Comparing Teleological Predictions with their Non-teleological Counterparts

The article ENCODE finds the human genome to be an active place, by John Timmer, is provacative. The issue it highlights serves as a useful focal point around which to contrast the predictive utility of a teleological approach with that of standard evolutionary thinking. This is particularly so since more data relevant to the junk DNA question soon will be forthcoming. From the article:

The big surprise in this work is that the genome is pervasively made into RNA.

The new study finds that essentially every base in the genome shows up in RNA at one point or another. This is despite the fact that most of these bases aren't doing anything: 95 percent of the genome isn't under selective pressure, and most of that 95 percent doesn't appear functional in an evolutionary sense.

My thinking is more in line with that of a commenter who pointed out that large stretches of DNA are under selective pressure. They are energetically costly and could perform some yet undiscovered function that enhances reproductive fitness. More from the article:

Personally, I fall into the "it's all junk" end of the spectrum. The all-junk view, in contrast, is consistent with current data.

"Current" is the operative word. The author's view is an inevitable by product of the lense through which he views evolution. If the process is devoid of teleology then junk appears inevitable. I have an opposite view and predict that most RNA transcription confers functional benefits to affected organisms.

It looks like they're choosing to define functional as "made into RNA," even though they recognize that much of the DNA that is made into RNAs clearly has no influence on survival or fitness. They're then using that skewed definition to claim the data shows that most of the genome is functional. Since most of the popular press produces accounts based on the press release, the public is going to be receiving a very distorted view of this work.

Maybe not. That depends on the ultimate resolution of the issue. It is wiser to state that we do not now know the relationship between RNAs and fitness. In any case why the rush to a conclusion? Mainstream evolutionists are endlessly patient with OOL research; cautioning us not to rush to judgement. But the rush here is dictated by the overarching paradigm. If evolution is a non-teleological process then it makes no sense to anticipate an absence of junk. But if junk eventually proves to be minimal, look for the scramble to adjust theory to data. All because science is self-correcting of course. Nothing to do with imperfect human perceptions.

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49 Responses to “Comparing Teleological Predictions with their Non-teleological Counterparts”

Raevmo Says:
June 16th, 2007 at 10:10 am
I wonder how you explain from a teleological viewpoint why some salamanders have 40 times the amount of DNA as humans. Do you really believe that salamanders need all that extra functionality?

Comment by Raevmo — June 16, 2007 @ 10:10 am

Thought Provoker Says:
June 16th, 2007 at 10:26 am
Hi Bradford,

My compliments on your fairly balanced treatment of this article and thank you for bringing it to our attention.

Let me address the part where I feel you gave into the temptation to employ some unwarranted shield bashing. You wrote…

In any case why the rush to a conclusion[?] Mainstream evolutionists are endlessly patient with OOL research; cautioning us not to rush to judgment. But the rush here is dictated by the overarching paradigm. If evolution is a non-teleological process then it makes no sense to anticipate an absence of junk.

Who is doing the rushing here? The author of the article suggest a spectrum of "…possible interpretations for all these extra transcripts" and described three possibilities. Yes, he gave his opinion as to which end of the spectrum he favored, but he did that to balance the popular media's (and your) rush to spin this as evidence for the "none of it's junk" end of the spectrum.

IMO, your echoing of John Timmer's call for restrain while offering you tentative opinion crossed the line into advocacy when you started imputing methods and motives on "mainstream evolutionists". You further aggravated this with an obviously sarcastic prediction…

But if junk eventually proves to be minimal, look for the scramble to adjust theory to data. All because science is self-correcting of course. Nothing to do with imperfect human perceptions.

Of course it has everything to do "…with imperfect human perceptions." Being an arrogant atheist myself, I assure you we don't question the unchanging perfection of the "reality-based" mechanistic universe. It is our human perceptions that change. If anything, our lack of faith in God is replaced with an even stronger faith in the perfection and consistency of reality.

While I was tempted to point out some of the specific arguments in this post at Panda's Thumb, I wouldn't want to risk swinging the pendulum too far to my side of this political argument. Therefore, I will return to the more neutral…

Let's do science!

I happen to think all this activity at the microscopic level is consistent with my "powered by quantum mechanics" hypothesis.

It might be "energetically costly" to keep the DNA/RNA engine constantly idling, but if there wasn't a mechanism by which quantum mechanics can do its weirdness, it couldn't force consistency in biological matter. Ergo, quantum mechanics must maintain a process that appears to be random and wasteful, but it is all in the name of forcing consistency of the universe, past, present and future.

Provoking Thought

Comment by Thought Provoker — June 16, 2007 @ 10:26 am

Bradford Says:
June 16th, 2007 at 11:54 am
Raevmo:

I wonder how you explain from a teleological viewpoint why some salamanders have 40 times the amount of DNA as humans. Do you really believe that salamanders need all that extra functionality?

Don't confuse the size of a program with its efficiency. Alternative splicing is a smart way of getting the most out of genes. There are other strategies as well.

Comment by Bradford — June 16, 2007 @ 11:54 am

Bradford Says:
June 16th, 2007 at 11:58 am
TP:

IMO, your echoing of John Timmer's call for restrain while offering you tentative opinion crossed the line into advocacy when you started imputing methods and motives on "mainstream evolutionists".

I am an advocate TP. That's part of the fun of blogging. Am I a fair advocate? I think so. At least most of the time. I believe mainstreamers box themselves in unnecessarily by excluding a teleological possibility a priori. But if they did not do so there would be no TT would there?

Comment by Bradford — June 16, 2007 @ 11:58 am

William Brookfield Says:
June 16th, 2007 at 12:02 pm
Hello everyone,

Just in case it is of interest, I have posted a bunch of articles related to this at my blog..

http://icon-rids.blogspot.com/

Comment by William Brookfield — June 16, 2007 @ 12:02 pm

Raevmo Says:
June 16th, 2007 at 12:24 pm
Bradford:

Don't confuse the size of a program with its efficiency. Alternative splicing is a smart way of getting the most out of genes. There are other strategies as well.

So you claim that most of the salamander's huge amount of DNA is somehow functional (to the individual salamander), but that it functions less efficiently than human DNA, perhaps because salamander genes don't undergo as much alternative splicing. That sounds like a testable idea: organisms with lots of DNA have a smaller proportion of genes that undergo alternative splicing. For starters, one could compare the salamanders with lots of DNA to their closest relatives with more modest C-values. Let's do science!

Comment by Raevmo — June 16, 2007 @ 12:24 pm

Bradford Says:
June 16th, 2007 at 12:30 pm
Raevmo:

That sounds like a testable idea: organisms with lots of DNA have a smaller proportion of genes that undergo alternative splicing. For starters, one could compare the salamanders with lots of DNA to their closest relatives with more modest C-values. Let's do science!

TP, your outlook is contagious.

Comment by Bradford — June 16, 2007 @ 12:30 pm

Bradford Says:
June 16th, 2007 at 12:36 pm
So you claim that most of the salamander's huge amount of DNA is somehow functional (to the individual salamander), but that it functions less efficiently than human DNA, perhaps because salamander genes don't undergo as much alternative splicing.

Ubiquitin and ubiquitinylation is another example of maximizing the impact of a gene. Add some post-translational modification to a protein and enhance the available options.

Comment by Bradford — June 16, 2007 @ 12:36 pm

Joy Says:
June 16th, 2007 at 1:32 pm
Well, the anti-ID goon squad is certainly up in arms about it (see the buzz over at science blogs). That's kind of interesting, particularly given the amount of CYA rhetoric being lobbed about how "everybody knew" junk DNA wasn't junk all along.

Razib over at Gene Expression has the fairest analysis of the bunch, though he does the double-back shuffle on "junk DNA" just like everybody else.

I'm delighted to see this provisional hypothesis from the antiquated ranks of genomic determinism being firmly falsified at long last. We've all seen too darned many bio-groupies and culture warriors through the years using junk DNA to argue vehemently against the possibility of design. [Case in point, Raevmo's posts to this thread.] Why, it's been one of their favorite weapons for so long you'd almost expect at least a minor mea culpa from at least one of them.

…or maybe not, considering that for the most prominant nay-sayers it's never been about the science anyway. Interestingly, a comment to Razib's post from Andras Pellionisz (with links to his own page, to the International PostGenetics Society and to a commercial enterprise he's associated with called FractoGene) indicates that there are quite a few enterprising specialists who never bought into the junk DNA idea.

Maybe they've all been so busy formulating their own post-genetic ideas that they just didn't care that Ohno had managed to put the brakes on scientific advancement for three decades with his dismissal of ~95% of the genome. At any rate, this falsification of the junk DNA paradigm will give those quiet folks the opportunity they've been waiting for to jump start things again. Thus I predict we'll be hearing from more and more of them in the coming weeks…

Comment by Joy — June 16, 2007 @ 1:32 pm

Joy Says:
June 16th, 2007 at 1:34 pm
Thanks for the link to your blog, William. It's getting to be quite the long list, isn't it? Â§;o)

Comment by Joy — June 16, 2007 @ 1:34 pm

Thought Provoker Says:
June 16th, 2007 at 1:50 pm
Hi Bradford,

You wrote…

I am an advocate TP. That's part of the fun of blogging. Am I a fair advocate? I think so. At least most of the time.

LOL Sarcastic remarks are rarely the sign of a "fair advocate". What if I reversed your argument and said"¦

"…the rush here is dictated by the overarching dogma. If evolution is a teleological process then it makes no sense to anticipate the presence of junk. But if junk eventually proves to be abundant, look for the scramble to adjust theory to data. All because the unnamed-but-known-to-be-intelligent designer's methods are mysterious of course. Nothing to do with religious apologetics."

Would that be "fair"

I would rather talk about science.

What did you think of my quantum powered explanation for this scientific evidence?

Doesn't it provide a nice mechanism regardless of the metaphysical beliefs behind it?

Provoking Thought

P.S. to Bradford. You wrote…

But if they did not do so there would be no TT would there?

Do you really want to get me started on TT's About Us description again?

Comment by Thought Provoker — June 16, 2007 @ 1:50 pm

William Brookfield Says:
June 16th, 2007 at 3:11 pm
Hi Joy.

Ohno had managed to put the brakes on scientific advancement for three decades with his dismissal of ~95% of the genome.

Dawkin's present position appears to be that 98 per cent of the human genome is junk..

http://www.skeptics.com.au/art...

Richard Dawkins "..there's lots more DNA that doesn't even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, "tandem repeats", and other nonsense which may be useful for forensic detectives but which doesn't seem to be used in the body itself.

Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.

Can we measure the information capacity of that portion of the genome which is actually used? We can at least estimate it. In the case of the human genome it is about 2%"

Andras Pellionisz long ago warned us about this stuff.

Comment by William Brookfield — June 16, 2007 @ 3:11 pm

Thought Provoker Says:
June 16th, 2007 at 4:01 pm
Hi All,

[big sigh]

Are you sure you wouldn't rather talk about science? It's a lot more interesting than spinning politics and history.

Oh Well…

Posts on Panda's Thumb and others are reacting to the ID movement's spin of trying to rush a conclusion that is favorable to creationism and ID. Hopefully, Bradford will ask ID proponents the same question he asked the opponents…

"In any case why the rush to a conclusion?"

The following are excepts from a Panda's Thumb post by Steve Reuland about an it's-all-junk article…

1. The whole history behind the "junk DNA" concept will have to wait for another day, but suffice it to say that the standard ID line on this is completely untrue. They claim that "Darwinists" thought the genome would be mostly non-functional, and that the "Darwinists" were surprised, recalcitrant, and stubborn to face the facts when things turned out differently. The article quotes Michael Behe as saying, "From the very beginning Darwinism thought whatever it didn't understand must be simple, must be nonfunctional. It's only in retrospect that Darwinists try to fit that into their theory."

As usual, Behe has his facts wrong. Prior to the advent of genomics, most strict Darwinians (i.e. those who believe that natural selection is everything) thought that the genome would be highly efficient and streamlined, that selection would mercilessly weed out any useless or wasteful sequences. Indeed, that largely seemed to be the case with bacteria. Although the strict Darwinian viewpoint had been losing ground by the early 70s, it was still quite puzzling when around 95% or more of eukaryotic genomes turned out to be non-coding. It required the non-Darwinian idea of neutral theory and much later the idea of selfish DNA to make sense of it all. To the extent that evolutionary theory had to retrospectively account for the evidence, Behe has it exactly backwards. The predominant adaptationist perspective had to give way to one that allowed for neutrality, contingency, ecology, and structural constraints. Only then did it occur to biologists that the whole genome need not be functional. The ID argument here is not only based on a false premise, it's an almost exact inversion of the truth.

2. Even more absurd, the article quotes Stephen Meyer as saying that, "It [this recent research] is a confirmation of a natural empirical prediction or expectation of the theory of intelligent design, and it disconfirms the neo-Darwinian hypothesis."

This, too, is utter nonsense. There is no logical connection between ID "theory" and the idea that the genome must be devoid of non-functioning DNA, because according to the IDists themselves, the "designer", along with its methods and its motives, cannot be defined. Nor have they come up with any model, coherent or otherwise, for how it was that living organisms came to be in their present state. Therefore, there aren't any constraints on what the "designer" may or may not do, and it (or they) could just as easily have added a bunch of non-functional DNA as made a genome that was 100% functional. Indeed, the IDists invoke this excuse all the time when dealing with the fact that many things in biology (not least of which is the genome) appear to be poorly or haphazardly designed. They even go so far as to say that it is a theological belief to state that a designer would have made efficient, highly functional designs. (One wonders how they could know it's theological if they don't know who the designer is.) We're not supposed to presume that the designer does things that make sense to us mere mortals. You see, he works in mysterious ways.

So Meyer's "prediction" here isn't a prediction at all, it's entirely post hoc reasoning. That makes Behe's quote from above not only wrong, but also deliciously ironic. We knew long before the ID movement began that at least some non-coding DNA would turn out to be functional, and molecular biologists were already busy searching for those functions back when the IDists were still calling themselves creationists. And now the IDists come along and retrospectively claim that they were the ones who predicted that non-coding DNA would be functional. Talk about shameless.

As for the bit about the research "disconfirm[ing] the neo-Darwinian hypothesis", that's so wildly wrong it doesn't require a detailed rebuttal. There's nothing about the neo-Darwinian synthesis that requires the genome to contain large amounts of non-functioning sequences. As previously stated, the default assumption among selectionists was that the genome would be fully functional. Meyer is simply engaging in dishonest and ignorant hyperbole.

3. Even if we assume for some reason that ID really does predict that all of the genome is functional, then so much the worse for ID. Neither this study nor any of the others that have appeared in recent years demonstrate that the entire genome is functional. What they show is that only a tiny percentage of the genome is functional. It's just a slightly larger tiny percentage than before. As the authors of the present study note, a mere 5% of the mammalian genome is conserved, suggestive of a function. Only 2% is protein coding, so the functional bits they're finding merely account for some of the discrepancy between the 2% that code for proteins and the 5% that we expect to be functional. I doubt there exists anywhere a competent molecular biologist who believes that all DNA is functional. The evidence strongly shows otherwise.

Not only does the vast majority of the genome have no known function, we have good reason to believe that much of it won't have a function because it consists of broken viruses, elements that rapidly duplicate, or degenerate gene copies. Many of these sequences are getting duplicated and deleted all the time, and vary not only between closely related species, but even between individuals within a species. Yet losing these sequences appears to have no consequence, and gaining new ones often causes disease by interrupting other sequences that are useful. Additionally, many non-coding sequences, particularly those from degenerate viruses and pseudogenes, accumulate mutations at the neutral rate. This wouldn't be happening if they were functional. Contrary to what the IDists believe, the non-functionality of these sequences isn't assumed by default, it's based on what we know about them.

The short version…

1. No or little DNA junk would be consistent with the basic Darwinian model, but reality is more complicated than that.

2. There is no ID model, therefore there are no ID predictions. How can ID make predictions when it refuses to even discuss possible motives for an unnamed designer?

3. However, if ID does predict a lack DNA junk then the existance of junk would be scientific falsification.

That being said, I will point out that accepting a mechanistic model that suggests quantum effects somehow influence DNA then most, if not all, of these complaints are invalidated.

Let's do science!

Provoking Thought

Comment by Thought Provoker — June 16, 2007 @ 4:01 pm

Raevmo Says:
June 16th, 2007 at 4:57 pm
Joy:

I'm delighted to see this provisional hypothesis from the antiquated ranks of genomic determinism being firmly falsified at long last. We've all seen too darned many bio-groupies and culture warriors through the years using junk DNA to argue vehemently against the possibility of design. [Case in point, Raevmo's posts to this thread.] Why, it's been one of their favorite weapons for so long you'd almost expect at least a minor mea culpa from at least one of them.

As usual, your comment amounts to little more than junk itself. The Nature paper (a veritable treasure trove of fascinating facts) shows that nearly all human nuclear DNA gets transcribed to some degree. That doesn't imply at all that all human DNA is functional. For example, over 25% of human DNA consists of (the remnants of) transposons, parasitic sequences that multiply themselves at the expense of their host (they can do damage by inserting themselves in functional genes.) Some species have even more junk, such as an amoebe with 200 times the human C-value. The Japanese pufferfish OTOH has only one seventh of the human C-value. You may find these facts inconvenient (or even a weapon) but that doesn't make them go away.

Comment by Raevmo — June 16, 2007 @ 4:57 pm

Joy Says:
June 16th, 2007 at 5:05 pm
William:

Andras Pellionisz long ago warned us about this stuff.

Strangely enough, this is the first I've heard of him. Tried to explore his site, but either it's besieged at present, or it's off-line for other reasons. Since much of the FractoGene site is held up for pending patents on the nanotech applications end, they must be really busy right now.

The PostGenetics site boasts 40 founders and members in 32 countries. Looks like not all geneticists were fooled into junk DNA as a culture war weapon. Have the warriors savaged any of these folks over the last 30 years for not buying the junk junk? Have they been treated as badly as telic thinkers and ID supporters here in the US?

I've got Pellionisz's Neural Geometry: Towards a Fractal Model of Neurons and will take some time to comb through it. When did you become familiar with his ideas, and what do you think about them?

Comment by Joy — June 16, 2007 @ 5:05 pm

Bilbo Says:
June 16th, 2007 at 5:07 pm
Hmmm…first TP argues that Darwinian theory predicts that most DNA will be functional. Then Raevmo argues that most DNA isn't functional. So does this mean that Raevmo isn't a Darwinian?

Comment by Bilbo — June 16, 2007 @ 5:07 pm

Raevmo Says:
June 16th, 2007 at 5:20 pm
Bilbo:

Hmmm"¦first TP argues that Darwinian theory predicts that most DNA will be functional. Then Raevmo argues that most DNA isn't functional. So does this mean that Raevmo isn't a Darwinian?

Old-fashioned Darwinian theory didn't really consider selection at levels other than the individual. Since the early seventies there has been growing awareness among the "Darwinians" that plenty of selection takes place at lower levels (parasitic "selfish" elements spreading at the expense of the individual host, cluttering genomes with junk) and higher levels (group selection or even species/clade level selection). So to answer your question, nope.

Comment by Raevmo — June 16, 2007 @ 5:20 pm

Joy Says:
June 16th, 2007 at 5:28 pm
TP:

That being said, I will to point out that accepting a mechanistic model that suggests quantum effects as somehow influencing DNA then most, if not all, of these complaints are invalidated.

I'd suspect that the biggest quantum effect influencing DNA would be electron sharing, which affects lots of molecular constructs in binding affinities and such, probably including state-switching. Jack Tuszinski has done some work suggesting superconductivity in the chromatin pi-stack during 'normal' operations - presenting genes and associated sequences for transcription moment-to-moment per the cell's requirements.

Superconductivity would mean that all the electrons in the chromatin are essentially acting as one electron. Perhaps the histone undercoding is directly affected by this too, as "live" chromatin is constantly oscillating - phasing in and out with new configurations. Superconductivity would allow the entire construct to be entangled, so all remotely sited adjuncts for the gene plus RNA codes that may be necessary for post-transcription alterations can be simultaneously presented as the full complementary suite. This is why Pellionisz's fractal idea is intriguing.

At any rate, we've known for awhile that a lot more was going on than the culture warriors wanted us to believe. Don't begrudge us a little gloating over their mass discomfort over this falsification of their favorite weapon. Everything else is just CYA after the fact. Â§;o)

Comment by Joy — June 16, 2007 @ 5:28 pm

Joy Says:
June 16th, 2007 at 5:56 pm
Raevmo:

As usual, your comment amounts to little more than junk itself. The Nature paper (a veritable treasure trove of fascinating facts) shows that nearly all human nuclear DNA gets transcribed to some degree. That doesn't imply at all that all human DNA is functional.

Well, since I'm not someone who ever predicted that all human DNA must be functional, perhaps you meant this insult for someone you've confused with me.

The Japanese pufferfish OTOH has only one seventh of the human C-value. You may find these facts inconvenient (or even a weapon) but that doesn't make them go away.

Hmmm… pufferfish. That's a Fugu, isn't it? Interestingly enough, Pellionisz has a paper confirming a prediction about them too, which you might be interested in.

Comment by Joy — June 16, 2007 @ 5:56 pm

CJYman Says:
June 16th, 2007 at 6:00 pm
Hello TP and Joy,

Is there any possibility that a logic gate could be so small and so near another logic gate that their operation would be affected by quantum effects?

Comment by CJYman — June 16, 2007 @ 6:00 pm

Thought Provoker Says:
June 16th, 2007 at 6:07 pm
Hi Joy,

After some stuff that most of us will just pretend to understand you wrote…

Don't begrudge us a little gloating over their mass discomfort over this falsification of their favorite weapon. Everything else is just CYA after the fact. Â§;o)

LOL

Ok, but you know your side will have its turn in experiencing mass discomfort too.

BTW, thank you for the link to Pellionisz's link. I have already started looking at it and feel another headache forming.

Should I assume that you are aware of Ouyang's and Awschalom's work on quantum spin transfers at room temperature?

You may have a huge lead on me in understanding this stuff. And granted, you are better trained than me in understanding all this "meaningless gibberish". But somehow, someway I am going to catch up.

Meanwhile, do you want to let the rest of the people in on this? Would you please post my "An Atheist's view of ID, Front Loading and Retrocausality"

As you can see by CJYman's comment, there would probably be interest.

MikeGene made the offer for a guest post, but he doesn't seem to be around. It wouldn't hurt to have Telic Thoughts have on record for a proposed model that may turn out to be very prophetic. Even if it came from an atheist. Especially if it came from an atheist. And if I make a fool of myself, who cares?

Regards,
TP

Comment by Thought Provoker — June 16, 2007 @ 6:07 pm

Thought Provoker Says:
June 16th, 2007 at 6:12 pm
Hi CJYman,

You asked…

Is there any possibility that a logic gate could be so small and so near another logic gate that their operation would be affected by quantum effects?

Would you be interested in reading about the beginnings of a computer made up of several such logic gates?

Look here.

The interesting thing about this one, is that it operates at room temperature. Other experments required very cold temperatures.

Regards,
TP

Comment by Thought Provoker — June 16, 2007 @ 6:12 pm

Raevmo Says:
June 16th, 2007 at 6:22 pm
Joy:

Hmmm"¦ pufferfish. That's a Fugu, isn't it? Interestingly enough, Pellionisz has a paper confirming a prediction about them too, which you might be interested in.

Yeah it is. Thanks for the link. I don't feel like reading the paper right now (I'm trying to watch The Hills Have Eyes II here). What prediction do you mean?

Comment by Raevmo — June 16, 2007 @ 6:22 pm

Joy Says:
June 16th, 2007 at 6:24 pm
TP:

Meanwhile, do you want to let the rest of the people in on this? Would you please post my "An Atheist's view of ID, Front Loading and Retrocausality"

Yeah, I'll post it. Give me a few minutes, okay?

Comment by Joy — June 16, 2007 @ 6:24 pm

Joy Says:
June 16th, 2007 at 6:27 pm
er… Which one should I use, TP?

Comment by Joy — June 16, 2007 @ 6:27 pm

Thought Provoker Says:
June 16th, 2007 at 6:29 pm
Hi Joy,

The last one. But beggers can't be choosers.

Thanks

Comment by Thought Provoker — June 16, 2007 @ 6:29 pm

Joy Says:
June 16th, 2007 at 6:36 pm
Done! It's on the front page now.

Comment by Joy — June 16, 2007 @ 6:36 pm

Thought Provoker Says:
June 16th, 2007 at 6:36 pm
Thanks

Comment by Thought Provoker — June 16, 2007 @ 6:36 pm

Bradford Says:
June 16th, 2007 at 6:51 pm
The whole history behind the "junk DNA" concept will have to wait for another day, but suffice it to say that the standard ID line on this is completely untrue. They claim that "Darwinists" thought the genome would be mostly non-functional, and that the "Darwinists" were surprised, recalcitrant, and stubborn to face the facts when things turned out differently.

The characterization of the "ID line" is what is untrue. Go back 4-5 years in forums where evolution, creation and intelligent design are discussed and contrast the number of Darwinian claims that fit the description of genomes being mostly non-functional with opposite claims. I first began to monitor discussion groups around five years ago and at that time anyone claiming that genomes were not primariliy junk was greeted with derision. The above is revisionist history.

Comment by Bradford — June 16, 2007 @ 6:51 pm

nickmatzke Says:
June 16th, 2007 at 6:53 pm
Basically all ID/creationist riffing on junk DNA is worthless, because they don't consider The Onion Test:

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

The onion, Allium cepa, is a diploid (2n = 16) plant with a haploid genome size of about 17 pg. Human, Homo sapiens, is a diploid (2n = 46) animal with a haploid genome size of about 3.5 pg. This comparison is chosen more or less arbitrarily (there are far bigger genomes than onion, and far smaller ones than human), but it makes the problem of universal function for non-coding DNA clear.

Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?

There you have it. The onion test. To be applied to any ambitious claims that a universal function has been found for non-coding DNA.

If you don't like onions, substitute ferns, salamanders, whatever. If you are a pufferfish, substitute humans.

PS: Junkdna.com is a crank website. FYI.

Comment by nickmatzke — June 16, 2007 @ 6:53 pm

Joy Says:
June 16th, 2007 at 6:59 pm
Raevmo:

What prediction do you mean?

One that kinda looks obvious from where I'm sitting, but made in an original "FractoGene" paper published in 2002. From the paper I linked:

Based on the prediction of "FractoGene, Fig.6. 18" (reproduced in Fig. 3. of this paper) that Fugu should exhibit a primitive P-cell arbor, while Danio should show an intermediate complexity, one of us suggested (AJP to Prof. G. SzÃ©kely on 7/4/2003) that a preliminary study be conducted to reveal the facts of neuroanatomy in the Fugu, and more recently in the Danio. While it is simplistic to imagine that total genome size would correlate linearly with specific organelle complexity, we were curious to examine P-cell presence and dendritic complexity in Fugu and Danio. That study is to be reported separately33. The authors have permitted us to refer to their results as "˜unpublished observations' for the Fugu. The Danio results (only partially available) and other comparisons are expected to blossom as a new branch of research.

I expect you might understand the details more than I could, computational genomics not being one of my specialties, and never having encountered "FractoGene" before… Â§;o)

Comment by Joy — June 16, 2007 @ 6:59 pm

Bradford Says:
June 16th, 2007 at 7:05 pm
Nick, why is it worthless to attempt to understand genomic dynamics? By non-coding I asssume you mean not coding for proteins but what seems more important to me, from all sorts of perspectives, is whether or not such non-coding DNA has functional value. Even if the value is marginal it is worth knowing.

Comment by Bradford — June 16, 2007 @ 7:05 pm

Joy Says:
June 16th, 2007 at 7:08 pm
Nick:

PS: Junkdna.com is a crank website. FYI.

How so? I only encountered Pellionisz today, in his comment to Razib's post. I couldn't access much of it for some reason, but what I did see seemed fairly legit. The paper I linked for Raevmo (one that I COULD access) was published in "The Cerebellum." Is that a crank journal?

Comment by Joy — June 16, 2007 @ 7:08 pm

Bradford Says:
June 16th, 2007 at 7:14 pm
Here is the link to the Junk DNA website Nick has called a crank website. Judge for yourself.

Comment by Bradford — June 16, 2007 @ 7:14 pm

Joy Says:
June 16th, 2007 at 7:17 pm
Bradford:

By non-coding I asssume you mean not coding for proteins but what seems more important to me, from all sorts of perspectives, is whether or not such non-coding DNA has functional value. Even if the value is marginal it is worth knowing.

I find myself wondering (maybe because my brain is sore from all this hoopla, trying to keep up, and now from Pellionisz's stuff) how much of the influence from 'fractal' repeats in the used-to-be junk might be pathological. I read almost daily reports from this group or that group that they've discovered genes for this disease or that disease or the other, but they hardly ever match, aren't deterministic, and only produce pathologies in some people.

I'd almost be willing to bet that if there's anything to what Pellionisz & Co. are proposing, we'll find more clues to actual disease states in the 'junk' than in the protein coders.

Comment by Joy — June 16, 2007 @ 7:17 pm

Bradford Says:
June 16th, 2007 at 7:32 pm
Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?

It is a mistake to equate genomic quantity with degree of function. An indication of a more advanced end product is efficiency of size. A good writer can concisely express a point that might take a less gifted one many times more words.

Comment by Bradford — June 16, 2007 @ 7:32 pm

Raevmo Says:
June 16th, 2007 at 7:45 pm
Bradford:

It is a mistake to equate genomic quantity with degree of function. An indication of a more advanced end product is efficiency of size. A good writer can concisely express a point that might take a less gifted one many times more words.

But what is your point? The onion example clearly shows that much of the genome has no function for the individual. Are you now saying that less gifted designers are responsible for the onions with lots of DNA? The children of a lesser God?

Comment by Raevmo — June 16, 2007 @ 7:45 pm

Bradford Says:
June 16th, 2007 at 7:59 pm
The onion example clearly shows that much of the genome has no function for the individual.

How do you know that?

Comment by Bradford — June 16, 2007 @ 7:59 pm

Raevmo Says:
June 16th, 2007 at 8:13 pm
How do you know that?

Two closely related species with very similar phenotypes and life cycle differ by an order of magnitude in DNA content. What is the most parsimonious inference? You figure it out. My take is that it blows an ID inference out of the water. As in devistatingly.

Comment by Raevmo — June 16, 2007 @ 8:13 pm

Bradford Says:
June 16th, 2007 at 8:50 pm
Two closely related species with very similar phenotypes and life cycle differ by an order of magnitude in DNA content. What is the most parsimonious inference? You figure it out.

The most accurate inference is the concern. That remains to be determined. A very simple mechanism could account for differences in quantity. Distance itself might have regulatory significance. It might be between a promotor region and some yet unknown regulatory element. There are other possibilities. The point is mainstreamers have been consistently wrong about genomic function. That is because their views are ideologically driven. Empiricism will win out in the end.

Comment by Bradford — June 16, 2007 @ 8:50 pm

Joy Says:
June 16th, 2007 at 11:36 pm
Oops. More junk bites the dust. Worse, it seems that at least some of the genomes published in the last 7 years were "incomplete" because the sequencers decided they didn't need to include DNA they'd been taught was mere junk.

We heard recently that the HGP conveniently left out gene copies too, which turned out to account for the actual differences between people. How neglectful of them. There's just no telling what we might find out if we go ahead and include the now known NOT to be junk DNA. And just to be thorough, they should probably sequence it all this time…

Comment by Joy — June 16, 2007 @ 11:36 pm

Bradford Says:
June 17th, 2007 at 6:59 am
Thanks for the link Joy.

"Most researchers thought heterochromatin had little or no function, because it appeared to lack the protein-coding genes that occur so richly in the chromosomes' more accessible and better-studied euchromatin," says Karpen, a senior scientist in Berkeley Lab's Life Sciences Division and an adjunct professor of cell and molecular biology at the University of California at Berkeley. "In recent years it has become apparent that heterochromatin is critical for many essential functions."

The study of genomes is a very dynamic field. It is wise to not dig in one's heels where change is coming fast and furious.

Comment by Bradford — June 17, 2007 @ 6:59 am

magnan Says:
June 17th, 2007 at 7:31 pm
Another thought: Is there a simple quantitative information theoretic way of showing that much of the supposedly "junk" DNA must be in some way functional? What I have in mind here is the total information content specified by the structure of an organism combined with the specification for its phylogenetic development from egg and sperm. If the genome must contain all of this information, a minimum number of nucleotides would be needed to encode it. For humans the protein-coding portion is supposedly only 2% or so of a total of 3 billion (60 million nucleotides). To be conservative, doubling that would get to around 120 million "letters" in the genetic alphabet and 5 million specified amino acid "words". This of course grossly oversimplified, but seems to be reasonable within maybe an order of magnitude. Following this approach, 5 million "words" would be equivalent to about 40 books of 400 pages with 40 lines per page and 8 numbers per line.

It seems clear to me at least that the protein coding portion of the genome is grossly inadequate to contain the necessary information. The 40 textbooks would barely be able to document the structures and developmental programs for the individual cell types themselves - the multiple coordinated molecular machines like the nucleus and organelles like mitochondria, ribosomes, Golgi apparatus, etc. etc. Even this must be infinitesimal compared to the informational equivalent of the body and brain including developmental programs. It must be truly astronomically huge. There are 10 trillion cells total. The brain is supposed to be the most complicated single object in the universe, containing 100 billion neurons each of which is connected to several thousand others in a very ordered structure.

What seems to be questionable from this very rough estimation is that even all of the nuclear DNA is enough.

Comment by magnan — June 17, 2007 @ 7:31 pm

Bradford Says:
June 17th, 2007 at 8:07 pm
Hi magnan. There are ways to determine function but it is not as straightforward as it seems. Knocking out essential genes can quickly indicate the nature and importance of their functions. The trouble is DNA may have function that is of marginal importance or expressed under unusual conditions. Redundancy can also make detection problematic.

We are still learning about functions we did not know existed. We are also learning that known functions can be more intricate than we believed. I suspect new information will provide more details of already known functions. I would not rule out the possibility of information storage in non-nucleic acids but think nuances on existing genetic codes are more likely.

Comment by Bradford — June 17, 2007 @ 8:07 pm

magnan Says:
June 18th, 2007 at 7:34 am
Thanks, Bradford. My point was that a very rough estimate of information content seems to indicate the need to utilize vastly more than the normally considered protein coding part of the genome, in order to specify the total physical design and development programs. This would imply that much of the "junk" DNA subject to the ENCODE research is somehow part of this information storage. Are you saying that you disagree? It seems to me multiple frame translation and other data compression techniques are unlikely to be able to compress the required information into the non-"junk" part of the genome.

Comment by magnan — June 18, 2007 @ 7:34 am

Bradford Says:
June 18th, 2007 at 8:14 am
magnan: Are you saying that you disagree? It seems to me multiple frame translation and other data compression techniques are unlikely to be able to compress the required information into the non-"junk" part of the genome.

I agree. I believe we will discover that the genomic activity we currently observe in non-protein coding portions of genomes are expressions of stored information which likely have regulatory functions. I occasionally come across speculation that some forms of RNA might have a yet unknown immunological function. If so that could explain why function is difficult to account for even when genomic regions are knocked down.

Comment by Bradford — June 18, 2007 @ 8:14 am

John Timmer Says:
June 18th, 2007 at 10:01 am
Technorati lead me to this response to my original write up at Ars Technica. I won't argue the junk/nonjunk issue here, since i had my say in my original article, but i was intrigued by this part of your write up:

Personally, I fall into the "it's all junk" end of the spectrum…The all-junk view, in contrast, is consistent with current data.
"Current" is the operative word. The author's view is an inevitable by product of the lense through which he views evolution. If the process is devoid of teleology then junk appears inevitable."

I'm left wondering why you have issues with the standard of evidence for scientific models. The best any scientific model, hypothesis, or theory can do is be consistent with the current body of data. After all, what are the alternatives? Being consistent with data that's out of date? Being inconsistent? By emphasizing the current aspect, you appear to be promoting a view that it's better to be consistent with data we don't yet have, and may never have.

Of course, to be useful, any scientific model needs to be potentially inconsistent with some data. This is where teleology (and string theory) runs into trouble. For teleology, either some hard predictions regarding the intended endpoint have to be made, or teleology is consistent with anything.

In general, folks at Discovery have emphasized that we can't know the goals of any designers, which leaves them with methodological problems. But, in the wake of this publication's presentation in the press, i'm seeing a lot of hard predictions in terms of "no junk = teleology". But these results, at best, shift the junk issue from DNA to RNA - we still don't know what these transcripts do, and there is no data that suggest they do anything. But, as mentioned by other posters here, there is evidence from organisms with compact genomes that all this RNA is dispensable. Which, by that hard prediction, makes teleology inconsistent with current data…

Comment by John Timmer — June 18, 2007 @ 10:01 am

Pellionisz Says:
June 19th, 2007 at 9:01 pm
pellionisz_at_junkdna.com says:

Indeed, the server of http://www.junkdna.com crashed under the tsunami set off by the (BTW not unexpected…) announcement of the 1% pilot-results of ENCODE, "officially" discarding the "genes/junk" dogma. The site is now running on a better protected and higher capacity server (same domain) - with extraordinary downloads.

Genomics was deliberately "framed" by the late Dr. Ohno in 1972 to be confined to "Genetics" - earlier he tried an even more dismissive adjective ("trash" DNA, 1970), but it did not stick.

The scientific misnomer is now reduced to a historical (and extremely harmful) moniker of a bygone era. In the PostModern era; PostGenetics ("Genomics beyond Genes"; http://www.postgenetics.org with 55 Founders and members from 35 Countries) focuses on the urgent agenda:

(1) Most of the media coverage would agree that "it is time to re-think Genetics". PostGenetics has been doing so (IPGS was the first organization that formally abandoned the "junk DNA" dogma on the 12 of October, 2006 in its "European Inaugural"). "If it is not Junk, what it is and how does it work?". Scientific theories were needed, and my FractoGene http://www.fractogene.com in 2002 was (and is) a contender for algorithmic design of the Genome

(2) Theories must be experimentally verifiable/refutable. FractoGene is supported by experimental evidence, published in refereed science journal (The Cerebellum); http://www.junkdna.com/fractog... All other theories are welcome - none should be opressed and/or underfunded

(3) Indeed, it has been proven for several hereditary diseases (and suspected in "most if not all" others) that "glitches" in the "junk DNA" cause lethal syndromes. (Friedreich' Spinocerebellar Ataxia is a specific example, for list see http://www.junkdna.com/junkdna... ). In the case of about a dozen or so diseases "fractal defects" have been identified in intronic and intergenic DNA; see http://www.fractogem.com

(4) "If genomics is a goldmine, where is the gold?" - was the question in 2003 (at the 50th Anniversary mtg of the Double Helix in Monterey, CA). Clearly, we have 99% of the (human) DNA to work with, but we have to "tool up" to the historical challenge. Dr. Capecchi's group went on record swiftly with an exemplary "tool" (how to mutate arrays of "junk"; putting visible question-marks on dogmatic views of evolution; http://www.junkdna.com/#non-ge... . Biotech industry will never be the same again… (Genes triggered Genentech, PostGenes trigger PostGeneTech…)

(5) Every paradigm-shift in Science (if profound enough) caused our philosophy to keep up with it. (Classic example; quantum mechanics resulting in the principle of uncertainty). The AI/Neural Network paradigm shift resulted in "Neurophilosophy", PostGenetics is likely to provoke new philosophies (look for World-Class Philosopher in the Board of International PostGenetics Society…)

IPGS is open for all in suitable categories.

Comments welcome here and at email address above;

Regards,
Dr. Pellionisz

Comment by Pellionisz — June 19, 2007 @ 9:01 pm

onething Says:
June 21st, 2007 at 1:22 am
William Brookfield,

Just in case it is of interest, I have posted a bunch of articles related to this at my blog..

I've tried and tried but I cannot log into your blog. I think Denise OLeary's blog has the same format and I had the same trouble.

Comment by onething — June 21, 2007 @ 1:22 am

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