Wednesday, September 26, 2007

Will the IDiots Make the Same Mistake with RNA that They Made with Junk DNA?

 
Robert Crowther (whoever that is) posted a similar question on the Intelligent Design Creationis blog of the Discovery Institute. His question was Will Darwinists Make the Same Mistake with RNA that They Made in Ignoring So-Called "Junk" DNA?.
One interesting thing that leapt out at me when reading this was the fact that, while many scientists now realize that it was a mistake to jump to the conclusion that there were massive amounts of "junk" in DNA (because they were trying to fit the research into a Darwinian model), they are on the verge of committing the same exact mistake all over again, this time with RNA.
In order to understand such a bizarre question you have to put yourself in the shoes of an IDiot. They firmly believe that the concept of junk DNA has been overturned by recent scientific results. According to them, the predictions of Intelligent Design Creationism have been vindicated and all of the junk DNA has a function.

Of course this isn't true but, unfortunately, there are some scientists whose level of intelligence is not much above that of the typical IDiot [Junk DNA in New Scientist] [The Role of Ultraconserved Non-Coding Elements in Mammalian Genomes].

Now the IDiots have turned their attention to RNA. They fell hook line and sinker for the hype about functional sequences in junk DNA and they're falling just as easily for the hype about new RNAs. They believe all those silly papers that attribute function to every concevable RNA molecule that has ever been predicted or detected in some assay.

The IDiots were wrong about junk DNA and they're wrong about RNA. The answer to my question is "yes," the IDiots will make the same mistake. You can practically count on it. The answer to Crowther's question is "no." Most (but not all) scientists did not fall for the spin on junk DNA and they realize that the vast majority of our genome is junk. In the long run, they will not fall for the claim that most of the junk DNA is functional because it encodes essential RNA molecules.

12 comments :

  1. Thanks for making these important points, Larry Moran. I'm a little bit confused, still, about the definition of junk DNA. I've heard Genomicron and Alex Pallazo (spelling) say that JUNK DNA is sections of the Genome with no described function. On the other hand, here it seems as if you are implying that JUNK DNA are sections of the genome that do not code for essential RNA etc.

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  2. Junk DNA is DNA that has no biological function.

    I think that lots of junk DNA can be transcribed. One obvious example is transcribed pseudogenes.

    If an RNA is essential then the gene for that RNA is not junk.

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  3. > According to them, the predictions of Intelligent Design Creationism have been vindicated and all of the junk DNA has a function.

    Well, no, IDiots aren't that idiotic, the point is that a measure of agnosticism is in order, if we found function for DNA which was said (proclaimed!) to be functionless. So we should not be so confident in such areas where we don't know.

    I suppose I need a jibe for the non-IDiots, let's see, if it's not an ID, it's an EGO! Evolution Gets Omnipotent.

    Let us hope--not a super-ego...

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  4. Robert Crowther (whoever that is)

    At the The Panda's Thumb he has been described as the Center (for the Renewal of) Science and Culture Media Complaints Division PR man.

    Note that the IDiots are catching up on proteomics and other descriptions of biomolecules and their functions in cells: Jonathan Wells is working on a forthcoming book about genetics titled The End of the Genetic Paradigm.

    More junk to debunk.

    I've heard Genomicron and Alex Pallazo (spelling) say that JUNK DNA is sections of the Genome with no described function.

    That is Alex Palazzo.

    I think Larry and TR Gregory may differ a bit in description:

    “Junk DNA”, which originally was coined in reference to now-functionless gene duplicates (i.e., true broken-down “junk”), is now used as “a catch-all phrase for chromosomal sequences with no apparent function” (Moore 1996). Its current usage also implies a lack of function which is accurate by definition for pseudogenes in regard to protein-coding, but which does not hold for all non-coding elements. [Bold added]

    Gregory wants to retire the concept:

    Because it is generally no longer applied in its original meaningful sense, because the type of DNA to which it actually relates now has a more descriptive name (pseudogenes), and because of its connotations of total phenotypic inertness, the term “junk DNA” should probably be abandoned in favour of less subjective terminology. "Non-coding DNA" serves this purpose quite well.

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  5. lee_merrill:

    the point is that a measure of agnosticism is in order

    The point is that we know the maximum amount of DNA that ought to have function. It is a prediction from evolutionary theory:

    5% of the genome sequence is conserved across mammals, and for about 60% of this (i.e., 3% of the genome) there is additional evidence of function. This includes the protein-coding exons as well as regulatory elements and other functional sequences. So, at this stage, we have increasingly convincing evidence of function for about 3% of the genome, with another 2% likely to fall into this category as it becomes more thoroughly characterized.

    This will be yet another test of evolutionary biology theory, in the years to come. Meanwhile the vacuous IDC refuses to make any specific predictions.

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  6. > The point is that we know the maximum amount of DNA that ought to have function. It is a prediction from evolutionary theory...

    Well, no, it's an observation from evolutionary theory, this measure--seems to me.

    But the point remains that what we don't know, we should say we don't know, rather than assume that because we see no function, there is no function.

    If tomorrow a discovery is made that non-coding DNA is (say) structurally important, or is needed for spacing the time between gene transcriptions, then this estimate of what is functional will increase?

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  7. lee_merrill:

    I can see how you don't like the observation, which of course is independent of the theory, and the prediction, but the fact remains that this is known to scientists.

    However, you yourself urged us to be agnostic on what we don't know, so why you would support wild guesses of function outside of those supportable 5 % is beyond reasonable understanding.

    Your last question is perhaps a statement that you don't understand what a prediction and its test means.

    The discussed estimate is AFAIK fairly robust, it will probably not change much with new data, which is why I suggested it could work as a test.

    Further a prediction must be based on data independent of its test data, or it wouldn't be a test.

    In this case the prediction is based on sequence conservation. While the test would consist of such functional data you describe.

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  8. lee_merrill says,

    But the point remains that what we don't know, we should say we don't know, rather than assume that because we see no function, there is no function.

    We know a lot more than you think. We know for instance, that most of the junk DNA is composed of small repetitive sequences. They are derived from known genes so they count as pseudogenes and they are defective. (There's a posting coming on this topic. I suspect there are readers who know where I'm going with recent posts.)

    We know that the junk DNA accumulates mutations at a rate consistent with no function. We know that the amount of junk DNA in different vertebrate species can vary by a factor of two or three suggesting that even the amount of DNA is not functional.

    We have a very sound knowledge of the basic processes of molecular biology and genetics and there's nothing that suggests this DNA could be functional. On the other hand, the fact that it could be junk is consistent with what we know about evolution and molecular biology.

    It's been known since the late 1960's that humans could not tolerate the genetic load if more than 5% of our genome were essential.

    Scientists have been looking for functions in junk DNA for 40 years without finding anything significant.

    Put all of this together and you can see that the concept of junk DNA is not just some wild speculation based on ignorance.

    But you already knew that, didn't you?

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  9. > However, you yourself urged us to be agnostic on what we don't know, so why you would support wild guesses of function...

    Well, no, I'm not saying there is (or is not) function.

    > We have a very sound knowledge of the basic processes of molecular biology and genetics and there's nothing that suggests this DNA could be functional.

    Nor was there (apparently) before the discovery of transcription controls in the junk! And maybe it's some functional tangent like timing control, or struts in the DNA for structure, or who knows what, some non-coding reason to have that DNA around that is still unlooked-for.

    > It's been known since the late 1960's that humans could not tolerate the genetic load if more than 5% of our genome were essential.

    That's interesting, I would hope to hear more about this some time?

    > Put all of this together and you can see that the concept of junk DNA is not just some wild speculation based on ignorance.

    Well yes, but what I mostly object to is proclamation of the label as a strong conclusion, a conclusive defeat of the poor IDiots. This would perchance bespeak a lack of objectivity.

    > But you already knew that, didn't you?

    Well, no--I am no biologist, nor the son of a biologist. I appreciate your replies to folks here, and your biologic...

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  10. Speaking as a population genetecist...

    I do think "junk DNA" is probably just a bad term. Sure, a large amount of DNA doesn't seem to have any known purpose. But lots of recent research, not just the ultraconserved sequences mentioned here, continues to suggest that some of that DNA might have a purpose (see , for example, Andolfatto 2005). That said, there's also a lot of stuff that almost certainly isn't directly adaptive -- the majority of the average plant genome, for example, is made up of transposons. But labeling it all "junk DNA" is sort of silly, an oversimplification that erroneously suggests that we know what most of that DNA is (or isn't) doing. Fact is, we still don't have a clue what most DNA that is clearly recongizable as a gene does. So, while I like a chance to jump on ID as much as the next guy, perhaps we should hold off on this one, or at least tone down the rhetoric.

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  11. lee_merrill says,

    Nor was there (apparently) before the discovery of transcription controls in the junk!

    I think you've been taken in by the recent hype. We've known about regulatory sequences in non-coding DNA since the 1960's. They were never, ever, thought to be junk DNA.

    Just because there are some modern scientists who apparently never read a textbook, does not mean that regulatory sequences have just been discovered.

    There's a brief description of genetic load here: [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome].

    Well yes, but what I mostly object to is proclamation of the label as a strong conclusion, a conclusive defeat of the poor IDiots. This would perchance bespeak a lack of objectivity.

    That's not the way I see it. I believe it is a strong conclusion based on four decades of research. You need to get past this idea that by calling something "junk" we are merely expressing our ignorance. That's not how it is at all. We really, really, do have evidence that most of the DNA in our genome has no function.

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  12. maundering gadabout says,

    But labeling it all "junk DNA" is sort of silly, an oversimplification that erroneously suggests that we know what most of that DNA is (or isn't) doing.

    I'm sorry, but I strongly disagree with this characterization of the discussion. We really do have a pretty good idea of what most of the DNA is (or isn't) doing. We haven't just been burying our heads in the sand for 40 years.

    Don't be taken in by the recent hype in the scientific literature. It's in the best interests of modern researchers to blow the trumpets whenever they discover some new little piece of DNA that has a function. Meanwhile, the big picture doesn't change.

    True, there are some papers that claim to have uncovered massive amounts of function in some of the noncoding DNA that we think of as junk. Those papers are very controversial. They are almost certainly wrong, in my opinion, because they conflict with so much evidence to the contrary.

    Fact is, we still don't have a clue what most DNA that is clearly recongizable as a gene does.

    Don't include me in that category. Yes, it's true that there are many putative genes in our genome who's function is currently unknown but that's not what you imply. You seem to be implying that we can't tell the difference between a gene and non-gene. That's a gross exaggeration. And in any case, it won't help your argument. All of the work in the past 15 years indicates that we tend to over-estimate the number of genes not under-estimate it.

    So, while I like a chance to jump on ID as much as the next guy, perhaps we should hold off on this one, or at least tone down the rhetoric.

    This isn't about the IDiots. I've been studying and teaching about the organization of genomes long before I was ever interested in Intelligent Design Creationism and long before any creationist ever heard of a genome. This is about legitimate science and how to interpret data and test hypotheses.

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