Mike Dunford posted Entry 3195 on June 17, 2007 11:03 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/3184

So-called “junk DNA” has been much the buzz lately. A recent (and outstandingly lousy) Wired magazine article on the topic uncritically printed assertions by the Discovery Institute’s lead hack Stephen Meyer that the discovery that some regions of DNA once thought to be functionless do have functions is, “a confirmation of a natural empirical prediction or expectation of the theory of intelligent design, and it disconfirms the neo-Darwinian hypothesis,” The author of the Wired article does not provide us with any explanation of how ID “theory” made that prediction, but a more recent article at the Discovery Institute’s Media Complaints Division does.

The basis for this astounding prediction (yes, I am using “astounding” sarcastically) is actually pretty simple, as Casey Luskin explains. “[D]esign theorists,” he tells us, “recognize that ‘Intelligent agents typically create functional things.’” That’s right. We can predict that noncoding DNA has some sort of function for the animal because we know that designers usually design functional things. If you have paid any sort of attention to what Intelligent Design proponents have said over the years, I should probably apologize to your next of kin, because there’s a pretty good chance that your head just exploded.

For the survivors, here’s why the sheer chutzpah of Casey’s assertion is enough to cause neurological overload.

Read more (at The Questionable Authority):

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Comment #183678

Posted by realpc on June 18, 2007 6:08 PM (e)

Darwinists like to point out examples of what they consider bad design in organisms, because it supports the no-design hypothesis.

Calling something “junk” because it is not understood is typical of materialist science.

If there is some kind of universal intelligence, on the other hand, we would not expect organisms to be full of useless junk.

So that is, obviously, why ID advocates predict useful and elegant designs, and why Darwinists predict haphazard and wasteful designs.

Comment #183685

Posted by PvM on June 18, 2007 7:01 PM (e)

Calling something Junk is a valid null hypothesis, calling it Design is typical of the ID non-science.

Your ‘prediction’ is meaningless as it lacks in any foundation of logic, let alone empirical data.

Comment #183686

Posted by Sir_Toejam on June 18, 2007 7:12 PM (e)

Has realpc EVER said anything not intended as bait?

seriously, why is it that PT contributors can’t figure out how to trashcan repeat trolls?

Comment #183694

Posted by AR on June 18, 2007 9:14 PM (e)

Re: Comment 183678 by the certified troll “realpc”:

If there is some kind of universal intelligence, on the other hand, we would not expect organisms to be full of useless junk.

This would be true if we knew what the “universal intelligence”, whatever this means, intended to do. What if that mysterious intelligence wanted to create a lot of useless junk for his (her, its) own unfathomable reasons? Since ID advocates refuse even speculate on the attributes and behavior of the “Creator,” they cannot make any real predictions whatsoever but always can pretend to have predicted everything and anything. They can always do so because their imaginary creator can supposedly to do anything and everything at whim.

Comment #183696

Posted by David Stanton on June 18, 2007 9:33 PM (e)

AR,

You are absolutely correct. However, if you want to claim that any intelligent designer had anything to do with designing any eukaryotic genomes, I guess you would have to at least attempt to explain the motivation for the following types of genetic elements:

SINES
LINES
Pseudogenes
Trinucleotide repeats in coding regions

Whenever ID proponents try to make postdictions, they still usually fail to learn the relevant science, so they usually still get it wrong.

Comment #183697

Posted by Henry J on June 18, 2007 10:42 PM (e)

Re “seriously, why is it that PT contributors can’t figure out how to trashcan repeat trolls?”

Cause they just evolve a new logon id when the old one stops working?

Henry

Comment #183706

Posted by Popper's ghost on June 19, 2007 1:55 AM (e)

Darwinists

Funny how you can tell from his very first word that realpc did not read, and is not responding to, Mike’s post at TQA.

Comment #183707

Posted by Popper's ghost on June 19, 2007 1:58 AM (e)

Cause they just evolve a new logon id when the old one stops working?

That’s no more responsive to what STJ wrote than realpc’s drivel is to what Dunford wrote.

Comment #183725

Posted by demallien on June 19, 2007 6:20 AM (e)

Actually PG, Henry has a point. If you stop responding to a known troll, because they’re a known troll, said troll will just change names and start again. In other words, Henry’s comment is a valid response to Sir TJ.

Comment #183726

Posted by demallien on June 19, 2007 6:20 AM (e)

Actually PG, Henry has a point. If you stop responding to a known troll, because they’re a known troll, said troll will just change names and start again. In other words, Henry’s comment is a valid response to Sir TJ.

Comment #183742

Posted by pwe on June 19, 2007 8:37 AM (e)

From the Wired article:

Catherine Shaffer/Wired wrote:

That’s why T. Ryan Gregory, an assistant professor in biology at the University of Guelph, believes that nonfunctional should be the default assumption. “Function at the organism level is something that requires evidence,” he said.

Sounds as a good idea. It’s junk, unless you can prove otherwise. Of course, since it’s in there, it serves some function, even if it only being there. But that a certain string of DNA has a particular function cannot be the à priori assumption.

Oh, yes, and the article isn’t too good – rather confusing.

- pwe

Comment #183770

Posted by Sir_Toejam on June 19, 2007 12:59 PM (e)

…and grady is just the Kansas curmudgeon yet again.

as to what henry said…

there’s this little thing called an IP address.

everybody has one.

even trolls.

I rather think that PT contibutors need a meeting to review posting policies and make a final decision about what to do with trolls, and follow through on that.

It’s not like people who violate posting rules have not been banned before.

Comment #183771

Posted by Sir_Toejam on June 19, 2007 1:01 PM (e)

man, it’s like people considering the “function” of DNA have never read The Selfish Gene.

Comment #183786

Posted by harold on June 19, 2007 2:40 PM (e)

realpc wrote -

Actually, let me begin by saying that, although I think it’s like shooting fish in a barrel, yes, it is instructive to show how wrong creationist posts are. It helps lurkers, especially those who may not be fully up to speed on the issue yet, to deal with similar types in their daily life.

Obviously, everybody has the right to reply or not, as they see fit, but I feel no special inhibition from shredding creationist nonsense.

Darwinists like to point out examples of what they consider bad design in organisms, because it supports the no-design hypothesis.

It supports that the particular feature under examination was not designed by a magical entity with human standards of what constitutes “good” or “bad” design, but that’s not why scientists point it out. They point it out because it’s what reality shows.

Note the use of the biased terminology “Darwinist”.

Calling something “junk” because it is not understood is typical of materialist science.

This is the exact opposite of the truth. First of all, science is characterized by admission of the existence of things that are not yet known; it is typically fundamentalist ideologies that insist that they can explain everything.

Second of all, it’s trivially obvious that the term “junk” is relatively seldom used in science, even though a great deal is unknown.

Note the use of the biased terminology “materialist”.

If there is some kind of universal intelligence, on the other hand, we would not expect organisms to be full of useless junk.

It is true that any biological feature that is less than perfectly functional more or less disproves the idea that it was magically created by a carefully planning “designer” with human standards of what is “useful” or “useless”. Thus, ID advocates realize that non-coding DNA alone explodes their agenda-driven drivel. (That’s true even if it has some low level of poorly regulated transcription, or if some or all of it serves some sequence-independent redundant function. I’m sure real scientists will discover more and more about DNA which is not part of the primary genome, but that won’t take away the problem for creationism.)

Technically, many might believe that there could still be a “universal intelligence” that either doesn’t magically squirt DNA into nuclei, or doesn’t share human standards, or has both of these characteristics. That, however, is not a scientific issue.

So that is, obviously, why ID advocates predict useful and elegant designs, and why Darwinists predict haphazard and wasteful designs.

Nonsense again. Scientists would equally expect many “useful and elegant” systems to result from the evolution of life. Of course, the terms above are purely subjective, but still, it’s not fair to say that scientists would describe biological systems as “haphazard and wasteful”

It is true that “ID advocates” are disproved whenever something that appears imperfect or puzzling to them, but can be explained by evolution, is observed.

It certainly does not follow that the theory of evolution suffers when systems are found to be elegant and efficient. The theory of evolution predicts that many such systems will be found.

It’s entertaining that ID/creationists always assume that if they can somehow “disprove evolution” their sectarian ideology will win by default, even though this would make no sense even if they could “diprove evolution”.

And of course, non-coding DNA does not, in itself, “prove evolution”, merely because it explodes ID/creationism. It’s just one more piece of evidence that supports the theory of evolution.

Comment #183791

Posted by Andrea Bottaro on June 19, 2007 3:19 PM (e)

With reference to trolls, just to be clear: we enjoy them just as little as everyone else. Those who also violate any PT rule and can be banned based on i.p. address, are. Some however post from dynamic i.p. addresses that cannot be banned without inconveniencing legitimate commenters. In those cases, we just move the nonsense comments to the Bathroom Wall, or delete them if appropriate.

Until we can get around doing so (and sometimes it may take a while), the best thing to do for everyone else is to just ignore the fools.

Comment #183806

Posted by realpc on June 19, 2007 6:00 PM (e)

I am not a creationist or a Christian. I am a skeptic. I believe the universe is made of information, not “matter,” and that it naturally evolves towards greater complexity.

Materialist science cannot explain the origin of new species, and it certainly can’t explain the origin of life. Neo-Darwinism is a weak theory, unsupported by evidence. It can explain adaptation in existing species, but not the development of new and more complex features.

When you insist that neo-Darwinism is adequate to explain the origin of new and more complex species, you are relying on materialist faith, not evidence or logic.

Christian creationism is not part of this debate. We are not debating whether life evolved or how long it took. We are not debating whether God looks like an old man or whether he wrote the bible. We are debating whether or not the universe is made out of information, intelligence, meaning. We are asking who is smarter, nature or ourselves.

It makes a big difference in how we think and live. If nature is mindless and evolution occurs by chance (yes, and natural selection), then we will respect and trust it less. If we see nature as an expression of infinite intelligence, far more complex than anything we can comprehend, we will be more ready to learn from it.

Materialist science has had some great successes and there is no reason to throw it away. But there is also no reason for not venturing beyond it.

Comment #183807

Posted by CJO on June 19, 2007 6:20 PM (e)

If nature is mindless and evolution occurs by chance (yes, and natural selection), then we will respect and trust it less. If we see nature as an expression of infinite intelligence, far more complex than anything we can comprehend, we will be more ready to learn from it.

The first sentence is bald assertion, nothing more. Care to back it up? (not sure whom I’m kidding)

The second is patently self-contradictory: If we (without rationale) decide the universe is “far more complex than anything we can comprehend” why would we think we could learn anything from it?

Comment #183808

Posted by David Stanton on June 19, 2007 6:30 PM (e)

I see realpc has tried to derail yet another thread. For those of you who are not familiar with his brand of argument, he uses the MSU method (making stuff up). Here is a list of some of the claims he has made on various threads. Of course he has presented absolutely no evidence for any of these claims and he has repeatedly failed to acknowledge any evidence to the contrary. Feel free to add to the list if I have missed anything.

(1) The “Law of Complexity” states that some things complexify themselves at some times by some unknown mechanism for some unknown reason.

(2) The “Theory of Creative Evolution” states that some things get better and better for some reason, or something like that.

(3) The “intelligence” of your body means that you can somehow create beneficial mutations whenever you need them and that this process is entirely “natural” even though there is no known mechanism by which it could occur.

(4) DNA does not “know” enough to “orchestrate” the process of development (and so apparently we don’t have any idea how it could possibly work).

(5) Development violates the laws of physics (not the known laws of physics just the unknown ones).

(6) “Natural” means understood by science (presumably anything not yet understood is not natural). I know, this directly contradicts number three, but I’m not the one making this stuff up.

(7) “Complexity” cannot be determined unless we know the purpose and function of something (apparently the complexity changes if the perceived purpose changes).

(8) We all exist in a shared virtual reality and the real reality is outside the matrix. (Wait I saw that movie, he might be right about this one. Anyway, I guess no one can prove him wrong).

(9) Humans are “newer” than dogs. (Even though Canis familiaris arose in Asia about 15,000 years ago). See Science 298:1610-1613 (2002) for example.

(10) AIDS is not caused by HIV.

Of course you are free to respond to realPC, after all no one can stop you. I would suggest that you at least try to keep him/her/it on topic, since threads seem to deteriorate rather quickly when he/she/it comes around. For example, the topic of this thread was supposed to be junk DNA. Could this be deduced from the last post made by realPC?

I don’t plan on responding to any of the baiting from realPC. He has a right to his opinions, but why should anyone else care? I would love to introduce realPC to ERV, but I already have too much respect for ERV to do that. Oh well, maybe they will meet some day. We can only hope.

Comment #183812

Posted by realpc on June 19, 2007 6:54 PM (e)

“If we (without rationale) decide the universe is “far more complex than anything we can comprehend” why would we think we could learn anything from it?”

Well just think about it. If something is so complex we can’t ever understand it completely, does that mean we can never understand it at all?

If someone is smarter than you are, does that mean you cannot learn anything from them? If nature is smarter than we are, does it follow we cannot learn anything from it?

Comment #183814

Posted by George Cauldron on June 19, 2007 8:57 PM (e)

Well just think about it. If something is so complex we can’t ever understand it completely, does that mean we can never understand it at all?

If someone is smarter than you are, does that mean you cannot learn anything from them? If nature is smarter than we are, does it follow we cannot learn anything from it?

Have you ever looked at your hands? I mean really looked at them?

What would chairs look like if knees bent backwards?

Comment #183815

Posted by qetzal on June 19, 2007 8:58 PM (e)

pwe wrote:

It’s junk, unless you can prove otherwise. Of course, since it’s in there, it serves some function, even if it only being there. But that a certain string of DNA has a particular function cannot be the à priori assumption.

We shouldn’t assume a sequence with no proven function is junk. That’s as unsupportable as assuming that every sequence does have a function. (Of course, if you have data to support that a sequence really is ‘junk’, that’s a different story.)

Also, I don’t think simple existence is really a function.

Comment #183816

Posted by Science Avenger on June 19, 2007 9:04 PM (e)

It’s possible I have the wrong troll, but isn’t he a fan of the invisible, unexplained, unevidenced genetic barrier which holds all evolution to the micro level, thus not allowing speciation?

Comment #183817

Posted by Science Avenger on June 19, 2007 9:08 PM (e)

We are asking who is smarter, nature or ourselves.

We wants it, yessssss, we do, precious.

Comment #183821

Posted by Popper's ghost on June 19, 2007 9:53 PM (e)

Actually PG, Henry has a point. If you stop responding to a known troll, because they’re a known troll, said troll will just change names and start again.

Do you have any idea what “non-responsive” means? It doesn’t mean that the statement was false, but that it was a non-sequitur. The question was “why is it that PT contributors can’t figure out how to trashcan repeat trolls?” The response about trolls changing their names is idiotic, because we’re talking about realpc here, and “realpc” isn’t some new name that no one has seen before. Sheesh.

Comment #183822

Posted by Popper's ghost on June 19, 2007 10:04 PM (e)

If you stop responding to a known troll, because they’re a known troll, said troll will just change names and start again.

Also, what you wrote is incredibly foolish on two other counts. One is that STJ referred to “trashcan”ning trolls, not merely shunning them. And if we were talking about shunning, what you’re saying in essence is that it’s useless to shun a troll because they’ll just change their name and you won’t recognize them as the same troll. One would have to be quite a fool not to grasp that that is not an argument for engaging trolls. So what is it an argument for? Well, nothing at all, it’s just a pointless observation that no action is perfect in its results – a rather pathetic approach to the world.

Comment #183830

Posted by Popper's ghost on June 19, 2007 10:17 PM (e)

Of course, since it’s in there, it serves some function, even if it only being there.

That’s rather raw teleology. “serves some function” is equivalent to “serves some purpose”, but there are no purposes for unplanned processes or entities. “function” must be viewed strictly operationally, in terms of what effect something has, but just “being there” is not an effect.

It’s junk, unless you can prove otherwise.

That’s a textbook example of the fallacy of argumentum ad ignorantiam. The effects, if any, of so-called (unfortunately) “junk” DNA are not negated by our failure to prove their existence.

Comment #183832

Posted by Popper's ghost on June 19, 2007 10:25 PM (e)

BTW

I am a skeptic. I believe [in fairy tales contradicted by mountains of evidence]

I doubt that we would have any trouble spotting this particular troll regardless of what name it went by.

Comment #183833

Posted by Dave Carlson on June 19, 2007 10:31 PM (e)

…and cue the pissing contest!

Comment #183834

Posted by PvM on June 19, 2007 10:33 PM (e)

That’s a textbook example of the fallacy of argumentum ad ignorantiam. The effects, if any, of so-called (unfortunately) “junk” DNA are not negated by our failure to prove their existence.

Lacking any evidence that it has function, the best assumption is the null hypothesis. Or we may as well accept that design is a better null hypothesis…

Comment #183835

Posted by Dave Carlson on June 19, 2007 10:33 PM (e)

Whoops. Wrong thread. Feel free to delete this and my previous comment

Comment #183837

Posted by Popper's ghost on June 19, 2007 10:45 PM (e)

Surely even you understand that a hypothesis is not an assumption. In any case, his statement went beyond assumption – he asserted that “junk” DNA has no function unless proven otherwise. That, as I said, is a classic, textbook case fallacy of argumentum ad ignorantiam.

Comment #183840

Posted by Sir_Toejam on June 19, 2007 11:01 PM (e)

design is a better null hypothesis…

how does one formulate design as null hypothesis to begin with?

Comment #183849

Posted by demallien on June 20, 2007 12:02 AM (e)

Sir_Toejam wrote:

how does one formulate design as null hypothesis to begin with?

Lol. It is a bit like “what is the sound of one hand clapping”, isn’t it! :-)

Comment #183853

Posted by Sir_Toejam on June 20, 2007 1:12 AM (e)

more like:

what isn’t the sound of one hand clapping.

Comment #183905

Posted by Raging Bee on June 20, 2007 12:59 PM (e)

The title was “Let’s Talk Junk,” and sure enough, RealBlitheringNewAgeyNoncompoop shows up to do just that. Why am I not surprised?

Comment #183908

Posted by Raging Bee on June 20, 2007 1:21 PM (e)

David: Thanks for the realridiculoustroll recap. I’d like to add my own wild guesses as to how he became what he is:

1) He pulled ahead in grade-school in science, and his parents and teachers praised him and kept on telling him how smart he was.

2) He thought to himself “I’m smart, my teachers tell me so; therefore I don’t need to study or do homework anymore.”

3) The rest of his generation pulled ahead of him while he rested on his laurels and thought he was still ahead.

4) He found a bunch of New Agey stuff about how “mianstream science” was incomplete, out of touch with the “human element,” and lacking in…well…something mainstream science couldn’t define exactly, which was why mainstream science was wrong, see, because it was heartless and inhuman and only dealt with things it could quantify.

5) It sounded sensible to him, and appealed to his vanity, because it allowed him to pretend he was still smarter than all those other kids who kept on learning science while he was pretending to know everything already. And since he was unusually smart (all his teachers in grade-school told him so, remember), if something sounded sensible to him, then it must be right; no further verification required.

6) Now he’s stuck in his own bubble-verse, where logic can’t be used to separate BS from fact, because logic itself is inhuman and untrustworthy; and he’s still the smartest kid in class, so no one can tell him he was ever wrong about anything.

Comment #183926

Posted by harold on June 20, 2007 4:33 PM (e)

David Stanton -

I was going to comment on how incredibly accurate your summary was.

Raging Bee -

That’s probably a pretty good guess, although I’m not sure about “3)”, in the sense that I’m not sure how well the “rest of his generation” has done overall. Also, his intense inflexibility and expressed disrespect for others (which are what make him a troll, not his new agey philosophy, which, HIV-denial and all, is far less offensive than the pseudo-theocratic brutality which the DI gang not so secretly endorse) suggest that their may be something more than just that going on.

I’ve known several people who fit the profile you give exactly, although last time I saw them they were still drummers in bad rock bands or aspiring actors. None of them were creationists per se.

(But I mainly knew them during the period between the fall of 70’s creationism and its ghoulish resurrection as 1999-2005 “ID”. I went through an entire biology degree thinking that “conservatives” pretended to “favor hard science” and never even knowing that creationism existed, and I was raised in a Baptist church - a liberal one, but still Baptist.)

Comment #183928

Posted by Raging Bee on June 20, 2007 5:04 PM (e)

I’ve known several people who fit the profile you give exactly, although last time I saw them they were still drummers in bad rock bands or aspiring actors.

And has RealBlitheringNewAgeyNoncompoop told us what his current job is? Perhaps one day we’ll see him in some seedy bar, rambling on about the scientists’ conspiracy while his bandmates try to get him back onstage to, like, do his actual job.

Or perhaps one of us has already seen him handing out LaRouchie pamphlets outside a subway station.

Comment #183933

Posted by realpc on June 20, 2007 6:18 PM (e)

All your guesses about me have been wrong. I’m not a drummer I’m a guitarist. No really, I have said it before, I am a software developer. I chose that career because it’s all logic with very little room for politics. The program runs or it doesn’t, no matter what your software ideology may be.

I would like to know how many computer scientists prefer IDE over NDE, relative to biologists. I have a suspicion we are more likely to be bothered by the weaknesses of NDE than you biologists are.

Comment #183934

Posted by David B. Benson on June 20, 2007 6:33 PM (e)

Well, I am a (retired) computer scientist. I am most impressed by the continued advances in

evolutionary algorithms,

which solve real-world problems, and which are designed to mimic biological evolution.

Comment #183935

Posted by Sir_Toejam on June 20, 2007 6:46 PM (e)

I chose that career because it’s all logic with very little room for politics.

BWAHAHAHAHAAHAH!

that is the damn funniest thing you’ve said since you came to PT.

now I don’t believe you’re actually in software development, either.

admit it:

the “real” in your handle is meant as irony, right, troll?

Comment #183943

Posted by harold on June 20, 2007 8:16 PM (e)

I am a software developer

My biology and medicine degrees tell me that computer scientists are completely wrong about programming. Except for David B. Benson.

Okay, for those who didn’t understand it, that was a joke. Creationist posters alway claim to be “computer scientists” or “engineers” (most of them are exaggerating at best) whose training somehow tells them that biologists are all wrong, without knowing anything about biology.

More irony is added by the fact that most biomedical science degrees require some computer science, physics, statistics, and so on, and encourage more, whereas computer science and engineering degrees (let alone associates degrees) don’t require any biology.

Comment #183946

Posted by David B. Benson on June 20, 2007 8:31 PM (e)

harold — Aha! Except at a few universities, such as this one, which require a semester of biology for all students, irrespective of major…

Comment #183947

Posted by Sir_Toejam on June 20, 2007 8:37 PM (e)

the reason I laughed so hard, is that I’ve done both:

advanced degree in zoology, published research in various behavioral ecology related issues.

and have been involved in game development and design, database and web programming and server applications.

one of the lessons I learned quite rapidly was that politics (in the form of personal ego issues) runs rampant in any business, let alone game development and even web programming.

the application of logic was far rarer in private business than I ever found it in academia, that’s for sure.

maybe realpc hasn’t made it past the data entry stage yet?

*snicker*

Comment #183950

Posted by David Stanton on June 20, 2007 9:16 PM (e)

Raging Bee and Harold,

Thanks guys, I appreciate the sentiments. I know I have posted this stuff before, (although I do keep updating), so I hope I am not boring anyone. However, I do think it is important to let people know what kind of logic to expect from realpc without actually responding to any of his metaphysical musings. He is not so bad really, at least compared to some rabid creationists. He will at least look at some scientific literature. However, I get the distinct impression that he is absolutely desperate to prevent any real scientific discussion, especially concerning the real thread topic. I have no idea why, but for evidence just look at what happened to the present thread. Maybe somebody does want to discuss metaphysics with him. I have no objection to that, but why must it be done here? If he doesn’t care about junk DNA, why post on this thread? And why does somebody always respond?

As for junk DNA, no one has chosen to respond to my challenge about SINES, LINES pseudogenes, etc. Maybe I didn’t state my metaphysical assumptions sufficiently clearly.

The human genome project has shown beyond a doubt that the human genome is a veritable wasteland of useless junk that barely manages to function. It has all of the properties that one would expect as a result of over four billion years of random mutation and natural selection. If it was designed by anyone, it was the worst job in the history of the universe. Still, I for one wouldn’t have it any other way.

Comment #183952

Posted by Henry J on June 20, 2007 9:26 PM (e)

Re “I would like to know how many computer scientists prefer IDE over NDE, relative to biologists.”

I’m a software engineer. But if I happen to wonder about something related to biology, I’ll go to a biologist to ask, not another engineer. After all, as you just pointed out (presumably without meaning to), computer scientists aren’t expected to be experts in biological science.

Henry

Comment #183990

Posted by realpc on June 21, 2007 5:49 AM (e)

“if I happen to wonder about something related to biology, I’ll go to a biologist to ask”

And if I have a health question I would ask an MD. And if the answer didn’t make sense to me, I would continue searching for information.

Being a software developer does not qualify me as an expert in biology. It doesn’t mean I am immune to political bias or any other human weakness. The average guy writing software probably doesn’t know, or care, much about biology.

I only mentioned it to correct someone’s wrong impression that I am anti-science and living in my parents’ basement playing drums.

I value logic and the scientific method. People who criticize scientific materialism are not all losers on drugs, which is what one commenter here assumed.

And my interest in evolution theory spans decades. I may be an amateur, but I am not a novice.

Comment #184000

Posted by realpc on June 21, 2007 6:31 AM (e)

“the human genome is a veritable wasteland of useless junk that barely manages to function. It has all of the properties that one would expect as a result of over four billion years of random mutation and natural selection.”

And that is exactly my point. Each time “junk” turns out to have a function, it’s considered a victory for ID.

I don’t think any of it is junk, but we’ll have to wait and see.

In the mean time, why not just say the function is unknown, rather than assume everything you don’t understand is worthless junk?

Comment #184011

Posted by David Stanton on June 21, 2007 8:05 AM (e)

realpc,

Thanks for posting on topic. Now, if you can demonstrate a function for the 200,000 SINES and the 800,000 LINES and the thousands of pseudogenes in the human genome, you will not only score a victory for ID, but you will probably win a Noble prize as well.

By the way, I am perfectly aware that some of them can have some sort of “function” some of the time by chance alone. However, the vast majority have no discernible function and in fact are most often deleterious. I am also aware that some of these elements can occasionally, by random mutation and natural selection, eventually assume some useful function, but of course that does not count as intelligent design. And no, you can’t just claim that RM and NS alone are not sufficient, that ia the point. This is exactly the pattern one would expect to see as the result of these processes, inefficiency, waste and poor “planning”.

Also, don’t try to use any metaphysical argument about the “intelligence of the human body” and how everything was all planned to work out for the best, unless of course you have some evidence this time.

You can’t have it both ways. If “each time junk is found to have a function it is considered a victory for ID” then each time junk is found to have no discernable function is should be considered a victory for RM/NS. If we subscribe to that logic, the score card so far is about 1:1,000,000. So, once again, either ID makes no real predictions whatsoever, or if it tries to, it is demonstrably wrong.

Comment #184018

Posted by Laser on June 21, 2007 8:31 AM (e)

And if I have a health question I would ask an MD. And if the answer didn’t make sense to me, I would continue searching for information.

And if every other MD you asked gave you the same answer, what would you do?

I think what you meant to say is that if the answer didn’t conform to your preconceived notion of the universe, you’d continue searching.

If there is some kind of universal intelligence, on the other hand, we would not expect organisms to be full of useless junk.

Why not? Why do you assume that the “universal intelligence” would not fill organisms with “useless junk”? Perhaps the “universal intelligence” had reasons that you can’t fathom, or perhaps it was playing a joke on us. This “universal intelligence” could have countless motives which could possibly explain every observation. Therefore, it explains nothing and is useless.

Comment #184019

Posted by realpc on June 21, 2007 8:40 AM (e)

David Stanton,

When something appears to have no function, maybe it’s just because you don’t understand it well enough. A non-programmer would look at a program and see nonsense, would never imagine what it’s function could be. I think it’s the same story with DNA.

What you perceive as “inefficiency, waste and poor planning” might just be beyond current biological understanding.

The more they learn about physics, the stranger and less comprehensible the universe seems. Biology is heading in that direction also – the more you learn about life the more baffling it will seem.

In my opinion, it will turn out that none of it is junk. The body as a whole is efficient and not cluttered with meaningless junk. The same for organs and cells. So we can reasonably expect the same for DNA. We just don’t undertand the code.

Comment #184023

Posted by David Stanton on June 21, 2007 9:32 AM (e)

realpc,

Thanks for responding. Perhaps I did not make myself clear. There are very good reasons, based on very good evidence, to conclude that there is absolutely no function for these elements. They are very well understood genetically. If you want to claim that there is some function, the burden of proof is on you to demonstrate that function. Claiming that others are ignorant in a field that you are unfamiliar with is not really a good way to argue.

As I already stated, a few of these elements might possibly perform some function, (although usually deleterious), eventually. However, by their very nature they are parasitic and useless to the host. No mater how many times and in how many ways they are demonstrated to be useless, someone can always claim that they might still have some unknown function, so what? Claiming that it might be true doesn’t make it true. Once again, the burden of proof is on those who oppose the consensus view.

I agree that the universe is stranger than we know, I just don’t agree that SINES are stranger than we know. In any event, thanks for addressing scientific issues.

Comment #184029

Posted by realpc on June 21, 2007 10:26 AM (e)

“There are very good reasons, based on very good evidence, to conclude that there is absolutely no function for these elements.”

Because they don’t code proteins? What about meta-programs? Sorry if I’m just ignorant, but I don’t see how you can be sure an element has no function.

Comment #184031

Posted by Robert King on June 21, 2007 10:57 AM (e)

realpc,

This has been noted elsewhere but have a look at this

http://genomicron.blogspot.com/2007/04/onion-tes…

The implication in the discussion from the Creationist side is that labelling junk-DNA as being junk is somehow insulting God. If researchers took that view they would be forced to do research based on theological rather than observational considerations. This would hinder progress. Say it’s not actually junk. Neverthless, treating it as junk for now, based on current (and overwhelming) evidence, is a faster way to finding its actual function than assuming that it isn’t junk and making specific efforts to discovering what its function (or functions) is.

Comment #184035

Posted by Glen Davidson on June 21, 2007 11:35 AM (e)

Like I’ve mentioned elsewhere, we’ve seen junk DNA arise from transposons, retroviruses, and duplications. There are regulatory elements that cut down on transposon replication, precisely because transposons can make huge amounts of junk. Slightly longer and shorter DNA among individuals of a species is common, due often to transposon insertions. Whole genome duplications have been observed, and appear to have happened many times during the course of vertebrate evolution (despite the fact that it is much better known among plants).

Charlie, of course, neither knows nor cares to learn about these matters. Just declare that, finding function for DNA where it was not previously known, is a prediction of ID, and you have the semblance of science, though not at all the real thing. And Charlie has never shown the slightest knowledge of, capacity in, or even the desire to learn science.

Like virtually all computer-programmer (he claims) ID proponents, he just insists that his ignorance is superiority, and yes (not coining a new phrase) it’s the sort of Newspeak that IDists use precisely because they can’t do any real science (Behe did in the past, but like it was with Gonzalez, continuing science has at least diminished once ID has taken hold, perhaps disappeared altogether).

Glen D
http://tinyurl.com/35s39o

Comment #184036

Posted by Raging Bee on June 21, 2007 11:41 AM (e)

Oblivious to the obvious, RealPretentiousNewAgeNoncompoop drones on…

I am a software developer. I chose that career because it’s all logic with very little room for politics.

So you work in a field that (you say) is “all logic,” therefore we’re expected to believe that everything you say is logical, even when you’re talking about something far outside your area of expertise? That’s one of the lamest atguments from authority I’ve ever heard. (BTW, I’ve done enough software development myself to know it’s NOT “all logic;” and those developers who think it is, don’t get very far.)

I would like to know how many computer scientists prefer IDE over NDE, relative to biologists. I have a suspicion we are more likely to be bothered by the weaknesses of NDE than you biologists are.

If none of them have actually PROVEN either theory wrong (what’s the difference again?), then there’s no reason to give a shit what “bothers” them. Or you.

All you’ve ever brought to any of the threads you’ve hijacked is ignorance and irrelevence. We may be wrong to think you’re on drugs, but given your consistently piss-poor quality of thought, we see no need to make any apology for our opinions. Grow up two decades and call us in the morning.

Comment #184039

Posted by Science Avenger on June 21, 2007 11:59 AM (e)

And now time for an update from Trollcenter:

“maybe”, conjecture, conjecture, “I think”,
“might”, “might”, baseless assertion, baseless assertion, baseless assertion, “In my opinion”, baseless assertion, baseless assertion, non-sequitor, baseless assertion, “I’m just ignorant”, “I don’t see how”.

Quite a performance there Bob, you can see why he’s still the champ.

Comment #184054

Posted by David Stanton on June 21, 2007 1:46 PM (e)

realpc wrotte:

“Sorry if I’m just ignorant, but I don’t see how you can be sure an element has no function.”

The point is not that you are ignorant, that is irrelevant. The point is that you have failed to demonstrate any function. I am not “sure” there is no function for every last one of these elements. No one really can be absolutely sure, or probably ever will be.

However, as others have pointed out already, there are a few facts that you will have to account for whether you eventually find any type of function for any of these elements or not:

(1) There are literally millions of copies of these things in the human genome. Even if all of them do serve a function, it must be a pretty inefficient one.

(2) When SINES and LINES transpose they often cause insertional mutagenesis. Depending on exactly where this occurs, which is for all practical purposes random, this can lead to reduced fitness, increased probability of disease and death.

(3) Most copies of SINES and LINES are not near a promoter sequence and so are not actively transcribed. A few master copies usually account for the vast majority of transposition events in most organisms, the rest are useless vestiges.

(4) SINES are too short to code for useful proteins. They are not expressed and mutate at a rate consistent with lack of functional constraint. There is no known mechanism by which they can be excised specifically and so they increase in copy number over time. They can serve as useful phylogennetic markers, from which we can perhaps conclude that their purpose is to provide evidence for macroevolution.

(5) Many pseudogenes are demonstrably mitochondrial in origin. They use a different genetic code than that used by nuclear genes, (or at least they used to), so it unlikely that they will ever be expressed in the nucleus. Even if they are expressed, the proteins cannot be imported into the mitochondria because they lack the proper signal sequences.

(6) All of the above elements can be dispensed with without loss of function. However, if these elements persist, there is some evidence to suggest that they can cause the extinction of entire lineages. This is in fact one hypothesis to account for the complete extinction of dinosaur lineages.

So, in conclusion, no, I’m not absolutely sure that absolutely none of these elements can ever serve any useful function. However, as I already stated, the burden of proof is on you. You must demonstrate the function and you must account for all of these observations. Good luck.

Comment #184077

Posted by realpc on June 21, 2007 5:59 PM (e)

First, I appreciate the openness of PT, and the patience of those here who are willing to debate with non-experts. I posted a comment at UD (which is moderated) yesterday and it never showed up. At least I can say whatever I want here.

I would like to share this, from http://www.i-sis.org.uk/MGEJ.php

Much of the fluidity of the genome is due to mobile genetic elements that respond to physiological and environmental signals to recraft genes and genomes, creating new patterns of gene expression, new proteins and new evolutionary opportunities.

Perhaps only 1% of the human genome codes for genes, and that’s what the human genome map contains. The rest is mainly repetitive DNA, commonly known as ‘junk DNA’.

However, evidence has been emerging that lurking within junk DNA are armies of transposons (mobile genetic elements) that play an indispensable role in ‘natural genetic engineering’ the genome. They make up nearly half of the human genome, and serve as ‘recombination hotspots’ for cutting and splicing, and hence reshuffling the genome. They are also a source of ready to use motifs for gene expression, as well as new protein-coding sequences.

These important transposons are scattered throughout the genome. There are two main categories: Long Interspersed Elements (LINEs) about 6.7 kilobasepairs in length and Short Interspersed Elements (SINEs) of several hundred basepairs.

Comment #184083

Posted by David Stanton on June 21, 2007 6:57 PM (e)

“They make up nearly half of the human genome, and serve as ‘recombination hotspots’ for cutting and splicing, and hence reshuffling the genome.”

Yes, and the vast majority of these types of genetic changes are deleterious as well. It simply cannot be argued that this supposed system is in any way designed or optomized. They can be important in the evolution of genome structure occasionally, but once again, through random changes that are usually deleterious. They can induce hybrid dysgenesis, which sometimes constrains evolution, but once again, it is a random and almost universally deleterious process. Why would “nearly half of the human genome” have to be devoted to “reshuffling” if it were initelligently designed in the first place? And, assuming that were some advantage to increased “reshuffling”, it could certainly be accomplished much more efficiently.

These elements do have genetic consequences. That does not imply that they have any true function,, purpose or meaning. Much more efficient systems could be designed to perform these functions if they were desirable, but these elements simply do not represent such a system. All the evidence indicates that these elements are tolerated and their consequences endured. They are eliminated if possible, but if not they can cause extinction.

These elements are viral in origin. They are parasites. They have consequences. Their presence has been endured and even adapted to, but intelligent design they are not. If God were even paying any attentioon to the human genome, why would she allow it to be taken over by parasites? These elements have a function in the human genome in exactly the same sense that malaria does. Unless of course you believe that malaria was also designed to improve human beings.

Comment #184130

Posted by realpc on June 22, 2007 5:50 AM (e)

“Why would “nearly half of the human genome” have to be devoted to “reshuffling” if it were initelligently designed in the first place?”

Possibly so that it can be responsive to an ever-changing environment, within and outside of the organism. The accepted theory has been, for a long time, that DNA does not change in response to external conditions, aside from changes that are completely random.

I think we’ll find that DNA is much more intelligent and adaptable than that.

Comment #184131

Posted by realpc on June 22, 2007 5:56 AM (e)

And, as I said before, we don’t see anything else in nature that’s inefficient and cluttered with junk.

So it would be odd if the genome, the center of life, were a chaotic mess.

Comment #184152

Posted by David Stanton on June 22, 2007 8:17 AM (e)

realpc,

Congratulations for keeping mostly to science. I mean it, I’m impressed. This kind of discussion is what PT should be all about, at least it seems that way to me.

Now, about that reshuffling hypothesis. It is an interesting specualtion. However, it fails to address most of the points I raisaed previously. It also fails to explain why only 1% of the genome is coding. It also fails to explain pseudogenes, trinucleotide repeats, introns amd almost every other type of “junk” found in the human genome.

As for the purpose of responding to a changing environment, that is another interesting speculation, but there are problems with that hypothesis as well.

(1) There is no known mechanism whereby chromosomal rearrangements can respond specifically to environmental conditions (including those mediated by retroviral transposons). So, once again, even if this were a consequence of all the junk in the genome, it still comes down to random changes followed by selection.

(2) There have not been any major interchromosomal rearrangements in the human lineage for millions of years (I can provide a reference if you want). The only major exception seems to be a single chromosomal fusion after the split from chimpanzees, but that was not mediated by retroviral transposons (again I can probably dig up the reference if necessary). So, if that is the purpose of all the junk, once again, terribly inefficient and not at all responsive to environmental change.

(3) High resolution FISH has revealed that there have been many small scale intrachromosomal rearrangements in the human lineage (reference somewhere in a pile my office). However, there is no evidence that these were mediated by transposons, no evidence that they are adaptive (most are probably neutral or deleterious), and no evidence that rhey persist for very long in evolutionary time. In short, they are random events, unrelated to the environment, that undergo selection after they arise.

So, in conclusion, there is no real evidence to suggest that these genetic elements are anything more than parasites that persist even though they are generally deleterious. They may increase the rate of some types of recombination events slightly, but only in a random way that is very inefficient, and certainly not in response to a changing environment.

By the way, we do indeed see many things in nature that are inefficient and cluttered with junk. Selection can be a very sloppy process and it has definate limitations. Once again, this is exactly what one would predict if random mutation and selection were the process responsible for biological diversity.

Comment #184177

Posted by realpc on June 22, 2007 10:54 AM (e)

“we do indeed see many things in nature that are inefficient and cluttered with junk. Selection can be a very sloppy process and it has definate limitations. Once again, this is exactly what one would predict if random mutation and selection were the process responsible for biological diversity.”

Ok, well, I respect your expert opinion. I do not perceive nature that way though, and I suspect we will gradually learn that it isn’t junk after all. Of course I am not an expert, have not devoted my life to biology, and no one can predict the future.

I think there is a random component to evolution, and I also think there is purpose. I think the entire system gropes its way towards greater complexity and intelligence.

Of course, as has been pointed out here many times, my philosophy is the opposite of the current scientific philosophy.

So we will see, if we live long enough. I think answers will come from biological computer science, which I would have chosen as a career if it had existed way back then.

Comment #184181

Posted by CJO on June 22, 2007 11:32 AM (e)

I do not perceive nature that way

If the history of science has a single take-home message of the sort that’ll fit on a T-shirt, it is:
“Unexamined perceptions about nature, especially beliefs about how nature should be, are almost always wrong.”

Comment #184182

Posted by Robert King on June 22, 2007 11:56 AM (e)

realpc,

The onion test is quite compelling, I think. But I’m curious why it matters so much to people whether some DNA is junk or not. Of course, it would be enormously interesting to know one way or another but many things in science are not fully understood - or current understanding is just plain wrong. But that’s the point of science. Labeling junk DNA “junk” makes no difference to its actual status which will eventually be determined if it hasn’t already. All science is tentative but, in practice, one has to go with the best judgment possible at any given time which is often - but not always - the consensus. Actually, in writing this I think I have answered my own question - people like absolute certainty while science can only provide the least uncertainty.

Comment #184187

Posted by realpc on June 22, 2007 12:52 PM (e)

I’m curious why it matters so much to people whether some DNA is junk or not.i

Robert King,

As David Stanton said, NDE predicts a lot of junk in DNA, and in nature in general. It’s no coincidence that it’s called “junk” rather than “as-yet not understood.”

IDE predicts elegant and efficient designs in nature. So they claim a victory when “junk” turns out to have a function. I think that’s more or less understandable.

I do not believe in a rigid form of ID theory, where some all-powerful diety planned everything out and zapped it into place. But I do believe nature is intelligent and creative and purposeful. I do not see junk in nature (unless you include human civilization in your definition of nature – we create plenty of junk).

I think there is lots of apparent randomness in nature, but what seems random from our perspective might be part of a creative process.

Comment #184189

Posted by David Stanton on June 22, 2007 1:09 PM (e)

realpc,

Thanks for being so civil anrd reasonable. You are of course entitled to your opinion. On this subject at least my opinion as an “expert” probably isn’t worth much more than yours. As you correctly point out, we don’t know everything and probably never will. So I guess I will just go on assuming that there is no real purpose to the process of random mutation and natural selecetion and you can go on assuming that there is some guiding force pushing life toward increased complexity. I would be more than happy to look at any evidence you might uncover in this regard. Until then, I guess we can respectfully agree to disagree. I freely admit that I could be wrong, but it is still up to you to prove it.

Now, about all that junk. Maybe others could give examples. Of course they should be examples that most likely have no useful function and are best explained by historical contingency rather that design or planning. Let me start out with vestigial organs such as whale hindlimb bones. They are obvioulsly homologous to terrestrial vertebrate hindlimb bones and yet whales do not have hindlimbs. It may be that they have taken on some function in the last few million years, but it certainly appears that they are just left-over junk that is practically useless now. They certainly aren’t what one would expect if whales were intelligently designed from scratch. The argument can be generalized to other types of vestigial organs as well, such as the nonfunctional eyes of some burrowing and cave-dwelling animals. Hopefully others will come up with many more interesting examples.

Comment #184194

Posted by harold on June 22, 2007 1:51 PM (e)

realpc -

You did manage to stay on topic, and I enjoyed reading this thread, since David Stanton’s posts were extremely well-organized and informative.

You are indeed welcome to your opinion. For the most part you were willing, throughout the discussion, to refrain from distorting David Stanton’s words.

I object to one thing that you said. I believe I corrected this once before. It is not an outright untruth, perhaps, nor does it necessarily represent bad faith on your part, although it has been corrected before.

As David Stanton said, NDE predicts a lot of junk in DNA

This is an oversimplification (and I think, an inaccurate paraphrase of David Stanton).

There is virtually no “junk DNA” in prokaryotic genomes. I don’t know what fraction of the DNA in the world belongs to prokaryotes, but a good deal does.

The theory of evolution does not necessarily predict “junk” in genomes. It differs from “intelligent design” in that it can explain the existence of the diverse things we lump together as “junk” DNA, right now, without hopeful reference to as yet undiscovered functions.

But based on what we know now, if we were to discover a new species of prokaryote (a not uncommon occurence) we would not predict that they would have “junk” DNA.

And the theory of evolution also predicts that many biological systems will appear remarkably efficient and finely adapted to their function.

Please, strive to be honest and accurate when describing what science would “predict”. It’s entirely up to you what you “believe”, but please don’t be dishonest about what others believe.

Comment #184195

Posted by realpc on June 22, 2007 1:55 PM (e)

David Stanton,

Thank you also. I learn a lot from these discussions and we can be respectful although we disagree.

“ They certainly aren’t what one would expect if whales were intelligently designed from scratch.”

Right, and I don’t believe anything was intelligently designed from scratch. I don’t think there’s an old guy up there at a drawing board. I think the universe is inherently creative, and that its designs unfold gradually, in a process of trial and error.

You can think of vestigial organs as junk, but maybe it just takes a long time for unused things to de-evolve completely. NDE predicts that useless organs will shrink, since they waste the organisms resources. Therefore, both IDE and NDE agree that nature should not be cluttered with junk. So actually, finding that something isn’t junk after all isn’t such a victory for IDE.

Comment #184197

Posted by David Stanton on June 22, 2007 2:07 PM (e)

Harold,

Thanks very much for the kind words. It means a lot to me coming from you. Thanks also for defending my integrity. Although I don’t think realpc wrote anything too outrageous, you are correct, that is not exactly what I said or exactly what I meant.

Comment #184198

Posted by Henry J on June 22, 2007 2:57 PM (e)

IDE predicts elegant and efficient designs in nature.

How does this prediction logically follow from the premise? As far as I can tell, both junky or not junky are consistent with the notion that something was deliberately engineered, at least unless one knows the methods and motives of the engineer(s).

Henry

Comment #184199

Posted by Henry J on June 22, 2007 3:03 PM (e)

I think there is a random component to evolution, and I also think there is purpose.

And how does that imply an active guiding force? Seems to me that if the one having the purpose notices that natural forces could produce an adequate result without guidance, then lack of guidance would not imply lack of purpose.

Henry

Comment #184204

Posted by David Stanton on June 22, 2007 3:24 PM (e)

Henry J,

You make excellent points. So I guess the question for realpc is this:

What predictions does your complexity hypothesis make and how are they different from those made using the more conventional RM/NS model? In other words, what evidence would convince you that your hypothesis had been falsified? I don’t have any particular need to falsify your hypothesis, but I do want to determine if it is in any way scientific and testable. We don’t seem to have gotten anywhere with the junk DNA argument, even though I still think the evidence is compelling.

Comment #184207

Posted by Robert King on June 22, 2007 4:46 PM (e)

realpc wrote:

I think there is lots of apparent randomness in nature, but what seems random from our perspective might be part of a creative process.

Randomness is a well defined concept. And there actually is real honest to goodness randomness in nature - the 2nd Law of Thermodynamics and, more generally, Statistical Mechanics (as a theory that makes testable predictions) rely on randomness. There is a lot of chaos (not quite the same as randomness) in the Solar System, in general, and obvious randomness in the asteroid belt. The notion that it must be part of a creative process is attributing to God what need not be attributed to him even if you are a Creationist. Also, randomness is still randomness even if God wanted or designed it that way.

Junk DNA or not junk DNA is irrelevant to ID as well because “no junk” is not an actual prediction of ID. It is really just speculation based on some people’s notion of how a designer might work. In principle something could be designed and have lots of hidden imperfections and so, since the Designer need not be a perfect God who does everything perfectly then that which is designed could include junk as well as flaws. If the ID community really wants “no junk” to be considered to be a real, and testable, prediction of ID then would a demonstration that it truly is junk invalidate ID?

And how do you explain the onions?

When the Bible says that God is not a God of disorder but of peace it is clearly equating disorder not with physical randomness but with the opposite of peace.

Comment #184208

Posted by Science Avenger on June 22, 2007 4:50 PM (e)

David Stanton said:

So I guess the question for realpc is this:

What predictions does your complexity hypothesis make and how are they different from those made using the more conventional RM/NS model?

No sir, the question is why you have chosen to steer a thread about the science of DNA to the implications of the Troll Hypothesis of Complexity, a hypothesis studied by, well, no one, not even its “author”.

I know you are amusing yourself, but let’s have a modocum of taste. There might be children present

Comment #184209

Posted by David Stanton on June 22, 2007 5:01 PM (e)

Science Avenger,

Perhaps you are right. Perhaps I have become too over indulgent. But we didn’t seem to be getting anywhere discussing the science. I was trying to see if realpc would make any testable predictions. After all, if millions of worthless parasites don’t count as junk then I guess we may never be able to convince anyone.

But still you are right. Who cares about a “hypothesis” that makes no predictions? I did ask for people to give examples of other kinds of junk, but I guess no one is interested in that either.

Comment #184210

Posted by Robert King on June 22, 2007 5:12 PM (e)

David,

Well I tried - how about the asteroid belt or the Kuiper belt?

Comment #184222

Posted by David Stanton on June 22, 2007 6:38 PM (e)

Robert,

Sorry, I forgot that you mentioned the onion test and the solar system. I do think the onion test is a good example. As for the solar system, I can understand why some would look at it and see order instead of chaos. Don’t get me wrong, I think you’re right. I just don’t think that we will be able to force anyone to admit that it is “junk”. After all, we do live on a priviliged planet you know. (Just kidding).

I was thinking of more biological examples, but there is no reasaon the argument could not be extended to astronomy as well. I guess this would be a kind of anti anthropic principle kind of thing.

Comment #184223

Posted by realpc on June 22, 2007 6:51 PM (e)

“if millions of worthless parasites don’t count as junk then I guess we may never be able to convince anyone.”

Your own theory, NDE, predicts that organisms will be efficient. These “worthless parasites” must be some kind of disadvantage, so individuals will more of them should gradually lose the competition for survival and reproduction.

Both NDE and IDE predict efficient designs.

As for what my theory, creative evolution, predicts – If the universe naturally tends to create life and increasingly complex systems, we would expect life to have originated and evolved in many different times and places. Finding evidence of life having existed on Mars, for example, would support my theory.

It also might predict the origin of life on earth in many times and places. (I don’t know how or if that could prediction could be tested.)

It would be very hard to explain NDE if evidence is ever found for my prediction.

Comment #184231

Posted by David Stanton on June 22, 2007 7:49 PM (e)

realpc,

Sorry, I don’t see how either of these predictions could not be accounted for by modern evolutionry theory. Also, if some guiding force were responsible for multiple failed origins of life on Earth and Mars it must be a pretty stupid force to have such a low success rate.

Comment #184232

Posted by PvM on June 22, 2007 8:46 PM (e)

PC wrote:

Both NDE and IDE predict efficient designs.

Nope, IDE predicts nothing since it cannot and will not address issues surrounding the designer. As far as NDE is concerned it predicts function not efficiency per se unless efficiency is a selectable and variation is present to find these more efficient solutions.

Comment #184234

Posted by Flint on June 22, 2007 8:52 PM (e)

In his book “Full House” Gould argued that there is indeed a “force” leading to generally increased complexity, which is actually an artifact of a statistical process. When lineages tend to grow both more and less complex almost equally, BUT there is a floor to complexity beneath which life can’t survive, then over time those lineages that become more complex cannot be counterbalanced by those becoming less complex.

Gould’s metaphor was a drunk on a sidewalk, equally likely to move toward the street as toward the walls of the buildings, but when the drunk hit the walls, he could go no further in that direction. When the drunk staggered toward the street, he had no such barrier and could keep going.

Mathematically, just moving at random, we’d expect to see the overwhelming majority of life hanging around the minimum complexity necessary to live, with a tiny percentage of lineages moving toward complexity. And by golly, that’s exactly what we see. There are three types of life - archaea, prokaryotes, and eukaryotes. Hard to tell which represents the greatest number of total cells, but it’s a close competetion. The first two are stone simple (with respect to what can survive), and a goodly chunk of the eukaryotes are protists, single-celled.

Humans see big complex life forms, even though as organisms these are in the tiny tiny minority, because they are visible and edible. We tend to ignore the bacteria. We get on the scales to see what “we” weigh, ignoring that more than half the cells we’re weiging are bacteria, which might account for 10% of the total scale reading. And some of which we couldn’t live without.

So while I suppose there’s nothing wrong with believing there some natural “force” pushing toward sophistication and complexity, the reality is that this perception is an artifact of our biases.

Comment #184238

Posted by David Stanton on June 22, 2007 9:40 PM (e)

Flint,

Excellent point. Perhaps that explains why, when I asked for examples of what would falsify the hypothesis, all I got were examples of what would be consistent with the hypothesis. And even those predictions could easily be consistent with modern evolutionary theory as well.

Seems that Science Avenger is right. If there is no way to falsify the hypothesis, it really isn’t science, so why discuss it al all?

Comment #184239

Posted by Henry J on June 22, 2007 9:41 PM (e)

Re “Finding evidence of life having existed on Mars, for example, would support my theory.”

Can you explain the logic you use to get from “life on Earth was deliberately engineered” to “somebody also put life on Mars”?

Another thought - if mutations really were being somehow guided, one would expect that beneficial mutations would be far more common than detrimental ones. As I understand it, what we see is just the opposite of that.

Henry

Comment #184277

Posted by Rolf Aalberg on June 23, 2007 4:26 AM (e)

Realpc wrote:

In my opinion, it will turn out that none of it is junk. The body as a whole is efficient and not cluttered with meaningless junk. The same for organs and cells. So we can reasonably expect the same for DNA. We just don’t undertand the code.

Maybe your opinion, but what about empirical support?

One of the methods I use(d) in the process of evolving my programs was by marking code sequences as comments, or putting them in a ‘Do While False’ loop to prevent the code from executing. What eventually became of the code is hard to say, it might be modified and put to some use, removed, or just stay there doing no harm. Surely others must have applied similar techniques although I don’t think I learned it from anyone.

Comment #184287

Posted by Torbjörn Larsson, OM on June 23, 2007 6:25 AM (e)

Flint wrote:

… a “force” leading to generally increased complexity, which is actually an artifact of a statistical process…. Mathematically, just moving at random, we’d expect to see the overwhelming majority of life hanging around the minimum complexity necessary to live, with a tiny percentage of lineages moving toward complexity. And by golly, that’s exactly what we see.

Thanks, I have often wondered what main stream biologists think here. I believe the above model is the impression you get if you hang around PT a lot/too much/not nearly enough, but I haven’t seen it as clearly expressed before.

So in physics speech, evolution is a symmetrical process (gain or loose function), but the initial and continuing boundary condition (function enough to replicate) is asymmetrical and would explain historical and current ‘function distribution’.

So what ‘function’ tail do we expect statistically? The usual expectation in complex and stratified cases are power functions, which makes for rather fat tails. Your description seems to concur.

Btw, does anyone know if there is any research in this area? Perhaps astrobiology interests or such? Or is it too premature/too complex?

[And if the thread needs to be on topic re non-coding DNA function, maybe a power distribution would describe a priori expectation on non-functional DNA remnants from “lost function” as well?]

Comment #184290

Posted by David Stanton on June 23, 2007 7:40 AM (e)

Torbjorn,

Yes, there is some research in this area. Unfortunately, progress has been hampered by an inability to define and quantify “complexity”. This is a discussion we have had many times here at PT. Maybe someone can come up with some references.

Comment #184321

Posted by Torbjörn Larsson, OM on June 23, 2007 11:14 AM (e)

David,

Thanks for taking time to answer! I see, the problem to define “complexity” for the task at hand is familiar (and, I guess, to characterize “function” in general) and explains well the current stumbling blocks.

Comment #184324

Posted by Science Avenger on June 23, 2007 12:02 PM (e)

Rolf Aalberg said:

Maybe your opinion, but what about empirical support?

He doesn’t bother with that. His opinion is sufficient on all things.

Comment #184789

Posted by Popper's Ghost on June 27, 2007 4:34 AM (e)

At any point in time, the maximum complexity of anything that has existed up until that time is no less than it was at any previous time – that’s logic; it’s a tautology: maximal historical complexity is necessarily non-decreasing. And, if increase or decrease in complexity via evolution is some sort of drunkard’s walk, then maximal historical complexity must generally increase over time (although not indefinitely, because of entropy and the eventual heat death of the universe; at some point before that, maximal historical complexity will permanently level off). This is all tautological – necessarily true. Yes, the “universe is inherently creative” – it must be. But this inherent creativity is deeply natural. To attribute such essential, tautological, creativity to “intelligence” is terribly foolish and confused.

The program runs or it doesn’t, no matter what your software ideology may be.

While some people are occasionally logical, generally people’s reasoning is riddled with errors (google Kahneman and Tversky), and some people almost never have a coherent thought without a great deal of external help. Without the hard reality of the computer not producing the results you want, your errors would be boundless in that field too. In science, rather than a computer producing the right results as the check that our work is correct, we have the empirical evidence against which our hypotheses and theories must be tested.

I would like to know how many computer scientists prefer IDE over NDE, relative to biologists. I have a suspicion we are more likely to be bothered by the weaknesses of NDE than you biologists are.

Among both computer scientists and biologists, acceptance of NDE is highly correlated with familiarity with the facts of biology and an ability to think logically.

Trackback: A Singular Lack of Imagination in ID

Posted by Threads from Henry's Web on June 18, 2007 10:14 AM

A post today dealing with junk DNA led me to some thinking about just how the nature of a designer might impact the nature of the things designed. It seems to me that no matter where we are looking for design, whether in the form of alien artifacts on...