Steve Reuland posted Entry 3189 on June 14, 2007 12:48 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/3178

Science journalism is a business filled with a few bright shining stars standing amidst a lot of writers whose stars are… let’s just say, they don’t shine as bright. Concerning the latter, there is a recent article in Wired magazine titled, One Scientist’s Junk Is a Creationist’s Treasure. It’s your standard attempt at journalistic “balance” that puts crackpots on an equal playing field with actual scientists whose work the former group misrepresents. There’s no excuse for this when a little background knowledge and a little more attention to what the real scientists are saying should show why the creationists are spouting nonsense.

As the title should tell you, the article has to do with so-called “junk DNA” and a recent paper concerning the opossum (Monodelphus domestica) genome. The authors of the paper found that a small fraction of transposable elements shared by the opossum and human genomes appear to contribute to host fitness, apparently by contributing to gene regulation. (Update: That particular paper isn’t involved with the opossum genome project; the conserved sequences are found within “boreoeutherians” which include primates, rodents, and carnivores – not the opossum.) This is a highly interesting if not exactly Earth shattering find.

Unfortunately, every time a new study comes along showing that some small fraction of so-called “junk DNA” turns out the have a function, the ID people do a strange sort of victory dance, as if this somehow proves that they’ve been right all along. In fact this is starting to become a frequent talking point with them. As with most creationists myths it’s taken on a life of its own, and I’m sure we’ll see it wandering around like a zombie for years to come in spite of the fact that it was DOA from the get-go. The new paper of course doesn’t support ID by any stretch of the imagination, nor do any recent findings concerning junk DNA, but the author of the Wired piece, Catherine Shaffer, just credulously repeats claims made by Michael Behe and Stephen Meyer as if they had some measure of legitimacy. Which is why it’s got Paul Nelson crowing about it. Below I will do the work that Shaffer didn’t and explain just how wrong these guys are.

The problem with the argument being put forth by the ID people is as follows:

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.

4. What makes all this exceptionally ridiculous is that the present study has inferred the functionality of some non-coding DNA based on its evolutionary conservation. In other words, if humans and opossums have stretches of DNA that are highly similar in sequence, then we conclude that selection must have been preserving those sequences during the eons since humans and opossums split off from a common ancestor. (Update: Again, the Lowe et al. paper did not include the opossum genome, but rather used the dog genome as the most distant from humans. Just think “dog” instead of “opossum”.) Given that Meyer and Nelson reject common ancestry, this particular method of analysis isn’t supposed to work according to their belief system. As Gill Bejerano, one of the study’s coauthors put it, “If you disbelieve this process, then from your perspective, we haven’t found anything interesting in the genome.” This should have tipped off the Wired author that she was dealing with crackpots, but for some reason it didn’t.

___________________________________________________________________________

So in conclusion, the IDists are claiming that they made a “natural empirical prediction” that has been successfully confirmed. The fact is however that they didn’t predict it, it isn’t correct, it doesn’t contradict mainstream theory, and the supposed confirmation is meaningless according to their own belief system. If that’s not enough to convince you these guys are nothing more than rank propagandists, not to worry: Stephen Meyer is working on a whole book of this nonsense called The DNA Enigma. We’ll get to see some junk for sure.

P.S. Larry Moran has more about the Wired article. And T. Ryan Gregory gives a brief history of junk DNA, again dispelling the IDist myth that “Darwinists” thought it was all non-functional. See also his onion test.

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Comment #183168

Posted by SteveF on June 14, 2007 5:25 PM (e)

As I mentioned at Larry’s blog, this new paper is significant:

http://www.nature.com/nature/journal/v447/n7146/…

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

From a BBC article:

“A close-up view of the human genome has revealed its innermost workings to be far more complex than first thought.

The study, which was carried out on just 1% of our DNA code, challenges the view that genes are the main players in driving our biochemistry.

Instead, it suggests genes, so called junk DNA and other elements, together weave an intricate control network.

The work, published in the journals Nature and Genome Research, is to be scaled up to the rest of the genome.”

http://news.bbc.co.uk/1/hi/sci/tech/6749213.stm

Comment #183172

Posted by Randall on June 14, 2007 5:49 PM (e)

To be fair, just because a DNA sequence mutates at a neutral rate doesn’t mean it’s non-functional. It could be very important that control sequence A and coding region B be 1000-1100 base pairs apart; which base pairs doesn’t matter, so that region mutates freely.

Of course, that doesn’t account for repeated motifs, obvious virus lysogenic-like material, pseudogenes, etc. I’m just pointing out that mutation doesn’t necessarily change “functional” DNA.

Comment #183174

Posted by Hawks on June 14, 2007 6:26 PM (e)

Given that Meyer and Nelson reject common ancestry, this particular method of analysis isn’t supposed to work according to their belief system.

And given that ID, as you said, does not say anything about the designer and so says nothing about whether or not common ancestry is “true”, no one is justified in using this study to claim that ID predicted anything. You can make some assumptions about the designer and accept that common ancestry has in fact happened (as Behe seems to have done), but then you are just justified in saying that “Beheism” predicts it.

ID predicts NOTHING!!!

Comment #183181

Posted by Bond; James Bond on June 14, 2007 9:51 PM (e)

I believe this recent study is very interesting to your topic in that it indicates that 100% of the genome may be poly-functional.
Would 100% poly-functionality in the genome be a evolutionary prediction or a ID prediction?

Encyclopedia Of DNA: New Findings Challenge Established Views On Human Genome
The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. “Our perspective of transcription and genes may have to evolve,” the researchers state in their Nature paper, noting the network model of the genome “poses some interesting mechanistic questions” that have yet to be answered.
Other surprises in the ENCODE data have major implications for our understanding of the evolution of genomes, particularly mammalian genomes. Until recently, researchers had thought that most of the DNA sequences important for biological function would be in areas of the genome most subject to evolutionary constraint — that is, most likely to be conserved as species evolve. However, the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution, at least when examined by current methods used by computational biologists.
According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species’ genomes contain a pool of functional elements, including RNA transcripts, that provide no specific benefits in terms of survival or reproduction.

The ENCODE consortium’s major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active.

http://www.sciencedaily.com/releases/2007/06/070…

Comment #183183

Posted by Steve Reuland on June 14, 2007 10:02 PM (e)

Bornagain777 wrote:

I believe this recent study is very interesting to your topic in that it indicates that 100% of the genome may be poly-functional.

It indicates nothing of the sort. If you read this article in Nature News for example, you learn that even the most radical of ENCODE researchers think that up to 20% of the genome may be functional. The rest think it’s lower.

If ID wants to claim 100% functionality of the genome as a prediction, fine with me. We can then safely conclude that it’s wrong.

Comment #183186

Posted by Jerry on June 14, 2007 10:47 PM (e)

Here’s a relevant paper that deserves more attention:

Marcelo A. Nóbrega, Yiwen Zhu, Ingrid Plajzer-Frick, Veena Afzal and Edward M. Rubin (1994). Megabase deletions of gene deserts result in viable mice. Nature 431, 988-993.

Comment #183187

Posted by Mike Klymkowsky on June 14, 2007 10:59 PM (e)

Jerry has it right, I believe – that genomic sequences are transcribed does not prove that they are functional. Only carefully done mutational/deletion studies can do that.

Believe it or not, though, scientists (and their university/institutional PR departments) like to make prosaic observations into earth shattering events.

At the same time, I cannot see how this relates to any prediction may by IDiots - or am I missing something deep here?

Comment #183189

Posted by Nick (Matzke) on June 14, 2007 11:38 PM (e)

SteveF writes:

As I mentioned at Larry’s blog, this new paper is significant

Um, this exact paper is what the Wired article was about, and is exactly what we are discussing. And the BBC article you link to isn’t much better than the other press coverage.

Bond, James Bond writes:

I believe this recent study is very interesting to your topic in that it indicates that 100% of the genome may be poly-functional.
Would 100% poly-functionality in the genome be a evolutionary prediction or a ID prediction?

What the heck does “100% poly-functionality” even mean? Evidently you think the study shows that 100% of junk DNA is functional, which is not what it shows, and the regular implication of this sort of thing in the media is exactly what we are complaining about.

Everyone read T. Ryan Gregory’s The Onion Test:

The onion test.

I am not sure how official this is, but here is a term I would like to coin right here on my blog: “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?

Comment #183192

Posted by Marc Geerlings on June 14, 2007 11:51 PM (e)

> At the same time, I cannot see how this relates to any prediction may by
> IDiots or am I missing something deep here?

Yes, you miss something deep here. Like vestigal organs, creationists/IDers oppose every claim that something in the (especially human) body is not perfect created. Surely a perfect creator wouldn’t deal with ‘junk’

I think they see this as a prediction by them and as a consequences every hint of something considered as junk or vestigal by those godless scientist turning out functional or with a purpose is a victory for them. They predict that everything will come out as perfect functional the end.

Comment #183208

Posted by Anna Lytickle on June 15, 2007 2:27 AM (e)

The Guardian (UK)

Other sequences of genetic code are thought to be “on standby”, awaiting a time further down the evolutionary path when they will be beneficial to human beings.

Now that would be a remarkable finding, though I suspect it says more about the quality of science writing on the Guardian since they dropped the regular science section. Predictory adaptation would, of course, be proof absolute of ID.

Comment #183211

Posted by SteveF on June 15, 2007 2:59 AM (e)

Nick,

According to Steve (and a linky in the article), the relevant paper is this one on the opossum:

“Thousands of human mobile element fragments undergo strong purifying selection near developmental genes.”

Whereas I referenced a paper that came out yesterday in Nature (and this is what the BBC article concerns itself with):

“Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.”

I agree with Steve that the Wired article is feeble, but I was wondering what people thought about this additional study.

Comment #183216

Posted by SteveF on June 15, 2007 3:24 AM (e)

This is taking balance to the extreme (i.e. completely making stuff up). Shaffer says in the comments:

“I interviewed five scientists for this article. Dr. Francis Collins, Dr. Michael Behe, Dr. Steve Meyers, Dr. T. Ryan Gregory, and Dr. Gill Bejerano. Each one is a gentleman and a credentialed expert either in biology or genetics.”

Comment #183218

Posted by Nick (Matzke) on June 15, 2007 3:36 AM (e)

Oops, my bad – I was somehow confusing different things. The marsupial genome paper actually came out long ago (well, early May) so I tuned it out for some reason. I agree the Wired article is about the marsupial genome – I guess we can add that it is six weeks late in addition to everything else.

Anyway, people have been arguing about the press coverage of the ENCODE project on various blogs – no one has a problem with the paper, which is interesting but not any kind of revolution in terms of understanding junk DNA.

The basic point of the ENCODE paper as far as I am interested in it:

1. They looked at a somewhat-but-not-completely representative 1% of the genome.

2. Most of the sample DNA is transcribed to RNA
2a. However I am told that much of that is low frequency transcription and could easily just be random due to the generality of the relevant enzymes

3. Only about 5% of the sampled DNA is evolutionarily conserved according to the ENCODE study (ah – the “present study” thing in the present PT post is what got me mixed up), which does not help arguments which say that all DNA is functional.

For more see genomicron: http://genomicron.blogspot.com/2007/06/more-abou…

Comment #183219

Posted by SteveF on June 15, 2007 4:07 AM (e)

Thanks Nick. There is also an article on it in today’s Science. Some people are predicting revolution, others being more cautious:

Given the traditional gene-centric perspective, that finding “is going to be very disturbing to some people,” says John Greally, a molecular biologist at Albert Einstein College of Medicine in New York City. On the other hand, says Francis Collins, director of the National Human Genome Research Institute (NHGRI) in Bethesda, Maryland, “we’re beginning to understand the ground rules by which the genome functions.”

http://www.sciencemag.org/cgi/content/full/316/5…

(subscription required I think)

Comment #183228

Posted by Popper's ghost on June 15, 2007 6:52 AM (e)

Other sequences of genetic code are thought to be “on standby”, awaiting a time further down the evolutionary path when they will be beneficial to human beings.

Ah yes, those sequences, with their little tiny brains, lungs, and mouths, legs, are awaiting, with bated breath, the day when, having trod further down the path, they can generously help out some human beings.

People are so clueless.

Comment #183229

Posted by Bond, James Bond on June 15, 2007 6:55 AM (e)

Steve Reuland wrote:

It indicates nothing of the sort. If you read this article in Nature News for example, you learn that even the most radical of ENCODE researchers think that up to 20% of the genome may be functional. The rest think it’s lower.
If ID wants to claim 100% functionality of the genome as a prediction, fine with me. We can then safely conclude that it’s wrong.

Yet the first sentence in the blog entry states:
The new data indicates the genome contains very little unused sequences and, in fact, is a complex, interwoven network.

I don’t think “very little unused sequences” means 20% functionality as you imply! I think very little unused sequences looks very suspiciously like ther fully functional genome predicted by ID.

Nick Matzke asks?
What the heck does “100% poly-functionality” even mean?

Yet, The first sentence in the second paragraph of the blog entry states:

The ENCODE consortium’s major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another.

“EXTENSIVE OVERLAPPING” is what poly-functionality means!

whats more is that ID will expect the data compression of the genome to be found to be several codes thick for much of the genome!

Comment #183239

Posted by Andrea Bottaro on June 15, 2007 8:38 AM (e)

The new data indicates the genome contains very little unused sequences and, in fact, is a complex, interwoven network.

I don’t think “very little unused sequences” means 20% functionality as you imply! I think very little unused sequences looks very suspiciously like ther fully functional genome predicted by ID.

If you think that, you are mistaken. The authors are careful to make a distinction between “biochemically active” (that is, transcribed into RNA) and functional (i.e. with a selectable effect on the phenotype). “Unused” in the sentence you quote just means “non-transcribed”, biochemically inactive. The fact that much of the intergenic DNA is transcribed at some level (and the level is often very low: although people have been looking at transcripts for decades, we are only becoming aware of this kind of RNA material now because of the increased sensitivity of our techniques and exponential growth of transcript sequence databases) doesn’t mean it actually has a selectable function.

Indeed, one of the interesting things the article proposes is that there are many active transcriptional elements in any genome that have no selectable function, are are poorly conserved, and rapidly come and go during evolution. However, once in a while one gets coopted into some regulatory role, explaining why a fraction of apparently phenotypically functional (selectable) regulatory elements are not evolutionarily conserved. This hypothesis would not work in the context of a 100% functional genome.

Comment #183247

Posted by Steve Reuland on June 15, 2007 10:25 AM (e)

I don’t think “very little unused sequences” means 20% functionality as you imply! I think very little unused sequences looks very suspiciously like ther fully functional genome predicted by ID.

Andrea already answered this, but let me point out that it is the ENCODE researchers who say 20%, not me. And that’s the high end.

If the researchers who worked on this project and published the paper think that 20% or less of the genome is functional, then you are obviously misinterpreting the paper (or rather the press release) if you think it says 100%.

Comment #183263

Posted by ck1 on June 15, 2007 12:04 PM (e)

The article in Nature on the massive ENCODE project is an an overview.

This overview is linked to a series of focused articles dealing with specific aspects of the project - these articles have now been published in a dedicated issue of Genome Research:

http://www.genome.org/current.shtml

The individual articles are open access.

Heavy-duty stuff and a lot to digest, but the issue begins with a “perspective” essay that summarizes the key findings and puts them into context. There are also two commentaries - one on what these findings mean for the definition of “gene” and the other is about phenotypes.

Comment #183264

Posted by harold on June 15, 2007 12:06 PM (e)

James Bond -

You seem to be missing a major point here.

Non-coding DNA is one of many massive problems for ID/creationism. Why would a designer use it every time he magically created a eukaryotic cell, if it was in any way imperfectly functional?

It is NOT a problem for science, nor is its lack - prokaryotes don’t have it.

When creationists gloat over some suggestion of function in non-coding DNA, they’re not scoring a point, they’re merely trying to get one major (and valid) penalty against them overturned on review, long after the fact. They’ve still lost the game, and in reality, the penalty still stands.

Comment #183265

Posted by harold on June 15, 2007 12:08 PM (e)

James Bond -

You seem to be missing a major point here.

Non-coding DNA is one of many massive problems for ID/creationism. Why would a designer use it every time he magically created a eukaryotic cell, if it was in any way imperfectly functional?

It is NOT a problem for science, nor is its lack - prokaryotes don’t have it.

When creationists gloat over some suggestion of function in non-coding DNA, they’re not scoring a point, they’re merely trying to get one major (and valid) penalty against them overturned on review, long after the fact. It doesn’t add a shred of support to their model if some of it has a function; they just think that it mildly reduces the impact of one of the thousands of pieces of evidence and logic against their model. They’ve still lost the game, and in reality, the penalty still stands.

Comment #183273

Posted by someguy on June 15, 2007 12:34 PM (e)

… a recent paper concerning the opossum (Monodelphis domestica) genome. The authors of the paper found that a small fraction of transposable elements shared by the opossum and human genomes appear to contribute to host fitness, apparently by contributing to gene regulation.

In the interest of accuracy, the opossum paper actually reported that of the (very small) fraction of all transposable elements that appear to contribute to regulatory elements in human, the majority were inserted after the opossum-human last common ancestor.

The implication is that this mechanism of evolutionary innovation may be more common than previously known examples have suggested (because the majority of putative regulatory elements are far more ancient, and may therefore have lost any resemblance to “modern” transposons).

Comment #183287

Posted by Steve Reuland on June 15, 2007 1:06 PM (e)

Marc Geerlings wrote:

Yes, you miss something deep here. Like vestigal organs, creationists/IDers oppose every claim that something in the (especially human) body is not perfect created. Surely a perfect creator wouldn’t deal with ‘junk’

Actually, I think there’s something a bit different going on. The ID/creationists can account for the existence of “junk” and other imperfections simply by invoking the mysterious ways of God. (Or, for the literalist set, The Fall.) After all, they’ve got the far more serious problem of evil to contend with, and they wave that away by saying it’s all part of some master plan.

I think where “junk DNA” hits them in the gut is on the subject of common descent. When humans and chimps, for example, contain identical or nearly identical functioning genes, the creationists claim that similar functions require similar solutions, so the Creator independently stuck the same thing in separately created species. However, this excuse doesn’t work with non-functional DNA. If both humans and chimps have the same non-functional DNA (and boy do we), then the only rational explanation for this is that it was derived from a common ancestor.

This puts the creationists in a serious bind. Although they could try to invoke the “wild and crazy God” hypothesis, doing so means that God made things look exactly as if evolution occurred. This is unsatisfying as it makes God out to be a trickster, and just as bad it requires them to admit that the evidence really does favor evolution. It’s much easier for them to deny that the sequences are non-functional to begin with. They’ve been doing this for a long time with vestigial organs, for example by saying that those tiny vestigial legs on fossil whales are really functional, so therefore there’s no reason to believe that whales came from land-dwelling ancestors.

So I think the bit about God not creating junk is simply a new twist on an old position that had been staked out for another reason entirely.

Comment #183293

Posted by CJO on June 15, 2007 1:48 PM (e)

It highlights a common thread in Creationist propaganda: The Big Lie.

Take the best evidence for evolution, play a game of “telephone” with it on the wingnut web, and then claim this garbled reiteration as a Creationist “prediction” to crow about with hollow triumphalism to the credulous and the already converted.

The Cambrian explosion? Selection-driven adaptive radiation into formerly unoccupied (well –non-existent, really) niches.

Irreducible Complexity? Basically evidence of a stochastic process at work, since the hallmarks of rational design at its best are simplicity and elegance, NOT needless complexity.

Complex Specified Information? Okay, Bill, explain this specification to me again. Sounds like function. Selectable function.

And now “junk” DNA. Utterly devastating, so the only way out is the Big Lie.

Comment #183294

Posted by Steve Reuland on June 15, 2007 2:01 PM (e)

someguy wrote:

In the interest of accuracy, the opossum paper actually reported that of the (very small) fraction of all transposable elements that appear to contribute to regulatory elements in human, the majority were inserted after the opossum-human last common ancestor.

You’re right. Actually, that particular paper (Lowe et al.) isn’t involved with the opossum genome project at all – that was a mix-up on my part. I had assumed that because the paper was mentioned in connection with the opossum project in the Wired article that it was part of it. At this point I’m left wondering why Shaffer even mentioned the opossum genome project.

In the Lowe et al. paper, the most distant mammal used was the dog, so that the mobile elements they found have been conserved since the carnivores split from the rodent/primate lineage around 100 MYA. Fortunately that doesn’t change anything I said about it, except where you see “opossum” you should think “dog”.

Comment #183296

Posted by someguy on June 15, 2007 2:28 PM (e)

At this point I’m left wondering why Shaffer even mentioned the opossum genome project.

Probably because the Lowe et al paper and the opossum paper came out at about the same time and reported similar findings. Easy to mix up if your science writing star doesn’t … shine that bright.

Comment #183300

Posted by harold on June 15, 2007 3:00 PM (e)

Steve Reuland -

Actually, I think there’s something a bit different going on. The ID/creationists can account for the existence of “junk” and other imperfections simply by invoking the mysterious ways of God. (Or, for the literalist set, The Fall.) After all, they’ve got the far more serious problem of evil to contend with, and they wave that away by saying it’s all part of some master plan.

True enough when they admit YEC, although it still provokes the awkward claim that God plugged a lot more DNA into eukaryotic, but not prokaryotic, genomes, after the “fall”.

But when they’re trying to do the “ID shuffle”, claiming “objective” evidence for a “designer”, they can’t very well make reference to the Garden of Eden.

Lying gets so complicated.

Comment #183354

Posted by Wade on June 15, 2007 11:00 PM (e)

harold wrote:

It is NOT a problem for science, nor is its lack - prokaryotes don’t have it.

Nick (Matzke) wrote:

3. Only about 5% of the sampled DNA is evolutionarily conserved according to the ENCODE study (ah – the “present study” thing in the present PT post is what got me mixed up), which does not help arguments which say that all DNA is functional.

I cannot believe people don’t see what “Junk DNA” really is. It is the body plan of higher organisms. That’s why prokaryotes don’t have any or very little - they don’t have body plans. That’s why it can be FUNCTIONAL but not conserved. Genome comparisons show that most higher organisms have very similar genes. The reason a human is not a chicken is not because we have different genes, it is because our Non-coding DNA specifies a completely different body plan, brain plan, etc. I don’t expect my body plan to be “conserved” with the chicken body plan. It’s obvious to me, but somehow the science community is “surprised” by the findings.

Comment #183369

Posted by Popper's ghost on June 16, 2007 2:34 AM (e)

I think very little unused sequences looks very suspiciously like ther fully functional genome predicted by ID.

NOTHING is predicted by ID. Try to get that through your martini-addled brain, Mr. Bond.

Comment #183370

Posted by Popper's ghost on June 16, 2007 2:36 AM (e)

It’s obvious to me

Lots of things are obvious to crackpots.

Comment #183378

Posted by Marc Geerlings on June 16, 2007 5:29 AM (e)

>I think very little unused sequences looks very suspiciously like ther fully
>functional genome predicted by ID.

>NOTHING is predicted by ID. Try to get that through your martini-addled brain, >Mr. Bond.

You’re right nothing is predicted by ID, however I will predict that there are two scenario’s exist that will give ID a major boost if they ever will become true:

1. DNA which is fully functional without a lot of “junk”.
2. “Junk” which gets incorporated into the working part, which will be seen as the “creator” had put all our functionality all ready in the DNA and it gets used when needed.

Your comment, how ever true it is, does not help to see in advance how research is gonna used against science. Better to be prepared then willfully ignorant of the danger!

Comment #183390

Posted by harold on June 16, 2007 9:09 AM (e)

Wade -

I cannot believe people don’t see what “Junk DNA” really is. It is the body plan of higher organisms. That’s why prokaryotes don’t have any or very little - they don’t have body plans. That’s why it can be FUNCTIONAL but not conserved. Genome comparisons show that most higher organisms have very similar genes. The reason a human is not a chicken is not because we have different genes, it is because our Non-coding DNA specifies a completely different body plan, brain plan, etc. I don’t expect my body plan to be “conserved” with the chicken body plan. It’s obvious to me, but somehow the science community is “surprised” by the findings.

Your language makes me suspect you may be joking, but putting that aside, this is an example of what I call a “good mistake” (but it’s only good if the person learns something by making it). Because it is a good observation that prokaryotes lack both a multicelluar body plan and significant amounts of non-coding DNA.

Here are the problems with this idea, though -

1. A fair amount is already known about development in multicelluar organisms, and so far, genes play a key role. It is certainly true to a large degree that it is your genes that make you a human, and not a chicken.
http://en.wikipedia.org/wiki/Hox
http://en.wikipedia.org/wiki/Body_plan
http://en.wikipedia.org/wiki/Evolutionary_develo…

2. Despite the recent discussion of the fact that some non-coding DNA is transcribed at a very low level, much, probably most, non-coding DNA lacks intact genetic structure. It doesn’t have the elements necessary to allow known transcription enzymes to transcribe it, or regulate its transcription. And there’s certainly no evidence that during embryogenesis, DNA transcription differs radically in a biochemical sense (of course the relative frequency of transcription of various genes differs wildly in different cells at different times). So it’s very hard to imagine how it could function as transcribed DNA. And obviously, transcription has to be tightly regulated during embryogenesis.

And if it’s not being transcribed to a significant degree, it wouldn’t be very reasonable, at this point in time, to think that it has much specific, controllable effect on cellular physiology by just sitting there.

3. Closesly related organisms have very similar genes, but even within the same species, non-coding DNA structure and sequences can vary a great deal, almost to the extent of being not very strongly correlated within species. So it’s more likely that genetic sequences explain the similarities.

4. Eukaryotes have a much more efficient way of packing DNA into cells, and more space to put it in. So accumulation of non-coding DNA would be expected to be selected against much less severely. Of course replicating extra sequences with each cell division requires slightly more energy, but that’s equally true of both prokaryotes and eukaryotes, whereas only prokaryotes have the “storage” issue. So it’s not necessarily unsurprising, at least in retrospect, that eukaryotes have non-coding DNA and prokaryotes don’t. (Note - this is not necessarily the ONLY reason but it may be one reason.)

If you’re just a citizen who had a thought, you may find this interesting.

If you’re a creationist I’ll get back an illogical and insulting reply, but someone else may find this interesting.

Comment #183391

Posted by harold on June 16, 2007 9:19 AM (e)

Marc Geerling -

You seem to be missing a major point here.

Non-coding DNA is one of many massive problems for ID/creationism. Why would a designer use it every time he magically created a eukaryotic cell, if it was in any way imperfectly functional?

But is NOT a problem for science, nor is its lack - prokaryotes don’t have it. Science can explain non-coding DNA, ID can’t, but take away the non-coding DNA and there are still millions of things that science can explain, and that ID not only can’t, but doesn’t even try to. Science doesn’t rely on non-coding DNA, science was going strong before non-coding DNA was discovered. But non-coding DNA devastates ID.

When creationists gloat over some suggestion of function in non-coding DNA, they’re not scoring a point, they’re merely trying to get one major (and valid) penalty against them overturned on review, long after the fact.

It doesn’t add a shred of support to ID if some or all non-coding DNA has some “function”; it just mildly reduces the impact of one of the thousands of pieces of evidence and logic against their model. Without non-coding DNA, ID makes no sense, with non-coding DNA, it makes no sense, but in the second case, there are .00001% more ways to explain why it makes no sense.

(See my post above for a partial explanation of why, even some of it is transcribed at a low level, most non-coding DNA probably doesn’t have the same kind of strong, specific functionality as genes.)

Comment #183393

Posted by Steve Reuland on June 16, 2007 9:26 AM (e)

Wade wrote:

I cannot believe people don’t see what “Junk DNA” really is. It is the body plan of higher organisms.

So do amoebae have a body plan? If not, why do they have junk DNA?

How about an onion? Does it have a body plan? Does one species of onion have such a radical different body plan that it needs twice the non-coding DNA as another species of onion within the same genus?

Comment #183400

Posted by Marc Geerlings on June 16, 2007 11:57 AM (e)

@Harold

I’m not missing to point, I agree completely with you that everything can explained by ID, but this is not a scientific battle. And Although ID doesn’t predict anything scientifically, it is front-loaded.

- Everything is created by a perfect creator.
- The creation is perfect and by creation they are only thinking about humans.

So they make prediction, not based on science at all, but that is no problem for them, because the majority of the people think if you put on a lab-coat and say a lot of science jargon, that is science. And if something that was called junk which builds human, isn’t junk after-all, this will be seen as a win for Jesus. I will give them wriggle room and maybe enough to convince a judge who is a little bit sympathetic. Again I’m not missing to point, I I only not convinced of the rationality of the majority of people in this world. I’m only saying try to think as the majority of people and especially as the people who try to get us back to the dark ages and have the power to do it. ID doesn’t explain anything scientifically but I think majority of people think it does.

Comment #183403

Posted by harold on June 16, 2007 12:50 PM (e)

Marc Geerlings -

I have a slightly optimistic reply to that.

One thing you may be experiencing is that a lot of people have a misunderstanding of the term “intelligent design”.

A lot of intelligent people initially think that it means what it sounds like it means - they more or less mistake it for simply accepting science without ruling out some kind of God, along the lines of Ken Miller.

Once they find out that ID means such things as claiming that the bacterial flagellum could not have evolved, but had to be specifically, magically created by a “designer”, or claiming that since we can tell that a beehive was designed by bees, therefore we should conclude that all living cells were “designed” by an “intelligent designer” that we ostensibly don’t know anything about, they tend to reject it.

Only time will tell, but the battle against ID has been relatively successful so far.

I also wrote a post about why non-coding DNA isn’t likely to be a major factor in body plan development. For some reason, it seems to have disappeared (it was extemely dry and scientific, not “abusive”). Hopefully it will reappear.

Comment #183410

Posted by Torbjörn Larsson, OM on June 16, 2007 1:18 PM (e)

harold wrote:

I also wrote a post about why non-coding DNA isn’t likely to be a major factor in body plan development. For some reason, it seems to have disappeared

It happened to me too on this very thread - once in a while a comment will come back with ‘Since you are a first time commenter, the comment will be held until approved” - at which point they are as likely to disappear as not.

My comment is now +24 h old and growing older by the minute. Frustrating, really.

Comment #183413

Posted by harold on June 16, 2007 1:51 PM (e)

Tobjorn Larsson -

I realize that hard-working volunteers run this site, and all I do is show up and comment once in a while, but still…

In fact, when I write anything inolved here, I usually copy it and paste into a text file, having been burned so many times (a much higher burn rate for attempted posts than any other site I am aware of).

Ironically, that “first time” message reassured me that the post had been registered, and I failed to do so.

It’s interesting to wonder what “first time” means. I took it to mean “first time you have posted on this particular thread”. Of course, that’s a somewhat inefficient standard for initiating a review, since it will force a review of regular posters’ contributions over and over again, for every new thread they post on.

An alternate explanation is that it’s meant to identify true first time posters, but worked wrong and misidentified us as first-timers. A true first time post would be a logical standard for review. Of course, that only works if you correctly identify first time posts.

So it’s either an inefficient screening system that worked correctly (it was our first post to this thread), or a potentially efficient screening system, but one that didn’t work correctly.

For the record, I only support “banning” anyone either for repetitive disruptiveness long after their points have been addressed, or for really serious abuse, such as actual practical threats, intense profanity, or the use of offensive ethnic, gender, or orientation slurs, or something equally offensive.

Otherwise, I say, let the trolls be heard - and answered.

Comment #183428

Posted by Steve Reuland on June 16, 2007 3:25 PM (e)

Harold, I published your comment, it should show up now. I have no idea why it was held as pending as I’m not the one who runs the site. I should have gotten an email about it, but either I didn’t get it or I didn’t notice it (which happens when you get 50+ emails per thread).

Comment #183448

Posted by raven on June 16, 2007 6:29 PM (e)

Just going to repost an old one. This junk DNA issue is just going around in circles. Some noncoding will have functions, some is just there. The wide variety of genome sizes among mammals tells one that right there. Plust 8% of the human genome is defective retroviruses left over from ancient battles.

raven on April 23, 2007 10:28 AM (e)

From www.genomesize.com
Human is 3.5 pg/cell

Number of mammals: 438
Smallest mammalian genome size: 1.73pg, Miniopterus schreibersi, Bent-winged bat
Largest mammalian genome size: 8.40pg, Tympanoctomys barrerae, Red viscacha rat
Mean for mammals: 3.47pg ± 0.04

Avian genome sizes tend to be smaller.

I’ve no doubt that much noncoding DNA is functional, introns, regulatory regions, etc..As shown by phylogenetic conservation.

Some of it is clearly probably just genome parasites and adventitious accumulations. This is implied by the fact that genome sizes vary widely even within mammals and between mammals and avians. Not seeing how or why the the actual functional genome varies all that much between say mammals. Does the red rat really have twice as many genes as a human? Or a bat half as many?

Comment #183479

Posted by Torbjörn Larsson, OM on June 17, 2007 1:18 AM (e)

harold wrote:

So it’s either an inefficient screening system that worked correctly (it was our first post to this thread), or a potentially efficient screening system, but one that didn’t work correctly.

In other news, dog bit man. :-)

But as the site and its scripts will soon be updated, I hope the next version will be more reliable.

Comment #184445

Posted by raven on June 24, 2007 3:34 PM (e)

Some of the noncoding DNA questions are empirically addressable. In the study below, the authors just deleted big chunks of DNA and made knockout mice from the cells. Nothing much happened even though some of the DNA was conserved from mice to humans.

Reference from “Jerry” previous thread:

1: Nature. 2004 Oct 21;431(7011):988-93.
Megabase deletions of gene deserts result in viable mice.Nóbrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM.
DOE Joint Genome Institute Walnut Creek, California 94598, USA.

The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially ‘disposable DNA’ in the genomes of mammals.