The creationist view of junk DNA

Here's a recent video podcast (Aug. 23, 1022) from the Institute for Creation Research (sic). It features an interview with Dr. Jeff Tomkins of the ICR where he explains the history of junk DNA and why scientists no longer believe in junk DNA.

Most Sandwalk readers will recognize all the lies and distortions but here's the problem: I suspect that the majority of biologists would pretty much agree with the creationist interpretation. They also believe that junk DNA has been refuted and most of our genome is functional.

That's very sad.

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Religion vs science (junk DNA): a blast from the past

I was checking out the science books in our local bookstore the other day and I came across Evolution 2.0 by Perry Marshall. It was published in 2015 but I don't recall seeing it before.

The author is an engineer (The Salem Conjecture) who's a big fan of Intelligent Design. The book is an attempt to prove that evolution is a fraud.

I checked to see if junk DNA was mentioned and came across the following passages on pages 273-275. It's interesting to read them in light of what's happened in the past four years. I think that the view represented in this book is still the standard view in the ID community in spite of the fact that it is factually incorrect and scientifically indefensible.

A theology student doesn't like Jerry Coyne's book Faith vs. Fact

A theology student named Derrick has written a review of Jerry Coyne's book Faith vs. Fact. He didn't like it very much. (Duh!) You can read his review at: Jerry Coyne, Faith Vs. Fact: Why Science and Religion Are Incompatible.

Before reading that review, let's make sure we understand Jerry's position. Here's what he says on page xx of his book.

My main thesis is narrower and, I think, more defensible: understanding reality, in the sense of being able to use what we know to predict what we don't, is best achieved using the tools of science, and is never achieved using the methods of faith. That is attested by the acknowledged success of science in telling us everything from the smallest bits of matter to the origin of the universe itself—compared with the abject failure of religion to tell us anything about gods, including whether they exist.

An Anglican says that science and religion don't conflict

Are you surprised to hear a religious person say that science and religion are not in conflict? Of course you aren't. That's just what you expect religious people to say.

Why in the world would Nature publish an article where an Anglican makes such a claim? [See Religion and science can have a true dialogue] And why in the world should its readers pay any attention at all to the nonsensical first paragraphs ...

I work for the Archbishops’ Council in the Church of England, and this summer I did something that many people would think is impossible. I sat in a dark lecture theatre engrossed in a computationally generated 3D journey through the Universe. Virtual stars whizzed past and seemed narrowly to miss colliding with my head as we accelerated through galaxies and past exploding stars. I listened to cosmologists speak on research into dark matter, particle physics, the rate at which the growth of the Universe is accelerating and the possibi­lity of multi­verses. I asked questions and they responded.

According to the popular narrative on the relationship between science and religion, this event should not have happened. The entire audience was made up of bishops and church leaders. Science and faith, we are constantly told, are in conflict and have little in common.

Really? What "popular narrative" says that Anglican church leaders can't learn about science? What "popular narrative" says that Anglicans cannot accept the findings of physics and cosmology? Who says that?

The problem here is not the ridiculous false claim but the fact that it's published in a leading science journal. I'm not aware of any Nature articles on the conflict between science and religion and the claim that belief in god(s) is not compatible with a scientific way of knowing. Why is Nature getting involved in this debate and why is it taking sides?

Read Jerry Coyne's take on this article at: Fulsome accommodationism in the journal Nature.¹

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1. Keep in mind that Jerry uses the word "accommodationist" to mean anyone, atheist or theist, who thinks that science and religion are compatible. In its original sense, the word "accommodationist" referred only to those people who Dawkins referred to as "Neville Chamberlain evolutionists." These appeasers were atheists who argued that science and religion are compatible. Only atheists can be accomodationists according to this original definition—they one I still adhere to. I don't think it's noteworthy that religious people try to make science and religion compatible.

Templeton gives $8 million to prove that there's more to evolution than natural selection

The Templeton Foundation will fund a group of researchers who promote something called "The Extended Evolutionary Synthesis" (EES). The grant is for $8 million (US). The project is headed by Kevin N, Laland of the University of St. Andrews (Scotland, UK) and Tobias Uller of Lund University in Sweden. You can read all about it at: Putting the Extended Evolutionary Synthesis to the Test.

There are two problems with this funding. The first is the source of the funds. I agree with Jerry Coyne and many others that Templeton Fund money is tainted because the clear purpose of the fund is to lend credence to religion [Templeton keeps up the woo]. Templeton will only fund projects that advance that objective.

The second problem is the science. The advocates of EES promote things like "developmental plasticity," "niche construction," "evo-devo," and "epigenetics"—all of these phenomena are supposed to play a major role in evolutionary theory, a role that is not covered by the Modern Synthesis.

I think that all of these processes may play a role in explaining the history of life on Earth¹ but so do plate tectonics, asteroid impacts, and endosymbiosis. The problem is that there's a difference between explaining the events behind the history of life and evolutionary theory. They are not the same thing.

The real question is whether any of these things need to be incorporated into modern evolutionary theory and whether they extend the Modern Synthesis. Personally, I don't think any of them make a significant contribution to evolutionary theory.

But my real beef is with the outdated view of evolution held by EES proponents. To a large extent they are fighting a strawman version of evolution. They think that the "Modern Synthesis" or "Neo-Darwinism" is the current view of evolutionary theory. They are attacking the old-fashioned view of evolutionary theory that was common in the 1960s but was greatly modified by the incorporation of Neutral Theory and increased emphasis on random genetic drift. The EES proponents all seem to have been asleep when the real revolution occurred.

When you listen to them, you get the distinct impression they have never read The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. I have no confidence in biologists who want to overthrow a view of evolutionary theory that's already been dead for half a century. I have no confidence in biologists who aren't at ease talking about non-adaptive evolution. This is the 21st century.²

Elizabeth Pennisi is all over this. She wrote an article for the April 22 (2016) edition of Science: Templeton grant funds evolution rethink. The opening sentence is very revealing ....

For many evolutionary biologists, nothing gets their dander up faster than proposing that evolution is anything other than the process of natural selection, acting on random mutations.

Damn right! I'm not an evolutionary biologist but my dander gets up whenever scientists make such a ridiculous claim.

Help is one the way, according to Elizabeth Pennisi because the Templeton Foundation is funding research to show that there's more to evolution than natural selection. Unfortunately, the "extended" version doesn't include random genetic drift and modern population genetics.

No wonder some evolutionary biologists are uneasy with an $8.7 million grant to U.K., Swedish, and U.S. researchers for experimental and theoretical work intended to put a revisionist view of evolution, the so-called extended evolutionary synthesis, on a sounder footing. Using a variety of plants, animals, and microbes, the researchers will study the possibility that organisms can influence their own evolution and that inheritance can take place through routes other than the genetic material.

I don't object to work on those subjects. My beef is with the idea that they pose a problem for our current understanding of evolutionary theory. More importantly, my main complaint is that the biologists who will spend all this money missed the real revolution that took place 50 years ago.

Here's how Pennisi describes the extended evolutionary synthesis. Her description is pretty accurate.

The extended evolutionary synthesis is a term coined in 2007 to imply that the preeminent current evolutionary theory, the so-called modern synthesis, needed to broaden its focus because it concentrated too much on the role of genes in evolution and lacked adequate incorporation of new insights from development and other areas of biology. The idea has gradually gathered momentum since its advocates first met in Germany in 2008 (Science, 11 July 2008, p. 196). Later, Kevin Laland, an evolutionary biologist at the University of St. Andrews in the United Kingdom, and several colleagues took up the cause, arranging for a point-counterpoint discussion in Nature in 2014 and a comprehensive review last year in the Proceedings of the Royal Society B's annual Darwin Review.

Advocates stress that animals, plants, and even microbes modify their environments, exhibit plasticity in their physical traits, and behave differently depending on the conditions they face. Chemical modifications of the DNA that affect gene activity—so-called epigenetic changes—seem to explain some of this flexibility. These and other factors suggest to some biologists that an organism's development is not simply programmed by the genetic sequences it inherits. For them, such plasticity implies that parents can influence offspring not just through their DNA but by passing on the microorganisms they host or by transmitting epigenetic marks to subsequent generations. “Innovation may be a developmental response that becomes stabilized through genetic changes,” explains Armin Moczek, an evolutionary developmental biologist at Indiana University, Bloomington.

Nor is evolution controlled only by natural selection, the winnowing process by which the fittest survive and reproduce, Laland and others argue. Organisms, by transforming their environments and responding to environmental factors, help control its course, they contend. As such, the extended synthesis “represents a nascent alternative conceptual framework for evolutionary biology,” Laland and dozens of colleagues wrote in a funding proposal to the Templeton Foundation last year.

This is a profoundly adaptationist view of evolutionary theory. The "extended" version merely adds a few more mechanisms that might improve adaptation.

Most of the EES proponents are working on animals, many are physiologists. They share an evo-devo view of evolution that emphasizes the role of natural selection. I share Michael Lynch's view that we live in a post-Darwinian world and nothing in evolution makes sense except in the light of population genetics. I agree with him that most scientists think of evolution as a soft science and that includes many biologists. It includes most of the EES proponents who probably couldn't tell you anything about population genetics beyond the fact that it's too mathematical. That doesn't stop them from criticizing modern evolutionary theory.

Natural selection is just one of several evolutionary mechanisms, and the failure to realize this is probably the most significant impediment to a fruitful integration of evolutionary theory with molecular, cellular, and developmental biology.

Michael LynchHere's a quote from Michael Lynch's book The Origins of Genome Architecture. In my view, it describes the group who were awarded $8 million to overthrow modern evolutionary theory.

Despite the tremendous theoretical and physical resources now available, the field of evolutionary biology continues to be widely perceived as a soft science. Here I am referring not to the problems associated with those pushing the view that life was created by an intelligent designer, but to a more significant internal issue: a subset of academics who consider themselves strong advocates of evolution but who see no compelling reason to probe the substantial knowledge base of the field. Although this is a heavy charge, it is easy to document. For example, in his 2001 presidential address to the Society for the Study of Evolution, Nick Barton presented a survey that demonstrated that about half of the recent literature devoted to evolutionary issues is far removed from mainstream evolutionary biology.

With the possible exception of behavior, evolutionary biology is treated unlike any other science. Philosophers, sociologists, and ethicists expound on the central role of evolutionary theory in understanding our place in the world. Physicists excited about biocomplexity and computer scientists enamored with genetic algorithms promise a bold new understanding of evolution, and similar claims are made in the emerging field of evolutionary psychology (and its derivatives in political science, economics, and even the humanities). Numerous popularizers of evolution, some with careers focused on defending the teaching of evolution in public schools, are entirely satisfied that a blind adherence to the Darwinian concept of natural selection is a license for such activities. A commonality among all these groups is the near-absence of an appreciation of the most fundamental principles of evolution. Unfortunately, this list extends deep within the life sciences.

The real revolution was the incorporation of nonadaptive mechanisms into evolutionary theory and the overthrow of adaptationism. That revolution is not complete. There are still thousands of biologists who remain strict Darwinists even as they try to promote different ways of achieving adaptation. Those biologists still dominate the popular press (e.g. Elizabeth Pennisi) and they are largely responsible for skepticism about junk DNA. That has to change. Evo-devo types need to listen to Michael Lynch when he says ...

Unfortunately, the emerging field of evolutionary developmental biology is based almost entirely on a paradigm of natural selection, and the near-absence of the concept of nonadaptive processes from the lexicon of those concerned with cellular and developmental evolution does not follow from any formal demonstration of the negligible contribution of such mechanisms but simply reflects the failure to consider them. [my emphasis ... LAM] There is no fundamental reason why cellular and developmental features should be uniquely immune to nonadaptive evolutionary forces. One could even argue that the stringency of natural selection is reduced in complex organisms with behavioral and/or growth from flexibilities that allow individuals to match their phenotypic capabilities to the local environment.

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1. Some of them are trivial and some are ineffective but that's been debated many times. I want to emphasize the fact that EES proponents don't understand modern evolutionary theory.

2. To be fair, some of these proponents do pay lip-service to non-adaptive evolution from time to time but it's clear that they don't really get it.