Saturday, October 3, 2009

Stephen Matheson: Talking Trash About Junk DNA

A reader upbraided me for my recent post on “junk” DNA and pointed me to the harsh words of evolutionist Stephen Matheson on “junk” DNA, which I had not seen before. Let’s have a look:

"Junk DNA" is a very popular subject among anti-evolution commentators. At the Discovery Institute (DI) and Reasons To Believe (RTB), as well as other creationist outlets, you can find ample discussion of "junk DNA" and why it matters to Christians who don't like evolution.

I've mentioned this topic several times myself, because I believe that the misuse of science by creationists is seldom more in evidence than when opponents of evolution confront genetics and genomics.

The opening move by evolutionists is to equate any and all skeptics as creationists.

As I've noted before, common descent provides a superior explanation for the extraordinary facts gleaned through comparative genomics

In the evolution genre, phrases like “common descent provides a superior explanation” are code for “the evidence falsifies creation.” The reasoning is always contrastive as Elliott Sober points out. Evolution and common descent are problematic, but there is no alternative. Of course that is a religious claim. But wait …

and there is no competing scientific explanation.

Not only is common descent the superior explanation, it is the only scientific explanation. This is a standard argument in the genre: make up your own definition of science which just so happens to exclude empirical approaches.

As I see it, a knowledgeable Christian person considering these data has exactly two rational alternatives: 1) acknowledge the explanatory power of common ancestry and accept its reality; or 2) acknowledge the appearance of common ancestry but deny its reality.

Well at least non Christians are allowed to follow the data. This is the usual “it’s either common descent or a cosmic conspiracy” false dichotomy. Appearance of common ancestry? That's strange, beyond speculation there is no explanation of how it would work. Matheson states that his writings are about scientific explanation. So far we have the usual evolutionary metaphysics and dogma.

Any other choice is indicative of ignorance or of some form of intellectual dishonesty.

It is the height of hypocrisy for evolutionists to be lecturing skeptics about their supposed intellectual dishonesty. Evolutionary thought is based on and motivated by non scientific, religious and philosophical, concerns which they mask as “just science.” It is rationalism masquerading as empiricism. And they then castigate skeptics as dishonest.

I have advocated the use of the concept of folk science to account for the tendency of some apologists (e.g., the "scholars" at Reasons To Believe) to misrepresent science

The ad hominem is another standard evolutionary attack. Credentials don’t matter. One can be a genuine scholar only if one accepts evolution.

in defense of their preconceived interpretive framework.

More hypocrisy as the evolutionists, who openly mandate naturalism, divine a preconceived framework in the work of those who (i) express none and (ii) find scientific problems with evolution.

Creationists insist that "junk DNA" is functional and therefore that evolutionary claims regarding its origin are mistaken.

This is not universally true, but it is a strong tendency that is worth pointing out. The “nature must be functional, and even perfect” view goes back to Paley and eighteenth century English natural theology, and was/is an important foil for Darwin and today’s evolutionists. However, history is on the natural theologian’s side as we continue to discover function for what evolutionists thought were useless structures.

Creationists of various stripes commonly claim that because evolutionary biologists automatically assumed that non-coding DNA lacked function, little or no research on the subject occurred for decades. That claim is doubly false: biologists have always adopted various stances on the functional roles of non-coding DNA, and consequently research into its function has proceeded apace.

Matheson freely generalizes about creationists but resists generalizations about evolutionists. It is true that various stances were adopted vis-à-vis “junk” DNA, but the view that it is non functional has been prevalent and used as an evolutionary apologetic.

Enormous numbers of DNA elements that make up the bulk of the human genome -- and most of its non-coding "junk" segments -- have been identified and are being actively investigated by molecular biologists. These elements are anything but mysterious: they are so-called mobile genetic elements of various kinds, with well-known properties. Their properties, and their use in scores of analyses of evolutionary relationships, are systematically omitted from creationist writings on the subject.

Good point. More needs to be written on these successful predictions of evolution. For instance, it needs to be pointed out that evolutionists turn these successes into compelling evidence by applying Darwin’s Principle.

The proteins that enable animals to smell are called olfactory receptors (ORs). The human genome contains about 800 OR genes, but more than half of them have been inactivated by mutation, yielding what are called pseudogenes. These "fossil genes" are found in precisely the same locations within the genome as are the fully-functional versions in other mammals (i.e., mice). Analysis of these genes and their properties has led to the construction of a highly coherent explanatory framework that accounts for the existence of these pseudogenes and the evolution of smell in vertebrates. Looking for a creationist approach to these data? The word 'olfactory' appears nowhere on RTB's website; at the DI, you'll find it in lots of articles...about stem cells.

Well I’ve written on pseudogenes, but that appears nowhere on Matheson’s website. Indeed, Matheson seems to avoid those pseudogenes that contradict the evolutionary expectations. Nor does he seem to consider non evolutionary explanations.

It certainly is true that there are plenty of evidences in biology that fit the evolutionary expectations. But there are plenty of evidences that do not, and many of them are staggering—far more so than the positive evidences (which are mainly circumstantial) are supportive.

The preponderance of empirical evidence does not bode well for evolution. Of course we can argue about how to weigh this evidence and that, and just where the theory stands. But the theory is unquestionably not a fact. This is different than saying it is not true.

When we say evolution is not a fact we are pointing out the state of our knowledge. We cannot conclude with any level of confidence that evolution is true or compelling. We certainly are in no position to equate it with the fact of gravity (something we sense every waking moment).

But this is precisely what evolutionists claim. They say evolution is every bit as much a fact as is gravity. They argue we know this from the scientific evidence. But this is unquestionably false.

The problem is not that evolutionists are hypothesizing a scientifically questionable theory—it is that they are mandating a scientifically questionable theory. This is what is so telling about evolution.

Sure evolution might be true. It does not seem likely from the science, but perhaps somehow, some way, it occurred.

Nonetheless evolutionists are certain they are right, and of course theirs is a metaphysical certainty. Religion drives science, and it matters.


  1. Sir, there is no such thing as an evolutionist, you create this straw man to bring up arguments up against to further your organizations propaganda and lies.

    What you are calling an evolutionist is actually practically every single scientist! Through many different disciplines from sub-branches of physics, chemistry, biology, geology correlations have been made with each other and with history and they have all provided and strengthened evolution to the level of practical truth.

    You are deliberately mis-representing ID with actual science and comparing your unfounded ideas with hypotheses. You take the latest ideas, which still need to proven out and use them as fodder to argue your case, whereas in fact, it is science working as it should; namely asking questions, coming up with falsifiable theories, and challenging each other.

    Intelligent design has consistently failed such a level of peer review and has not produced a single peer-reviewed paper; you exist in on an intellectual island kibitzing at those who are honestly attempting to understand our universe.

    You do your religion a dis-service.

  2. Wrong, it is a demonstrable scientific fact that evolution occurs and is an actual phenomenon, in the same way it is with gravity;

    You can complain all you want that this is only 'microevolution' but it is still, according to basic population genetics, evolution. It is still an actual process that we can observe and understand. NOBODY HAS EVER EVEN OBSERVED 'MICRO' DESIGN OR 'MICRO' CREATION.
    Even if simply observing 'microevolution' and then extrapolating it to much larger scales were the only evidence we had for evolution in general it would still be infinitely superior to all proposed alternatives.

  3. It is a fact that evolution happens; that biodiversity and complexity does increase, that both occur naturally only by evolutionary means.

    It is a fact that alleles vary with increasing distinction in reproductive populations and that these are accelerated in genetically isolated groups.

    It is a fact that natural selection, sexual selection, and genetic drift have all been proven to have predictable effect in guiding this variance.

    It is a fact that significant beneficial mutations do occur and are inherited by descendant groups, and that multiple independent sets of biological markers exist to trace these lineages backwards over many generations.

    It is a fact that birds are a subset of dinosaurs the same way humans are a subset of apes, primates, eutherian mammals, and vertebrate deuterostome animals.

    It is a fact that the collective genome of all animals has been traced to its most basal form, and that those forms are also indicated by comparative morphology, physiology, and embryological development.

    It is a fact that everything on earth has definite relatives either living nearby or evident in the fossil record.

    It is a fact that the fossil record holds hundreds of definitely transitional species even according to its strictest definition, and that both microevolution and macroevolution ( have been directly-observed.

    Evolution is a fact!

  4. Dr. Hunter,

    The comments from rabid Darwinists are hilarious. They make such a caricature of themselves and prove every point you are trying to make about them. They seem to think that screaming "evolution is a fact" enough times will make it true.

    Many of them are blind fools who are incapable of seeing the facts, especially in genetics, that contradict Darwinian evolution, many of which you have pointed out very succinctly.

    I am a graduate student studying computer science. In my area of study, I have never seen science conducted in such a shoddy manner as I have witnessed in evolutionary biology. Massive amounts of contradictory evidence is either shoehorned into the theory, or ignored. It's mind boggling to me.

  5. Interesting how neither Mr Hunter nor his 'fan' limbo give an alternative explanation for why humans and chimps share thousands of pseudogenes in the same places in their genomes.
    Even YEC biologist Todd Wood admits, "it is difficult to explain why pseudogenes with the exact same substitutions or deletions would be shared between species that did not share a common ancestor."

    Or why many of those pseudogenes show clear evidence of being adapted to a prior manner of life (such as the vitellogenin gene used for egg yolk that is found in humans, chimps and other placental mammals) but is in the same place and is functional in egg-laying mammals like the platypus.

    No, we have nothing but complaints, and moaning about various anomalies that Mr Hunter declares can not be explained by evolution. How do you know that, sir? What don't you go to the next meeting of evolutionary biologists near you and present this stuff and make a case for your alternative? Or would that be too much like actual science?

    I notice elsewhere that Mr Hunter has an article about Sean Carroll presenting SINES and LINES as evidence for evolution. Another excerpt from the book in question is;
    "There are some individuals with scientific credentials who doubt or deny certain elements of evolutionary science that are widely accepted by the scientific community; some may even doubt the entire theory. But getting a doctoral degree and making negative statements are relatively easy - making new, verifiable discoveries is an altogether different matter. The deniers specialize in rhetoric and mining of quotes."

    I think that sums you and the ID movement up rather well. I suggest you get yourself down to the 'Biologic Institute' and help out. After all the entire output of it with all its ‘researchers’ so far is easily exceeded by any reasonably productive individual scientist.

  6. Who said I was a YEC and what does that have to do with anything in this post? Attacking a strawman won't help your crusade :-)

    Darwin was wrong about virtually everything important, that's obvious to anyone who objectively looks at the facts. The fact that some chose to practically deify the man just makes me scratch my head and wonder.

  7. Limbo, I did not say anywhere that you were a YEC. If you are incapable of reading and understanding English that is not my fault. If you are I suggest you read what I wrote again, and try to point to where I said you were a YEC.

    I notice neither you nor your fellow evolution-denier Mr Hunter can give me an explanation for the data I presented.

    So far, in 150 years, no data has cropped up that challenges the basic ideas Darwin proposed: modern species arose through descent with modification through natural selection. Moreover, every new advance in biology has confirmed these ideas at ever-increasing levels of detail.

  8. "So far, in 150 years, no data has cropped up that challenges the basic ideas Darwin presented ..."

    This is an astonishing mis representation of science, but it is typical. Evolutionists hold that there is no evidence against their theory. What an indictment against evolutionary thought.

    It would be like saying there is no evidence against geocentrism.

  9. "So far, in 150 years, no data has cropped up..."

    What about the fossil record, including the Cambrian explosion? Where's the progressive, step-wise change from simple to complex?

    What about the discovery that the DNA of living things like the sea anemone, which have been around since the Cambrian (500,000,000 odd years ago), have DNA every bit as complex as modern creatures?

    How do these facts confirm Darwin's theories, "at an ever increasing level of detail", as you put it.

    I guess the part I don't get is this: why do we need to overreach so badly when the picture of what really happened is so unclear? I have nothing against proposing theories in an attempt to explain the origin of living things, but why do they have to be presented with such certainty, and why do those who point out the obvious problems have to be treated with such contempt?

  10. Whether or not you guys like at that is the position of the scientific community.

    This is not to say evolution explains absolutely everything and that we know all the details, of course we don't. But that is not the case for any scientific theory, and if that eventually becomes the state of affairs scientists will have nothing more to do. Many theories have obvious problems with them, such as our understanding of gravity, or our obviously flawed classic model of atomic structure. However, there are basic ideas within these 'theories' that have been established beyond any reasonable doubt;
    - atoms exist
    - gravity is a natural phenomena causing objects with mass to attract each other
    - living organisms are descended from common ancestors and natural selection played a role in the diversification

    Could anybody here name me a single working paleontologist, at a research institution and with a record of scientific publications in the field, who thinks that the Cambrian slow fuse poses a problem for the theory of evolution? I don't just want quote-mined articles. I want to be able to contact the scientist in question so that I can verify his/her position.

  11. "living organisms are descended from common ancestors and natural selection played a role in the diversification'

    That's pretty watered down and vague, especially "ancestors" and "played a role". Where did these ancestors come from, and how many were there? And, of course natural selection played a role in diversification. Nobody questions that.

    That statement is completely compatible with ID too. The devil is in the details.

  12. That was what I meant when I said "So far, in 150 years, no data has cropped up that challenges the basic ideas Darwin proposed: modern species arose through descent with modification through natural selection. Moreover, every new advance in biology has confirmed these ideas at ever-increasing levels of detail." So I am glad you now agree with me.

    From a scientific viewpoint it isn't really important whether or not it is compatible with ID, as ID isn't a scientific idea. No aspect of ID creationism comes even close to qualifying as science. ID in a general sense as a philosophical position is of course compatible with evolution.

  13. "So far, in 150 years, no data has cropped up that challenges the basic ideas Darwin proposed: modern species arose through descent with modification through natural selection"

    You're equivocating all over the place, namely in what Darwin actually proposed, and in what modern day evolutionary theory (neo Darwinism) claims to explain (and the metaphysical baggage that comes with those explanations). That's where the overreach comes in.

  14. Darwins though that cells were simple blobs of jelly. Its noot too hard to imagine that developing from random accidents. But now we know that the simplest cell is at least as complex as a city. This is much harder to explain in Darwinian terms. And Darwin thought that heredity was controlled by blobby things called gemules. Gemules were thougt to be very mammiabel. Now that heredity is controlled by genes, which are passed down intact as discrete units from parent to offspring, unless an accident occurs. This makes it much harder to account for the variation tha natural selection acts on.

  15. There are from 2 million to 10 million species that exist now. There have been anywere from 20,000,000 to 1,000,000,000 species that are now extinct. If only 1% of these case of speciation left a trace in the fossil record, then there would be 200,000 to 10,000,000 transtional fossils. That is a lot more than the 3 dozen or so posted on the talkorigins list. And some of those transitons are transitions between major groups, not species to species. Evolution means species to species change, so some of those transitions a not really evidence of evolution.

  16. sorry, typo

    "mammiabel"should be malliable.