Saturday, December 02, 2006

The IDiots Don't Understand Junk DNA

So what else is new?

The chief IDiot (Casey Luskin) over at Discovery Institute claims that junk DNA is a science-stopper. This is such old news.

Every time scientists find a function for some non-coding DNA we are treated to another diatribe against junk DNA. In fairness, it's not just the IDiots who do this. Some so-called scientists are just as guilty. They don't understand junk DNA.

Here's a clue. Junk DNA is DNA that has no function. It is not non-coding DNA. Lots of non-coding DNA has a function (regulatory sequences, origins of replication, centromeres, telomeres, SARs, etc. etc). But, in mammals, most of it doesn't. Most of the human genome is junk.

Just because we discover a function for some little bit of non-coding DNA does not mean that all of it has a function. Use your head. This is elementary rationalism. Oops, I almost forgot, that's not their strong point.

Think of pseudogenes or degenerative alu sequences, for example. They will always be junk DNA.

19 comments :

  1. I certainly agree with what you are saying about Casey Luskin’s statements.
    However, being a molecular biologist rather then an evolutionary biologist I have some problems with your definition of junk DNA:

    "Here's a clue. Junk DNA is DNA that has no function. … Think of pseudogenes or degenerative alu sequences, for example. They will always be junk DNA."

    IMO the term is rather operationally then in depth defined. It is used in cases in which we can’t ascribe any function to a given piece of DNA. However, this doesn’t mean lack of function. Indeed, it really depends on the perspective of the researcher. E.g., when I worked on the promoter of a mammalian gene that contains long stretches of GGA repeats we initially did not think that this sequence may have any function. Indeed, such sequences are excluded from blast searches due to their low complexity and their relatively high frequency in eukaryotic genomes (provided one doesn’t switch off the low complexity filter). However, when we found out that the very same sequence is conserved in other sequences we made deletion mutants that showed that this “junk” is essential for the transcription of the gene.
    In addition, one should keep the following points in mind:
    Lack of function only means lack of function under the very experimental settings used to investigate a sequence (e.g. differential methylation of ALU elements may play a role in gene regulation). A sequence may lack a function for the genome it is located in but may well have a function for itself (e.g. retrotransposition of functional ALU elements)
    Any stretch of sequence may have had a function in ancestors or may develop some function in the future (e.g. exonization of ALU elements). In addition one should be aware that “function” does not necessarily mean “beneficial” (e.g., there are cases in which a retrotransposed ALU elements caused genetic diseases).
    Thus, “junk DNA” means “we currently don’t have a clue about the sequence in question”. However, this statement always contains the subtext “but we will work like hell on it if we should get any hints that the sequence might be functional in some interesting way”.

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  2. I don't disagree. There will always be cases where some bits of DNA that we currently include in the "junk" category turn out to have a function.

    That's not the point. The point is that we are extremely confident that a large amount of the mamalian genome really is junk. It's not just a definition based on ignorance. We've been working on the problem for over thirty years.

    You don't dismiss all this data and call the whole concept of junk DNA into question just because some little bit of functional DNA has been discovered. That's what's happening all too often, and unfortunately, it's being done by people who should known better.

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  3. Since intelligent design is rhetoric, not science, it's hardly surprising that IDers use scientific terms in any way they find rhetorically advantageous.

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  4. Casey Luskin is not overly bright. But i think I can match this story. In a recent debate about ID at Cornell, Hannah Maxson characterized Heisenberg's uncertainty priciple as a 'science stopper'.

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  5. Hannah Maxson, word has it, is a triple major in chemistry, physics and mathematics.

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  6. I am not sure that name calling really helps in figuring out the very likely potential of 98.7% of human DNA playing role(s) in DNA function.

    Why call ID-ots those who were actually much closer to scientific findings (that an ever-increasing part of "junk DNA" is definitely anything but "junk") than most (not all) primitive Darwinists, who maintained that function of DNA can be understood by ignoring 98.7% of it (that was "junk")?

    The fact is, that primitive Darwinism actually has a rather formidable problem with "junk DNA". The notion is in direct conflict with the axiom that "the survival of the fittest" would simply squeeze out in evolution anything that is not functional - or even outright harmful (as well known glitches in "junk DNA" clearly are).

    Why don't BOTH SIDES drop all "name calling" and "pseudo-debates" and simply focus ON THE SCIENTIFIC CHALLENGE that 98.7% of the human DNA poses?

    Ample scientific background is provided e.g. at http://www.junkdna.com/new_citations.html

    For those who wish to plunge into the algorithmic (hardest of hard core) approaches, see e.g. quantitative predictions of the "FractoGene" approach at http://www.fractogene.com , now with experimental support published in peer-reviewed science journal

    http://www.junkdna.com/fractogene/05_simons_pellionisz.pdf

    pellionisz_at*NOSPAM*_junkdna.com

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  7. "Why call ID-ots those who were actually much closer to scientific findings (that an ever-increasing part of "junk DNA" is definitely anything but "junk")"

    Being lucky that a non-science based claim accidentially fits with scientific findings doesn't make IDists babble more reasonable. Science always includes the possibility of unintentional errors. However, it is the very nature of science to correct errors and wrong assumptions and it has indeed done so over centuries. In contrast ID is creationism in disguise not willing and indeed unable to overcome its dogma of a designer. Thus, guys like Casey Luskin play in a completely different league and it is not only fair but absolutely necessary to keep them out of science

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  8. Dr. Andras J. Pellionisz says,

    The fact is, that primitive Darwinism actually has a rather formidable problem with "junk DNA". The notion is in direct conflict with the axiom that "the survival of the fittest" would simply squeeze out in evolution anything that is not functional - or even outright harmful (as well known glitches in "junk DNA" clearly are).

    I agree. Ultra-Darwinians like Richard Dawkins and Daniel Dennett have a problem with junk DNA. It doesn't fit into their worldview.

    That's a problem they'll have to deal with. It's not a problem for pluralists like me.

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  9. I am certain in time we will understand that the term "junk DNA" is a gross misnomer. On what authority do I make such a claim? Well, not much. I am not a geneticist or a molecular biologist. In fact, I only know slightly more about DNA than the average college educated person. However, as a software developer I have a vague idea of how many bytes of code is needed to make complex software programs. And to think that something as complicated as a human being is encoded in only 3 billion base pairs of DNA is astounding. I think it's more probable that the human DNA which we have discovered so far doesn't contain all the information required to produce humans. I wouldn't be suprised if more DNA, or some other kind of information, is discovered.

    http://randystimpson.blogspot.com/2007/06/junk-dna-is-myth.html

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  10. Intelligent Designer says,

    I am certain in time we will understand that the term "junk DNA" is a gross misnomer. On what authority do I make such a claim? Well, not much.

    That's correct, you are not knowledgeable enough about the subject to have an informed opinion.

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  11. Let me be more specific. To be more specific, since DNA alphabet consists of 4 nucleobases, we can represent a nucleobase with 2 bits data. This means that 4 base pairs can be represented by a byte of data and approximately 4 million base pairs can be represented by a megabyte of data. This means that the entire human genome can be represented by only 750MB of data. To suggest that 97% of DNA is junk implies the implausible -- that less than 23MB of DNA is not junk. Microsoft Word has a size of 12MB.

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  12. A bacterial genome is about 4 million base pairs and there's no junk. Thus, 1MB of data is sufficient for an ordinary bacterial cell.

    Mammals have 23X more data. That seems quite reasonable to me. Why is it a problem for you?

    Your entire argument is based on ignorance of basic biology. Why do you think anyone should listen to you?

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  13. I hope you aren't suggesting that human beings are only 23 times as complex as bacteria. If that is what you believe why should anyone listen to you?

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  14. Intelligent Designer says,

    I hope you aren't suggesting that human beings are only 23 times as complex as bacteria. If that is what you believe why should anyone listen to you?

    I'm saying that humans only need 23X as much functional DNA. I base my statement on scientific facts. What evidence do you have?

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  15. Which scientific facts tell us that humans only needs 23X as much fuctional DNA is bacteria? Since you are so sure of that, tell me how much DNA is dedicated to the following human functions or features.

    1) Tissue repair
    2) The immune system
    3) The formation of our bone structure
    4) Eye sight
    5) ... 23) Pick the ones you know most about
    24)The brain

    Feel free to provide your estimates in terms of B where B is the amount of DNA in a bacteria.

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  16. It would make biologists' work a lot easier if there were "brain DNA" and "eye DNA".

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  17. I don't know Devin. If hypothetically there were bits of DNA that were categorically brain or eye, then what would stop biology from having a bit of DNA for my cute dimples or my chiseled chin? It would be a nightmare of DNA to sort through and nothing would get done. Clearly modern molecular biology is superior.

    Also, to intelligent designer: 3 billion base pairs includes the junk DNA. There really isn't any other source of DNA in the human cells, except for mitochondria. Furthermore, DNA was established to be the molecule of heredity way back-- there is no other molecule. Hence, when given the fact that humans have 23 times more DNA than bacteria, logic demands the conclusion that it must be at least sufficient. Of course, it is more than sufficient as any biologist will tell you. Returning to my satirical example, organisms don't work by dedicating volumes of data for traits. It all returns to an overarching theme in biology, that complex things can arise out of simple things. Demanding answers to your non sequiturs won't help you understand that.

    I also find it odd that a software developer compared DNA to a text file, rather than to a computer program. I'm personally insulted in the same way rednecks take offense to evolution: I'm not made up of no ASCII!

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  18. Dunbar says,

    I also find it odd that a software developer compared DNA to a text file, rather than to a computer program.

    Microsoft Word is not a text file. It is an executable program used to create Word documents.

    Dunbar says,

    given the fact that humans have 23 times more DNA than bacteria, logic demands the conclusion that it must be at least sufficient

    But humans have 750 more times DNA than bacteria. My point is that given our perceived complexity compared to bacteria, it isn't plausable to think that we have only 23 times as much functional DNA as bacteria and to consider the rest junk.

    Since neither you, nor I or any one else knows what the vast majority of DNA does, let's try to estimate a lower bound for a plausable amount of functional DNA. Now when it comes to estimates, it's standard practice in my industry to estimate the parts and add them together to get an estimate for the whole. That is what I propose we do.

    Let's start with the ability to perform tissue repair (I wish my car could do that). So Professor Morgan, would you guestimate that this feature deserves .2B, .5B, B, 2B, 5B or something way more or less?

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  19. Since neither you, nor I or any one else knows what the vast majority of DNA does, let's try to estimate a lower bound for a plausable amount of functional DNA. Now when it comes to estimates, it's standard practice in my industry to estimate the parts and add them together to get an estimate for the whole. That is what I propose we do.

    One does not have to know what the vast majority of DNA does in order to characterise it. By definition, a gene must have some sort of functional product, be it RNA or protein. For instance, any microarray will demonstrate that only a small percentage of the human genome codes for protein-- all without knowing what sort of function such protein may code for. Since scientists have indeed characterised much of the human genome as having no function, all with good evidence, it is foolish to suggest that you have evidence to the contrary. Simply stating your incredulity isn't good enough. By example, you perceive humans to be more complex than bacteria, which is gross hubris. There is no doubt that humans have specific adaptations that bacteria do not have, but bacteria perform practically all of the complex metabolic processes essential for life, from photosynthesis to the citric acid cycle to even digestion in our guts. The collective genetic variation in our gut flora is probably greater than our own.
    Thus, it is not inconceivable that humans only have 23 times more functional DNA than the average bacterium (where did the number come from incidentally?). Your demands for estimates do not serve your premise at all, because the genome doesn't work like that. Most genes cannot be categorically labelled as serving one function. By analogy, a same piece of operating code may allow two different programs to access memory or do similar tasks. If you insist on treating every trait in humans like it requires a sacred amount of DNA, then of course you will arrive at your erroneous conclusion that all of our genome must be put to use.

    Instead of posting a very old thread, it may be advisable to read all the past posts on junk DNA. I have helpfully included such a search: http://sandwalk.blogspot.com/search?q=junk+dna

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