Required reading for the junk DNA debate

This is a list of scientific papers on junk DNA that you need to read (and understand) in order to participate in the junk DNA debate. It's not a comprehensive list because it's mostly papers that defend junk DNA and refute arguments for massive amounts of function. The only exception is the paper by Mattick and Dinger (2013).¹ It's the only anti-junk paper that attempts to deal with the main evidence for junk DNA. If you know of any other papers that make a good case against junk DNA then I'd be happy to include them in the list.

If you come across a publication that argues against junk DNA, then you should immediately check the reference list. If you do not see some of these references in the list, then don't bother reading the paper because you know the author is not knowledgeable about the subject.

Brenner, S. (1998) Refuge of spandrels. Current Biology, 8:R669-R669. [PDF]

Brunet, T.D., and Doolittle, W.F. (2014) Getting “function” right. Proceedings of the National Academy of Sciences, 111:E3365-E3365. [doi: 10.1073/pnas.1409762111]

Casane, D., Fumey, J., et Laurenti, P. (2015) L’apophénie d’ENCODE ou Pangloss examine le génome humain. Med. Sci. (Paris) 31: 680-686. [doi: 10.1051/medsci/20153106023] [The apophenia of ENCODE or Pangloss looks at the human genome]

Cavalier-Smith, T. (1978) Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox. Journal of Cell Science, 34(1), 247-278. [doi: PDF]

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]

Doolittle, W.F., Brunet, T.D., Linquist, S., and Gregory, T.R. (2014) Distinguishing between “function” and “effect” in genome biology. Genome biology and evolution 6, 1234-1237. [doi: 10.1093/gbe/evu098]

Doolittle, W.F., and Brunet, T.D. (2017) On causal roles and selected effects: our genome is mostly junk. BMC biology, 15:116. [doi: 10.1186/s12915-017-0460-9]

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

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

Graur, D. (2017) Rubbish DNA: The functionless fraction of the human genome Evolution of the Human Genome I (pp. 19-60): Springer. [doi: 10.1007/978-4-431-56603-8_2 (book)] [PDF]

Graur, D. (2017) An upper limit on the functional fraction of the human genome. Genome Biology and Evolution, 9:1880-1885. [doi: 10.1093/gbe/evx121]

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

Graur, D., Zheng, Y., and Azevedo, R.B. (2015) An evolutionary classification of genomic function. Genome Biology and Evolution, 7:642-645. [doi: 10.1093/gbe/evv021]

Gregory, T. R. (2005) Synergy between sequence and size in large-scale genomics. Nature Reviews Genetics, 6:699-708. [doi: 10.1038/nrg1674]

Haerty, W., and Ponting, C.P. (2014) No Gene in the Genome Makes Sense Except in the Light of Evolution. Annual review of genomics and human genetics, 15:71-92. [doi:10.1146/annurev-genom-090413-025621]

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]

Mattick, J. S., and Dinger, M. E. (2013) The extent of functionality in the human genome. The HUGO Journal, 7:2. [doi: 10.1186/1877-6566-7-2]

Five Things You Should Know if You Want to Participate in the Junk DNA DebateMorange, M. (2014) Genome as a Multipurpose Structure Built by Evolution. Perspectives in biology and medicine, 57:162-171. [doi: 10.1353/pbm.2014.000]

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]

Ohno, S. (1972) An argument for the genetic simplicity of man and other mammals. Journal of Human Evolution, 1:651-662. [doi: 10.1016/0047-2484(72)90011-5]

Ohno, S. (1972) So much "junk" in our genome. In H. H. Smith (Ed.), Evolution of genetic systems (Vol. 23, pp. 366-370): Brookhaven symposia in biology.

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

Rands, C. M., Meader, S., Ponting, C. P., and Lunter, G. (2014) 8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage. PLOS Genetics, 10:e1004525. [doi: 10.1371/journal.pgen.1004525]

Thomas Jr, C.A. (1971) The genetic organization of chromosomes. Annual review of genetics, 5:237-256. [doi: annurev.ge.05.120171.001321]

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1. The paper by Kellis et al. (2014) is ambiguous. It's clear that most of the ENCODE authors are still opposed to junk DNA even though the paper is mostly a retraction of their original claim that 80% of the genome is functional.

I'm going to a birthday party!

It's Bruce Alberts' 80th birthday party in San Francisco. There will be food, wine, cake, and (probably) dancing but first you go to the symposium on education.

Bruce Alberts’ 80th Birthday Gathering and Symposium
Saturday, April 14
Symposium on Science Education and Science Policy in Honor of Bruce Alberts’ 80th Birthday
(At the Metropolitan Club, 640 Sutter St., San Francisco 94102)

9a Guests arrive and register

10a Introduction by Master of Ceremonies Gregor Eichele

10:10a Session 1 How do we convey the importance of science to the public?
Moderator: Maureen Munn
Panelists: Janet Coffey, Will Colglazier, Janet English, Caroline Kiehle

11:40a Break

12p Buffet Lunch served in the Garden Room

1:30p Session 2 Innovations in Teaching and Learning in Higher Education
Moderators: Doug Kellogg and Kimberly Tanner.
Panelists: Judy Miner, Sally Pasion (one more panelist TBA)

2:30p Coffee and tea break

3p Session 3 Challenges Facing the Next Generation of Scientists
Moderators: Cynthia Fuhrmann and Bill Theurkauf.
Panelists: Marc Kirschner, Barry Selick, Nolan Sigal

4p Break

4:30p Session 4 Science Policy
Moderators: Mary Maxon and Jason Rao
Panelists: Bill Colglazier, Haile Debas, Donna Riordan, Keith Yamamoto

5:30p Elaine Bearer’s Duet for clarinet and viola: “Replication Machine”

6:15p Reception at Metropolitan Club Bar (4th Floor)

7p Buffet Dinner (Metropolitan Club Main Dining Hall — 4th Floor) Ending at 9:30p.

Sunday, April 15

10a - 2p Drop-in Brunch for all hosted at Beth Alberts’ home

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Photo: Bruce Alberts with his first three graduate students: Glenn Herrick (right), Keith Yamamoto (left), Larry Moran (middle right), Bruce Alberts (middle left).

Cafe Scientific Mississauga: The Good, Bad, & Natural

Dan Riskin: The Good, Bad, & Natural: What Mother Nature says
about morality?

Thursday, April 12, 2018
7:30 - 10:00 pm
The Franklin House
263 Queen Street S
Streetsville (Mississauga), Ontario, Canada

"People often act like “natural” is synonymous with “good.” Using heinous examples from the scientific literature, Dan Riskin will blow the hinges off that misconception. Then he’ll give some thoughts about where, if not from nature, the roots of human morality might lie.

Dan Riskin, PhD, is a television personality, scientist, author, and podcaster. He is best known as the co-host of Discovery's flagship science program, Daily Planet, and as the host of Animal Planet's show about parasites, Monsters Inside Me. To make science accessible and interesting to wide audiences, Dan has appeared as a guest on The Tonight Show with Jay Leno, The Late Late Show with Craig Ferguson, The Dr. Oz Show, and on several news outlets, including CP24, CTV, CNN, and CBS. Dan has published more than 20 papers in scientific journals, and his first popular book, Mother Nature is Trying to Kill You was a Canadian bestseller.

IMPORTANT:
This meetup starts 30 minutes later than our regular meeting time to give Dan time to drive to Mississauga from Scarborough.
You are welcome to come at 7 or 7:30, but don't expect the talk to begin before 8 pm. It will definitely be worth it."

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Subhash Lakhotia: The concept of 'junk DNA' becomes junk

Continuing my survey of recent papers on junk DNA, I stumbled upon a review by Subash Lakhotia that has recently been accepted in The Proceedings of the Indian National Science Academy (Lakhotia, 2018). It illustrates the extent of the publicity campaign mounted by ENCODE and opponents of junk DNA. In the title of this post, I paraphrased a sentence from the abstract that summarizes the point of the paper; namely, that the 'recent' discovery of noncoding RNAs refutes the concept of junk DNA.

Lakhotia claims to have written a review of the history of junk DNA but, in fact, his review perpetuates a false history. He repeats a version of history made popular by John Mattick. It goes like this. Old-fashioned scientists were seduced by Crick's central dogma into thinking that the only important part of the genome was the part encoding proteins. They ignored genes for noncoding RNAs because they didn't fit into their 'dogma.' They assumed that most of the noncoding part of the genome was junk. However, recent new discoveries of huge numbers of noncoding RNAs reveal that those scientists were very stupid. We now know that the genome is chock full of noncoding RNA genes and the concept of junk DNA has been refuted.

Peter Larsen: "There is no such thing as 'junk DNA'"

The March 2018 issue of Chromosome Research is a Special Issue on Transposable Elements and Genome Function. I found it as I was doing my routine search for papers on junk DNA in order to see whether scientists are finally beginning to understand the issue. Peter Larsen (guest editor) wrote the introduction to the special issue. He says ...

There is no such thing as “junk DNA.” Indeed, a suite of discoveries made over the past few decades have put to rest this misnomer and have identified many important roles that so-called junk DNA provides to both genome structure and function (this special issue; Biémont and Vieira 2006; Jeck et al. 2013; Elbarbary et al. 2016; Akera et al. 2017; Chen and Yang 2017; Chuong et al. 2017). Nevertheless, given the historical focus on coding regions of the genome, our understanding of the biological function of non-coding regions (e.g., repetitive DNA, transposable elements) remains somewhat limited, and therefore, all those enigmatic and poorly studied regions of the genome that were once identified as junk are instead best viewed as genomic “dark matter.”

What's In Your Genome? - The Pie Chart

Here's my latest compilation of the composition of the human genome. It's depicted in the form of a pie chart.¹ [UPDATED: March 29, 2018]

What is "dark DNA"?

Some DNA sequencing technologies aren't very good at sequencing and assembling DNA that's rich in GC base pairs. What this means is that some sequenced genomes could be missing stretches of GC-rich DNA if they rely exclusively on those techniques. This difficult-to-sequence DNA was called "dark DNA" in a paper published last summer (July 2017).

The paper looked at some missing genes in the genome of the sand rat Psammomys obesus. The authors initially used a standard shotgun strategy in order to sequence the sand rat genome. They combined millions of short reads (&lt200 bp) to assemble a complete genome. A large block of genes seemed to be missing—genes that were conserved and present in the genomes of related species (Hargraves et al., 2017). They knew the genes were present because they could detect the mRNAs corresponding to those genes.

Making Sense of Genes by Kostas Kampourakis

Kostas Kampourakis is a specialist in science education at the University of Geneva, Geneva (Switzerland). Most of his book is an argument against genetic determinism in the style of Richard Lewontin. You should read this book if you are interested in that argument. The best way to describe the main thesis is to quote from the last chapter.

Here is the take-home message of this book: Genes were initially conceived as immaterial factors with heuristic values for research, but along the way they acquired a parallel identity as DNA segments. The two identities never converged completely, and therefore the best we can do so far is to think of genes as DNA segments that encode functional products. There are neither 'genes for' characters nor 'genes for' diseases. Genes do nothing on their own, but are important resources for our self-regulated organism. If we insist in asking what genes do, we can accept that they are implicated in the development of characters and disease, and that they account for variation in characters in particular populations. Beyond that, we should remember that genes are part of an interactive genome that we have just begun to understand, the study of which has various limitations. Genes are not our essences, they do not determine who we are, and they are not the explanation of who we are and what we do. Therefore we are not the prisoners of any genetic fate. This is what the present book has aimed to explain.

Is evolutionary psychology a deeply flawed enterprise?

We were discussing the field of evolutionary psychology at our local cafe scientific meeting last week. The discussion was prompted by watching a video of Steven Pinker in conversation with Stephen Fry. I pointed out that the field of evolutionary psychology is a mess and many scientists and philosophers think it is fundamentally flawed. The purpose of this post is to provide links to back up my claim.

Can the Dunning-Kruger effect be reversed?

The Dunning-Kruger Effect was first proposed in a classic 1999 paper (Kruger and Dunning, 1999).¹ People suffering from this effect show one of two characteristics. If they are not knowledgeable about a subject they tend to overestimate their ability. If they are experts in a subject they tend to underestimate their ability (see figure).

The phenomenon is more significant in people who overestimate their ability because it includes a large number of people who are making decisions on subjects that they know little about. Because of the Dunning-Kruger effect, they are confident that their decisions are based on facts and evidence. That's bad enough, but there's another aspect to this problem—why do these people seem to be incapable of recognizing that they are suffering from the Dunning-Kruger effect? Here's how Kruger and Dunning explain this ...

Junk DNA and selfish DNA

Selfish DNA is a term that became popular with the publication of a series of papers in Nature in 1980. The authors were referring to viruses and transposons that insert themselves into a genome where they exist solely for the purposes of propagating themselves. These selfish DNA sequences are often thought, incorrectly, to be the same as the Selfish Genes of Richard Dawkins¹ [Selfish genes and transposons]. In fact, "selfish genes" refers to the idea that some DNAs enhance fitness and the frequency of these genes will increase in a population through their effect on the vehicle that carries them. It's an adaptationist view of evolution. The selfish DNA of transposons and viruses is quite different. These sequences only propagate themselves—the fitness of the organism is largely irrelevant. These elements do not contribute directly to the adaptive evolution of the species.

Transposons and integrated viruses are subjected to mutation just like the rest of the genome. Deleterious mutations cannot be purged by natural selection because inactivating a transposon has no effect on the fitness of the organism.² As a result, large genomes are littered with defective transposons and bits and pieces of dead transposons. This is not selfish DNA by any definition. It is junk DNA [What's in Your Genome?].

Human genome books

Theme
Genomes
& Junk DNA

I'm trying to read all the recent books on the human genome and anything related. There are a lot of them. Here's a list with some brief comments. You should buy some of these books. There are others you should not buy under any circumstances.

Test your irony meter

The irony meter was a running joke on the newsgroup talk.origins back in the last century. Our irony meters were supposed to protect us from the craziness of creationists but as soon as we built a really good irony meter a new bit of creationist crazy came along and fried it. Apparently Jesus and Mo have the same problem.

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Scientists fight back against fake news and pseudoscience

You probably know that climate change is real and humans are a major cause of global warming. You probably know that life has evolved and the Biblical story of creation is false. Scientists have been actively promoting these ideas for decades and they've been relatively successful in most countries. What you may not know is that these are just two of the many controversial claims that scientists are fighting. You may even have been tricked into believing some of the other pseudoscientific claims that are out there.

Dirty bacteria

Did you know that the dirt in your local park is full of bacteria? Each scoop of soil contains millions of bacteria. And it's not just in your local park, soil bacteria are everywhere. This is part of the reason why the total mass of bacteria on the planet outweighs all of the eukayotes combined, including elephants and whales.

There are hundreds of different species of bacteria in your local dirt. They are as different from each other as moose and mushrooms.

Did you ever wonder whether the bacteria in Australian soil are similar to the bacteria in Austrian soil? Delgado-Baquerizo and his colleagues did, so they tested soils from all over the world. The results are published in a recent issue of Science (Delgado-Baquerizo et al., 2018).

The answer is yes ... and no. They looked at 237 locations on all continents except Antarctica. Most samples had about 1000 different species—the authors call them "phylotypes" because it's hard to define what a species is in bacteria. Only a small number of species (phylotypes) were found in all locations (511 out of 25,224 = 2%) but they accounted for almost half of the total mass. Here's how the authors describe their result ...

Together, our results suggest that soil bacterial communities, like plant communities, are typically dominated by a relatively small subset of phylotypes.

Most of those 511 dominant phylotypes fall into two large and diverse clades (phyla?): Proteobacteria and Actinobacteria. The distribution is shown in Figure 1 of the paper (left). It illustrates a little-known fact about bacteria; namely, that they are a very diverse group. Scientists are only beginning to explore this diversity. Only 18% of the 511 dominant phylotypes were previously known to science!

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Image Credit: Bacillus Sp. soil bacteria from The ecology of soil-borne human diseases

Delgado-Baquerizo, M., Oliverio, A.M., Brewer, T.E., Benavent-González, A., Eldridge, D.J., Bardgett, R.D., Maestre, F.T., Singh, B.K., and Fierer, N. (2018) A global atlas of the dominant bacteria found in soil. Science, 359(6373), 320-325. doi: doi: 10.1126/science.aap9516

Happy Darwin Day 2018!

Charles Darwin, the greatest scientist who ever lived, was born on this day in 1809 [Darwin still spurs tributes, debates] [Happy Darwin Day!] [Darwin Day 2017]. Darwin is mostly famous for two things: (1) he described and documented the evidence for evolution and common descent and (2) he provided a plausible scientific explanation of evolution—the theory of natural selection. He put all this in a book, The Origin of Species by Means of Natural Selection published in 1859—a book that spurred a revolution in our understanding of the natural world.

Modern evolutionary theory has advanced well beyond Darwin's theory but he still deserves to be honored for being the first to explain evolution and promote it in a way that convinced others. Here's one passage from the introduction to Origin of Species.

Although much remains obscure, and will long remain obscure, I can entertain no doubt, after the most deliberate and dispassionate study of which I am capable, that the view which most naturalists entertain, and which I formerly entertained—namely, that each species has been independently created—is erroneous. I am fully convinced that species are not immutable; but that those belonging to what are called the same genera are lineal descendants of some other and generally extinct species, in the same manner as the acknowledged varieties of any one species are the descendants of that species. Furthermore, I am convinced that Natural Selection has been the main but not exclusive means of modification.

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One philosopher's view of random genetic drift

Random genetic drift is the process whereby some allele frequencies change in a population by chance alone. The alleles are not being fixed or eliminated by natural selection. Most of the alleles affected by drift are neutral or nearly neutral with respect to selection. Some are deleterious, in which case they may be accidentally fixed in spite of being selected against. Modern evolutionary theory incorporates random genetic drift as part of population genetics and modern textbooks contain extensive discussions of drift and the influence of population size. The scientific literature has focused recently on the Drift-Barrier Hypothesis, which emphasizes random genetic drift [Learning about modern evolutionary theory: the drift-barrier hypothesis].

Most of the alleles that become fixed in a population are fixed by random genetic drift and not by natural selection. Thus, in a very real sense, drift is the dominant mechanism of evolution. This is especially true in species with large genomes full of junk DNA (like humans) since the majority of alleles occur in junk DNA where they are, by definition, neutral.¹ All of the data documenting drift and confirming its importance was discovered by scientists. All of the hypotheses and theories of modern evolution were, and are, developed by scientists.

Nothing in biology makes sense except in the light of population genetics.

Michael Lynch
You might be wondering why I bother to state the obvious; after all, this is the 21st century and everyone who knows about evolution should know about random genetic drift. Well, as it turns out, there are some people who continue to make silly statements about evolution and I need to set the record straight.

One of those people is Massimo Pigliucci, a former scientist who's currently more interested in the philosophy of science. We've encountered him before on Sandwalk [Massimo Pigliucci tries to defend accommodationism (again): result is predictable] [Does Philosophy Generate Knowledge?] [Proponents of the Extended Evolutionary Synthesis (EES) explain their logic using the Central Dogma as an example]. I looks like Pigliucci doesn't have a firm grip on modern evolutionary theory.

His main beef isn't with evolutionary biology. He's mostly upset about the fact that science as a way of knowing is extraordinarily successful whereas philosophy isn't producing many results. He loves to attack any scientist who points out this obvious fact. He accuses them of "scientism" as though that's all it takes to make up for the lack of success of philosophy. His latest rant appears on the Blog of the American Philosophers Association: The Problem with Scientism.

I'm not going to deal with the main part of his article because it's already been covered many times. However, there was one part that caught my eye. That's the part where he lists questions that science (supposedly) can't answer. The list is interesting. Pigliucci says,

Next to last, comes an attitude that seeks to deploy science to answer questions beyond its scope. It seems to me that it is exceedingly easy to come up with questions that either science is wholly unequipped to answer, or for which it can at best provide a (welcome!) degree of relevant background knowledge. I will leave it to colleagues in other disciplines to arrive at their own list, but as far as philosophy is concerned, the following list is just a start:

• In metaphysics: what is a cause?
• In logic: is modus ponens a type of valid inference?
• In epistemology: is knowledge “justified true belief”?
• In ethics: is abortion permissible once the fetus begins to feel pain?
• In aesthetics: is there a meaningful difference between Mill’s “low” and “high” pleasures?
• In philosophy of science: what role does genetic drift play in the logical structure of evolutionary theory?
• In philosophy of mathematics: what is the ontological status of mathematical objects, such as numbers?

[my emphasis LAM]

Before getting to random genetic drift, I'll just note that my main problem with Pigliucci's argument is that there are other definitions of science that render his discussion meaningless. For example, I prefer the broad definition of science—the one that encompasses several of the Pigliucci's questions [Alan Sokal explains the scientific worldview][Territorial demarcation and the meaning of science]. The second point is that no matter how you define knowledge, philosophers haven't been very successful at adding to our knowledge base. They're good at questions (see above) but not so good at answers. Thus, it's reasonable to claim that science (broad definition) is the only proven method of acquiring knowledge. If that's scientism then I think it's a good working hypothesis.

Now back to random genetic drift. Did you notice that one of the questions that science is "wholly unequiped" to answer is the following: "what role does genetic drift play in the logical structure of evolutionary theory?" Really?

Pigliucci goes on to explain what he means ...

The scientific literature on all the above is basically non-existent, while the philosophical one is huge. None of the above questions admits of answers arising from systematic observations or experiments. While empirical notions may be relevant to some of them (e.g., the one on abortion), it is philosophical arguments that provide the suitable approach.

I hardly know what to say.

How many of you believe that the following statements are true with respect to random genetic drift and evolutionary theory?

1. The scientific literature on all the above is basically non-existent.
2. The philosophical literature is huge.
3. The question does not admit of answers arising from systematic observations or experiments.
4. It is philosophical arguments that provide the suitable approach.

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1. There are some very rare exceptions where a mutation in junk DNA may have detrimental effects.

We live in the age of bacteria

I'm sad because we now have almost a whole generation of young people who know very little about Stephen Jay Gould. (He died of cancer in 2002.) I was thinking of this yesterday as I was preparing a post on bacteria. Gould's 1996 book, Full House, is about fundamental misconceptions of evolution and progress and it contains the following passage (p. 176) ...

We live now in the "Age of Bacteria." Our planet has always been in the "Age of Bacteria," ever since the first fossils—bacteria, of course—were entombed in rocks more than three and a half billion years ago.

On any possible, reasonable, or fair criterion, bacteria are—and always have been—the dominant forms of life on earth.

Listen to him make this point twenty years ago ...

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Junior scientist snowflakes

A recent letter in Nature draws attention to a serious (?) problem in modern society; namely, the persecution of junior scientists by older scientists who ask them tough questions. Anand Kumar Sharma warns us: "Don’t belittle junior researchers in meetings". Here's what he says, ...

The most interesting part of a scientific seminar, colloquium or conference for me is the question and answer session. However, I find it upsetting to witness the unnecessarily hard time that is increasingly given to junior presenters at such meetings. As inquisitive scientists, we do not have the right to undermine or denigrate the efforts of fellow researchers — even when their reply is unconvincing.

It is our responsibility to nurture upcoming researchers. Firing at a speaker from the front row is unlikely to enhance discussions. In my experience, it is more productive to offer positive queries and suggestions, and save negative feedback for more-private settings.

Are splice variants functional or noise?

This is a post about alternative splicing. I've avoided using that term in the title because it's very misleading. Alternative splicing produces a number of different products (RNA or protein) from a single intron-containing gene. The phenomenon has been known for 35 years and there are quite a few very well-studied examples, including several where all of the splice regulatory factors have been characterized.

The Salzburg sixty discuss a new paradigm in genetic variation

Sixty evolutionary biologists are going to meet next July in Salzburg (Austria)to discuss "a new paradigmatic understanding of genetic novelty" [Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses]. You probably didn't know that a new paradigm is necessary. That's because you didn't know that the old paradigm of random mutations can't explain genetic diversity. (Not!) Here's how the symposium organizers explain it on their website ...

How many lncRNAs are functional?

There's solid evidence that 90% of your genome is junk. Most of it is transcribed at some time but the transcripts are transient and usually confined to the nucleus. They are junk RNA [Functional RNAs?]. This is the view held by many experts but you wouldn't know that from reading the scientific literature and the popular press. The opposition to junk DNA gets much more attention in both venues.

There are prominent voices expressing the view that most of the genome is devoted to producing functional RNAs required for regulating gene expression [John Mattick still claims that most lncRNAs are functional]. Most of these RNAs are long noncoding RNAs known as lncRNAs. Although most of them fail all reasonable criteria for function there are still those who maintain that tens of thousands of them are functional [How many lncRNAs are functional: can sequence comparisons tell us the answer?].

ENCODE's false claims about the number of regulatory sites per gene

Some beating of dead horses may be ethical, where here and there they display unexpected twitches that look like life.

Zuckerkandl and Pauling (1965)

I realize that most of you are tired of seeing criticisms of ENCODE but it's important to realize that most scientists fell hook-line-and-sinker for the ENCODE publicity campaign and they still don't know that most of the claims were ridiculous.

I was reminded of this when I re-read Brendan Maher's summary of the ENCODE results that were published in Nature on Sept. 6, 2012 (Maher, 2012). Maher's article appeared in the front section of the ENCODE issue.¹ With respect to regulatory sequences he said ...

The consortium has assigned some sort of function to roughly 80% of the genome, including more than 70,000 ‘promoter’ regions — the sites, just upstream of genes, where proteins bind to control gene expression — and nearly 400,000 ‘enhancer’ regions that regulate expression of distant genes ... But the job is far from done, says [Ewan] Birney, a computational biologist at the European Molecular Biology Laboratory’s European Bioinformatics Institute in Hinxton, UK, who coordinated the data analysis for ENCODE. He says that some of the mapping efforts are about halfway to completion, and that deeper characterization of everything the genome is doing is probably only 10% finished.

What's in Your Genome?: Chapter 5: Regulation and Control of Gene Expression

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! The first chapter is an introduction to genomes and DNA [What's in Your Genome? Chapter 1: Introducing Genomes ]. Chapter 2 is an overview of the human genome. It's a summary of known functional sequences and known junk DNA [What's in Your Genome? Chapter 2: The Big Picture]. Chapter 3 defines "genes" and describes protein-coding genes and alternative splicing [What's in Your Genome? Chapter 3: What Is a Gene?]. Chapter 4 is all about pervasive transcription and genes for functional noncoding RNAs [What's in Your Genome? Chapter 4: Pervasive Transcription].

Chapter 5 is Regulation and Control of Gene Expression.

Chapter 5: Regulation and Control of Gene Expression

What do we know about regulatory sequences?

The fundamental principles of regulation were worked out in the 1960s and 1970s by studying bacteria and bacteriophage. The initiation of transcription is controlled by activators and repressors that bind to DNA near the 5′ end of a gene. These transcription factors recognize relatively short sequences of DNA (6-10 bp) and their interactions have been well-characterized. Transcriptional regulation in eukaryotes is more complicated for two reasons. First, there are usually more transcription factors and more binding sites per gene. Second, access to binding sites depends of the state of chromatin. Nucleosomes forming high order structures create a "closed" domain where DNA binding sites are not accessible. In "open" domains the DNA is more accessible and transcription factors can bind. The transition between open and closed domains is an important addition to regulating gene expression in eukaryotes.

The limitations of genomics

By their very nature, genomics studies look at the big picture. Such studies can tell us a lot about how many transcription factors bind to DNA and how much of the genome is transcribed. They cannot tell you whether the data actually reflects function. For that, you have to take a more reductionist approach and dissect the roles of individual factors on individual genes. But working on single genes can be misleading ... you may miss the forest for the trees. Genomic studies have the opposite problem, they may see a forest where there are no trees.

Regulation and evolution

Much of what we see in evolution, especially when it comes to phenotypic differences between species, is due to differences in the regulation of shared genes. The idea dates back to the 1930s and the mechanisms were worked out mostly in the 1980s. It's the reason why all complex animals should have roughly the same number of genes—a prediction that was confirmed by sequencing the human genome. This is the field known as evo-devo or evolutionary developmental biology.

           Box 5-1: Can complex evolution evolve by accident?

Slightly harmful mutations can become fixed in a small population. This may cause a gene to be transcribed less frequently. Subsequent mutations that restore transcription may involve the binding of an additional factor to enhance transcription initiation. The result is more complex regulation that wasn't directly selected.

Open and closed chromatin domains

Gene expression in eukaryotes is regulated, in part, by changing the structure of chromatin. Genes in domains where nucleosomes are densely packed into compact structures are essentially invisible. Genes in more open domains are easily transcribed. In some species, the shift between open and closed domains is associated with methylation of DNA and modifications of histones but it's not clear whether these associations cause the shift or are merely a consequence of the shift.

           Box 5-2: X-chromosome inactivation

In females, one of the X-chromosomes is preferentially converted to a heterochromatic state where most of the genes are in closed domains. Consequently, many of the genes on the X chromosome are only expressed from one copy as is the case in males. The partial inactivation of an X-chromosome is mediated by a small regulatory RNA molecule and this inactivated state is passed on to all subsequent descendants of the original cell.

           Box 5-3: Regulating gene expression by
           rearranging the genome

In several cases, the regulation of gene expression is controlled by rearranging the genome to bring a gene under the control of a new promoter region. Such rearrangements also explain some developmental anomalies such as growth of legs on the head fruit flies instead of antennae. They also account for many cancers.

ENCODE does it again

Genomic studies carried out by the ENCODE Consortium reported that a large percentage of the human genome is devoted to regulation. What the studies actually showed is that there are a large number of binding sites for transcription factors. ENCODE did not present good evidence that these sites were functional.

Does regulation explain junk?

The presence of huge numbers of spurious DNA binding sites is perfectly consistent with the view that 90% of our genome is junk. The idea that a large percentage of our genome is devoted to transcriptional regulation is inconsistent with everything we know from the the studies of individual genes.

           Box 5-3: A thought experiment

Ford Doolittle asks us to imagine the following thought experiment. Take the fugu genome, which is very much smaller than the human genome, and the lungfish genome, which is very much larger, and subject them to the same ENCODE analysis that was performed on the human genome. All three genomes have approximately the same number of genes and most of those genes are homologous. Will the number of transcription factor biding sites be similar in all three species or will the number correlate with the size of the genomes and the amount of junk DNA?

Small RNAs—a revolutionary discovery?

Does the human genome contain hundreds of thousands of gene for small non-coding RNAs that are required for the complex regulation of the protein-coding genes?

A “theory” that just won’t die

"... we have refuted the specific claims that most of the observed transcription across the human genome is random and put forward the case over many years that the appearance of a vast layer of RNA-based epigenetic regulation was a necessary prerequisite to the emergence of developmentally and cognitively advanced organisms." (Mattick and Dinger, 2013)

What the heck is epigenetics?

Epigenetics is a confusing term. It refers loosely to the regulation of gene expression by factors other than differences in the DNA. It's generally assumed to cover things like methylation of DNA and modification of histones. Both of these effects can be passed on from one cell to the next following mitosis. That fact has been known for decades. It is not controversial. The controversy is about whether the heritability of epigenetic features plays a significant role in evolution.

           Box 5-5: The Weismann barrier

The Weisman barrier refers to the separation between somatic cells and the germ line in complex multicellular organisms. The "barrier" is the idea that changes (e.g. methylation, histone modification) that occur in somatic cells can be passed on to other somatic cells but in order to affect evolution those changes have to be transferred to the germ line. That's unlikely. It means that Lamarckian evolution is highly improbable in such species.

How should science journalists cover this story?

The question is whether a large part of the human genome is devoted to regulation thus accounting for an unexpectedly large genome. It's an explanation that attempts to refute the evidence for junk DNA. The issue is complex and very few science journalists are sufficiently informed enough to do it justice. They should, however, be making more of an effort to inform themselves about the controversial nature of the claims made by some scientists and they should be telling their readers that the issue has not yet been resolved.

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Sex isn't as beneficial as you might think

One of the most interesting topics in my molecular evolution class was the discussion over the importance of sex. Most students seem to think the problem is solved. They were taught that sex increases variation in a population and this gives sexual populations an evolutionary advantage. The fact that sex (recombination) breaks up as many linkages as it creates makes the explanation much less viable. The fact that there's very little evidence to support the claim comes as quite a surprise to my students. Sex is still one of the greatest mysterious in evolutionary biology [What did Joe Felsenstein say about sex?] [Everything you thought you knew about sex is probably wrong].

Kevin Laland's view of "modern" evolutionary theory (again)

Kevin Laland has just published another critique of modern evolutionary theory. This one appears in Aeon [Evolution unleashed]. His criticism is based on a naive and outdated view of modern evolutionary biology. That view has been widely criticized in the past but Laland continues to ignore such criticisms [e.g. Kevin Laland's new view of evolution].

Here's how he describes the state of modern evolutionary biology.

If you are not a biologist, you’d be forgiven for being confused about the state of evolutionary science. Modern evolutionary biology dates back to a synthesis that emerged around the 1940s-60s, which married Charles Darwin’s mechanism of natural selection with Gregor Mendel’s discoveries of how genes are inherited. The traditional, and still dominant, view is that adaptations – from the human brain to the peacock’s tail – are fully and satisfactorily explained by natural selection (and subsequent inheritance). Yet as novel ideas flood in from genomics, epigenetics and developmental biology, most evolutionists agree that their field is in flux. Much of the data implies that evolution is more complex than we once assumed.

Herding Hemingway's Cats by Kat Arney

Kat Arney has written a very good book on genes and gene expression. She covers all the important controversies in a thorough and thoughtful manner.

Kat Arney is a science writer based in the UK. She has a Ph.D. from the University of Cambridge where she worked on epigenetics and regulation in mice. She also did postdoc work at Imperial College in London. Her experience in the field of molecular biology and gene expression shows up clearly in her book where she demonstrates the appropriate skepticism and critical thinking in her coverage of the major advances in the field.

Calculating time of divergence using genome sequences and mutation rates (humans vs other apes)

There are several ways to report a mutation rate. You can state it as the number of mutations per base pair per year in which case a typical mutation rate for humans is about 5 × 10^-10. Or you can express it as the number of mutations per base pair per generation (~1.5 × 10^-8).

You can use the number of mutations per generation or per year if you are only discussing one species. In humans, for example, you can describe the mutation rate as 100 mutations per generation and just assume that everyone knows the number of base pairs (6.4 × 10⁹).

How much mitochondrial DNA in your genome?

Most mitochondrial genes have been transferred from the ancestral mitochondrial genome to the nuclear genome over the course of 1-2 billion years of evollution. They are no longer present in mitochondria but they are easily recognized because they resemble α-proteobacterial sequences more than the other nuclear genes [see Endosymbiotic Theory].

This process of incorporating mitochondrial DNA into the nuclear genome continues to this day. The latest human reference genome has about 600 examples of nuclear sequences of mitochondrial origin (= numts). Some of them are quite recent while others date back almost 70 million years—the limit of resolution for junk DNA [see Mitochondria are invading your genome!].

Lateral gene transfer in eukaryotes - where's the evidence?

Lateral gene transfer (LGT), or horizontal gene transfer (HGT), is widespread in bacteria. It leads to the creation of pangenomes for many bacterial species where different subpopulations contain different subsets of genes that have been incorporated from other species. It also leads to confusing phylogenetic trees such that the history of bacterial evolution looks more like a web of life than a tree [The Web of Life].

Bacterial-like genes are also found in eukaryotes. Many of them are related to genes found in the ancestors of modern mitochondria and chloroplasts and their presence is easily explained by transfer from the organelle to the nucleus. Eukaryotic genomes also contain examples of transposons that have been acquired from bacteria. That's also easy to understand because we know how transposons jump between species.

Contaminated genome sequences

The authors of the original draft of the human genome sequence claimed that hundreds of genes had been acquired from bacteria by lateral gene transfer (LGT) (Lander et al., 2001). This claim was abandoned when the "finished" sequence was published a few years later (International Human Genome Consortium, 2004) because others had shown that the data was easily explained by differential gene loss in other lineages or by bacterial contamination in the draft sequence (see Salzberg, 2017).

Parental age and the human mutation rate

Theme

Mutation

-definition
-mutation types
-mutation rates
-phylogeny
-controversies

Mutations are mostly due to errors in DNA replication. We have a pretty good idea of the accuracy of DNA replication—the overall error rate is about 10^-10 per bp. There are about 30 cell divisions in females between zygote and formation of all egg cells. In males, there are about 400 mitotic cell divisions between zygote and formation of sperm cells (Ohno, 2019) . Using these average values, we can calculate the number of mutations per generation. It works out to about 130 mutations per generation [Estimating the Human Mutation Rate: Biochemical Method].

This value is similar to the estimate from comparing the sequences of different species (e.g. human and chimpanzee) based on the number of differences and the estimated time of divergence. This assumes that most of the genome is evolving at the rate expected for fixation of neutral alleles. This phylogenetic method give a value of about 112 mutations per generation [Estimating the Human Mutation Rate: Phylogenetic Method].

The third way of measuring the mutation rate is to directly compare the genome sequence of a child and both parents (trios). After making corrections for false positives and false negatives, this method yields values of 60-100 mutations per generation depending on how the data is manipulated [Estimating the Human Mutation Rate: Direct Method]. The lower values from the direct method call into question the dates of the split between the various great ape lineages. This controversy has not been resolved [Human mutation rates] [Human mutation rates - what's the right number?].

It's clear that males contribute more to evolution than females. There's about a ten-fold difference in the number of cell divisions in the male line compared to the female line; therefore, we expect there to be about ten times more mutations inherited from fathers. This difference should depend on the age of the father since the older the father the more cell divisions required to produce sperm.

This effect has been demonstrated in many publications. A maternal age effect has also been postulated but that's been more difficult to prove. The latest study of Icelandic trios helps to nail down the exact effect (Jónsson et al., 2017).

The authors examined 1,548 trios consisting of parents and at least one offspring. They analyzed 2.682 Mb of genome sequence (84% of the total genome) and discovered an average of 70 mutations events per child.¹ This gives an overall mutation rate of 83 mutations per generation with an average generation time of 30 years. This is consistent with previous results.

Jónsson et al. looked at 225 cases of three generation data in order to make sure that the mutations were germline mutations and not somatic cell mutations. They plotted the numbers of mutations against the age of the father and mother to produce the following graph from Figure 1 of their paper.

Look at parents who are 30 years old. At this age, females contribute about 10 mutations and males contribute about 50. This is only a five-fold difference—much lees than we expect from the number of cell divisions. This suggests that the initial estimates of 400 cell divisions in males might be too high.

An age effect on mutations from the father is quite apparent and expected. A maternal age effect has previously been hypothesized but this is the first solid data that shows such an effect. The authors speculate that oocyotes accumulate mutations with age, particularly mutations due to strand breakage.

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Of these, 93% were single nucleotide changes and 7% were small deletions or insertions.

Jónsson, H., Sulem, P., Kehr, B., Kristmundsdottir, S., Zink, F., Hjartarson, E., Hardarson, M.T., Hjorleifsson, K.E., Eggertsson, H.P., and Gudjonsson, S.A. (2017) Parental influence on human germline de novo mutations in 1,548 trios from Iceland. Nature, 549:519-522. [doi: 10.1038/nature24018]

Ohno, M. (2019) Spontaneous de novo germline mutations in humans and mice: rates, spectra, causes and consequences. Genes & genetic systems 94:13-22. [doi: 10.1266/ggs.18-00015]

The history of DNA sequencing

This year marks the 40th anniversary of DNA sequencing technology (Gilbert and Maxam, 1977; Sanger et al., 1977)¹ The Sanger technique soon took over and by the 1990s it was the only technique used to sequence DNA. The development of reliable sequencing machines meant the end of those large polyacrylamide gels that we all hated.

Pyrosequencing was developed in the mid 1990's and by the year 2000 massive parallel sequencing using this technique was becoming quite common. This "NextGen" sequencing technique was behind the massive explosion in sequences in the early part of the 21st century.²

Even newer techniques are available today and there's a debate about whether they should be called Third Generation Sequencing (Heather and Chain, 2015).

Nature has published a nice review of the history of DNA sequencing (Shendure et al., 2017). I recommend it to anyone who's interested in the subject. The figure above is taken from that article.

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1. Many labs were using the technology in 1976 before the papers were published.

2. New software and enhanced computer power played an important, and underappreciated, role.

Heather, J.M., and Chain, B. (2015) The sequence of sequencers: The history of sequencing DNA. Genomics, 107:1-8. [doi: 10.1016/j.ygeno.2015.11.003]

Maxam, A.M., and Gilbert, W. (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Methods in enzymology, 65:499-560. [doi: 10.1016/S0076-6879(80)65059-9]

Sanger, F., Nicklen, S., and Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, 74:5463-5467. [PDF]

Shendure, J., Balasubramanian, S., Church, G.M., Gilbert, W., Rogers, J., Schloss, J.A., and Waterston, R.H. (2017) DNA sequencing at 40: past, present and future. Nature, 550:345-353. [doi: 10.1038/nature24286]

Escape from X chromosome inactivation

Mammals have two sex chromosomes: X and Y. Males have one X chromosome and one Y chromosome and females have two X chromosomes. Since females have two copies of each X chromosome gene, you might expect them to make twice as much gene product as males of the same species. In fact, males and females often make about the same amount of gene product because one of the female X chromosomes is inactivated by a mechanism that causes extensive chromatin condensation.

The mechanism is known as X chromosome inactivation. The phenomenon was originally discovered by Mary Lyon (1925-2014) [see Calico Cats].

Creationists questioning pseudogenes: the GULO pseudogene

This is the second post discussing creationist¹ papers on pseudogenes. The first post addressed a paper by Jeffrey Tomkins on the β-globin pseudogene [Creationists questioning pseudogenes: the beta-globin pseudogene]. This post covers another paper by Tomkins claiming that the GULO pseudogenes in various primate species are not derived from a common ancestor but instead have been deactivated independently in each lineage.

The Tomkins' article was published in 2014 in Answers Research Journal, a publication that describes itself like this:

ARJ is a professional, peer-reviewed technical journal for the publication of interdisciplinary scientific and other relevant research from the perspective of the recent Creation and the global Flood within a biblical framework.

Creationists questioning pseudogenes: the beta-globin pseudogene

Jonathan Kane recently (Oct. 6, 2017) posted an article on The Panda's Thumb where he claimed that Young Earth Creationists often don't get enough credit for raising serious issues about evolution [Five principles for arguing against creationism].

He mentioned some articles about pseudogenes as prime examples. I asked him for references and he responded with two articles by Jeffrey Tomkins that were published on the Answers in Genesis website. The first was on the β-globin pseudogene and the second was on the GULO pseudogene. Both articles claim that these DNA sequences aren't really pseudogenes because they have functions.

I'll deal with the β-globin pseudogene in this post and the GULO pseudogene in a subsequent post.

Historical evolution is determined by chance events

Modern evolutionary theory is based on the idea that alleles become fixed in a population over time. They can be fixed by natural selection if they confer selective advantage or they can be fixed by random genetic drift if they are nearly neutral or slightly deleterious [Learning about modern evolutionary theory: the drift-barrier hypothesis]. Alleles arise by mutation and the path that a population follows over time depends on the timing of mutations [Mutation-Driven Evolution]. That's largely a chance event.

Sequencing human diploid genomes

Most eukaryotes are diploid, including humans. They have two copies of each autosome. Thousands of human genomes have been sequenced but in almost all cases the resulting genome sequence is a mixture of sequences from homologous chromosomes. If a site is heterogeneous—different alleles on each chromosome—then these are entered as variants.

What's in Your Genome?: Chapter 4: Pervasive Transcription (revised)

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! The first chapter is an introduction to genomes and DNA [What's in Your Genome? Chapter 1: Introducing Genomes ]. Chapter 2 is an overview of the human genome. It's a summary of known functional sequences and known junk DNA [What's in Your Genome? Chapter 2: The Big Picture]. Chapter 3 defines "genes" and describes protein-coding genes and alternative splicing [What's in Your Genome? Chapter 3: What Is a Gene?].

Chapter 4 is all about pervasive transcription and genes for functional noncoding RNAs. I've finally got a respectable draft of this chapter. This is an updated summary—the first version is at: What's in Your Genome? Chapter 4: Pervasive Transcription.

Cold Spring Harbor tells us about the "dark matter" of the genome (Part I)

This is a podcast from Cold Spring Harbor [Dark Matter of the Genome, Pt. 1 (Base Pairs Episode 8)]. The authors try to convince us that most of the genome is mysterious "dark matter," not junk. The main theme is that the genome contains transposons that could play an important role in evolution and disease.

Winter is coming ... I want this for Xmas (or whenever)

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Experts meet to discuss non-coding RNAs - fail to answer the important question

The human genome is pervasively transcribed. More than 80% of the genome is complementary to transcripts that have been detected in some tissue or cell type. The important question is whether most of these transcripts have a biological function. How many genes are there that produce functional non-coding RNA?

There's a reason why this question is important. It's because we have every reason to believe that spurious transcription is common in large genomes like ours. Spurious, or accidental, transcription occurs when the transcription initiation complex binds nonspecifically to sites in the genome that are not real promoters. Spurious transcription also occurs when the initiation complex (RNA plymerase plus factors) fires in the wrong direction from real promoters. Binding and inappropriate transcription are aided by the binding of transcription factors to nonpromoter regions of the genome—a well-known feature of all DNA binding proteins [see Are most transcription factor binding sites functional?].

The Extended Evolutionary Synthesis - papers from the Royal Society meeting

I went to London last November to attend the Royal Society meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives [New Trends in Evolutionary Biology: The Program].

The meeting was a huge disappointment [Kevin Laland's new view of evolution]. It was dominated by talks that were so abstract and obtuse that it was difficult to mount any serious discussion. The one thing that was crystal clear is that almost all of the speakers had an old-fashioned view of the current status of evolutionary theory. Thus, they were for the most part arguing against a strawman version of evolutionary theory.

The Royal Society has now published the papers that were presented at the meeting [Theme issue ‘New trends in evolutionary biology: biological, philosophical and social science perspectives’ organized by Denis Noble, Nancy Cartwright, Patrick Bateson, John Dupré and Kevin Laland]. I'll list the Table of Contents below.

Most of these papers are locked behind a paywall and that's a good thing because you won't be tempted to read them. The overall quality is atrocious—the Royal Society should be embarrassed to publish them.¹ The only good thing about the meeting was that I got to meet a few friends and acquaintances who were supporters of evolution. There was also a sizable contingent of Intelligent Design Creationists at the meeting and I enjoyed talking to them as well² [see Intelligent Design Creationists reveal their top story of 2016].

Niles Eldredge explains punctuated equilibria

Lots of people misunderstand punctuated equilibria. It's a theory about small changes leading to speciation. In many cases the changes are so slight that you and I might not notice the difference. These are not leaps or saltations and there are no intermediates or missing links. The changes may be due to changes in the frequency of one or two alleles.

Punctuated equilibria are when these speciation events take place relatively quickly and are followed by much longer periods of stasis (no change). Niles Eldredge explains how the theory is derived from his studies of thousands of trilobite fossils.

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Niles Eldredge explains hierarchy theory

You may not agree but you should at least know what some evolutionary biologists are thinking.

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