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Are Falk, Miller, Dawkins, Ayala Socially Guilty? — Highlights of Pellionisz and Sternberg


We have been occasionally graced at UD by visits of DNA researcher Andras Pellionisz who wrote:

the issue of “Junk” DNA itself is much more vital for human kind, since hundreds of millions are dying of “Junk DNA diseases” while the urgency of plunging into active research is overlooked because on ANY ideological grounds.

Those looking at


will realize that for those to whom SCIENCE of “junk” DNA is still not the “mainstream” are socially guilty because of putting priority on ideology over survival.

Hundreds of millions of patients don’t appreciate delay of medicine by ideology.

DNA Researcher Andras Pellionisz

Darwinists like Falk, Miller, Ayala, and Dawkins have generally argued DNA is mostly “junk”, the by-product of mindless Darwinian processes. The pro-junk, anti-mind Darwinist position is what Dr. Pellonisz has labeled a “socially guilty” position.

Personally, I’m ambivalent to the question of whether these Darwinists are socially guility or not. The point remains, however, that the issue of “junk” DNA is of great medical significance.

Recently at EN&V, evolutioanry biologist Richard Sternberg highlights some of the latest issues regarding DNA. I save the technical disucssions for the comment section.

In the mean time, I will highight Sternberg’s framing of the junk DNA issue through his version of Arthur C. Clarke and Stanley Kubrick’s 2001 a Space Odyssey. [Incidentally 2001 a Space Odyssey is not too far from some conceptions of Intelligently Designed Evolution (a view Pellionisz seems almost sympathetic to, and one that Hoyle accepted).]

Moon Mysteries and the Lunarlogos Foundation
Suppose you are keenly interested in the topography of one of the moons, named Y6-9. Suppose also that the books you first select to read on the topic are popular works, written by “experts” who are “living legends.” As you read through the works, you find paragraphs here and there about how utterly decrepit Y6-9 is, and how this space body exemplifies eons of random events. The authors argue that we already knew all there was to know about that moon back in 1859, and that the evidence demonstrates either that God doesn’t exist or that the deity left the cosmos to itself after the Big Bang.

You find, however, that these books almost totally ignore the findings of the billion-dollar missions sent to the surface of Y6-9 since the 1960s. Indeed, there is next to nothing in them about Y6-9’s actual geology.

So you contact the Lunarlogos Foundation, a Christian group that promotes such books. You tell them that you have a few specific questions about the Y6-9 mission findings. The response you get is that because you are a layman, you would not be able to comprehend the details. Besides, the Lunarlogos folks say, the mainstream experts have spoken authoritatively about the subject and that should be enough for you. As a consolation, though, they send you a CD that has songs that are sung by one of their founding members.
Somewhat disgruntled, you decide to spend a day at a university library. You ask a librarian for maps of Y6-9 and technical journals that discuss its features. An hour or so later, with stacks of data before you, something catches your eye—something never mentioned in any of the books you’ve read. Sitting in a Y6-9 crater is a large monolith. High resolution photos reveal it to be rectangular in shape, with a polished surface, and composed of some dense black material. This must be a mistake, you think. So you look at other craters on Y6-9 and many of them also contain the same kind of monolith. You discern their overall distribution to be non-random—and the monoliths themselves are highly non-random. Then, after consulting the literature, you learn: The existence of such objects has been known for over two decades. In fact, one of the experts of Lunarlogos wrote about them in the technical reports of the Y6-9 probe missions.

Now, more than disgruntled, you decide to write about what you have learned, citing the relevant literature in case someone might want to read about this topic themselves. After posting what you write on the Internet, Lunarlogos posts their reply. Their response reads something like this:

Okay. Sure. There are obnoxious monoliths littering Y6-9…everybody knows this. In fact, there are about a million of them. But they got there because of degenerative cosmic processes. While many of the structures Mr. X mentioned are suggestive of some possibly unknown cause that we have never denied, it is almost certain that much, if not most, of the Y6-9 surface is without any remarkable features. Besides, why would God put them there? They are simply nonsensical.

We have one more thing to say. We don’t appreciate how disrespectful Mr. X has been to our team of experts. Although Mr. X is a Ph.D. planetary scientist, he is not as qualified to write on this subject as scientists approved by Lunarlogos. So we ask him, for the sake of having meaningful dialogue: Please stop writing about this subject.

A Lunarlogos sympathizer writes on another blog:

We think you’re a nice guy, but your arguments are insane.

Here are the links to the rest of Sternberg’s essays which are rich with the technical details of his argument against Falk’s view.

Beginning to Decipher the SINE Signal


Discovering Signs in the Genome by Thinking Outside the BioLogos Box


Ayala and Falk Miss the Signs in the Genome

In light of the potential medical importance of junk DNA researchers, it is apparent the issues surrounding ID vs Darwin debate are more than religious, social or political. Real science and important scientific questions are being explored by Pellionisz and his colleagues at the HoloGenomics Society, Sternberg at the Biologic Institute, and John Sanford at Cornell and Logos Research.

Casey Luskin offers his viewpoint: Does Darrel Falk’s Junk DNA Argument for Common Descent Commit “One of the Biggest Mistakes in the History of Molecular Biology”?

Since Ayala won the Templeton prize,,,, "The Templeton Prize honors a living person who has made an exceptional contribution to affirming life’s spiritual dimension, whether through insight, discovery, or practical works." http://www.templetonprize.org/abouttheprize.html ,,,I'm left severely wondering exactly how is Ayala "affirming life's spiritual dimension" when he is vehemently opposed to any ID inference whatsoever in biology? Seems very clear to me he is trying his utmost to belittle "life's spiritual dimension". ,,,This following video shows Ayala getting "whomped", as one Ayala sympathizer put it, by Dr. Craig Is Intelligent Design Viable? http://www.youtube.com/view_play_list?p=C34CF609D7F22AD6 Come to think of it, I believe if anyone has really made exceptional contribution to affirming life’s spiritual dimension, and make people think seriously about that issue, it would be Dr. Craig. bornagain77
Knockout experiments will likely show that there is some functional toleration in the loss of the "junk" regions. However I point out on mathematical grounds alone, that knockout experiments are a terrible method of determining function or lack thereof. See: Airplane Magnetos Contingency Designs and Reasons ID will Prevail. If the regions can be knocked-out, but are redundantly functional (that is they are like spare tires and spare navigation systems, etc.) then those are systems that evidence function that emerged outside of natural selection, and to quote Darwin:
"If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."
That would be the junk DNA regions. It is already well known that most molecular evolution must be independent of natural selection. This hypothesis (neutral evolution) has been used to argue in favor of junk DNA. What if we discover features of the genome which can't be attributable to : 1. Darwinian evolution 2. Neutral evolution 3. chemical and physical law It is circumstantially suggestive of Intelligent Design. I've already suggested, on scientific (not theological) grounds alone that an Intelligent Designer may exist. See: Quantum Enigma of Consciousness, The Identity of the Designer. Even granting that ID might be a fringe hypothesis, it has the advantage over a self-contradictory Darwinian account of "junk" DNA, because the ID mechanism is at least free of the contradictions Sternberg highlights. scordova
von Sternberg comments on how Ayala and his Darwinist friends reason with Square Circles. Ayala and friends simultaneously argue that similar regions between rats and mice are the product of Darwinian processes because they are identical, and they are identical because they are functional, but while functional they are simultaneously functionless because they don't code for proteins and they look like junk to Darwinists. Modern neo-Darwinism reasons in square circles. This isn't science, this isn't even reasonable speculation. Reasonable specualtions should be free of self-contradiction!!!:
Thinking Like a Darwinian Experts such as John Avise, Francisco Ayala, Francis Collins, and Darrel Falk tell us that we must think like Darwinians before we can begin to make sense of the data, since nothing else is scientific, or indeed even reasonable. So let’s play along and think like Darwinians, limiting ourselves to what Collins and his colleagues have authoritatively provided. Recall that they are: •Chance mutations continually degrade genomes that are largely junk •SINEs are for the most part nonsensical junk •Natural selection is the sole creative force in evolution •Except when genetic drift (neutral evolution) is also a factor We can call this conceptual scheme the “BioLogos box.” We’ll start, then, with chance mutations. We know that the enzymes encoded by the L1 retrotransposon copy and paste SINEs into mammalian genomes. So perhaps this is the causative agent that acts independently of primary DNA sequence? And since L1 is present in all mammalian genomes, we may just be on the trail of the “conserved cause.” But wait. L1 also mobilizes itself. This is a problem, for when we compare LINE and SINE distributions along chromosomes, it is clear that in the regions where the former is abundant the latter is not, and vice versa. Remember the graph (from Figure 9d of Ref. 1): But we have no plausible mechanistic explanation for why the mouse L1 machinery would have pasted B1s/B2s/B4s—over twenty-two million years, no less—into the same general locations and at much the same densities, as the rat L1 machinery pasted ID elements over the same period of time. Not to fear. We still have to consider that worker of miracles, natural selection. This mechanism eliminates harmful features while preserving those that enhance survival. So let’s construct a hypothesis: Mouse and rat SINE distributions reflect the differential removal of these DNA repeats from regions where their presence would be harmful. In other words, we predict that sequences where mouse B1s/B2s/B4s and rat IDs peak in density are segments of the genome that are largely junk; conversely, in the sections where these SINEs taper off, functional coding regions are to be found. Does this hypothesis point in the right causal direction? I don’t think so. Here is why. Remember the statement made by Falk in defense of Ayala contra Meyer:
He [Ayala] does say that on average there are about 40 copies of Alu sequences between every two genes, but this is simply a fact.
Well, both Falk and Ayala are correct—and that is the problem with the selection hypothesis. Protein-coding genes make up only ~1.5% of the mammalian genome. Where do the peaks of B1s/B2s/B4s and IDs occur along the mouse and rat chromosomes, respectively? In and around the ~1.5% of the genome that is protein-coding. Remember the following statement in the sentence of the Nature paper quoted above1:
The cause of the unusual distribution patterns of SINEs, accumulating in gene-rich regions where other interspersed repeats are scarce, is apparently a conserved feature, independent of the primary sequence of the SINE... (Italics mine.)
Whatever the mystery cause is, it plucked out the species-specific SINEs from the junkety-junk LINE regions, and piled them high around the “twenty-five thousand genes” of the mouse and rat. Or it directed the SINEs to rain down on the gene-rich regions and in much lesser amounts elsewhere. This contradicts our selection hypothesis, unless the SINEs are doing something important in and around those protein-coding regions. But since so much ink has been spilled arguing that nothing of the sort is the case—these are junk elements, even harmful—we must turn to some other factor. Reaching into the BioLogos box, we now pull out “genetic drift.” Neutral evolution means that a mutation—regardless of whether it is beneficial, neutral, or negative—can become fixed or lost in a lineage solely by chance. With respect to a SINE insertion, its persistence in a lineage would have to be a genetic coin toss: If heads, the SINE stays in a site; if tails, it is lost. So for a pure neutralist model to account for the graphs we have seen, ~300,000 random mutation events in the mouse have to match, somehow, the ~300,000 random mutation events in the rat. What are the odds of that?
Ayala given the Templeton? No surprise: See: Templeton's Love Affair with Darwinism scordova
Yep, that's the same Ayala: Francisco Ayala, the winner of the 2010 Templeton Prize. Allen_MacNeill
You are not referring to the Ayala who won the prize of the Templeton Foundation, do you? osteonectin
I think Dr von Sternberg is to be commended for, if not making a prediction, starting down the path to making a prediction. He has identified the distribution of SINEs (at a level smaller than the isochore) as a possible signal. I look forward to hearing more about how he will decide if it is a signal. Otherwise he just spent three posts trying to piddle on BioLogos with little to show for it. Nakashima
Off topic: Rube Goldberg and his Cartoon Machines - video http://www.history.com/shows/modern-marvels/videos/rube-goldbergs-cartoon-machines#rube-goldbergs-cartoon-machines bornagain77

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