Monday, October 24, 2011

Stephen Meyer Talks About Junk DNA

Stephen C. Meyer has a Ph.D. degree (1991) in the History and Philosophy of Science from Cambridge University in the UK. He is currently Program Director of the Center for Science and Culture at the Discovery Institute in Seattle, Washington, USA.

Meyer's book, Signature in the Cell: DNA and the Evidence for Intelligent Design, is an attempt to present Intelligent Design Creationism as genuine science. I'll have more to say about this later but for now I want to concentrate on one particular aspect of his case.

Mayer claims that one requirement of a genuine scientific theory is the ability to make falsifiable predictions. Does Intelligent Design Creationism make such predictions? Yes, one of the predictions is that genomes will not contain very much junk DNA. It will be instructive to see how Intelligent Design Creationists handle this issue, especialy since I've just finished a thorough review of The Myth of Junk DNA by Jonathan Wells.

Here's what Meyer says about junk DNA.
Consider the case of so-called junk DNA—the DNA that does not code for proteins found in the genomes of both one-celled organisms and multicellular plants and animals. The theory of intelligent design and materialistic evolutionary theories (both chemical and biological) differ in their interpretation of so-called junk DNA. Since neo-Darwinism holds that new biological information arises as a result of a process of mutational trial and error, it predicts that nonfunctional DNA would tend to accumulate in the genomes of eukaryotic organisms (organisms whose cells contain nuclei). Since most chemical evolutionary theories also envision some role for chance interactions in the origin of biological information, they imply that nonfunctional DNA would have similarly accumulated in the very first simple (prokaryotic) organisms—as a kind of remnant of whatever undirected process first produced functional information in the cell. For this reason, most evolutionary biologists concluded upon the discovery of nonprotein-coding DNA that such DNA was "junk." In their view, discovery of the nonprotein-coding regions confirmed the prediction or expectation of naturalistic evolutionary theories and disconfirmed an implicit prediction of intelligent design.
As I explained in my review of Wells' book, this historical description differs substantially from the truth (i.e. it's a lie). It is not true that neo-Darwinists, or any other advocates of evolution, "predicted" that junk DNA would accumulate in eukaryotic genomes. It is not true that the "discovery" of nonprotein-coding DNA "confirmed the prediction or expectation of naturalistic evolutionary theories." Lots of nonprotein-coding DNA was known to have a function even as far back as 1970.

It's not even true that the presence of true junk DNA (as opposed to nonprotein-coding DNA) was a prediction of evolutionary theory. It looks like Meyer is just parroting the views of Jonathan Wells without applying the requisite skepticism and critical thinking.
As Michael Shermer argues, "Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragmented copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution." Or as Ken Miller argues: "The critics of evolution like to say that the complexity of the genome makes it clear that it was designed .... But there's a problem with that analysis, and it's a serious one. The problem is the genome itself: it's not perfect. In fact, it's riddled with useless information, mistakes, and broken genes .... Molecular biologists actually call some of these regions 'gene deserts,' reflecting their very nature." Or as philosopher of science Philip Kitcher puts it, "If you were designing the genomes of organisms" you would not fill them up with junk."
Shermer, Miller, Kitcher ... don't those names sound familiar? It's the same cast of characters that Wells refers to in his book. What they're saying is that, based on scientific evidence, some genomes have lots of junk DNA and this doesn't fit with the idea of Intelligent Design Creationism. They are correct.

ID advocates advance a different view of nonprotein-coding DNA. The theory of intelligent design predicts that most of the nonprotein-coding sequences in the genome should perform some biological function, even if they do not direct protein synthesis. ID theorists do not deny that mutational processes might have degraded or "broken" some previously functional DNA, but we predict that the functional DNA (the signal) should dwarf the nonfunctional DNA (the noise), and not the reverse. As William Dembski explained and predicted in 1998: "On an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function." The discovery in recent years that non-protein coding DNA performs a diversity of important biological functions has confirmed this prediction. It also decisively refutes prominent critics of intelligent design—including Shermer Miller and Kitchener—who have continued to argue (each as recently as 2008) that the genome is composed of mostly useless DNA.
There you have it. Intelligent Design Creationism is a valid scientific theory because it makes a falsifiable prediction. It predicts that most of our genome will contain functional sequences and only a small amount can be junk.

This prediction has been falsified. Most of our genome is junk. I wonder how long it's going to take before the IDiots realize that they've hitched their theory to a falling star. I wonder how they're going to handle the truth when it finally dawns on they that they are wrong. (I expect a lot of backpeddaling and no outright admission that their "scientific theory" has been falsified.)
Contrary to their claims, recent scientific discoveries have shown that the nonprotein-coding regions of the genome direct the production of RNA molecules that regulate the use of the protein-coding regions of DNA. Cell and genome biologists have also discovered that the supposedly "useless" nonprotein-coding regions of the genome: (1) regulate DNA replication, (2) regulate transcription, (3) mark sites for programmed rearrangements of genetic material, (4) influence the proper folding and maintenance of chromosomes, (5) control the interactions of chromosomes with the nuclear membrane (and matrix), (6) control RNA processing, editing, and splicing, (7) modulate translation) (8) regulate embryological development, (9) repair DNA, and (10) aid in immunodefense of fighting disease among other functions. In some cases, "junk" DNA has even been found to code functional genes.
What an impressive list! Unfortunately for Meyer, none of these functional regions of DNA were ever thought to be junk. Collectively they account for only a few percent of the genome. He probably got all of his scientific information from a fellow IDiot—I wonder who?
Overall, the nonprotein-coding regions of the genome function much like an operating system in a computer that can direct multiple alterations simultaneously. Indeed, far from being "junk," as materialistic theories of evolution assumed, the nonprotein-coding DNA directs the use of other information in the genome, just as an operating system directs the use of the information contained in various application programs stored in a computer. In any case, contrary to the often heard criticism that the theory makes no predictions, intelligent design not only makes a discriminating prediction about the nature of "junk DNA"; recent discoveries about nonprotein-coding DNA confirm the prediction that it makes.
Oops, sorry to disappoint you Stephen Meyer, but you're dead wrong about the facts. The Intelligent Design Creationism prediction has been falsified. Our genome is full of junk DNA. The evidence has allowed us to discriminate between evolution and "God did it." Guess who lost?

Take your friend Jonathan out for a beer, You're both going to need it.


29 comments:

  1. "There you have it. Intelligent Design Creationism is a valid scientific theory because it makes a falsifiable prediction. It predicts that most of our genome will contain functional sequences and only a small amount can be junk.

    This prediction has been falsified. Most of our genome is junk. I wonder how long it's going to take before the IDiots realize that they've hitched their theory to a falling star. I wonder how they're going to handle the truth when it finally dawns on they that they are wrong. (I expect a lot of backpeddaling and no outright admission that their "scientific theory" has been falsified.)"

    I find it strange that you are willing to rely on such a naive version of Popperian falsificationism in defining what is "scientific theory". Surely, there must be more to it than "if it's falsifiable, it's scientific" -- i.e., if the results of the falsification clear and they are not accepted, then you're doing pseudoscience instead of science.

    If a group or viewpoint just brazenly ignores falsifications, then surely they are missing an important part of the role that falsification is supposed to play in science, even if we decide to follow Popper's 1960s-level definition of science.

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  2. I wonder how long it's going to take before the IDiots realize that they've hitched their theory to a falling star. I wonder how they're going to handle the truth when it finally dawns on they that they are wrong. (I expect a lot of backpeddaling and no outright admission that their "scientific theory" has been falsified.)

    You still give Wells, Meyer, et al., too much credit. They *do* realize they're wrong. Wells' and Meyer's books *are* their handling of the truth - deny at all costs, brazen it out, the best defense is a good(?) offense.

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  3. NickM says,

    I find it strange that you are willing to rely on such a naive version of Popperian falsificationism in defining what is "scientific theory".

    I do no such thing. I think it's stupid to rely on falsification to determine what is science and what is not.

    My definition of science is that it's a way of knowing that relies on evidence, rationalism, and healthy skepticism.

    Perhaps you were confusing my version of the philosophy of science with that of the philosopher of science, Stephen Meyer?

    Or maybe you didn't detect the sarcasm?

    I think that most of Intelligent Design Creationism is science—it's just bad science.

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  4. I think that most of Intelligent Design Creationism is science—it's just bad science.

    I think both you and those of us who believe ID is *not* science are partly agenda-driven. You want to make sure ID folk and other creationists can't hide from science behind NOMA or something similar. We want to make sure ID folk and other creationists don't get a constitutional "free pass" to offer their religiously driven curricula in U.S. schools.

    I'm not sure such agenda-driven definitions are the best way to arrive at criteria for what is "not science" vs. what is "bad science." I will suggest, however, that simply because ID is not appropriately taught in schools as science is no reason that it can't be discussed as an example of how not to do science.

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  5. Jud says,

    I think both you and those of us who believe ID is *not* science are partly agenda-driven. You want to make sure ID folk and other creationists can't hide from science behind NOMA or something similar.

    I don't know what you mean by "agenda-driven." I don't believe that there's any other way of knowing other than science. What kind of "agenda" do you think I have other than getting at the truth?

    We want to make sure ID folk and other creationists don't get a constitutional "free pass" to offer their religiously driven curricula in U.S. schools.

    I understand YOUR agenda. You want to use the courts and the constitution (instead of science) to protect you from religious fundamentalists.

    How's that working out so far? Does the current generation of students understand evolution and reject creationism?

    ... simply because ID is not appropriately taught in schools as science is no reason that it can't be discussed as an example of how not to do science.

    I've always been in favor of teaching about Intelligent Design Creationism in science classes.

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  6. @Larry Moran I've always been in favor of teaching about Intelligent Design Creationism in science classes.

    I assume teaching about ID is different than teaching ID.

    Would you also teach about homeopathy, acupuncture, chiropractic and other psuedo-sciences that make claims about the nature of reality ?

    At some point you're going to run out of time to teach real science.

    I guess this could be relegated to an introductory science course.

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  7. Larry said
    My definition of science is that it's a way of knowing that relies on evidence, rationalism, and healthy skepticism.

    What about curiosity? None of the prominent IDers seem to be very interested in the identity of the designer, let alone the means by which he/she/it engineers living organisms. They are very unwilling to speculate on these matters. This I consider the most clearcut sign that ID is not science.

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  8. Dr. Moran writes:

    I understand YOUR agenda. You want to use the courts and the constitution (instead of science) to protect you from religious fundamentalists.

    Fairly close. I wish to use all three, including science, to (1) prevent creationism from being taught in schools as fact, and (2) permit teaching about ID creationism and various other forms of bad science or not-science to encourage critical thinking by students. Not just "this is right, this is wrong" but why they are right or wrong, and the essential roles of the processes that produced the right and wrong conclusions.

    How's that working out so far? Does the current generation of students understand evolution and reject creationism?

    Though the sorts of polls I've seen aren't the most reliable windows into attitudes and understanding among the student age group, let's assume for the sake of this discussion that the understanding of evolution and rejection of creationism among students in the USA is (1) not good overall; and (2) worse than in almost all other developed countries.

    On the other hand, the same can be said of USA students with regard to their understanding of math, physics, etc. - not great in general, and behind that of students in nearly all other developed countries. Thus I'm not sure the lack of success in teaching evolution can be laid in significant part at the door of the legal fight to keep religious instruction (as opposed to discussions about religion) out of schools. I think "how that's working out for us" can be described as successful to the extent that it has prevented many USA students in state-run schools from being instructed in various forms of religious cant, including creationism, as factual biology, history, etc.

    "... simply because ID is not appropriately taught in schools as science is no reason that it can't be discussed as an example of how not to do science."

    I've always been in favor of teaching about Intelligent Design Creationism in science classes.

    Yes, I think we pretty well agree here. One thing I'm not clear on, though (and the source of my "agenda-driven" comment) is this: Quite often when you say ID is bad science, rather than not science, that is juxtaposed with comments by you that ID can be critically examined with the tools of science. This seems to me to indicate that you think if ID is classified as not science, then perhaps there is an argument that science should not be able to critically examine it. Is my impression of what you think incorrect?

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  9. I thought junk DNA was a big surprise and faced opposition at the beginning. In Fisher&co.'s early neo-darwinian framework that included only functional alleles that are affected by selection and drift, what you would not expect is a lot of DNA just sitting there.

    Another question. I don't think you can make any prediction regarding the intentions and thoughts of a supernatural creator. It's not really a prediction, it's just a guess. Maybe the Designer wanted to put all that junk DNA there for some mysterious purpose because His ways are mysterious. Who knows? In my opinion trying to read the mind of the Maker isn't science, it's theology.

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  10. NickM:
    "even if we decide to follow Popper's 1960s-level definition of science"
    Popper's ideas, especially the demarcation criterion discussed here, is from the 1930s. Regardless, no one seems to have done better.
    As far as IDiots being scientific, Moran is saying ID, insofar as it is testable, could be called scientific. The IDiots are clearly not scientific since they ignore, and in fact lie, about the results of those tests. So, according I think to Lakatos, ID, as a research program and an activity carried out by IDiots, is degenerate, and not scientific.

    Judd:
    "I'm not sure such agenda-driven definitions are the best way to arrive at criteria for what is "not science" vs. what is "bad science.""
    Even outside of any agenda, ID can be seen as bad, downright terrible, science. Also, lets not forget to consider the agenda of the IDists, for lots of them, its a Trojan Horse.

    Judd
    "Simply because ID is not appropriately taught in schools as science is no reason that it can't be discussed as an example of how not to do science."
    Lets pretend a school district does just that, what will happen? They will immediately be sued for discrimination against a religion.
    Besides, any discussion of 'an example of bad science' that uses creationism will be pointless, most people recognize it as utterly stupid, better to look at examples of honest attempts at science that failed /because/ the workers deviated from scientific norms (perhaps the rejection of continental drift as a good example)

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  11. SChenck writes:

    Lets pretend a school district does just that, what will happen? They will immediately be sued for discrimination against a religion.

    Oh I don't know. We learned about the motions of the planets, Galileo, the opposition of the Church, etc., and I didn't hear of any Catholic parents or organizations suing the school.

    And when PBS's science series, "Nova," had a program on Kitzmiller v. Dover, the PBS web site featured related teacher resources. I don't recall any lawsuits stemming from teachers using the program in their classrooms.

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  12. Schenk:

    Also, lets not forget to consider the agenda of the IDists, for lots of them, its a Trojan Horse.

    Good point. One only has to look at many of the regular posters and commenters on, say, Uncommon Descent, to see that the science is almost immaterial, other than as an opportunity to shove a bunch of pamphlets in the hands of the vaguely curious.

    I wonder if the fundamental driver is 'separation of church and state' - not an issue here in the UK, where, oddly, religious instruction is the only mandatory subject, and yet it has no nationally set curriculum - teach whatever wibble you like, but teach something, lest people get the idea that one can live wibble-free!.

    But 'over there', AIUI getting ID in school would be the only way, and perhaps a lot of the claptrap about "science is a religion" stems from a second-front strategy - if "they" get their materialistic religion taught, why can't we, we pay our tax dollars too yadda yadda.

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  13. Jud:
    "I didn't hear of any Catholic parents or organizations suing the school.[and after Nova did some shows on evolution] I don't recall any lawsuits stemming from teachers using the program in their classrooms."
    I think that a lot of the Evangelicals out there are just wackier than the Catholics, especially on this issue, they seem to consider it a fundamental issue for their religion. And as far as not suing PBS, I think that the reaction would be different if its the schools, they'll interpret it as forced indoctrination by the state.
    Obviously this is all speculation, but who could've forseen that they'd sue school districts to attempt to get YEC and the like INTO the schools!

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  14. Jud:
    "I didn't hear of any Catholic parents or organizations suing the school.[and after Nova did some shows on evolution] I don't recall any lawsuits stemming from teachers using the program in their classrooms."
    I think that a lot of the Evangelicals out there are just wackier than the Catholics, especially on this issue, they seem to consider it a fundamental issue for their religion. And as far as not suing PBS, I think that the reaction would be different if its the schools, they'll interpret it as forced indoctrination by the state.
    Obviously this is all speculation, but who could've forseen that they'd sue school districts to attempt to get YEC and the like INTO the schools!

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  15. Corneel said...

    None of the prominent IDers seem to be very interested in the identity of the designer

    That's because they know who the designer is, they just aren't honest enough to admit that it's their invisible S&M buddy in the sky.

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  16. Corneel:
    None of the prominent IDers seem to be very interested in the identity of the designer

    Steve Oberski:
    That's because they know who the designer is, they just aren't honest enough to admit that it's their invisible S&M buddy in the sky.


    If one isn't too concerned about one's sanity, a poke round Uncommon Descent is a ... ummm ... revelation. Some skip daintily round the "who-is-the-designer" issue, others dive right in fully clothed. Which is just infuriating. Because a designer can plausibly make things out of bits and pieces it finds lying around. But turns out this designer can make matter and energy and space and time as well, and fiddle with them ad hoc.

    For light relief, try this UD randomiser someone's built - a 'random' selection below.

    Interesting that undesigned phrases can still amuse - a random increase in unspecified ribticklosity (UR), essentially through a process of recombination. Though obviously, one has to be selective.

    "EO Wilson is an entity that can do work – chemical or mechanical."

    "...as a hero of the modern day whale, a primate, became Homo Sapiens"

    "...they were made by scientists who were tossing junior on the assumption that he exists"

    "feathers an adaptation to the redox potential in inorganic molecules."

    "the ID proponents are literally surrounded by mice"

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  17. Interesting!
    http://www.physorg.com/news/2011-10-junk-dna-differences-humans-chimps.html

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  18. The importance of junk DNA:
    http://www.mobilednajournal.com/content/2/1/13/abstract

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  19. @Peter B,

    Have you seen the papers that discuss LINE/SINE/etc targeting from the element's perspective?

    Ex. here's an old review...
    http://microb230.med.upenn.edu/PDF%20Library/BushmanReview.Cell115.pdf

    In my opinion, the paper you link to observes something then attempts to argue correlation=causation. This error plagues many bioinformatic studies at the moment.

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  20. I really have to hand it to Wells et al. They have managed to convince their followers that a theory that has natural selection as a major mechanism is utterly unable to account for the alleged functionality of DNA. If this is not evidence that creationists can be made to believe anything as long as it buttresses their preconceptions, then nothing can be.

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  21. It's amazing that the paper that PeterB referenced takes no account of polymorphism of retroelement insertions. They seem to assume that all the observed insertions in both species are fixed, when a number of recent papers have shown that a large portion of the observed human insertions are dimorphic. It is hard to tell from these papers which and how many insertions are fixed (the folks at dbRIP are working on enumerating the ones that are near fixation in a future release of the database.) Until this is sorted out, any conclusion about the effect of new TE insertions on species differences is premature. You can't account for species differences with insertions that are present at low frequency.

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  22. It is not true that neo-Darwinists, or any other advocates of evolution, "predicted" that junk DNA would accumulate in eukaryotic genomes. It is not true that the "discovery" of nonprotein-coding DNA "confirmed the prediction or expectation of naturalistic evolutionary theories."

    It looks like the atheist evolutionists are the ones back tracking. Say hi to George Carlin when you meet him in Hell.

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  23. dude you should take this post down...because it makes you look foolish in light of this:

    http://io9.com/5940974/so+called-junk-dna-could-be-keeping-you-alive

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    1. It's certainly true that somebody looks foolish.

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  24. Hello,

    I'm not a scientist (and dont' pretend to be) and so am curious to see if your thoughts on this subject have changed any since the recent Nature article published (discussed in NY Times here: http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?_r=0). (By the way, I was researching that article when I found this post.)

    According to this article, as much as 80% of what we thought was junk DNA isn't (and that number could go up). Just so you know, I am in general some type of ID proponent but am really just looking at these various issues as a layman and would appreciate your insight.

    Best,
    Paul

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    1. The ENCODE claim has been discussed on the blogs and in numerous scientific articles.

      Most knowledgeable scientists recognize that the ENCODE Consortium over-interpreted their data. It's simply NOT TRUE that 80% of our genome has a function. It appears that the people responsible for this false claim were not familiar with the extensive literature on junk DNA.

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    2. As I said before, I am somewhat inclined to accept some form of ID and so was very interested in this study, but admit I was a bit skeptical of a such a dramatic increase in the amount of functional DNA. I suspect that some criticisms of the conclusion will show up in Nature too, but one probably shouldn't expect to see as much media attention directed at those (it seems our media tends toward the sensational so defenses of longer-held beliefs tend to get short shrift). Thanks for offering your thoughts on this.

      Best,
      Paul

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  25. Any thoughts on this one:

    http://www.genengnews.com/insight-and-intelligenceand153/what-junk-dna-it-s-an-operating-system/77899872/

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    Replies
    1. Another example of a bad journalist (Patricia Fitzpatrick Dimond) and bad journalism.

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