Ian Musgrave posted Entry 2390 on June 19, 2006 07:32 AM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/2385

Over at Uncommon Descent William Dembski is linking to the random mutation site with approval. Claiming to be a “ Darwinian Evolution Experiment”, all it is is a simple random mutation generator. To be “Darwinian”, a system has to have selection as well. No selection, as in this case, well, it’s a waste of space. So why is Dembski linking to a site that he knows is a attacking a strawman version of evolution? Maybe its a bit of street theatre to distract people from the fact that he is happy with Ann Coulters appalling book, you know, the one where she falsley accuses honest scientists of fraud?

If you want to see a real Darwinian Evolution Experiment pop over to Zachriel’s Word Mutagenation and Phrasenation pages, where mutation and selection is used. Not only only do you get to evolve plain English words and phrases (the thing that the random mutation site claims you can’t do), you get to look at the code and see how it is done! Extra cool. If you are hankering for an old style Dawkins Weasel program, I maintain an archive here.

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Comment #106542

Posted by Flint on June 19, 2006 8:11 AM (e)

Just out of curiosity, has anyone found a creationist who does an honest job of figuring selection into his calculations. Offhand, I can’t recall a case of a creationist who even *recognizes* that selection exists. In all the thousands of repetitions of the 747 in a junkyard, not one nod in the direction of selection. Like the concept simply cannot penetrate the creationist brain.

So I don’t believe Dembski realizes that mutation without selection is a strawman. For him, there is no selection. He has to my knowledge never registered that it exists or what it might imply. I think Dembski instinctively tunes selection out because his convictions cannot allow it, and then tunes out the fact that he’s done so.

Comment #106594

Posted by Bob O'H on June 19, 2006 9:31 AM (e)

Maybe its a bit of street theatre to distract people from the fact that he is happy with Ann Coulters appalling book, you know, the one where she falsley accuses honest scientists of fraud?

There’s another theory that he’s trying to hide his Danish rotteness.

Either way, it’s good times for UD-watchers at the moment.

Bob

Comment #106596

Posted by Chris Hyland on June 19, 2006 9:45 AM (e)

Flint wrote:

For him, there is no selection. He has to my knowledge never registered that it exists or what it might imply.

I did ask on another thread for an example of a creationist calculation of information in evolution that actually models the branching and pruning of natural selection but was told:

I would just say that it’s not hugely relevant

Comment #106604

Posted by Jonathan Abbey on June 19, 2006 10:18 AM (e)

This is actually sort of interesting, in that there are so many ways this random mutator does not capture the complexity of living organisms, and their response to mutation. It might be fun to try and explain some of the dynamics that escapes the model, here.

One big, obvious problem with this simulation is not just that there is no selection (as a poster on UD says, you can always just hit back and try again), but that there is also no replication. If you’ve only got one individual, giving birth to one child in each generation, you’re not going to experience much evolutionary success. If this model were to take a sentence, make 10 million copies of it, and start letting them mutate and reproduce differentially, you could get rater better dynamics.

To a point at least. Another crucial difference is that in living systems, the genome is the recipe for ‘baking the cake’, rather than a blueprint, and slight alterations in the recipe for a living thing can perturb the entire development of the organism, with all sorts of mechanisms helping to constrain the result into something reasonable, according to the organism’s innate capacity for dealing with a variety of insults and sub-optimum environmental conditions. English is a terribly rigid system by comparison, with a simple binary correct/incorrect decision rule for grammatical and syntactical correctness.

Another difference is that this mutator just shows point mutations, there is no mechanism for splicing in redundant copies of portions of the text to serve as a reserve pool of functionality while one or the other copy undergoes additional mutation. Even if such were to happen, the strict rules of English would make the result seem far more bizarre and disturbing to us than gene duplication is to many organisms.

Another difference is that sexual reproduction is not modelled in any way, so there is no mixing of viable alleles into new combinations.

Surely there are more?

Comment #106605

Posted by T_U_T on June 19, 2006 10:20 AM (e)

simple random mutation generator

I just wonder what the author of this bioinformatics masterpiece wants to show by writing a deliberately nonfunctional program… Does he think that by producing an example that doesn’t work at all he somehow refutes the entire idea ? Anyone can write a basic math program that doesn’t get the numbers right faster than I can type this post : int main(){ printf( “2 * 2 = 5\n” ); return 0; } Does that imply that basic math doesn’t work as well ?

Comment #106606

Posted by Jonathan Abbey on June 19, 2006 10:25 AM (e)

Zachriel’s page has some good analysis of the mathematics of a mutating system of English words, though the mutation he is using is at the level of substituting English words for English words, not doing letter changes.

Comment #106611

Posted by Jim Wynne on June 19, 2006 10:41 AM (e)

The inimitable DaveScot correctly (for a change) points out that the cited entry at UD was not authored by Dembski. In the ensuing comments, one tinabrewer waxes skeptical over the importance of selection, apparently believing that unless there’s some type of new and improved selection that she hasn’t heard of, selection isn’t all that significant:

It interests me, in reading the comments that follow this post at PT, that the PT people seem convinced that “selection” is so terribly significant in evolution. There seems to be some muddy water on this one, for everyone concerned. I myself have always felt, just at a gut level, that the aspect of random mutations is the only really controversial aspect of RM+NS, since to me, natural selection is just an obvious uncreative static mechanism. Are they referring to other popular new selection mechanisms, and how significant are these in the overall story?

Comment #106613

Posted by normdoering on June 19, 2006 11:00 AM (e)

Jim Wynne wrote:

The inimitable DaveScot correctly (for a change) points out that the cited entry at UD was not authored by Dembski.

http://www.uncommondescent.com/index.php/archives/1234

Is Dembski even saying anything about what’s going on with his site? He doesn’t bother to correct wrong ideas that his fans shoot off.

Comment #106616

Posted by Pete Dunkelberg on June 19, 2006 11:21 AM (e)

Ian’s Weasel page
http://www.health.adelaide.edu.au/Pharm/Musgrave/essays/whale.htm
has lots of good stuff.

Comment #106619

Posted by Julie Stahlhut on June 19, 2006 11:31 AM (e)

The great divide:

“I myself have always felt, just at a gut level…” – tinabrewer

“… I try not to think with my gut.” – Carl Sagan

Comment #106621

Posted by Erasmus on June 19, 2006 11:41 AM (e)

I believe Stephen Colbert pointed out that he and GW are both ‘gut thinkers’ and don’t need to rely on the truthiness of ‘facts’. god what an hilarious analogy.

Comment #106624

Posted by DragonScholar on June 19, 2006 11:57 AM (e)

I have to say it’s really an incredibly amateurish example.
1) No example of selection.
2) It utilizes language as its example. Language works by a series of interreated symbol systems used by the observer, and communication breaks down if you interfere with these enough. It doesn’t compare well to genetic information, in my opinion.
3) It then argues that randomness is irrelevant for science and thus evolution. I’m still figuring out the logic that if it involves randomness it’s not science.
4) He has a disclaimer at the end that is exceptionally sad. Scroll all the way to the bottom (it’s too large to post politely). Roughly he reveals his ignorance of genetics and experimental design - by his words, it seems that no one could ver do an experiment on evolution because it’d be Intelligent Design since it involves a designer.

I also admit I take this rather personally. I’ve been doing a site of random creativity. for quite some time and *I* never get used as an example of justifying Intelligent Design.

Comment #106630

Posted by Tyranossaurus on June 19, 2006 12:50 PM (e)

If randomness is so utterly useless then why do spamers use random generators to fool filters?

Comment #106632

Posted by JohnK on June 19, 2006 12:59 PM (e)

Engineer Perry Marshall, creator of the linked random mutation site, can be seen debating in a long thread on IIDB. Utterly impervious to criticism.
(Unfortunately, a few of his interrogators choose wrong lines of attack on Marshall’s main claim and no one rolled up their sleeves and gave the general explanation of how the genetic code could have evolved naturally from the RNA world (RNA synthetases, selection for replication effectiveness & efficency, etc.), so Marshall now boasts he carried the day.)

Comment #106633

Posted by Jacques on June 19, 2006 1:00 PM (e)

“by his words, it seems that no one could ver do an experiment on evolution because it’d be Intelligent Design since it involves a designer.”

Typical ID catch-22. I’ve seen them argue that a mathematical model that showes how the (adaptive) information content of genomes can increase in time is not a valid argument since the model was intelligently designed. This must be the 6th law of thermodynamics: just when you think they can’t get more stupid, they pull it off anyway.

Comment #106638

Posted by Scott on June 19, 2006 1:23 PM (e)

Actually, human language seems to me to be a pretty good example of evolution. Everyone knows that French, Spanish, and Italian all “evolved” (in some sense) from Latin, all since the time of Christ. However, to randomly change words (or letters) in a modern French sentence and expect to still have a valid modern French sentence is laughable. [Well, okay. French is a bad example. You can change all sorts of letters in a French sentence, and it’s *still* unpronounceable. :-) ] It’s also laughable that that one should expect to be able to change random words or letters in a modern French sentence and eventually come up with a valid modern Spanish sentence, with each change resulting in some valid sentence in some modern language. Same is true for Latin to modern French. Yet we *know* that such changes occurred. Over time. Over *lots* of time. The language itself changed, so that these seemingly “random” changes actually were meaningful at the time they were used, even though those changes may no longer make sense to us today.

Has anyone seen a comparison of the parallels between the evolution of human language, and the evolution of species?

Comment #106644

Posted by k.e. on June 19, 2006 1:45 PM (e)

And yet the letters which make up the words are only a symbolic reference to the spoken language. Mere tokens or hieroglyphs, not to be confused with words themselves and words (an aural media) with meaning or the message.
The idolaters slavishly revere words and sentences. So it is appropriate to beat them with their own idols.

Comment #106647

Posted by Jim Wynne on June 19, 2006 1:50 PM (e)

Scott wrote:

Has anyone seen a comparison of the parallels between the evolution of human language, and the evolution of species?

Robert Pennock does a good treatment of the subject in his book Tower of Babel

Comment #106648

Posted by k.e. on June 19, 2006 1:55 PM (e)

And yet the letters which make up the words are only a symbolic reference to the spoken language. Mere tokens or hieroglyphs, not to be confused with words themselves and words (an aural media) with meaning or the message.
The idolaters slavishly revere words and sentences. So it is appropriate to beat them with their own idols.

Comment #106651

Posted by Wesley R. Elsberry on June 19, 2006 2:23 PM (e)

So I don’t believe Dembski realizes that mutation without selection is a strawman. For him, there is no selection. He has to my knowledge never registered that it exists or what it might imply. I think Dembski instinctively tunes selection out because his convictions cannot allow it, and then tunes out the fact that he’s done so.

This is not correct. Dembski attempts to calculate an upper bound on information that may be fixed by natural selection per generation in this essay.

From these observations it is clear that selection can accumulate a lot of information over successive generations. As is noted Joklik and WillettÕs (1976, p. 78) microbiology text, ÒWithin a short period, often as short as 20 minutes, a bacterium can create a complete duplicate of itself, which in turn is capable of duplicating.Ó Over a billion years, at one bit of information introduced every twenty minutes, selection could in principle produce 26 trillion bits of information, certainly enough to handle any conceivable genome. Nonetheless, from these observations it is equally clear that selection can only produce a very limited amount of information at any one generation. 100 bits is certainly too generous. The most fecund breeders with which I am familiar are certain fish whose spawn include a hundred million eggs. A realistic upper limit on the amount of biological information introduced by selection is therefore around 30 bits. For many organisms it is far less. Mammals, for instance, have an upper limit of about 5 bits of information per generation through selection.

Just because the analysis alluded to is incompetent doesn’t mean it doesn’t exist.

Comment #106654

Posted by Flint on June 19, 2006 2:46 PM (e)

Wesley,

Thanks for the reference. Sounds to me as though Dembski really does address selection here, but does so in order to dismiss it as so inadequate to produce what we observe as not really to exist in practice after all.

In other words, he is *explicitly* tuning it out. Or have I misunderstood his intent here?

Comment #106656

Posted by Ben on June 19, 2006 3:10 PM (e)

Having been intimately involved in the nitty gritty of natural selection I’m just flabergasted that creationists can’t possibly understand how vitally important selection is to the process. I think that fundamentalists huge problem with sex in general definately colors their understanding and perspective when it comes to natural selection.

It’s just so amazingly simple. I’ve had offspring. They are like me and my wife… only a little bit different. But I recongnize things I “selected” in my wife (or she selected in me) that are in my children…. This sort of thing goes on for a billion years and those incremental changes become monumental.

You add in environmental factors and some random mutation and it becomes staggeringly obvious..

I have come to the conclusion that if you are even remotely capable of functioning at a relatively high mental capacity and you don’t believe, when push comes to shove, in evolution then you have severe emotional problems, or are really lacking in imagination.

It’s really hard not to turn a post into a rant…. I’m really just amazed that people don’t accept evolution as fact….

Comment #106661

Posted by Inoculated Mind on June 19, 2006 3:32 PM (e)

I think Dembski has made it clear over the years that he believes that genes pop entirely out of random noise - so I think selection hasn’t sunk in.

You know what I noticed about that typing monkey website? They only seem to count the shakespeare that is correct from the beginning. So there could be several sentences of shakespeare in the middle, but they’re not counted. Evolution works from every beginning and end part of genes. If it is selectable it is selectable - it doesn’t have to be right at the beginning only.

It would be interesting to see a program specifically created to show how shakespeare could evolve over time with incremental steps of mutation and selection. All the first website is doing is saying that the chance of getting the entire thing in one fell swoop is incredibly small. Which no one disputes.

Comment #106674

Posted by Torbjörn Larsson on June 19, 2006 4:13 PM (e)

I’m sure other examples of selection has been offered here, as in prototyping and markets. For example, I’ve succeeded in establishing a healthy population of my favourite sugarfree soda at the closest store by selection on an initially random sample. (I’m also sure that an IDier identifies that with intelligent design by the store owner, instead of an automatic reaction from the market mechanism. Sigh!)

Dragon says:
“by his words, it seems that no one could ver do an experiment on evolution because it’d be Intelligent Design since it involves a designer.”

Yes, it’s reminding of the QM observer that quantum babblers use for special appeals to explain consciousness (or souls, as they want to have it). Here another experimental artifact is taken in custody to purportedly support a dualistic world view.

There are ways to “unobserve” QM, but they have some small problems as all QM interpretations. (Consistent histories with decoherence by thermodynamic equilibria observers, such as the vacuum itself - problems with selection rules. Manyworlds with decoherence without observers - problems with randomness.) So they also don’t sell easily, if the public doesn’t want to listen to the message.

Comment #106681

Posted by wamba on June 19, 2006 4:50 PM (e)

from the fact that he is happy with Ann Coulters appalling book, you know, the one where she falsley accuses honest scientists of fraud?

Nothing new there, I just finished reading Icons of Evolution by Jonathan Wells.

Comment #106684

Posted by DragonScholar on June 19, 2006 5:10 PM (e)

wamba wrote:

I just finished reading Icons of Evolution by Jonathan Wells.

Is there a place that compiles science-focused reviews of such books? It’d be very useful to have a quick reference to anti-science books like that.

Comment #106686

Posted by steve s on June 19, 2006 5:26 PM (e)

TalkOrigins is pretty much your first place to look for things like that, AFAIK.

http://www.talkorigins.org/faqs/wells/

Comment #106693

Posted by PaulC on June 19, 2006 5:52 PM (e)

The strawman cited here is especially bad because it doesn’t take even selection into account. But another thing missing is any appreciation of the role of populations in actual evolution.

Obviously if there were just one organism, and it had an offspring of exactly 1 before dying, then mutation would not be very helpful given any probability less than 1 that a mutation would lead to non-viable offspring. That would even hold if (contrary to out experience) most actually were beneficial. You could add selection to this strawman example, and you’d still be able to prove the obvious, but in a slightly more subtle way.

In real-life population dynamics, the next generation must have at least the potential to be greater than the current generation by some percentage. Without any limiting factors, this leads to exponential population growth, which is obviously unsustainable, but the percentage of viable offspring (perhaps altered by mutation rate) is not a limiting factor provided there are enough total offspring. Ultimately, the limiting factors may involve food, disease, predation, etc.

Warning, I am not a biologist so somebody correct me if I say something stupid below:

(a) The usual case is that the offspring of some organism has either no significant mutations or maybe some neutral ones. By this I mean the offspring that make it to the point of actually being born, hatching, germinating, etc. Any genetic variation is mostly due to the combination of parents’ genes.

(b) A less usual case is that the offspring has a deleterious mutation (that makes it less fit).

(c ) An even less usual case is that the offspring has a beneficial mutation (that makes it more fit).

Case (b) isn’t going to hurt you provided your overall rate of reproduction is high enough. Errors don’t happen exclusively in biological systems, after all. They happen in “intelligently designed” manufactured products too. As long as they don’t happen too often, their cost is borne by the successful copies.

Case (c ) is rare enough that you could ignore it in oversimplistic models of living things. If you’re running a farm or a pedigree dog breeder, say, you might classify anything out of the ordinary as a defect without hurting your yield. However, in nature, there is nobody making this arbitrary distinction. In short, there is nothing to stop evolution from happening, so why would you not expect it to happen?

The point that I think people really miss is that the main engine that enables evolution is not mutation, but the opposite: the extraordinarily accurate reproduction of an enormous amount of genetic material across generations. If the next generation were simply riddled with random generations with significant effects on phenotype, then evolution could not progress. Of course, without any mutation it would not progress either. But with a relatively low rate of mutation including some tiny fraction that are beneficial, evolution is the expected outcome.

Comment #106695

Posted by PaulC on June 19, 2006 5:58 PM (e)

I wrote: “would not be very helpful given any probability less than 1 that a mutation would lead to non-viable offspring.”

I inverted my logic midway through. I meant to say that if you had any probability greater than 0 that a mutation would lead to non-viable offspring, then the “give birth to one child and die” method would eventually fail, even if you had an unrealistically high probability of beneficial ones. So even if you tried to incorporate selection into the silly example on the linked web page, you would still have a very poor model of what evolution entails.

Comment #106696

Posted by PaulC on June 19, 2006 6:02 PM (e)

I wrote: “riddled with random generations” and meant “riddled with random mutations”

Sorry for not catching these in preview mode. It’s amazing how much the errors stick out after posting.

Comment #106702

Posted by Bill Gascoyne on June 19, 2006 6:28 PM (e)

I’m not sure whether to cheer or scream:

Scientists Taking Cues From Nature

Maybe a bit OT, but the article actually quotes Dembski, which unfortunately means that someone is paying attention to him.

Comment #106703

Posted by Longhorn on June 19, 2006 6:32 PM (e)

A kind of event that has contributed significantly to the differences among nearly all sexually reproducing organisms is sexual reproduction. I’m quite different than either of my parents. Though I may have been born with some new mutations, they have not had a signficant affect on my observable traits. Yet I’m still significantly different than either of my parents. I’m as different as I am from them largely because they sexually reproduced with each other.

A lot of people seem not to realize how important sexual reproduction was in causing the differences among nearly all sexually reproducing organisms. Whales are as different as they are from their land mammal ancestors partly because vast numbers and combinations of organisms sexually reproduced. Sexual reproduction was one of keys to causing the differences that have existed among nearly all sexually reproducing organisms that have lived on earth.

Also, lateral transfer is a kind of event that was important in causing the differences among many asexually reproducing organisms.

Comment #106706

Posted by Longhorn on June 19, 2006 6:45 PM (e)

One thing sexual reproduction does is that it sometimes causes an organisms to have two versions of a recessive gene. And an organism having two versions of a recessive gene can trigger an observable trait.

On a different note, sometimes I wonder whether sexual reproduction and varying levels of reproduction success, by themselves, caused a population of land mammals to evolve into whales. But I do have my doubts. Can sexual reproduction and varying levels of reproductive success cause nostrils to evolve into blow holes? I don’t know. But I do have my doubts. I don’t experience sexual reproduction absent mutations to gametes causing that level of difference across sexual generations. I suspect that mutations to sex cells were important, as well. But then again, Pakicetus evolved into whales in about 15 million years. And I have no concept of that length of time.

Comment #106733

Posted by Lurker on June 19, 2006 9:27 PM (e)

Most trained scientists accept RM+NS evolution, however some don’t. A smaller group of trained scientists think it’s wrong, way wrong.

My question is this:
Which group is right and how do you know they are right?

If the experts themselves can’t agree then what should the average Joe think about this? Let me run through some responses that I think will come up and offer my comments. If you have other answers please post them.

1) “The majority opinion says…” - as you know this is an appeal to popularity and is a logical fallacy. Anyway, I want to know how you know the minority opinion isn’t correct.

2) “The evidence clearly shows…” - not according to the minority opinion of experts in the field. How do you know the majority opinion has it right?

3) “They aren’t real scientists” - they probably aren’t ‘True Scotsmen’ either. Try again.

Comment #106735

Posted by Flint on June 19, 2006 9:47 PM (e)

Lurker:

I vote for candidate #2. The evidence rules. Yes, a tiny handful of Devout Fundamentalists have decided that the evidence doesn’t matter, or that the evidence MUST ratify their religious convictions because God said so. But this is a misuse of evidence. And those who disagree about the evidence, instructively, have been 100% totally unable to come up with a single test, hypothesis, or course of investigation that might even *begin* to produce different evidence more in accordance with their faith.

Saying “my faith is incompatible with the evidence, therefore the evidence is wrong” isn’t really a sincere disagreement about the evidence. Instead, it’s (I will presume) a sincere inability to rectify a conflict rationally.

(Oh yes, I hope you have noticed that this tiny minority of ‘experts’ does no research, publishes nothing, has failed to convince any judge, and with almost no exceptions is untrained specifically in what they claim “expertise” in. You HAVE noticed this, haven’t you?)

Comment #106736

Posted by snaxalotl on June 19, 2006 9:47 PM (e)

program Godsim()
repeat
{
print(“obey!\nburn in hell!\nbananas!\n”)
call divineintervention(random(99999))
}

Comment #106745

Posted by Longhorn on June 19, 2006 10:23 PM (e)

Lurker wrote: “Most trained scientists accept RM+NS evolution, however some don’t.”

Lurker, I urge you to read posts 106703 and 106706, my previous posts in this thread. “RM+NS” are not the only kids of events that were important in terms of causing the differences between bacteria and elephants. For instance, sexual reproduction was hugely important.

As to your question, a tiny percentage of experts don’t accept that self-replicating molecules that were on earth about 3.8 billion years ago evolved through reproduction into all the complex organisms that have lived on earth. I think when a non-expert experiences this sort of massive agreement on the part of experts it is relevant to what the non-expert is justified in believing. However, the non-expert still should acquaint oneself with the relevant data. Here is a link to an article that presents some of the data that has helped me determine that cells evolved into elephants:

http://www.talkorigins.org/faqs/comdesc/

I also recommend Ernst Mayr’s book What Evolution Is, which was published in 2001. Mayr was a great biologist, and he wrote the book for a general audience.

It is important to note that we are getting a more detailed understanding of the kinds of events that caused cells to evolve into elephants. For instance, we are getting a deeper understanding of the kinds of events that trigger mutations to sex cells.

Comment #106746

Posted by Ian Musgrave on June 19, 2006 10:25 PM (e)

Jim Wynne wrote:

In Comment #106611,
The inimitable DaveScot correctly (for a change) points out that the cited entry at UD was not authored by Dembski.

Ooohh, did I mix up Dembski and Someone Else? Just like Ann Coulter mixed up EB Ford and HBD Kettlewell? Funny, Dembksi was happy with that, so people should be unconcerned that he got mixed up with Someone Else. On the other hand, Dembski has claimed responsibility for all Ann Coulter’s errors with regard to evolution, so he should take responsibility for the errors on his own blog. Or maybe I’m just engaging in a little Street Theatre.

Comment #106747

Posted by Henry J on June 19, 2006 10:31 PM (e)

Re “Can sexual reproduction and varying levels of reproductive success cause nostrils to evolve into blow holes? I don’t know. But I do have my doubts.”

And actually answering that question would seem to require a rather compute-intensive simulation.

Henry

Comment #106748

Posted by Sir_Toejam on June 19, 2006 10:33 PM (e)

. “RM+NS” are not the only kids of events that were important in terms of causing the differences between bacteria and elephants.

nor is RM the only method for inducing genetic change (not that it’s always that random to begin with).

horizontal gene transfers can also play a role, as well as chromosal doubling, etc.

there are lots of ways of modifying a genome significantly other than just straight mutation of the genome itself.

It’s not the source of the change in genome that’s the important part, it’s that there IS some change that results in a phenotype (either fully expressed or while in development) that selection can act upon.

even then, significant change can occur without significant selective pressures as well. That’s where the hypothesis of neutral mutation comes from.

so while RM + NS is a component of the ToE, and a useful place to begin explaining the basics of the theory, it isn’t the theory as a whole.

Comment #106750

Posted by Longhorn on June 19, 2006 11:11 PM (e)

Henry wrote: “And actually answering that question would seem to require a rather compute-intensive simulation.”

I’m not sure that is true. I think it is important to get a better understanding of how much genetic and phenotypic difference can be caused by the first phase of meiosis. Can it be really significant – like a mutation to a gamete? And some people might even know how much genetic and phenotypic difference can be caused by the first phase of meiosis. I’m not one of those people.

I also think that if we learn more about the organisms that are the closest living land mammal relatives to whales, and if we can compare their genome with a whale genome, that would help a lot in terms of helping us determine how significant mutations to sex cells were (versus vast numbers and combinations of organisms sexually reproducing) in terms of causing the differences between whales and their most recent land mammal ancestors.

It is important to note that I share ancestors with all the chimpanzees that are alive today. And one particularly important difference between my genome and theirs is a chromosomal fusion. So what happened is that one of my ancestors (a long time ago) was born with a chromosomal fusion. It had 47 chromosomes. Two of its direct descendents reproduced, resulting in (following meiosis and fertilization) an organism with only 46 chromosomes, the number we have today. Interestingly, chromosomal fusions are actually not that uncommon in the animal world. Moreover, chromosomal fusions are a kind of mutation that occurs to sex cells. It suspect that this chromosomal fusion was important in terms of causing the differences between humans and chimpanzees. But how important? Had the split already occurred? Was it the proximate cause of the split?

I tend to think that some mutations were important in causing a population of land mammals to evolve into whales. Because I just don’t experience sexual reproduction causing events as significant as the kind that caused nostrils to evolve into blow holes. Mutation to gametes preceding fertilization seems to be the combination of events that we experience causing the biggest differences between parent and offspring. For instance, that caused the elephant man, humans with blue eyes and (I believe) the coats of black panthers (also known as melanistic jaguars).

However, it is also important to keep in mind the vast periods of time we are talking about. It is hard for me to extrapolate from my own experience to 15 million years. And a lot of the differences that dogs exhibit were caused by meiosis and sexual reproduction. I suspect that both mutations to sex cells and sexual reproduction were kinds of events that were important in causing the difference between whales and their land mammal ancestors.

If mutations were indeed important in causing nostrils to evolve into blow wholes, how many mutations were involved?

Comment #106751

Posted by Anton Mates on June 19, 2006 11:21 PM (e)

Lurker wrote:

If the experts themselves can’t agree then what should the average Joe think about this?

Perhaps the average Joe could get off his average derriere and try to figure out who really is an expert, and why they disagree?

1) “The majority opinion says…” - as you know this is an appeal to popularity and is a logical fallacy. Anyway, I want to know how you know the minority opinion isn’t correct.

It’s not a logical fallacy unless you try to use it in a logical proof; majority opinion can be excellent supporting evidence, provided you know something about how individuals are making their choice and why they might disagree. If 99 people peek in that kennel over there and tell you there’s a cat in it, and 1 person says no, it’s a dog, what are you going to conclude pending further information? Personally, I’m going with it being a cat, and that one guy was blind, insane, a liar or doesn’t know much about animals.

Mind, there are certainly instances where majority opinion tells you nothing, and there are much better ways to reach on opinion on scientific matters–see below–but calling its use a “logical fallacy” is simply incorrect. And if one can’t be bothered to look into a scientific question in detail, heck yeah, go for the majority expert opinion. You won’t always be right, but you’re playing the odds.

2) “The evidence clearly shows…” - not according to the minority opinion of experts in the field. How do you know the majority opinion has it right?

As Flint says, this is the big one. How do you know? Because you check. What is the evidence? Is each expert in question actually expert in that area? Do they actually refer to the available evidence? Is their chain of argument cogent?

For a concrete example, Michael Behe disagrees with pretty much everyone in immunology about what the evidence says on immune system evolution. However, as we saw at the Kitzmiller trial, Michael Behe cheerfully admits not having looked at the evidence in question, and says he has no need to. We can now forget about what Michael Behe says on this matter. Next!

The lovely thing about science is that everybody can get a grasp on it if they try hard enough. We can’t all be Darwin or Faraday or Einstein, but we can examine their theories, check the sources of their data and confirm that the data support the theory. It takes time and effort, though, and if you don’t have that to spare, it’s back to the majority expert opinion. That’s why we have professional scientists–to find out for us the stuff we don’t want to find out for ourselves.

3) “They aren’t real scientists” - they probably aren’t ‘True Scotsmen’ either. Try again.

You think someone might be using the “no true Scotsman” fallacy? Check. Find out if the person in question actually grew up in Scotland or not.

Not sure whether someone’s a “real scientist” or a “real expert?” Check. Find out if the person does science, and whether there’s any evidence for this other than their say-so. Have they published? Have they made discoveries others are building on? Is their research in the area on which they claim to be an expert? Do they have degrees in this area, and if so, where from, and what work did they do to get it? How are they viewed by other scientists/experts who in turn have a legitimate claim in the area?

I realize it can be difficult and exhausting to do all this investigation, which is why sooner or later you have to return to majority expert opinion. For instance, I know there are a few self-labeled physicists–some even with degrees and a publishing record–who think QM or relativity are “wrong, very wrong” and Newton had it right all along. But I really haven’t time to examine the work and credentials of each in detail, so I’m going to have to go with the Orthodox Mainstream Physics Establishment’s opinion that they’re shooting blanks.

Comment #106753

Posted by Longhorn on June 19, 2006 11:25 PM (e)

Hi, Sir T. Good luck to England in the World Cup.

nor is RM the only method for inducing genetic change (not that it’s always that random to begin with).

What do you mean by “method for inducing genetic change?” Sexual reproduction can cause “genetic change,” at least given what I think you mean by that. As you know, the first phase of meiosis often results in a genome that is fairly significantly different than the genome that precedes the phase.

Also, you mention “random mutation.” I have never fully understood what people mean by “random mutation.” Do they mean “uncaused event?” The idea of an “uncaused event” doesn’t make sense to me, at least at the non-quantum level. And even at the quantum level it doesn’t make that much sense to me. Mutations are caused. For instance, some mutations are caused by exposure to a certain level of radiation.

Maybe they mean that humans are unable predict when a given mutation will occur. Okay sure. There are a lot of things I can’t predict. I can’t predict if England will beat Sweden. But if England does beat Sweden, it is not an “uncaused event.” A number of factors will be involved. For instnce, presumably Rio Ferdinand will play a good game.

Comment #106755

Posted by Henry J on June 19, 2006 11:27 PM (e)

Re “1) “The majority opinion says…” - as you know this is an appeal to popularity and is a logical fallacy.”

Er, no, that’s not an appeal to popularity. It has nothing to do with how many (if any) of those scientists actually like the conclusion, it’s whether they think the evidence supports it.

Also consider how many of the minority are in the right field, and whether their argument(s) are based on evidence or not. Case in point: I.D. pushers keep saying they have “explanation” but never get around to saying what that explanation actually is.

Henry

Comment #106758

Posted by Henry J on June 19, 2006 11:54 PM (e)

Re “if we learn more about the organisms that are the closest living land mammal relatives to whales,”

Hippotamus, iirc.

Henry

Comment #106761

Posted by Anton Mates on June 20, 2006 12:26 AM (e)

Longhorn wrote:

nor is RM the only method for inducing genetic change (not that it’s always that random to begin with).

What do you mean by “method for inducing genetic change?” Sexual reproduction can cause “genetic change,” at least given what I think you mean by that. As you know, the first phase of meiosis often results in a genome that is fairly significantly different than the genome that precedes the phase.

I think he’s simply agreeing with you. Sexual reproduction, mutation and horizontal transfer all result in genetic change.

Also, you mention “random mutation.” I have never fully understood what people mean by “random mutation.” Do they mean “uncaused event?” The idea of an “uncaused event” doesn’t make sense to me, at least at the non-quantum level. And even at the quantum level it doesn’t make that much sense to me. Mutations are caused. For instance, some mutations are caused by exposure to a certain level of radiation.

Maybe they mean that humans are unable predict when a given mutation will occur. Okay sure. There are a lot of things I can’t predict. I can’t predict if England will beat Sweden. But if England does beat Sweden, it is not an “uncaused event.” A number of factors will be involved. For instnce, presumably Rio Ferdinand will play a good game.

Yes, “random” refers to predictability, not to cause. In particular, mutations are unpredictable even in principle (unless someone comes up with a deterministic successor to quantum theory, anyway), and what statistical regularities they do have are uncorrelated with their “value” in terms of selection.

Comment #106765

Posted by H. Humbert on June 20, 2006 1:19 AM (e)

Lurker, whether or not evolution and speciation occurs it isn’t a debate between two opposing groups of scientists. It’s between religious fundamentalists and everyone else.

There isn’t a single evolution-denier who didn’t arrive at that conclusion because of their religious beliefs. If there was legitimate scientific doubt on the matter then it would be more than just the religious nutters more that willing to step forward and point it out. But there isn’t. You have to honestly ask yourself, why is that?

Comment #106766

Posted by Sir_Toejam on June 20, 2006 1:21 AM (e)

I think he’s simply agreeing with you. Sexual reproduction, mutation and horizontal transfer all result in genetic change.

yes, but specifically the reason i left out sexual reproduction is that a very large proportion of organisms don’t reproduce sexually, yet there is still genetic variability for selection to act on, and that’s specifically the kind of variability I wanted to address.

well, I guess that’s rather obvious, since sexual reproduction is an evolved trait to begin with

;)

Anton also answered the “random” question in the same manner i was considering it as well.

Truly, it is an overgeneralized term for “non-deterministic”, so in that sense, all mechanisms for inducing genetic variability could be considered “random” to a greater or lesser extent.

typically, we usually consider the “random” mutation of genetic material to be due to either physical processes (mutagenics like radiation damage or chemical damage), or transcription errors, for example. In this sense, they are relatively non-deterministic, as there is a wide probability distribution surrounding where an event like this is likely to occur on a genome, as well as what the exact result of an event will be.

Things like horizontal gene transfer can be a bit more predictable, as we are usually dealing with known genetic code insertions (in the case of viruses, for example), but there is still some unpredictability involved in where an insertion/deletion event will occur, and how specifically it will interact with the genome as a whole.

Then, sexual reproduction is much more predictable, as often we can predict specific traits resulting from specific crosses (which, I’m sure every one of us who took molecular and population genetics got entirely sick of doing after the thousandth time ;) ); but even then, not always, and some traits are heavily tied to the specific environmental cicrumstances present during their experession, and it becomes much harder to predict how the trait will end up expressing itself specifically.

However, the bottom line is that the use of the term “random” is merely meant as a purely overgeneralized descriptor, used when one doesn’t want to detail all the probability distributions and other factors that lie behind the use of the term itself.

Unfortunately, as we have seen repeatedly, those unfamiliar (or those who choose to intentionally misrepresent) use these generalizations to make unwarranted assumptions and conclusions about (not just the ToE), that most often result in mischaracterization of science.

They don’t want you to look behind the scenes to learn the reality of the theories involved, but prefer to oversimplify, in order to make good sound bites and mislead.

Even a narrower scope like a scientific law, often is grossly oversimplified by those who want to make an illegitamate argument.

take the 2LOT as a perfect case on point.

Comment #106793

Posted by Chris Hyland on June 20, 2006 6:10 AM (e)

If mutations were indeed important in causing nostrils to evolve into blow wholes, how many mutations were involved?

The answer probably involves comparing the development of whales and hippos, and trying to discover the genes responsible for blowholes/noses. Hopefully then the difference will be differences in gene expression during development, and the number of mutations probably less than enough to have occured in 15 million years.

Comment #106794

Posted by Andrew McClure on June 20, 2006 6:39 AM (e)

So I was reading over this discussion earlier today, and thinking about some of the comments…

DragonScholar wrote:

I have to say it’s really an incredibly amateurish example.
1) No example of selection.
2) It utilizes language as its example. Language works by a series of interreated symbol systems used by the observer, and communication breaks down if you interfere with these enough. It doesn’t compare well to genetic information, in my opinion.

…something that occurred to me was that you really don’t ever see any particularly good “product demos” of evolution, so to speak. You rarely see one of these little computer “evolution simulator” programs living up to the level of clarity and intuitiveness that you’d get out of, I dunno, an Exploratorium exhibit or something. Most attempts to model evolutionary processes seem to tend to turn out either so simplistic they don’t make an impression on anyone, or so arcane that you don’t really understand what’s happening in the model unless you understand biology quite a bit already.

On the one hand, we have the straw man models the creationists come up with, like this monkey shakespeare program, which don’t even attempt to model reality.

On the other hand though what we have are the IT IS A WEASEL style programs, which are a neat little demonstration of the mechanism of selection, but don’t really do anything else. They’re not trying to do anything more than demonstrate selection in action, of course; the point is mostly to show how drastically different from the “junkyard” scenario things become if you implement just one or two of the basic mechanisms of real-world evolution. These programs do a very good job at what they’re meant to do. But if you’re looking for any particularly meaningful model of evolutionary processes, they aren’t it.

(On the third hand we have genetic-algorithm software, which works and does lots of interesting stuff, but the point isn’t so much to model real-world evolution; the point is to be useful for some computing task. Moreover, such things are usually nontrivial to explain to someone unfamiliar with the idea of, say, an “algorithm”.)

If there’s a fourth hand, I wouldn’t know what it is at the present time.

Anyway, there’s a couple of problems I see with the WEASEL program if you’re trying to use it as a demonstration of the idea that mutation+natural selection can generate interesting things rather than just shuffle random bits around. One, the WEASEL programs ignore most of the mechanisms that appear in real-world evolutionary processes (like populations, regulatory sequences, sex… we seem to be building a longish list of such mechanisms in the thread above). Two, like DragonScholar mentions, language is brittle and maybe not a very good medium for the programs to use as their “genetic material”. Three, and this is the one that’s interesting to me, the Weasel programs don’t seek fitness. They just seek one specific string. The programs are given one specific, fixed destination, rather than being given a fitness landscape and told to find a destination. This last thing is of particular interest to me in context of this current discussion, because the WEASEL algorithms fail to show any “ingenuity”. It is one thing to show that a stochastic algorithm can reconstruct a sentence that a human has specified. It is something more interesting to show that a genetic algorithm can solve a problem. (We can find plenty of examples of genetic processes solving problems in biological systems, of course, but this doesn’t help much when faced with someone studiously determined to ignore all evidence that comes out of the biological sciences.)

I kind of wonder: if rolling a die and seeing if the face came up SHAKESPEARE isn’t a very good demonstration of the power of evolutionary processes (and I think everyone here agrees it isn’t); and if a simple simulation of natural selection where the fitness function is the hamming distance from the sentence “METHINKS IT IS LIKE A WEASEL” is lacking as well (and I sort of think it is); then what might be an example of a good simulation, possibly something that could be stuck up on a web page somewhere?

Thinking about this for awhile, it occurred to me that images might be a much more suitible form of output than text would for an analogue of the WEASEL programs, becuase:

1. Images can be meaningful without following the strict and very artificial rules of language, and
2. it’s much easier to optimize an image for a “purpose” than it is to do so for a sentence. For example, you could run some kind of genetic algorithm for a long time in hopes of finding something that “looks like a panda”, without having any specific picture of a panda in mind. And anyway
3. Oooh pictures pretty shiny.

I’m a bit afraid that this post up to this point is a little bit stream-of-consciousness, so I hope I’m not just rambling here. But where I’m going with all of this is, I got kind of bored this evening, so I slapped something together in half an hour that tries to generate images by a sort of improvised genetic algorithm (I assume there’s a goodly number of very similar programs floating around the internet already, but again, I was bored). This consists of a small perl program with a CGI interface that iteratively mucks about with individual pixels in GIF images the same way the WEASEL programs muck about with individual letters in sentences. So far it doesn’t really seem to work very well.

What the program does is take a pool of images (randomly generated, to begin with), and “breed” them against each other by randomly copying each individual pixel from one of the two parent images into the corresponding position in the child image. (The point is to mimic genetic recombination. Also, to mimic mutation, there is a small, like 1 in 16 or 1 in 256 or something, chance that a pixel will be copied “wrong” and randomly swap to some other color.) The user then gets to select, based on whatever criteria they like, which child from each pairing gets to survive into the next generation. Once the pool for the next generation is full, the parents are tossed and the process starts over. In theory, if you run this enough times, you should be able to generate nearly any image you like. In practice there are a couple of problems. First off, even in a small (say, 32x32) image there’s a lot of stuff going on, and it’s hard for a human observer to distinguish any meaningful difference at all between the initial set of images. Second off, mutation adds information only relatively slowly, and a human user (i.e. me) is only going to sit through about four or ten generations before getting frustrated and bored and giving up. In this amount of time, you can usually manage to a achieve very small goal (say: creating a small black blotch in one corner of the image) but certainly not anything on the scale of “generate a picture of a Panda”. I’m pretty confident, however, that if instead of having the selection be done by human input, you let an image-recognizing neural net or something determine fitness, you’d get much more meaningful results, since that could more easily be run through the thousands of generations that would be necessary for the model to do anything meaningful.

Anyway, if you want to play around with this, the files are linked below, assuming you know Perl. No, there isn’t that much to them. (To make these work, save them in a CGI-capable directory as “index.pl” and “evo.pm”, and put in the same directory a world-writable subdirectory named “i” for it to save images in.) I will probably play around with the parameters some more later to see if I can tease the program into doing anything interesting.

http://vote.grumpybumpers.com/evo/index.txt
http://vote.grumpybumpers.com/evo/evo.pm.txt

I’d host running versions of these myself, but the current rudimentary interface generates somewhat unpleasant quantities of disk-space-eating temp files (the files are small, but there are a lot of them), so I don’t know what would do to my poor little hosting provider to link the live version from Panda’s Thumb…

Comment #106804

Posted by 'Rev Dr' Lenny Flank on June 20, 2006 7:11 AM (e)

Most trained scientists accept RM+NS evolution, however some don’t. A smaller group of trained scientists think it’s wrong, way wrong.

Most trained scientists accept that the earth revolves around the sun, however some don’t. A smaller group of trained scientists think it’s wrong, way wrong.

http://www.fixedearth.com

http://www.biblicalastronomer.org

How oh how can we tell which is right?

Comment #106805

Posted by 'Rev Dr' Lenny Flank on June 20, 2006 7:14 AM (e)

I suppose then that the fact that learned Biblical scholars can’t agree on “what the Bible really means”, indicates that the Bible is wrong.

Right, Carol?

Comment #106812

Posted by Keith Douglas on June 20, 2006 8:27 AM (e)

Jacques: Confusing the model with its referents is not surprising in an essentially idealist world view …

Inoculated Mind: What would be much more interesting and much harder to do would be to evolve any play at all, not just Hamlet. After all, this would reduce the artificial “directionality” to the system.

Lurker: #2, basically. However, one has to remember that science does not (especially in the more advanced fields) produce heaps of data but instead systems of hypotheses weaved out of data (so to speak) and tested against yet more. Further, data themselves are not collected mindlessly but refined and processed. If all that gets rolled into evidence, then yes, #2.

Longhorn: “Random” here means “independent of the use to the organism” or something like that. (See various works on randomness and also on causality by various philosophers for more on this sort of use.)

Comment #106818

Posted by Longhorn on June 20, 2006 9:59 AM (e)

Anton Mates wrote:

In particular, mutations are unpredictable even in principle (unless someone comes up with a deterministic successor to quantum theory, anyway), and what statistical regularities they do have are uncorrelated with their “value” in terms of selection.

It seems possible that, in at least some populations, the frequency of mutation increases when the organisms are under some kind of stress, for instance, nutrient deficient environments. Is it possible? If it is, this correlation might suggest that organisms are physically predisposed to mutate more frequently under certain conditions. Perhaps populations might have tended to have greater reproductive success when their rates of mutation were higher in stressful conditions, resulting in an evolved trait, namely the predisposition to mutate more frequently under certain conditions.

Of course there is not a gene that regulates mutation rates. But maybe the macro-organism is, in its totality, an organism that has a disposition to mutate more frequently under certain conditions.

Comment #106823

Posted by Anton Mates on June 20, 2006 10:43 AM (e)

Longhorn wrote:

It seems possible that, in at least some populations, the frequency of mutation increases when the organisms are under some kind of stress, for instance, nutrient deficient environments. Is it possible?

Oh, without a doubt. The overall mutation rate, and even the rate of a particular sort of mutation (e.g. point mutation A->T) in a particular stretch of DNA, can be affected both by environmental factors (like a particular chemical mutation) and by genetic factors governing DNA topology, repair and so forth.

Here for instance is a study where E. coli was bred to have a higher mutation rate than normal.

Comment #106826

Posted by Longhorn on June 20, 2006 11:02 AM (e)

Oh, without a doubt. The overall mutation rate, and even the rate of a particular sort of mutation (e.g. point mutation A->T) in a particular stretch of DNA, can be affected both by environmental factors (like a particular chemical mutation)

Right. I know that events in the environment can trigger mutations.

and by genetic factors governing DNA topology, repair and so forth.

Thanks

Here for instance is a study where E. coli was bred to have a higher mutation rate than normal.

Thanks

Comment #106831

Posted by Longhorn on June 20, 2006 11:19 AM (e)

I wrote:

It seems possible that, in at least some populations, the frequency of mutation increases when the organisms are under some kind of stress, for instance, nutrient deficient environments. Is it possible?

I’m not sure why I asked that question. I already realized that events in the environment can trigger mutations. I guess what I should have asked is whether, in some cases, evolution and reproductive success has contributed to some populations having the mutation rates that they have had. And, according to Anton and the information he linked to, it looks like evolution and reproductive success has contributed to populations having the mutations rates that they have had.

One interesting note is that, according to studies done by the geneticist John Drake, some species have importantly different mutation rates than do other species. These different mutation rates most likely have something to do with the size of the genomes involved. A larger genome provides more opportunity for mutation. However, it may be that reproductive success has contributed to some populations having the mutations rates that they have.

Comment #106832

Posted by PaulC on June 20, 2006 11:24 AM (e)

I wanted to concur with some of the comments about sexual reproduction and other kinds of gene transfer. Mutation gets all the attention (probably from comics and B-movies about radioactivity) but a lot of adaptation occurs without it.

I believe that evolution would be extremely slow if mutation were the only mechanism for genetic variation. It is possible through sexual reproduction to combine two successful adaptations in the same individual even if they arose independently. The extent to which these adaptations are combined is random, but one usually receives copies of genes that already do something useful. Selection then enriches the sample space so it is somewhat biased towards those genetic combinations that are most useful in the current environment. (Note: I don’t know the details on the peppered moth studies, but I would imagine that such a rapid adaptation was caused by a combination of existing genes for pigmentation rather than any significant mutation).

If the above were not true, then one would expect genetic algorithms to perform no better than simple monte carlo algorithms when in fact genetic algorithms are better at search kinds of optimizations (and don’t help much or at all in certain others).

I realize that mutation does play a significant role, but I think it is overemphasized, especially by critics. Randomness in general gets overemphasized. You need some variability, but evolution is no more random than the process that gets all the air out of a hole in a beachball.

Comment #106848

Posted by Longhorn on June 20, 2006 12:34 PM (e)

PaulC wrote:

I wanted to concur with some of the comments about sexual reproduction and other kinds of gene transfer. Mutation gets all the attention (probably from comics and B-movies about radioactivity) but a lot of adaptation occurs without it.

A question I have is this: How important was mutation in terms of contributing to the differences between whales and their most recent land-mammal ancestors?

One reason I ask is that I have experience with dogs. I like dogs. And I know that all dogs descended from a population of wolves that lived on earth perhaps 130,000 years ago. And some dogs are remarkably different than others, for instance, Chihuahuas and Saint Bernards. How much of a role did mutation play in causing the differences among dogs? I’m sure that plain old sexual reproduction played an enormous role in bringing about these differences. Within the population of wolves that evolved into all these dogs, there was already a significant amount of genetic material present in the population. With different combinations of these organisms reproducing over 130,000 years, you are going to get some really significant differences. And just look at dog-breeders. They know how to combine certain dogs to get very refined traits. Saint Bernards are wonderful at rescuing people in cold weather. Chihahuas are small and ugly. Dobermans are sleek and fierce. Bulldogs have an incredibly powerful bite.

Now extrapolate that out 15 million years. Could plain old sexual reproduction have been the driving force in resulting in a population of land mammal changing into whales? I don’t know. I am sure that sexual reproduction did play a very important role. But were mutations important as well? For instance, did some mutations contribute to the fluke on the whale’s tail? Did some mutations contribute to the nostrils evolving into blow holes? I wonder. I don’t experience mere sexual reproduction (absent mutations) causing that level of phenotypic change across generations. And we do see mutations that occur to sex cells causing some bigger leaps from parents to offspring. For instance, the elephants man and fruit flies with legs for antennae. And cycloptic lambs. And people with multiple digits. But then again 15 million years is a long time.

One thing that is clear is that sexual reproduction contributed significantly to the differences between whales and their land mammal ancestors. For one, sexual reproduction can combine two sequences of DNA, one inherited from the mother and one inherited from the father. And each of these sequences can affect a trait. This combining of the two genes can result in an intensification of the trait, for instance, the rhino’s horn and the giraffe’s neck.

However, as Sir Toejam was good to note, in terms of geologic time, sexual reproduction is a recent phenomenon. It may have first evolved 1.5 billion years ago. And even before sexual reproduction evolved we obviously still had many organisms having different genomes than their parents did. However, compare the degree of difference among organisms before sexual reproduction evolved and after it evolved. The degree of difference is remarkably different before and after the evolution of sexual reproduction. Most asexually reproducing organisms are much more alike than most sexually reproducing organisms. For instance, I’m quite different than elephants. Also, in the vast majority of cases, asexually reproducing organisms are much more like their parent than sexually reproducing organisms are like their parents. In sum, I think sexual reproduction played a huge role in causing the differences among nearly all sexually reproducing organisms.

Comment #106852

Posted by Lurker on June 20, 2006 12:48 PM (e)

'Rev Dr' Lenny Flank wrote:

Most trained scientists accept that the earth revolves around the sun, however some don’t. A smaller group of trained scientists think it’s wrong, way wrong.

http://www.fixedearth.com

http://www.biblicalastronomer.org

How oh how can we tell which is right?

One way to answer this is to say personal experience tells you the minority opinion is wrong. However, when it comes to evolution, the personal experience of the minority group says they have the correct interpretation of the evidence. So really you haven’t answered the question.

Comment #106853

Posted by Aureola Nominee, FCD on June 20, 2006 12:56 PM (e)

One way to answer this is to say personal experience tells you the minority opinion is wrong. However, when it comes to evolution, the personal experience of the minority group says they have the correct interpretation of the evidence.

What is this supposed to mean? Even with heliocentrism the “personal experience of the minority group says they have the correct interpretation of the evidence.”

Alas, arguments from personal experience are inconclusive, unless one has evidence to show in support. Which evolutionary biologists have (plenty of), and geocentric astronomers have not.

Comment #106854

Posted by GuyeFaux on June 20, 2006 12:59 PM (e)

One way to answer this is to say personal experience tells you the minority opinion is wrong. However, when it comes to evolution, the personal experience of the minority group says they have the correct interpretation of the evidence. So really you haven’t answered the question.

Personal experience would tell us the Sun revolves around the Earth (which personal experience tells us is flat).

Comment #106856

Posted by Lurker on June 20, 2006 1:08 PM (e)

H. Humbert wrote:

Lurker, whether or not evolution and speciation occurs it isn’t a debate between two opposing groups of scientists. It’s between religious fundamentalists and everyone else.

There isn’t a single evolution-denier who didn’t arrive at that conclusion because of their religious beliefs. If there was legitimate scientific doubt on the matter then it would be more than just the religious nutters more that willing to step forward and point it out. But there isn’t. You have to honestly ask yourself, why is that?

Not a single one? Somehow I doubt that.

Anyway, you’re using this argument to avoid my question. Use another scientific fact if you want - say the Big Bang. There’s a minority opinion there too. Tell me how you know the majority opinion is correct when there is some disagreement among the experts who are trained in such matters and who have looked at the evidence only to conclude differently. Do you simply side with the majority because there are more of them and is that a wise thing to do? I’m curious.

Comment #106857

Posted by Longhorn on June 20, 2006 1:12 PM (e)

Paul C wrote:

I wanted to concur with some of the comments about sexual reproduction and other kinds of gene transfer.

It is important not to think of sexual reproduction merely as a kind of “gene transfer.” “Gene transfer” suggests that the genome is being transferred from parent(s) to offspring with the various nucleotides in a fairly similar sequence. Meanwhile, sexual reproduction includes the first phase of meiosis, which results in many of paternal nucleotides and many of the maternal nucleotides breaking apart and then reforming in a very different order than the order that preceded the breaking apart. The first phase of meiosis results in a pretty dramatic transformation in the sequences of the nucleotides that make up the genome.

Here is Mayr on what happens at the genetic level during sexual reproduction:

“It took more than 100 years of study to achieve a full understanding of the meaning and process of sexual reproduction. Darwin searched unsuccessfully all his life for the source of genetic variation. It required knowledge of the process of gamete formation and the difference between genotype and phenotype and their roles in natural selection, as well as an understanding of population variation.

“August Weismann and a group of cytologists found the answer. They showed that in sexual reproduction, gamete formation is preceded by two special cell divisions. During the first division, homologous maternal and paternal chromosomes attach themselves tightly to each other and then may break at one or several places. The broken chromosomes exchange parts with each other so that they now consist of a mixture of paternal and maternal chromosome pieces. This process is called crossing over…In the second cell division preceding the formation of the gametes, the chromosomes do not divide, but one of each pair of homologous chromosomes goes randomly to one daughter cell and the other chromosome to the other daughter cell. As a result of this ‘reduction division’ the ‘haploid’ number of chromosomes in each gamete is half that of the ‘diploid’ chromosome number of the zygote produced by the fertilized egg. This sequence of two cell divisions preceding gamete formation is called meiosis” (What Evolution Is, p. 103-4).

Comment #106859

Posted by Lurker on June 20, 2006 1:20 PM (e)

Alas, arguments from personal experience are inconclusive, unless one has evidence to show in support. Which evolutionary biologists have (plenty of), and geocentric astronomers have not.

Personal experience would tell us the Sun revolves around the Earth (which personal experience tells us is flat).

The pile of evidence must be interpreted by the experts. The interpretation process is a ‘personal experience’ so personal experience can’t be dismissed altogether.

What is considered relevant evidence, how much weight should be assigned to each piece of evidence and how much evidence do we need are questions that need to be answered by these people. It’s a pretty subjective process since there are no objective standards available to help us answer these questions. Scientists on both sides have looked at the evidence and reached different conclusions. Who’s right and how can we confirm this?

Comment #106860

Posted by Longhorn on June 20, 2006 1:26 PM (e)

Lurker wrote:

Tell me how you know the majority opinion is correct when there is some disagreement among the experts who are trained in such matters and who have looked at the evidence only to conclude differently. Do you simply side with the majority because there are more of them and is that a wise thing to do? I’m curious.

The same way you determine that the earth is not flat disk that rests on the back of the giant tortoise. For one, experience as much of the alleged events as you can.

Of course, you are reliant on the experts to some extent. For instance, presumably you don’t have the technology to observe what happens at the genetic level when organisms sexually reproduce, or the technology or expertise to calculate the age of the known of universe, or the technology to calculate the age of certain important fossils. I recognize that this is a pain. But that’s life. We all have limitations in terms of time, expertise, energy, abilities and technology. But we often can do quite a bit of leg work.

Comment #106866

Posted by Longhorn on June 20, 2006 1:31 PM (e)

Scientists on both sides have looked at the evidence and reached different conclusions. Who’s right and how can we confirm this?

Cells evolved into elephants. And I’ve presented a link to an article that presents some of the data that can help one determine this. I also recommend Mayr’s book What Evolution Is.

Comment #106878

Posted by guthrie on June 20, 2006 1:35 PM (e)

Anyway, you’re using this argument to avoid my question. Use another scientific fact if you want - say the Big Bang. There’s a minority opinion there too. Tell me how you know the majority opinion is correct when there is some disagreement among the experts who are trained in such matters and who have looked at the evidence only to conclude differently. Do you simply side with the majority because there are more of them and is that a wise thing to do? I’m curious.

I dont know about everyone else, but I tend to distinguish stuff that clearly fits all available data, and that nobody argues agout, really. Examples such as the structure of benzene, or, more controversially, relativity, which has passed every test so far proposed for it.
Then you go to the big bang theory. This is still somewhat in flux, they had to add in inflation to make the numbers work out, which is a hint that it isnt quite right. In a case like this, you simply have to have patience, and accept that the majority “opinion” is the best answer we have so far, i.e. as of June 2006, the Big Bang theory is the most all encompassing, and accurate cosmological model so far proposed and tested. This does not mean it is THE TRUTH, or that it will not be superseded.
So, in cases where there are genuine disagreements between large numbers of experts, I reccomend patience, and a dose of scepticism.

But this does not apply in the case of evolutionary biology. No theory with better explanatory power has been proposed; no attack on it has been substantiated using the scientific method. The final step in distinguishing between worthy and unworthy “experts” is to look at what experiments they are doing to test their theories. In teh case of evolutionary biologists- lots of experiments.
IN the case of ID’ists and creationists- none that I am aware of.

Comment #106885

Posted by Aureola Nominee, FCD on June 20, 2006 1:40 PM (e)

Lurker:

when scientists have different opinions on how to interpret data, they discuss among themselves until a general consensus arises.

This is exactly the situation with the theory of evolution, as well as heliocentrism.

Does this guarantee that scientists have reached the Truth™?

No, of course. That’s not even the reason for doing science. Only that they have done their best given the current state of our knowledge.

The only way to overthrow the general consensus of scientists on anything is to pile up more evidence, not to handwave and claim that expert consensus isn’t relevant because a few contrarians are unconvinced. Live with it.

Comment #106911

Posted by PaulC on June 20, 2006 1:57 PM (e)

Lurker:

Do you simply side with the majority because there are more of them and is that a wise thing to do? I’m curious.

This kind of question presupposes that all beliefs are the same. I have a lot of working assumptions in my mind and would be at a loss without them, but I’m not sure what it is to “side with” a group of people? Do I need to take a loyalty oath?

In some cases, I really have no basis for a belief other than an appeal to authority. E.g., it’s my understanding that mainstream scientists have strong evidence that some form of the Big Bang is correct and that the steady state universe is incorrect. But that’s an area that I have not evaluated. It’s not that I “side with” the majority, but there is a proposition in my head along with the equivalent of a footnote explaining what it’s doing there. If I had a chance to bet my own money against somebody finding new evidence supporting the steady state view, I might do that. This is connected with a meta-belief that in practice authorities who study an issue carefully often have some basis for their conclusion, which often turns out to be correct. It might not be true in any particular case, but I don’t think I’d go wrong placing my money on that side consistently given no better basis.

In other cases I actually have a chance to evaluate the evidence and the reasoning. For instance, I can tell you with near certainty whether a member of a certain class of discrete algorithms will finish in a reasonable amount of time with the correct answer. I can usually provide a mathematical proof in fact. It’s still possible that I could be wrong, and I have made enough mistakes in the past. But I have very high confidence in my judgment.

Evolution falls in the middle ground. I’m not a biologist, so my means of evaluating the evidence is not as rigorous as it could be. However, there’s a preponderance of evidence for common descent as well as genetic variation. Go to any natural history museum and you will see that directly. I am also familiar with thought experiments and simulations that make a convincing case for evolution-like processes on a smaller scale. Given that we need some way to explain the diversity of life on earth, it is really not much of a leap for me to look at other kinds of examples of self-organization and genetic algorithms (that I can evaluate very rigorously) and conclude that over the time scales and populations involved, these would probably be adequate to explain what we see. Evolution would happen independent of any other “design” events since nothing would stop it in light of what we now know for certain. In fact, it occurs often enough to be observed directly on human time scales. Absent any direct evidence of a “designer”, the most reasonable conclusion is that evolution is the whole story.

But to recap, I don’t just jumble my beliefs together in my brain. Each one has some kind of justification attached to it, some more rigorous than others. If a belief ever fails to apply, I would revisit its justification and see where it errs. I don’t “side with” beliefs. I merely make my decisions using them as provisional assumptions.

Comment #106918

Posted by GuyeFaux on June 20, 2006 2:03 PM (e)

Scientists on both sides have looked at the evidence and reached different conclusions. Who’s right and how can we confirm this?

Of course, it would be a lie to claim that there are not divergent theories within neo-Darwinism. This results in vigorous and fruitful scientific debate, resulting in new experiments and overall a better understanding of the science. As a lay observer, I think it’s impossible to absolutely to chose sides within the debate.

However, ID people and Creationists are not participating in this scientific debate; they start and end with their subjective distate of evolutionary theory.

Comment #106921

Posted by GSLamb on June 20, 2006 2:08 PM (e)

Lurker wrote:

Tell me how you know the majority opinion is correct when there is some disagreement among the experts who are trained in such matters and who have looked at the evidence only to conclude differently. Do you simply side with the majority because there are more of them and is that a wise thing to do? I’m curious.

I am getting pretty tired of this trend of using “Fair and Balanced” as a way of attacking people/theories.

Scientist A: I have done countless studies and years of research on X. The data clearly shows that X = Y.

Scientist B: Bah! {waves hand dismissively}

Which of these seem more thought out? Should we place equal weight behind these ideas?

Majority opinion does not dictate truth. Majorities can be wrong. Scientific truth is based upon testable hypotheses. Not only must you have an ‘opinion’, but this hypothesis must be testable. You should be able to say if X, then we should see Y.

Evolutionary theory does that. So far, the ‘minority view’ has yet to show evidence and testable hypotheses to back their claims. I put more weight behind thousands of experiments and years of data than hand-waving and just-so stories.

Here’s the kicker, though. Should someone come along with a better theory, one that explains the observed data and predicts results better than current evolutionary theory, that will gain majority consensus.

This has been the homework of ID, YEC, and the others. Sadly, none of them have tried. All they have done is attempt to poke holes in the current theory. You cannot build a house by telling your neighbor he built his house wrong.

Comment #106923

Posted by Coin on June 20, 2006 2:14 PM (e)

Lurker wrote:

The pile of evidence must be interpreted by the experts.

Not really. You are just as free to look at the pile of evidence yourself. Helpfully, evolutionary biology is one of those cases where the experts have consistently provided detailed explanations of why and how they reached the interpretations they did.

Lurker wrote:

It’s a pretty subjective process since there are no objective standards available to help us answer these questions.

Not really. The entire point of the process is to be objective. This is the entire reason why the scientific process is considered valuable, because it’s one of the closest things to an objective method of determining answers humankind has, when it’s followed. Just because you don’t agree with the standards scientists use to weigh and select the value and trustworthiness of evidence doesn’t mean that those standards are subjective.

Now, of course there are going to be edge cases where the scientific method cannot conclusively come to a finding, and it requires a subjective value judgement to judge the worthiness of the different possibilities the scientific process presents. In these cases the scientifically correct thing to do would be to gather more evidence.

But, of course, evolution is not one of those edge cases; the evidence behind the theory of evolution is so overwhelming and consistent that you have to throw out nearly all the evidence science has ever collected before the case for evolutionary speciation is no longer clear and compelling. The big bang, on the other hand, is one of these ambiguous edge cases (in some ways– the question these days isn’t so much “did it happen”, but “exactly how and why did it happen”), and this is precisely what makes it a fascinating and important research subject.

Comment #106933

Posted by Tom Curtis on June 20, 2006 4:54 PM (e)

Andrew Mclure:

Anyway, if you want to play around with this, the files are linked below, assuming you know Perl. No, there isn’t that much to them. (To make these work, save them in a CGI-capable directory as “index.pl” and “evo.pm”, and put in the same directory a world-writable subdirectory named “i” for it to save images in.) I will probably play around with the parameters some more later to see if I can tease the program into doing anything interesting.

Perhaps it would be easier to link to a site on Biomorphs:

http://www.rennard.org/alife/english/biomintrgb.html

Better yet would be a link to Darwin Pond, which demonstrates natural selection, not artificial selection (like WEASEL programs and Biomorphs) and is fun to play with:

http://www.ventrella.com/Darwin/darwin.html

Comment #106935

Posted by Tom Curtis on June 20, 2006 5:22 PM (e)

Longhorn:

A question I have is this: How important was mutation in terms of contributing to the differences between whales and their most recent land-mammal ancestors?

One reason I ask is that I have experience with dogs. I like dogs. And I know that all dogs descended from a population of wolves that lived on earth perhaps 130,000 years ago. And some dogs are remarkably different than others, for instance, Chihuahuas and Saint Bernards. How much of a role did mutation play in causing the differences among dogs? I’m sure that plain old sexual reproduction played an enormous role in bringing about these differences.

Granting that sexual reproduction played that role in the diversification of dogs, it is still not that significant as a source of long term genome diversity. To see this, suppose that all genes in modern dogs were found in their wolf ancestors; ie, that all the differences between dog breeds are brought about by reshuffling combinations of alleles, and not by the introduction of new alleles. What would follow from this is that individual dog breeds have significantly less genetic diversity than the original wolf population, so that they would be approaching a limit to how much further selection could influence their traits. In fact, excluding the introduction of new alleles by mutation, all members of the more extreme breeds (such as chihuahuas) should be effectively genetic clones.

For further selection to be effective, the genetic diversity has to be renewed by mutation. So while sexual reproduction may be the main factor in generating initial varieties, over the long term of 10’s of millions of years, it is the mutations that are the effective source of variety.

Where sexual reproduction is truly important for the long term of evolution is the ability it provides to uncouple beneficial mutations from harmful mutations in the same genome; and to combine beneficial mutations from a variety of ancestors into one genome. This increases the pace at which sexually reproducing species can evolve relative to non-sexually reproducing species by about fifty percent.

Comment #106942

Posted by Longhorn on June 20, 2006 6:15 PM (e)

Tom Curtis wrote:

Granting that sexual reproduction played that role in the diversification of dogs, it is still not that significant as a source of long term genome diversity. To see this, suppose that all genes in modern dogs were found in their wolf ancestors; ie, that all the differences between dog breeds are brought about by reshuffling combinations of alleles, and not by the introduction of new alleles.

Thanks. But is it reasonable to characterize sexual reproduction merely as “reshuffling combinations of alleles?” Isn’t the first phase of meiosis doing something more than that? It can result in significantly different sequences of nucleotides. In other words, you might have sequence ATCGATCG that becomes GCGATATG. Then there is the fertilization event that puts these brand new sequences of nucleotides next to each other. That causes significant genetic and phenotypic diversity. Just look at humans. I’m very different than either of my parents. I received 23 chromosomes from my father, and 23 from my mother. The 23 chromosomes I received from my father consist of nucleotides that are in a very different sequence than are the nucleotides in his 46 chromosomes. The 23 chromosomes I received from my mother consist in nucleotides that are in a very different sequence than are the nucleotides in her 46 chromosomes. Sexual reproduction is not a blending process.

Also, there was a significant amount of genetic material present in that population of wolves that evolved into dogs.

What would follow from this is that individual dog breeds have significantly less genetic diversity than the original wolf population, so that they would be approaching a limit to how much further selection could influence their traits. In fact, excluding the introduction of new alleles by mutation, all members of the more extreme breeds (such as chihuahuas) should be effectively genetic clones.

So you are saying that much of the variation that we see in dogs was caused by mutations? Do you have evidence for that or something that I could read? I know that in breading certain dogs, you can get very different offspring. I see it. Especially over numerous. Though I suspect some of these dogs have some new mutations, they don’t appear to be any big deal in terms of their phenotypes. The offspring are as different as they are from their parents because their parents reproduced. I suspect that sexual reproduction played a very large role in causing the variation among dogs. First, sexual reproduction happens very frequently. Second, it results in offspring that are significantly different than their parents. Dogs don’t give birth to elephants. But dogs can birth to offspring that are quite different than they are. Finally, we are talking about massive lengths of time.

Here is a quote from Mayr on the importance of sexual reproduction/genetic recombination in evolution:

“Evolution in sexually reproducing organisms consists of genetic changes from generation to generation in populations, from the smallest local deme to the aggregate of interbreeding populations in a biological species. Numerous processes, particularly mutation, contribute to these genetic changes to supply the phenotypic variation needed by selection. The most important factor is recombination, which is largely responsible for the virtually inexhaustible supply of new genotypes in every generation” (What Evolution Is, p. 157).

Comment #106945

Posted by Longhorn on June 20, 2006 6:56 PM (e)

It does seem to me that there has been limits to the phenotypic diversity that sexual reproduction has brought about. For instance, if humans keep on reproducing for 20 million years, I tend to doubt we would get a human with a rhino-like horn, unless there are some mutations that occur affecting the nose bone. A rhino-like horn is a significantly different trait than what any human has now, though I know some humans with some pretty darn big noses and big bumps on their noses. Moreover, the combination of events that seems to bring about the biggest change from parent(s) to offspring is sexual reproduction plus mutations to gametes.

Comment #106947

Posted by 'Rev Dr' Lenny Flank on June 20, 2006 7:01 PM (e)

One way to answer this is to say personal experience tells you the minority opinion is wrong.

Of course, everyone ELSE also claims that THEIR “personal experience” tells them that YOUR opinion (and by the way, fundamentalism is a minority within Christianity) is wrong. (shrug)

However, when it comes to evolution, the personal experience of the minority group

You mean the IDers ….?

says they have the correct interpretation of the evidence.

How can they tell?

So really you haven’t answered the question.

Actually I did. You just weren’t bright enough to catch it. (shrug)

Comment #106948

Posted by 'Rev Dr' Lenny Flank on June 20, 2006 7:02 PM (e)

Not a single one? Somehow I doubt that.

Then name one. (shrug)

Comment #106950

Posted by Sir_Toejam on June 20, 2006 7:07 PM (e)

unless there are some mutations that occur affecting the nose bone.

after all the discussion so far, it really surprises me that you forgot to include the selection half of the equation.

If there was a significant selective pressure (for example, chicks dig guys with horns - even small ones- over guys that don’t) favoring the development of human “horns”, the likelihood of a trait like that spreading throughout a population would be much higher.

with 6 billion humans on the planet, I rather doubt there HASN’T been a mutation of one kind or another that produced a human “horn” or something similar.

If it’s a heritable trait, and chicks dig it…

a lot of us might be sporting horns in a relatively short (hundreds of thousands of years; maybe even less) time.

Comment #106951

Posted by 'Rev Dr' Lenny Flank on June 20, 2006 7:09 PM (e)

Scientists on both sides have looked at the evidence and reached different conclusions.

Um, no. Scientists have studied the evidence and concluded that life evolves. On the other side, a small group of religious nuts has decided that evolution is against their religion.

If you disagree, please please by all means go ahead and name five non-religious scientists who disagree with evolution.

Heck, name ONE.

And you still have not answered MY question about a movoing earth. After all, there too, by your own standards, are two groups of scientists who have studied the evidence and reached different conclusions.

So how do YOU decide whether or not the earth revolves around the sun …. ……?

It’s a simple question. Why are you so reluctant to answer it?

Comment #106956

Posted by Sir_Toejam on June 20, 2006 7:15 PM (e)

[quote]It does seem to me that there has been limits to the phenotypic diversity[/quote]

ahh, rethinking your post here, I see what you were trying to emphasize now.

to some extent, that is true, but it really is on a scale of probabilities. new traits are appearing all the time, you just don’t hear about them much.

It truly is amazing the kinds of bizarre phenotypes that have occured in humans over recorded history; and with 6 billion of us, it’s hard to rule much out.

but, yes, the probability of any specific aberrant trait can be quite low.

Comment #106960

Posted by David Sadler on June 20, 2006 7:25 PM (e)

Hello to the group,

If Dembski likes Coulter, well, that’s a problem, but I see no great problem with his random mutation generator. I would have more of a problem with one that is programmed to target a mutation and then select it for survival as is suggested by the initiator of this thread. That’s intelligent design isn’t it?

This mutation and selection creative force is interesting. Before life there was no life. How did mutation and selection work on lifeless, non-reproducing clumps of whatever to build a non-living organism awaiting only the spark of life to bring it to life as the first living thing in the cosmos?

Thanks,

David Sadler
www.david-sadler.org

Comment #106962

Posted by steve s on June 20, 2006 7:41 PM (e)

it wouldn’t.

Comment #106963

Posted by Torbjörn Larsson on June 20, 2006 7:44 PM (e)

“Use another scientific fact if you want - say the Big Bang. There’s a minority opinion there too.”

What minority opinion would that be? Big bang is considered a fact in much the same way evolution is. The observed radiation relicts (cosmic microwave background radiation) together with other observations serve to do this. Exactly as the observed fossil relicts together with other observations makes common descent with variation a fact.

The discussion now is about which mechanisms were acting and how they work. ( http://cosmicvariance.com/2006/03/16/wmap-results-cosmology-makes-sense/ ) Similar to the current discussions of mechanisms within evolution. The difference is that it is a younger science with fewer observations.

BTW, I don’t get guthrie’s commentary about inflation. It is ad hoc, but it explains many details of bigbang and cosmology, and there are theories explaining its mechanisms. Currently it is the most favored explanation. (See the link above.)

Inflation is not a hint of anything wrong AFAIK but supports the bigbang theory nicely. It explains the flatness of the universe which no other mechanism does for general relativity cosmologies. It explains observed density variations by blowing up initial quantum variations. Finally it extends the principle of universalness by making our universe a non special universe among infinitely many others in some variants of endless inflation multiverse theory.

Comment #106968

Posted by Torbjörn Larsson on June 20, 2006 8:05 PM (e)

David says:

“How did mutation and selection work on lifeless, non-reproducing clumps of whatever to build a non-living organism awaiting only the spark of life to bring it to life as the first living thing in the cosmos?”

If you look at abiogenesis ideas, for example pre-RNA and RNA worlds, you see that variation and selection works there too. But it works differently since you start out with chemistries with production instead of replication. Subsequent developments which gave more or less faithful replication as the fitter systems still doesn’t give you “mutation” as we know it. It isn’t until genetic material appear and gave faithful replication you can start discussing in terms of mutations.

BTW, defining “life” and its demarcation properties (“spark of life”? naa, don’t think so.) are as hard to define as the concept of “species”. It is as futile to point at any individual system and say “it was the first living thing” on earth as to point at any individual organism and say “it was the first gobbledygook”. We know it when we see it, though.

And how do you know that life on earth was first? With the number of galaxies and considering the young age of the earth, the way to bet is that it wasn’t.

Comment #106971

Posted by Torbjörn Larsson on June 20, 2006 8:11 PM (e)

“It isn’t until genetic material appear and gave faithful replication you can start discussing in terms of mutations.”

Umm, that goes for “natural selection” as well since it also assumes replicting systems. Before that it is ordinary selection, I think.

Comment #106973

Posted by Torbjörn Larsson on June 20, 2006 8:20 PM (e)

David says:

“I would have more of a problem with one that is programmed to target a mutation and then select it for survival as is suggested by the initiator of this thread. That’s intelligent design isn’t it?”

If you read the thread you can see that this is a tripple straw man. It isn’t proposed, any proposal similar to it isn’t ID, any proposal similar to evolution isn’t ID.

Congratulations, I haven’t seen so much straw in one place before!

Comment #106974

Posted by David Sadler on June 20, 2006 8:31 PM (e)

REF: Comments #106960, 68, 71

“How did mutation and selection work on lifeless, non-reproducing clumps of whatever to build a non-living organism awaiting only the spark of life to bring it to life as the first living thing in the cosmos?”
- dss -

Torbjörn Larsson said:

“… it works differently since you start out with chemistries with production instead of replication.”

“… “natural selection” … assumes replicting systems. Before that it is ordinary selection …”

What is the survivability or “production” benefit or advantage for any such change in non-living matter leading that matter to change in the direction of a non-living organism waiting for life to enable it to reproduce thereby allowing natural selection to begin?

David Sadler
www.david-sadler.org

Comment #106976

Posted by steve s on June 20, 2006 8:40 PM (e)

Hey David, you know what else gets me? These evolutionists talk about ‘gene duplication’. They say ‘gene duplication’ is sooooo important for evolution. But how was there ‘gene duplication’ before there were genes, huh? The Darwinists gloss over that little problem with their fairy tale.

Comment #106977

Posted by 'Rev Dr' Lenny Flank on June 20, 2006 8:42 PM (e)

awaiting only the spark of life

(sigh)

There is no “spark of life”.

Vitalism has been dead for well over a century. Do try and keep up, would you?

Comment #106978

Posted by PaulC on June 20, 2006 8:55 PM (e)

David Sadler:

I see no great problem with his random mutation generator.

I see no problem if you’re trying to illustrate what happens when you insert random errors in strings repeatedly. But if the point was to support any claim about evolution, then you should have a system that resembles evolution in some fashion.

It’s true: the English language did not evolve on old modems without error correcting protocols, nor could it. Quick, somebody inform the media!

Comment #106980

Posted by PaulC on June 20, 2006 8:57 PM (e)

Lenny:

There is no “spark of life”.

Now he tells me. You mean I just wasted months and thousands of dollars constructing a huge lightning rod and digging up body parts?

Comment #106982

Posted by Tom Curtis on June 20, 2006 9:21 PM (e)

Longhorn:

Thanks. But is it reasonable to characterize sexual reproduction merely as “reshuffling combinations of alleles?” Isn’t the first phase of meiosis doing something more than that? It can result in significantly different sequences of nucleotides. In other words, you might have sequence ATCGATCG that becomes GCGATATG. Then there is the fertilization event that puts these brand new sequences of nucleotides next to each other. That causes significant genetic and phenotypic diversity. Just look at humans. I’m very different than either of my parents. I received 23 chromosomes from my father, and 23 from my mother. The 23 chromosomes I received from my father consist of nucleotides that are in a very different sequence than are the nucleotides in his 46 chromosomes. The 23 chromosomes I received from my mother consist in nucleotides that are in a very different sequence than are the nucleotides in her 46 chromosomes. Sexual reproduction is not a blending process.

I think for practical purposes, sexual reproduction is a shuffling process that gives you at random, one of the two alleles of each gene from your mother, and one of the two from your father. It is possible that a crossover could take place within the sequence of a gene, and thus create new alleles, but I suspect the possibility is largely irrelevant to the course of evolution.

You should remember that less than 5% of the human genome codes for any gene, so the chance of crossover within a gene sequence in a given meiotic division is small (about 1 in 7). This assumes that there is no mechanism ensuring crossovers occur outside of coding sequences, which would greatly surprise me. This is because if a crossover is not perfectly aligned within a gene sequence, it is almost certain to be disastrous in that it will generate a multiple basepair deletion or repeat, or a frameshift.

Assuming there is perfect alignment, a crossover within the sequence will only generate a new allele if the crossover occurs between two distinct alleles, and if the difference between the alleles are on different sides of the crossover point. That later requires that the alleles differ in at least two loci, at a minimum. Considering the number of genes in which humans do not diverge from chimps at all, the number distinct alleles that effect protein sequence within a interbreeding human population would be very small.

So while meiosis is probably a mechanism of mutation, it is probably a very rare one, paling into insignificance compared to mutations resulting from mitosis, and heat.

So you are saying that much of the variation that we see in dogs was caused by mutations? Do you have evidence for that or something that I could read? I know that in breading certain dogs, you can get very different offspring. I see it. Especially over numerous. Though I suspect some of these dogs have some new mutations, they don’t appear to be any big deal in terms of their phenotypes.

Actually, for some breeds (such as chihauhua’s and daschunds) mutations have almost certainly been necessary to achieve their current form. For others this is not so, though they will still typically have many alleles not present in their ancestral population. German Shepherd like dogs could easily be bred to from wolf stock without additional mutations, but almost certainly they still possess alleles not present in the ancestral wolf population.

What I am actually saying, however, is that as selection continues to drive a population’s traits in a particular direction, a greater and greater percentage of the alleles effecting that trait will be new mutations that were not present in the ancestral population. If this were not so, in the limit we would have the absurd situation were all the current diversity of vertebrate life comes about from simple reshuffling the alleles present in on of Pikaia’s close cousins.

As for the scale at which, relative to a given time, most new alleles are new mutations, I cannot say. I suspect most of the differences between ourselves and chimpanzees would be due to new mutations. That does not deny that the initial divergence would have come about be sorting amongst pre-existing alleles. The difference between Lucy and chimp ancestor contemporary might be largely due to different combinations of alleles widely present in an ancestral population. (Nor is it to deny that to a first approximation in terms of physiology, we are chimps.) The difference between whales and hippos, on the other hand, would be almost entirely due to new alleles not present in their common ancestor.

Here is a quote from Mayr on the importance of sexual reproduction/genetic recombination in evolution:

“Evolution in sexually reproducing organisms consists of genetic changes from generation to generation in populations, from the smallest local deme to the aggregate of interbreeding populations in a biological species. Numerous processes, particularly mutation, contribute to these genetic changes to supply the phenotypic variation needed by selection. The most important factor is recombination, which is largely responsible for the virtually inexhaustible supply of new genotypes in every generation” (What Evolution Is, p. 157).

New genotypes, not new alleles. A genotype is the whole genome of an individual, and a new genotype is created each time you reshuffle the pre-existing alleles in meiosis.

Comment #106983

Posted by Longhorn on June 20, 2006 9:23 PM (e)

Sir T, thanks for the good comments.

T wrote:

after all the discussion so far, it really surprises me that you forgot to include the selection half of the equation.

I didn’t forget. But, as you know, varying levels of reproduction success didn’t by itself cause a population of land mammals to evolve into whales. Essential to this population transforming in the way that it did was the genetic and phenotypic differences that existed among many of the members of this population. And this genetic and phenotypic variation occurred partly because of sexual reproduction. However, as you suggest, this wonderful evolutionary change happened partly because some organisms produced offspring and other organisms did not.

Comment #106985

Posted by Henry J on June 20, 2006 9:27 PM (e)

Re “Where sexual reproduction is truly important for the long term of evolution is the ability it provides to uncouple beneficial mutations from harmful mutations in the same genome; and to combine beneficial mutations from a variety of ancestors into one genome. This increases the pace at which sexually reproducing species can evolve relative to non-sexually reproducing species by about fifty percent.”

Fifty percent? All that expense and stuff for just half again? Huh.

Henry

Comment #106987

Posted by David Sadler on June 20, 2006 9:57 PM (e)

PaulC said regarding the random generator, “[if] the point was to support any claim about evolution, then you should have a system that resembles evolution in some fashion.”

Evolution says random mutations and natural selection builds more complex organisms. Right?

What magic creative force caused non-living matter to organize into the first living entity?

I know, evolutionists have a problem with the term ‘life’ or ‘living’ because the theory just doesn’t address that, so just ignore life for now. What creative force or benefit directs the building of non-living matter towards an organization that leads to life sustaining assembly?

David Sadler
www.david-sadler.org

Comment #106988

Posted by David Sadler on June 20, 2006 10:14 PM (e)

Lenny said, “There is no “spark of life.”

Okay. But do you agree there are things that are living and things that are non-living? Do you agree that a person who is living can die and once dead they are no longer living?

I’m not trying to be cute. I just wish to hear from you that there is life and non-life.

David Sadler
www.david-sadler.org

Comment #106989

Posted by Longhorn on June 20, 2006 10:17 PM (e)

Tom Curtis, thank you very much. That was very helpful and interesting. I appreciate your taking the time.

It is possible that a crossover could take place within the sequence of a gene, and thus create new alleles, but I suspect the possibility is largely irrelevant to the course of evolution.

Why do you say that?

Actually, for some breeds (such as chihauhua’s and daschunds) mutations have almost certainly been necessary to achieve their current form.

What reason is there to believe that?

You may well be right. But even if that is true, I suspect that Chihuahuas are as different as they are from their wolf ancestors partly because of sexual reproduction. Sexual reproduction is frequent and results in offspring that are quite different than their parents. Sexual reproduction also results in an organism with a genome that is significantly different than either of its parents has. And we know that genotype affects phenotype. Finally, 130,000 years is a long time.

I suspect most of the differences between ourselves and chimpanzees would be due to new mutations.

What reason is there to believe that? I suspect that mutations played an important role in bringing about the differences between humans and chimps. For one, I have 46 chromosomes and chimps have 48. That has got to be important, right? However, I submit that sexual reproduction also played a significant role in bringing about the differences between humans and chimps. Sexual reproduction is frequent and results in offspring that are quite different than their parents. Sexual reproduction also results in an organism with a genome that is significantly different than that of either of its parents has. And we know that genotype affects phenotype. Finally, we are talking about massive lengths of time, maybe 5.5 million years. And look how different I am from my parents. I’m not an elephant. But I’m very different than they are.

The difference between whales and hippos, on the other hand, would be almost entirely due to new alleles not present in their common ancestor.

Amost entirely? I wonder. Why do you say that? Mutations were probably important. But really significant beneficial mutations seem to be a small percentage of all mutations. And humans (and probably whales) have between 20,000 to 25,000 genes. So there would have to be multiple beneficial mutations affecting the same body part, for instance, the air pathway. I’m sure mutations were important. But I suspect that sexual reproduction and the combining of certain genetic sequences was also important. If we breed certain rhinos, we can get bigger and bigger horns. Obviously there is a limit. We are not going to get a horn that is 50 feet long. But we can get ones that are pretty big, especially if keep breeding the rhinos with the longest horn and if we nurture the long-horned rhinos the way we do Chihuahuas. Over long periods of time Chihuahuas wouldn’t do well out in the savannah on their own.

Do you think the evolution of nostrils to blowholes in whales was caused by multiple mutations? How many mutations do you think that would have taken?

Also, just to clarify, you think the alleles present in whales that were not present in Pakicetus were caused by mutation rather than by meiosis?

New genotypes, not new alleles. A genotype is the whole genome of an individual, and a new genotype is created each time you reshuffle the pre-existing alleles in meiosis.

I don’t see what you mean? Could you elaborate on that? Is Mayr wrong?

Comment #106995

Posted by steve s on June 20, 2006 10:30 PM (e)

Okay. But do you agree there are things that are living and things that are non-living? Do you agree that a person who is living can die and once dead they are no longer living?

As Wodehouse would say, my jaw dropped so hard it’s a wonder it didn’t come off its hinges.

Comment #106996

Posted by Anton Mates on June 20, 2006 10:34 PM (e)

David Sadler wrote:

What magic creative force caused non-living matter to organize into the first living entity?

I know, evolutionists have a problem with the term ‘life’ or ‘living’ because the theory just doesn’t address that, so just ignore life for now. What creative force or benefit directs the building of non-living matter towards an organization that leads to life sustaining assembly?

Um, if we’re ignoring “life,” why ask that last question? It’s not any more relevant to evolutionary theory because you asked it in a more roundabout way.

But the short (and, again, non-evolutionary) answer would be “chemistry,” which isn’t really any more “magic” than the forces which caused a big cloud of gas and dust to organize into the solar system.

Comment #107000

Posted by Andrew McClure on June 20, 2006 10:43 PM (e)

Tom Curtis: Very neat links, thanks!

Comment #107001

Posted by Rilke's Granddaughter on June 20, 2006 10:44 PM (e)

Sadler wrote:

What magic creative force caused non-living matter to organize into the first living entity?

Chemistry.

Comment #107002

Posted by David Sadler on June 20, 2006 10:48 PM (e)

Steve said, “… evolutionists talk about ‘gene duplication’. They say ‘gene duplication’ is sooooo important for evolution. But how was there ‘gene duplication’ before there were genes, huh? The Darwinists gloss over that little problem with their fairy tale.”

Hi, Steve,

Evolutionary theory just can’t handle the question of how non-life became life. It can not handle why non-living matter organized itself into a configuration or assemblage capable of becoming alive.

Obviously, at some point non-life became alive in the Evolutionist creation story, but as you say, they gloss over the problem. If they would really think about that for just a little while in search for an answer, they might instead produce some questions about the absence of any chemical or physical creative force to organize non-living matter in such a fashion.

I would just like to hear someone try to answer the question. No where in nature do we see assemblages capable of living that are not alive. Do we?

David Sadler
www.david-sadler.org

Comment #107005

Posted by David Sadler on June 20, 2006 10:57 PM (e)

To this question…

“What creative force or benefit directs the building of non-living matter towards an organization that leads to life sustaining assembly?”

… Anton and Rilke answered, “chemistry.”

That is a claim without proof, is it not?

Can you point to the lab and chemist that can mix chemicals into an assemble of a non-living cell even with the aid of a super computer?

Can you point to any natural non-living entity that has all the parts of a living cell?

David Sadler
www.david-sadler.org

Comment #107006

Posted by Andrew McClure on June 20, 2006 11:01 PM (e)

David Sadler wrote:

What magic creative force caused non-living matter to organize into the first living entity?

I see no reason to think magic must have been involved.

But here is a 1-paragraph summary of one hypothesis as to what may have predated the universal common ancestor. In short, there are chemical reactions which naturally form the building blocks living things are made from; these reactions can be induced in a lab, and the conditions under which these chemical reactions naturally happen may have been possible at certain points in the earth’s history.

So far, little is known about abiogenesis. Scientists seem to be reaching a consensus that self-catalyzing strands of RNA predated “organisms” as we think of them today, but exactly what happened before that is beyond the ability of science to say at the present time.

David Sadler wrote:

Evolutionary theory just can’t handle the question of how non-life became life.

That is because it is not part of evolution. Evolutionary theory explains the diversity and development of new life forms. It does not explain where the single common ancestor came from because that is a different subject explained by different theories. It is for the same reason that scientific theories about the origin of hurricanes do not explain why earthquakes occur. It is for the same reason that maps of the United States usually do not show the location of Ottowa.

David Sadler wrote:

No where in nature do we see assemblages capable of living that are not alive. Do we?

Viruses, prions. Endospores, maybe.

The problem with this discussion is you are using the word “life” as if it means something specific. Perhaps it would help if you defined exactly what you believe this word means.

Comment #107009

Posted by Sir_Toejam on June 20, 2006 11:13 PM (e)

But here is a 1-paragraph summary of one hypothesis as to what may have predated the universal common ancestor.

David, if you get a chance to read Dawkin’s Blind Watchmaker, he uses an interesting analogy of how clay particles can “self organize” and “replicate” in a stream bed, IIRC. I always thought that was a useful explanation for thought purposes, to give an idea of how molecules can do these things without significant external input.

Comment #107012

Posted by David Sadler on June 20, 2006 11:29 PM (e)

Hi, Andrew,

I appreciate you trying on this question.

You said, “Evolutionary theory explains the diversity and development of new life forms. It does not explain where the single common ancestor came from because that is a different subject explained by different theories.”

I was taught differently and those teachings are still everywhere.

google: ‘primordial soup first cell evolution’

You get things like this…
How Life First Bubbled Up
http://www.astrobio.net/news/modules.php?op=modload&name=News&file=article&sid=1175&mode=thread&order=0&thold=0

It says, “A central question in evolution is how simple versions of these cells, or vesicles, first arose and began the process of competition that drove the evolution of life.”

The rest of the article is speculation because no one knows as you and this article admits. This is an odd situation for the “Evolution is Fact” crowd that wishes exclusive exposure in our public schools.

Were you not taught the primordial soup component of evolution in school?

David Sadler
www.david-sadler.org

Comment #107014

Posted by Sir_Toejam on June 20, 2006 11:36 PM (e)

The rest of the article is speculation because no one knows as you and this article admits. This is an odd situation for the “Evolution is Fact” crowd that wishes exclusive exposure in our public schools.

awww, and here I thought you might actually have honest questions.

Instead, you’re just a troll, aren’t you?

as to whether I myself was ever taught that abiogenisis was part of the ToE, no. I guess my teachers were a little smarter than yours.

go figure.

Comment #107015

Posted by David Sadler on June 20, 2006 11:37 PM (e)

Hi, Sir_Toejam,

I have read Dawkin’s Blind Watchmaker and am aware of the clay and water idea. You say that, “molecules can do these things without significant external input.” Do you know of any experiment using clay and running water or any example in nature of non-living assemblages capable of living but which are not alive as the result of such interaction between clay and water?

David Sadler
www.david-sadler.org

Comment #107017

Posted by Sir_Toejam on June 20, 2006 11:39 PM (e)

sorry, you’ve made yourself clear. You’re not really interested in information, but only your agenda.

if you’ve read Dawkins, you can just as easily go and check the references listed in the book yourself.

bye bye.

Comment #107018

Posted by Anton Mates on June 20, 2006 11:41 PM (e)

Longhorn wrote:

Tom Curtis wrote:

Granting that sexual reproduction played that role in the diversification of dogs, it is still not that significant as a source of long term genome diversity. To see this, suppose that all genes in modern dogs were found in their wolf ancestors; ie, that all the differences between dog breeds are brought about by reshuffling combinations of alleles, and not by the introduction of new alleles.

Thanks. But is it reasonable to characterize sexual reproduction merely as “reshuffling combinations of alleles?” Isn’t the first phase of meiosis doing something more than that? It can result in significantly different sequences of nucleotides. In other words, you might have sequence ATCGATCG that becomes GCGATATG.

That would generally be classed under “mutation,” as such a sequence change would actually produce a new allele, not simply reshuffle them.

Then there is the fertilization event that puts these brand new sequences of nucleotides next to each other. That causes significant genetic and phenotypic diversity. Just look at humans. I’m very different than either of my parents. I received 23 chromosomes from my father, and 23 from my mother. The 23 chromosomes I received from my father consist of nucleotides that are in a very different sequence than are the nucleotides in his 46 chromosomes. The 23 chromosomes I received from my mother consist in nucleotides that are in a very different sequence than are the nucleotides in her 46 chromosomes.

Your DNA sequences shouldn’t be very different from those of either parent, or you probably wouldn’t have made it this far! As I recall from intro genetics, double or triple crossovers are quite rare, so it’s unlikely that any of your chromosomes is any more weirdly arranged than one end of mom’s stitched to the other end of dad’s.

So you are saying that much of the variation that we see in dogs was caused by mutations? Do you have evidence for that or something that I could read?

Well, there’s Lindblad-Toh et al., “Genome sequence, comparative analysis and haplotype structure of the domestic dog” (Nature, 2005). They say, “Grey wolf and dog are most closely related (0.04% and 0.21% sequence divergence in nuclear exon and intron sequences, respectively).” .04% or .21% may not sound like a lot of difference, but the dog genome’s about 2.5 billion bases total, so that’s a lot of mutations.

I know that in breading certain dogs, you can get very different offspring. I see it. Especially over numerous. Though I suspect some of these dogs have some new mutations, they don’t appear to be any big deal in terms of their phenotypes. The offspring are as different as they are from their parents because their parents reproduced.

I think you’re reasoning backwards here. Most mutations (in offspring that survive to adulthood, anyway) produce little or no visible effect, so usually you can chalk down the difference between parent and offspring to sexual recombination. However, the few mutations that do have an obvious effect can have a huge one–albinism, gigantism, dwarfism, and so forth. Those are rare, but over evolutionary timespans they’re incredibly important. Moreover, without mutation sexual reproduction would do nothing for variation–different combinations of alleles would be impossible if mutation hadn’t created different alleles per gene in the first place!

Remember, too that wolf offspring tend to look much more like either parent than do the offspring of a pair of randomly-chosen dogs. You get surprising-looking mutts precisely because there’s all this variation in the dog gene pool and combining two randomly-drawn genomes tends to give you unexpected results–that doesn’t happen with wolves. That suggests that dogs have a lot of genetic variation (of a particular sort, at least, with gross morphological consequences) that wolves lack. And that implies that that variation’s due to mutation since dogs split off from wolves.

Put another way, if modern dog breeds are simply particular assortments of extant wolf genes, then we’d expect the occasional wolf to be born looking at least vaguely like one breed or another, but that doesn’t happen. OTOH, if modern dog breeds are distinctive because of particular mutations, then it makes sense that that doesn’t happen, because the particular suite of mutations distinguishing a given dog breed from a wolf is highly unlikely ever to occur again.

I suspect that sexual reproduction played a very large role in causing the variation among dogs. First, sexual reproduction happens very frequently.

So does mutation. Nachmana & Crowella (“Estimate of the Mutation Rate per Nucleotide in Humans,” Genetics 2000) estimate that each human has about 175 mutations vs. their parents–most not being in coding regions, of course.

Comment #107021

Posted by Rilke's Granddaughter on June 20, 2006 11:49 PM (e)

In the somewhat unlikely event that you’re actually interested in answers, rather than simply repeating ad nauseum your inaccurate beliefs about science, I’ll respond.

Sadler wrote:

Hi, Andrew,

I appreciate you trying on this question.

You said, “Evolutionary theory explains the diversity and development of new life forms. It does not explain where the single common ancestor came from because that is a different subject explained by different theories.”

I was taught differently and those teachings are still everywhere.

No, they are not everywhere. They aren’t in Minnesota, University of Chicago, Notre Dame, or Johns Hopkins.

google: ‘primordial soup first cell evolution’

You get things like this…
How Life First Bubbled Up
http://www.astrobio.net/news/modules.php?op=modl…

It says, “A central question in evolution is how simple versions of these cells, or vesicles, first arose and began the process of competition that drove the evolution of life.”

The rest of the article is speculation because no one knows as you and this article admits.

Perhaps you should re-read the article; it is talking the evolution of the first replicators - not how those replicators arose. This kind of confusion is frequent in non-scientists.

This is an odd situation for the “Evolution is Fact” crowd that wishes exclusive exposure in our public schools.

We teach that the theory of evolution is fact because it is the best explanation to fit the observation that evolution has occured. It is backed by more data more solidly than pretty much any scientific theory going.

Were you not taught the primordial soup component of evolution in school?

No, my teachers were intelligent. Apparently your’s were somewhat lacking.

Comment #107022

Posted by Andrew McClure on June 20, 2006 11:54 PM (e)

David Sadler wrote:

I was taught differently and those teachings are still everywhere.

It is possible. I hear there are various problems with the public schools in certain areas.

However, I must admit, I find an alternate possibility also likely: Maybe you weren’t taught any differently, you just happened to have a biology class at some point in your life in which the primordial soup hypothesis or something like it was brought up, and it’s just that you either weren’t paying attention or didn’t understand exactly what was being presented to you.

David Sadler wrote:

Were you not taught the primordial soup component of evolution in school?

Nope.

Though a girl in my high school did replicate the Miller-Urey experiment as her senior project.

Either way, whether they are often discussed together or not– “evolution” is a big and vague term, it’s easy for stuff to get lumped in with it– abiogenesis is not part of evolutionary theory, and the validity of the theory of evolution is in no way dependent on anything that predates the universal common ancestor. Meanwhile I would find it highly questionable to speak of the primordial soup or RNA world hypotheses as “component[s] of evolution”, since while evolutionary processes certainly would have played a part in the continuing development of such proto-life forms, it is not certain to me that the mechanisms of evolution would have worked in the same way we understand it to work in modern, cellular organisms (or even that we can yet say for certain what the exact mechanisms of evolution in such an environment would have been). I think both are worthy of being taught in schools since they are valid scientific theories, but the differences between them are important to understand.

By the way, I’m still curious what exactly you think “life” means.

Comment #107023

Posted by Anton Mates on June 20, 2006 11:56 PM (e)

David Sadler wrote:

To this question…

“What creative force or benefit directs the building of non-living matter towards an organization that leads to life sustaining assembly?”

… Anton and Rilke answered, “chemistry.”

That is a claim without proof, is it not?

No. It is easy to prove that natural chemical reactions can produce a replicator; even the creationist’s caricature “a whole lot of atoms banged into each other just so…” is clearly not physically impossible. What is not yet known is the feasibility and likelihood of each particular chemical pathway leading to a replicator. The field of pre-biotic chemistry is concerned with exploring this.

Can you point to the lab and chemist that can mix chemicals into an assemble of a non-living cell even with the aid of a super computer?

Any of them, if they’ve got a planet-sized lab and several million years to kill. Most prebiotic chemists, of course, are looking for ways to streamline this a bit.

Can you point to any natural non-living entity that has all the parts of a living cell?

Such an entity would be a contradiction in terms, unless you believe in vitalism.

Comment #107024

Posted by PaulC on June 21, 2006 12:02 AM (e)

David Sadler:

What magic creative force caused non-living matter to organize into the first living entity?

That process was neither magic nor a “force” (a term with a specific meaning in a scientific context) and for that matter, it was not evolution.

Darwinian evolution cannot begin until you have replicating cells capable of passing genes to the next generation and altering these genes. As I noted in a much earlier post, the next generation also has to have the potential of being larger than the current one by some percentage or else there is no way for successful genes to proliferate. The silly text randomizing applet is missing all of these things as well as selection, so it is not relevant to a discussion of evolution.

By the way, the process of getting from non-living matter to living matter is usually called abiogenesis, and it’s not very well understand, particularly as compared to evolution. My (non-scientific) hunch is that it will be understood well in the next few decades, but this has no relevance to a discussion of evolution, a non-controversial scientific principle that applies to living things (or more generally, thing that can reproduce themselves). By definition the question of the appearance of the first self-reproducing entity lies outside its scope.

Comment #107026

Posted by David Sadler on June 21, 2006 12:18 AM (e)

Hi, Sir_Toejam,

My questions are honest. I’m just trying to see if anyone has any better answers than the last time I had a discussion on this subject many years ago.

I see more and more evolutionists coming over to the ID side especially since the conclusion of the Human Genome Project. The amount of information required simply has been a tipping point for many who now find the ID model easier to believe than the random assemblage of non-living matter into life capable entities.

You said, “as to whether I myself was ever taught that abiogenisis was part of the ToE, no. I guess my teachers were a little smarter than yours.”

I’m sure my teachers didn’t understand it either and they taught what was in the text books.

I was taught evolution exclusively until I graduated from college. Right after that, I read some books offering scientific criticism of evolution and over a period of years I accepted ID as the model that best explains what we can actually observe and test.

I won’t be here long. Just taking a break from research on a New Energy article I’m writing. It’s interesting what people will believe in the absence of evidence. Then I read this article in today’s news…

http://www.uncommondescent.com/index.php/archives/1173
Respected Cornell geneticist rejects Darwinism in his recent book
Genetic Entropy & the Mystery of the Genome
by John Sanford

I added it to my evolution file and saw this…

http://abcnews.go.com/US/wireStory?id=315976
Famous Atheist Now Believes in God
Antony Flew: One of World’s Leading Atheists Now Believes in God, More or Less, Based on Scientific Evidence
The Associated Press

The link is no longer any good, but genetic complexity has brought Flew over to the ID side.

I see there is still a lot of ‘maybe’ and ‘if’ and ‘possibly’ in the explanations of evolution. ‘Maybe this happened. It could happen this way.’ Things like that. That hasn’t changed. What I do see changing is the number of people becoming aware of genetic complexity due to the visibility of GM food, cloning, the HGP and such. Slowly, attitudes are changing and I believe the glory days of Darwin are definitely over. The discovery of DNA can’t be put back into the bottle. The Internet is also a factor in this emerging awareness. The controlled media now has competition. All sides can be heard now if one is willing to listen.

David Sadler
www.david-sadler.org

Comment #107027

Posted by Sir_Toejam on June 21, 2006 12:18 AM (e)

Though a girl in my high school did replicate the Miller-Urey experiment as her senior project.

really? That’s pretty cool. Not exactly your standard high school fare.

did she successfully replicate it, is the big question :)

Comment #107028

Posted by Sir_Toejam on June 21, 2006 12:19 AM (e)

I see more and more evolutionists coming over to the ID side

nope. not honest.

like i said, you’ve made yourself clear.

Comment #107029

Posted by Sir_Toejam on June 21, 2006 12:22 AM (e)

offering scientific criticism of evolution

no such animal exists.

If you took the time to even understand what “scientific” means, you could grasp that on your own.

evidently, not only were your teachers extremely deficient on their knowledge of theory, but on their very knowledge of the scientific process itself.

You should sue your school for lax teaching standards.

Comment #107030

Posted by Sir_Toejam on June 21, 2006 12:26 AM (e)

The link is no longer any good, but genetic complexity has brought Flew over to the ID side.

IIRC, there’s a reason your link doesn’t work anymore. didn’t he “fly right back” shortly thereafter?

better check that one a bit further….and you still haven’t listed any evolutionary biologists that have “seen the error of their ways”.

nope, pretty clear your just a standard issue creobot, spending the night trolling.

You should go before you embarass yourself any further.

Comment #107031

Posted by Sir_Toejam on June 21, 2006 12:29 AM (e)

oh, and one last thing, before you wax philosophical about “all the evidence against the ToE from my idiotic non-evolutionary biologist sources, you might try checking the index to creationist claims over on the Talkorigins.org archive.

I’m sure whatever you think is so novel has already been claimed by a hundred or more creobots before you, and refuted after the first time posted.

the links to the talkorginis archive is right on the front page of PT, from there it’s easy enough to get to the index of creationist claims.

go there and stop wasting everybody’s time, including your own.

Comment #107033

Posted by Andrew McClure on June 21, 2006 12:35 AM (e)

Though a girl in my high school did replicate the Miller-Urey experiment as her senior project.

really? That’s pretty cool. Not exactly your standard high school fare.

did she successfully replicate it, is the big question :)

This was for my high school’s big difficult Chemistry II AP class… The class had a final project of the student’s choosing in place of a final exam. It was a widely known fact that the maximum score on this project was always a 99, no matter what. The teacher was of the opinion that a score of 100 was perfect, and nobody is perfect, so the most you can get is a 99.

By the conclusion of her project the girl who did the Miller-Urey thing could show that she had produced, while not as many of the amino acids that Miller-Urey did, she had in fact successfully synthesized some of them.

I wasn’t there, but the teacher’s response was later paraphrased to me as something like “OK, you created life, so you get a 99.5”.

Comment #107034

Posted by Sir_Toejam on June 21, 2006 12:39 AM (e)

she had in fact successfully synthesized some of them.

nice! from what I’ve heard, it’s not that easy of an experiment to duplicate, even for grad students.

but then, O-chem lab was one of my worst subjects as an undergrad :)

Comment #107035

Posted by Jonathan Abbey on June 21, 2006 12:42 AM (e)

David Sadler wrote:

I see more and more evolutionists coming over to the ID side especially since the conclusion of the Human Genome Project. The amount of information required simply has been a tipping point for many who now find the ID model easier to believe than the random assemblage of non-living matter into life capable entities.

Really? Name two.

Comment #107041

Posted by Tom Curtis on June 21, 2006 1:49 AM (e)

Longhorn:

It is possible that a crossover could take place within the sequence of a gene, and thus create new alleles, but I suspect the possibility is largely irrelevant to the course of evolution.

Why do you say that?

I thought I had explained. The reasons are:

a) Crossovers within a gene sequence are (probably) relatively uncommon compared to normal point mutations?

This follows from the simple fact that gene sequences are so small a portion of the overall genetic sequence. Most crossovers will fall in non-coding sequences. In fact, as inexact crossovers within a coding sequence are likely to render a gene unfunctional, it is likely that mechanisms have evolved favouring crossovers in non-coding sequences, so that crossovers in sequences are likely to be far rarer than a simple statistics on sequence length would indicate. In contrast, it is likely that every human zygote has, on average 10 point mutations which have an effect on the phenotype, and far more that effect the sense of codons in coding sequences but are neutral in effect.

b) Inexact crossovers are likely to be so deleterious that they will be eliminated immediately and have no long term effect on evolution.

c) Exact crossovers, ie, crossovers within a coding sequence that do not cause frameshift, deletion or duplication, are likely to not increase the number of alleles.

If the male sequence is AAAAA, and the female sequence is aaaba, a crossover at between the second two points will produce two varients (one discarded are random), AAaba, and aaAAA. But these two variants are only the original two variants. No new alleles have been produced. (Note: case only indicates parental origin of sequence.) Only if there are two differences between the two alleles, and the crossover point lies between the two will a new allele be produced. Even then, it will not be different in principle to a point mutation producing the same effect.

Which brings us to point

d) Because the effective alleles variants amongst humans are so few for any given gene, the chance of a crossover producing a significant variant are minor.

By effective allele, I mean an allele that effects protein sequence, and has a physiological effect. I believe that for most human genes, there are very few effective variants, and most of those differ in only one location, so that for the majority of genes, an exact crossover would not produce new alleles.

You may well be right. But even if that is true, I suspect that Chihuahuas are as different as they are from their wolf ancestors partly because of sexual reproduction. Sexual reproduction is frequent and results in offspring that are quite different than their parents. Sexual reproduction also results in an organism with a genome that is significantly different than either of its parents has. And we know that genotype affects phenotype. Finally, 130,000 years is a long time.

I don’t think you are following the logic of the situation.

If a population is under selection for a trait, alleles not favourable to that trait get eliminated from the gene pool. These are replaced by mutation so that the genetic diversity remains fairly constant in the long term. The result is that when further selection occurs, the next population will have a combination of original and mutant alleles. Because some of the original alleles get eliminated after each round of selection, each round results in successively fewer original alleles surviving, and consequently a higher proportion of mutant alleles in the gene pool.

Think of a battalion of infantry. After each battle a portion of its soldiers are killed, and replaced by new recruits. After each successive battle, fewer and fewer of the members of the batalion are survivers of the original battalion. If, in each battle, 5% are killed, after 10 battles only 60% of the battalion are original members. After 20 battles only 36%; after 50 battles, 8%. (The formula is ((1 - proportion killed) to the power of the number of battles).)

Now instead of a battalion, consider our original population of wolves. Suppose (which seems very conservative) that Chihuahuas have all the alleles present in the original stock except for 5%. On this analogy, after a million years, only 60% alleles of the Chihuahua descendants will have come from their wolf ancestors. After 2 million, only 36%; after 5 million, only 8%. So while sexual recombination is the most important factor in producing variety for selection over the short term (with only 5% of the variety coming from mutation), it is of minor relevance in the long term (accounting for only 8% of alleles).

Now, this analysis tacitly assumes that elimination of alleles is solely a matter of chance, whereas it is really a matter of selection and chance. So no doubt numerous alleles will survive because no close variant of the allele can improve fitness. But most of these hoary veterans are found in areas where there is little variation due to selection. They are found amongst our 60 odd percent of genes which have close analogues in yeast, and which consequently have little to do with morphology or behaviour of canines as such.

And this analysis, that the majority of alleles for a variable trait get eliminated in the long term of selection, must be correct. If it is not, we are committed to the majority of alleles in modern humans having existed in the first pre-cambrian worm that exploited sexual reproduction, and who is the ancestor not just of all humans, but of all mosquitoes and snails as well.

Comment #107050

Posted by Lurker on June 21, 2006 2:17 AM (e)

Dr. Lenny wrote:

Um, no. Scientists have studied the evidence and concluded that life evolves. On the other side, a small group of religious nuts has decided that evolution is against their religion.

If you disagree, please please by all means go ahead and name five non-religious scientists who disagree with evolution.

Heck, name ONE.

OK, John A. Davidson. If you say he’s not a ‘real scientist’ qualified to have an opinion on such things then please by all means go ahead and give me the official definition of ‘real scientist’ so I’ll know.

Yep, we’re all biased. So what? A religious person may be acting out of bias OR they may be as neutral/objective as humanly possible. I could be biased and as such I could be wrong about my conclusions…..so could you.

And that’s my question - how do you know the group with the minority opinion reached the wrong conclusion due to bias? What is the objective criteria for determining such a thing?

And you still have not answered MY question about a movoing earth. After all, there too, by your own standards, are two groups of scientists who have studied the evidence and reached different conclusions.

So how do YOU decide whether or not the earth revolves around the sun …. ……?

It’s a simple question. Why are you so reluctant to answer it?

I agree with the majority opinion because it seems reasonable to me. I can’t prove they are right anymore than you can.

Now how about you answer MY question instead of dancing around it…how do you know the group with the minority opinion reached the wrong conclusion due to bias?

Comment #107052

Posted by Andrew McClure on June 21, 2006 2:29 AM (e)

OK, John A. Davidson.

The 19th-century Canadian politician?

Comment #107062

Posted by Aureola Nominee, FCD on June 21, 2006 6:44 AM (e)

Lurker:

Each of us is a minority of one. Of course, when we have to interact with anybody else we need to work from a shared description of reality. The consensus of scientists is just that: a shared description of reality.

It can be wrong. The minority view might be more right. So, what do we do?

We look for further evidence. In the meantime, we adopt the description of reality shared by most experts. It really is as simple as that.

A sign that a minority view might be correct is that it gains acceptance out of the weight of evidence. A sign that a minority view is due to bias is that it gains acceptance due to other reasons.

With evolution, as well as with heliocentrism, this is precisely what happened: the (then) minority views that evolution happens and that the sun does not revolve around the earth won on the field of evidence. The (now) minority contrary views appeal only to people with a theological axe to grind. For the moment, the case is closed.

Yet, in science “cases” do not get “closed”; if those now in the minority manage to produce enough evidence to convince the majority, the pendulum may well swing the other way. But it takes way more than a declaration of contrariness.

Comment #107063

Posted by Popper's Ghost on June 21, 2006 7:01 AM (e)

One way to answer this is to say personal experience tells you the minority opinion is wrong. However, when it comes to evolution, the personal experience of the minority group says they have the correct interpretation of the evidence. So really you haven’t answered the question.

Yeah, it’s a real problem when the only kind of argument you understand is an argument from authority. Then you are left, like Lurker, asking over and over “But how do we know which authority is right?”

Comment #107064

Posted by 'Rev Dr' Lenny Flank on June 21, 2006 7:03 AM (e)

Hey Sadler, do you know what a “blithering idiot” is?

You are “blithering”.

Comment #107065

Posted by 'Rev Dr' Lenny Flank on June 21, 2006 7:08 AM (e)

OK, John A. Davidson.

BWA HA HA HA AH AHA HA AH !!!!!!!!!!!!!!!!

And that’s my question - how do you know the group with the minority opinion reached the wrong conclusion due to bias? What is the objective criteria for determining such a thing?

It’s called “the scientific method”. I’m quite sure you’ve never heard of it.

I agree with the majority opinion because it seems reasonable to me. I can’t prove they are right anymore than you can.

Tell you what, Lurker, I have a way to test your idea that “science is just an opinion, and no one can tell whether your opinion or mine is right”. Near my house is the Sunshine Skyway Bridge. I’d be very happy to take you there, where you can loudly declare that the “majority opinion” that “gravity pulls things down” isn’t any more capable of proof than the “minority opinion” that “gravity doesn’t pull things down”. Then you can jump off the bridge to demonstrate the equal validity of your “minority opinion”.

Are you game?

Comment #107067

Posted by 'Rev Dr' Lenny Flank on June 21, 2006 7:10 AM (e)

who now find the ID model

Even the luminaries at Discovery Institute now admit that there isn’t any “ID model” to teach, and have given up entirely on ID in favor of “teaching the controversy about evolution”.

Do TRY and keep up, would you … ?

Comment #107069

Posted by 'Rev Dr' Lenny Flank on June 21, 2006 7:17 AM (e)

I won’t be here long.

I don’t blame you.

Comment #107070

Posted by Popper's Ghost on June 21, 2006 7:23 AM (e)

how do you know the group with the minority opinion reached the wrong conclusion due to bias?

By examining the evidence. Duh.

Comment #107074

Posted by Popper's Ghost on June 21, 2006 7:49 AM (e)

Syntax Error: mismatched tag 'quote'

Comment #107075

Posted by Popper's Ghost on June 21, 2006 7:52 AM (e)

David Sadler wrote:

What magic creative force caused non-living matter to organize into the first living entity?

You only need a magic creative force if you think that living matter differs from non-living matter by virtue of having some magical quality or essence; that’s the ancient but obsolete view known as vitalism. But we now know that “life” is simply matter arranged in certain ways that produce certain functions or attributes such as metabolism, growth, reproduction, etc. When one gives up the notion that magic must have been involved, then it becomes an area for empirical investigation, i.e., science. And scientists are working on it, while IDiots say “it was designed”, which says nothing useful at all.

I see more and more evolutionists coming over to the ID side especially since the conclusion of the Human Genome Project.

No you don’t; you’re lying.

Respected Cornell geneticist rejects Darwinism in his recent book

What a surprise it is to find out that, after an unpleasant divorce, he became a born again Christian and young earth creationist. Gee, I wonder if that, rather than the scientific evidence, might have led him to reject “Darwinism”.

The link is no longer any good, but genetic complexity has brought Flew over to the ID side.

Flew is a confused old philosopher who doesn’t know diddly squat about abiogenesis. He was misled by religious zealot Gerald Schroeder. Flew has stated: “I now realize that I have made a fool of myself by believing that there were no presentable theories of the development of inanimate matter up to the first living creature capable of reproduction.”

That this is the best that you can do says a lot.

Comment #107076

Posted by Popper's Ghost on June 21, 2006 8:02 AM (e)

Yet, in science “cases” do not get “closed”; if those now in the minority manage to produce enough evidence to convince the majority, the pendulum may well swing the other way. But it takes way more than a declaration of contrariness.

It’s not really accurate that cases do not get closed in science. No evidence can possibly contradict the belief that the earth goes around the sun. New evidence may refine the details of our understanding of the orbit, but they won’t change the already observed facts. And that refined understanding will not possibly ever include the notion that the orbit of the earth around the sun is affected by undetectable pixies.

Comment #107077

Posted by Aureola Nominee, FCD on June 21, 2006 8:15 AM (e)

Popper’s Ghost:

Every object in the Solar System moves along elliptical orbits, with one of the foci located in the theoretical “centre of mass” of the whole system (and even this is an approximation).

This “centre of mass” is located inside the Sun, but not in its geometric centre; so, the Sun is no more “fixed” than the Earth.

That’s what I meant when I said that no case is ever closed in science. To quote from Isaac Asimov:

[W]hen people thought the Earth was flat, they were wrong. When people thought the Earth was spherical they were wrong. But if you think that thinking the Earth is spherical is just as wrong as thinking the Earth is flat, then your view is wronger than both of them put together.

The heliocentric model of the Solar System was wrong. Of course the geocentric model was more wrong, yet the case was not closed, after all.

Of course, colloquially I will cheerfully say that the planets of our system revolve “around the Sun”. But that’s not the point.

Comment #107087

Posted by Longhorn on June 21, 2006 8:47 AM (e)

Anton Mates wrote:

That would generally be classed under “mutation,” as such a sequence change would actually produce a new allele, not simply reshuffle them.

My point is this: The first phase of meiosis often results in a sequence of nucleotides being in a significantly different order than what preceded the first phase. So, for instance, we may have the following sequence at particularly location on a chromosomes:

AC
AT
CT
GC
AC
GC
AC

After crossing over, we may have this sequence:

AC
AT
CT
GC
AT
GC
AT

That is significant. For genotype affects phenotype, and we have a new sequence.

Well, there’s Lindblad-Toh et al., “Genome sequence, comparative analysis and haplotype structure of the domestic dog” (Nature, 2005). They say, “Grey wolf and dog are most closely related (0.04% and 0.21% sequence divergence in nuclear exon and intron sequences, respectively).” .04% or .21% may not sound like a lot of difference, but the dog genome’s about 2.5 billion bases total, so that’s a lot of mutations.

How do you know that those sequences were caused by mutations? Second, how do you know that those sequences are those ones that made the key difference?

You get surprising-looking mutts precisely because there’s all this variation in the dog gene pool and combining two randomly-drawn genomes tends to give you unexpected results—that doesn’t happen with wolves. That suggests that dogs have a lot of genetic variation (of a particular sort, at least, with gross morphological consequences) that wolves lack. And that implies that that variation’s due to mutation since dogs split off from wolves.

But do you know that it is mutation that is causing the difference? The first phase of meiosis causes a fairly significant difference.

So does mutation. Nachmana & Crowella (“Estimate of the Mutation Rate per Nucleotide in Humans,” Genetics 2000) estimate that each human has about 175 mutations vs. their parents—most not being in coding regions, of course.

But beneficial mutations are a small percentage of all mutations.

Comment #107089

Posted by Popper's Ghost on June 21, 2006 8:54 AM (e)

But that’s not the point.

Well you’ve clearly missed the point, as you are addressing a strawman. I never said anything about the sun being “fixed”. It’s absurd to say the heliocentric model of the solar system was wrong, as the earth does go around the sun – which is not to say that it goes around its geometric center. There is no such thing as “the” heliocentric model of the solar system; models evolve. As I stated, “New evidence may refine the details of our understanding of the orbit”.

Comment #107090

Posted by Popper's Ghost on June 21, 2006 8:56 AM (e)

BTW, you say “that’s what I meant when I said that no case is ever closed in science”, but I think I understand what you meant better than you do – people commonly forget the context in which they make their statements, and the context here is about evolution. The case is closed that evolution occurs.

Comment #107092

Posted by Longhorn on June 21, 2006 8:58 AM (e)

Tim Curtis, thanks.

Most crossovers will fall in non-coding sequences.

That is very interesting. I didn’t know that. Do you have a link where I can learn more about that?

I don’t think you are following the logic of the situation.

If a population is under selection for a trait, alleles not favourable to that trait get eliminated from the gene pool. These are replaced by mutation so that the genetic diversity remains fairly constant in the long term. The result is that when further selection occurs, the next population will have a combination of original and mutant alleles. Because some of the original alleles get eliminated after each round of selection, each round results in successively fewer original alleles surviving, and consequently a higher proportion of mutant alleles in the gene pool.

Think of a battalion of infantry. After each battle a portion of its soldiers are killed, and replaced by new recruits. After each successive battle, fewer and fewer of the members of the batalion are survivers of the original battalion. If, in each battle, 5% are killed, after 10 battles only 60% of the battalion are original members. After 20 battles only 36%; after 50 battles, 8%. (The formula is ((1 - proportion killed) to the power of the number of battles).)

Now instead of a battalion, consider our original population of wolves. Suppose (which seems very conservative) that Chihuahuas have all the alleles present in the original stock except for 5%. On this analogy, after a million years, only 60% alleles of the Chihuahua descendants will have come from their wolf ancestors. After 2 million, only 36%; after 5 million, only 8%. So while sexual recombination is the most important factor in producing variety for selection over the short term (with only 5% of the variety coming from mutation), it is of minor relevance in the long term (accounting for only 8% of alleles).

Now, this analysis tacitly assumes that elimination of alleles is solely a matter of chance, whereas it is really a matter of selection and chance. So no doubt numerous alleles will survive because no close variant of the allele can improve fitness. But most of these hoary veterans are found in areas where there is little variation due to selection. They are found amongst our 60 odd percent of genes which have close analogues in yeast, and which consequently have little to do with morphology or behaviour of canines as such.

And this analysis, that the majority of alleles for a variable trait get eliminated in the long term of selection, must be correct. If it is not, we are committed to the majority of alleles in modern humans having existed in the first pre-cambrian worm that exploited sexual reproduction, and who is the ancestor not just of all humans, but of all mosquitoes and snails as well.

I’m sorry, but I don’t see what you are getting at. If it is not inconvenient, could you explain it another way? Thanks

Comment #107093

Posted by Aureola Nominee, FCD on June 21, 2006 9:04 AM (e)

I think I understand what you meant better than you do.

I think you might - just might - wish to reconsider the stunning idiocy of this sentence.

Who needs IDiots, when we have idiots on our own side?

Comment #107094

Posted by Popper's Ghost on June 21, 2006 9:11 AM (e)

I think I understand what you meant better than you do.

I think you might - just might - wish to reconsider the stunning idiocy of this sentence.

The stunning idiocy is your ad hominem response when I just explained what I meant by it. I suggest that you don’t have a very good grasp of cognition nor a good theory of meaning.

Who needs IDiots, when we have idiots on our own side?

Indeed, idiots who argue that the earth doesn’t go around the sun. Next you’ll be telling us that the moon doesn’t go around the earth. Wow, relativity, what a concept! But it’s stupid, idiotic, and moronic to introduce it here in the grand strawman fashion that you have.

Comment #107095

Posted by PaulC on June 21, 2006 9:13 AM (e)

On the subject of vitalism, I’ve often wondered what percentage of Americans really grasp the fact that vitalism is fully discredited.

Obviously the people pushing ID have to be careful to avoid the impression of being vitalists, and are quick to call everything under the sun a “machine.” But I doubt it fully sinks in, as the blithering of a recent contributor to this comment board has made clear.

I’m of the view that the non-vitalist theory of life is far more counterintuitive than evolution. If you believe a cell can do all the things we see it do, including differentiate into heterogeneous populations capable of forming things like elephant tusks, then it’s not much of a stretch to suppose its descendants can evolve over generations.

The development process from embryo to adult really looks like a miracle. We have good reason to think every step is the result of chemistry and physics, but we haven’t filled in all the gaps. For some reason, most creationists are not stupid enough to look for their god in these fleeting gaps. Why is that? The main difference, I guess, is that we can replay development in the lab. But I think that objectively speaking, it is much harder to believe a single cell can hold the recipe for a cheetah running at 60 mph then it is to believe humans and chimps share a common ancestor.

Comment #107096

Posted by Aureola Nominee, FCD on June 21, 2006 9:20 AM (e)

Popper’s Ghost:

I know what my point was, and you do not, your idiotic contention notwithstanding.

The only strawmen here are yours. Science is not in the business of making final pronouncements on Truth™, and theories are always - always - open to revision. THAT was my point. Your insistence to the contrary counts exactly for nothing.

With this, I’ll stop answering your idiotic declarations. You are welcome to your tiny, selfreferential world of arrogance; what I regret is that you pretend you are on the side of science.

Comment #107097

Posted by Longhorn on June 21, 2006 9:21 AM (e)

Tim Curtis wrote:

Where sexual reproduction is truly important for the long term of evolution is the ability it provides to uncouple beneficial mutations from harmful mutations in the same genome; and to combine beneficial mutations from a variety of ancestors into one genome. This increases the pace at which sexually reproducing species can evolve relative to non-sexually reproducing species by about fifty percent.

Here is what Mayr says on sexual reproduction: “The process of sexual reproduction makes far more new phenotypes available for natural selection than does mutation of any other process. It is the major source of variation found in populations of sexual species. This capacity for the production of large amounts of variation would seem to be the major selective advantage of sexual reproduction (see the special section ‘The Evolution of Sex,’ Science 281(1988): 1979-2008). It is this capacity for recombination that gives sexual reproduction its enormous evolutionary importance” (What Evolution Is, p. 105).

It seems clear that sex has contributed significantly to the differences among organisms. Sex is frequent. Sex results in significantly different genotypes and phenotypes. Beneficial mutations are a small percentage of all mutations. And sex often results in offspring having two versions of a beneficial gene.

Tim, the more I learn from you, I’m sure mutation played a huge role in causing a population of land mammals to evolve into whales. Out of curiosity, do you have any rough estimate on how many mutations it took for this populations’ nostrils to evolve into blow holes?

And you are saying that mutation is the only cause of the rhino’s horn? I’m sure mutation was important. But sex was important, too. For one thing, sex results in offspring with two versions of the gene that causes big-hornedness.

Comment #107098

Posted by Longhorn on June 21, 2006 9:24 AM (e)

Aureola Nominee wrote:

The only strawmen here are yours. Science is not in the business of making final pronouncements on Truth™, and theories are always - always - open to revision. THAT was my point. Your insistence to the contrary counts exactly for nothing.

Aureola, the earth is not flat disk that that rests on the back of a giant tortoise. I know that. And we are not going to learn otherwise. That is just the way it is.

Comment #107100

Posted by Popper's Ghost on June 21, 2006 9:26 AM (e)

The only strawmen here are yours. Science is not in the business of making final pronouncements on Truth™, and theories are always - always - open to revision. THAT was my point. Your insistence to the contrary counts exactly for nothing

You’re going out of your way to be stupid. I explicitly noted that theories are open to revision. Nonetheless, science does make final pronouncements on truth. There was once a debate as to whether rockets could reach the moon; we now know the truth of the matter. There was once a debate as to whether the continents can move; we now know the truth of the matter. There was once a debate as to whether evolution occurs; we now know the truth of the matter. Those are the facts, your stupid strawman blatherings and capital letters notwithstanding. The notion that science does not make final pronouncements on truth is itself a pronouncement on truth; it’s a silly and naive dogma that shallow thinking people like yourself toss around without examination.

Comment #107101

Posted by Longhorn on June 21, 2006 9:27 AM (e)

I wrote:

Here is what Mayr says on sexual reproduction: “The process of sexual reproduction makes far more new phenotypes available for natural selection than does mutation of any other process.”

That was a typo. Mayr’s quote actually is: “The process of sexual reproduction makes far more new phenotypes available for natural selection than does mutation or any other process.”

Comment #107102

Posted by Popper's Ghost on June 21, 2006 9:30 AM (e)

Aureola, the earth is not flat disk that that rests on the back of a giant tortoise. I know that. And we are not going to learn otherwise. That is just the way it is.

Quite so. The pathetically arrogant Aureola Nominee just can’t stand that someone contradicted her/him/it, and can’t conceive that such a person isn’t an idiot, or is “on the side of science”. I refuse to be that stupid – I know that neither of us are idiots, and both of us are on the side of science.

Comment #107103

Posted by Aureola Nominee, FCD on June 21, 2006 9:31 AM (e)

Longhorn:

That’s why people should distinguish between data and theories. The proverbial “Precambrian rabbit” is always a possibility.

As I said, colloquially I will cheerfully say “the Earth goes around the Sun, not vice versa”; and I have no doubts that evolution is a fact, and that the current theory of evolution will be further refined but not upturned.

Colloquially, evolutionary biologists sometimes speak of organisms “evolving this or that trait in order to achieve this or that result”.

Both are perfectly acceptable shorthands for describing situations that, scientifically, are much more complicated than that.

Comment #107104

Posted by Longhorn on June 21, 2006 9:33 AM (e)

Popper’s Ghost wrote:

You’re going out of your way to be stupid. I explicitly noted that theories are open to revision. Nonetheless, science does make final pronouncements on truth. There was once a debate as to whether rockets could reach the moon; we now know the truth of the matter. There was once a debate as to whether the continents can move; we now know the truth of the matter. There was once a debate as to whether evolution occurs; we now know the truth of the matter. Those are the facts, your stupid strawman blatherings and capital letters notwithstanding. The notion that science does not make final pronouncements on truth is itself a pronouncement on truth; it’s a silly and naive dogma that shallow thinking people like yourself toss around without examination.

Popper’s Ghost, please be civil. Even though this is only a blog, feelings can still get hurt. And civil discourse tends to be more beneficial.

Comment #107105

Posted by Longhorn on June 21, 2006 9:37 AM (e)

Aureola wrote:

That’s why people should distinguish between data and theories. The proverbial “Precambrian rabbit” is always a possibility.

I’m afraid I don’t see your point. The earth is not a flat disk that rests on the back of a giant tortoise.

Comment #107107

Posted by Popper's Ghost on June 21, 2006 9:40 AM (e)

Popper’s Ghost, please be civil. Even though this is only a blog, feelings can still get hurt. And civil discourse tends to be more beneficial.

I suggest that you talk to Aureola, since he/she/it was the one who started tossing around ad hominems about idiocy.

To recap: I said that the earth goes around the sun; I never used the term “heliocentric model”. Aureola now refers to “perfectly acceptable shorthands for describing situations that, scientifically, are much more complicated than that”. In other words, what I wrote was perfectly acceptable; in other words, Aureola attacked a strawman. My point was that Aureola’s statement about cases not getting closed in science was too strong, because it was made in reference to finding enough evidence to convince the majority of scientists that evolution has not occurred. But that will never happen – that case is closed. The context was never “refinement of theories”, so that whole thread is a strawman.

Comment #107108

Posted by Aureola Nominee, FCD on June 21, 2006 9:50 AM (e)

Longhorn:

May I suggest that Great A’Tuin is incompatible with the evidence we have collected so far? May I suggest that that is not a matter of theory?

May I also suggest that we were NOT talking about the fact of evolution, but about the theory of evolution, and that my reference to the need for anyone wishing to support a contrary view (such as John Davison, for instance) need to get busy and collect evidence that supports their minority view?

Now, do you see where the strawman was? It was in pretending that I was talking about the fact of evolution, while I was talking of the theory of evolution. This equivocation should be the exclusive domain of IDiots, but apparently someone on our side does it, too.

And of course, when someone claims to know what I meant better than I did, I lose any respect I have for him.

Comment #107110

Posted by Popper's Ghost on June 21, 2006 9:57 AM (e)

Now, do you see where the strawman was? It was in pretending that I was talking about the fact of evolution, while I was talking of the theory of evolution.

This is plainly dishonest. Your statement was “if those now in the minority manage to produce enough evidence to convince the majority, the pendulum may well swing the other way”. The way was “earth goes around sun” and the other way was “sun goes around earth”. Clearly, no evidence will swing us from the former to the latter. And the context was Lurker’s statements about minority versus majority views of evolution. This has nothing to do with refinements of the theory, but whether evolution occurs.

Comment #107112

Posted by Aureola Nominee, FCD on June 21, 2006 10:05 AM (e)

Just for reference, here is the very first post I made on this thread, responding to Lurker:

One way to answer this is to say personal experience tells you the minority opinion is wrong. However, when it comes to evolution, the personal experience of the minority group says they have the correct interpretation of the evidence.

What is this supposed to mean? Even with heliocentrism the “personal experience of the minority group says they have the correct interpretation of the evidence.”

Alas, arguments from personal experience are inconclusive, unless one has evidence to show in support. Which evolutionary biologists have (plenty of), and geocentric astronomers have not.

I don’t know whether other people were asleep, but this was the context: “interpretation of evidence”.

If this is dishonest on my part, fine: then I am dishonest. However, I am fully convinced that the accumulation of evidence can overturn specific interpretations of it.

Comment #107113

Posted by Popper's Ghost on June 21, 2006 10:06 AM (e)

And of course, when someone claims to know what I meant better than I did, I lose any respect I have for him.

I have a friend who wrote a thesis on theories of causation, then had a serious motorcycle injury, smashing his head into a telephone pole. While his neurologist told him that the tests said he was ok, he could only understand 1/4 of his own thesis. Presumably there were people who could then understand more of it than he. So one need not be an idiot to think that person A could understand something written by person B better than person B does. While brain injury could be the cause, so could the mere passage of time. People reinterpret their past writings and past behaviors in terms of their current mental states, and there’s no law of physics that says that the author of a passage is the best interpreter of the meaning of the passage. Anyway, I was being a bit flip, but you reacted like a raging ahole.

Comment #107115

Posted by Grey Wolf on June 21, 2006 10:11 AM (e)

Longhorn: read Strata, by Terry Pratchett, to see a “rabbit in the Cambrian” at an universal level. There is *always* a way to show that some of our scientific theories are wrong.

Of course, as we research them more and more and accumulate evidence, they tend to what I see as the “thursdaism event horizon”*, and when it is close enough we can probably ignore the possibility of them ever being found mistaken, but science never intersects the truth, only asymptotically gets closer to it.

Hope that helps,

Grey Wolf

*i.e. “Nothing has evolved because we were created last Thursday with memories implanted”. It remains a possibility, always, (always discarded because of Occam, of course) and as we research anything, the number of opposing hypothesis become more and more thurdaism. It is an event horizon because there is no hypothesis more utterly useless than thurdaism, of course

Comment #107116

Posted by Longhorn on June 21, 2006 10:13 AM (e)

Aureola wrote:

May I suggest that Great A’Tuin is incompatible with the evidence we have collected so far? May I suggest that that is not a matter of theory?

May I also suggest that we were NOT talking about the fact of evolution, but about the theory of evolution, and that my reference to the need for anyone wishing to support a contrary view (such as John Davison, for instance) need to get busy and collect evidence that supports their minority view?

Now, do you see where the strawman was? It was in pretending that I was talking about the fact of evolution, while I was talking of the theory of evolution. This equivocation should be the exclusive domain of IDiots, but apparently someone on our side does it, too.

And of course, when someone claims to know what I meant better than I did, I lose any respect I have for him.

OK. But my point is that the earth is not a flat disk that rests in the back of a giant tortoise. Whatever label you want to use for that claim (“theory” “knowledge-claim” “belief” “fact”) , the earth is not a flat disk that rests in the back of a giant tortoise.

Also, Popper’s Ghost has an important point. You have suggested something like the following: no claims are known to be true. But you seem to be advancing that claim as something you know to be true. That suggests logical inconsistency, and I’m not warranted in accepting a claim that is logically inconsistent. Now maybe you would say: I’m merely justified in believing (but I don’t know) that no claims are known to be true. OK. But then what do you do with the claim that the earth is not a flat disk that rests on the back of a giant tortoise? What do you do with the claim that some humans have walked on the moon? Maybe you want to say that I don’t know that. OK. I can live with that, as long as it is understood that I am, at the very least, very warranted in inferring that some humans have walked on the moon and that the earth is not a flat disk that rests on the back of a giant tortoise.

Comment #107117

Posted by Aureola Nominee, FCD on June 21, 2006 10:17 AM (e)

It’s a pity, then, that I had not suffered a potentially devastating brain injury in between my posting of the comment in question and your reply.

And, if I may point it out, you were not being “a bit glib”: you were simply wrong, and arrogantly assuming something about me which you couldn’t possibly know.

I would have reacted less intensely had you stated that you understood the implications of my words better than I did (and even this would have been wrong, since you didn’t know whether I understood those implications better than you, worse than you, or just as well as you).

Then you compounded this with accusing me of not tolerating diversity of opinion. Well, in that at least you may be right: I dismiss offhand people who claim to know what I mean better than I do. I think that you might do likewise, and rightfully call such people “idiots”.

Comment #107119

Posted by Popper's Ghost on June 21, 2006 10:25 AM (e)

Longhorn: read Strata, by Terry Pratchett, to see a “rabbit in the Cambrian” at an universal level. There is *always* a way to show that some of our scientific theories are wrong.

Even finding a pre-Cambrian rabbit fossil would not falsify the theory of evolution. It might have early on when there was much less data available and the theory was in its infancy. But now, whatever explanation might be found for the pre-Cambrian fossil, it would be integrated into the theory. Rather than Terry Pratchett, I would look more toward philosopher of science A.F. Chalmers’ book “What is this thing called Science?” to understand the evolution of scientific theories. It’s important to keep in mind that “the theory of evolution” is a term without a fixed referent. Since the fact of evolution is already established, there will always be some theory to explain it.

Comment #107120

Posted by Aureola Nominee, FCD on June 21, 2006 10:27 AM (e)

Longhorn:

You have suggested something like the following: no claims are known to be true.

Not as far as I can tell. I have suggested something like the following: in science no cases are closed. As I see it, there is evidence, and there are theories that interpret the evidence. Evidence may point us towards one interpretation with enormous strength (such as with biological evolution) or lower strength (such as with cosmogonic theories); it is not a matter of switches being thrown, ON/OFF, TRUE/FALSE. Clearly, to upturn a particular theory - a particular interpretation of the evidence - would require contrary evidence. So, every theory is accepted only provisionally, insofar as no contrary evidence surfaces, and it gets tweaked or, occasionally, discarded and replaced if such evidence does surface.

Really, I don’t see why this should be regarded as controversial: it is a strength of science, not a weakness.

Comment #107124

Posted by Longhorn on June 21, 2006 10:34 AM (e)

Not as far as I can tell. I have suggested something like the following: in science no cases are closed.

What do you mean by “science?” And is that claim “in science no cases are closed” logically inconsistent? You seem to be saying that the case is closed that, in science, no cases are closed. I urge you to focus in the self-referential issue.

Also, the earth is not a flat disk that rests on the back on the back of a giant tortoise.

Comment #107126

Posted by Aureola Nominee, FCD on June 21, 2006 10:36 AM (e)

Grey Wolf:

science never intersects the truth, only asymptotically gets closer to it.

Beautifully put.

Comment #107127

Posted by Popper's Ghost on June 21, 2006 10:38 AM (e)

It’s a pity, then, that I had not suffered a potentially devastating brain injury in between my posting of the comment in question and your reply.

It’s a pity that your reading skills are so poor, since I noted that brain injury is not a requirement.

And, if I may point it out, you were not being “a bit glib”

I said I was being a bit “flip”, and now you are claiming to know that I wasn’t. Sheesh but you are an arrogant and hypocritical %#%@.

arrogantly assuming something about me which you couldn’t possibly know

I didn’t assume anything about you; I said I think I understand what you wrote better than you.

I would have reacted less intensely had you stated that you understood the implications of my words better than I did

Your quibbles just get more and more stupid.

Then you compounded this with accusing me of not tolerating diversity of opinion.

I didn’t accuse you of any such thing; you’re hallucinating. What I said was that you couldn’t conceive of me saying what I did without my being an idiot, or not being on the side of science. Your comment about “on the side of science” is completely idiotic, but I know you’re not an idiot, nor are against science, just because you occasionally lapse into idiocy.

Well, in that at least you may be right: I dismiss offhand people who claim to know what I mean better than I do. I think that you might do likewise, and rightfully call such people “idiots”.

No, I wouldn’t, because I’m not one, and I have already explained exactly how I think that can be the case, so I certainly wouldn’t think that someone who said so was an idiot; sheesh.

I think we’ve abused this board enough with this crap. I’m out of here.

Comment #107128

Posted by Aureola Nominee, FCD on June 21, 2006 10:41 AM (e)

Longhorn:

What do you mean by “science?”

Very interesting. What do you mean by science?

And is that claim “in science no cases are closed” logically inconsistent?

No, it isn’t.

You seem to be saying that the case is closed that, in science, no cases are closed.

This is not a scientific theory.

I urge you to focus in the self-referential issue.

I urge you not to confuse the different levels. Remarks about the nature of science are not scientific theories.

Comment #107130

Posted by Aureola Nominee, FCD on June 21, 2006 10:46 AM (e)

Syntax Error: mismatched tag 'quote.'

Comment #107131

Posted by Aureola Nominee, FCD on June 21, 2006 10:49 AM (e)

Popper’s Ghost, first you said I did not tolerate being contradicted, now you claim you never accused me of not tolerating other opinions?

I suggest you might have comprehension problems with your own words, let alone mine.

Comment #107132

Posted by Longhorn on June 21, 2006 10:51 AM (e)

Grey Wolf wrote:

Longhorn: read Strata, by Terry Pratchett, to see a “rabbit in the Cambrian” at an universal level. There is *always* a way to show that some of our scientific theories are wrong.

What do you mean by “scientific theories?” Your claim seems logically inconsistent. You seem to be advancing the claim as one that cannot be wrong.

And with all due respect, I also think the claim is nonsense. The earth is not a flat disk that rests on the back of a giant tortoise. And I share ancestors with Bear from “BJ and the Bear.” Here is a link:

http://groups.msn.com/BJandTheBearFanClub/bjandthebearphotos.msnw

Comment #107134

Posted by Longhorn on June 21, 2006 10:55 AM (e)

Aureola wrote:

Very interesting. What do you mean by science?

I only used the word to ask how you were using it.

Also, the earth is not flat disk that rests on the back of a giant tortoise. That is just the way it is. It is good to come to terms with that.

Comment #107136

Posted by MartinM on June 21, 2006 10:57 AM (e)

Longhorn wrote:

What do you mean by “scientific theories?” Your claim seems logically inconsistent. You seem to be advancing the claim as one that cannot be wrong.

You need to distinguish between statements made within some epistemic framework, and statements made about some epistemic framework.

Comment #107137

Posted by Lurker on June 21, 2006 10:58 AM (e)

Dr. Lenny wrote:

BWA HA HA HA AH AHA HA AH !!!!!!!!!!!!!!!!

Nice. It doesn’t prove your point though. Let me demonstrate how: “BWA HA HA HA AH AHA HA AH ! Dr. Lenny is obviously wrong.” Have I proved you are wrong? No. Try again.

It’s called “the scientific method”. I’m quite sure you’ve never heard of it.

Yes the scientific method. The same method used by the minority opinion. Answer my question.

Are you game?

We’re not talking about gravity are we? Anyway, there is NO minority opinion in the scientific community when it comes to falling off bridges is there?

Comment #107138

Posted by PaulC on June 21, 2006 10:58 AM (e)

Popper’s Ghost:

So one need not be an idiot to think that person A could understand something written by person B better than person B does. While brain injury could be the cause, so could the mere passage of time.

Neither is necessary. First off, it’s always possible that I could write something that happens to be true, but have a fragile grasp of it. I might even construct a logical argument in such a way and verify it step by step to my own satisfaction–ruling out mere luck. Someone with a deeper understanding of the domain might see my argument, immediately have a coherent grasp of where it is going, and suggest a simplified version. This happens all the time in mathematics.

In the above case, the “passage of time” might enhance rather than degrade understanding. If I have been studying a topic, I might have a deeper grasp of my own writing a year after writing it and forgetting about it.

In a more formal context, it’s easy to write things that mean something, but which nobody understands very well at the time. The clearest case I can think of involves computer programs. But if that’s cheating, note that an algorithm can be stated quite precisely in English. For instance, there is an old sorting method called Shell Sort, http://en.wikipedia.org/wiki/Shell_sort notable not because it is the best method, but because it has been so hard to pin down its asymptotic complexity. You could argue that Shell (the inventor) understood only that he had come up with a sorting method that seemed better than some others he knew. Over time, people actually understood what he had come up with to a deeper degree than those who preceded them.

A similar phenomenon occurs with games. It should be clear to anyone who has ever invented a new game or a variation on an old one that it does not automatically make you the best player. While you can lay down a set of rules that you understand formally, it’s entirely possible–and frequent–that a better player can beat you at these same rules the first time you put them in play. I would say that in a rigorous sense that player “understood” what you said better than you did.

BTW, I’m sorry about your friend. That’s really a tragic story.

Comment #107139

Posted by Longhorn on June 21, 2006 11:02 AM (e)

Martin wrote:

You need to distinguish between statements made within some epistemic framework, and statements made about some epistemic framework.

Okay. But what do you mean by “scientific theory?”

Also, the earth is not a flat disk that rests on the back of a giant tortoise. And some humans have walked on the moon.

Comment #107140

Posted by Popper's Ghost on June 21, 2006 11:04 AM (e)

Popper’s Ghost, first you said I did not tolerate being contradicted, now you claim you never accused me of not tolerating other opinions?

Sigh. You said I accused you of not tolerating “diversity of opinion”. Somehow I’m not surprised that you think that’s the same as my stating that you can’t tolerate being contradicted.

I suggest you might have comprehension problems with your own words, let alone mine.

But I do understand the (large) difference between the two.

Comment #107141

Posted by Lurker on June 21, 2006 11:06 AM (e)

Popper's Ghost wrote:

Yeah, it’s a real problem when the only kind of argument you understand is an argument from authority. Then you are left, like Lurker, asking over and over “But how do we know which authority is right?”

You assume I’m confused because I asked some questions. Wrong-o. I know how this process works. I wanted to see if anyone here knows. So far Dr. Lenny has failed miserably.

Comment #107144

Posted by Popper's Ghost on June 21, 2006 11:10 AM (e)

BTW, I’m sorry about your friend. That’s really a tragic story.

While he was still an undergrad, the great American analytical philosopher David Lewis recognized his brilliance and took him under his wing, and when Lewis went from UCLA to Princeton, my friend went with him; it was in Princeton that he had the accident, which nipped an incredibly promising career in the bud. I hear that he’s now a law professor in the midwest somewhere.

Comment #107146

Posted by Aureola Nominee, FCD on June 21, 2006 11:16 AM (e)

Longhorn:

Science is basically the systematic collection and interpretation of evidence, following a process generally known as “the scientific method”.
What is the point you are trying to make with this question?

Comment #107147

Posted by Lurker on June 21, 2006 11:20 AM (e)

Aureola Nominee wrote:

However, I am fully convinced that the accumulation of evidence can overturn specific interpretations of it.

I agree, however your statement is looking to the future for answers. What about today’s interpretation? That’s what I’m talking about.

Comment #107148

Posted by Aureola Nominee, FCD on June 21, 2006 11:21 AM (e)

Popper’s Ghost:

You know, I suspected you might try the wordplay approach. Yet, I’m supposed to be the dishonest one, the one hallucinating…

What a blank you are, in the arsenal of science.

Comment #107151

Posted by Aureola Nominee, FCD on June 21, 2006 11:23 AM (e)

Lurker:

today, the evidence points massively in the direction of the theory of evolution and away from any alternatives, so much that it would be perverse to withhold provisional acceptance of it.

Comment #107152

Posted by Popper's Ghost on June 21, 2006 11:26 AM (e)

You know, I suspected you might try the wordplay approach. Yet, I’m supposed to be the dishonest one, the one hallucinating…

Well, it’s more plausible that you’re dishonest than that you really don’t understand the difference between not tolerating diversity of opinion and not tolerating being contradicted. The former has much greater scope than the latter, and I did not accuse you of it.

What a blank you are, in the arsenal of science.

It’s quite lovely the way you keep turning away from opportunities to not be an ahole.

Comment #107154

Posted by Aureola Nominee, FCD on June 21, 2006 11:32 AM (e)

Popper’s Ghost:

Diversity without contradiction sounds like a very dull diversity to me. Anyway, please feel free to continue offending me. I think that qualifies you way more than I could ever hope to.

Comment #107156

Posted by Longhorn on June 21, 2006 11:34 AM (e)

Science is basically the systematic collection and interpretation of evidence, following a process generally known as “the scientific method”.

That is not enough information for me to determine whether I should accept your claim that nothing is known in science. It is just not enough information. Maybe I should go do something else.

Your claim may be tautological. You may be using the word “science” so that a necessary condition for “science” is that no science claims are known to be true or false. Tautological claims are known to be true. But they are not very interesting. It would be like saying: “all bachelors are unmarried males.”

Also, I wanted to see if your claim is logically inconsistent. And I’m still not sure. You are advancing the claim as one that is settled. But it’s hard for me to tell whether your claim “in science, nothing is settled” is “science” or “non-science.”

Finally, the earth is not a flat disk that rests on the back of a giant tortoise. Whether we call that “science” or “non-science,” it is good to focus on the idea that the earth is not flat disk that rests on the back of a giant tortoise. It grounds us.

What is the point you are trying to make with this question?

To see if I should accept your claim. Also, because I wonder if your claim is logically inconsistent. And I need more information to determine that.

Comment #107160

Posted by Popper's Ghost on June 21, 2006 11:39 AM (e)

Anyway, please feel free to continue offending me. I think that qualifies you way more than I could ever hope to.

Well, if that’s so, then once must consider your calling me an idiot, a “blank”, etc. It’s your own words that qualify you as a hypocritical ahole.

As for “diversity without contradiction”, that’s your silly wordplay; I said nothing about it. No doubt you tolerate a diversity of contradictory opinions, in the abstract. It’s when you, personally, are contradicted that you go all raving ego-defensive.

Comment #107163

Posted by Aureola Nominee, FCD on June 21, 2006 11:50 AM (e)

Longhorn:

maybe you are right: with the background noise of goalpost-moving that someone else is generating it is difficult to continue trying to concentrate, and we might be better off letting the thread go.

Anyway, in a sense yes, my remark was tautological just as much as (a+b)^2 = a^2 + 2ab + b^2 is tautological.

I was simply restating, for the benefit of someone who insisted on dismissing scientists’ consensus as somehow uncertain, that that consensus is basically all we can hope for, and that the theory of evolution is as close to certainty as we can hope to be.

The fact of evolution, on the other hand, is as certain as the fact that the Earth is not the Discworld, i.e. I would sooner doubt my sanity than those facts.

Comment #107165

Posted by Popper's Ghost on June 21, 2006 11:55 AM (e)

maybe you are right: with the background noise of goalpost-moving that someone else is generating it is difficult to continue trying to concentrate, and we might be better off letting the thread go.

Oh poor baby. I moved no goalpost, and you are truly pathetic.

Comment #107166

Posted by Popper's Ghost on June 21, 2006 12:02 PM (e)

I was simply restating, for the benefit of someone who insisted on dismissing scientists’ consensus as somehow uncertain, that that consensus is basically all we can hope for, and that the theory of evolution is as close to certainty as we can hope to be.

But our acceptance of the theory of evolution isn’t dependent upon consensus, it’s dependent on the evidence. That was my point (and that of others) to Lurker earlier, when I noted that, if the only sort of argument one accepts is an argument from authority, then one is left with asking, as Lurker does, how do we know which authority to believe. Unfortunately, that is how many people see science – as a series of statements from authorities – because they don’t have the tools to evaluate scientific arguments. And this is why the IDists are able to make headway with their rhetoric about “controversy”.

Comment #107171

Posted by fnxtr on June 21, 2006 12:08 PM (e)

I recommend Ben Bova’s “Mercury” for its depiction of Bishop Danvers.

And a saucer of milk each for Popper and Aureola.

Comment #107174

Posted by Aureola Nominee, FCD on June 21, 2006 12:14 PM (e)

Acceptance of the theory of evolution among biologists and very well informed laypeople is based on the evidence.

Acceptance of the theory of evolution among the remaining 99+% or humankind is predicated on recognition of one’s own limitations, i.e. in deferring to expert authority.

Otherwise, you are stuck: you cannot tell the “minority biologists” (all one or two of them) that they are wrong on the basis of evidence, because they can always turn around and say “nope, evidence supports MY position”. And you are back to square one.

But you can tell them “well, state your case and let’s see whether we have overlooked something; in the meantime, though, this is what most biologists agree upon.”

The key part of this is “in the meantime”. Right here and now, we have a consensus, i.e. to the best of our ability this is a good approximation of reality. Should something radically new turn out, we can revise this; and we keep looking.

Comment #107178

Posted by steve s on June 21, 2006 12:19 PM (e)

IDK if Popper moved any goalposts, but the guys at Uncommonly Dense sure did.

Comment #107185

Posted by Popper's Ghost on June 21, 2006 12:48 PM (e)

Acceptance of the theory of evolution among biologists and very well informed laypeople is based on the evidence.

Acceptance of the theory of evolution among the remaining 99+% or humankind is predicated on recognition of one’s own limitations, i.e. in deferring to expert authority.

I don’t think it takes being all that well informed; as I said, I think it depends on being able to evaluate scientific arguments. I know plenty of people who are not all that well informed about the evidence for evolution but can readily see through the counterarguments. This can be a bit subtle; if someone claims that there is no evidence for evolution, as Ann Coulter does, that’s not a scientific argument, it’s an unsupported claim that is implausible on its face. The fact that virtually all biologists accept that evolution has occurred is itself evidence, not mere consensus, because such uniformity would be implausible in the absence of evidence … if you have some understanding of how the scientific community works. But if you think that scientists are just a big cult or a cabal of self-serving money grubbers, or are trying to destroy religion, etc., then it’s possible to dismiss the relevance of the uniformity.

Otherwise, you are stuck: you cannot tell the “minority biologists” (all one or two of them) that they are wrong on the basis of evidence, because they can always turn around and say “nope, evidence supports MY position”. And you are back to square one.

Of course I can tell them that they are wrong on the basis of the evidence, because they are and I can show them the evidence and give the arguments for what the evidence supports. We would only be back to square one if “naysaying [is] an argument”, but it isn’t. It doesn’t matter what they say, it matters what arguments they give … as you note:

But you can tell them “well, state your case and let’s see whether we have overlooked something; in the meantime, though, this is what most biologists agree upon.”

and I would say, this is what the evidence and reasoning indicates. If I’m not familiar with the evidence or the reasoning about it, then I would want to look at it before adding the consensus view to my set of beliefs. That most biologists agree on something is, again, itself evidence … pretty strong evidence that that is the best supported position. But I take it that way because I have a good understanding of how science works in practice. But I think it’s dangerous to accept consensus views in general. I don’t accept the consensus view that God exists, and I didn’t accept the consensus view that there were WMDs in Iraq. For me it depends on what mechanisms are behind the formation of the consensus.

Comment #107198

Posted by Aureola Nominee, FCD on June 21, 2006 1:32 PM (e)

Oh, sorry. I thought we were discussing about science, not theology or the current U.S. administration’s fantasies.

I would be willing to defer to a consensus of experts on the existence of gods if such people as “experts on the existence of gods” existed. I am not aware of their existence, though.

I, for one, was willing to defer to a consensus of experts on the existence of WMDs in pre-invasion Iraq. Unfortunately for… well, basically for all of us, Bush & Co. were not willing to do likewise, and when the experts told them that those WMDs were not there, they pressed on regardless.

Comment #107199

Posted by Aureola Nominee, FCD on June 21, 2006 1:33 PM (e)

AFAIK, “appeal to authority” is not a logical fallacy; “appeal to false authority” is.

Comment #107212

Posted by Grey Wolf on June 21, 2006 2:17 PM (e)

All quotes from Popper’s Ghost

Even finding a pre-Cambrian rabbit fossil would not falsify the theory of evolution.

What about finding a fossilized plesiosaur holding a placard which read, “End Nuclear Testing Now”?

But now, whatever explanation might be found for the pre-Cambrian fossil, it would be integrated into the theory.

Or the theory would have to be scraped because it turns out that Q engineered everything. Or that Loki did create Earth and everything in it last Thursday.

Rather than Terry Pratchett, I would look more toward philosopher of science A.F. Chalmers’ book “What is this thing called Science?” to understand the evolution of scientific theories.

Yes, *if* you wanted to understand the evolution of scientific theories. If you wanted to learn to cook, I’m sure there are good books on the subject in your local library. But since that was not the point of the book recommendation, I wonder why you went on that tangent. I was offering you a funny example of a “rabbit in Cambrian” that neatly eviscerates the theory of evolution and, indeed, the fact of evolution. The book, no need to say, is fiction. Science fiction, in fact. I’d normally wouldn’t bother pointing it out (it’s Pratchett, after all), but Popper seems determined to ignore the point, so I thought I’d better spell it out, just in case.

Since the fact of evolution is already established, there will always be some theory to explain it.

And again, I repeat: there is no such thing as “established fact” in science. Yes, Last Thurdaism is unlikely enough to be ignored, but you cannot discard it except via Occam. It remains a possible explanation that fits all (and any!) of the facts.

All evidence, coupled with Occam’s razor, points to evolution as the explanation for the diversity of life in this planet. However, science cannot say it is the Truth because science does not deal with Truth but with reasonable hypothesis.

You are so driven to be Right in your conversation with Aureola that you have stopped listening, though, so I won’t bother with you. My points might have been good or bad, but you didn’t address them at all.

Hope that helps,

Grey Wolf

Comment #107213

Posted by Popper's Ghost on June 21, 2006 2:20 PM (e)

Oh, sorry. I thought we were discussing about science, not theology or the current U.S. administration’s fantasies.

When one deals with a concept used within some context, it is sometimes necessary to examine it in a broader context in order see what role it is playing in the context under discussion. What I tried to point out is that consensus among scientists is special because of the operation of the special characteristics of scientific method – which is not something that people who don’t understand scientific arguments are likely to understand. If they accept consensus among scientists on the same basis as they accept consensus among other populations on other sorts of issues, then they are using too weak a criterion, IMO.

I, for one, was willing to defer to a consensus of experts on the existence of WMDs in pre-invasion Iraq. Unfortunately for… well, basically for all of us, Bush & Co. were not willing to do likewise, and when the experts told them that those WMDs were not there, they pressed on regardless.

Members of the Bush administration, as well as press, have repeatedly claimed that everyone believed there were WMDs. Of course, they don’t mean every man, woman and child; when they get more specific, they refer to every intelligence agency, saying that it’s not just U.S. agencies. If one looks closely, one finds that the consensus is overstated, but when it comes to U.S. agencies, the Bush administration (largely Cheney; this was dealt with in last night’s FrontLine, “The Dark Side”) pressured them to say what they wanted to hear. So, the experts did not tell them, or us, that the WMDs were not there – I don’t know where you got the idea that Bush & Co. were not deferring to the experts. But they didn’t so much defer as drive the intelligence reports to fit their agenda. The intelligence process was corrupted, some experts were silenced, and some didn’t say what they really believed. There was enough “minority” information available – from Scott Ritter, for instance – to give me serious doubt about the claims. But the “expert consensus” most readily available to average Americans is the one that Colin Powell presented to the U.N., which resulted in rave reviews from the media, and the majority of Americans supporting Bush’s drive to war. It’s that consensus that I did not accept; I watched Powell’s presentation carefully and skeptically and I came to a quite different conclusion.

AFAIK, “appeal to authority” is not a logical fallacy; “appeal to false authority” is.

Neither is a logical fallacy; appeal to authority is an informal fallacy. The fallacy is called “appeal to authority” or “fallacious appeal to authority”, not “appeal to false authority”, but of course it deals with appeals to the claims of people lacking adequate authority. But just because an appeal to a legitimate authority doesn’t come under the named fallacy doesn’t mean that P follows from “authority claimed P”. As stated by

http://www.nizkor.org/features/fallacies/appeal-to-authority.html

It should be noted that even a good Appeal to Authority is not an exceptionally strong argument. After all, in such cases a claim is being accepted as true simply because a person is asserting that it is true. The person may be an expert, but her expertise does not really bear on the truth of the claim. This is because the expertise of a person does not actually determine whether the claim is true or false. Hence, arguments that deal directly with evidence relating to the claim itself will tend to be stronger.

Which is pretty much what I said.

Comment #107214

Posted by Popper's Ghost on June 21, 2006 2:24 PM (e)

You are so driven to be Right in your conversation with Aureola that you have stopped listening, though, so I won’t bother with you.

You, like Aureola, seem to be very fond of ad hominems and insults. If you won’t bother with me, then I wonder what you were doing typing all that.

In any case, there are established facts in science, and it’s simply perverse to deny it.

Comment #107216

Posted by Grey Wolf on June 21, 2006 2:28 PM (e)

All quotes by longhorn

What do you mean by “scientific theories?”

The descriptions of the facts and extrapolations thereof arrived to through the scientific method

Your claim seems logically inconsistent. You seem to be advancing the claim as one that cannot be wrong.

My claim was not a scientific theory, so it was not contained within the claim. Indeed, it is more in the nature of an axiom.

And with all due respect, I also think the claim is nonsense. The earth is not a flat disk that rests on the back of a giant tortoise. And I share ancestors with Bear from “BJ and the Bear.”

Did either of you even bother to read my post beyond the first line? What if the Earth was created last Thursday, as a flat disk on top of A’ Tuin, and every evidence was created by Loki to hide it from you? Possible? yes. Likely? no. Occam? discards it. Science? Doesn’t deal in truths, but in conclusions from evidence. But assumes, as an axiom, that the evidence is not deliberately misleading .

As I told Popper, try reading my post before jumping down my throat.

Hope that helps,

Grey Wolf

Comment #107217

Posted by Popper's Ghost on June 21, 2006 2:31 PM (e)

P.S.

Yes, Last Thurdaism is unlikely enough to be ignored, but you cannot discard it except via Occam. It remains a possible explanation that fits all (and any!) of the facts.

If you want to insist upon this, then you must also accept that it is not an “established fact” that you were born of human parents, that you drive whatever sort of car you think you drive, that George Bush is president of the U.S., etc. etc. It has nothing to do with “science”, and everything to do with empirical epistemology. When we use the word “fact” in connection with empirical claims, the word has built into it certain epistemological assumptions, and the word “establish” has a certain meaning in regard to empirical processes. Thus, there really are established facts even though it is logically conceivable that they could be false.

Comment #107218

Posted by Aureola Nominee, FCD on June 21, 2006 2:39 PM (e)

It should be noted that even a good Appeal to Authority is not an exceptionally strong argument. After all, in such cases a claim is being accepted as true simply because a person is asserting that it is true. The person may be an expert, but her expertise does not really bear on the truth of the claim. This is because the expertise of a person does not actually determine whether the claim is true or false. Hence, arguments that deal directly with evidence relating to the claim itself will tend to be stronger.

Emphasis added. You will note that this quote speaks in relative, not absolute terms.

And the experts on Iraqi WMDs were the UN inspectors, and they were pretty much unanimous in denying that Iraq was bristling with nearly-finished or even launch-ready WMDs.

If I have the power to intimidate experts to say what I want them to say, basically I’ve blown away any legitimate authority those experts might have, and any appeal to their “authority” becomes fallacious.

Comment #107221

Posted by GuyeFaux on June 21, 2006 2:48 PM (e)

Tell you what, Lurker, I have a way to test your idea that “science is just an opinion, and no one can tell whether your opinion or mine is right”. Near my house is the Sunshine Skyway Bridge…

Ah, creationists dabbling in post-modernism.

Comment #107222

Posted by Popper's Ghost on June 21, 2006 2:52 PM (e)

Emphasis added. You will note that this quote speaks in relative, not absolute terms.

Nor did I say anything about absolute terms; again, I said pretty much what Nizkor says. But emphasizing “exceptionally” in “not an exceptionally strong argument” kind of misses the point, since that is usually a euphemism for “a pretty weak argument”.

And the experts on Iraqi WMDs were the UN inspectors, and they were pretty much unanimous in denying that Iraq was bristling with nearly-finished or even launch-ready WMDs.

This looks like a bit of a “true Scotsman” argument. There are many who would – and did – argue that the UN inspectors were only shown what SH wanted them to see. It would help to go back and look at the Colin Powell presentation to see what he presented as the WMD threat. One of the elements was the claim that there was a large amount of material that wasn’t accounted for in what the inspectors had catalogued.

If I have the power to intimidate experts to say what I want them to say, basically I’ve blown away any legitimate authority those experts might have, and any appeal to their “authority” becomes fallacious.

It’s always possible for the process to be corrupted; that was my point, that it’s necessary to look at the process by which consensus is developed.

Comment #107224

Posted by Longhorn on June 21, 2006 2:59 PM (e)

Much earlier in this thread, I wrote:

I suspect that sexual reproduction played a very large role in causing the variation among dogs. First, sexual reproduction happens very frequently.

Anton Mates responded:

So does mutation.

And I responded:

But beneficial mutations are a small percentage of all mutations.

My point – that beneficial mutations are a small percentage of all mutations – is not important to whether I am warranted in inferring that sexual reproduction caused some of the significant differences that exist among dogs and between, say, humans and chimps. For although mutations that are reproductively advantageous are a small percentage of all mutations, mutations are ubiquitous. They are so frequent in fact that even if reproductively advantageous mutations are a small percentage of all mutations, mutation still could have been by far the most important factor (along with selection) in causing the significant differences among all organisms. In a nutshell, a small percentage of X can still be an enormously large number. For instance, a small percentage of the space in the known universe is occupied by stars, and there are billions and billions of stars in the known universe.

Partly because of the helpful posts by Anton and Tim Curtis, it is clear to me that new mutations played an important role in causing the hugely significant differences that exist among at least many, if not all, sexually reproducing organisms. First, mutation to gametes is what we observe that tends to cause some of the most anomalous differences between parents and offspring. Second, we know that humans and chimps share common ancestors, and the human genome and chimp genome have important differences that clearly were caused by mutation. For instance, humans have 46 chromosomes, and chimps 48. Chromosomal fusions are kind of mutation.

The question, however, is how important has sexual reproduction been in causing the differences among organisms. Well, first, I’m as different as I am from my parents because of sexual reproduction. Though I may have been born with some new mutations to my coding DNA, any new mutations I was born with have not had a significant affect on my observable traits.

However, did sexual reproduction directly cause any of the more significant differences that exist in the animal kingdom? For instance, how much of the difference between whales and Pakicetus was caused by vast numbers and combinations of organisms sexually reproducing? I’m not sure. It is clear that sexual reproduction at least enabled that transformation to occur. Specifically, sexual reproduction at least did something to enable mutations (plus selection) to cause these big differences, for instance, sexual reproduction protected the organisms from disease as mutations caused the important phenotypic change. For one, the difference among asexually reproducing organisms are fairly trivial compared to the differences among whales and their most recent land mammal ancestors. The whole animal kingdom changed dramatically after sexual reproduction evolved. Just compare.

But has sexual reproduction merely protected organisms from disease and deleterious mutations while reproductively helpful mutations (and selection) caused the most significant differences in the animal kingdom? Maybe. But I tend to doubt it. I tend to think sexual reproduction has caused some of the important differences among nearly all sexually reproducing organisms. First, sexual reproduction can result in the existence of an organisms with two versions of a reproductively beneficial gene. Both of its parents can have that sequence, and pass it down to the offspring. For example, the rhino’s horn is as big as it is partly because various members of this population have sexually reproduced.

Second, meiosis results in cells that are significantly different than somatic cells. The nucleotides that make up the gametes are in a significantly different sequence than they are in somatic cells, and the gametes tend to have half the number of chromosomes of somatic cells.

Finally, the fertilization event puts two fairly significantly different combinations of chromosomes next to each. The chromosomes don’t blend; they don’t even touch each other. And then the proteins caused by the genome help build the organism.

However, I also think that rhinos have the horns they do because various members of the population had mutations to cause the build up of the bone on the ends of their noses. Because it is clear that all organisms descended from self-replicating molecules; we don’t experience sexual reproduction causing anomalous traits like horns; and we do experience mutations to gametes causing the most anomalous differences between parents and offspring.

Comment #107229

Posted by Sir_Toejam on June 21, 2006 3:07 PM (e)

Popper’s Ghost -

Just curious;

Did you ever use the name “Morbius” here on PT by any chance?

Comment #107231

Posted by Aureola Nominee, FCD on June 21, 2006 3:14 PM (e)

It’s always possible for the process to be corrupted; that was my point, that it’s necessary to look at the process by which consensus is developed.

You won’t get any disagreement from me on this specific point. Of course the process of how a consensus is developed is all-important; I like to think of this process as an integral part of the scientific method.

And maybe it’s because I am not living in the U.S., but the discussion about the credibility of UN weapons inspectors vs. US official statements sounded pretty unconvincing to the rest of the world (except for the famous Coalition of the Willing).

Comment #107233

Posted by Sir_Toejam on June 21, 2006 3:33 PM (e)

lurker:

when lenny laughed at you (as we all did, although more privately), the reasons were twofold:

1. You spelled your hero’s name wrong, it’s Davison, not Davidson.

and

2. He really is completely insane. not only is is his PEH listed as “crankiest” in the evolution section on crank.net, but have you check out his blog? It’s tens of pages and hundreds of posts of JAD arguing with invisible phantoms, and rants, that if they came from my own father, would suggest he be commited for observation.

JAD didn’t abandon the ToE, he abandoned reality altogether (somwhere around the mid 80’s). That’s why he was stripped of his teaching duties at UV, and granted “emeritus” status. it’s the least embarassing way for a univeristy to rid itself of potential liability suit.

You might as well hold Charles Manson as an opponent of a scientific theory.

If you actually want to argue the case that his PEH has evidentiary support, please do.

that would be a real hoot!

Comment #107239

Posted by Steviepinhead on June 21, 2006 3:47 PM (e)

I understand that the following is a picky aside to Longhorn’s main points, but a rhino’s “horn” is not an outgrowth of bone.

The “horn” is a compacted mass of hair and related keratin material: sometimes the horns can “fray” due to wear and tear, and even appear a little raggedy and hairy.

Ref.:http://www.sosrhino.org/knowledge/faq.php.

Comment #107245

Posted by Henry J on June 21, 2006 3:58 PM (e)

Re “My point — that beneficial mutations are a small percentage of all mutations — is not important to whether I am warranted in inferring that sexual reproduction caused some of the significant differences that exist among dogs and between, say, humans and chimps. For although mutations that are reproductively advantageous are a small percentage of all mutations, mutations are ubiquitous.”

My guess is that both mutation and recombination were prerequisit to at least a lot of the diversity in plant, animals, and fungi. Mutation creates bits of variety, and recombination produces different mixes of those bits. Can’t really get there without both, or at least not nearly as quickly.

Henry

Comment #107249

Posted by Sir_Toejam on June 21, 2006 4:10 PM (e)

actually, in at least angiosperms, a recent paper was released this month (Genome Research: 16:738-749) with further evidence (and a spiffy new analytical technique) to indicate that genome-wide duplications played a significant role in generating diversity.

Yeah, it’s a complicated world out there.

Comment #107273

Posted by Tom Curtis on June 21, 2006 6:29 PM (e)

Longhorn:

Tim Curtis, thanks.

Most crossovers will fall in non-coding sequences.

That is very interesting. I didn’t know that. Do you have a link where I can learn more about that?

Actually, this claim was a deduction of mine from the facts that uneven crossovers withing genes would almost invariably disable the gene, and thus be harmful; and that a mechanism to avoid crossovers within coding sequences (ie, to hit the 95% of non-coding DNA rather than the 5% of coding DNA) would be much easier to evolve than a mechanism to ensure exact alignment.

But on your request, I have found the following review article:

http://www.genesdev.org/cgi/content/full/11/20/2600

In S. cerevisiae, hot spots correspond to the sites of the meiosis-specific DSBs that initiate recombination. DSBs do not occur at a specific DNA sequence, but rather are dispersed throughout a region of 50-200 bp at each locus examined (de Massy et al. 1995; Liu et al. 1995; Xu and Kleckner 1995; Xu and Petes 1996). Almost all breaks occur in intergenic regions that contain transcription promoters, but transcription is not required for DSB induction (White et al. 1992; Wu and Lichten 1994). Hot spots correspond to nuclease-hypersensitive sites in chromatin isolated from vegetative cells, and these regions undergo meiosis-specific modifications that increase their susceptibility to nuclease digestion (Ohta et al. 1994; Wu and Lichten 1994; Fan and Petes 1996). However, an open chromatin configuration must not be the only determinant of DSB formation because there is an imperfect correlation between the level of nuclease hypersensitivity and the probability of cleavage (Wu and Lichten 1995; Fan and Petes 1996).

Note that DSBs (and hence crossovers) occur in intergenic (ie, between gene) sequences, at or near transcription promoters. The do not occur at a specific sequence, but within a 50 to 200 bp of the promoter sequence. This means that even if they occured at a promotor sequence for an actual gene as opposed to a promotor sequence near a pseudogene or tandem repeats, the break would probably not occur in the coding sequence. It also means that if they occured within a coding sequence, the sequences might be mismatched by up to 150 bps, which would be almost invariably catastrophic for protein function.

I also found this article, which is of interest, but not necessarily directy relevant:

http://www.sciencedaily.com/releases/2002/08/020830072103.htm

Both tend to support my private theory that the most important function of much of “junk DNA” is to provide buffer zones so that meiosis can occur outside of genes. If this is so, it is important that it exists, but not important how much exists or as to its particular sequence.

(By the way, its Tom, not Tim.)

I’m sorry, but I don’t see what you are getting at. If it is not inconvenient, could you explain it another way? Thanks

I do not think I can explain it more clearly in a small space. The essential points are:

Not all original alleles will survive a sustained period of selection;

Lost alleles will be replaced by the formation of new alleles by mutation so that, in the long term the amount of genetic variety is near constant;

So after a sustained period of selection, the gene pool of a population will consist of some percentage of original alleles, plus some new alleles;

Because this is a reiterated process, after a very long period of sustained selection (or containing major intervals of sustained selection), the proportion of original alleles must fall until they represent only a tiny minority of all alleles present in the gene pool.

This is the same logic that applies to species. The species extant today are almost exactly those that were extant 100 thousand years ago. There have been some losses which on average have been replaced by new species. (Where in the midst of a human caused mass extinction so this is not entirely true, but over most periods it would be.) It would be wrong to argue that because of this, the species that exist in 50 million years would be largely those that exist today. On the contrary, if only 5% of species are lost and replaced every million years, in 50 million years only 8% of species will be survivors from the present. (Actually, no species would survive from the present, though some genii would, but this approximation will do for the purposes of illustration.)

Comment #107286

Posted by Longhorn on June 21, 2006 7:15 PM (e)

Tom, thanks for the information.

Note that DSBs (and hence crossovers) occur in intergenic (ie, between gene) sequences, at or near transcription promoters. The do not occur at a specific sequence, but within a 50 to 200 bp of the promoter sequence. This means that even if they occured at a promotor sequence for an actual gene as opposed to a promotor sequence near a pseudogene or tandem repeats, the break would probably not occur in the coding sequence. It also means that if they occured within a coding sequence, the sequences might be mismatched by up to 150 bps, which would be almost invariably catastrophic for protein function.

As I understand that article (and the language isn’t easy for me), it doesn’t say that “most crossovers will fall in non-coding sequences.” It says: “DSBs do not occur at a specific DNA sequence, but rather are dispersed throughout a region of 50-200 bp at each locus examined (de Massy et al. 1995; Liu et al. 1995; Xu and Kleckner 1995; Xu and Petes 1996).” As I understand that sentence, most crossovers don’t occur at a particular sequence but occur all over a particular region. And it doesn’t say, or suggest to me, that said region is non-coding. Now it might tend to be non-coding. And maybe that is a reasonable inference, given that a significant amount of the entire genome is non-coding. But meiosis is usually presented to the general reader as occurring in coding DNA. I would characterize Dawkins in that manner, though that might not be totally fair. At least there is no suggestion made by any author I’ve read that crossovers tend to occur in non-coding DNA.

Mayr goes out of his way to stress how important sex has been to evolution. It would seem to me that if most of the crossovers occur in non-coding DNA, he wouldn’t have emphasized sex as much as he did.

However, even if most crossovers do occur in non-coding regions, sex could still have contributed to important differences among sexually reproducing organisms. For we still have the reduction phase of meiosis and the fertilization events. The latter puts two different sets of chromosomes together and builds the organism from that blueprint.

Comment #107293

Posted by Longhorn on June 21, 2006 7:35 PM (e)

Tom wrote:

I do not think I can explain it more clearly in a small space. The essential points are:

Not all original alleles will survive a sustained period of selection;

Lost alleles will be replaced by the formation of new alleles by mutation so that, in the long term the amount of genetic variety is near constant;

So after a sustained period of selection, the gene pool of a population will consist of some percentage of original alleles, plus some new alleles;

Because this is a reiterated process, after a very long period of sustained selection (or containing major intervals of sustained selection), the proportion of original alleles must fall until they represent only a tiny minority of all alleles present in the gene pool.

This is the same logic that applies to species. The species extant today are almost exactly those that were extant 100 thousand years ago. There have been some losses which on average have been replaced by new species. (Where in the midst of a human caused mass extinction so this is not entirely true, but over most periods it would be.) It would be wrong to argue that because of this, the species that exist in 50 million years would be largely those that exist today. On the contrary, if only 5% of species are lost and replaced every million years, in 50 million years only 8% of species will be survivors from the present. (Actually, no species would survive from the present, though some genii would, but this approximation will do for the purposes of illustration.)

Maybe I’m not quite seeing your point. But some populations of organisms don’t change much over millions and millions of years. Some of today’s bacteria is very similar to bacteria that we had 3 billion years ago. As I understand it, cockroaches are very similar today to what they were millions and millions of years ago.

But then some series of events triggers important changes among the members of the populations. Which events? For asexually reproducing organisms, mutation, lateral transfer and varying levels of reproductive success (aka natural selection) were key.

But in sexually reproducing organisms, we also have this thing called sexual reproduction. It seems really important in terms of causing the changes among populations of sexual reproducers. It is hugely correlated with massive changes in the animal kingdom. It’s exciting. It’s fun. And the offspring gets a period to develop within its mother’s womb before its thrust out into the cold, cruel world. We know that sexual reproduction can cause pretty significant change from parents to offspring. And we know that sexual reproduction occurs frequently. We know its not harmful, although it can be painful for the woman. And we know that it can combine two versions of a gene, each of which is reproductively helpful. This combining of the gene often accentuates the trait, as we see with rhinos and giraffes. So for instance, say organism O is born with a new mutation M. Let’s say M contributes to a trait that helps O live and reproduce. Let’s say some of O’s descendents are also born with this mutation. And let’s say some of them reproduce with each other. This can cause the existence of an organisms with two copies of mutation M. And this can contrubte to an intensification of the trait connected to M.

So, what I’m saying is that sex seems really important in terms of causing the differences that exist among sexual reproducers.

Comment #107296

Posted by Tom Curtis on June 21, 2006 7:42 PM (e)

Longhorn:

The question, however, is how important has sexual reproduction been in causing the differences among organisms. Well, first, I’m as different as I am from my parents because of sexual reproduction. Though I may have been born with some new mutations to my coding DNA, any new mutations I was born with have not had a significant affect on my observable traits.

Better to say easily observable traits. The vast majority of mutations that become selected for have effects that cannot be detected except by statistical analysis over large populations. You may be the first bearer of a mutation that will transform human history, but if you were, odds are you would never know it.

For instance, how much of the difference between whales and Pakicetus was caused by vast numbers and combinations of organisms sexually reproducing? I’m not sure. It is clear that sexual reproduction at least enabled that transformation to occur. Specifically, sexual reproduction at least did something to enable mutations (plus selection) to cause these big differences, for instance, sexual reproduction protected the organisms from disease as mutations caused the important phenotypic change.

Yes, but the colission of India with Asia provided a fertile, shallow sea ideal for the evolution of whales. This, like the protection from disease, or the warm bloodedness of mammals are important historical facts (and traits) relevant to the specific evolution of whales, but are not relevant to the theoretical issue at hand. Thus, the resistance to disease resulting from sexual reproduction is an equivalent trait to the restance to disease provided by the vertebrate immune system - but there is not reason to have a discussion as to which is more important for evolution, mutation or the vertebrate disease system. Neither is disease resistance confered by sexual reproduction germaine to this discussion.

For one, the difference among asexually reproducing organisms are fairly trivial compared to the differences among whales and their most recent land mammal ancestors. The whole animal kingdom changed dramatically after sexual reproduction evolved. Just compare.

This is a matter of perspective. Morphologically there is little difference between a bacteria and an archeabacteria, but biochemically there is a much greater difference between them than there is between us and yeast. This reflects the relative time it took to evolve eukaryotic cells from prokaryotic cells compare to the time it takes to evolve complex multicellurity given eukaryotic cells. This coupled with the large number of multicellular creatures that have reverted to asexual reproduction suggests that it is eukaryotic cells, not sexual reproduction which was the important precondition for the explosion in multicellular diversity. This is not to say that sexual reproduction does not accelerate evolution. It does! But it is not implicated in the diversity of forms that evolution has generated.

First, sexual reproduction can result in the existence of an organisms with two versions of a reproductively beneficial gene. Both of its parents can have that sequence, and pass it down to the offspring. For example, the rhino’s horn is as big as it is partly because various members of this population have sexually reproduced.

This is not so much a function of sexual reproduction as of diploidy. Polyploidy at some stage of the reproductive cycle is probably necessary for sexual reproduction, but that stage could be very brief (and is is some species), and a-sexual creatures can also be diploid.

Further, it is not clear that it is an advantage. Haploid creatures derive the whole of a given protein from just on version of a gene. Given your rhino example, a haploid “rhino” with allele H, would probably have as strong a horn as a diploid with alleles H/H, and stronger than a rhino with alleles H/h. Indeed, often polyploid creatures transcribe from just one of two versions of a gene, or from just one in a particular cell. Only in partially dominant traits do both copies get transcribed to a significant degree.

Where diploidy is very important is that it shields organisms from recessive lethal genes.

Second, meiosis results in cells that are significantly different than somatic cells. The nucleotides that make up the gametes are in a significantly different sequence than they are in somatic cells, and the gametes tend to have half the number of chromosomes of somatic cells.

SFAIK, the nucleotides sequence in chromosomes from the father/mother are the same in the sperm/egg as they are in somatic cells. The sequences are different from either sequence possessed by the father/mother; but that is because of crossovers which, as discussed in a previous post, typically do not occur inside coding sequences, so typically do not form new alleles to be selected. Just now combinations of alleles within the genome.

Nor do I think the haploid part of the vertebrate haplo/diploid life cycle is particularly significant (beyond one feature) to evolution, being, as it is, very short in duration, and entirely protected from adverse environments.

Finally, the fertilization event puts two fairly significantly different combinations of chromosomes next to each. The chromosomes don’t blend; they don’t even touch each other. And then the proteins caused by the genome help build the organism.

This is just a redescription of diploidy, which was your first point, so I refer you to comments above.

I’ll discuss what I think is the significance of sexual reproduction for evolution in a following post to keep posts to (an almost) reasonable length.

Comment #107307

Posted by Tom Curtis on June 21, 2006 8:12 PM (e)

Longhorn:

Maybe I’m not quite seeing your point. But some populations of organisms don’t change much over millions and millions of years. Some of today’s bacteria is very similar to bacteria that we had 3 billion years ago. As I understand it, cockroaches are very similar today to what they were millions and millions of years ago.

But then some series of events triggers important changes among the members of the populations. Which events? For asexually reproducing organisms, mutation, lateral transfer and varying levels of reproductive success (aka natural selection) were key.

If you are looking for the explanation for adaptive radiations (such as the Cambrian “explosion”) we are discussing entirely the wrong area. The explanation for stability in species, and also for wild diversification lies primarily in ecology. We know this because mutations occur at a sufficient pace to drive evolution at a rate thousands of times faster than that which has been observed over the long term of geological history. Given a population of moderate size (100,000 individuals), and a relatively shor period (100,000 years) every possible point mutation will have occured in some individual that survives to adulthood, on average 10 times.

That is why, when a major ecological catastrophe (a mass extinction) occurs, evolution occurs at a very rapid rate. But after that, things settle down over the long period because ecological niches are relatively stable, and their occupants well established and hard to displace. That is why “living fossils” invariably come from very stable environments. The Coelocanth comes from ocean depths, the most ecological stable environment known. Cockroaches live in leaf litter, which is far more stable in temperature and moisture than the rest of the forest. Indeed the ecological differences between Carboniferous and Quaternary leaf litter are minimal; and the difference between Permian and Quaternary tropical river banks are also minimal. That is also why islands are hotbeds of evolution. Mutation rates and sexual activity are no more phrenetic in Hawaii than on the US mainland, but speciation is much more rapid in Hawaii because so few ecological niches had original occupants, and because extinctions are far more common (because of small species numbers).

In the long course of evolution, some adaptive radiations have been caused by new structures (genetic, as in pax gene duplication, or morphological, as in the evolution of lungs and tetrapod limbs) have opened up a vista of ecological niches previously unachievable. But the process that formed these novel structures are just the normal processes of evolution. They have astonishing consequences because of the ecological possibilities they open rather than because of some astonishing fact about their formation.

Comment #107308

Posted by 'Rev Dr' Lenny Flank on June 21, 2006 8:14 PM (e)

The pathetically arrogant Aureola Nominee just can’t stand that someone contradicted her/him/it

Damn. I’ll be picking pieces of my irony meter out of the walls for WEEKS now.

Comment #107309

Posted by Coin on June 21, 2006 8:18 PM (e)

Those things are dangerous.

Comment #107313

Posted by Tom Curtis on June 21, 2006 8:39 PM (e)

Longhorn:

As I understand that article (and the language isn’t easy for me), it doesn’t say that “most crossovers will fall in non-coding sequences.” It says: “DSBs do not occur at a specific DNA sequence, but rather are dispersed throughout a region of 50-200 bp at each locus examined (de Massy et al. 1995; Liu et al. 1995; Xu and Kleckner 1995; Xu and Petes 1996).” As I understand that sentence, most crossovers don’t occur at a particular sequence but occur all over a particular region.

Almost all breaks occur in intergenic regions that contain transcription promoters, but transcription is not required for DSB induction (White et al. 1992; Wu and Lichten 1994).

“Intergenic regions” meaning “regions between genes” as “international flights” mean “flights between nations”; and in contrast to “intragenic regions” (or “infragenic”), ie, regions within genes. Coding DNA, of course, are genes, although not all genes need be coding sequences of DNA (depending on how you define it.) So if “almost all breaks occur in intergenic regions” than almost all breaks occur in the regions of DNA between genes (and hence between rather than in coding DNA sequences).

However, assuming (which is not obvious) that the transcription promoters near which crossover occurs are transcription promotors for active genes (which I think unlikely for reasons given), then the crossover occurs withing a region from 50 to 250 bp of such promoters. This gives the possibility that they are all upstream of the promoter which means they are not in the coding DNA which lies downstream. It also opens the possibility that, unless the promoter contains a TATA box, that crossovers downstream of the promoter will still miss the coding sequence because eukaryotic promoters can lie several kilobases upstream of the sequence whose transcription they promote.
http://en.wikipedia.org/wiki/Promoter

IMO, however, if crossovers typically occured at transcription promoters near gene sequences, saying that they almost always occured in intergenic regions would be fundamentally misleading, in that most crossovers, in that instance, would not lie between genes, but in genes.

Comment #107315

Posted by Longhorn on June 21, 2006 9:10 PM (e)

“Intergenic regions” meaning “regions between genes” as “international flights” mean “flights between nations”; and in contrast to “intragenic regions” (or “infragenic”), ie, regions within genes. Coding DNA, of course, are genes, although not all genes need be coding sequences of DNA (depending on how you define it.) So if “almost all breaks occur in intergenic regions” than almost all breaks occur in the regions of DNA between genes (and hence between rather than in coding DNA sequences).

Are you saying that most crosses occur in “junk DNA?” I’m finding this discussion to be a little unclear.

It seems reasonable that most crossovers do not cause sequences from one parent to get stuck in a particular gene of the sequences of the other parent. But it does seem not seem reasonable to me that most crossovers occur in junk DNA. Is that what you are saying?

Comment #107316

Posted by Longhorn on June 21, 2006 9:17 PM (e)

I wrote:

But it does seem not seem reasonable to me that most crossovers occur in junk DNA. Is that what you are saying?

I meant it ods not seem reasonable to me that…

Tom wrote:

This is not to say that sexual reproduction does not accelerate evolution. It does! But it is not implicated in the diversity of forms that evolution has generated.

What reason is there to believe that sexual reproduction “is not implicated in the diversity of forms that evolution has generated?”

Comment #107317

Posted by Longhorn on June 21, 2006 9:21 PM (e)

Further, it is not clear that it is an advantage. Haploid creatures derive the whole of a given protein from just on version of a gene. Given your rhino example, a haploid “rhino” with allele H, would probably have as strong a horn as a diploid with alleles H/H…

Do you have a link or any evidence for that?

Comment #107318

Posted by Longhorn on June 21, 2006 9:24 PM (e)

This is a matter of perspective.

No, it’s not. Look at the difference between elephants and frogs and humans.

This reflects the relative time it took to evolve eukaryotic cells from prokaryotic cells compare to the time it takes to evolve complex multicellurity given eukaryotic cells. This coupled with the large number of multicellular creatures that have reverted to asexual reproduction suggests that it is eukaryotic cells, not sexual reproduction which was the important precondition for the explosion in multicellular diversity.

Here is that quote from Mayr again:

“The process of sexual reproduction makes far more new phenotypes available for natural selection than does mutation or any other process. It is the major source of variation found in populations of sexual species. This capacity for the production of large amounts of variation would seem to be the major selective advantage of sexual reproduction (see the special section ‘The Evolution of Sex,’ Science 281(1988): 1979-2008). It is this capacity for recombination that gives sexual reproduction its enormous evolutionary importance” (What Evolution Is, p. 105).

Comment #107320

Posted by Longhorn on June 21, 2006 9:28 PM (e)

This is just a redescription of diploidy, which was your first point, so I refer you to comments above.

I don’t see your point.

Comment #107324

Posted by Longhorn on June 21, 2006 10:18 PM (e)

Here is a quote from Dawkins:

“Sexual selection produces quirky, whimsical evolution that runs away in apparently arbitrary directions, feeding on itself to produce wild flights of evolutionary fancy” (The Ancestor’s Tale, p. 263).

Comment #107325

Posted by Tom Curtis on June 21, 2006 10:19 PM (e)

Longhorn, IMO, short responces of the form of “what is your evidence for that” are impolite. They are impolite because the place on your interlocuter the entire burden of sustaining the discussion - of providing evidence and reasons - without accepting any of that burden yourself. They also show no engagement with reasons or evidence already provided because they require no engagement to be uttered. Further, as they can be endlessly repeated, and as any cogent responce (other than “just because” or equivalents) must be longer, they result in an exponential increase in the amount of informatin your interlocuter must provide to sustain the discussion.

That pattern of responces is often used as tactic by creationists. Any evolutionist explanation is subjected to multiple brief requests for further explanation, and any responce to those is treated the same. When, at the end of the day the evolutionist cannot keep up with the exponential increase of requests for links and information, the creationist claims to have won the debate because of the number of unanswered questions, even though they have not provided any reasons justifying their position.

I am assuming you are making your short responces not as a debating tactic, but out of thoughtlessness and laziness. Regardless, I am at the end of my tether. The answers to all of your latest barrage of questions are already contained in the prior discussion.

On the assumption that you genuinely want to learn about this topic, here is one more usefull link:

http://en.wikipedia.org/wiki/Evolution_of_sex

By the way, IMO, with no reasons given, sexual reproduction is important to evolution because:

a) It allows a greater amount of variety to be sustained in a population of a given size, given equivalent mutation rates; and

b) It allows a significantly greater effective mutation rate to be sustained than would otherwise be the case.

Both have significant effects on the pace of evolution, but except in that they generate “frozen accidents”, have little effect on end outcomes.

Comment #107328

Posted by Sir_Toejam on June 21, 2006 10:30 PM (e)

Regardless, I am at the end of my tether.

I applaud your patience, Tom!

maybe I’ve spent too much time here, but I doubt i would have gotten past the second “do you have evidence for that?” type of response.

Comment #107329

Posted by Longhorn on June 21, 2006 10:35 PM (e)

maybe I’ve spent too much time here, but I doubt i would have gotten past the second “do you have evidence for that?” type of response.

That is BS. What am I suppose to do? There were unsubstantiated claims, and I’m skeptical of some of them.

What am I suppose to? At what point do you thin I’m wrong.

Maybe you can help.

Comment #107330

Posted by Longhorn on June 21, 2006 10:37 PM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #107331

Posted by Longhorn on June 21, 2006 10:41 PM (e)

The answers to all of your latest barrage of questions are already contained in the prior discussion.

I disagree. Please give me one example.

Comment #107332

Posted by Longhorn on June 21, 2006 10:47 PM (e)

Tom wrote:

This coupled with the large number of multicellular creatures that have reverted to asexual reproduction suggests that it is eukaryotic cells, not sexual reproduction which was the important precondition for the explosion in multicellular diversity.

Here is what Mayr says:

No matter what the selective advantage of sexual reproduction may be, that it does have an advantage is clearly indicated by the consistent failure of all attempts to return to asexuality. Obligatory asexuality is not found among higher plants, but agamospermy, seed production without fertilization, is widespread (Grant 1981). Uniparental reproduction, however, is more frequent than sexual reproduction in certain protists, fungi, and some groups of nonvascular plants. It is the exclusive mode of reproduction in the prokaryotes, in which unidirectional gene transfer provides genetic variation.

Comment #107335

Posted by Sir_Toejam on June 21, 2006 11:28 PM (e)

What am I suppose to? At what point do you thin I’m wrong.

look, at some point you have to start grasping the things Anton and Tom are trying to point out.

The frustration comes in when, instead of indicating by example that you have grasped what either of them said, you instead ask them to keep doing the work of showing references to you to detail or explain it better.

it’s not necessarily that anyone thinks you dishonest, but one does get the impression that you could just as easily do some of the work yourself.

it’s not all that hard.

An online forum isn’t really the ideal location for an in depth course of instruction, after all.

aside from that, I was merely pointing out my own shortcomings wrt patience.

In fact, If the same series of questions were directed at myself, I would have posted something very similar to what i just said above, but far earlier than Tom did.

really, it’s meant as a postive suggestion that since you exhibit real interest in the topic, that you spend more time reading some basic texts on the issue (apart from Myers).

In fact, as usual for most with an interest in the subject of evolution and reproduction, I always recommend Futuyma’s Evolutionary Biology as an excellent reference and instructional work.

do remember that the focus of this thread was simply the lack of recognition of the second half of the RM+NS equation by just about any creobot you can name.

If you do wish to continue an online discussion, I would suggest you open a topic over at the ATBC area (link on the front page of PT). that will get lots of individual input, and you can investigate different directions as much as you’d like.

Comment #107336

Posted by Tom Curtis on June 21, 2006 11:32 PM (e)

Longhorn:

That is BS. What am I suppose to do? There were unsubstantiated claims, and I’m skeptical of some of them.

What am I suppose to? At what point do you thin I’m wrong.

What you ought not to do is to assume your interlocuter will give you a basic education in biology.

You are asking interesting questions, and they are relevant and important. However, they cannot be meaningfully discussed without some basic understanding. At a minimum:

You should know the difference between a gene, a genotype, and a gene pool;

You should know the difference between the quesions:

What is sexual reproduction and why is sexual reproduction sustained by natural selection?

What is the effect of sexual reproduction on the path and long term outcomes of evolution?

What is sexual selection, and how does it occur?

These are very distinct questions, and have distinct answers. However, you have just shown by your Dawkins quote (and your most recent Mayr quote) that you do not understand them to be distinct.

Having got a basic understanding of the issues involved, it is quite appropriate to ask for further clarification or evidence; but you ought also to be trying to follow explanations and reasons as given. At a minimum, you should be able to summarise the reasons and evidence already given to you in your own words; and be able to see why someone would consider them relevant. When asking for further clarrification and reasons, you should at least provide that summary so that your interlocuter can see you are trying to understand what they said. You should also provide the reasons for your own beliefs. If you can’t do either, then either you do not understand the subject well enough to analyze reasons when given, or your interlocuter is terminally confused. There have been enough signs in this case for me to conclude that it is the former.

Comment #107337

Posted by Anton Mates on June 21, 2006 11:42 PM (e)

Longhorn wrote:

As I understand that sentence, most crossovers don’t occur at a particular sequence but occur all over a particular region. And it doesn’t say, or suggest to me, that said region is non-coding. Now it might tend to be non-coding. And maybe that is a reasonable inference, given that a significant amount of the entire genome is non-coding. But meiosis is usually presented to the general reader as occurring in coding DNA.

“Meiosis” is a process that involves the entire cell and its genome–coding and non-coding DNA alike.

I would characterize Dawkins in that manner, though that might not be totally fair. At least there is no suggestion made by any author I’ve read that crossovers tend to occur in non-coding DNA.

Aside from the sources Tom provided, there is much more non-coding DNA than coding DNA in a eukaryotic genome, so statistically most crossovers should occur in non-coding DNA. Can you explain why it seems “unreasonable” to you that they should do so?

Returning to your earlier example,

My point is this: The first phase of meiosis often results in a sequence of nucleotides being in a significantly different order than what preceded the first phase. So, for instance, we may have the following sequence at particularly location on a chromosomes:

AC
AT
CT
GC
AC
GC
AC

After crossing over, we may have this sequence:

AC
AT
CT
GC
AT
GC
AT

1) The above would be a mutation by definition, particularly if it occurred in a coding region. Just because it occurs during meiosis doesn’t mean it’s not a mutation.

2) I’m not sure how the above could result from crossover. I’m assuming here that the two columns of bases each represent a single strand from one of the two chromatids–if so, generally crossover should just switch pairs of horizontally-adjacent bases. That doesn’t seem to be what you’ve done above.

Respectfully, I would suggest reading the genetics section in a good bio textbook–Neil Campbell’s “Biology”, maybe. I wish I could remember the name of my intro genetics textbook.

Comment #107338

Posted by Sir_Toejam on June 21, 2006 11:55 PM (e)

I think the text used in my undergrad genetics course was simply Genetics, by F. Ayala.

It was a decent enough treatise.

Comment #107348

Posted by Sir_Toejam on June 22, 2006 12:11 AM (e)

meh, it doesn’t look like that textbook is available any more.

hmm.

interestingly, a good reference for molecular genetics is not as easy to google as I would have thought.

Comment #107355

Posted by Tom Curtis on June 22, 2006 1:01 AM (e)

A good site for online textbooks:

http://textbookrevolution.org/biology/

A good highschool level textbook on Meiosis:

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Meiosis.html

Comment #107356

Posted by Sir_Toejam on June 22, 2006 1:31 AM (e)

hmm. I really couldn’t find a good undergrad level molecular genetics text using either google or google scholar. i searched amazon too, to no avail.

interesting.

well, the reference to Futuyma’s Evolutionary Biology works here too. He does cover the basic relevant aspects of both the molecular and population genetics. Just not in as much depth as I would normally recommend.

a good used copy can be had cheap:

http://www.amazon.com/gp/offer-listing/0878931899/ref=dp_olp_2/102-5562519-3020154?%5Fencoding=UTF8

Comment #107368

Posted by Longhorn on June 22, 2006 5:57 AM (e)

Tom wrote:

Having got a basic understanding of the issues involved, it is quite appropriate to ask for further clarification or evidence; but you ought also to be trying to follow explanations and reasons as given. At a minimum, you should be able to summarise the reasons and evidence already given to you in your own words; and be able to see why someone would consider them relevant. When asking for further clarrification and reasons, you should at least provide that summary so that your interlocuter can see you are trying to understand what they said. You should also provide the reasons for your own beliefs. If you can’t do either, then either you do not understand the subject well enough to analyze reasons when given, or your interlocuter is terminally confused. There have been enough signs in this case for me to conclude that it is the former.

I know people who were signficantly taller than either of his parents. I believe Kareem Abdul Jabbar is an example. Kareem was probably taller than anybody in his sexual lineage. I doubt mutation contributed to this. Nutrtion probably played a role. But he was as tall as he was because his parents reproduced. And his mother had genes for “tallness,” and his father had genes for “tallness.”

Had did giraffe’s necks get so long. Partly because of the same kind of event. You keep combining giraffes with some of the lonngest necks in the population, and the necks keep getting longer and longer and longer.

There are limits, of course. But those necks can get pretty darn long, just through combining different combinations of giraffes.

Comment #107369

Posted by Longhorn on June 22, 2006 6:02 AM (e)

Anton wrote:

Aside from the sources Tom provided, there is much more non-coding DNA than coding DNA in a eukaryotic genome, so statistically most crossovers should occur in non-coding DNA. Can you explain why it seems “unreasonable” to you that they should do so?

First, I might be wrong. I don’t know. But I question it because of the way meiosis presented in various things that I’ve read. It is presented as if it doesn’t occur to the junk DNA. It is presented as if it occurs to the part of the genome that codes. Do you have understanding that the crossovers usually do occur to the junk the DNA? I would be interested in that.

Comment #107370

Posted by Longhorn on June 22, 2006 6:06 AM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #107371

Posted by Longhorn on June 22, 2006 6:12 AM (e)

Anton wrote:

Aside from the sources Tom provided, there is much more non-coding DNA than coding DNA in a eukaryotic genome, so statistically most crossovers should occur in non-coding DNA.

Unless I am misunderstanding the article that Tom linked to, the article does not show that most cross-overs occur in “non-coding DNA.” It shows that most crossover don’t break up existing genes. The genes stay in tack for the most part. That is how I understand this sentence: “Almost all breaks occur in intergenic regions that contain transcription promoters, but transcription is not required for DSB induction (White et al. 1992; Wu and Lichten 1994).” In other words, the crossovers occur so that the breaks occur in between two genes. But I might be wrong.

Comment #107373

Posted by Longhorn on June 22, 2006 6:19 AM (e)

Tom wrote:

What is the effect of sexual reproduction on the path and long term outcomes of evolution?

That is the question I’m interested in. I’m also interested on the degree to which sexual reproduction contributed to less massive anatomical differences.

But I’m interested, for instance, the kinds of events that contributed to the giraffe’s getting so long. I’m interested in the kinds of events that resulted in the whales nostril’s evolving into blow holes. I’m interested in the kinds of events that resulted in elephants having such long trunks.

I’m sorry if my questions have been annoying. But there was no intent on my part to be provocative.

Comment #107374

Posted by Longhorn on June 22, 2006 6:23 AM (e)

Anton wrote:

2) I’m not sure how the above could result from crossover. I’m assuming here that the two columns of bases each represent a single strand from one of the two chromatids—if so, generally crossover should just switch pairs of horizontally-adjacent bases. That doesn’t seem to be what you’ve done above.

If I understand what you are saying, it is essentially what I’ve done. I’ve merely switched three pairs of nucleotides. I thought that that sometimes occurs during meiosis. But maybe I’m wrong.

Comment #107377

Posted by Longhorn on June 22, 2006 6:36 AM (e)

Sir Toejam wrote:

look, at some point you have to start grasping the things Anton and Tom are trying to point out.

From your perspective, what have I not grasped?

really, it’s meant as a postive suggestion that since you exhibit real interest in the topic, that you spend more time reading some basic texts on the issue (apart from Myers).

I have read more than a little in order to determine what kinds of events have contributed to significant diversity among organisms. I’m specifically interested in the degree to which sexual reproduction contributed to significant anatomical diversity. I’m interested, for instance, in the series of events that resulted in nostrils evolving into blow holes. I’m especially interested in the extent to which sexual reproduction contributed to this transformation. I’ve read Dawkins, Mayr, Sean Carroll, Lewontin, Gould, Ridley and Futuyma. I’ve also read Daniel Dennett.

Comment #107381

Posted by 'Rev Dr' Lenny Flank on June 22, 2006 7:14 AM (e)

What am I suppose to do?

Go to a library (the big building with all the books in it) and ask the nice librarian there to show you where all the beginner’s science books are.

Come back when you know what the hell you are talking about.

It’s not our job to give you a basic science education, and it’s not our job to explain all the things you don’t know to your satisfaction.

And if you want to shoot your mouth off about “all scientists in the world are wrong !!!!!!!!”, you’ll look a lot less like an uneducated pig-ignorant idiot if you, uh, actually know what you are talking about.

Just some friendly advice.

Comment #107382

Posted by Longhorn on June 22, 2006 7:17 AM (e)

Go to a library (the big building with all the books in it) and ask the nice librarian there to show you where all the beginner’s science books are.

Could you be specific? What am I getting wrong? I didn’t say any scientist was wrong.

Comment #107383

Posted by 'Rev Dr' Lenny Flank on June 22, 2006 7:20 AM (e)

I’ve read Dawkins, Mayr, Sean Carroll, Lewontin, Gould, Ridley and Futuyma. I’ve also read Daniel Dennett.

Read them again. And have an educated perosn explain all the big words to you.

Comment #107384

Posted by Longhorn on June 22, 2006 7:22 AM (e)

Lenny, what have I said that you disagree with?

Comment #107399

Posted by Anton Mates on June 22, 2006 8:37 AM (e)

Longhorn wrote:

Aside from the sources Tom provided, there is much more non-coding DNA than coding DNA in a eukaryotic genome, so statistically most crossovers should occur in non-coding DNA.

Unless I am misunderstanding the article that Tom linked to, the article does not show that most cross-overs occur in “non-coding DNA.” It shows that most crossover don’t break up existing genes.

But these mean exactly the same thing: gene = coding DNA sequence!

Comment #107438

Posted by Longhorn on June 22, 2006 12:06 PM (e)

Anton wrote:

But these mean exactly the same thing: gene = coding DNA sequence!

Yeah, after reading it again and thinking more about it, “intergenic” is considered non-coding.

Also, the organism that the article about is S. cerevisiae, also known as yeast. According to the article, crossovers usually occur in the intergenic regions of yeast. However, the article also includes the following:

“In many organisms, recombination is concentrated in gene-rich regions (e.g., Civardi et al. 1994; Gill et al. 1996). In contrast, in C. elegans, recombination occurs preferentially in gene-poor regions (Barnes et al. 1995); mutation of the rec-1 gene abolishes this bias (Zetka and Rose 1995b). In mice and human males, crossing over occurs at higher-than-average frequencies near telomeres (for review, see Ashley 1994). Curiously, these telomere-proximal recombination exchanges are not associated with detectable recombination nodules, suggesting that these events are mechanistically distinct from other exchanges. A special case of a recombination hot spot is the pseudoautosomal region that serves as the site of pairing and exchange between the X and Y chromosomes in mammals (for review, see Rappold 1993)” (emphasis added).

Here is the whole relevant part of the article:

“Meiotic recombination events are not uniformly distributed throughout the genome (for review, see Lichten and Goldman 1995). Instead, the frequency of meiotic exchange per unit physical distance can vary by several orders of magnitude from one region to another, even within a single chromosome. Considerable attention has focused on recombination hot spots, which are sites or regions in which recombination occurs at frequencies significantly higher than the average for the overall genome.

“In S. cerevisiae, hot spots correspond to the sites of the meiosis-specific DSBs that initiate recombination. DSBs do not occur at a specific DNA sequence, but rather are dispersed throughout a region of 50-200 bp at each locus examined (de Massy et al. 1995; Liu et al. 1995; Xu and Kleckner 1995; Xu and Petes 1996). Almost all breaks occur in intergenic regions that contain transcription promoters, but transcription is not required for DSB induction (White et al. 1992; Wu and Lichten 1994). Hot spots correspond to nuclease-hypersensitive sites in chromatin isolated from vegetative cells, and these regions undergo meiosis-specific modifications that increase their susceptibility to nuclease digestion (Ohta et al. 1994; Wu and Lichten 1994; Fan and Petes 1996). However, an open chromatin configuration must not be the only determinant of DSB formation because there is an imperfect correlation between the level of nuclease hypersensitivity and the probability of cleavage (Wu and Lichten 1995; Fan and Petes 1996).”

“A well-characterized recombination hotspot in S. pombe is defined by the ade6-M26 mutation. Unlike other eukaryotic hot spots, M26 activity depends on a specific DNA sequence: 5’-ATGACGT-3’ (Schuchert et al. 1991). This heptamer serves as a binding site for a heterodimeric protein, Mts1/Mts2, whose activity is required for hot spot activity (Wahls and Smith 1994; Fox et al. 1997). Chromatin structure appears to play a role in regulating recombination in fission yeast, just as it does in budding yeast. The M26 mutation causes a dramatic increase in meiotic induction of a nuclease hypersensitive site in the ade6 promoter, and it creates a new hypersensitive site at the position of the M26 mutation (located ~400 bp downstream) (Mizuno et al. 1997). Both the promoter and M26 are required for hot spot activity (Zahn-Zabal et al. 1995). The position of the lesion that initiates recombination, either in the presence or in the absence of the M26 mutation, is not known.

“Little is known about the molecular basis of hot spot activity in systems other than fungi. In many organisms, recombination is concentrated in gene-rich regions (e.g., Civardi et al. 1994; Gill et al. 1996). In contrast, in C. elegans, recombination occurs preferentially in gene-poor regions (Barnes et al. 1995); mutation of the rec-1 gene abolishes this bias (Zetka and Rose 1995b). In mice and human males, crossing over occurs at higher-than-average frequencies near telomeres (for review, see Ashley 1994). Curiously, these telomere-proximal recombination exchanges are not associated with detectable recombination nodules, suggesting that these events are mechanistically distinct from other exchanges. A special case of a recombination hot spot is the pseudoautosomal region that serves as the site of pairing and exchange between the X and Y chromosomes in mammals (for review, see Rappold 1993).”

It is important to note that even if crossovers tend to occur in ares of some organisms that are not gene rich, that is not that important to whether sexual reproduction has been important in contributing to some of the significant diversity among sexual reproducers. For crossover do seem to occur in gene rich areas for some organisms. More importantly, we also have the key aspect of sexual reproduction, which is the fertilization event. It places the two distinct groups of chromosomes next to each other. The chromosomes don’t blend. The don’t touch each other. And from their you get an organism like Kareem Abdul Jabbar.

Kareem may have been born with some new mutations. But if he was, those mutations probably were not the cause of his being the height that he is. Nutrition was important. And he got genes that, when put together, contributed to him being the height that he is. Some organisms end up having traits that are more pronounced than either of their parents. The combination of genes contributed.

Comment #107549

Posted by Anton Mates on June 22, 2006 11:10 PM (e)

Longhorn wrote:

But these mean exactly the same thing: gene = coding DNA sequence!

Yeah, after reading it again and thinking more about it, “intergenic” is considered non-coding.

Also, the organism that the article about is S. cerevisiae, also known as yeast. According to the article, crossovers usually occur in the intergenic regions of yeast. However, the article also includes the following:

“In many organisms, recombination is concentrated in gene-rich regions (e.g., Civardi et al. 1994; Gill et al. 1996). In contrast, in C. elegans, recombination occurs preferentially in gene-poor regions (Barnes et al. 1995); mutation of the rec-1 gene abolishes this bias (Zetka and Rose 1995b). In mice and human males, crossing over occurs at higher-than-average frequencies near telomeres (for review, see Ashley 1994). Curiously, these telomere-proximal recombination exchanges are not associated with detectable recombination nodules, suggesting that these events are mechanistically distinct from other exchanges. A special case of a recombination hot spot is the pseudoautosomal region that serves as the site of pairing and exchange between the X and Y chromosomes in mammals (for review, see Rappold 1993)” (emphasis added).

As far as I can see, there’s no conflict here. Crossovers can occur within gene-rich regions without occurring actually within individual genes. This is actually what you’d expect if sexual reproduction is intended to safely boost variation–if a crossover point occurs within a gene-rich region it’s likely to end up swapping a few whole genes, but if it doesn’t occur within an actual gene, it’s not going to swap incomplete pieces of genes, and thus no individual gene’s sequence is altered. In other words, no mutation occurs. Thus recombination will independently assort existing alleles without generating new and probably lousy-functioning ones.

Kareem may have been born with some new mutations. But if he was, those mutations probably were not the cause of his being the height that he is.

Probably not, but Kareem also isn’t remarkably tall given his genetic background–there’re lots of seven-footers in West Africa. I know nothing of his particular people of origin or family history, but if he has some extremely tall distant relatives, that supports his height being due to a particular assortment of extant alleles. Maybe neither of his parents got that exact combo, but the population as a whole occasionally produces someone who does, and Kareem was one of them.

That reasoning doesn’t really work for dog evolution from wolves, because we don’t see the occasional wolf who’s, say, even half as small as a Chihuahua. That suggests that Chihuahuas are packing some combo of mutant growth alleles that aren’t individually found in any wolf.

Comment #107572

Posted by Wayne E Francis on June 23, 2006 3:09 AM (e)

I’ve got through about half the posts in this thread and I’m surprised that no one has pointed out why dogs have so many different varieties that basically come down to visual differences.

Dogs, all breeds, and wolves are the SAME species. There is very little genetic difference between a Chihuahua, Saint Bernard and a grey wolf. About the same genetic difference between You and someone that lives next door to you or even half way around the world.

The differences we see in dogs is no different from differences in humans. It’s expressions of genes that cause slight differences in people. Do you have blue eyes or brown, grey or green or something in between? (hey that rhymes) Do you have Blonde hair or black, brown or red or are you bald instead? (hehehe to easy). Are you as tall as Robert Pershing Wadlow, short as Verne Troyer or maybe even shorter? Do you have muscles like Phil Hill or can run like Michael Johnson, do you have reflexes of a 7 year old boy or or or ….ok I’ve run out of the patience to continue rhyming.

This is the reason why if you let a pack of dogs into the wilds they will, over a course of many generations, “revert back to gray wolves”. It isn’t that mutations are slowly turning them into gray wolves. They are Canis Lupus. They have just been selected to produce certain traits. Its like 2 short people have a kid their child is more likely to be short. The big thing about dog breeds being different from gray wolves seems to come mostly from the trait making them more docile. Breeding wolves and selecting them for being more docile shows that this also has many secondary effects like:
1. coat colour and pattern changes
2. floppy ears
3. Upturned tail
4. smaller brain

What is the evidence for this you say? Well they’ve tested it. Not only for wolves but another member of the Canidae family the Red Fox or Vulpes Vulpes. Not only is the Red Fox a different species it is a member of a different Genus. Despite this Red Foxes when breed and selectively breed for docile traits show the same changes as happens with Grey Wolves.

From American Scientist Vol 87 No 2
“Other physical changes mirror those in dogs and other domesticated animals. In our foxes, novel traits began to appear in the eighth to tenth selected generations. The first ones we noted were changes in the foxes’ coat color, chiefly a loss of pigment in certain areas of the body, leading in some cases to a star-shaped pattern on the face similar to that seen in some breeds of dog. Next came traits such as floppy ears and rolled tails similar to those in some breeds of dog. After 15 to 20 generations we noted the appearance of foxes with shorter tails and legs and with underbites or overbites. The novel traits are still fairly rare. Most of them show up in no more than a few animals per 100 to a few per 10,000. Some have been seen in commercial populations, though at levels at least a magnitude lower than we recorded in our domesticated foxes.”

So this seems to something genetically tied to, atleast, the Canidea family but maybe even the order of Carnivors.

The reason dogs revert back to wolves is because they ARE wolves. Wolves are more suited to life in the wild then dogs are. Thus if you put dogs in the wild they’ll do what they do. They’ll form packs. They’ll hunt. They’ll breed. Over generations the more aggressive wolves will do better. They’ll be head of the pack. They’ll breed more. They’ll be more healthy because they eat better.

After many generations where that original pack of dogs is now looking like a normal pack of wolves you could do a 2nd test. Have people move into their territory. Watch what happens over generations. You’ll see that it’s the more docile wolves that approach the settlements more. They’ll eat the scraps of food humans throw away. The more docile they are the more they’ll encroach on the settlements. Being more docile the humans will start to tame them. The humans can then selectively breed for certain traits. But the basic mutt is there….its just a docile wolf. The visual differences between these dogs and wolves are VERY superficial and really not much different then differences between humans.

So people should stop using dogs as a great example of “Macro Evolution”
Don’t get me wrong Macro Evolution, better called just “Evolution” does occur. Dogs are not a different species then wolves and shouldn’t be said to be.

In a case where you have true speciation where Species A splits into 2 species and over large amounts of time you get species A and B. Species B evolves differently then species A due to many factors. Species A may even change over these long periods of time. In any case if you dumped Species B back into Species A environment and real speciation occurred you would not see Species B “revert back” to Species A.

Dog are only separated from wolves by 10k years or so. Just like you could take a human from 10k years ago and they would still be able to have children with modern humans. 10k years ago qualifies as “modern human”.
Step back 2 million years ago this wouldn’t be the case. Sticking humans alone in a jungle won’t make them revert back to some ancient ape any more then sticking a wolf in an African environment would make them turn into a Hyena. They may evolve into a similar predator but they would not be the same species or even genus.

Comment #107685

Posted by Longhorn on June 23, 2006 7:19 PM (e)

Anton wrote:

Crossovers can occur within gene-rich regions without occurring actually within individual genes.

Sure. But I’m not so interested in what can occur. I’m more interested what does occur and what usually does occur. I don’t know how frequent it is for breaks to occur in the middle of a gene. But I do understand that the chromosomes pieces that swap usually (but not always) are on the same loci of the two chromosomes involved in a swap. Moreover, the first phase of meiosis does result in new sequences of nucleotides than what existed before the phase, and often significantly different sequences. In fact, in at least some organisms, recombination creates protein sequence diversity at a faster than does mutation. I provide the link below.

Here is a good quote from Mayr on meiosis:

“It took more than 100 years of study to achieve a full understanding of the meaning and process of sexual reproduction. Darwin searched unsuccessfully all his life for the source of genetic variation. It required knowledge of the process of gamete formation and the difference between genotype and phenotype and their roles in natural selection, as well as an understanding of population variation.

“August Weismann and a group of cytologists found the answer. They showed that in sexual reproduction, gamete formation is preceded by two special cell divisions. During the first division, homologous maternal and paternal chromosomes attach themselves tightly to each other and then may break at one or several places. The broken chromosomes exchange parts with each other so that they now consist of a mixture of paternal and maternal chromosome pieces…In the second cell division preceding the formation of the gametes, the chromosomes do not divide, but one of each pair of homologous chromosomes goes randomly to one daughter cell and the other chromosome to the other daughter cell. As a result of this ‘reduction division’ the ‘haploid’ number of chromosomes in each gamete is half that of the ‘diploid’ chromosome number of the zygote produced by the fertilized egg. This sequence of two cell divisions preceding gamete formation is called meiosis” (p. 103-4).

“Two processes during meiosis achieve a drastic recombination of the parental genotypes: (1) crossing-over during the first division and (2) the random movement of homologous chromosomes to different daughter cells (gametes) during the reduction division…These, in turn, produce unique phenotypes, providing unlimited new material for the process of natural selection (What Evolution Is, p. 103-4).”

Moreover, if, during meiosis, a break does occur in the middle of a gene, the one chromosome usually receives a piece of chromosome from the other chromosome that consists in the same number of nucleotides as the piece lost in the swap, and the piece received comes from the same location on chromosome as the piece lost.

Finally, according to an article published in April of 2005 the Proceedings of the National Academies of Sciences of the United States of America (PNAS), “intragenic recombination rapidly creates protein sequence diversity compared with random mutation.” Here is the abstract:

“Intragenic recombination rapidly creates protein sequence diversity compared with random mutation, but little is known about the relative effects of recombination and mutation on protein function. Here, we compare recombination of the distantly relate-lactamases PSE-4 and TEM-1 to mutation of PSE-4. We show that, among lactamase variants containing the same number of amino acid substitutions, variants created by recombination retain function with a significantly higher probability than those generated by random mutagenesis. We present a simple model that accurately captures the differing effects of mutation and recombination in real and simulated proteins with only four parameters: (i) the amino acid sequence distance between parents, (ii) the number of substitutions, (iii) the average probability that random substitutions will preserve function, and (iv) the average probability that substitutions generated by recombination will preserve function. Our results expose a fundamental functional enrichment in regions of protein sequence space accessible by recombination and provide a framework for evaluating whether the relative rates of mutation and recombination observed in nature reflect the underlying imbalance in their effects on protein function.”

Here is a link to the abstract and full article: http://www.pnas.org/cgi/content/abstract/102/15/5380

Moreover, according to the authors:

“One question raised by our observations is whether relative rates of intragenic mutation and recombination reflect the underlying imbalance in their effects on protein function. This question can be partly answered. In both natural and laboratory evolution, recombination allows creation of broad sequence diversity with relatively low cost in loss of function compared to mutation. Pathogens under immune surveillance wage combinatorial warfare with their hosts, recombining homologous surface proteins to create folded proteins with diverse epitopes to escape immune responses (13, 42). In the laboratory, gene shuffling (25) and site-directed recombination (27) have proven useful in evolving new enzyme functions by generating diversity while preserving overall fold. By contrast, mutation allows access to only narrow regions of sequence space because of its deleterious effects, although it can be used to search exhaustively for local optima inaccessible by recombination. Our results may explain why recombination is so strongly favored when diversity is the goal: Intragenic recombination efficiently creates protein sequence diversity while conserving structure via preservation of interactions (24), symmetry, and conservatively chosen substitutions. Conservation of fold allows exploration of function.” (emphasis added)

So, intragenic recombination probably has been important in causing protein sequence diversity, and probably contributed to the differences among dogs. It seems to cause to significant protein sequence diversity without the cost to the organism that mutations often do.

But I believe that an evolutionary important aspect of sex is the fertilization event. I touched on this earlier.

Probably not, but Kareem also isn’t remarkably tall given his genetic background—there’re lots of seven-footers in West Africa. I know nothing of his particular people of origin or family history, but if he has some extremely tall distant relatives, that supports his height being due to a particular assortment of extant alleles. Maybe neither of his parents got that exact combo, but the population as a whole occasionally produces someone who does, and Kareem was one of them.

But my point is we often see organisms that have a more pronounced trait than either of their parents. And sexual reproducers often come into being with a trait that no one their sexual lineage possessed, and a new mutation did not cause the difference. Just look at certain mutts that are different than any dog I‘ve ever seen. And Kareem’s height might be another example. Mark Eaton was 7’5”. He was a great shot-blocker. Unfortunately, he didn’t have much of an offensive game. He was slow and plodding.

The professional wrestler The Big Show is a huge guy. I don’t know how big his parents are.

Also, my understanding is that in the 1800s plant breeders were able to significantly increase the sugar content of plants through breeding. My understanding is that they got the content from 5% to 17%. That is pretty significant.

But, as I’ve suggested, I think there are limits to how much phenotypic diversity has come from sexual reproduction. The saber tooth’s cat teeth got longer and longer and longer. And I’m sure sexual reproduction played a huge role. But there is going to come a point where I don’t sexual reproduction can get the trait any more pronounced. But I’d like to have a better understanding of where that point is. I don’t think whales evolved from land mammals merely through sexual reproduction. Mutations were important, too.

Here is a link to some more information on breeding:

http://necsi.org/projects/evolution/breeding/like_natural/like_natural.html

That reasoning doesn’t really work for dog evolution from wolves, because we don’t see the occasional wolf who’s, say, even half as small as a Chihuahua.

I have never seen a wolf get born who is half as small as a Chihuahua. And maybe no person has seen this occur. And maybe that has never happened. But that doesn’t enable you and me to determine that Chihuahuas are as different as they are from their wolf ancestors solely or mostly because of accumulated mutations. We are talking about 130,000 years. A lot can happen in that amount of time, a lot of little changes can add up over such vast periods of time. That a change does happen in one reproduction event doesn’t enable us to determine that it has never happened. Especially when reproduction events are so frequent and we are talking about such long periods of time.

An important issue of this: How much of the difference between dogs and wolves was caused by mutation versus sexual reproduction? I don’t know. There are genomes are very similar. Here is a quote that appeared in an article in National Geographic (From Wolf to Woof):

“Genetic studies show that dogs evolved from wolves and remain as similar to the creatures from which they came as humans with different physical characteristics are to each other, which is to say not much difference at all. ‘Even in the most changeable mitochondrial DNA markers, dogs and wolves differ by not much more than one percent,’ says Robert Wayne, a geneticist at the University of California at Los Angeles.”

Here is the link to the cover, which has a good photograph of a wolf and a little dog:

http://www7.nationalgeographic.com/ngm/data/2002/01/01/html/ft_20020101.1.html

The question is what events caused the difference sequences, mutation, sexual reproduction or both? I think probably both. The population of wolves that evolved into dogs had significant genetic diversity. You could put their sequences in many different orders. The first phase of meiosis puts sequences in different orders. And fertilization puts the two groups of chromosomes next to each other.

But one of the key aspects is this. A dog might have a new mutation that contributes to a trait. Two of its descendents have that same mutation. They reproduce. Sometimes this results in the trait being more pronounced than it was in the first organism to have the mutation. We see this Kareem Abdul Jabbar and the breading that occurred to get certain brighter colors in flowers and sheep with longer hair and stronger horses. And stronger larger cows for eating.

Finally, Chris Colby writes the following: “Recombination creates new combinations of alleles. Alleles that arose at different times and different places can be brought together. Recombination can occur not only between genes, but within genes as well. Recombination within a gene can form a new allele. Recombination is a mechanism of evolution because it adds new alleles and combinations of alleles to the gene pool.” Here is the link:

http://www.talkorigins.org/faqs/faq-intro-to-biology.html

Comment #107708

Posted by Anton Mates on June 23, 2006 9:24 PM (e)

Wayne E Francis wrote:

I’ve got through about half the posts in this thread and I’m surprised that no one has pointed out why dogs have so many different varieties that basically come down to visual differences.

Dogs, all breeds, and wolves are the SAME species. There is very little genetic difference between a Chihuahua, Saint Bernard and a grey wolf. About the same genetic difference between You and someone that lives next door to you or even half way around the world.

True, but more than anything that’s an illustration of why “genetic difference” measures aren’t massively useful for making species distinctions. There are lots of bird and insect sibling species, for instance, where we still can’t reliably distinguish them genetically, but they certainly know the difference when it comes to mating. Sometimes a small genetic change is critical. In the case of dogs and wolves, it produces things like a hundredfold-reduction in adult body mass, which is otherwise pretty much unheard of in a single mammalian species.

I certainly agree that dogs and wolves are the same species–in fact, I wonder if the entire genus Canis couldn’t be equally “correctly” classified as a single species, since they all hybridize fairly frequently. I’m just saying, raw “genetic difference” is a poor way to make that decision. If all dogs except Chihuahuas were wiped out–and through some miracle, Chihuahuas found a stable niche in, I dunno, the fields of Ohio–it would be much harder to make the case that they’re the same species as wolves.

The differences we see in dogs is no different from differences in humans. It’s expressions of genes that cause slight differences in people.

Thing is, a change in gene expression is a genetic change. It’s just a mutation to a regulatory gene rather than to a gene coding for some extranuclear protein. So, continuing from my comments above, here’s an example of a “small” genetic change that turns out to really really matter, by affecting the regulation of lots of other genes.

This is the reason why if you let a pack of dogs into the wilds they will, over a course of many generations, “revert back to gray wolves”. It isn’t that mutations are slowly turning them into gray wolves.

I’d disagree with this. Precisely because they aren’t steadily reversing all the mutations that turned them from wolves into dogs, they don’t revert back to wolves. Probably the populations of once-domestic dogs which have been wild for the longest are the dingo and New Guinea singing dog. While they have certain traits in common with wolves–notably, enlarged carnassials and once-a-year estrus cycles–they clearly aren’t becoming wolves either morphologically or behaviorally. They’re off on their own evolutionary tracks.

It may be that small populations of feral dogs in, say, North America have become close-to-indistinguishable from wolves or coyotes, but I’d suspect that that’s due more to interbreeding with wild canids.

Breeding wolves and selecting them for being more docile shows that this also has many secondary effects like:
1. coat colour and pattern changes
2. floppy ears
3. Upturned tail
4. smaller brain

What is the evidence for this you say? Well they’ve tested it. Not only for wolves but another member of the Canidae family the Red Fox or Vulpes Vulpes. Not only is the Red Fox a different species it is a member of a different Genus. Despite this Red Foxes when breed and selectively breed for docile traits show the same changes as happens with Grey Wolves.

From American Scientist Vol 87 No 2
“Other physical changes mirror those in dogs and other domesticated animals. In our foxes, novel traits began to appear in the eighth to tenth selected generations. The first ones we noted were changes in the foxes’ coat color, chiefly a loss of pigment in certain areas of the body, leading in some cases to a star-shaped pattern on the face similar to that seen in some breeds of dog. Next came traits such as floppy ears and rolled tails similar to those in some breeds of dog. After 15 to 20 generations we noted the appearance of foxes with shorter tails and legs and with underbites or overbites. The novel traits are still fairly rare. Most of them show up in no more than a few animals per 100 to a few per 10,000. Some have been seen in commercial populations, though at levels at least a magnitude lower than we recorded in our domesticated foxes.”

Note, though, that the authors still attribute these changes to mutation–just mutations in regulatory genes.

“Belyaev believed that similarity in the patterns of these traits was the result of selection for amenability to domestication. Behavioral responses, he reasoned, are regulated by a fine balance between neurotransmitters and hormones at the level of the whole organism. The genes that control that balance occupy a high level in the hierarchical system of the genome. Even slight alterations in those regulatory genes can give rise to a wide network of changes in the developmental processes they govern. Thus, selecting animals for behavior may lead to other, far-reaching changes in the animals’ development. Because mammals from widely different taxonomic groups share similar regulatory mechanisms for hormones and neurochemistry, it is reasonable to believe that selecting them for similar behavior—tameness—should alter those mechanisms, and the developmental pathways they govern, in similar ways.”
(Emphasis added).

So people should stop using dogs as a great example of “Macro Evolution”
Don’t get me wrong Macro Evolution, better called just “Evolution” does occur. Dogs are not a different species then wolves and shouldn’t be said to be.

I don’t think anyone who uses that example (here, anyway) is considering dogs as a different species than wolves. But colloquially, “macroevolution” means not merely speciation but also evolution leading to “big” changes, and wolf-to-dog is a great example of that. In contrast, a lot of other macroevolution examples, as in Nereis or Drosophila, provide great examples of incipient speciation, but not much obvious morphological or behavioral change, so the layperson might understandably repeat the old “Well, they’re still just flies/worms” line. So I think the dog example has its place.

Darwin, after all, used another domestic animal–the pigeon–as his chief example of the power of selection.

Comment #107719

Posted by Longhorn on June 23, 2006 9:57 PM (e)

Wayne Francis wrote:

Dog are only separated from wolves by 10k years or so.

My understanding is that they are separated by between 100,000 and 130,000 years.

Here is a link:

http://www.pbs.org/wgbh/evolution/library/01/5/l_015_02.html

Comment #107722

Posted by Sir_Toejam on June 23, 2006 10:03 PM (e)

domesticated 130k years ago, yes, but active selective breeding programs are likely far more recent.

I think this is what he was referring to.

Comment #107723

Posted by Sir_Toejam on June 23, 2006 10:05 PM (e)

OTOH, he could have been relying on the same dates that are commonly quoted in several older textbooks, I could be wrong.

Comment #107725

Posted by Anton Mates on June 23, 2006 10:19 PM (e)

Longhorn wrote:

Moreover, the first phase of meiosis does result in new sequences of nucleotides than what existed before the phase, and often significantly different sequences. In fact, in at least some organisms, recombination creates protein sequence diversity at a faster than does mutation.

Again, what you’re describing is a mutation in the general sense–it’s simply a mutation which is due to intragenic recombination rather than, say, a stray gamma ray. (Some sources may speak of “intragenic recombination” versus “random mutation,” but I think that’s just terminological shorthand.) So you’re really asking the question: Of the mutations which arise and become fixed in a population, how many of them are due to intragenic recombination? I don’t think anyone knows the answer to that yet, and no doubt it varies wildly between taxa.

Finally, according to an article published in April of 2005 the Proceedings of the National Academies of Sciences of the United States of America (PNAS), “intragenic recombination rapidly creates protein sequence diversity compared with random mutation.” Here is the abstract:

Note that this paper doesn’t tell you how often intragenic recombination occurs. Perusing the online literature provides answers ranging from “very rarely” to (in the case of one particular human locus) “often enough to contribute more variants than the inferred point mutations did.” So it doesn’t seem like there’s a general consensus on this.

But my point is we often see organisms that have a more pronounced trait than either of their parents. And sexual reproducers often come into being with a trait that no one their sexual lineage possessed, and a new mutation did not cause the difference. Just look at certain mutts that are different than any dog I‘ve ever seen.

Well, you’d need actual evidence for this–you don’t know, for instance, that that mutt didn’t have a cousin to his great-uncle who happened to have the same trait. And you’d have to check, as you mentioned earlier, that the trait is actually genetic and not environmentally induced (like increased body size due to a richer diet.) And you certainly don’t know that a new mutation didn’t cause the difference.

Comment #107733

Posted by Longhorn on June 23, 2006 10:50 PM (e)

Again, what you’re describing is a mutation in the general sense—it’s simply a mutation which is due to intragenic recombination rather than, say, a stray gamma ray. (Some sources may speak of “intragenic recombination” versus “random mutation,” but I think that’s just terminological shorthand.) So you’re really asking the question: Of the mutations which arise and become fixed in a population, how many of them are due to intragenic recombination? I don’t think anyone knows the answer to that yet, and no doubt it varies wildly between taxa.

The point is that the genetic sequence is caused by the chromosomes swapping nucleotides. I’m talking about the event that caused the nucleotides to be in the order than they are in.

Again, what you’re describing is a mutation in the general sense—it’s simply a mutation which is due to intragenic recombination rather than, say, a stray gamma ray. (Some sources may speak of “intragenic recombination” versus “random mutation,” but I think that’s just terminological shorthand.) So you’re really asking the question: Of the mutations which arise and become fixed in a population, how many of them are due to intragenic recombination? I don’t think anyone knows the answer to that yet, and no doubt it varies wildly between taxa.

The point is that the sequence of nucleotides is caused by the chromosomes swapping nucleotides.

Note that this paper doesn’t tell you how often intragenic recombination occurs. Perusing the online literature provides answers ranging from “very rarely” to (in the case of one particular human locus) “often enough to contribute more variants than the inferred point mutations did.” So it doesn’t seem like there’s a general consensus on this.

I haven’t see anything that says “very rarely” when it comes to mammals or highly complex organisms. Here is the quote from the article that Tom Curtis linked to:

In many organisms, recombination is concentrated in gene-rich regions (e.g., Civardi et al. 1994; Gill et al. 1996). In contrast, in C. elegans, recombination occurs preferentially in gene-poor regions (Barnes et al. 1995); mutation of the rec-1 gene abolishes this bias (Zetka and Rose 1995b). In mice and human males, crossing over occurs at higher-than-average frequencies near telomeres (for review, see Ashley 1994). Curiously, these telomere-proximal recombination exchanges are not associated with detectable recombination nodules, suggesting that these events are mechanistically distinct from other exchanges. A special case of a recombination hot spot is the pseudoautosomal region that serves as the site of pairing and exchange between the X and Y chromosomes in mammals (for review, see Rappold 1993)” (emphasis added).”

Well, you’d need actual evidence for this—you don’t know, for instance, that that mutt didn’t have a cousin to his great-uncle who happened to have the same trait.

Fair enough. But what are you saying? That breeding hasn’t caused any trait to be more significant than what preceded the breeding? That would be an unreasonable claim. Look at the coats of certain animals. So how did you think saber tooth cats teeth so long? Solely by multiple mutation hitting the one gene, or the few genes, that affect teeth length? What the giraffe’s neck? Multiple mutations hitting the genes that affect neck length. I bet sexual reproduction played an important role. Just as it did in the creation of Michael Jordan and Pele and Kareem. And Hulk Hogan.

And you’d have to check, as you mentioned earlier, that the trait is actually genetic and not environmentally induced (like increased body size due to a richer diet.)

The Big Show is not as big as he is just because of diet.

And you certainly don’t know that a new mutation didn’t cause the difference.

In some cases I think I do. Like Michael Jordan’s ability at basketball.

Comment #107735

Posted by Longhorn on June 23, 2006 11:03 PM (e)

Here is a quote on the increase on the sugar content of the sugar beet through breeding:

“In the United States, sugar beets are grown extensively from Michigan to Idaho and in California, accounting for more than half of United States sugar production. Since the 18th cent. selective breeding has raised the root’s sucrose content from 2% or 4% to 15% and even 20%.”

Here is a link:

http://www.encyclopedia.com/html/b/beet.asp

Comment #107745

Posted by Anton Mates on June 24, 2006 12:40 AM (e)

Longhorn wrote:

The point is that the genetic sequence is caused by the chromosomes swapping nucleotides. I’m talking about the event that caused the nucleotides to be in the order than they are in.

Right–that was recombination, and it produced a mutation.

Note that this paper doesn’t tell you how often intragenic recombination occurs. Perusing the online literature provides answers ranging from “very rarely” to (in the case of one particular human locus) “often enough to contribute more variants than the inferred point mutations did.” So it doesn’t seem like there’s a general consensus on this.

I haven’t see anything that says “very rarely” when it comes to mammals or highly complex organisms. Here is the quote from the article that Tom Curtis linked to:

None of the quote you provided speaks to the above question, though. This paper says that “Intragenic recombination is a relatively rare, but evolutionarily important phenomenon occurring in mitosis and meiosis in a wide variety of organisms,” although they proceed to prove that it’s not particularly rare in the ciliate they’re writing about. In this study on corn, they get recombination frequencies generally below 1/10,000. It certainly seems that recent work in humans is arguing for increased importance of recombination in producing mutations.

Fair enough. But what are you saying? That breeding hasn’t caused any trait to be more significant than what preceded the breeding?

No, of course not. But breeding is just evolution where we control the fitness landscape. The successes of breeding are due to exactly the same mechanisms powering natural evolution–which include mutation (which itself includes intragenic recombination) and independent assortment due to other recombination events. In other words, it doesn’t make sense to say “If you can do it through breeding, mutation must not have been important.” In fact, generally breeders are more dependent on mutation since they’re working with a smaller population, hence there’s a bottleneck effect stifling initial variation.

And you’d have to check, as you mentioned earlier, that the trait is actually genetic and not environmentally induced (like increased body size due to a richer diet.)

The Big Show is not as big as he is just because of diet.

Not sure what that has to do with anything…. Anyway, according to Wiki, the Big Show has acromegaly, which generally isn’t heritable at all–it’s due to a spontaneous pituitary tumor. So that’s environment, not genetics.

And you certainly don’t know that a new mutation didn’t cause the difference.

In some cases I think I do. Like Michael Jordan’s ability at basketball.

Ok…how do you know?

Comment #107795

Posted by Wayne Francis on June 24, 2006 9:29 AM (e)

Anton Mates wrote:

Thing is, a change in gene expression is a genetic change. It’s just a mutation to a regulatory gene rather than to a gene coding for some extranuclear protein. So, continuing from my comments above, here’s an example of a “small” genetic change that turns out to really really matter, by affecting the regulation of lots of other genes.

Actually I believe from what I’ve read that the changes we see from wolves to dogs and dogs back to wolves is a positive feed back mechanism that can be altered and reversed.

When left to breed freely, dogs revert to a generalized pariah-type often associated with the dingo or pariah dog of India or generic husky Ñ a medium-sized, prick-eared animal with a ginger, black, black and tan, white, and parti-colored coats,” notes Derr. He adds: “The dog doesn’t have to revert to the wolf. The dog is a wolf Ñ albeit a wolf who exists in human society.

They don’t need to look like grey wolves. Point is they loose all the differences we see very quickly. The positive feedback promotes more aggressive dogs. More aggressive dogs loose the distinctive traits of individual dog breeds. Even the dogs brains get bigger. Seems that, in at least C. Lupus, aggressiveness has a direct correlation to brain size and intelligence. While you might think your pet dog is smarter then a wild grey wolf you should realize that your dog is just more attuned to human interaction then the grey wolf is.

C.Lupus is a species simply because in many instances if you throw a subspecies of Canis Lupus into the wild with another subspecies of Canis Lupus they will often interbreed.

Now sure there is an issue of say a Chihuahua breeding with a grey wolf because of the size but you’d find that the signals that the Chihuahua puts off, pheromones, are still very similiar. This is why many breeds of dogs would interbreed with wolves very easily.

Probably the populations of once-domestic dogs which have been wild for the longest are the dingo and New Guinea singing dog. While they have certain traits in common with wolves—notably, enlarged carnassials and once-a-year estrus cycles—they clearly aren’t becoming wolves either morphologically or behaviorally. They’re off on their own evolutionary tracks.

Is a bit misleading. Yes they are changing. Why aren’t they just like grey wolves? Because they are in a different environment to grey wolves.
If left alone they would become their own species. But the 10-100 thousand years is a evolutionary drop in the bucket. Grab a human from 100k years ago and I’d wager they’d breed pretty successfully with “Modern Humans”.

My point is this, and I hate the term, “Macro Evolution” most often does not occur in a small amount of time. Even so say wolves where started to be domesticated 130k years ago. Are today’s wolves genetically the same as those from 130k years ago? How much difference is there. What is the difference from the 130k year old wolves and today’s domesticated dog breeds? All in all….very little. Just because things look visually different doesn’t mean much. Humans are very diverse. Our primary sense is sight. We notice visual differences more then any other sense. C. Lupus has very acute sense of smell. The smell of that Chihuahua is much more important to that wolf deciding if the Chihuahua is its next lunch or how the wolf will be able to root the Chihuahua.

There is a reason dogs sniff each others butts….it isn’t because they like the smell of poo. So while you see massive differences between dog breeds don not equate that to the dogs seeing massive differences between subspecies.

Give the dingo in Australia a million years or more and I would not be surprised that the dingo could be classified as a new species. But until dingoes stop sniffing the butts of domesticated dogs and thinking “Hmmm I wouldn’t mind rooting this one” I’ll classify, along with most other people that understand the species, them as the same species.

So I put it badly that dogs will revert to grey wolves. They will change into a common pariah-type….which is wolf enough for me. Either way they don’t have big issues breeding with wolves in the wild.

To a great example of evolution is genus Equus. We have lots of data about it and can see large scale changes that dwarf the minor changes we see in C.Lupis. Why is this….because evolution at the species level will always be concidered by creationist to only be “Micro evolution”. To get “Macro Evolution” you need to look at the Genus level and higher. There are 3 species of “Zebras”. Try to convince a creationist of this and you’ll hear a bunch of nonsense and babbling. But if we look at just these 3 species in the genus Equus you can see truely large differences between them. Most people might look at the 3 together and just see 3 black and white striped horses but tho they look very similiar there are levels magnitude more difference between then any 2 breeds of C. Lupus. Just because they are closer in size and shape and colour doesn’t mean much.

Comment #107814

Posted by stevaroni on June 24, 2006 11:06 AM (e)

Give the dingo in Australia a million years or more and I would not be surprised that the dingo could be classified as a new species.

I’ve often mused about exactly where to draw the line on the “species” thing.

Imagine if 19th century Europe knew nothing about the history of domestic dogs, and one of the “voyages of discovery” had stumbled across an island populated by chihuahuas and great danes - the same species but (probably) mechanically incapable of interbreeding.

Anybody want to lay money against the idea that they would have been declared different species in 1850, in 1920 someone would cross-breed them and people would think of the chiu-dane like a horse-zebra mix, and someone else would write a research paper in the 90’s analyzing their DNA and declaring them the same species?

Comment #107826

Posted by Longhorn on June 24, 2006 12:12 PM (e)

Anton wrote:

Right—that was recombination, and it produced a mutation.

The point is that the sequence of nucleotides was caused by the swapping of nucleotides from various chromosomes.

None of the quote you provided speaks to the above question, though. This paper says that “Intragenic recombination is a relatively rare, but evolutionarily important phenomenon occurring in mitosis and meiosis in a wide variety of organisms,”

Do they say what organisms?

In this study on corn, they get recombination frequencies generally below 1/10,000. It certainly seems that recent work in humans is arguing for increased importance of recombination in producing mutations.

You can call it a mutation if you want. But it is important to understand which series of events caused the nucleotides to be in the sequence that they are in. And that was the swapping of nucleotides by some chromosomes during the first phase of meiosis.

In other words, it doesn’t make sense to say “If you can do it through breeding, mutation must not have been important.”

I didn’t say mutation has not been important in producing differences among organisms. And I didn’t mean to suggest it. My point is that sexual reproduction has been important in causing differences among sexually reproducing organisms.

In fact, generally breeders are more dependent on mutation since they’re working with a smaller population, hence there’s a bottleneck effect stifling initial variation.

Do you have a link?

Not sure what that has to do with anything…. Anyway, according to Wiki, the Big Show has acromegaly, which generally isn’t heritable at all—it’s due to a spontaneous pituitary tumor. So that’s environment, not genetics.

That’s a good point.

Ok…how do you know?

Correlations. New mutation in organisms aren’t correlated with people to be able to jump that high and have that good coordination. And the combining of chromosomes during sex is.

Also, look at the sugar content of beets.

Comment #107828

Posted by Longhorn on June 24, 2006 12:21 PM (e)

Anton wrote: “This paper says that ‘Intragenic recombination is a relatively rare, but evolutionarily important phenomenon occurring in mitosis and meiosis in a wide variety of organisms,’ although they proceed to prove that it’s not particularly rare in the ciliate they’re writing about.”

What do you mean by “intragenic recombination?” Do you mean the swapping of nucleotides that occurs among coding DNA? Or do you mean recombination that causes a “new allele?” The paper you linked to was published in 1998. The one I linked to was published in 2005. Here is what it says:

“Intragenic recombination rapidly creates protein sequence diversity compared with random mutation, but little is known about the relative effects of recombination and mutation on protein function.”

Anton, why is this important to you? What is your point in all this?

Comment #107830

Posted by Longhorn on June 24, 2006 12:36 PM (e)

None of the quote you provided speaks to the above question, though.

Anton, what “question” are you talking about?

Comment #107833

Posted by Longhorn on June 24, 2006 1:10 PM (e)

Here is a link to a study on corn:

http://www.pnas.org/cgi/content/full/99/2/1082?ijkey=0a23271149e8c0537a818b76f5c3dec06fb37d55

According to the study, “Recombination was almost 2 orders of magnitude higher in the distal side, which is gene-dense and lacks retrotransposons, than in the proximal side, which is gene-poor and contains a large cluster of methylated retrotransposons.”

Comment #107957

Posted by Henry J on June 24, 2006 6:46 PM (e)

Re “I’ve often mused about exactly where to draw the line on the “species” thing.”

I’m left with the impression that there is no “line”. It’s a bit like looking at a tree branch that divides into two branches furthur up, and trying to decide exactly where the boundaries are. But the only places with unambiguous boundaries are where the interconnections have died (gone extinct).

Henry

Comment #108115

Posted by Anton Mates on June 25, 2006 2:04 AM (e)

Wayne Francis wrote:

Actually I believe from what I’ve read that the changes we see from wolves to dogs and dogs back to wolves is a positive feed back mechanism that can be altered and reversed.

When left to breed freely, dogs revert to a generalized pariah-type often associated with the dingo or pariah dog of India or generic husky, a medium-sized, prick-eared animal with a ginger, black, black and tan, white, and parti-colored coats,” notes Derr. He adds: “The dog doesn’t have to revert to the wolf. The dog is a wolf, albeit a wolf who exists in human society.

They don’t need to look like grey wolves. Point is they loose all the differences we see very quickly.

But…not to be contrary, but they don’t. They retain many of those differences, which is why they become pariah-type or husky-type rather than wild-grey-wolf-type. Don’t get me wrong, I fully agree that they’re still wolves, and that they were always wolves. But they don’t get more wolfy–more like their wild ancestors–when they go feral, except insofar as wild-wolf-like traits like aggression and tooth morphology are independently selected for. Unless washed out by hybridization, feral dog populations don’t become indistinguishable from wild wolf populations.

C.Lupus is a species simply because in many instances if you throw a subspecies of Canis Lupus into the wild with another subspecies of Canis Lupus they will often interbreed.

That’s not a sufficient criterion for genus Canis, though, as I’ll discuss more below.

Probably the populations of once-domestic dogs which have been wild for the longest are the dingo and New Guinea singing dog. While they have certain traits in common with wolves—notably, enlarged carnassials and once-a-year estrus cycles—they clearly aren’t becoming wolves either morphologically or behaviorally. They’re off on their own evolutionary tracks.

Is a bit misleading. Yes they are changing. Why aren’t they just like grey wolves? Because they are in a different environment to grey wolves.

Not really–well, it might be true for the singing dog. But a lot of the enviroments dingoes, for instance, hunt in, are very similar to ancestral habitats of the grey wolf. (In fact, I believe they overlap a bit in SE Asia.)

Conversely, I can’t think of any case where a feral dog population ended up just like grey wolves, in any environment–except again maybe where they could hybridize.

Just because things look visually different doesn’t mean much. Humans are very diverse. Our primary sense is sight. We notice visual differences more then any other sense. C. Lupus has very acute sense of smell. The smell of that Chihuahua is much more important to that wolf deciding if the Chihuahua is its next lunch or how the wolf will be able to root the Chihuahua.

Again, I disagree…wolves do have small dogs for lunch fairly frequently (relative to how often they encounter them unprotected), as do coyotes. OTOH, I haven’t personally ever heard of a wolfdog or coydog which was a cross with a very small dog breed. Size really does matter; even aggressive domestic dogs sometimes view Chihuahuas as prey. Gene flow between sympatric grey wolf and Chihuahua populations would be close to zero.

Give the dingo in Australia a million years or more and I would not be surprised that the dingo could be classified as a new species. But until dingoes stop sniffing the butts of domesticated dogs and thinking “Hmmm I wouldn’t mind rooting this one” I’ll classify, along with most other people that understand the species, them as the same species.

As will I.

So I put it badly that dogs will revert to grey wolves. They will change into a common pariah-type….which is wolf enough for me. Either way they don’t have big issues breeding with wolves in the wild.

Well, here’s the problem with those criteria. If pariah-type dogs are (grey) wolf enough for you, what about coyotes and (to a lesser extent) jackals? Why aren’t they wolfy enough?

Take the New Guinea singing dog–not that I’m obsessed (quite) with these guys, but they’re just such a great example. As genus Canis goes, they’re wacky. In terms of phenotype–both morphology and behavior–they’re definitely less wolfish than coyotes. They’ve got uvulas. They vocalize with highly FM howls and high-frequency trills. They initiate play by a stalking posture rather than a play bow. They drop their ears forward in submission instead of folding them back. They toss their heads to the side when excited. The females yelp repetitively and experience abdominal contractions for several minutes during mating, and while they normally have a single estrus cycle per year, they can come back into estrus immediately if they don’t get impregnated the first time. All this stuff is unique among the entire Canidae, let along genus Canis.

They also have an open-mouthed play bite (which coyotes do, but wolves and dogs don’t). They readily and skillfully climb trees and rocky terrain, unlike wolves, coyotes or other dogs (or almost any canid besides red foxes). And of course their small size and relatively short legs are very un-wolflike. The singing dog is such a unique critter that the researcher who first discovered it labeled it as a separate species, Canis hallstromi, and some taxonomists (almost the only ones studying it) still concur. Yet genetic analysis shows that it’s very definitely a descendant of domestic dogs.

Now, for your second criterion. Can they hybridize with wolves? Of course. But the entire genus Canis can hybridize. Coyotes hybridize like crazy with both wolves and dogs, to the point where in some areas of eastern North America, almost all the apparent “wolves” genotype as coyotes. In fact, it’s still an open question whether the “red wolf” is or was ever a separate canid species, as opposed to an extremely common coyote-wolf hybrid. The singing dog, of course, never would naturally hybridize with wolves due to geographic barriers.

So. If the singing dog looks and acts less like a wolf than a coyote does–if it’s less likely to hybridize with a wolf than a coyote is–then why should we include it in C. lupus when the coyote’s a separate species?

To a great example of evolution is genus Equus. We have lots of data about it and can see large scale changes that dwarf the minor changes we see in C.Lupis. Why is this….because evolution at the species level will always be concidered by creationist to only be “Micro evolution”. To get “Macro Evolution” you need to look at the Genus level and higher. There are 3 species of “Zebras”. Try to convince a creationist of this and you’ll hear a bunch of nonsense and babbling. But if we look at just these 3 species in the genus Equus you can see truely large differences between them. Most people might look at the 3 together and just see 3 black and white striped horses but tho they look very similiar there are levels magnitude more difference between then any 2 breeds of C. Lupus. Just because they are closer in size and shape and colour doesn’t mean much.

Size means a lot. For that matter, so do shape and colour. Size affects speed, calorie requirements, ability to bring down large prey or defend against predators, etc. Head shape affects bite strength and brain size. Leg length affects running speed and efficiency and ability to move through snow. Colour affects camouflage ability and visual distinctiveness. There’s a reason you see lots of feral shepherd mixes and not too many feral pugs.

But, sure, you could find lots of taxa with more variation than C. lupus. Zebras, definitely. Darwin’s finches, too. Thing is, C. lupus is something we’ve seen evolve, which is not the case for such wild taxa. Most laypeople accept that all those diverse breeds of dogs did come from wolves not too long ago, and that understanding can be very instructive. (Not all accept this, though–my grandfather recalls a Creationist student who told him there were two Boston bulldogs on the ark!) Again, there’s a reason Darwin introduced evolution with domestic pigeons.

The more examples the better, I say–bring up zebras, bring up finches, bring up Hawaiian drosophila. But don’t leave out the domestic lineages, with their unique advantages of unparalleledly rapid evolution in certain aspects, and directly-observed evolutionary history.

Comment #108434

Posted by Anton Mates on June 26, 2006 1:37 AM (e)

Longhorn wrote:

I didn’t say mutation has not been important in producing differences among organisms. And I didn’t mean to suggest it. My point is that sexual reproduction has been important in causing differences among sexually reproducing organisms.

I don’t disagree; I don’t think anyone here does.

In fact, generally breeders are more dependent on mutation since they’re working with a smaller population, hence there’s a bottleneck effect stifling initial variation.

Do you have a link?

Google “dog genome” and look at any of the more recent papers; most of them discuss the bottlenecks at the initial domestication and the founding of initial modern breeds.

Correlations. New mutation in organisms aren’t correlated with people to be able to jump that high and have that good coordination. And the combining of chromosomes during sex is.

I’m not sure how precisely you’re using the term “correlation” there. But every human ever born, good jumper, lousy jumper or mediocre jumper, is the product of “the combining of chromosomes during sex;” thus it is mathematically impossible for jumping ability to be correlated with that.

I think you might mean that there are no mutations in humans which are individually associated with jumping ability, while there are new allelic combinations due to sex which are so associated. Is that correct? If so, I’d like to know your sources.

Also, look at the sugar content of beets.

That doesn’t tell you much–the beet plants could have acquired mutations for greater sugar content during the course of artificial breeding, or they could have recombined existing alleles with the same effect, or both.

Anton wrote: “This paper says that ‘Intragenic recombination is a relatively rare, but evolutionarily important phenomenon occurring in mitosis and meiosis in a wide variety of organisms,’ although they proceed to prove that it’s not particularly rare in the ciliate they’re writing about.”

What do you mean by “intragenic recombination?” Do you mean the swapping of nucleotides that occurs among coding DNA? Or do you mean recombination that causes a “new allele?”

Intragenic recombination is defined as the former, and usually it results in the latter (and is the only type of recombination which does so.)

The paper you linked to was published in 1998. The one I linked to was published in 2005. Here is what it says:

“Intragenic recombination rapidly creates protein sequence diversity compared with random mutation, but little is known about the relative effects of recombination and mutation on protein function.”

Which, again, doesn’t tell you anything about the relative contributions of intragenic recombination versus other forms of mutation to a given evolutionary lineage.

In other words, that paper is saying, “Intragenic recombination, when it happens, can produce variation faster than other forms of mutation (IIRC they were comparing it specifically to point mutations.” It’s not saying how often that actually happens.

Anton, why is this important to you? What is your point in all this?

Well, initially it seemed you were looking for some information on evolution, and I wanted to provide what I could. I’m not really sure what you’re looking for at this point, so perhaps there’s no reason to continue. But I have learned more about the importance of intragenic recombination as a result of this discussion, for which I’m grateful.

Comment #108496

Posted by Henry J on June 26, 2006 10:44 AM (e)

So intragenic recombination could insert (or delete) one or two base pairs from a gene? (i.e., a frame shift).

I recall reading that chlorophyll originated from a frame shift; was that likely to have been from a recombination event?

Henry

(Btw, the spelling checker doesn’t like “intragenic”.)

Comment #108506

Posted by Anton Mates on June 26, 2006 11:19 AM (e)

Henry J wrote:

So intragenic recombination could insert (or delete) one or two base pairs from a gene? (i.e., a frame shift).

Doesn’t look like it…at least, that would require a recombination error where the two gene copies failed to line up correctly.

A quick & dirty online search doesn’t turn up any papers where frameshift mutations are attributed to intragenic recombination, and the Drummond et al. paper Longhorn referenced above is arguing for the superiority of recombination over other mutation sources precisely because it doesn’t produce mutations of that sort, which are more likely to be nonfunctional.

I did notice one or two papers describing intragenic recombination as a means of correcting frameshift mutations, but *cough* didn’t read ‘em.

So I’d say any given frameshift is unlikely to be due to recombination.

Comment #108608

Posted by Henry J on June 26, 2006 10:10 PM (e)

Re “So I’d say any given frameshift is unlikely to be due to recombination.”

Oh. Well, so much for that idea, then.

Henry

Comment #108728

Posted by Longhorn on June 27, 2006 10:45 AM (e)

Anton wrote:

Google “dog genome” and look at any of the more recent papers; most of them discuss the bottlenecks at the initial domestication and the founding of initial modern breeds.

I didn’t see anything on that. Do you have a link?

I’m not sure how precisely you’re using the term “correlation” there. But every human ever born, good jumper, lousy jumper or mediocre jumper, is the product of “the combining of chromosomes during sex;” thus it is mathematically impossible for jumping ability to be correlated with that.
I think you might mean that there are no mutations in humans which are individually associated with jumping ability, while there are new allelic combinations due to sex which are so associated. Is that correct? If so, I’d like to know your sources.

Michael Jordan didn’t have new mutations to cause him to jump the way he did. That was my point. Do you disagree?

Intragenic recombination is defined as the former, and usually it results in the latter (and is the only type of recombination which does so.)

That is not how I was using the term. I was just meaning nucleotide sequences caused by the swapping of nucleotides in coding DNA during the first phase of meiosis. And I don’t think that is how the authors of the paper are using the term. I think they just mean nucleotide sequences caused by the swapping of nucleotides in coding DNA. But I might be wrong.

Which, again, doesn’t tell you anything about the relative contributions of intragenic recombination versus other forms of mutation to a given evolutionary lineage.
In other words, that paper is saying, “Intragenic recombination, when it happens, can produce variation faster than other forms of mutation (IIRC they were comparing it specifically to point mutations.” It’s not saying how often that actually happens.

It is saying that intragenic recombination happens more frequently than random mutation. Here is the exact quote: “Intragenic recombination rapidly creates protein sequence diversity compared with random mutation, but little is known about the relative effects of recombination and mutation on protein function.”

I’m not really sure what you’re looking for at this point, so perhaps there’s no reason to continue.

My point is that sex has been important in causing the differences among sexually reproducing organisms.

Comment #108729

Posted by Longhorn on June 27, 2006 10:48 AM (e)

Anton wrote:

That doesn’t tell you much—the beet plants could have acquired mutations for greater sugar content during the course of artificial breeding, or they could have recombined existing alleles with the same effect, or both.

My point is that sexual reproduction was important in increasing the content of sugar beets.

Comment #108732

Posted by Longhorn on June 27, 2006 11:08 AM (e)

Anton, I found some discussion of the “bottleneck.” For instance, here is something from National Geographic:

In addition, the data suggests how dogs were domesticated. The amount of genetic diversity across breeds is consistent with a “bottleneck”—a strong reduction in genetic variety—that occurred between 10,000 and 15,000 years ago.

“This bottleneck is likely to have been [due to] domestication,” Ellegren said.

Within breeds there are also signs of strong bottlenecks just 50 to 200 years ago, suggesting most dog breeds have a very recent origin.

Here is the link: http://news.nationalgeographic.com/news/2005/12/1207_051207_dog_genome.html

But that is not so much what I’m interested in. Here is the quote of yours that I’m interested in:

In fact, generally breeders are more dependent on mutation since they’re working with a smaller population, hence there’s a bottleneck effect stifling initial variation.

I want to know what evidence there is that “breeders are more dependent on mutation since they’re working with a smaller population.”

Comment #108740

Posted by Longhorn on June 27, 2006 11:48 AM (e)

I wrote:

I want to know what evidence there is that “breeders are more dependent on mutation since they’re working with a smaller population.”

It might be that mutations have contributed to the diversity that we see among some dogs. But I think it is clear that sexual reproduction was important in causing the diversity among dogs. First, we know that sexual reproduction causes differences from parent(s) to offspring; for instance, I’m as different as I am from my parents largely, if not entirely, because they reproduced with each other. Second, sexual reproduction is common. Apparently, intragenic recombination occurs more frequently than do mutations. Finally, we know that sex frequently causes observable traits when an organism inherits particular genes from each parent. So, for instance, one might have the color eyes one has because one inherited particular genes from one’s father and particular genes from one’s mother.

Let’s say that, within a population of beets, there are 30 different genes that contribute to sugar content. Sexual reproduction can combine all 30 of those genes together in some organisms. And as a result, the organism may have a higher sugar content than the other members of its population.

Comment #108762

Posted by Anton Mates on June 27, 2006 12:46 PM (e)

Longhorn wrote:

Google “dog genome” and look at any of the more recent papers; most of them discuss the bottlenecks at the initial domestication and the founding of initial modern breeds.

I didn’t see anything on that. Do you have a link?

Probably the most important paper is here.

Michael Jordan didn’t have new mutations to cause him to jump the way he did. That was my point. Do you disagree?

Yes. Have you established that none of Jordan’s ancestors or relatives have a comparable genetic talent for jumping? Have you examined the genomes of Jordan and his parents, listed all of his mutations and confirmed that none of them are relevant to this talent? If not, you don’t have evidence for this claim. I don’t deny the possibility, but you need evidence.

That is not how I was using the term. I was just meaning nucleotide sequences caused by the swapping of nucleotides in coding DNA during the first phase of meiosis.

Um…that’s what you said before, and I agreed that that’s how the term is defined. I don’t understand your disagreement here.

Which, again, doesn’t tell you anything about the relative contributions of intragenic recombination versus other forms of mutation to a given evolutionary lineage.
In other words, that paper is saying, “Intragenic recombination, when it happens, can produce variation faster than other forms of mutation (IIRC they were comparing it specifically to point mutations.” It’s not saying how often that actually happens.

It is saying that intragenic recombination happens more frequently than random mutation. Here is the exact quote: “Intragenic recombination rapidly creates protein sequence diversity compared with random mutation, but little is known about the relative effects of recombination and mutation on protein function.”

No, nothing in that quote refers to the relative frequencies of the two processes.

But that is not so much what I’m interested in. Here is the quote of yours that I’m interested in:

In fact, generally breeders are more dependent on mutation since they’re working with a smaller population, hence there’s a bottleneck effect stifling initial variation.

I want to know what evidence there is that “breeders are more dependent on mutation since they’re working with a smaller population.”

A bottleneck, as mentioned above, causes a “reduction in genetic variety.” That means that there are fewer alleles available for each gene, therefore combining alleles can’t do as much and mutations are more necessary.

Let’s say that, within a population of beets, there are 30 different genes that contribute to sugar content. Sexual reproduction can combine all 30 of those genes together in some organisms. And as a result, the organism may have a higher sugar content than the other members of its population.

But once all those genes (actually, alleles) have been combined, you hit a dead end. If your beet already had the best possible combo of existing alleles in terms of sugar content, and there was no mutation, further breeding would not produce any improvement.

In practice, this doesn’t happen–sugar beets keep getting sweeter, high-oil corn keeps improving its oil content, and so forth–therefore mutation must be adding alleles that weren’t there before.

Comment #108777

Posted by Longhorn on June 27, 2006 1:31 PM (e)

Yes. Have you established that none of Jordan’s ancestors or relatives have a comparable genetic talent for jumping? Have you examined the genomes of Jordan and his parents, listed all of his mutations and confirmed that none of them are relevant to this talent? If not, you don’t have evidence for this claim. I don’t deny the possibility, but you need evidence.

Maybe I didn’t make my point clear enough. Jordan was not born with a new mutation that gave him that ability. In other words, when his parents had sex, a mutation to his father’s sperm did not cause that ability.

Maybe mutations in the past contributed to his jumping ability.

Comment #108780

Posted by Longhorn on June 27, 2006 1:44 PM (e)

No, nothing in that quote refers to the relative frequencies of the two processes.

Yes it does. Here is the sentence: “Intragenic recombination rapidly creates protein sequence diversity compared with random mutation.” In others, combination creates diversity faster than mutation does.

A bottleneck, as mentioned above, causes a “reduction in genetic variety.” That means that there are fewer alleles available for each gene, therefore combining alleles can’t do as much and mutations are more necessary.

That there was a bottleneck does not enable you or me to reasonably infer that mutation caused the diversity subsequent to the bottleneck. For it is clear that vast numbers and combinations of organisms sexually reproducing was correlated with the diversity subsequent diversity. Maybe mutation also contributed to the diversity.

But once all those genes (actually, alleles) have been combined, you hit a dead end. If your beet already had the best possible combo of existing alleles in terms of sugar content, and there was no mutation, further breeding would not produce any improvement.

In practice, this doesn’t happen—sugar beets keep getting sweeter, high-oil corn keeps improving its oil content, and so forth—therefore mutation must be adding alleles that weren’t there before.

You don’t know that mutation caused the differences. What evidence do you have for that? We know that beets have more sugar content now than they did in the 1840s. Sexual reproduction could have caused that by itself. Or maybe mutation plus sexual reproduction. What evidence do you have that it is mutation plus sexual reproduction. I’m not sure if it is just sexual reproduction or both.

Comment #108783

Posted by Longhorn on June 27, 2006 1:49 PM (e)

I wrote:

For it is clear that vast numbers and combinations of organisms sexually reproducing was correlated with the diversity subsequent diversity.

I meant that vast numbers and combinations of organisms sexually reproducing was correlated with the diversity subsequent to the bottleneck.

Comment #108788

Posted by Longhorn on June 27, 2006 2:05 PM (e)

Anton wrote:

In practice, this doesn’t happen—sugar beets keep getting sweeter, high-oil corn keeps improving its oil content, and so forth—therefore mutation must be adding alleles that weren’t there before.

We agree that the sugar content of the beets has increased. The questions is: Which events have caused this increase in the sugar content? I suppose there are two possibilities.

1. Sexual reproduction.

2. Sexual reproduction plus mutation.

Even if mutation has contributed to the increased sugar content, it hasn’t caused this increase by itself. For sexual reproduction has combined in particular organisms those genes that increase sugar content. In other words, let’s say beet A is born with nucleotide sequence X. Let’s say X is a combination of nucleotides that didn’t exist in either of As parents. X occurred during the reproductive event that resulted in beet A coming into being. And let’s say X caused beet A to have higher sugar content than its parents have. Moreover, let’s say beet B came into being with sequence Y. And Y caused B to have higher sugar content than its parents have. We can breed beet and A and beet B. The offspring can have both sequence X and gene Y. And that can cause the offspring of X and Y to have higher sugar content than either X or Y has.

Comment #108791

Posted by Longhorn on June 27, 2006 2:22 PM (e)

I wrote:

And that can cause the offspring of X and Y to have higher sugar content than either X or Y has.

I meant that that can cause the offspring of A and B to have higher sugar content than either A or B has.

Comment #108798

Posted by Longhorn on June 27, 2006 3:05 PM (e)

Anton, earlier in the thread, you wrote the following:

Moreover, without mutation sexual reproduction would do nothing for variation—different combinations of alleles would be impossible if mutation hadn’t created different alleles per gene in the first place!

I’m not sure what you mean by that. Obviously, sexual reproduction is a recently evolved activity; it didn’t exist 3 billion years ago. So mutations that occurred in the distant passed contributed to the very existence of sexual reproduction.

However, now that sexual reproduction has evolved, sexual reproduction has contributed significantly to phenotype diversity. You and I agree on that. The question is: are there any cases in which significant phenotype diversity occurred without mutation playing an important role? It’s hard to say. I’m different from my parents in terms of our observable traits. And mutation played no role in our observable traits being as different as they are. But the difference between me and my parents is less – though arguably not a huge amount less – than the difference between wolves and German Shepards. Was mutation important in causing the difference between wolves and German Shepards? I don’t know. But I do know that sexual reproduction was important in causing the differences between wolves and German Shepards, for:

1. Sexual reproduction is frequent.

2. Apparently sexual reproduction creates protein sequence diversity at a faster rate than mutation does.

3. My phenotype is very different from the phenotypes of my parents, and mutation played no role in our phenotypes being as different as they are.

4. A population of wolves that lived about 130,000 years ago evolved into all the dogs that are alive today. 130,000 years is a fairly long time.

5. Sexual reproduction can contribute to an organism having a trait if the organism inherits an analogous sequence of nucleotides from each of its parents.

6. Sexual reproduction sometimes combines genes in one organism so that it results in the organism having a more pronounced trait than any members of its sexual lineage has.

Comment #108808

Posted by Henry J on June 27, 2006 3:39 PM (e)

Don’t I recall that for some protein the coding gene is split up into sections that might be in way different locations in the chromosomes? In that case could recombination change a protein formula without being technically intragenic?

Henry

Comment #108871

Posted by Anton Mates on June 27, 2006 8:51 PM (e)

Longhorn wrote:

Yes. Have you established that none of Jordan’s ancestors or relatives have a comparable genetic talent for jumping? Have you examined the genomes of Jordan and his parents, listed all of his mutations and confirmed that none of them are relevant to this talent? If not, you don’t have evidence for this claim. I don’t deny the possibility, but you need evidence.

Maybe I didn’t make my point clear enough. Jordan was not born with a new mutation that gave him that ability. In other words, when his parents had sex, a mutation to his father’s sperm did not cause that ability.

Yes, you’ve said this several times. What you haven’t done is provide any evidence for this claim. How do you know what abilities Jordan’s individual mutations did or did not cause? How do you know Jordan even has an exceptional jumping ability not shared by anyone else in his family?

No, nothing in that quote refers to the relative frequencies of the two processes.

Yes it does. Here is the sentence: “Intragenic recombination rapidly creates protein sequence diversity compared with random mutation.” In others, combination creates diversity faster than mutation does.

“Faster” in the sense of “per event,” not “per unit time.” They’re saying that 10 recombination events produce more diversity than 10 point mutations, but that tells you nothing about how long it takes 10 of each to occur.

(If, BTW, you follow their citations in that section, the cited sources provide some cases where recombination events which leave viable offspring do happen more frequently than point mutation events doing the same. But that still doesn’t tell you how often the two events occur, period. One of the points of the paper above is that recombination could be rarer than other forms of mutation but still contribute more diversity to viable offspring, because it produces functional alleles more often than they do.)

That there was a bottleneck does not enable you or me to reasonably infer that mutation caused the diversity subsequent to the bottleneck. For it is clear that vast numbers and combinations of organisms sexually reproducing was correlated with the diversity subsequent diversity. Maybe mutation also contributed to the diversity.

By definition, if new alleles are found that weren’t in the ancestral population, that’s mutation. An increase in genetic diversity (in terms of number of alleles per locus) subsequent to a bottleneck can only be due to mutation. It may be primarily mutation which occurred during recombination, but it’s still mutation.

But once all those genes (actually, alleles) have been combined, you hit a dead end. If your beet already had the best possible combo of existing alleles in terms of sugar content, and there was no mutation, further breeding would not produce any improvement.

In practice, this doesn’t happen—sugar beets keep getting sweeter, high-oil corn keeps improving its oil content, and so forth—therefore mutation must be adding alleles that weren’t there before.

You don’t know that mutation caused the differences. What evidence do you have for that?

I don’t think I can explain it more clearly than I did above. Without the appearance of new alleles, which is by definition mutation, sugar content would eventually plateau when the breeder happened to get plants with the optimal combination of existing alleles.

I don’t think I can provide much else which is useful to this conversation. But, again, I’m sure you would find it rewarding to take a class on genetics if possible, and/or read a textbook on the subject.

Comment #108873

Posted by Anton Mates on June 27, 2006 9:07 PM (e)

Henry J wrote:

Don’t I recall that for some protein the coding gene is split up into sections that might be in way different locations in the chromosomes? In that case could recombination change a protein formula without being technically intragenic?

Hmm, I’ve never heard of that. (Which means nothing about whether it’s true or not.) I’ve heard of proteins being made of smaller subunits, each of which is coded for in a different location–hemoglobin is one IIRC–but each subunit’s coding sequence was considered a separate gene, so that would still be intergenic.

If you can find an example, I’d love to see it.

Comment #108883

Posted by Longhorn on June 27, 2006 9:58 PM (e)

Anton, would you be interested in talking on the phone? This is interesting, and it looks like we are running out of time. You can call me collect.

You wrote:

Yes, you’ve said this several times. What you haven’t done is provide any evidence for this claim. How do you know what abilities Jordan’s individual mutations did or did not cause?

I’m saying the mutation didn’t occur during the very reproductive event that resulted in the creation of the gametes that brought us Michael Jordan. It didn’t occur in the egg-cell that became Jordan or the sperm-cell that became Jordan. Because those kinds of events are correlated with longer limbs and fast-twitch muscles occurring in one person. There is no way. That is impossible. We are talking about long limbs that have developed over millions of years. And muscles that have developed over millions of years.

Are you saying that a single mutation that occurred in Michael Jordan’s father sperm caused Michael Jordan to be that good at basketball? That’s ridiculous. That is not the kind of event we experience happening in the animal kingdom.

How do you know Jordan even has an exceptional jumping ability not shared by anyone else in his family?

They may have. That is a real possibility. In fact, I’m sure people in Jordan’s ancestral line were pretty darn good jumpers. In some way, that is my very point. My point is that no mutation that occurred in parents’ very gametes caused Jordan to be able to play basketball the way he does.

Comment #108887

Posted by Longhorn on June 27, 2006 10:18 PM (e)

“Faster” in the sense of “per event,” not “per unit time.”

Why do you say that? Also, that probably is not true. A single mutations occurs really fast. They are boomb pop. Quick.

What the author is saying is that over the course of reproductive generations, recombination causes protein sequence diversity at a faster rate than does mutation. That is the way I read it, anyway. Are you saying that they are saying that a mutation takes longer to occur than a recombination event? I don’t think they are saying that.

Comment #108892

Posted by Longhorn on June 27, 2006 10:24 PM (e)

By definition, if new alleles are found that weren’t in the ancestral population, that’s mutation. An increase in genetic diversity (in terms of number of alleles per locus) subsequent to a bottleneck can only be due to mutation. It may be primarily mutation which occurred during recombination, but it’s still mutation.

First, what do you mean by “allele?” Moreover, Chris Colby writes the following: “Recombination creates new combinations of alleles. Alleles that arose at different times and different places can be brought together. Recombination can occur not only between genes, but within genes as well. Recombination within a gene can form a new allele. Recombination is a mechanism of evolution because it adds new alleles and combinations of alleles to the gene pool.”

Here is the link:

http://www.talkorigins.org/faqs/faq-intro-to-bio…

Comment #108894

Posted by Longhorn on June 27, 2006 10:28 PM (e)

I don’t think I can explain it more clearly than I did above. Without the appearance of new alleles, which is by definition mutation, sugar content would eventually plateau when the breeder happened to get plants with the optimal combination of existing alleles.

There would be limits to how much sugar content can be increase by sexual reproduction. But my point is that it may be that sexual reproduction caused all of the increase in sugar content of the beets that occurred during breeding. And if sexual reproduction did not cause all of the increase, it was at least hugely important in causing the increase.

Comment #108895

Posted by Longhorn on June 27, 2006 10:35 PM (e)

Anton, here is a quote from another article on meiosis and “new alleles:“ “During meiosis, alleles are shuffled and new alleles are created.” Here is the link:

http://www.virtuallaboratory.net/Biofundamentals/lectureNotes/Topic5-2_LifeCycle.htm

Comment #108897

Posted by Longhorn on June 27, 2006 10:40 PM (e)

I wrote:

I’m saying the mutation didn’t occur during the very reproductive event that resulted in the creation of the gametes that brought us Michael Jordan. It didn’t occur in the egg-cell that became Jordan or the sperm-cell that became Jordan.

Maybe I should be clearer. Any new mutations that occurred in the gametes of Michael Jordan’s father and/or the gametes of his mother did not contribute to Jordan being as good a basketball player as he is

Because those kinds of events are correlated with longer limbs and fast-twitch muscles occurring in one person.

I meant those kinds of events are not correlated.

Comment #108903

Posted by Henry J on June 27, 2006 11:37 PM (e)

Anton,
Re “I’ve heard of proteins being made of smaller subunits, each of which is coded for in a different location”

That may be the sort of thing I was thinking of.

Henry

Comment #108917

Posted by Longhorn on June 28, 2006 12:46 AM (e)

Here is a good quote from Mayr on the importance of genetic recombination in sexual reproducers:

“Evolution in sexually reproducing organisms consists of genetic changes from generation to generation in populations, from the smallest local deme to the aggregate of interbreeding populations in a biological species. Numerous processes, particularly mutation, contribute to these genetic changes to supply the phenotypic variation needed by selection. The most important factor is recombination, which is largely responsible for the virtually inexhaustible supply of new genotypes in every generation. Selection, then, is responsible for the elimination of all but on the average two of the offspring of two parents. Those individuals that are best adapted to the abiotic and biotic environment have the greatest chance to be among the survivors. This process favors the development of new adaptations and the acquisition of evolutionary novelties, thus leading to evolutionary advance, as stated in the language of evolutionary biology” (What Evolution Is, p. 157).

Also, here is a quote from a book by A.B. Korol, I.A. Preygel and S.I. Preygel entitled Recombination, Variability and Evolution (1994):

“Estimates from various Drosophila species indicate that 25-40% of variation of fitness observed in natural populations is regenerated by crossing over in one generation from the gene content of a randomly drawn chromosome pair. This lead Dobzhansky to conclude that a temporary arrest of the mutation process would not result in a significant decrease in variation over a large number of generations.

“In fact, variation generated de novo by the mutation process is lower by orders of magnitude. This is particularly the case in view of the large amount of genetic variability (and heterozygosity) present in natural populations discovered in the 1960s by the method of protein electrophoresis and subsequently confirmed at the DNA level (Hubby and Lewontin, and many others). All other things being equal, genetic variance for a sexual population with free recombination may be several times that for a population with no recombination” (p. 10).

Comment #109536

Posted by David Sadler on June 30, 2006 7:38 PM (e)

Hi, Rilke’s Granddaughter,

You are very wise.
How did the first replicators arise?
Did they arise all over the planet independently?
Or did they arise in one or two locations and then spread out?

Thanks,
David

Comment #109537

Posted by David Sadler on June 30, 2006 8:02 PM (e)

The intelligent design model explains why the fossil record shows the sudden appearance of fully-formed, fully-differentiated and fully-functional life forms.

The Darwinian model demands a fossil record that blurs life forms between the form they were and the form into which they are changing in the never-ending diversification of one life-form into many life different and distinct life forms.

This sudden appearance in the fossil record gave Darwin pause, yet it is ignored and waved-off as not important by today’s true believers of Evolution.

Can anyone help Darwin out on this point?

David Sadler

“There is another and allied difficulty which is much more serious. I allude to the manner in which species belonging to the main divisions of the animal kingdom suddenly appear in the lowest known fossiliferous rocks.”
– Charles Darwin, The Origin of Species –

“The abrupt manner in which whole groups of species appear in certain formations has been urged by several paleontologists … as a fatal objection to the belief of the transmutation of species. If numerous species, belonging to the same genera or families, have really started into life at once, that fact would be fatal to the theory of evolution through natural selection. For the development by this means of a group of forms all of which are (according to the theory) descended from some one progenitor, must have been an extremely slow process; and the progenitors must have lived long before their modified descendants.”
– Charles Darwin, The Origin of Species –

“Most of the museums classify the deepest rocks that contain fossils of multicelled organisms as Cambrian rocks. Dr. Preston Cloud, writing in Geology magazine in 1973 stated that not a single indisputable multicellular fossil had been found anywhere in the world in a rock supposedly older than Cambrian rocks. But in the Cambrian rocks is found a multitude of highly complex creatures with no ancestors. These rocks contain fossils of trilobites, brachiopods, corals, worms, pelecy-pods (clams), and soft-bodied creatures like jellyfish. As stated in a 1961 book, Prehistoric Life on Earth, ‘The invertebrate animal phyla are all represented in Cambrian deposits.’ It was then believed that vertebrates had not appeared until the Lower Ordovician, but in 1977 fully developed heterostracan vertebrate fish fossils were discovered in the Upper Cambrian of Wyoming. The discovery, reported in Science magazine, May 5, 1978, placed every major animal phylum (group) in the Cambrian rocks. This extremely significant information comes as quite a shock to most people for it is not discussed in school or in university textbooks. The museum officials, however, freely talked about the explosive appearance of complex life in the Cambrian rocks. They explained that the sudden appearance of all animal phyla with no ancestors was called the ‘Cambrian Explosion.’”
– Luther Sunderland, Darwin’s Enigma –

“To the question why we do not find rich fossil-iferous deposits belonging to these assumed earliest periods prior to the Cambrian system, I can give no satisfactory answer.”
– Charles Darwin, The Origin of Species, p. 309 –

Comment #109539

Posted by Steviepinhead on June 30, 2006 8:20 PM (e)

Just what we need, another clueless moro–

Excuse me, I got carried away there for a second. But it does get old.

Let’s just say instead another clueless, quote-mining, strawman-erecting, refuted-“critique” recycling, close-minded, evidence-ignoring, anti-intellectual, pizza-hating, true-believing lackey of the creaIDiot scam artists.

But who knows, maybe he’s polite to his mother and dad, even after they ground him for bringing home those terrible grade reports…

Kid, get a clue. Go check out your fusty claims on TalkOrigins. They’re so nicely indexed, even you can probably find them in a jiffy. Then, when you’ve learned a little, come back with some actual evidence and knowledge and give us a whirl again. You’ll probably still be a moro–er, all that other stuff, but at least you might be a little more entertaining.

At the moment, you’re just a stale bore.

Comment #109540

Posted by Coin on June 30, 2006 8:34 PM (e)

David Sadler wrote:

The intelligent design model explains why the fossil record shows the sudden appearance of fully-formed, fully-differentiated and fully-functional life forms…

… “Poof!”

Comment #109541

Posted by 'Rev Dr' Lenny Flank on June 30, 2006 9:12 PM (e)

The intelligent design model

What intelligent design model?

Nelson says there ain’t one, Gilder says there ain’t one, and Johnson says there ain’t one.

You know something they don’t?

Comment #109544

Posted by Bruce Thompson GQ on June 30, 2006 10:19 PM (e)

David Sadler wrote:

The intelligent design model explains why the fossil record shows the sudden appearance of fully-formed, fully-differentiated and fully-functional life forms…

Poof on earth

Poof on Mars

Indicating:
1. poor aim
2. spill over
3. drive by poofing with a shot gun

Delta Pi Gamma (Scientia et Fermentum)

Comment #109545

Posted by David Sadler on June 30, 2006 10:20 PM (e)

Flank, Coin and Steviepinhead - probably your real names - couldn’t even begin to answer Darwin and Sunderland so you insult the poster. How intellectual and scientific. How mature.

This is why IDers win public debates with Darwinists and why Darwinism is on the way out.

Yes, hearing the words of evolutionists questioning their own theory is too much to handle for the true believers. It’s heresy in the church of Macro-Evolution.

Comment #109550

Posted by Anton Mates on June 30, 2006 11:59 PM (e)

Start here, David, and perhaps move on to this.

Suffice to say, Darwin was a very cautious thinker and searched for every possible hole or defect in his theory. That’s called being a good scientist. Why IDers openly criticize him for rigorously applying critical thinking to his own theories, I’ll never understand.

As to why they would use a source 150 years out of date to discuss the Cambrian explosion…that I understand all too well.

Comment #109554

Posted by David Sadler on July 1, 2006 1:19 AM (e)

Hi, Anton,

Let’s move forward then.

“What is so frustrating for our present purpose is that it seems almost impossible to give any numerical value to the probability of what seems a rather unlikely sequence of events…. An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle.
– Francis Crick, Nobel Prize winner and co-discoverer of DNA, Life Itself, p. 79 –

“I don’t know how long it is going to be before astronomers generally recognize that the combinatorial arrangement of not even one among the many thousands of biopolymers on which life depends could have been arrived at by natural processes here on the earth. Astronomers will have a little difficulty in understanding this because they will be assured by biologists that it is not so, the biologists having been assured in their turn by others that it is not so. The “others” are a group of persons who believe, quite openly, in mathematical miracles. They advocate the belief that tucked away in nature, outside of normal physics, there is a law which performs miracles (provided the miracles are in the aid of biology). This curious situation sits oddly on a profession that for long has been dedicated to coming up with logical explanations of biblical miracles…. It is quite otherwise, however, with the modern miracle workers, who are always to be found living in the twilight fringes of thermodynamics.”
– Fred Hoyle, “The Big Bang in Astronomy,” New Scientist, v. 92, no. 1280, November 19, 1981, p. 521-27 [explaining that “there are 2,000 complex enzymes required for a living organism but not a single one of these could have formed on earth by random, shuffling processes in even 20 billion years,” comments by Luther Sunderland, Darwin’s Enigma] -

Comment #109559

Posted by David Sadler on July 1, 2006 1:43 AM (e)

Hi, Anton,

The author of http://www.talkorigins.org/indexcc/CC/CC300.html uses a lot of qualifiers ‘may’ ‘probably’ and so on.

What leaps out is that the author is pushing back the sudden appearance of the life forms but they are still fully formed, fully functional and fully differentiated. Their appearance is sudden.

If all these life forms are the end result of the slow process of mutation, selection and differentiation, where are the ‘morphs’ between A and Z?

If all life emerged and differentiated from a single organism or even (by some miracle) a thousand living cells of different types, mutation and morphing had to be the rule, not the exception. Since mutation is going to produce as many mistakes as successes and if fossilization is a rare event, then fossilization would snapshot the rule, not the exception. Yet what stands out and what the author you suggested above is saying is that the fossil record snapshots unique life forms that can be classified with their own name thus differentiating them from other similarly differentiated life forms.

The fossil record observes sudden appearance of fully functional, fully differentiated life forms, when the math of (first life + mutation = how many species?) is an incredible equation missing only the proof of all this mutation and change in the fossil record. Considering the number of mutations required to get a positive mutation, the majority of the mutations would have produced a mass of grossly deformed and classifiable creatures. Yet, as any trip to the museum shows, the life forms are very nicely unique, functional and fully formed.

The linked author did nothing to counter the essential claim of Darwin or the evolution critics of his day regarding the point of sudden appearance. He merely ‘pushed’ the dates back.

Do you see the point?

Comment #109561

Posted by David Sadler on July 1, 2006 1:57 AM (e)

Here are some more quotes, many from well known evolutionists. Insulting me will not change the quotes for the facts which these men were confronting regarding their profession…

David Sadler

“The known fossil record fails to document a single morphological transition and hence offers no evidence that the gradualistic model of Darwinism can be correct. Doubts about gradualistic evolution have been for long years suppressed.”
– Steven Stanley Professor of paleontology at Johns Hopkins University, –

“We paleontologists have said that the history of life [the fossils] supports the story of gradual adaptive change, all the while knowing that it does not.”
– Niles Eldridge –

“Each new generation, it seems, produces a few young paleontologists eager to document examples of evolutionary change in their fossils… of the gradual progressive sort. The fossils, rather than exhibiting the expected pattern, just seem to persist virtually unchanged. This extraordinary conservatism looks to the paleontologist keen on finding evolutionary change as if no evolution has occurred. These studies are considered ‘failures’ and are not even published. Paleontologists see stasis [no change] as ‘no results’ rather than a contradiction of the prediction of gradual progressive evolutionary change.”
– Niles Eldridge –

“That theory [macroevolution] as a general proposition is effectively dead despite its persistence as textbook orthodoxy.”
– Stephen Jay Gould, professor of paleontology at Harvard and a preeminent figure in evolution theory wrote in Paleobiology –

“Darwin’s theory of natural selection has never had any proof. There may be wide discrepancies within species (microevolution), but the gaps with between the species (macroevolution) cannot be bridged.”
– Richard Goldschmidt, professor of geology at the University of California at Berkeley –

“Evolution has not taught us how birds descended from reptiles, mammals from earlier quadrupeds, quadrupeds from fishes or vertebrates from invertebrates. To seek the stepping stones between the gaps is to seek in vain, forever.”
– D’Arcy Thompson in one of the great classics of biology On Growth and Form –

“Species appear in the sequence very suddenly, show little or no change during their existence in the record, then abruptly go out of the record. It is rarely clear that the descendants were actually better than their predecessors… biological improvement is hard to find.”
– From the Bulletin of Chicago’s Field Museum of Natural History –

“This is true of all 32 orders of mammals. In no case is an approximately continuous sequence of one order to another known. The break is so sharp and the gap so large that the origin of the order is speculation. The absence of transitional forms is not confined to mammals. It is an almost universal phenomenon and has long been noted by paleontologists.”
– George Gaylord Simpson who preceded Gould at Harvard –

“Most species exhibit no directed change during their tenure on Earth, nor does a species arise gradually by the steady transformation of its ancestry. It appears all at once and fully formed.”
– Stephen Jay Gould, professor of paleontology at Harvard writing in Natural History –

“Modern gorillas, orangutans, and chimpanzees spring out of nowhere, as it were. They are here today, they have no yesterday.”
– Donald J. Johanson (discoverer of Lucy) –

“The first and most important steps of animal evolution are even more obscure than those of plant evolution.”
– Boston University biologist Paul Weiss –

“We are in the dark concerning the origins of insects.”
– French zoologists, Pierre-P. Grasse –

“The lungfish, like every other group of fish that I know, have their origins firmly based on nothing.”
– Said E. White, world-class authority on lungfishes –

“The origins of the higher categories are shrouded in mystery; they appear abruptly in the fossil record without evidence of transitional forms.”
– David Raup, professor of geology at the University of Chicago –

“I fully agree with your comments on the lack of direct illustration of evolutionary transitions in my book. If I knew of any, fossil or living, I would certainly have included them. You suggest that an artist should be used to visualize such transformations, but where would he get the information from? I could not, honestly, provide it, and if I were to leave it to artistic license, would that not mislead the reader?”
– Dr. Colin Paterson, author of “Evolution” for the British Museum of Natural History in a letter to Luther Sunderland dated April 10, 1979 –

Comment #109587

Posted by Jim Wynne on July 1, 2006 8:56 AM (e)

Sadler wrote:

What leaps out is that the author is pushing back the sudden appearance of the life forms but they are still fully formed, fully functional and fully differentiated. Their appearance is sudden.

What seems to not be fully formed, functional and differentiated is your ability to understand what you’ve read. As you appear to be reasonably intelligent, this means that the suppression of your facilities is willful. But humor us for a moment, if you will, and assume that you’re wrong and that biological evolution is well established. What would a life form that is not fully formed, fully functional and fully differentiated look like. Help us, David. What should we be looking for? Something half cat and half dog?

Comment #109613

Posted by Torbjörn Larsson on July 1, 2006 12:04 PM (e)

The midsummer holiday was long and eventful, apparently so was this thread.

David says:
“What is the survivability or “production” benefit or advantage for any such change in non-living matter leading that matter to change in the direction of a non-living organism waiting for life to enable it to reproduce thereby allowing natural selection to begin?”

A combination of raw material production and products that produced fastest and was most robust to environmental change become the more common. Of those systems, those that had the ability to somewhat reproduce would be amongst the most common. And so on.

I agree with ‘Rev’, you argue like a vitalist. There was no non-living organism (an organism is by definition living) and it wasn’t ‘waiting’. As in evolution, the fittest survived. It is merely that before reproduction you can’t say “natural” selection since it assumes replication.

Comment #109616

Posted by Torbjörn Larsson on July 1, 2006 12:13 PM (e)

David says:

“But do you agree there are things that are living and things that are non-living?”

There is a difference between “life” and “being alive”. Life started once about 3 billion of years ago, and haven’t stopped since. Evolution tells us it is this “life” that has branched out in the currently living organisms. In a very real sense each organism starts to die as soon as it is spawned off as an individual - sooner or later it will stop metabolise. Defining “being alive” has a different meaning for higher organisms though - as soon as our brains are dead we are medically and legally dead.

Comment #109620

Posted by Torbjörn Larsson on July 1, 2006 1:00 PM (e)

David says:

“Let’s move forward then.” And continues, to again, discuss abiogenesis though it has nothing to do with evolution and the fossil record.

As Anton has already explained: “It is easy to prove that natural chemical reactions can produce a replicator; even the creationist’s caricature “a whole lot of atoms banged into each other just so…” is clearly not physically impossible. What is not yet known is the feasibility and likelihood of each particular chemical pathway leading to a replicator. The field of pre-biotic chemistry is concerned with exploring this.”

Comment #109626

Posted by Torbjörn Larsson on July 1, 2006 1:12 PM (e)

David says:

“What leaps out is that the author is pushing back the sudden appearance of the life forms but they are still fully formed, fully functional and fully differentiated. Their appearance is sudden.”

That isn’t what he says. He presents earlier fossils to answer the claim on “the Cambrian explosion, with no ancestral fossils”. The earlier in strata you look the lifeforms are smaller and harder to fossilise by their internal construction. The record naturally and predictively peter out. The earliest fossils are traces in seabeds, mineralised colonies of bacterias or traces of bactrias in rocks. We don’t expect fossils of early life such as RNA worlds.

Fossils do not appear suddenly. Their appearance and the progressively richer record is explained by evolution and contradicts creationism. Do you see the point?

Comment #109627

Posted by Torbjörn Larsson on July 1, 2006 1:15 PM (e)

David says:

“Here are some more quotes, many from well known evolutionists.”

You are quotemining, expressing quotes out of context. This will not impress anyone and move a discussion further. Make a point instead.

Comment #109629

Posted by Torbjörn Larsson on July 1, 2006 1:41 PM (e)

“Life started once about 3 billion of years ago,”

Lest someone starts to argue age, let me rephrase to “Life started once billion of years ago,”

Comment #109636

Posted by Torbjörn Larsson on July 1, 2006 2:14 PM (e)

BTW, if I come out as concentrated on David here, I noted the interesting discussion about modelling observational facts and theories on one side and philosophical claims on Truth on the other. OTOH, it is a complicated mess where different models are feasible, quite like QM interpretations, thus conflict prone. :-)

Comment #109714

Posted by Anton Mates on July 1, 2006 10:06 PM (e)

David Sadler wrote:

Let’s move forward then.

I notice that, in “moving forward,” the topic seems to have shifted from the Cambrian Explosion to abiogenesis…almost as if the progress of evolutionary biology has helped to explain the former and make the latter accessible to research and discussion. That’s interesting, isn’t it?

“What is so frustrating for our present purpose is that it seems almost impossible to give any numerical value to the probability of what seems a rather unlikely sequence of events…. An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle.
— Francis Crick, Nobel Prize winner and co-discoverer of DNA, Life Itself, p. 79 —

Well, let’s see what Crick said with Orgel twelve years later, in “Anticipating an RNA World: Some Past Speculations on the Origin of Life: Where Are They Today?”

“How clearly did we anticipate the exciting experimental discoveries of the last decade? We must confess that we did not anticipate them at all! We discussed a number of hypothetical schemes for the origins of our genetic system and touched on each of the major features of the RNA world hypothesis. However, we did not ourselves search for, nor did we encourage others to search for, relics of the RNA world in contemporary organisms. We took it for granted that RNA-based catalysis was necessarily less efficient than protein-based catalysis, and consequently that RNA catalysts had been superseded by protein enzymes in every case. The same assumption led us to underestimate the potential complexity of an RNA world.”

“How much influence did our speculations have on the subsequent development of the subject? Very little. We doubt that Cech or Altman were aware of our papers when they made their important discoveries. The lesson is clear: speculation is fun, but even correct hypotheses without experimental follow-up are unlikely to have much effect on the development of biology.”

Later,

“We did not seriously consider the possibility that there was a midwife, a replicating pre-RNA world of quite differentchemistry based, for example, on clays, as suggested by Cairns-Smith (11), or an alternative organic polymer (12). Such a pre-RNA world would have possessed the catalytic activity necessary to start the RNA world but it may not have needed to transfer its genetic information directly to that of the new (RNA) replication system. We now find this idea attractive. Whether molecular relics of a pre-RNA world still exist remains to be seen.”

Being able to change one’s mind is a very important talent for a good scientist, and Crick is to be commended here. Incidentally, Crick also wrote,

“The age of the earth is now established beyond any reasonable doubt as very great, yet in the United States millions of Fundamentalists still stoutly defend the naive view that it is relatively short, an opinion deduced from reading the Christian Bible too literally. They also usually deny that animals and plants have evolved and changed radically over such long periods, although this is equally well established. This gives one little confidence that what they have to say about the process of natural selection is likely to be unbiased, since their views are predetermined by a slavish adherence to religious dogmas.”

“I don’t know how long it is going to be before astronomers generally recognize that the combinatorial arrangement of not even one among the many thousands of biopolymers on which life depends could have been arrived at by natural processes here on the earth. Astronomers will have a little difficulty in understanding this because they will be assured by biologists that it is not so, the biologists having been assured in their turn by others that it is not so. The “others” are a group of persons who believe, quite openly, in mathematical miracles. They advocate the belief that tucked away in nature, outside of normal physics, there is a law which performs miracles (provided the miracles are in the aid of biology). This curious situation sits oddly on a profession that for long has been dedicated to coming up with logical explanations of biblical miracles…. It is quite otherwise, however, with the modern miracle workers, who are always to be found living in the twilight fringes of thermodynamics.”
— Fred Hoyle, “The Big Bang in Astronomy,” New Scientist, v. 92, no. 1280, November 19, 1981, p. 521-27 [explaining that “there are 2,000 complex enzymes required for a living organism but not a single one of these could have formed on earth by random, shuffling processes in even 20 billion years,” comments by Luther Sunderland, Darwin’s Enigma] -

Fred Hoyle, of course, was an astronomer and not a biologist, which made him a poor authority on whether and how biologists might be misinforming astronomers. His errors in applying combinatorics to abiogenesis have been well documented-you may wish to start here.

Comment #109719

Posted by Anton Mates on July 1, 2006 10:44 PM (e)

David Sadler wrote:

The author of http://www.talkorigins.org/indexcc/CC/CC300.html… uses a lot of qualifiers ‘may’ ‘probably’ and so on.

Surely you aren’t objecting to this? Don’t you think such qualifiers may sometimes be appropriate when discussing events 600 million years ago?

What leaps out is that the author is pushing back the sudden appearance of the life forms but they are still fully formed, fully functional and fully differentiated. Their appearance is sudden.

That probably wouldn’t have “leapt out” if you had read so far as Response 1.

And, as others asked, what sort of unformed, nonfunctional life would you expect to see in the fossil record?

If all these life forms are the end result of the slow process of mutation, selection and differentiation, where are the ‘morphs’ between A and Z?

I hope you realize that you’re essentially asking why we haven’t dug up the fossils of every viable organism which ever lived. I can explain why this is an unrealistic aspiration if you’d like, but it should suffice to consider the sheer number of fossilizable life forms that have lived and died on this planet, and compare the total size of our museum collections.

Yet what stands out and what the author you suggested above is saying is that the fossil record snapshots unique life forms that can be classified with their own name thus differentiating them from other similarly differentiated life forms.

Anything can be classified with its own name–particularly if it turns up rarely enough that you don’t have much like it. Conversely, there are fossils which are so plentiful and vary so continuously that it’s quite difficult to classify or label them. One of the more amusing such cases is that of fossil hominids, as touched on here (although I saw more on this in a lecture by Jeff McKee and I don’t recall if the comparison in question is available anywhere online). Creationists all agree that such fossils are either “apes” or “men,” but the transitional fossils are labeled “definitely man” by some creationists and “definitely ape” by others!

The fossil record observes sudden appearance of fully functional, fully differentiated life forms, when the math of (first life + mutation = how many species?) is an incredible equation missing only the proof of all this mutation and change in the fossil record. Considering the number of mutations required to get a positive mutation, the majority of the mutations would have produced a mass of grossly deformed and classifiable creatures. Yet, as any trip to the museum shows, the life forms are very nicely unique, functional and fully formed.

Actually, every living human carries on the order of a hundred new mutations. Yet, with the exception of Paris Hilton, we generally aren’t grossly deformed and unclassifiable. Most mutations are neutral, not negative.

Aside from that, you’re making the implicit assumption that a population would have to carry all those negative mutations along with the positive ones. But that’s not how evolution works. If a thousand individuals in a population are born with negative mutations and a single one is born with a positive mutation, the thousand negative mutations will vanish from the population as their bearers are reproductively out-competed, while the positive mutation will (on average, at least) persist and flourish. That’s the “selection” in “natural selection.”

Here are some more quotes, many from well known evolutionists. Insulting me will not change the quotes for the facts which these men were confronting regarding their profession…

Quote-mining does not an argument make. Those “evolutionists” remained evolutionists after making those quotes, which alone should tell you you’re misinterpreting them. Unless you honestly believe that periodically biologists whisper to one another–or openly publish(!?)–the equivalent of “Hey, did you know our discipline is one giant fraud?”, then go right back to work and forget about it.

Comment #109724

Posted by RBH on July 1, 2006 11:20 PM (e)

Anton Mates wrote

One of the more amusing such cases is that of fossil hominids, as touched on here (although I saw more on this in a lecture by Jeff McKee and I don’t recall if the comparison in question is available anywhere online). Creationists all agree that such fossils are either “apes” or “men,” but the transitional fossils are labeled “definitely man” by some creationists and “definitely ape” by others!

The paradigmatic figure for that general comparison is on Talkorigins. Which skull is human and which is “ape” is not agreed amongst creationists. See here for various creationist classifications.

RBH

Comment #109738

Posted by Pastor Bentonit on July 2, 2006 1:04 AM (e)

Ministry of Truth wrote:

This is why IDers win public debates with Darwinists and why Darwinism is on the way out.

HAHAHAHAHAHAHAHAHAHAHAHAHA!

Then why do IDers lose every scientific debate and every court case?

Now go annoy someone else, troll.

Comment #109772

Posted by Anton Mates on July 2, 2006 11:02 AM (e)

RBH wrote:

The paradigmatic figure for that general comparison is on Talkorigins. Which skull is human and which is “ape” is not agreed amongst creationists. See here for various creationist classifications.

Wonderful, thanks for pulling that up.

Comment #109808

Posted by Torbjörn Larsson on July 2, 2006 7:39 PM (e)

“relics of the RNA world in contemporary organisms”

Ooops, I completely forgot that class of fossils. The scarcity still applies, I guess.

““Life started once about 3 billion of years ago,”

Lest someone starts to argue age, let me rephrase to “Life started once billion of years ago,””

Today I have the energy to check: “life is theorized to have evolved from non-life somewhere between 3.5 to 3.9 billion years ago.” “3500 Ma Lifetime of the last universal ancestor; the split between the bacteria and the archaea occurs.” “In 2002, William Schopf of UCLA published a controversial paper in the scientific journal Nature arguing that geological formations such as this possess 3.5 billion year old fossilized algae microbes.” (Wikipedia).

Um, either my memory didn’t completely expire during midsummer festivities, or I made a lucky guess.

Comment #117601

Posted by kilroy on August 7, 2006 4:07 AM (e)

>> This program starts with “seed” words

And where did these seed words come from?

Comment #117605

Posted by Popper's ghost on August 7, 2006 5:29 AM (e)

It doesn’t matter. One creationist said “Just try a little experiment yourself. Start with a short 2 or 3-letter word …”; he didn’t say where the word should come from. And now another creationist illustrates his failure to comprehend by asking a pointless and irrelevant question.

P.S. This thread is 7 weeks old. Surely there must be something more recent that creationists can ask foolish questions about.