Sandwalk: Kat Arney defends junk DNA

Thursday, July 28, 2022

Kat Arney defends junk DNA

I'm a big fan of Kat Arney and I loved her 2016 book Herding Hemingway's Cats where she interviews a number of prominent scientists. If you haven't read it you should try and get a copy even if it's just to read the chapters on Mark Ptashne, Dan Graur, and Adrian Bird. The last chapter begins with an attempt to interview Evelyn Fox Keller but don't be put off by that because the rest of the chapter is very scientific.

Kar Arney gets mentioned a couple of times in my book and I quote her opinion of epigenetics from the chapter on Adrian Bird. She has a much better understanding of genes, genomes, and junk DNA that every other person who's ever written a book on those subjects. I especially like what she has to say about her journey of discovery on page 259 near the end of the book.

Things that I thought were solid fact have been exposed as dogma and scientific hearsay, based on little evidence but repeated enough times by researchers, textbooks, and journalists until they feel real.
Kat Arney (2016)

Kat Arney has just (July 28, 2022) posted a Genetics Society podcast on Genetics Unzipped. The main title is Does size matter when it comes to your genes and the subsections are "Where have all the genes gone?" "Genes or junk?" and "Are you more special than an onion?" You can listen to the podcast on that site (24 minutes) or read the entire transcript.

I don't entirely agree with everything she says in the podcast but she should be applauded for defending junk DNA in the face of all the scientific hearsay that out there. Good for her.

Here's three things that I might have said differently.

I don't agree with her historical account of estimates of the number of genes in the human genome [False History and the Number of Genes 2010]. The knowledgeable experts in the field were predicting about 30,000 genes and their estimates weren't far off. The figure below is from Hatje et al. (2019). Note the anomalous estimates from the GeneSweep lottery and the EST data. The EST data were known to be highly suspect. This is important because the false narrative promotes the idea that scientists knew very little about the human genome before the sequence was published and it promotes the idea that there's some great mystery (too few genes) that needs to be solved.
I disagree with her statement that "actual genes makes up less than 2% of all the DNA in the whole human genome." My disagreement depends somewhat on the definition of a gene but that's not really controversial. We're talking about the molecular gene and that's defined as "A gene is a DNA sequence that is transcribed to produce a functional product" [What Is a Gene?]. There are exceptions but this is the best definition we have. The fact that a great many scientists are confused about this is no excuse. Genes include introns so the typical human gene is quite large. In fact, about 45% of the human genome is devoted to genes. This is a far cry from the small percentage (<2%) that consists only of coding regions.

Kat Arney says, "So, given that most of our genome isn’t actually genes, what does the rest of it do? Well, it’s complicated, and there’s still a lot we don’t know." My quibble here is subtle but I think it's important. I think we have a pretty good handle on the functional parts of our genome and I don't expect any surprises. We know that about 10% of our genome is conserved and we can account for most of that functional DNA. The rest is not a mystery. We know that most of it consists of various flotsam and jetsam related to transposons and things like pseudogenes and dead viruses. This is junk DNA by any definition and we should stop pretending that it's a big mystery. When we say that 90% of our genome is junk that's not a reflection of ignorance; it's an evidence-based conclusion.

Hatje, K., Mühlhausen, S., Simm, D., and Kollmar, M. (2019) The Protein-Coding Human Genome: Annotating High-Hanging Fruits. BioEssays, 0(0), 1900066. [doi: 10.1002/bies.201900066]

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)

Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)

Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Peter Atkins

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake. Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory. Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change. Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance. Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change. Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat. Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is True

I once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000

It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma

One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick

There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner

An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins

Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod

The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.

Richard Lewontin

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Thursday, July 28, 2022

Kat Arney defends junk DNA

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