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Monday, August 05, 2019

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.
Take the issue of so-called junk DNA, or "non-coding DNA" as it's known today.1 We are aware that 3 percent of the human genome codes for proteins.2 In 1972, a scientist coined the term junk DNA to describe the 97 percent of DNA with no known function.3 Some scientists still maintain that large portions of the genome are useless accretions of evolutionary garbage.4

The ENCODE project ("Encyclopedia of DNA Elements") was started in 2003 to find all the functional elements of the human genome. The 'New York Times' announced, "Bits of Mystery DNA, Far from 'Junk,' Play Crucial Role," and went on to say.
The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as "junk" but that turns out to play critical roles in controlling how cells, organs and other tissues behave. The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches.5
Science magazine's report was entitled. "ENCODE Project Writes Eulogy for Junk DNA." There is no such thing as junk in the trunk when it comes to DNA.6

A tiny contingent of diehard junk-DNA advocates, such as Larry Moran of the University of Toronto, insisted that the ENCODE announcement was a "media fiasco."7 ENCODE found over 80 percent of the genome is involved in RNA production, DNA expression, or replication, for at least one cell type. ENCODE has expanded into a family of investigations into noncoding DNA functions. 8

Do Larry Moran and other junk-DNA advocates also happen to share any particular bias with respect to religion? Check and see for yourself.

If we assume purposelessness in evolution, as is done in the 1.0 version, it's logical to expect a lot of junk. If we assume a designer, we assume there's a purpose to its inclusion, and therefore, look into it until we discover it's not really junk after all. 9


The people who say parts of DNA are junk say so out of ignorance, not knowledge. They don't know how to build a cell or a genome. They don't know what everything does. The burden of proof that junk DNA is truly junk is on them. Until they understand everything and can explain every nuance of the genome's operation in precise detail—until they can build a cell from scratch—their job is not done.... 10

Any scientist who takes his work seriously has no choice but to say, "I don't know what it function is, but my job is to fully engage in the systematic study of the structure and behavior of this until I do. So until I have a complete working model that describes the entire system in exact detail, I have no right to assume these stretches of DNA are junk.

1. Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means
2. It's no more than 1%. [What's In Your Genome? - The Pie Chart] [How many protein-coding genes in the human genome?]
3. He's referring to the paper by Susumu Ohno (1972). Ohno did not say that 97% of our genome is junk and he did not say or imply that all noncoding DNA was junk. He estimated that no more than 6% of our genome could be devoted to genes and he knew that some of the noncoding parts include promoters, regulatory sequences, and centromeres. [Required reading for the junk DNA debate]
4. Today, a majority of knowledgeable scientists agree that most of our genome is junk and the number is growing every year as more and more scientists become aware of the overwhelming evidence for junk DNA. [What is the dominant view of junk DNA?]
5. The New York Times is not a reliable source of information about science.
6. Science is usually a reliable source of scientific information but in this case Elizabeth Pennisi gets it all wrong [Science Writes Eulogy for Junk DNA ].
7. [The ENCODE publicity campaign of 2007] [The truth about ENCODE]
8. [ENCODE's false claims about the number of regulatory sites per gene] [What did the ENCODE Consortium say in 2012?]
9. Atheism does not predict anything about the composition of our genome or any other genome. From our knowledge of biochemistry and evolution, we might have guessed that most genomes would be packed with functional sequences because junk DNA is likely to be deleterious. Natural selection should eliminate junk DNA in populations undergoing strong selection. That's what we see in bacterial populations. The discovery of massive amounts of junk DNA in mammals conflicted with this simple understanding of evolution but it was consistent with the view of evolution that was developed in the late 1960s. That view allowed for the expansion of the genome by adding junk DNA in populations that were not under strong selection. With respect to the existence of junk DNA, it doesn't matter whether you are a believer or not. What matters is whether you accept scientific evidence or reject it. Many believers reject science because of their religious bias.
10. Only one side of this debate is basing their view on ignorance and lack of knowledge and it's not the scientists. There is plenty of evidence for junk DNA [Five Things You Should Know if You Want to Participate in the Junk DNA Debate].


John Harshman said...


Joe Felsenstein said...

If we assume purposelessness in evolution, as is done in the 1.0 version, it's logical to expect a lot of junk.

I recall that in the 1970s there were many evolutionary biologists who were astonished that so much of the genome was crap. We assumed that natural selection would have eliminated that. It took some more careful thought to see that sequences like families of transposons could accumulate without being immediately screened out.

In creationists' revision of history, we were all predicting lots of junk in the genome. That's certainly not the way I remember it.

Larry Moran said...

Your memory is accurate; furthermore, even today there are still lots of evolutionary biologists who are skeptical of junk DNA because they assume it would have been eliminated by natural selection.

Arlin said...

Also in the 1970s apparently there were many scientists surprised at neutrality and stochasticity. According to Grodwohl, many theoreticians were engaged in looking for the maximization principle in evolution. When this research program imploded, people like Lewontin and Kimura went looking for other opportunities.

I have a favorite quotation to reflect the change in attitude that happened as a result of the molecular revolution. Originally, King and Jukes (1969) invoked the correlation between amino acid frequency in proteins, and codon number in the genetic code, as evidence of neutrality. King later retracted this and argued that such a correlation follows if evolution is a stochastic mutation-limited process, even if fixations are selective. Maynard Smith (1975) recites this argument and then says:

"Hence the correlation does not enable us to decide between the two [i.e., neutrality and selection]. However, it is worth remembering that *if* we accept the selectionist view that most substitutions are selective, we cannot at the same time assume that there is a unique deterministic course for evolution. Instead, we must assume that there are alternative ways in which a protein can evolve, the actual path taken depending on chance events. This seems to be the minimum concession the selectionists will have to make to the neutralists; they may have to concede much more." (p. 106)

Joe Felsenstein said...

Grodwohl starts by quoting me. I don't think that "this research program imploded". It just turned out that the theory was too intractable to find out what quantity was maximized in deterministic models of population genetics. If such a quantity were findable, it would not have been mean fitness but it would have reflected fitness as well as recombination, and yes, mutation. There would also be some stochastic version, maximizing some properties of the distributions of gene frequencies. Alas, not solvable analytically. But I still argue, worth looking for, as it would give us a succinct picture of how the details of evolutionary and genetic processes compromise adaptation.

Joe Felsenstein said...

I would add, and many molecular biologists who are so fascinated by the analogy between a cell and a machine that they are sure that all those details of the genome must reflect subtle functions of the machine. And so ignorant of population genetics that they don't understand the arguments against having that many finely-adapted features of the cell. And besides, think of all the grants that can be applied for to work all this out.

Larry Moran said...

It's true that many (most?) biochemists and molecular biologists don't understand modern evolutionary theory. I used to attend meetings of biochemistry and molecular biology instructors and most of them couldn't explain why the amino acid sequences of most proteins were different in different species.

We also know that most of the ENCODE labs, consisting of hundreds of scientists, couldn't interpret their results correctly.

Fair Witness said...

Marshall has his own brand of ID that says life did evolve, but only because a creator front-loaded the first genome with all the knowledge of HOW to evolve. I once asked him to point out all the "self-modifying code" that would be required for this to be true. He deflected by naming several researchers who supposedly had already done this (they haven't).

Larry Moran said...

This is the problem with non-experts who write about evolution. They think they understand what's going on because they rely on other "experts" who teach them about evolution. But if you aren't a biologist you can't tell which experts to believe and which ones to reject. That's when you start to look foolish writing a book on a subject you know very little about.

Joe Felsenstein said...

There is the insurmountable problem of how, once you load an early eukaryote with all the information needed to make an elephant and a redwood tree, etc., do you keep that from mutating away? But I suppose Marshall doesn't mean that, but that mutation, selection, and other evolutionary forces will do the job, but only after Marshall's special evolution code has been inserted into the cell. He doesn't explain how these forces are prevented from working without this special code.

Fair Witness said...

Larry, were you not aware of Marshall's blog posts for which you were the topic?