Tara Smith posted Entry 1573 on October 11, 2005 12:45 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/1568

It’s always nice when there’s a groundbreaking article in the literature, and the subject just happens to be your baby. My current research focuses on Streptococcus agalactiae (group B streptococcus, GBS), a bacterium that is the leading cause of neonatal meningitis in the United States. It also is a leading cause of invasive infection in the elderly, and can cause sepsis and toxic shock-like syndrome in healthy adults. No vaccine is currently available.

But what’s garnered attention recently hasn’t been any clinical presentations or new case reports of GBS disease; it’s the bacterium’s DNA. Specifically, the whole genomic sequences of 8 different strains of GBS, and the conclusions the authors have come to regarding bacterial genetic diversity–that it may be “endless.”

Continue reading (at Aetiology).

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Comment #51910

Posted by Norman Doering on October 11, 2005 12:57 PM (e)

“…the conclusions the authors have come to regarding bacterial genetic diversity—that it may be ‘endless.’”

Oh my gawd! There really are a couple billion monkeys typing away for a few billion years… but the typerwriter only has four keys, A, C, G and T.

Comment #51911

Posted by Steviepinhead on October 11, 2005 12:59 PM (e)

It’s time to say, “Thanks, Tara!” for a series of great posts over the last several days.

Comment #51913

Posted by Bayesian Bouffant, FCD on October 11, 2005 1:14 PM (e)

How clever of the Designer not to paint himself into a corner…

Comment #51929

Posted by BlastfromthePast on October 11, 2005 2:24 PM (e)

Where’s NS in all of this? If there is an infinite diversity, then obviously NS is not operative–or else it would pick one over the other. Now if NS cannot act on bacteria, then how did bacteria evolve?

I await enlightened responses.

Comment #51932

Posted by Bayesian Bouffant, FCD on October 11, 2005 2:36 PM (e)

Where’s NS in all of this?

I can only assume you mean noodle specificity. Evidence of His Noodly Appendage is all around us.

Comment #51933

Posted by Tara Smith on October 11, 2005 2:47 PM (e)

Blastfromthepast wrote:

Where’s NS in all of this? If there is an infinite diversity, then obviously NS is not operative—or else it would pick one over the other. Now if NS cannot act on bacteria, then how did bacteria evolve?

I await enlightened responses.

Huh. I’m not really sure where to begin. First, I have no idea how you came to the conclusion that if there is “infinite diversity,” then “obviously NS is not operative.” NS is one of the factors that would lead to that very diversity, as isolates pick up new genes in the environment that give them a selective advantage in their local population. However, what may give one isolate an advantage at a particular time in a particular environment may be detrimental to another isolate in another time in a different environment–therefore, a great deal of diversity will be seen in the global GBS population, although obviously only limited diversity may be seen locally. Does that clarify it at all?

I have no idea how you go from your first statement to your conclusion that NS can’t act on bacteria. Either I’m not seeing several steps in your logic, or you’ve bypassed them.

Comment #51934

Posted by Steviepinhead on October 11, 2005 2:47 PM (e)

Blast, Blast, Blast. When will you learn that you need to invest the time and energy to actually gain some rudimentary understanding of this stuff before you launch once more into your open mouth, insert foot routine.

Mutatation generates variation. The diversity of life-forms is the expected result. Within any given amount of time, natural selection begins to winnow that diversity within any given niche of any given prevailing environment, but those niches and environments don’t simply stand still as time marches on. Because both the variation generated by the life-forms and the variation-winnowing environment are moving targets, the fitness match between life-form and environment never reaches perfection.

Otherwise we wouldn’t have a diverse biome in the first place, just one not-very-interesting species of slime covering one not-very-interesting ball of rock (if that; one suspects that overly-boring “environments” most likely don’t give rise competing replicators in the first place).

Reality is messier than you might like. You can get used to it, or you can keep wishing that it will turn out to conform to your rather simplistic and boring fantasies, but you can’t do both.

Comment #51938

Posted by Russell on October 11, 2005 3:09 PM (e)

Tara Smith wrote:

I have no idea how you go from your first statement to your conclusion that NS can’t act on bacteria. Either I’m not seeing several steps in your logic, or you’ve bypassed them.

I may be able to help you with that.

See, if there’s “infinite diversity”, that means that every possible permutation of sequence exists within the world’s population of S. agalactiae. So, if the genome is, say 4x10^6 basepairs, there are at least 4^(4x10^6) different versions of S. agalactiae out there. And, while that’s a pretty large number, it’s not quite infinite, so we have to allow for the fact that there’s really no hard and fast limit to the genome size, thus extending our very large number to infinity.

And, of course, an unspoken assumption in Blast’s devastatingly incisive query is that all of these infinite sequences are equally represented in the population of S. agalactiae; in other words its genome is entirely random! Don’t you see? Blast has just disproved evolution… again!

That and the fact that Blast is a committed creationist should clear things up.

Hope that helps.

Comment #51940

Posted by Flint on October 11, 2005 3:13 PM (e)

One pictures colonies of bacteria each evolving like mad to adapt to a few somewhat different (and changing) square millimeters of environment, and being able to do so indefinitely. Given enough difference in territorities, the right rate of change, and an extensive enough buffet of mutations to choose from, and it would be astounding if something totally novel did NOT evolve from NS at work.

Comment #51951

Posted by Tara Smith on October 11, 2005 3:59 PM (e)

Thanks, Russell–it’s so much clearer now. :)

Comment #51954

Posted by RBH on October 11, 2005 4:38 PM (e)

I’ll only remark that “infinite” and “endless” are not synonyms.

RBH

Comment #51959

Posted by RBH on October 11, 2005 5:10 PM (e)

In the context of the paper under discussion, neither “endless” nor “infinite” are justified. From the abstract of the paper at issue:

Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes. (Bolding added)

“Vast” is neither “endless” (in the sense that we’ll continue finding new ones no matter how long we look) nor “infinite” (in the sense that the number of existing unique genes is greater than any arbitrarily large number).

RBH

Comment #51960

Posted by Tara Smith on October 11, 2005 5:27 PM (e)

Very true. I think I cribbed “endless” from one of the write-ups about this paper. The authors consistently use “vast” throughout the manuscript.

Comment #51968

Posted by ben on October 11, 2005 6:18 PM (e)

Blast, I’m not sure how NS acts here, but I did notice that if you magnify the image really really big, you can see an extremely clear image of Bill Dembski in the pupil of the bacteria’s eye.

Comment #51988

Posted by BlastfromthePast on October 11, 2005 8:41 PM (e)

Russell wrote:

And, of course, an unspoken assumption in Blast’s devastatingly incisive query is that all of these infinite sequences are equally represented in the population of S. agalactiae; in other words its genome is entirely random! Don’t you see? Blast has just disproved evolution… again!

I see you’ve finally seen the light. As I said before, I await an enlightened response. (Or, shall we see yet another ad hoc explanation?)

RBH wrote:

“Vast” is neither “endless” (in the sense that we’ll continue finding new ones no matter how long we look) nor “infinite” (in the sense that the number of existing unique genes is greater than any arbitrarily large number).

I took a quick look at the article and didn’t see either the word “endless” nor “infinite.” Let this be a cautionary tale, though, that words do have repercussions. My argument still stand; it’s just that its merits are not as “vast” as they were before.

To “ben”, all I can say is that if you want to be snide, then go ahead and be snide. Nonetheless, there is plenty that science can’t explain. And if that annoys you, then maybe that’s a sign you’ve made science your god.

Comment #51989

Posted by Flint on October 11, 2005 8:48 PM (e)

Nonetheless, there is plenty that science can’t explain. And if that annoys you, then maybe that’s a sign you’ve made science your god.

I hope we can distinguish between what science can not explain, and what science has not explained. It’s annoying for someone to imply that what science might explain someday can’t be explained at all. Since I have absolutely no idea where to draw the line, and just extrapolating from what science has done, I personally would feel very uncomfortable relying on the unexplainability of anything. Faith in our eternal ignorance is pretty empty, all in all.

Comment #51991

Posted by 'Rev Dr' Lenny Flank on October 11, 2005 8:53 PM (e)

Blast, why on earth should anyone care in the slightest about your uneducated uninformed opinions?

Comment #51992

Posted by 'Rev Dr' Lenny Flank on October 11, 2005 8:55 PM (e)

Nonetheless, there is plenty that science can’t explain.

No kidding. Maybe that’s why scientists still have jobs, and haven’t all retired to the Bahamas by now.

Alas for you (and other IDers) “can’t explain” isn’t the same as “will not EVER explain”. Every time people like you have made that bet, they have lost. Every single time.

How many times do you need to sit on a stove before learning that it burns your ass?

Comment #51993

Posted by BlastfromthePast on October 11, 2005 8:56 PM (e)

Flint wrote:

It’s annoying for someone to imply that what science might explain someday can’t be explained at all.

Yes, science is an “all knowing” god.

Comment #51996

Posted by Moses on October 11, 2005 9:07 PM (e)

Comment #51993

Posted by BlastfromthePast on October 11, 2005 08:56 PM (e) (s)

Yes, science is an “all knowing” god.

Just a tool used by some clever apes. Unlike your non-existent religious icon that explains and does nothing.

Comment #52001

Posted by Norman Doering on October 11, 2005 10:23 PM (e)

BlastfromthePast asked: “Where’s NS in all of this? If there is an infinite diversity,…”

There’s not “infinite” diversity. You have to get used to the fact that sometimes biologists speak with a bit of poetic license. There is merely more diversity than they can get their heads around at the moment.

What it means is that for these bacteria is that the fitness landscape is not a lifeless desert with only a few oasis to survive in, but a raging jungle where many diverse gene sequences can survive. They can tolerate a lot of diversity and not get selected out. It means life is easy for them.

Comment #52006

Posted by Steve S on October 11, 2005 10:57 PM (e)

I get the sense that Blast is pretty young. He seems to just not be familiar with some common ideas. For instance

Comment #51929

Posted by BlastfromthePast on October 11, 2005 02:24 PM (e) (s)

Where’s NS in all of this? If there is an infinite diversity, then obviously NS is not operative—or else it would pick one over the other. Now if NS cannot act on bacteria, then how did bacteria evolve?

He wouldn’t have said this if he knew that ‘infinite’ is not the same as ‘exhaustive’.

Comment #52008

Posted by Steve S on October 11, 2005 11:04 PM (e)

I estimate that Blast is about 18.

Comment #52010

Posted by BlastfromthePast on October 11, 2005 11:36 PM (e)

Norman Doerring wrote:

What it means is that for these bacteria is that the fitness landscape is not a lifeless desert with only a few oasis to survive in, but a raging jungle where many diverse gene sequences can survive. They can tolerate a lot of diversity and not get selected out. It means life is easy for them.

Spoken like a true Darwinist—–all metaphor and no substance.

There’s an article out about missense mutations which points out that one missense mutation is almost the same as another missense mutation–outside the funtional sites. Again, mutations, sequences, permutations, all, basically outside the putative influence of NS.

I used to think that RM+NS actually had a role in biology. It now is starting to look as though there’s no such thing as a “random mutation”, and, hence, that there doesn’t appear to be much to NS to act on, meaning that NS is just some trite historical invention which will one day (very soon) be hoisted upon the dustheap of ideas.

Steve S wrote:

I estimate that Blast is about 18.

I’m flattered. But since I have a degree in zoology, and a degree in engineering, you’ll agree that I’m just a little older than that.

Moses wrote:

Unlike your non-existent religious icon that explains and does nothing.

Thanks for your very scientific analysis.

*************I’m still waiting for an enlightened response.************

Comment #52011

Posted by Steve S on October 12, 2005 12:18 AM (e)

Given how you talk, and what you don’t seem to know about, I don’t see any reason to believe that you have degrees in zoology and engineering. I’ll stick with my guess that you’re 18 until I see evidence otherwise.

Comment #52012

Posted by BlastfromthePast on October 12, 2005 12:54 AM (e)

Steve S wrote:

Given how you talk, and what you don’t seem to know about, I don’t see any reason to believe that you have degrees in zoology and engineering. I’ll stick with my guess that you’re 18 until I see evidence otherwise.

I’m still waiting for an enlightened response. Why don’t you show me how much you know.

Comment #52013

Posted by Steve S on October 12, 2005 1:07 AM (e)

Yeah, well, given your loopy comments about Integrals and such, I don’t think it’s worth my time trying to educate you. I’ll let someone else waste his time trying to enlighten you.

Comment #52014

Posted by Norman Doering on October 12, 2005 1:42 AM (e)

BlastfromthePast “Spoken like a true Darwinist——-all metaphor and no substance.”

My words were metaphors, but things like “fitness landscapes” while being metaphoric are still genuine and precise mathematics used evolutionary programming and genetic algorithms, not just biology.

http://en.wikipedia.org/wiki/Fitness_landscape

The term was coined by Sewall Wright:
http://en.wikipedia.org/wiki/Sewall_Wright

BlastfromthePast “There’s an article out about missense mutations which points out that one missense mutation is almost the same as another missense mutation—outside the funtional sites.”

Link the article so people know what you’re talking about. What you’re saying just looks dead wrong. Missense mutations or nonsynonymous mutations is where a nucleotide is changed which results in a different amino acid. This in turn can cause diseases such as Epidermolysis bullosa and sickle-cell disease. How can that be “almost the same as another” if some cause disease and others don’t or different diseases.

What you’re saying makes no sense.

BlastfromthePast “Again, mutations, sequences, permutations, all, basically outside the putative influence of NS.”

That’s just dead wrong. The ID people are lying to you.

BlastfromthePast “I used to think that RM+NS actually had a role in biology.”

They do! Anyone who says different is lying to you or you have misunderstood.

BlastfromthePast “It now is starting to look as though there’s no such thing as a ‘random mutation,’”…

A better word would be unguided mutation, mutations have causes and there are other mechanisms at work changing the genome, but the randomness is seen in the pointless death and disease in organisms.

BlastfromthePast “… and, hence, that there doesn’t appear to be much to NS to act on, meaning that NS is just some trite historical invention which will one day (very soon) be hoisted upon the dustheap of ideas.”

Natural selection works outside of biology. It’s why buggy whips and model-T Fords are now pretty much extinct. Natural selection even works on things designed by intelligent agencies.

You have so little idea about what you’re talking about and you’re being lied to on top of that.

You very clearly represent the tragedy of education ID causes.

Comment #52016

Posted by sanjait on October 12, 2005 3:18 AM (e)

Nice post Tara Smith. This is an interesting finding. As a pathogen microbiologist, I’ve always felt that the “species” definition is only weakly applicable to bacteriology in general. This casts an interesting shadow on the evo-ID debate. The IDists are always saying there are no transitional forms, but in the microbial world where the “species” (or “kind” as creationists like to refer to it) are so blurred, the vast continuum of genetic diversity we observe, along with our continuing elucidation of the fitness advantages of certain genes in select environments leaves little need for conjecture and extrapolation to see evolution taking place.

I don’t know much about GBS S. agalactiae, but if it is anything like GAS S. pyogenes, the observation of genetic instability is not too surprising. If I remember correctly (and I may be mixing up my recollections from my basic path micro class, so correct me if I’m wrong), the group A’s, which cause the well known strep throat, are individually extremely susceptible to the adaptive immune response. I’m not sure how Blast claims this is problematic for evolutionary thoery, but just as higher eukaryotes have evolved hypervariant proteins to recognize antigens, like antibodies and T-cell receptors, some pathogens have evolved hypervariant regions using different mechanisms. GAS M proteins, the outer surface that is presented the immune system, is a classic example of how genetic instabilit/hypervariance provide a selective advantage by preventing the mammalian herds from acquiring adaptive immunity to the organism. HIV is another example. It is likely that we will find many organisms that are susceptible to adaptive immunity in fact use extreme variance to evade the immune response.

Since Blast seems to have missed the implication of these findings I’ll spell it out: we are observing the processes of mutation and selection causing significant genetic changes in real time (over only the last few decades in both Strep and HIV), and we have a pretty plausible theory regarding the fitness advantage conferred by such changes.

Comment #52018

Posted by Pastor Bentonit on October 12, 2005 4:11 AM (e)

Blast wrote:

I’m flattered. But since I have a degree in zoology, and a degree in engineering, you’ll agree that I’m just a little older than that.

Is it only me, or do they actually clone little DaveScots in engineering schools? Or was it evopeaches? And do they all get assigned an IQ of 144 at graduation? So many questions, so few answers…

Comment #52031

Posted by Moses on October 12, 2005 8:01 AM (e)

*************I’m still waiting for an enlightened response.************

You’ve received many enlightened responses, to which you’ve closed your eyes and stuck your fingers in your ears and gone “la la la la la la.” Your behavior is akin to many a small child who doesn’t want to hear I’m not dropping everything and running out to get them that toy they just saw on TV.

So I play the daddy card: “No. Because. End of story.” Rather than get into an argument and empower a small child who has little knowledge, a immature capacity for judgment and a decided capacity to act on irrational whims.

I will say this, your obvious grandiosity is amusing. You are really stuck on yourself and clearly express the condescending and inflexible demeanor of a classic narcissist as you bray incessantly, and screech triumphantly, about things you clearly do not understand.

Comment #52032

Posted by Tara Smith on October 12, 2005 8:08 AM (e)

sanjait wrote:

Nice post Tara Smith. This is an interesting finding. As a pathogen microbiologist, I’ve always felt that the “species” definition is only weakly applicable to bacteriology in general. This casts an interesting shadow on the evo-ID debate. The IDists are always saying there are no transitional forms, but in the microbial world where the “species” (or “kind” as creationists like to refer to it) are so blurred, the vast continuum of genetic diversity we observe, along with our continuing elucidation of the fitness advantages of certain genes in select environments leaves little need for conjecture and extrapolation to see evolution taking place.

Absolutely. ‘Course, then at least YECs retreat to “but they’re still bacteria!,” so apparently all bacteria are of one “kind” despite the extreme diversity at the DNA level, while humans and chimps, despite near 100% DNA identity, are obviously different “kinds.” I love the mental disconnect.

I don’t know much about GBS S. agalactiae, but if it is anything like GAS S. pyogenes, the observation of genetic instability is not too surprising. If I remember correctly (and I may be mixing up my recollections from my basic path micro class, so correct me if I’m wrong), the group A’s, which cause the well known strep throat, are individually extremely susceptible to the adaptive immune response. I’m not sure how Blast claims this is problematic for evolutionary thoery, but just as higher eukaryotes have evolved hypervariant proteins to recognize antigens, like antibodies and T-cell receptors, some pathogens have evolved hypervariant regions using different mechanisms. GAS M proteins, the outer surface that is presented the immune system, is a classic example of how genetic instabilit/hypervariance provide a selective advantage by preventing the mammalian herds from acquiring adaptive immunity to the organism. HIV is another example. It is likely that we will find many organisms that are susceptible to adaptive immunity in fact use extreme variance to evade the immune response.

Yep. The M and M-like proteins in GAS are actually a great example of an “increase in information” as well, since they are products of a single gene which duplicated and subsequently diverged, to produce proteins which have different biological functions. And as you mentioned, the M proteins are targets of the human adaptive immune system (we make antibodies against them, to put it simply), so there are well over 100 variations of this protein, and the antibodies aren’t cross-protective. (That is, even if we’re immune to one, we can still be infected by strains that carry one of the other varieties). My dissertation work was on the regulation of this genetic regulon, so it’s another one of my babies. :) And currently, my project with GBS involves studying another (thus far uncharacterized) region of hypervariable genes, which I think may play a similar role in GBS as the M proteins play in GAS.

One thing about these organisms, though–they’re not easily transformed. I can’t tell you how long it took me to electroporate a stupid plasmid into a strain of GAS when I was a grad student. GBS is similar. So I have to wonder, are phage mediating most of this diversity? Or are there signals in their natural environments that make them more transformable? We’ve spent so much time studying gene regulation in pure cultures, hopefully we can move toward a more realistic model with all the new genetic toys and answer some of these questions.

Comment #52034

Posted by Pastor Bentonit on October 12, 2005 8:30 AM (e)

Tara Smith wrote:

,One thing about these organisms, though—they’re not easily transformed. I can’t tell you how long it took me to electroporate a stupid plasmid into a strain of GAS when I was a grad student. GBS is similar. So I have to wonder, are phage mediating most of this diversity? Or are there signals in their natural environments that make them more transformable? We’ve spent so much time studying gene regulation in pure cultures, hopefully we can move toward a more realistic model with all the new genetic toys and answer some of these questions.

Tell me about it. Electroporation of Bacillus thuringiensis or protoplast transformation of B. subtilis is not exactly easy either…makes you long for lab strains of E. coli optimised for transormation. I think both your answers apply, by the way. Phage transduction in the Bacillus cereus group was performed in soil microcosms set up at our lab many years ago.

Comment #52035

Posted by Tara Smith on October 12, 2005 8:38 AM (e)

Yeah, it’s probably a little bit of both. I did a lot of transduction experiments with GAS and A25 phage to get random transposon knockouts, and those were always relatively easy.

Comment #52039

Posted by Russell on October 12, 2005 9:05 AM (e)

RE: transformation of various streptococci and bacilli. Here’s a naive question from someone who’s never tried to transform any bacteria except E. coli. Are all gram-positives similarly resistant to transformation?

Comment #52040

Posted by Tara Smith on October 12, 2005 9:09 AM (e)

Nope. Streptococcus pneumoniae, for instance, is naturally transformable–and it’s been hypothesized that’s probably one reason why GAS and GBS remain almost universally penicillin-sensitive, while S. pneumo has long been resistant.

Comment #52041

Posted by Robert M. on October 12, 2005 9:13 AM (e)

It’s always amazing for me to come to fora where real scientists hang out and talk about their work. It’s amusing to contrast the comments of the biologists with the anti-evolution trolls.

I’m de-lurking to prove that not all engineers are insular idiots. The underlying mathematical order in biology–the simple mechanisms that lead to all the complexity we see–is fascinating to me, and I appreciate people who write interesting stuff at the level of a reasonably intelligent layman.

Articles like this are cool, and serve to underscore the everyday importance of evolutionary theory for working biologists. I can’t imagine having to contend with people who dispute the existence of Maxwell’s equations; you all have my support and sympathy!

Comment #52042

Posted by Pastor Bentonit on October 12, 2005 9:27 AM (e)

Hi Robert, and welcome to PT! I did not imply btw, that all engineers are “insular idiots”…just the DaveScot clones. [rant]Some days I just get tired and picture them as one Über-Troll with maybe multiple personality disorder (for instance, evopeach has been overly aggressive and vitriolic lately…see the ARN threads). Agreed, science is so much more interesting in the long run, than random psychopathology.[/rant] ;-)

Comment #52056

Posted by Russell on October 12, 2005 11:21 AM (e)

Streptococcus pneumoniae, for instance, is naturally transformable…

I guess a moment’s reflection might have spared me the trouble asking. Now that I think about it, Avery & McLeod used exactly this phenomenon and this organism to demonstrate that DNA is, in fact, the genetic material.

D’oh!

Comment #52060

Posted by shenda on October 12, 2005 12:08 PM (e)

Hi Tara,

Great post!

A few questions, if you have the time:

How do you define a population of bacteria? Is the bacteria in one puddle the same population as the bacteria in the puddle two blocks down?

How rapidly can bacterial populations (such Streptococcus agalactiae) spread geographically?

Why is this vast diversity such a surprise? Considering a) the large total population of this bacterium, and b) that it is spread out across the planet in a vast numbers of populations, and c) how easily it adopts new genes, wouldn’t it be more surprising if this diversity did not exist?

Shenda

Comment #52063

Posted by sanjait on October 12, 2005 12:46 PM (e)

“One thing about these organisms, though—they’re not easily transformed. I can’t tell you how long it took me to electroporate a stupid plasmid into a strain of GAS when I was a grad student. GBS is similar. So I have to wonder, are phage mediating most of this diversity? Or are there signals in their natural environments that make them more transformable? We’ve spent so much time studying gene regulation in pure cultures, hopefully we can move toward a more realistic model with all the new genetic toys and answer some of these questions.”

“Tell me about it. Electroporation of Bacillus thuringiensis or protoplast transformation of B. subtilis is not exactly easy either…makes you long for lab strains of E. coli optimised for transormation.”

I just have to concur for a moment. Our lab works on Mycobacteria, and they are no day at the beach either. They can transform, but the worst part is sequencing a knockout mutant afterwards. I guess other people can use ligated loops or hybridization to locate a transposon, but we use a fun method called nested suppression PCR, which is basically a semi-specific PCR voodoo ceremony with about a 5% unpredictable success rate. It could be worse I guess, the lab across from ours studies Chlamydia, which have no known methods for genetic manipulation. They just use the guess and check method with natural mutant phenotype isolates.

Regarding the issue of transformability in vivo: I don’t know how an IDist perspective would tackle the issue of diversity in natural isolates, but thinking about the evolutionary origin of their diversity, there are at least 3 possibilites: 1. The variant genes in the pan-genome are the result of LGT events, which seems likely since you are talking about phages and such. There should be a genetic trace for this, in the form of similarity to other organisms, att sites, IS elements, etc. If this is the case, the organisms with which the genes share similarity should give clues to both the source and environement in which the transformations take place. 2. The bacteria creates novel genes through genetic instability. This seems unlikely offhand, but if the pan-genome appears paralagous but not homologous to other strep spp., that would support this hypothesis. 3. The isolates are all descended from a more complex organsims. In Mycobacteria, there are purely environmental species (e.g. M. smegmatis, opportunistic pathogens (e.g.M. avium, and obligate pathogens (M. tuberculosis and M. leprae). Generally, it appears as though the more pathogenic strains evolved from the less pathogenic, and in the process they lost a lot of genes. They gained a few virulence factors, but overall the pathogenic ones are quite a bit smaller. This hypothesis may not apply, as I don’t know offhand the location of S. agalactiae on the bacterial tree or their degree of core gene similarity to each other (as in, are they really one “species”?), but if there are environmental ancestors this may apply.

I too appreciate informed discussion, and also notice how it contrasts sharply with IDists baseless conjecture and wordplay coupled with an utter lack of working knowledge. Every time I read a post from Blastfromthepast I just want to show him the NCBI BLAST server. And on that note, I should get back to my bench…

Comment #52064

Posted by Tara Smith on October 12, 2005 12:55 PM (e)

Hi Shenda,

Great questions!

How do you define a population of bacteria? Is the bacteria in one puddle the same population as the bacteria in the puddle two blocks down?

Boy, that really depends, and it’s pretty subjective. Basically, a “population” of bacteria can be anything the researcher wants it to be, from a pure culture expanded from one starter colony where we’re looking for SNPs, to all the bacteria in a certain niche in the body, to all the bacteria of a certain species in a certain geographical region. It’s not anything that’s taxonomic, like “species,” so it’s up to the discretion of the investigator. So, in response to your question, they could be the same population, depending on the question the researcher is asking.

How rapidly can bacterial populations (such Streptococcus agalactiae) spread geographically?

It’s really not known, because there’s not great surveillance for this organism. Most of what we know comes from states or countries that track invasive cases of GBS disease, but that’s only a subset of all the isolates out there. We know that it can be transmitted vertically (mother to baby), by direct contact (such as contaminated hands), and by sexual contact, but we really have no idea how fast one clone could spread across a country, or around the world. The answer would seem to be, “not too fast,” because the isolates we culture from invasive cases and pregant women here in the US are pretty different from ones that are found in, say, Japan. But if there was a strong selective pressure that would contribute to increased spread, who knows how quickly it could go. For example, serotype V isolates, which were unheard of prior to the 1980s, are now found frequently in adults who develop sepsis from GBS, and these isolates are more commonly resistant to erythromycin and clindamycin. Was that a factor in their spread? Probably, but it’s hard to say because we just don’t have the surveillance data.

Why is this vast diversity such a surprise? Considering a) the large total population of this bacterium, and b) that it is spread out across the planet in a vast numbers of populations, and c) how easily it adopts new genes, wouldn’t it be more surprising if this diversity did not exist?

Well, diversity was expected, but nothing on the order of as many as 33 unique genes per isolate. One reason is because GBS doesn’t very easily adopt new genes, at least, as far as we can tell in the laboratory. It’s not a DNA “scavenger” like some bacterial species are. Additionally, there has been this meme in GBS epidemiology (finally dissipating, it seems) that isolates within a serotype are fairly clonal. The work I did for my postdoc (which we’re still finalizing for publication) argues against that, and having this paper to cite as a reference will go a long way toward furthering that case.

Comment #52069

Posted by shenda on October 12, 2005 1:08 PM (e)

Hi Tara,

Thank you.

Comment #52070

Posted by Tara Smith on October 12, 2005 1:13 PM (e)

sanjait wrote:

I just have to concur for a moment. Our lab works on Mycobacteria, and they are no day at the beach either. They can transform, but the worst part is sequencing a knockout mutant afterwards. I guess other people can use ligated loops or hybridization to locate a transposon, but we use a fun method called nested suppression PCR, which is basically a semi-specific PCR voodoo ceremony with about a 5% unpredictable success rate. It could be worse I guess, the lab across from ours studies Chlamydia, which have no known methods for genetic manipulation. They just use the guess and check method with natural mutant phenotype isolates.

Heh. voodoo PCR, I know it well. :) And yes, others have it worse off–but it’s still nice to vent once in awhile.

Regarding the issue of transformability in vivo: I don’t know how an IDist perspective would tackle the issue of diversity in natural isolates, but thinking about the evolutionary origin of their diversity, there are at least 3 possibilites: 1. The variant genes in the pan-genome are the result of LGT events, which seems likely since you are talking about phages and such. There should be a genetic trace for this, in the form of similarity to other organisms, att sites, IS elements, etc. If this is the case, the organisms with which the genes share similarity should give clues to both the source and environement in which the transformations take place.

Sure–if we have the sequences of the organisms they came from (or their similar relatives). But remember just how many bacterial species we’re totally clueless about, especially in the throat, vaginal, and GI tracts, where GBS hang out. Anyhoo, I’m sure someone at TIGR will play around with this.

2. The bacteria creates novel genes through genetic instability. This seems unlikely offhand, but if the pan-genome appears paralagous but not homologous to other strep spp., that would support this hypothesis.

And this would probably be easier to check. They’d have to be pretty divergent not to show up on their screen, though.

3. The isolates are all descended from a more complex organsims. In Mycobacteria, there are purely environmental species (e.g. M. smegmatis, opportunistic pathogens (e.g.M. avium, and obligate pathogens (M. tuberculosis and M. leprae). Generally, it appears as though the more pathogenic strains evolved from the less pathogenic, and in the process they lost a lot of genes. They gained a few virulence factors, but overall the pathogenic ones are quite a bit smaller. This hypothesis may not apply, as I don’t know offhand the location of S. agalactiae on the bacterial tree or their degree of core gene similarity to each other (as in, are they really one “species”?), but if there are environmental ancestors this may apply.

There aren’t any that I’m aware of, but as you can imagine, most of the focus on these organisms are on the ones that are pathogens for humans and animals. Strep are also closely related to enterococci, which can be found in the environment without animal hosts, but I have no idea how long ago they diverged or what the ancestral phylogeny looks like there. I know that in the comparisons I’ve seen between GBS, GAS, and Strep pneumo, you don’t see any of that. I’d guess that the diversity is mostly due to LGT, with probably a little bit of your second point (genetic instability and variation) and maybe a tad of your third point (gene loss) thrown in there.

Comment #52074

Posted by Bob O'H on October 12, 2005 1:39 PM (e)

Sorry to be a grouch, but how can they have any confidence in an extrapolation from a sample size of 8 individuals? I was looking at these problems a couplke of years ago (in a community ecology context), and I honestly don’t think you can do better than put bounds on the number of clones, even with large sample sizes. Basically, there are many ways of doing the extrapolation, and no way of knowing which is the best.

Oh no! I’ve just checked the paper, and they used an exponential model. When I used that model, it managed to estimate a number of species less than the observed number. OK, it’ll work differently for different problems, but still.

They say this in their conclusion:

Our data clearly show that the strategy to sequence one or two genomes per species, which has been used during the first decade of the genomic era, is not sufficient and that multiple strains need to be sequenced to understand the basics of bacterial species.

I’d want to add an “or eight” in there.

Of course, I’m not arguing that the diversity isn’t huge, only that the data doesn’t demonstrate that. And the fact that GBS has all this spare DNA kicking about is interesting enough: it should keep a few students and post-docs in beer for several years.

Bob

Comment #52077

Posted by Tara Smith on October 12, 2005 2:00 PM (e)

Not grouchy at all, and I’d guess that even the authors would mostly agree with you. They mention that their confidence intervals are huge, and I’d assume most people would take their figures with a grain of salt. But it still represents a push to change the way researchers see GBS, and hopefully there will be much less of the “a serotype II is a serotype II is a serotype II,” or “we have the genome sequence already–why bother with more?” kind of thinking.

Comment #52118

Posted by BlastfromthePast on October 12, 2005 11:13 PM (e)

Norman Doerring wrote:

Link the article so people know what you’re talking about. What you’re saying just looks dead wrong.

http://raven.bioc.cam.ac.uk/~mdepristo/files/dep…

Moses wrote:

You’ve received many enlightened responses, to which you’ve closed your eyes and stuck your fingers in your ears and gone “la la la la la la.”

Please point out to me ONE such “enlightened response.” Just one.

Norman Doerring wrote:

Natural selection works outside of biology. It’s why buggy whips and model-T Fords are now pretty much extinct. Natural selection even works on things designed by intelligent agencies.

This statement is embarrassingly indefensible. It even has a name: “Berra’s Blunder”. You can look it up in Icons of Evolution. Why don’t we just replace NS with the phrase “feedback mechanism”? It has the merits of conveying the same sense as that of using NS, while focusing in more on what is actually taking place: feedback.

sanjait wrote:

Nice post Tara Smith. This is an interesting finding. As a pathogen microbiologist, I’ve always felt that the “species” definition is only weakly applicable to bacteriology in general. This casts an interesting shadow on the evo-ID debate. The IDists are always saying there are no transitional forms, but in the microbial world where the “species” (or “kind” as creationists like to refer to it) are so blurred, the vast continuum of genetic diversity we observe, along with our continuing elucidation of the fitness advantages of certain genes in select environments leaves little need for conjecture and extrapolation to see evolution taking place.

This is the kind of quote that professional biologists–steeped as they are in neo-Darwinism–don’t think twice about, but that drive those of us who have no confidence at all in NS wildly crazy.

It’s an appeal to use the “microbial” world to demonstrate “transitional” forms——-BUT….……, “the “species” definition is only weakly applicable to bacteriology in general.” Do you see the contradiction here? Bacteria have all kinds of “transitional forms”; but a “transition” to what—–since you can’t define a “species.”

And, oh, Robert, do you see that this isn’t exactly like dealing with Maxwell’s Equations?

Comment #52122

Posted by Norman Doering on October 13, 2005 3:06 AM (e)

BlastfromthePast wrote: “This statement is embarrassingly indefensible. It even has a name: “Berra’s Blunder”. You can look it up in Icons of Evolution.”

No it’s not indefensible. For one thing, I’m not saying the same thing as Berra, and for another, Wells missed the point or lied about the point of Berra’s metaphor. So you missed on two counts.

There’s a reason we don’t buy model-Ts that’s different than why we don’t buy old style Corvettes. The old style Corvette would still be about as functional as the new style but the model-T isn’t. The model-T can no longer compete in the “natural” environment of human marketing desires. Any modern car would beat a model-T on all points.

If you doubt that, then practice what you preach and throw away your car and drive a model-T and then tell me it’s as functional as a modern car.

I said: Natural selection works outside of biology. It’s why buggy whips and model-T Fords are now pretty much extinct. Natural selection even works on things designed by intelligent agencies.

The point you don’t yet grasp is that selection can operate independently from random mutation. The environment selects the most fit. That’s so true it’s almost just a tautology.

How can you deny selection, both natural and human, is beyond me.

As for the random – well, if mutations aren’t at least sometimes random then your designer God purposely gives horrible genetic diseases to many men and animals.

What Wells did with Berra was a dishonest form of quote mining.

Berra’s analogy of the corvettes was used at the end of a section on human evolution and discussion of how evolutionary biologists piece together the fossil evidence to generate the hypothesized lineage of descent of homo sapiens. He used the Corvette as an example of how cars can be very similar or very different.

Here’s the last paragraph from Berra’s “Evolution and the myth of creationism” (just before the Corvette figure):

“…the accelerating pace of hominid fossil discoveries is truly dazzling. In darwin’s time, only a few neanderthal remains were known, and they were misunderstood. today we have a whole cast of characters in the drama of human evolution. these fossils are the hard evidence of human evolution. they are not figments of scientific imagination. if the australopithecines, homo habilis and h. erectus, were still alive today, and if we could parade them before the world, there could be no doubt of our relatedness to them. it would be like attending an auto show. if you look at a 1953 corvette and compare it to the latest model, only the most general resembleances are evident, but if you compare a 1953 and a 1954 corvette, side by side, then a 1954 and a 1955 model, and so on, the descent with modification is overwhelmingly obvious. This is what paleoanthropologists do with fossils, and the evidence is so solid and comprehensive that it cannot be denied by reasonable people. there are quibbles about individual relationships, but each new discovery helps fine-tune our increasingly detailed knowledge of human evolution.”

Regardless of whether think Berra made a “blunder” or not, what point do you think he was trying to make with the analogy?

Comment #52152

Posted by shenda on October 13, 2005 9:58 AM (e)

Blast wrote:

“Please point out to me ONE such “enlightened response.” Just one.”

Post# 52001, 51989, 51934, 51933.

Just because you disagree with them does not make them invalid or “unenlightened”.

Comment #52181

Posted by BlastfromthePast on October 13, 2005 12:58 PM (e)

shenda wrote:

Just because you disagree with them does not make them invalid or “unenlightened”.

First, thank you for being polite. I’m not too familiar with that on this blog.

Second, the fact is that, yes, you’re right, I don’t find their responses “enlightened.” And it’s because there’s several problems that I see that are simply glided over. The respondants assume NS really exists, so they see it everywhere and explain everything in terms of it.

First problem: This is a quote from Tara’s column:

Many species of bacteria are DNA scavengers, receiving new pieces of DNA via horizontal gene transfer. Some take these up easily–they are said to be “naturally transformable.” With others, it’s more difficult for new DNA to get in. In many cases, bacteriophages may bring new genes in when they infect a bacterium. However they’re introduced, this sharing of genes in bacteria is an extremely common phenomenon. Anyone who is familiar with the phenomenon of antibiotic resistance knows that one way this can spread among organisms is via horizontal transfer of these genes, often on little bits of DNA called plasmids.

Genes are being transferred. Large portions of DNA are being swapped. Traditional neo-Darwinism says that “random” mutations occur, basically these are changes of single-nucleotides. These mutations, in turn, bring about changes in proteins, which now can themselves produce further changes to the organism. Then along comes NS, and it chooses between the “changed” and “unchanged” organisms. That’s more or less the theory.

And yet, here we have whole “genes” (1,000 nucleotides on average) being swapped, taken into an organism, and it’s still a BACTERIUM! So if a PATTERNED sequence of 1,000 nucleotides doesn’t change a bacterium into something else, then how will a “single-nucleotide” change make a difference?

Second problem: This process cannot be totally random. Yes, there’s a random element to it; viz., that the genetic material that is swapped from one particular bacterium with another bacterium is done at random. However, this process is deterministic–it follows some rules. So the (I used the term “putative” in an earlier post) mutations that occur happen not willy-nilly, but according to set rules.

Third problem: Bacteria–I read this somewhere–have 80% of their genome that is stable, while 20% is constantly changing. If you suppose that NS is functioning to maintain the 80% stable, then what is happening to the other 20%? If NS is acting, then what is its verdict? What final form is the “best-suited” given the environment? NS seems not to have an answer. Therefore, it is logical to assume that the 20% of the genome that is constantly adapting itself, is adapting itself INDEPENDENTLY of NS. This throws into question the entire role of NS. It would appear that bacteria simply have an INNATE capacity to adapt to their environment in a way that is PRE-ADAPTED. Hence there is no need to invoke NS.

Fourth problem: If 20% of a genome is in constant flux, then it would appear that be the most likely candidate for evolving into a new, and different “life-form.” And yet, bacteria remain bacteria, millenium after millenium. If one of the most simple of life-forms, with 20% of its genome constantly changing, can’t “evolve” under the influence of NS, then what of more advanced and complicated life-forms?

Fifth problem: The fact that this 20% seems to be able to take on almost any form (not in a single organism, but via a procession of changed organisms), this means that the “possibility” of random sequence space–without chemically pre-ordained stopping points (i.e., without “favored” places in the probability space of bacterial genomes, as Dawkins imagines)–is indeed demonstrated, and, thus, actually bolsters some of the probability assumptions that ID makes.

I would consider an “enlightened” response one that could give me reasonable answers to these problems.

Comment #52182

Posted by CJ O'Brien on October 13, 2005 1:05 PM (e)

Blast:

It’s an appeal to use the “microbial” world to demonstrate “transitional” forms———-BUT………., “the “species” definition is only weakly applicable to bacteriology in general.” Do you see the contradiction here? Bacteria have all kinds of “transitional forms”; but a “transition” to what——-since you can’t define a “species.”

Yeah, it’s almost like nearly ALL the forms are transitional, isn’t it?
Your error is in believing that’s a problem for evolution. It’s not. It’s a big problem for the Biblical concept of “kinds” though, isn’t it?

See, your basline assumption is that, in order for there to be evolution, there has to be a “target,” another species, that a given one is evolving “toward.”

But that’s not the case. Organisms change. Lineages diverge. People come along after the fact and try, for purposes of classification, to make all that diversity fit into little boxes calle “species.” But that’s post-hoc. There’s no requirement that the concept of species needs to be clearly defined for natural selection to do its work.

Comment #52185

Posted by Flint on October 13, 2005 1:47 PM (e)

Blast wrote:

Flint wrote:

It’s annoying for someone to imply that what science might explain someday can’t be explained at all.

Yes, science is an “all knowing” god.

Hard to know quite what to make of this response, which very carefully ignores entirely the point it is supposedly responding to.

Let’s say, just for discussion, that there are things science can’t explain for two distinct reasons: the first, because we simply don’t know enough yet, but will eventually. Indeed, go back to ANY prior time (even yesterday) and there will be things unexplained then which are explained now. The second reason is, perhaps there are things science CAN NOT explain under any conceivable circumstances.

Even if we grant this distinction, we have no means of drawing a line between them. CAN we explain someday what we currently can’t? Who can possibly know this? Blast seems convinced that those who recognize that science HAS explained what were once mysteries, and continues to do so on a steady continuing basis, are somehow saying that there is nothing science can’t explain, and are therefore worshipping science as their god. But this doesn’t follow logically or even sensibly. It’s a projection of Belief by a Believer onto everyone else whether it applies or not. In this case, it does NOT apply so emphatically that Blast’s invalid projection is nearly a complete non sequitur. Blast seems to be projecting that unBelievers are saying that science can explain either everything or nothing. It doesn’t explain everything, therefore anyone who thinks it can explain anything has propped up a false god.

Meanwhile, Blast seems to be saying “NS either explains ALL we see, or it explains NONE of it. Since it clearly doesn’t explain everything, it is a useless illusion, QED.” Complex multifaceted dynamic adaptive processes just don’t fit Blast’s either/or mentality, therefore they can’t be happening. Sure does make things simple, I guess.

Incidentally, this is why people have difficulty accepting Blast’s degree in engineering. If nothing else, an engineering degree should immerse the student in complex feedback processes. But I work with devout engineers in Alabama, and I can tell you that when their faith is threatened, their engineering training and discipline vanishes like the proverbial soap bubble. Suddenly processes become fixed and unchanging, probabilities become absolutes, evidence is abandoned in favor of preference, analysis gives way to memorization, honesty is trampled by need. Truth trumps reality without skipping a beat.

Comment #52191

Posted by CJ O'Brien on October 13, 2005 2:05 PM (e)

So if a PATTERNED sequence of 1,000 nucleotides doesn’t change a bacterium into something else, then how will a “single-nucleotide” change make a difference?

A single nucleotide change in the right place can in fact make the same difference. And all “mutants” have a variant allele, and they are not “something else” either, but they have a whole different gene too. Not sure where you’re going with this.

Second problem: This process cannot be totally random. Yes, there’s a random element to it; viz., that the genetic material that is swapped from one particular bacterium with another bacterium is done at random. However, this process is deterministic—it follows some rules.

All “random” really means in the context of mutations is that a mutation occurs without reference to its effect on phenotype. They’re not taken to be “uncaused” events, or necessarily “random” in a metaphysical sense. So the observation that lateral transfer of genetic material is the same is not a coherent objection to orthodox theory

Third problem: Bacteria—I read this somewhere—have 80% of their genome that is stable, while 20% is constantly changing. If you suppose that NS is functioning to maintain the 80% stable, then what is happening to the other 20%? If NS is acting, then what is its verdict? What final form is the “best-suited” given the environment?

I am suspicious of all such tidy percentages—bacteria are far too diverse for any such generalization to be enlightening. For the sake of argument, however, let’s just go with it.
“NS functioning to maintain…” simply means that alterations to that 80% are not selected for, meaning that a change in the genome at certain loci is almost certainly deletrious. We see the same effect in “higher” organisms and the conservation of early developmental pathways. NS “functions” by differential survival and reproduction. That’s it. It’s always operative where diversity exists that contributes to differential reproductive success. And again you’re locked into “kinds.” There is no “final form.” Lineages diverge. Some are more fecund in a given environment. The descendants of those lineages will come to predominate in that environment. Rinse and repeat.

Fourth problem: If 20% of a genome is in constant flux, then it would appear that be the most likely candidate for evolving into a new, and different “life-form.” And yet, bacteria remain bacteria, millenium after millenium. If one of the most simple of life-forms, with 20% of its genome constantly changing, can’t “evolve” under the influence of NS, then what of more advanced and complicated life-forms?

Teleology’s got you bad. You’re assuming that the theory calls for all lifeforms to be “striving” for the next rung on the ladder. But that’s exactly what 150 years of evolutionary thought has shown us is not occuring, despite our human desire to see such “progress” in the natural world. Bacteria are hugely successful organisms. They are arguably the most “highly evolved” creatures on the planet. Selection pressure is acting on a given lineage to be good bacteria, not to try to be an amoeba. You’re injecting discredited pre-Darwinian evolutionary concepts into your criticisms.

the “possibility” of random sequence space—without chemically pre-ordained stopping points (i.e., without “favored” places in the probability space of bacterial genomes, as Dawkins imagines)—is indeed demonstrated

You lost me. I need a clarification of your objection here.
I guess you’re saying that there’s too much diversity for natural selection to act on, thus the diversity was “front loaded” or some such?
If that’s it, then what I’d like to know is: when? How? If present bacteria are descendents of past bacteria, how do you keep a given environment from favoring a given lineage, regardless of the total diversity in a population?

Comment #52204

Posted by BlastfromthePast on October 13, 2005 3:41 PM (e)

CJ O'Brien wrote:

Your error is in believing that’s a problem for evolution. It’s not. It’s a big problem for the Biblical concept of “kinds” though, isn’t it?

No, it’s not a problem at all–it’s “one” kind, i.e., bacteria, under many different forms.

CJ O'Brien wrote:

See, your basline assumption is that, in order for there to be evolution, there has to be a “target,” another species, that a given one is evolving “toward.”

But that’s not the case. Organisms change. Lineages diverge.

You make my point: without a target, bacteria just change, and change, and change–and they don’t become gorillas.

Flint wrote:

Meanwhile, Blast seems to be saying “NS either explains ALL we see, or it explains NONE of it. Since it clearly doesn’t explain everything, it is a useless illusion, QED.”

A year ago I was quite comfortable thinking that NS could explain “microevolution.” I’m no longer comfortable with that explanation. I’m just more aware–not in any small part from this blog–of experiments and such which call into question NS’s role altogether.

Regarding “all knowing” science: it is one thing to say that science will be able to answer questions that before seemed unanswerable. It’s quite another to think that science has all the answers. You seemed to be taking that latter position; but, from what you just wrote, I think your position is more balanced. But let’s point out a thing or two: can science “explain” why gravity exists? Science knows that it does exist. It can explain how it works. It can predict what it might do. But whence gravity? In a billion years, will science be able to determine whence gravity? Even if gravity is broken down into something more elementary, whence those elemental entities?

Electrons and protons have equal but opposite charges. Those charges are unchanging. Why do they not change? Why is their magnitude what it is?

An analogy: Euclidean geometry has certain basic postulates. The rest flows from those postulates. Science can discover what flows from the “postulates”, but it can never explain the postulates in, and of, themselves.

CJ O'Brien wrote:

A single nucleotide change in the right place can in fact make the same difference.

Is this an article of Darwinian faith?

CJ O'Brien wrote:

“NS functioning to maintain…” simply means that alterations to that 80% are not selected for, meaning that a change in the genome at certain loci is almost certainly deletrious. We see the same effect in “higher” organisms and the conservation of early developmental pathways. NS “functions” by differential survival and reproduction. That’s it. It’s always operative where diversity exists that contributes to differential reproductive success. And again you’re locked into “kinds.” There is no “final form.” Lineages diverge. Some are more fecund in a given environment. The descendants of those lineages will come to predominate in that environment. Rinse and repeat.

This is the Canon of Darwinism. It’s a pat answer. But two questions: if an elephant produces only a small number of babies over its long lifetime, then how did it ever evolve when bacteria, that reproduce constantly, still remain bacteria. And in terms of fitness, if a mother with Tay-Sachs disease has seven children, and an Olympian athlete has two, who’s the more fit?

CJ O'Brien wrote:

Bacteria are hugely successful organisms.

You miss my point entirely. You live in a world where bacteria and other life forms exist. But, bacteria lived at a time when it was probably the ONLY life form around. So it was infinitely successful compared to anything else. If you’re argument is that it hasn’t changed because of its success, well, why did it evolve in the first place? If it doesn’t evolve, then no other life forms would be here.

CJ O'Brien wrote:

You lost me. I need a clarification of your objection here.

Dawkins way of getting around the incredible improbability of extant, specific genomic sequences is to say that some particular sequences just happen to be favored by NS. (Of course, if you don’t accept NS, then this argument fails. And hence his argument is ciruclar.) But the fact that bacteria can’t seem to “find” any such preferred sequences (i.e., the 20% keeps changing) implies that no such preference exists. You see, in fact you do need teleology. Bacteria represent an absence of teleology (no final form), which only demonstrates that when “final forms” (stable, specific sequence spaces) are encountered, they weren’t stabilized by chance.

Comment #52205

Posted by Steviepinhead on October 13, 2005 3:47 PM (e)

Good old Blast. Everytime he runs into an obstacle, he ignores it, bounces off, and heads off full tilt for the next obstacle, which he will smack into and ignore. He never actually gets anywhere, of course, but he sure does expend a lot of energy converting momentum into acoustic vibrations.

No one expects bacteria to suddenly mutate–in one micro or macro step, so don’t do your usual dance with those prefixes, please!–into NONbacteria. Anymore than–to use the useful (for almost anyone but Blast, but then we’re not really talking for his benefit) analogy of Berra’s given above–we would expect the carts or chariots of old to suddenly change into elegant 17th Century French carriages or 1954 Corvettes. Or cats to turn into dogs.

What we do expect is what we actually see: 1954 Corvettes becoming 1955 Corvettes. Wild grasses becoming heavier-stalked wild strains becoming–over hundreds and thousands of years–domesticated grains. Bacterial strain A differentiating into strains A1-A8, and then into A1a-g, and then into …

Does Blast really think the first archaic bacteria that started differentiating into eubacteria got there all in one step? Of course not, and somewhere in the cobwebbed attics of his mind, at least a few of his neurons must realize this. But a strain of archaic bacteria became a slightly-more-eubacteria-like strain. And, later, a strain of eubacteria became slightly more yeast-like. Or proto-yeast like, or whatever terminology jogs your jets.

(All without “knowing” where they were headed, or whether they were ever gonna get there, in a contingent universe, can we grok that simple idea, and hold it in mind with these two or three other simple ones, and then also try to juggle with the concept that two or three simple mechanisms interacting and reiterating, can generate highly complex resulting patterns? Or is that too much for the cobwebbed neurons?)

And then one strain of proto-yeast or proto-algae mutated to become a tad more like something that was going to eventually, after many more mutation and selection events, become something more like a multicellular plant or animal.

At this point, though, I always feel like someone shouting very slowly and very futilely at someone who speaks some different language entirely. We of course know, after many earlier replays of these same sorts of conversations with Blast, that no amount of evidence and no amount of explanation or argumentation, will ever drag those few mutinous neurons of his to the forefront of his mind.

Why? Not because the evidence is lacking or because the argumentation is, among reasonable open-minded persons, unconvincing. But because Blast is engaged, within the arena of his own mind, in a process of actively and incessantly suppressing what some few of his neurons, and the grat weight of the outside evidence, are trying to tell him.

And after a period of bafflement, internal struggle, and suppression, back Blast will come, like a windup toy surrounded by blocks he can’t quite fit between, to begin bouncing off them all over again.

The entertainment value of watching this has begun to pall. It would simply be pitiful–and mean to make fun of–if it wasn’t for that element of willful suppression of thought.

Comment #52212

Posted by Flint on October 13, 2005 4:57 PM (e)

Well, once more for grits and shins.

Blast:

No, it’s not a problem at all—it’s “one” kind, i.e., bacteria, under many different forms.

Finally, at very long last, a creationist has defined what a “kind” really IS. It’s a category of convenience for organisms of arbitrary difference! Of course, the bacteria “kind” varies much more than, say, the “mammal kind”. Probably more than the “chordate kind”. I always suspected the definition of “kind” was elastic without limit. If the creationist fantasy ever came true and a dog DID give birth to a cat, no problem. They are both STILL members of the “dat kind”.

without a target, bacteria just change, and change, and change—and they don’t become gorillas.

Except, of course, for the once-bacteria that over a couple billion years DID become gorillas. But we won’t count those. How about those bacteria that became eukaryotic at all? We won’t count those either. This is like arguing that nobody ever leaves Dallas, because those who do aren’t in Dallas anymore, and therefore don’t belong to the population under discussion!

A year ago I was quite comfortable thinking that NS could explain “microevolution.” I’m no longer comfortable with that explanation.

I think you are underscoring what I already wrote. When NS was the ONLY mechanism you knew about, you were willing to concede it minimal scope. But now that you’re aware of other mechanisms, you’ve changed your mind. Kind of like conceding that one might conceivably walk from one spot in Dallas to another, but couldn’t conceivably walk all the way to Fort Worth (macro-walking). But now that you’ve discovered cars and planes and buses, you’ve decided walking won’t even work within the Dallas city limits.

can science “explain” why gravity exists? Science knows that it does exist. It can explain how it works. It can predict what it might do. But whence gravity? In a billion years, will science be able to determine whence gravity?

This is the canonical reductio ad absurdum argument. The universe is what it is, there are fundamental “laws” (perhaps arbitrarily encompassed for analytic convenience). It’s not a failure of science to concede that the “ultimate cause” of these laws appears arbitrary. If, like a child, you keep asking “why” enough times, sooner or later you will reach the point where human investigation is limited to what IS. If you wish to go one step further and say “beyond here lies magic” (or one or more gods, or the supernatural, or whatever you Believe), that’s your privilege.

But not knowing the “ultimate cause” of gravity or the charge on the electron doesn’t prevent us from finding coherent explanations for how life changes over time. This is *almost* your prior argument that since we cannot know everything, we can’t know anything. What’s different is, our inability to know everything only seems to prevent us from knowing anything that conflicts with your faith. You’re perfectly comfortable with explanations much less obvious, attested by far fewer facts, of far greater ambiguity, with a far higher probability of being all wet, provided your faith is not challenged by them. Hell, engineering itself is the art of being “close enough.” Which often isn’t very, if it doesn’t need to be.

if an elephant produces only a small number of babies over its long lifetime, then how did it ever evolve when bacteria, that reproduce constantly, still remain bacteria.

Already answered, though I doubt you’ll like the answer. Those bacteria that still remain bacteria, are still bacteria. You have chosen to pretend that those that evolved AWAY from being bacteria even exist. This is a creationist misconception so hoary even AiG discourages its use: If eukaryotes evolved from bacteria, why are there still bacteria! As though you think this makes sense.

in terms of fitness, if a mother with Tay-Sachs disease has seven children, and an Olympian athlete has two, who’s the more fit?

This objection is perhaps even older than the last canard. Evolution by natural selection is a statistical phenomenon. We’re talking about tiny differences in survival rates. Nobody has ever made the argument (except dummies making strawmen) that ALL the “fittest” offspring survive, and ALL the rejects never breed. It’s an elementary statistical exercise (Dawkins goes through it once again in The Ancestor’s Tale) to calculate how many generations it takes for a beneficial mutation to spread through a population given a 1% improvement in the probability of breeding. The answer is always the same: not too damn many.

(Of course, if you don’t accept NS, then this argument fails. And hence his argument is ciruclar

How foolish. 2+2 is still 4, nothing circular about it, EVEN IF you reject this sum because you don’t like it or your faith opposes it.

But the fact that bacteria can’t seem to “find” any such preferred sequences (i.e., the 20% keeps changing) implies that no such preference exists. You see, in fact you do need teleology.

And once more for the world! The bacteria that are still bacteria, are still bacteria. Those that were once bacteria but are no more would flat refute this repeated blind spot, which is probably why you simply refuse to credit this process. Nobody has EVER left Dallas, because 100% of the people in Dallas right now are STILL THERE! Absolute proof, according to Blast.

Blind spot indeed.

Comment #52213

Posted by Tara Smith on October 13, 2005 5:07 PM (e)

Tara Smith wrote:

‘Course, then at least YECs retreat to “but they’re still bacteria!,” so apparently all bacteria are of one “kind” despite the extreme diversity at the DNA level, while humans and chimps, despite near 100% DNA identity, are obviously different “kinds.”

Blast wrote:

And yet, here we have whole “genes” (1,000 nucleotides on average) being swapped, taken into an organism, and it’s still a BACTERIUM!

*slaps forehead*

I’ve had meetings all day and have another one to get to in an hour, but thanks to everyone else for dealing with Blast’s, um, “challenges.”

Comment #52215

Posted by Henry J on October 13, 2005 5:15 PM (e)

What if we define “kind” to mean all the descendants from a distinct abiogenesis event?

(Should I say “abiogenesis” or just “biogenesis” in that question?)

Henry

Comment #52217

Posted by CJ O'Brien on October 13, 2005 5:24 PM (e)

I said: “A single nucleotide change in the right place can in fact make the same difference.” Where the “difference” is “the same” as Blast’s “PATTERNED sequence of 1,000 nucleotides.”
And Blast replied, “Is this an article of Darwinian faith?”

No. It’s a simple ramification of a discrete, combinatorial system. Single “letter” substitutions, additions or deletions can have disproportionate effects at crucial points, changing the entire “sense” of a gene. Take a toy example where you have a repetitive sequence, like …ACGACGACGACG… Now, at random, throw a T in there: …ACGATCGACGACG… Do you see how that has an effect beyond the single addition? Every triplet down the line from the T has changed, potentially causing that stretch of the genome to code for a different protein, all with one little “letter.”

But two questions: if an elephant produces only a small number of babies over its long lifetime, then how did it ever evolve when bacteria, that reproduce constantly, still remain bacteria. And in terms of fitness, if a mother with Tay-Sachs disease has seven children, and an Olympian athlete has two, who’s the more fit?

Blast, you know what “fitness” means, right? It’s an average over a population. It is understood that individual instances may not conform to the average (i.e. sometimes a perfectly “fit” animal gets killed in a freak rockslide or something, and sometimes a pathetic weakling gets lucky). But, over many individuals and many generations, the old bell-curve will out. And that’s the driver of the whole shebang. Call it a “pat” answer if it makes you feel better thinking of me as a Darwinbot or something, but it’s the right answer, and repeated enough times to people who obstinately refuse to see what’s before their eyes, it starts to sound pretty “pat.” See, it’s really easy to defend the truth. No rhetorical backflips required.

Comment #52230

Posted by BlastfromthePast on October 13, 2005 7:15 PM (e)

I must say, you guys are very entertaining; all wet,…..but very entertaining.

Tara wrote:

*slaps forehead*

I’ve had meetings all day and have another one to get to in an hour, but thanks to everyone else for dealing with Blast’s, um, “challenges.”

Don’t hurt yourself!

But I think you missed my point: neo-Darwinism insists that single-nucleotide mutations can eventually bring about macroevolution. Yet, a whole gene is imported, and a simple system–a single cell–doesn’t change phenotypically. So, then, what’s the hope of a single-nucleotide mutation doing this?

CJ O'Brien wrote:

Blast, you know what “fitness” means, right? It’s an average over a population.

It is if you want it to be. But Darwin didn’t know about population genetics, and his was the “survival of the fittest.” So, obviously, fitness also applies to individuals.

Flint wrote:

Except, of course, for the once-bacteria that over a couple billion years DID become gorillas. But we won’t count those. How about those bacteria that became eukaryotic at all? We won’t count those either. This is like arguing that nobody ever leaves Dallas, because those who do aren’t in Dallas anymore, and therefore don’t belong to the population under discussion!

We know that eukaryotes and gorillas exist, and that bacteria exist. What we don’t know is that RM+NS brought this about. To take the fact that all these exist as proof of RM+NS is simply to beg the question. It’s arguing in a circle: How did eukaryotes and gorillas come about from bacteria? By RM+NS. How do we know that RM+NS really works? Because bacteria became eukaryotes and gorillas. No one (except YEC’s) disputes that evolution occurred. It’s the mechanism of the evolution that is in dispute.

Flint wrote:

Evolution by natural selection is a statistical phenomenon.

ID is a statistical argument refuting neo-Darwinism.

Flint wrote:

And once more for the world! The bacteria that are still bacteria, are still bacteria. Those that were once bacteria but are no more would flat refute this repeated blind spot, which is probably why you simply refuse to credit this process. Nobody has EVER left Dallas, because 100% of the people in Dallas right now are STILL THERE! Absolute proof, according to Blast.

You’re missing my argument. If you think of the 20% of the genomes of this “species” of bacteria as tumblers, randomly tumbling from A to G to T to C, at each position, then you have an unimaginably large probability space. Dawkins effectively argues that this isn’t possible, and that it isn’t possible because preferences exist throughout this space, preferences–along the lines of your favorite analogy–allow organisms to “get out of Dodge.” This finding about this type bacteria challenges Dawkins views–and his arguments about such space.

Comment #52234

Posted by Flint on October 13, 2005 8:15 PM (e)

Blast:

You are most amazingly hard of listening.

Darwin didn’t know about population genetics, and his was the “survival of the fittest.” So, obviously, fitness also applies to individuals.

How is Darwin’s knowledge of population genetics relevant? Certainly fitness applies to individuals. But fitness is only one factor influencing reproduction. Plain chance plays a very large role as well. So what? How many times does anyone need to repeat that even a TINY reproductive advantage quickly spreads through a population, before you realize that this truth isn’t going to go away no matter how determinedly you ignore it. As you just did again.

We know that eukaryotes and gorillas exist, and that bacteria exist. What we don’t know is that RM+NS brought this about.

You are playing word games here. In an absolutist sense, we don’t “know” anything. We might have been created 10 seconds ago - we cannot “know” this is not true! Instead, what we have is probably the best-attested, most robust and solid scientific explanation mankind has ever developed. Yes, we’re all aware that if conflicts with your faith, so nothing short of absolute (and hence impossible) knowledge will satisfy you. Which your general approach strongly indicates you’d deny even if it were presented. I pointed out earlier that you are perfectly satisfied with ORDERS OF MAGNITUDE less confidence, where your faith is not challenged. You can pretend you don’t notice this either, but nobody is fooled.

ID is a statistical argument refuting neo-Darwinism.

No, it’s not a statistical argument. It is based on no data, no research, nothing but the Will To Believe. What some ID people do is ASSUME goddidit, dismiss a couple of truly vacuous strawmen, and conclude that their assumption is correct after all. This isn’t a statistical argument except in the desperate imaginations of those unable to admit even to themselves that maybe reality matters. Your claim here is flat dishonest. Your other arguments risk not being taken seriously when some of your arguments are outright lies. ID in its pure form simply says “My faith says my particular god did stuff science explains differently. Therefore science is wrong.” Everything else is just window dressing.

Dawkins effectively argues that this isn’t possible, and that it isn’t possible because preferences exist throughout this space, preferences—along the lines of your favorite analogy—allow organisms to “get out of Dodge.” This finding about this type bacteria challenges Dawkins views—and his arguments about such space.

No, you are once again determinedly ignoring the point that everyone else has made in every way they can think of to communicate it to you. The process you describe produces WILDLY DIFFERENT organisms. Indeed, the prokaryotic “Dodge” is being left wholesale, creating endless new Dodges, which in turn are left wholesale.

To pretend you can’t see this, you keep saying “but they are still bacteria”. But the category bacteria is mucking HUGE. FAR larger in DNA space than the entire animal kingdom. As I wrote earlier, you tried to duck this question by lumping the entire universe of bacteria together as being a single “kind”. But if this is true, there are really only two “kinds” of life: those of one cell, and those of more than one. Otherwise, you are simply selecting an arbitrary category you make up to suit your needs, that serves no purpose OTHER than to defend you against the facts.

Just where do you draw the boundaries of Dodge, then? At two cells? At some aspect of the description of any given cell? How do you categorize the archaea?

Comment #52235

Posted by Russell on October 13, 2005 8:17 PM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #52236

Posted by Russell on October 13, 2005 8:20 PM (e)

(oops.)

neo-Darwinism insists that single-nucleotide mutations can eventually bring about macroevolution

Where did you get that idea?

Comment #52242

Posted by RBH on October 13, 2005 9:06 PM (e)

Russell beat me to it. Where on earth did Blast get that notion? It belies any tenuous claim he might have had that he knows something about the theory he criticizes. But as Casey Luskin and his leaders teach us, that’s not a necessary qualification to shoot off one’s mouth about evolution.

RBH

Comment #52245

Posted by 'Rev Dr' Lenny Flank on October 13, 2005 9:14 PM (e)

No, it’s not a problem at all—it’s “one” kind, i.e., bacteria, under many different forms.

How do you know?

And why, then, isn’t ALL LIFE one “kind” — i.e., under many different forms?

And anyway, why areyou bringing up all this creationist “kinds” crapola, Blast —– I thought ID and creationism were supposed to be like oil and water.

Or are IDers just lying to us when they claim that?

Are you aware that “evolution only within kinds” is one of the defining charatceristics given for creation “science”? Are you telling us now that ID and creationism are, after all, the same thing?

No *WONDER* none of your fellow IDers ever comes to your defense, Blast. I’m sure they all cringe every time you post anything. But at least you haven’t (yet) reached the level of Appleton and Jabriol, who still remain the only creationists I’ve ever seen who OTHER CREATIONISTS told to shut up because they made creationism look bad.

Something for you to aspire to, Blast.

Comment #52260

Posted by Norman Doering on October 14, 2005 1:08 AM (e)

Where in Genesis does it say God made bacterial kind? Genesis only talks about two groups (two kingdoms), plants and animals.

Where do you draw the line between bacterial kind and some other kind that’s not bacterial? What makes this “kind” a kind distinct from another kind?

Comment #52268

Posted by Russell on October 14, 2005 7:18 AM (e)

Ever wonder where the moniker “BlastFromThePast” might come from? My current hypothesis: It’s Dave Cerutti (sp?) again, reliving the fun he had with “Admonitus”.

OK, Dave. “Blast” has run his course. We’ve got to that Phil Hendrie moment where the fake assertions can’t get any more absurd, and the audience either gets the joke, or it doesn’t.

Comment #52279

Posted by rdog29 on October 14, 2005 11:36 AM (e)

Just picked up on this thread, and in my haste to post a comment perhaps I’ve missed where this has been addressed….

Anyway, going back to Blast’s original post:

The degree of genetic diversity is a problem for evolutionary theory how???

Did evolutionary theory ever claim to place an upper limit on the amount of diversity? Or does ID, um, “Theory” make a prediction as to how much diversity should be present? And if so, does it provide a better explanation of the phenonenon than does evolutionary theory?

Did it ever occur to you that the amount of diversity observed may be a consequence of the local variation in selective pressures operating at any given time? I guess not - BAM! It’s instantly evidence for design, right?

It’s obvious, Blast, that you didn’t learn much in your school days, that is, if you indeed hold the degrees you claim. Possession of impressive-sounding credentials does not necesarily make for good thinking. Look at Duane Gish, my personal favorite poster child for Well-Credentialed Nincompoop.

As for the snideness of the comments, I (we) make no apologies. You are a moron and you deserve them.

Comment #52283

Posted by rdog29 on October 14, 2005 11:42 AM (e)

Oh, and by the way, Blast:

Just how the hell do you define a “kind”?

What is the metric for deciding how far apart, genetically, two organisms must be before they are considered different “kinds”???

Or don’t you bother with such a “pathetic level” of detail?

Comment #52285

Posted by Steviepinhead on October 14, 2005 11:56 AM (e)

Spin this one, Blast:

http://www.msnbc.msn.com/id/9686843/
Reuters 10/23/2005:
Mysterious microbe retrofits itself with plant
One-celled organisms capture algae, perhaps taking evolutionary leap

Fondly, SP.

Comment #52290

Posted by Steviepinhead on October 14, 2005 12:09 PM (e)

Oh, and a side note to Michael Behe, this new little beasty is–guess what!– a flagellate! In fact, both the new bacteria and its algal symbiote are flagellates, and when one engulfs the other, the latter loses its marvelous little tail. How very odd!

Yes, this indeed appears to be your very, very most favorite “unevolvable” biological mechanism, captured in the midst of, um, evolving.

Of course, Mr. Behe, I’m sure the well-funded DI will now divert a little of its cashflow from PR and lawsuits, and will send you off pronto to do some actual scientific research into this interesting new development. Right?

Do keep us here at Panda’s Thumb posted on the progress of the funding and outfitting of your research expedition (heck, I’m sure you wouold have already told us about this yourself, but you’re probably too busy getting geared up–hey, we understand, this must be a pretty exciting moment for you!).

Comment #52291

Posted by Steviepinhead on October 14, 2005 12:20 PM (e)

Of course, Blast, we here at PT realize that this newly-discovered bacteria–strange and novel as it seems at first glance–is still just one of that large and varied, but basically unitary, bacterial “kind”. I mean, we certainly realize that, struggle as they might to evolve into something different and novel, bacteria are destined forever to remain just bacteria….However much this particular bacteria may enjoy giving its impression of simultaneously being a member of the, um, algal “kind”.

But, what the heck, algae, bacteria, they’re probably all members of that well-known super-“kind”: bALGteria. Or is it bactALGAEia?

Well, anyway, I’m sure you know the kind I’m talking about.

Comment #52298

Posted by Norman Doering on October 14, 2005 1:26 PM (e)

Steviepinhead wrote: “Spin this one, Blast:…One-celled organisms capture algae, perhaps taking evolutionary leap.”

If there ever is a new theory that accounts for the diversity of life and replaces Darwinism it won’t be called “Intelligent Design,” it will be called Margulism, after Lynn Margulis.

Figure out what that means, Blast - if you haven’t run off.

Comment #52307

Posted by geogeek on October 14, 2005 3:53 PM (e)

Mysterious microbe retrofits itself with plant
One-celled organisms capture algae, perhaps taking evolutionary leap

Oh my god, that’s so cool. I dig the microphotographs.

I must admit that, as a geologist/mostly geochemist/hard rock type, my biology is pretty basic, but I did take a biological oceanography class in grad school. We got one class period on whales and fish. I was shocked – shocked! – to find out that 90% of the class was about little planktons and bacteria because most of the biology in the oceans is about the tiny guys (not just eubacteria and archea but also the eukaryotic phytoplankton, and, well, we do have to count in the multicellular zooplankton). I recall getting very confused about how biologists can divide bacteria into species at all once I learned that they “share” genetic information back and forth within generations, i.e. that a bacterium could change its genome by snugging up to another bacterium and swapping some DNA. The new genome, then, is not the result of mutation but is passed to future generations. Am I recalling this correctly? Does this make the definition of species sort of irrelevant for bacteria?

I was also really horrified to find out that viruses leave their disgusting DNA in other people’s cells (people being used in the sense of “kind”, i.e. an arbitrarily sized grouping of organisms, in this case all cellular life).

Hanging around with biological oceanography types I have also over-heard them say things like “We’ve found more unknown bacteria in the last five years than all known marine bacteria, and we have no idea what they’re doing out there.” If I recall correctly, this is because hunting the wily bacterium is truly hit-and-miss as far as reproducing populations. Instead what they do is pull up a jug of water and look at all the DNA. Huge numbers of DNA sequences are recognizable as belonging to bacteria, but not known bacteria, and are sufficiently different from one another to be considered different species. Any general comments from the biologists?

Comment #52321

Posted by BlastfromthePast on October 14, 2005 8:34 PM (e)

Norman Doerring wrote:

If there ever is a new theory that accounts for the diversity of life and replaces Darwinism it won’t be called “Intelligent Design,” it will be called Margulism, after Lynn Margulis.

Norman, would you like to read my copy of Acquired Genomes?

In fact, the kind of scenarios that Margulis talks about are fully consistent with ID. It will be interesting to see how wide-spread a phenomena symbiosis is. Remember, ID doesn’t say evolution didn’t happen; it says that Darwin didn’t get it right.

Comment #52322

Posted by 'Rev Dr' Lenny Flank on October 14, 2005 8:50 PM (e)

Norman, would you like to read my copy of Acquired Genomes?

He’d probably prefer that YOU read it, junior, and then have an educated person explain it all to you.

Or do *I* have to teach you more basic biology, after I’ve already taught you such things that you never heard of as Waddington, Baldwin, Pakicetus and Caudipteryx.

I charge $50/hour for science tutoring, Blast. You’ll get my bill.

Of course, you could always continue to get your, uh, “science” information from websites run by “ecological visionaries”. (snicker) (giggle)

In fact, the kind of scenarios that Margulis talks about are fully consistent with ID.

Of *course* they are. *EVERYTHING* is fully consistent with ID. That’s mostly because ID doesn’t, well, actually *SAY* anything. (shrug)

ID doesn’t say evolution didn’t happen; it says that Darwin didn’t get it right.

Duuuhhhhhhhhhh. We already KNEW that Darwin didn’t get it right. After all, Darwin didn’t even know what a “gene” is.

In case you didn’t notice, Blast, Darwin is … well … dead. Has been. For an awfully long time now.

Also, in case you didn’t notice, science has advanced a wee bit in the 100-plus years since Darwin’s death.

Do try and keep up, would you? (sigh)

Comment #52324

Posted by Timothy Chase on October 14, 2005 9:50 PM (e)

Lenny – I should have guessed! This really is one of your favorite haunts, isn’t it?

Comment #52326

Posted by Timothy Chase on October 14, 2005 10:01 PM (e)

Norman wrote:

If there ever is a new theory that accounts for the diversity of life and replaces Darwinism it won’t be called “Intelligent Design,” it will be called Margulism, after Lynn Margulis.

Figure out what that means, Blast - if you haven’t run off.

No, Norman. It will be called just what it is called today – the science of evolutionary biology. No individual is equal to everything which has been contributed, whether in terms of various Lamarckian mechanisms, lateral gene transfer, endosymbiosis, our understanding of the roles of retroelements, regulatory DNA, polyploidy, punctuated equilibria, etc.. Are you beginning to get the picture? Or should I use smaller words?

Comment #52327

Posted by Timothy Chase on October 14, 2005 10:05 PM (e)

Woops! Sorry. Misunderstood the conversation. Many apologies, Norman!

Comment #52328

Posted by Timothy Chase on October 14, 2005 10:07 PM (e)

I guess that is what I get for coming-in in the middle.

Comment #52332

Posted by Norman Doering on October 15, 2005 2:35 AM (e)

Timothy Chase wrote: “It will be called just what it is called today — the science of evolutionary biology.”

Of course, I didn’t replace that term – I said Margulism would replace Darwinism. Mostly because Lynn Margulis might deserve an equal place of honor.

Question for all of you – Is Darwin’s “Origin of Species” even worth reading these days as a biology text (granting its an important historical text). Darwin was arguing without a lot of the information we now have and we can all point to more evidence that Darwin ever had. Don’t we have better books now?

How far has the modern synthesis moved away from Darwin?

Comment #52334

Posted by 'Rev Dr' Lenny Flank on October 15, 2005 6:57 AM (e)

Lenny — I should have guessed! This really is one of your favorite haunts, isn’t it?

I enjoy de-balling ID/creationists, wherever they are. :>