Junk & Jonathan: Part 3—The Preface

Here's the preface to The Myth of Junk DNA by the IDiot, Jonathan Wells. After each paragraph I've inserted a short version of the truth just so you don't get misled by all the untruths and distortions that are found in creationist books.

See:

Junk & Jonathan: Part I—Getting the History Correct

Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?

Jonathan, Moonies, and Junk DNA

The discovery in the 1970s that only a tiny percentage of our DNA codes for proteins prompted some prominent biologists at the time to suggest that most of our DNA is functionless junk. Although other biologists predicted that non-protein-coding DNA would turn out to be functional, the idea that most of our DNA is junk became the dominant view among biologists.

• It's true that in the 1970s the experts in the study of genomes proposed that most of our genome is junk.
• It's not true that they thought non-coding DNA had no function. Functions of non-coding DNA were well-established by 1970.
• The idea that most of our genome is junk was never the "dominant" view among biologists even though it's correct.

That view has turned out to be spectacularly wrong. Since 1990--and especially after completion of the Human Genome Project in 2003--many hundreds of articles have appeared in the scientific literature documenting the various functions of non-protein coding DNA, and more are being published every week.

• It's not true that the idea of a large amount of junk DNA has turned out to be "spectacularly wrong."
• It's true that there have been lots of examples of of novel functions for small pieces of the genome that were previously lumped into the junk DNA category. These dozens of functional parts of the genome may amount to as much as 1-2% of the genome (probably less).

Ironically, even after evidence for the functionality of non-protein coding DNA began flooding into the scientific literature, some leading apologists for Darwinian evolution ratcheted up claims that "junk DNA" provides evidence for their theory and evidence against intelligent design. Since 2004, biologists Richard Dawkins, Douglas Futuyma, Kenneth Miller, Jerry Coyne and John Avise have published books using this argument. So have philosopher of science Philip Kitcher and historian of science Michael Shermer. So has Francis Collins, former head of the Human Genome Project and present director of the National Institutes of Health, despite the fact that he co-authored some of the scientific articles providing evidence against "junk DNA."

• It's true that well-established bits of junk DNA—like known pseudogenes—have been effectively used to challenge the idea that our genome appears designed. Those examples remain powerful, and true, examples of evolution that cannot be explained by Intelligent Design Creationism. They have not been refuted and they have not been explained by the IDiots.

These authors claim to speak for "science," but they have actually been promoting an anti-scientific myth that ignores the evidence and relies on theological speculations instead. For the sake of science, it's time to expose the myth for what it is.

• The truth is that those authors still speak for science and truth and their evidence is sound.
• Wells, on the other hand, speaks for the other side.

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Genomes
& Junk DNA

Far from consisting mainly of junk that provides evidence against intelligent design, our genome is increasingly revealing itself to be a multidimensional, integrated system in which non-protein-coding DNA performs a wide variety of functions. If anything, it provides evidence for intelligent design. Even apart from possible implications for intelligent design, however, the demise of the myth of junk DNA promises to stimulate more research into the mysteries of the genome. These are exciting times for scientists willing to follow the evidence wherever it leads.

• It's certainly true that non-coding DNA performs a wide variety of functions. Some of them are listed in various postings under Genomes & Junk DNA
• It's certainly not true that the organization of our genome—the majority of which is junk—provides evidence of intelligent design.
• It's certainly not true that the idea of junk DNA is a myth.
• It's true that these are exciting times and that smart people must follow the evidence wherever it leads even if it refutes cherished religious beliefs.

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[Hat Tip: Preface to The Myth of Junk DNA by Jonathan Wells]

Junk & Jonathan: Part 13—Chapter 10

This is part 13 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

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The title of Chapter 10 is "From Junk DNA to a New Understanding of the Genome." It's a very misleading title since the bulk of the chapter is an attempt to refute the arguments of various evolutionary biologists.

In this chapter, we return to the arguments based on junk DNA that we encountered in Chapter 2. Richard Dawkins, Kenneth Miller, Michael Shermer, Francis Collins, Philip Kitcher, Jerry Coyne and John Avise all claimed that most of our DNA is nonfunctional junk, and that this provides evidence for Darwinian evolution and against intelligent design (ID).

Wells' statement is very misleading. He's confusing the argument about conserved pseudogenes with a claim that most of our genome is junk. Several of these authors have pointed out that the presence of similar pseudogenes at the same location in the genomes of different species (e.g. humans and chimps) is powerful evidence of descent from a common ancestor. They also point out that the IDiots have a hard time explaining such observations [Creationist Logic]. (In fact, no IDiot has ever offered a satisfactory explanation.)

Nessa Carey doesn't understand junk DNA

Nessa Carey is a science writer with a Ph.D. in virology and she is a former Senior Lecturer in Molecular Biology at Imperial College, London.

She has written a book on junk DNA but it's not available yet (in Canada). Judging by her background, she should be able to sort through the controversy and make a valuable contribution to informing the public but, as we've already noted Nessa Carey and New Scientist don't understand the junk DNA debate.

Casey Luskin has a copy of the book so he wrote a blog post on Evolution News & Views. He's thrilled to find someone else who dismisses junk DNA and "confirms" the predictions of Intelligent Design Creationism. I hope Nessa Carey is happy that the IDiots are pleased with her book [New Book on "Junk DNA" Surveys the Functions of Non-Coding DNA].

Junk & Jonathan: Part 5—Chapter 2

This is part of my review of The Myth of Junk DNA. For a list of other postings on this topic see the link to Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

Chapter 2 is Junk DNA: The Last Icon of Evolution? It's mostly an explanation of how the concept of junk DNA fits into evolution. According to Wells, Darwin's theory of evolution by natural selection explains how living things descend with modification from a common ancestor. (Recall that Wells rejects common ancestry.) Wells explains that Darwin's original idea has been extended with the discovery of DNA. He describes "neo-Darwinism" like this ...

According to neo-Darwinism, traits are passed on by genes that reside on microscopic thread-like structures in the cells called chromosomes, and new traits arise from accidental genetic mutations.

In order to clear up any confusion, Wells tells us that, "... I will use "Darwinism" in the rest of the book to mean both Darwin's theory and neo-Darwinism" (p. 19). This is important since it's clear that he's talking about the theory of natural selection when he talks about Darwinism or neo-Darwinism.

Wells describes how Ohno coined the term "junk" DNA in 1972 then quotes Richard Dawkins as a supporter of junk. He states his belief that a couple of papers on selfish DNA in 1980 were taken as evidence of junk. He concludes that ...

... some biologists were skeptical of the notion of "junk DNA" from the very beginning—though most accepted it.

Wells fails to distinguish between those biologists who recognize the existence of junk DNA (e.g. pseudogenes) and those who thought that most of our genome is junk. I still believe that only a minority of biologists think that most our genome is junk. I also think that many biologists make a distinction between "junk" and "selfish." I know I do. In my mind "selfish" DNA, such as active transposons or endogenous retroviruses, isn't junk.

Next comes a couple of pages under the subheading "Using Junk DNA as Evidence for Darwinism and Against Intelligent Design." The usual suspects are mentioned. He quotes Ken Miller, Douglas Futuyma, Michael Shermer, Francis Collins, Phil Kitcher, Jerry Coyne, and John Avise. Although their emphasis varies, they all make the point that the presence of junk DNA in our genome is not consistent with intelligent design. It is, however, consistent with evolution (but not natural selection).

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Genomes
& Junk DNAIt's important to note that biologists don't, with rare exceptions, claim that the presence of junk DNA is evidence for Darwinism or evolution. It's consistent with our understanding of modern evolutionary theory but compact genomes with no junk would also be consistent with evolution, especially evolution by natural selection.

Most of these writers are pointing out how difficult it is for Intelligent Design Creationists to make their case in light of massive amounts of junk in our genome. They are mostly arguing against design and not for evolution.¹ This point will come up again in Chapter 10.

Wells concludes with ...

The arguments by Dawkins, Miller, Shermer, Collins, Kitcher, Coyne and Avise rest on the assumption that most non-coding DNA is junk, without any significant biological function. Yet a virtual flood of recent evidence shows that they are mistaken: Much of the DNA they claim to be "junk" actually performs important functions in living cells.

The stage is set. In the rest of the book, Jonathan Wells will try and convince us that most of the DNA in our genome is not junk. Pay attention 'cause it's important to keep the main focus of the dispute in center stage. What the scientists are saying is that there's a lot of junk in our genome and, in order to blunt that attack on design, Wells has to show that there's not very much junk DNA (perhaps none). It won't be sufficient to show that a few percent here and there aren't junk. Any amount of junk DNA is a threat to the basic concept of intelligent design. That's why the IDiots are so worried.

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1. I often make the same argument against adaptationists. Some of them see design by natural selection as the dominant feature of evolution but that's not what our genome tells us. There's no illusion of apparent design in our genome sequence.

Darwinists Don't Believe in Junk DNA

The "news" on Uncommon descent continues to amaze me. Today they put up a post with an ironic title: Sometimes, one runs into ID opponents who are just so confused ….

It caught my attention because my name was mentioned. Apparently some "ID opponent" read my take-down of Jonathan Wells' book The Myth of Junk DNA. This prompted the following response from "news" (lawyer, Barry Arrington).

"The Myth of Junk DNA" is actually quite easy to read. We’ve excerpted a number of passages here at UD. The interesting part is that Darwinists thought that the presence of huge amounts of junk DNA was evidence for their position.

If Barry Arrington had bothered to read my review of Wells' book he would know that this is a lie. You can read the entire series of posts at: The Myth of Junk DNA by Jonathan Wells but I want to draw your attention specifically to my comments on the history of the controversy: Junk & Jonathan: Part 1—Getting the History Correct] [Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?].

Jonathan Wells illustrates zombie science by revisiting junk DNA

Jonathan Wells has written a new book (2017) called Zombie Science: More Icons of Evolution. He revisits his famous Icons of Evolution from 2000 and tries to show that nothing has changed in 17 years.

I wrote a book in 2000 about ten images images, ten "icons of evolution," that did not fit the evidence and were empirically dead. They should have been buried, but they are still with us, haunting our science classrooms and stalking our children. They are part of what I call zombie science.

I won't bore you with the details. The icons fall into two categories: (1) those that were meaningless and/or trivial in 2000 and remain so today, and (2) those that Wells misunderstood in 2000 and are still misunderstood by creationists today.

Brandeis professor demonstrates his ignorance about junk DNA

Judge Starling (Dan Graur) has alerted me to yet another young biologist who hasn't bothered to study the subject of genomes and junk DNA [An Ignorant Assistant Professor at @BrandeisU Explains “Junk DNA”].

This time it's Assistant Professor of Biology Nelson Lau. He studies Piwi proteins and PiRNAs.

Lau was interviewed by Lawrence Goodman, a science communication officer at Brandeis University: DNA dumpster diving. The subject is junk DNA and you will be astonished at how ignorant Nelson Lau is about a subject that's supposed to be important in his work.

How does this happen? Aren't scientists supposed to be up-to-date on the scientific literature before they pass themselves off as experts? How can an Assistant Professor make such blatantly false and misleading statements about his own area of research expertise? Has he never encountered graduate students, post-docs, or mentors who would have corrected his misconceptions?

Here's the introduction to the interview,

Since the 1960s, it's largely been assumed that most of the DNA in the human genome was junk. It didn't encode proteins -- the main activity of our genes-- so it was assumed to serve no purpose. But Assistant Professor of Biology Nelson Lau is among a new generation of scientists questioning that hypothesis. His findings suggest we've been wrong about junk DNA and it may be time for a reappraisal. If we want to understand how our bodies work, we need to start picking through our genetic garbage.

BrandeisNow sat down with Lau to ask him about his research.

There's nothing wrong with being a "new generation" who questions the wisdom of their elders. That's what all scientists are supposed to do.

But there are certain standards that apply. The most important standard is that when you are challenging other experts you'd better be an expert yourself.

First off, what is junk DNA?
About two percent of our genome carries out functions we know about, things like building our bones or keeping the heart beating. What the rest of our DNA does is still a mystery. Twenty years ago, for want of a better term, some scientists decided to call it junk DNA.

Dan has already addressed this response but let me throw in my own two cents.

There was never, ever, a time when knowledgeable scientists said that all 98% of the DNA that wasn't part of a gene was junk. Not today, not twenty years ago (1996), and not 45 years ago.

There has never been at time since the 1960s when all non-gene DNA was a mystery. It certainly isn't a mystery today. If you don't know this then you better do some reading ... quickly. Google could be your friend, Prof. Lau, it will save you from further embarrassment. Search on "junk DNA" and read everything ... not just the entries that you agree with.

I added a bunch of links at the bottom of this post to help you out.

Is it really junk?
There’s two camps in the scientific community, one that believes it doesn’t do anything and another that believes it’s there for a purpose.

And you’re in the second camp?
Yes. It's true that sometimes organisms carry around excess DNA, but usually it is there for a purpose. Perhaps junk DNA has been coopted for a deeper purpose that we have yet to fully unravel.

It is possible that the extra DNA in our genome has an unknown deeper purpose but right now we have more than enough information to be confident that it's junk. You have to refute or discredit all the work that's been done in the past 40 years in order to be in the second camp.

I strongly suspect that Prof. Lau has not done his homework and he doesn't know the Five Things You Should Know if You Want to Participate in the Junk DNA Debate.

What possible "deep purpose" could this DNA have?

Maybe when junk DNA moves to the right place in our DNA, this could cause better or faster evolution. Maybe when junk genes interacts with the non-junk ones, it causes a mutation to occur so humans can better adapt to changes in the environment.

Most of the undergraduates who took my course could easily refute that argument. I'm guessing that undergraduates in biology at Brandeis aren't as smart. Or maybe they're just too complacent to challenge a professor?

We've got a serious problem here folks. There are scientists being hired at respectable universities who aren't keeping up with the scientific literature in their own field. How does this happen? Are there newly hired biology professors who don't understand evolution?

Eddy, S.R. (2012) The C-value paradox, junk DNA and ENCODE. Current Biology, 22:R898. [doi: 10.1016/j.cub.2012.10.002]

Niu, D. K., and Jiang, L. (2012) Can ENCODE tell us how much junk DNA we carry in our genome?. Biochemical and biophysical research communications 430:1340-1343. [doi: 10.1016/j.bbrc.2012.12.074]

Doolittle, W.F. (2013) Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. (USA) published online March 11, 2013. [PubMed] [doi: 10.1073/pnas.1221376110]

Graur, D., Zheng, Y., Price, N., Azevedo, R. B., Zufall, R. A., and Elhaik, E. (2013) On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution published online: February 20, 2013 [doi: 10.1093/gbe/evt028

Eddy, S.R. (2013) The ENCODE project: missteps overshadowing a success. Current Biology, 23:R259-R261. [10.1016/j.cub.2013.03.023]

Hurst, L.D. (2013) Open questions: A logic (or lack thereof) of genome organization. BMC biology, 11:58. [doi:10.1186/1741-7007-11-58]

Kellis, M., Wold, B., Snyder, M.P., Bernstein, B.E., Kundaje, A., Marinov, G.K., Ward, L.D., Birney, E., Crawford, G. E., and Dekker, J. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. (USA) 111:6131-6138. [doi: 10.1073/pnas.1318948111]

Morange, M. (2014) Genome as a Multipurpose Structure Built by Evolution. Perspectives in biology and medicine, 57:162-171. [doi: 10.1353/pbm.2014.000]

Palazzo, A.F., and Gregory, T.R. (2014) The Case for Junk DNA. PLoS Genetics, 10:e1004351. [doi: 10.1371/journal.pgen.1004351]

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Stephen Meyer Talks About Junk DNA

Stephen C. Meyer has a Ph.D. degree (1991) in the History and Philosophy of Science from Cambridge University in the UK. He is currently Program Director of the Center for Science and Culture at the Discovery Institute in Seattle, Washington, USA.

Meyer's book, Signature in the Cell: DNA and the Evidence for Intelligent Design, is an attempt to present Intelligent Design Creationism as genuine science. I'll have more to say about this later but for now I want to concentrate on one particular aspect of his case.

Mayer claims that one requirement of a genuine scientific theory is the ability to make falsifiable predictions. Does Intelligent Design Creationism make such predictions? Yes, one of the predictions is that genomes will not contain very much junk DNA. It will be instructive to see how Intelligent Design Creationists handle this issue, especialy since I've just finished a thorough review of The Myth of Junk DNA by Jonathan Wells.

Here's what Meyer says about junk DNA.

Junk DNA causes cancer

This is a story about misleading press releases. The spread of misinformation by press offices is a serious issue that needs to be addressed.

The Institute of Cancer Research in London (UK) published a press release on July 19, 2022 with the provocative title: ‘Junk’ DNA could lead to cancer by stopping copying of DNA. The first three sentences tell most of the story.

Scientists have found that non-coding ‘junk’ DNA, far from being harmless and inert, could potentially contribute to the development of cancer.

Their study has shown how non-coding DNA can get in the way of the replication and repair of our genome, potentially allowing mutations to accumulate.

It has been previously found that non-coding or repetitive patterns of DNA – which make up around half of our genome – could disrupt the replication of the genome.

Nobody ever said that junk DNA was "inert and harmless;" in fact it is assumed to be slightly deleterious and only gets fixed because it is invisible to natural selection in small populations (Nearly Neutral Theory). And no intelligent scientist equates noncoding DNA and junk DNA, even by implication. But in any case, this article isn't about all junk DNA, it's about certain small stretches of repetitive DNA that interfere with replication so that the resulting mutations have to be fixed by repair mechanisms. The most likely sequences to interfere with replication are repeats of CG or (CG)_n repeats. As the authors point out in the discussion, these repeats are "extremely rare" in all genomes, including the human genome, suggesting that they are under negative selection.

Other, more common, repeats also show detectable in vitro interference with replisomes at replication forks. The errors introduced by replication stalling can be repaired but some of them will escape repair causing mutations. It's not clear to me why mutations in junk DNA are a problem. That's not explained in the paper.

Here's the paper.

Casas-Delucchi, C.S., Daza-Martin, M., Williams, S.L. et al. (2022) Mechchanism of replication stalling and recovery within repetitive DNA. Nat Commun 13:3953 [doi: 10.1038/s41467-022-31657-x]

Accurate chromosomal DNA replication is essential to maintain genomic stability. Genetic evidence suggests that certain repetitive sequences impair replication, yet the underlying mechanism is poorly defined. Replication could be directly inhibited by the DNA template or indirectly, for example by DNA-bound proteins. Here, we reconstitute replication of mono-, di- and trinucleotide repeats in vitro using eukaryotic replisomes assembled from purified proteins. We find that structure-prone repeats are sufficient to impair replication. Whilst template unwinding is unaffected, leading strand synthesis is inhibited, leading to fork uncoupling. Synthesis through hairpin-forming repeats is rescued by replisome-intrinsic mechanisms, whereas synthesis of quadruplex-forming repeats requires an extrinsic accessory helicase. DNA-induced fork stalling is mechanistically similar to that induced by leading strand DNA lesions, highlighting structure-prone repeats as an important potential source of replication stress. Thus, we propose that our understanding of the cellular response to replication stress may also be applied to DNA-induced replication stalling.

The word "junk" does not appear anywhere in the paper and the word "cancer" appears only once in the text where it refers to a "cancer-associated" mutation in yeast. This makes me wonder why the press release uses both of these words so prominently. Does anybody have any ideas?

Perhaps it has something to do with a quotation from Gideon Coster, who is described as the study leader. He says,

We wanted to understand why it seems more difficult for cells to copy repetitive DNA sequences than other parts of the genome. Our study suggests that so-called junk DNA is actually playing an important and potentially damaging role in cells, by blocking DNA replication and potentially opening the door to cancerous mutations.

I find it strange that he refers to "so-called junk DNA" in the press release but didn't mention it in the peer-reviewed paper. He also didn't emphasize cancerous mutations in the paper.

The press release contain another quotation, this time it's from Kristian Helin who is the Chief Executive of The Institute of Cancer Research. He says,

This study helps to unravel the puzzle of junk DNA – showing how these repetitive sequences can block DNA replication and repair. It’s possible that this mechanism could play a role in the development of cancer as a cause of genetic instability – especially as cancer cells start dividing more quickly and so place the process of DNA replication under more stress.

It's unclear to me how studying these mutation-inducing repeats could help "unravel the puzzle of junk DNA" but that's probably why I'm not the chief executive of a cancer research insitute. I'm so stupid that I didn't even known there WAS a "puzzle" of junk DNA to be unravelled!

It's time for scientists to speak out against press releases like this one. It misrepresents the results and their interpretation as published after undergoing peer review. Intead, the press release is used as a propaganda exercise to promote the personal views of the scientists—views that they couldn't publish. This is what happened with ENCODE and it's becoming more and more common. The fact that, in this case, the personal views of these scientists are flawed only makes the situation worse.

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Can the AI program ChatGPT pass my exam?

There's a lot of talk about ChatGPT and how it can prepare lectures and get good grades on undergraduate exams. However, ChatGPT is only as good as the information that's popular on the internet and that's not always enough to get a good grade on my exam.

ChatGPT is an artificial intelligence (AI) program that's designed to answer questions using a style and language that's very much like the responses you would get from a real person. It was developed by OpenAI, a tech company in San Francisco. You can create an account and log in to ask any question you want.

Several professors have challenged it with exam questions and they report that ChatGPT would easily pass their exams. I was skeptical, especially when it came to answering questions on controversial topics where there was no clear answer. I also suspected that ChatGPT would get it's answers from the internet and this means that popular, but incorrect, views would likely be part of ChatGPT's response.

Here are my questions and the AI program's answers. It did quite well in some cases but not so well in others. My main concern is that programs like this might be judged to be reliable sources of information despite the fact that the real source is suspect.

Creationists admit that junk DNA may not be a "myth" after all

Creationists in general, and Intelligent Design Creationists in particular, feel very threatened by the idea that most of our genome is junk. We know why they feel threatened: it's because a genome full of junk doesn't seem like something gods would design on purpose. It's pretty hard to reconcile junk DNA with with gods that spend so much effort designing bacterial flagella.

The creationists get very excited whenever a group of scientists publish evidence for function in junk DNA and they could hardly contain themselves when the ENCODE preliminary results were published in 2007 because the ENCODE Consortium said that most of the human genome was functional. You will recall that the creationists fell hook line and sinker for the ENCODE publicity hype in September 2012 when the ENCODE leaders came right out and said that their analysis of the entire genome shows there is almost no junk in the human genome.

The creationists, just like the ENCODE leaders, were very resistant to all of the scientific evidence for junk DNA. Both groups showed a remarkable ignorance of four decades of work leading to the conclusion that our genomes are full of junk DNA [see ENCODE, Junk DNA, and Intelligent Design Creationism ]. Creationists, and even some scientific opponents of junk DNA, quote Jonathan Wells' book The Myth of Junk DNA as an authority of the issue.

Now, I wrote a pretty extensive review of The Myth of Junk DNA showing where mistakes were made and why the evidence still favored lots of junk DNA in our genome [The Myth of Junk DNA by Jonathan Wells]. That was in 2011. Here's how Jonathan Wells responded ... [Jonathan Wells Sends His Regrets].

Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.

The ENCODE Consortium has decided that it had better backtrack a little on the subject of junk DNA. Their recent PNAS article (Kellis et al., 2014) pretends that the publicity hype of September 2012 never existed and, even if it did, they may have been right to conclude that 80% of our genome is functional. It all depends on how you define function. Apparently they have just discovered that lots of scientists define it in a way that the ENCODE Consortium overlooked in September 2012.

Now they just want to make sure that everyone knows they have done their homework and they acknowledge that there's a wee bit of a controversy—but they weren't wrong! They just have a different way of defining function.

This puts some of the creationists in a difficult position. Some of them are actually willing to conceded that there's a lot of junk DNA in our genome while other are only willing to concede that the case for function may not be quite as rock solid as they thought.

Here's how an anonymous creationist explains the backtracking of the ENCODE Consortium on Evolution News & Views (sic): Defining "Functional": The Latest from ENCODE.

He/she starts off with the obligatory snipe at "Darwinists" and the obligatory misrepresentation of the case for junk DNA. He/she is referring to the Kellis et al. paper ...

First, the paper is a remarkably restrained and balanced response to some of the rather intemperate criticisms of ENCODE from hard-core Darwinists who insist that (a) ONLY an evolutionary approach yields valid information about functionality, (b) evolutionary theory necessarily implies that most of our DNA is junk, and (c) junk DNA provides evidence that Darwinian evolution is a fact. In other words this paper is a model of rational and civil scientific discourse, in contrast to what we have come to expect from some hard-core Darwinists.

(See the quote above from Jonathan Wells for an example of "a model of rational and civil scientific discourse.")

The Evolution News & Views post concludes with ...

The authors conclude that all three approaches must be taken into account, though a simple intersection of the three (which would include only DNA sequences that meet the test of functionality for all three approaches) would be far too restrictive. Unfortunately, the authors do not specify exactly how the three approaches could be integrated to yield a single reliable estimate of the percentage of functional DNA.

So the debate continues.

Believe it or not, that last sentence ("So the debate continues") is pretty remarkable considering that the creationists have steadfastly refused to admit that there is a scientific debate. Over the past decade, they have consistently claimed that the evidence is in and it shows that gods did it after all most of our genome is functional.

Maybe I'm being overly optimistic but it looks to me like some creationists are actually disagreeing with Jonathan Wells. Stay tuned.

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Kellis, M. et al. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. (USA) April 24, 2014 published online [doi: 10.1073/pnas.1318948111 ]

Intelligent design creationists think junk DNA is a placeholder for ignorance

Paul Nelson is a Senior Fellow of the Discovery Institute—the most important source of intelligent design propaganda. Paul and I have been disagreeing about science for many years. He is prone to interpret anything he finds in the scientific literature as support for the idea that scientists have misunderstood their subject matter and failed to recognize that science supports intelligent design. My goal has always been to try and explain the actual science and why his interpretations are misguided. I have not been very successful.

The photo was taken in London (UK) in 2016 at a meeting on evolution. It looks like I'm holding my breath because I'm beside a creationist but I assure you that's not what was happening. We actually get along quite well in spite of the fact that he's wrong about everything. :-)

Intelligent Design Creationists Attempt to (re)Define Junk DNA

Paul McBride is causing quite a stir among the creationists. His review of Science & Human Origins was so devastating that they couldn't ignore it.

Jonathan McLatchie (Jonathan M) is the latest creationist to attempt a defense of the home team. He concentrates on defending the Intelligent Design Creationist position on junk DNA [A Response to Paul McBride on Junk DNA].

On this topic (junk DNA), the IDiots make a lot of errors. One of them is to deliberately conflate "junk DNA" and "noncoding DNA" so that when they come up with evidence for function in noncoding DNA they can tout this as evidence against junk DNA. This error is so pervasive in the IDiot literature that Paul McBride even predicted that Casey Luskin would make this mistake in the book.

Denis Noble writes about junk DNA

I have read Dance to the Tune of Life. It's a very confusing book for several reasons. Denis Noble has a very different perspective on evolution and what evolutionary theory needs to accomplish. He thinks that life is characterized by something he calls "Biological Relativity." I don't disagree. He also thinks that evolutionary theory needs to incorporate everything that has ever happened in the history of life. That's where we part company.

I'm working slowly on a book about genomes and junk DNA so I was anxious to see how Noble deals with that subject. I tend to judge the quality of books and articles by the way they interpret the controversy over junk DNA. Here's the first mention of junk DNA from page 89. He begins by saying that it's difficult to explain development and the diversity of tissues in multicellular organisms. He continues with,

Junk & Jonathan: Part 12—Chapter 9

 
This is part 12 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

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The title of Chapter 9 is "Summary of the Case for Functionality in Junk DNA." It is Wells' attempt to summarize the "evidence" he has presented so far.

Wells tells us that the "evidence" falls into two broad categories: (1) evidence that putative junk is probably functional, and (2) evidence that small specific bits of the genome are functional.

Within the first category there are two subdivisions: (1a) evidence that most of the genome is transcribed, and (1b) genome comparisons. Let's look at these two subcategories.

Junk & Jonathan: Part 10—Chapter 7

This is part 10 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links below. For other postings on junk DNA check out the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

The American Society of Plant Biologists embarrasses itself by publishing "New functions for 'junk' DNA?"

Theme Genomes & Junk DNAThe American Society of Plant Biologists has put out a press release with the title New functions for 'junk' DNA?.

Non-coding DNA sequences found in all plants may have undiscovered roles in basic plant development and response to the environment.

DNA is the molecule that encodes the genetic instructions enabling a cell to produce the thousands of proteins it typically needs. The linear sequence of the A, T, C, and G bases in what is called coding DNA determines the particular protein that a short segment of DNA, known as a gene, will encode. But in many organisms, there is much more DNA in a cell than is needed to code for all the necessary proteins. This non-coding DNA was often referred to as "junk" DNA because it seemed unnecessary. But in retrospect, we did not yet understand the function of these seemingly unnecessary DNA sequences.

We now know that non-coding DNA can have important functions other than encoding proteins. Many non-coding sequences produce RNA molecules that regulate gene expression by turning them on and off. Others contain enhancer or inhibitory elements. Recent work by the international ENCODE (Encyclopedia of DNA Elements) Project (1, 2) suggested that a large percentage of non-coding DNA, which makes up an estimated 95% of the human genome, has a function in gene regulation. Thus, it is premature to say that "junk" DNA does not have a function—we just need to find out what it is!

I've sent a link to this post to Tyrone Spady [tspady@aspb.org] who is listed as the contact person at The American Society of Plant Biologists and to Gregory Bertoni [gbertoni@aspb.org] who is listed as Science Editor, The Plant Cell.

I'll keep it simple for them.

1. "This non-coding DNA was often referred to as "junk" DNA ..." No reputable group of scientists ever said that all non-coding DNA is junk. No scientist who understands genomes would ever say that today. [Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means]
2. "We now know that non-coding DNA can have important functions other than encoding proteins." We have known that for fifty years. Is that what American plant biologists think of as a recent discovery worthy of mention in a 2014 press release? [What's in Your Genome?]
3. "Recent work by the international ENCODE (Encyclopedia of DNA Elements) Project (1, 2) suggested that a large percentage of non-coding DNA, which makes up an estimated 95% of the human genome, has a function in gene regulation." It is true that the ENCODE Consortium claimed that most of our genome is functional. However, good scientists know that this claim is disputed and the best scientists know that it is wrong. Where does that leave American plant biologists? [Science still doesn't get it] [Ford Doolittle's Critique of ENCODE ]
4. "Thus, it is premature to say that "junk" DNA does not have a function—we just need to find out what it is!" There is abundant evidence that most of that extra DNA in our genome really is junk. It is not some mysterious black box as you imply. [Non-Darwinian Evolution in 1969: The Case for Junk DNA ] [Five Things You Should Know if You Want to Participate in the Junk DNA Debate]

It's bad enough having to teach biology to creationists but when you also have to teach it to biologists, you know we're in big trouble.

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Junk & Jonathan: Part 11—Chapter 8

This is part 11 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

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The title of Chapter 8 is "Some Recent Defenders of Junk DNA." It is Wells' attempt to deal with a very small percentage of the criticisms of his claim.

He begins with a reference to a 2003 paper that reported on transcription of a pseudogene and proposed a function for that transcript. He then references a 2006 paper that refutes the earlier study showing that the pseudogene transcript has no function. Good for Wells. That means he is aware of the fact that some of the work he references has not been reproduced. It's bizarre that Wells devotes three paragraphs to the discredited reference in Junk & Jonathan: Part 7—Chapter 4 and only mentions in passing that the result has been challenged.

He returns to this result in Chapter 8 and all but admits that the original result—so prominently presented in Chapter 3—is no longer valid. However, Wells can't leave it at that. The 2006 paper by Gray et al. went on to point out that some creationist literature had written up the earlier incorrect result and claimed that this was support for functional "junk DNA" and support for intelligent design creationism. The authors conclude their paper with ...

Furthermore, because Mkrn1-p1 is a nonfunctional pseudogene and does not trans-regulate its source Mkrn1 gene as claimed (6–9), our work reestablishes the evolutionary paradigm supported by overwhelming evidence that mammalian pseudogenes are indeed inactive gene relics.

Answering Barry Arrington's challenge: Darwinism predicted junk DNA

In my first post [Answering Barry Arrington's challenge: Darwinism] I established that Barry Arrington's version of "Darwinism" is actually "Neo-Darwinism" or the "Modern Synthesis." We all know why Intelligent Design Creationists would rather use "Darwinism"—this explains why they deliberately change the meaning to make it look like they understand evolution

Arrington's version of "Darwinism can be seen in the Uncommon Descent glossary. It focuses on natural selection as the mechanism of evolution and doesn't mention Neutral Theory of random genetic drift.

Barry Arrington's challenge to me is ...

The Function Wars: Part II

This is Part II of several "Function Wars"¹ posts. The first one is on Quibbling about the meaning of the word "function" [The Function Wars: Part I].

The ENCODE legacy

I addressed the meaning of "function" in Part I It is apparent that philosophers and scientists are a long way from agreeing on an acceptable definition. There has been a mini-explosion of papers on this topic in the past few years, stimulated by the ENCODE Consortium publicity campaign where the ENCODE leaders clearly picked a silly definition of "function" in order to attract attention.

Unfortunately, the responses to this mistake have not clarified the issue at all. Indeed, some philosophers have even defended the ENCODE Consortium definition (Germain et al., 2014). Some have opposed the ENCODE definition but come under attack from other scientists and philosophers for using the wrong definition (see Elliott et al, 2014). The net effect has been to lend credence to the ENCODE Consortium’s definition, if only because it becomes one of many viable alternatives.