Saturday, October 14, 2017

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.

Wednesday, October 11, 2017

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.

Wednesday, September 13, 2017

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.

Monday, September 11, 2017

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.

Saturday, September 09, 2017

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.

Wednesday, August 30, 2017

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?].

Sunday, August 27, 2017

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].

Friday, August 25, 2017

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.



Niles Eldredge explains hierarchy theory

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



How much of the human genome is devoted to regulation?

All available evidence suggests that about 90% of our genome is junk DNA. Many scientists are reluctant to accept this evidence—some of them are even unaware of the evidence [Five Things You Should Know if You Want to Participate in the Junk DNA Debate]. Many opponents of junk DNA suffer from what I call The Deflated Ego Problem. They are reluctant to concede that humans have about the same number of genes as all other mammals and only a few more than insects.

One of the common rationalizations is to speculate that while humans may have "only" 25,000 genes they are regulated and controlled in a much more sophisticated manner than the genes in other species. It's this extra level of control that makes humans special. Such speculations have been around for almost fifty years but they have gained in popularity since publication of the human genome sequence.

In some cases, the extra level of regulation is thought to be due to abundant regulatory RNAs. This means there must be tens of thousand of extra genes expressing these regulatory RNAs. John Mattick is the most vocal proponent of this idea and he won an award from the Human Genome Organization for "proving" that his speculation is correct! [John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research]. Knowledgeable scientists know that Mattick is probably wrong. They believe that most of those transcripts are junk RNAs produced by accidental transcription at very low levels from non-conserved sequences.

Monday, August 07, 2017

A philosopher defends agnosticism

Paul Draper is a philosopher at Purdue University (West Lafayette, Indiana, USA). He has just (Aug. 2, 2017) posted an article on Atheism and Agnosticism on the Stanford Encyclopedia of Philosophy website.

Many philosphers use a different definition of atheism than many atheists. Philosophers tend to define atheism as the proposition that god(s) do not exist. Many atheists (I am one) define atheism as the lack of belief in god(s). The distinction is important but for now I want to discuss Draper's defense of agnosticism.

Keep in mind that Draper defines atheism as "god(s) don't exist." He argues, convincingly, that this proposition cannot be proven. He also argues that theism—the proposition that god(s) exist—can also not be proven. Therefore, the only defensible position for a philosopher like him is agnosticism.

Friday, August 04, 2017

To toss or not to toss?

Now that I'm officially retired I've been cleaning out my office at the university and transferring all the important stuff to my home office. I'm taking advantage of this opportunity to throw out everything that I don't want any more. Eventually I'll have to vacate my university office because it's due to be renovated and transferred to another department.

Some stuff is easy to toss out and some stuff is easy to keep. It's the other stuff that causes a problem. Here's an example ....


These are the manuals that came with my very first PC back in 1981. I know I'll never use them but I'm kinda attached to them. Are they antiques yet?


Thursday, July 27, 2017

talk.origins evolves

The newsgroup talk.origins was created more than 30 years ago. It's been a moderated newsgroup for the past twenty years. The moderator is David Greig and the server, named "Darwin," has been sitting in my office for most of that time. I retired on June 30th and my office is scheduled for renovation so Darwin had to move. Another complication is that the moderator is moving from Toronto to Copenhagen, Denmark.

So talk.origins evolves and the server is moving elsewhere. Goodby Darwin.



Friday, July 14, 2017

Bastille Day 2017

Today is the Fête Nationale in France known also as "le quatorze juillet" or Bastille Day.

This is the day in 1789 when French citizens stormed and captured the Bastille—a Royalist fortress in Paris. It marks the symbolic beginning of the French revolution although the real beginning is when the Third Estate transformed itself into the National Assembly on June 17, 1789 [Tennis Court Oath].

Ms. Sandwalk and I visited the site of the Bastille (Place de la Bastille) when we were in Paris in 2008. There's nothing left of the former castle but the site still resonates with meaning and history.

One of my wife's ancestors is William Playfair, the inventor of pie charts and bar graphs [Bar Graphs, Pie Charts, and Darwin]. His work attracted the attention of the French King so he moved to Paris in 1787 to set up an engineering business. He is said to have participated in the storming of the Bastille but he has a history of exaggeration and untruths so it's more likely that he just witnessed the event. He definitely lived nearby and was in Paris on the day in question. (His son, my wife's ancestor, was born in Paris in 1790.)

In honor of the French national day I invite you to sing the French national anthem, La Marseillaise. An English translation is provided so you can see that La Marseillaise is truly a revolutionary call to arms. (A much better translation can be found here.)1



1. I wonder if President Trump sang La Marseillaise while he was at the ceremonies today?

Check out Uncertain Principles for another version of La Marseillaise—this is the famous scene in Casablanca.

Reposted and modified from 2016.

Revisiting the genetic load argument with Dan Graur

The genetic load argument is one of the oldest arguments for junk DNA and it's one of the most powerful arguments that most of our genome must be junk. The concept dates back to J.B.S. Haldane in the late 1930s but the modern argument traditionally begins with Hermann Muller's classic paper from 1950. It has been extended and refined by him and many others since then (Muller, 1950; Muller, 1966).

Thursday, July 06, 2017

Scientists say "sloppy science" more serious than fraud

An article on Nature: INDEX reports on a recent survey of scientists: Cutting corners a bigger problem than research fraud. The subtitle says it all: Scientists are more concerned about the impact of sloppy science than outright scientific fraud.

The survey was published on BioMed Central.

Tuesday, July 04, 2017

Another contribution of philosophy: Bernard Lonergan

The discussion about philosophy continues on Facebook. One of my long-time Facebook friends, Jonathan Bernier, took up the challenge. Bernier is a professor of religious studies at St. Francis Xavier University in Nova Scotia, Canada. He is a card-carrying philosopher.1

The challenge is to provide recent (past two decades) examples from philosophy that have lead to increased knowledge and understanding of the natural world. Here's what Jonathan Bernier offered.
But to use just one example of advances in philosophical understanding, UofT (specifically Regis College) houses the Lonergan Research Institute, which houses Bernard Lonergan's archives and publishes his collected works. Probably his most significant work is a seven-hundred-page tome called Insight, the first edition of which was published in 1957. It is IMHO the single best account of how humans come to know anything that has ever been written. The tremendous fruits that it has wrought cannot be summarized in a FB commend. Instead, I'd suggest that you walk over and see the friendly people at the LRI. No doubt they could help answer some of your questions.
Here's a Wikipedia link to Bernard Lonergan. He was a Canadian Jesuit priest who died in 1984. Regis College is the Jesuit College associated with the University of Toronto.

Is Jonathan Bernier correct? Is it true that Lonergan's works will eventually change the way we understand learning?


Note: In my response to Bernier on Facebook I said, "I guess I'll just have to take our word for it. I'm not about to walk over to Regis College and consult a bunch of Jesuit priests about the nature of reality." Was I being too harsh? Is this really an examples of a significant contribution of philosophy? Is it possible that a philosopher could be very wrong about the existence of supernatural beings but still make a contribution to the nature of knowledge and understanding?

1. Jonathan Bernier tells me on Facebook that he is not a philosopher and never claimed to be a philosopher.

Monday, July 03, 2017

Contributions of philosophy

I've been discussing the contributions of philosophy on Facebook. Somebody linked to a a post on the topic: What has philosophy contributed to society in the past 50 years?. Here's one of contributions ... do you agree?
Philosophers, historians, and sociologists of science such as Thomas Kuhn, Paul Feyerabend, Bruno Latour, Bas van Fraassen, and Ian Hacking have changed the way that we see the purpose of science in everyday life, as well as proper scientific conduct. Kuhn's concept of a paradigm shift is now so commonplace as to be cliche. Meanwhile, areas like philosophy of physics and especially philosophy of biology are sites of active engagement between philosophers and scientists about the interpretation of scientific results.


Sunday, July 02, 2017

Confusion about the number of genes

My last post was about confusion over the sizes of the human and mouse genomes based on a recent paper by Breschi et al. (2017). Their statements about the number of genes in those species are also confusing. Here's what they say about the human genome.
[According to Ensembl86] the human genome encodes 58,037 genes, of which approximately one-third are protein-coding (19,950), and yields 198,093 transcripts. By comparison, the mouse genome encodes 48,709 genes, of which half are protein-coding (22,018 genes), and yields 118,925 transcripts overall.
The very latest Ensembl estimates (April 2017) for Homo sapiens and Mus Musculus are similar. The difference in gene numbers between mouse and human is not significant according to the authors ...
The discrepancy in total number of annotated genes between the two species is unlikely to reflect differences in underlying biology, and can be attributed to the less advanced state of the mouse annotation.
This is correct but it doesn't explain the other numbers. There's general agreement on the number of protein-coding genes in mammals. They all have about 20,000 genes. There is no agreement on the number of genes for functional noncoding RNAs. In its latest build, Ensemble says there are 14,727 lncRNA genes, 5,362 genes for small noncoding RNAs, and 2,222 other genes for nocoding RNAs. The total number of non-protein-coding genes is 22,311.

There is no solid evidence to support this claim. It's true there are many transcripts resembling functional noncoding RNAs but claiming these identify true genes requires evidence that they have a biological function. It would be okay to call them "potential" genes or "possible" genes but the annotators are going beyond the data when they decide that these are actually genes.

Breschi et al. mention the number of transcripts. I don't know what method Ensembl uses to identify a functional transcript. Are these splice variants of protein-coding genes?

The rest of the review discusses the similarities between human and mouse genes. They point out, correctly, that about 16,000 protein-coding genes are orthologous. With respect to lncRNAs they discuss all the problems in comparing human and mouse lncRNA and conclude that "... the current catalogues of orthologous lncRNAs are still highly incomplete and inaccurate." There are several studies suggesting that only 1,000-2,000 lncRNAs are orthologous. Unfortunately, there's very little overlap between the two most comprehensive studies (189 lncRNAs in common).

There are two obvious possibilities. First, it's possible that these RNAs are just due to transcriptional noise and that's why the ones in the mouse and human genomes are different. Second, all these RNAs are functional but the genes have arisen separately in the two lineages. This means that about 10,000 genes for biologically functional lncRNAs have arisen in each of the genomes over the past 100 million years.

Breschi et al. don't discuss the first possibility.


Breschi, A., Gingeras, T.R., and Guigó, R. (2017) Comparative transcriptomics in human and mouse. Nature Reviews Genetics [doi: 10.1038/nrg.2017.19]

Genome size confusion

The July 2017 issue of Nature Reviews: Genetics contains an interesting review of a topic that greatly interest me.
Breschi, A., Gingeras, T. R., and Guigó, R. (2017). Comparative transcriptomics in human and mouse. Nature Reviews Genetics [doi: 10.1038/nrg.2017.19]

Cross-species comparisons of genomes, transcriptomes and gene regulation are now feasible at unprecedented resolution and throughput, enabling the comparison of human and mouse biology at the molecular level. Insights have been gained into the degree of conservation between human and mouse at the level of not only gene expression but also epigenetics and inter-individual variation. However, a number of limitations exist, including incomplete transcriptome characterization and difficulties in identifying orthologous phenotypes and cell types, which are beginning to be addressed by emerging technologies. Ultimately, these comparisons will help to identify the conditions under which the mouse is a suitable model of human physiology and disease, and optimize the use of animal models.
I was confused by the comments made by the authors when they started comparing the human and mouse genomes. They said,
The most recent genome assemblies (GRC38) include 3.1 Gb and 2.7 Gb for human and mouse respectively, with the mouse genome being 12% smaller than the human one.
I think this statement is misleading. The size of the human genome isn't known with precision but the best estimate is 3.2 Gb [How Big Is the Human Genome?]. The current "golden path length" according to Ensembl is 3,096,649,726 bp. [Human assembly and gene annotation]. It's not at all clear what this means and I've found it almost impossible to find out; however, I think it approximates the total amount of sequenced DNA in the latest assembly plus an estimate of the size of some of the gaps.

The golden path length for the mouse genome is 2,730,871,774 bp. [Mouse assembly and gene annotation]. As is the case with the human genome, this is NOT the genome size. Not as much mouse DNA sequence has been assembled into a contiguous and accurate assembly as is the case with humans. The total mouse sequence is at about the same stage the human genome assembly was a few years ago.

If you look at the mouse genome assembly data you see that 2,807,715,301 bp have been sequenced and there's 79,356,856 bp in gaps. That's 2.88 Gb which doesn't match the golden path length and doesn't match the past estimates of the mouse genome size.

We don't know the exact size of the mouse genome. It's likely to be similar to that of the human genome but it could be a bit larger or a bit smaller. The point is that it's confusing to say that the mouse genome is 12% smaller than the human one. What the authors could have said is that less of the mouse genome has been sequenced and assembled into accurate contigs.

If you go to the NCBI site for Homo sapiens you'll see that the size of the genome is 3.24 Gb. The comparable size for Mus musculus is 2.81 Gb. That 15% smaller than the human genome size. How accurate is that?

There's a problem here. With all this sequence information, and all kinds of other data, it's impossible to get an accurate scientific estimate of the total genome sizes.


[Image Credit: Wikipedia: Creative Commons Attribution 2.0 Generic license]

Tuesday, June 27, 2017

Debating alternative splicing (Part IV)

In Debating alternative splicing (Part III) I discussed a review published in the February 2017 issue of Trends in Biochemical Sciences. The review examined the data on detecting predicted protein isoforms and concluded that there was little evidence they existed.

My colleague at the University of Toronto, Ben Blencowe, is a forceful proponent of massive alternative splicing. He responded in a letter published in the June 2017 issue of Trends in Biochemical Sciences (Blencowe, 2017). It's worth looking at his letter in order to understand the position of alternative splicing proponents. He begins by saying,
It is estimated that approximately 95% of multiexonic human genes give rise to transcripts containing more than 100 000 distinct AS events [3,4]. The majority of these AS events display tissue-dependent variation and 10–30% are subject to pronounced cell, tissue, or condition-specific regulation [4].

Monday, June 26, 2017

Debating alternative splicing (Part III)

Proponents of massive alternative splicing argue that most human genes produce many different protein isoforms. According to these scientists, this means that humans can make about 100,000 different proteins from only ~20,000 protein-coding genes. They tend to believe humans are considerably more complex than other animals even though we have about the same number of genes. They think alternative splicing accounts for this complexity [see The Deflated Ego Problem].

Opponents (I am one) argue that most splice variants are due to splicing errors and most of those predicted protein isoforms don't exist. (We also argue that the differences between humans and other animals can be adequately explained by differential regulation of 20,000 protein-coding genes.) The controversy can only be resolved when proponents of massive alternative splicing provide evidence to support their claim that there are 100,000 functional proteins.

Saturday, June 24, 2017

Debating alternative splicing (part II)

Mammalian genomes are very large. It looks like 90% of it is junk DNA. These genomes are pervasively transcribed, meaning that almost 90% of the bases are complementary to a transcript produced at some time during development. I think most of those transcripts are due to inappropriate transcription initiation. They are mistakes in transcription. The genome is littered with transcription factor binding sites but only a small percentage are directly involved in regulating gene expression. The rest are due to spurious binding—a well-known property of DNA binding proteins. These conclusions are based, I believe, on a proper understanding of evolution and basic biochemistry.

If you add up all the known genes, they cover about 30% of the genome sequence. Most of this (>90%) is intron sequence and introns are mostly junk. The standard mammalian gene is transcribed to produce a precursor RNA that is subsequently processed by splicing out introns to produce a mature RNA. If it's a messenger RNA (mRNA) then it will be translated to produce a protein (technically, a polypeptide). So far, the vast majority of protein-coding genes produce a single protein but there are some classic cases of alternative splicing where a given gene produces several different protein isoforms, each of which has a specific function.

Friday, June 23, 2017

Debating alternative splicing (part I)

I recently had a chance to talk science with my old friend and colleague Jack Greenblatt. He has recently teamed up with some of my other colleagues at the University of Toronto to publish a paper on alternative splicing in mouse cells. Over the years I have had numerous discussions with these colleagues since they are proponents of massive alternative splicing in mammals. I think most splice variants are due to splicing errors.

There's always a problem with terminology whenever we get involved in this debate. My position is that it's easy to detect splice variants but they should be called "splice variants" until it has been firmly established that the variants have a biological function. This is not a distinction that's acceptable to proponents of massive alternative splicing. They use the term "alternative splicing" to refer to any set of processing variants regardless of whether they are splicing errors or real examples of regulation. This sometimes makes it difficult to have a discussion.

In fact, most of my colleagues seem reluctant to admit that some splice variants could be due to meaningless errors in splicing. Thus, they can't be pinned down when I ask them what percentage of variants are genuine examples of alternative splicing and what percentage are splicing mistakes. I usually ask them to pick out a specific gene, show me all the splice variants that have been detected, and explain which ones are functional and which ones aren't. I have a standing challenge to do this with any one of three sets of genes [A Challenge to Fans of Alternative Splicing].
  1. Human genes for the enzymes of glycolysis
  2. Human genes for the subunits of RNA polymerase with an emphasis on the large conserved subunits
  3. Human genes for ribosomal proteins
I realize that proponents of massive alternative splicing are not under any obligation to respond to my challenge but it sure would help if they did.

Thursday, June 22, 2017

Are most transcription factor binding sites functional?

The ongoing debate over junk DNA often revolves around data collected by ENCODE and others. The idea that most of our genome is transcribed (pervasive transcription) seems to indicate that genes occupy most of the genome. The opposing view is that most of these transcripts are accidental products of spurious transcription. We see the same opposing views when it comes to transcription factor binding sites. ENCODE and their supporters have mapped millions of binding sites throughout the genome and they believe this represent abundant and exquisite regulation. The opposing view is that most of these binding sites are spurious and non-functional.

The messy view is supported by many studies on the biophysical properties of transcription factor binding. These studies show that any DNA binding protein has a low affinity for random sequence DNA. They will also bind with much higher affinity to sequences that resemble, but do not precisely match, the specific binding site [How RNA Polymerase Binds to DNA; DNA Binding Proteins]. If you take a species with a large genome, like us, then a typical DNA protein binding site of 6 bp will be present, by chance alone, at 800,000 sites. Not all of those sites will be bound by the transcription factor in vivo because some of the DNA will be tightly wrapped up in dense chromatin domains. Nevertheless, an appreciable percentage of the genome will be available for binding so that typical ENCODE assays detect thousand of binding sites for each transcription factor.

This information appears in all the best textbooks and it used to be a standard part of undergraduate courses in molecular biology and biochemistry. As far as I can tell, the current generation of new biochemistry researchers wasn't taught this information.

Jonathan Wells talks about junk DNA

Watch this video. It dates from this year. Almost everything Wells says is either false or misleading. Why? Is he incapable of learning about genomes, junk DNA, and evolutionary theory?



Some of my former students

Some of my former students were able to come to my retirement reception yesterday: Sean Blaine (left), Anna Gagliardi, Marc Perry.




Hot slash buns

I love hot "cross" buns but now we buy the atheist version.



I retired after 39 years and they gave me an old used book

... but it was a rather special book ...



Wednesday, June 21, 2017

John Mattick still claims that most lncRNAs are functional

Most of the human genome is transcribed at some time or another in some tissue or another. The phenomenon is now known as pervasive transcription. Scientists have known about it for almost half a century.

At first the phenomenon seemed really puzzling since it was known that coding regions accounted for less than 1% of the genome and genetic load arguments suggested that only a small percentage of the genome could be functional. It was also known that more than half the genome consists of repetitive sequences that we now know are bits and pieces of defective transposons. It seemed unlikely back then that transcripts of defective transposons could be functional.

Part of the problem was solved with the discovery of RNA processing, especially splicing. It soon became apparent (by the early 1980s) that a typical protein coding gene was stretched out over 37,000 bp of which only 1300 bp were coding region. The rest was introns and intron sequences appeared to be mostly junk.

Tuesday, June 20, 2017

On the evolution of duplicated genes: subfunctionalization vs neofunctionalization

New genes can arise by gene duplication. These events are quite common on an evolutionary time scale. In the current human population, for example, there are about 100 examples of polymorphic gene duplications. These are cases where some of us have two copies of a gene while others have only one copy (Zarrie et al., 2015). Humans have gained about 700 new genes by duplication and fixation since we diverged from chimpanzees (Demuth et al., 2006). The average rate of duplication in eukaryotes is about 0.01 events per gene per million years and the half-life of a duplicated gene is about 4 million years (Lynch and Conery, 2003).

The typical fate of these duplicated genes is to "die" by mutation or deletion. There are five possible fates [see Birth and death of genes in a hybrid frog genome]:
  1. One of the genes will "die" by acquiring fatal mutations. It becomes a pseudogene.
  2. One of the genes will die by deletion.
  3. Both genes will survive because having extra gene product (e.g. protein) will be beneficial (gene dosage).
  4. One of the genes acquires a new beneficial mutation that creates a new function and at the same time causes loss of the old function (neofunctionalization). Now both genes are retained by positive selection and the complexity of the genome has increased.
  5. Both genes acquire mutations that diminish function so the genome now needs two copies of the gene in order to survive (subfunctionalization).

Monday, June 19, 2017

Austin Hughes and Neutral Theory

Austin Hughes (1949 - 2015) died a few years ago. He was one of my favorite evolutionary biologists.

Chase Nelson has written a nice summary of Hughes' work at: Austin L. Hughes: The Neutral Theory of Evolution. It's worth reading the first few pages if you aren't clear on the concept. Here's an excerpt ...
When the technology enabling the study of molecular polymorphisms—variations in the sequences of genes and proteins—first arose, a great deal more variability was discovered in natural populations than most evolutionary biologists had expected under natural selection. The neutral theory made the bold claim that these polymorphisms become prevalent through chance alone. It sees polymorphism and long-term evolutionary change as two aspects of the same phenomenon: random changes in the frequencies of alleles. While the neutral theory does not deny that natural selection may be important in adaptive evolutionary change, it does claim that natural selection accounts for a very small fraction of genetic evolution.

A dramatic consequence now follows. Most evolutionary change at the genetic level is not adaptive.

It is difficult to imagine random changes accomplishing so much. But random genetic drift is now widely recognized as one of the most important mechanisms of evolution.
I don't think there's any doubt that this claim is correct as long as you stick to the proper definition of evolution. The vast majority of fixations of alleles are likely due to random genetic drift and not natural selection.

If you don't understand this then you don't understand evolution.

The only quibble I have with the essay is the reference to "Neutral Theory of Evolution" as the antithesis of "Darwinian Evolution" or evolution by natural selection. I think "Neutral Theory" should be restricted to the idea that many alleles are neutral or nearly neutral. These alleles can change in frequency in a population by random genetic drift. The key idea that's anti-Darwinian includes that fact plus two other important facts:
  1. New beneficial alleles can be lost by drift before they ever become fixed. In fact, this is the fate of most new beneficial alleles. It's part of the drift-barrier hypothesis.
  2. Detrimental alleles can occasionally become fixed in a population due to drift.
In both cases, the alleles are not neutral. The key to understanding the overall process is random genetic drift not the idea of neutral alleles—although that's also important.
Originally proposed by Motoo Kimura, Jack King, and Thomas Jukes, the neutral theory of molecular evolution is inherently non-Darwinian. Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance.
I would just add that it's Neutral Theory PLUS the other effects of random genetic drift that make evolution much more random than most people believe.

Austin Hughes was a skeptic and a creative thinker who often disagreed with the prevailing dogma in the field of evolutionary biology. He was also very religious, a fact I find very puzzling.

His scientific views were often correct, in my opinion.
In 2013, the ENCODE (Encyclopedia of DNA Elements) Project published results suggesting that eighty per cent of the human genome serves some function. This was considered a rebuttal to the widely held view that a large part of the genome was junk, debris collected over the course of evolution. Hughes sided with his friend Dan Graur in rejecting this point of view. Their argument was simple. Only ten per cent of the human genome shows signs of purifying selection, as opposed to neutrality.


Saturday, June 17, 2017

I coulda been an astronomer

A long time ago I used to belong to the Royal Astronomical Society (amateur astronomers) in Ottawa (Canada). That's me on the right with some of my friends. We were testing our sun filters and getting ready to see Venus when the sun went down.

In spite of this promising beginning, I decided to go into biology because it was harder and more interesting.





Tuesday, June 06, 2017

June 6, 1944

Today is anniversary of D-Day—the day British, Canadian, and American troops landed on the beaches of Normandy.1

For baby boomers it means a day of special significance for our parents. In my case, it was my father who took part in the invasions. That's him on the right as he looked in 1944. He was an RAF pilot flying rocket firing typhoons in close support of the ground troops. During the initial days his missions were limited to quick strikes and reconnaissance since Normandy was at the limit of their range from southern England. During the second week of the invasion (June 14th) his squadron landed in Crepon, Normandy and things became very hectic from then on with several close support missions every day.

Stephen Meyer "predicts" there's no junk DNA

Here's an interview with Stephen Meyer on the Evolution 2.0 website: Stephen Meyer Debates Perry Marshall – Intelligent Design vs. Evolution 2.0. I'm posting some remarks by Stephen Meyer in order to preserve them for posterity. Meyer should know by now that the evidence for junk DNA is very solid and the ENCODE declarations are wrong. The fact that he persists in spreading false information about the ID "prediction" is revealing.

Tuesday, May 30, 2017

Imagine 7


I'll be at Imagine 7 this weekend. Are you going? Contact me if you want to get together.


We are scientists


You can tell we are scientists because we're all wearing lab coats.

Left to right: David Isenman, Larry Moran, Marc Perry, Kim Ellison, Trevor Moraes, Mike Ellison.

The photo was taken in the biochemistry department labs at the University of Toronto (Toronto, Canada).




Three generations of scientists


Bottom row, left to right.

Marc Perry: Bioinformatics researcher and former graduate student in my lab.
Mike Ellison: Professor, University of Alberta (Alberta, Canada) and former graduate student in the lab of my colleague David Pulleyblank.
Trevor Moraes: Professor in my department at the University of Toronto and former graduate student with Mike Ellison.
Kim (Bird) Ellison: Professor at the University of Alberta, former undergraduate student in my lab (where she met Mike Ellison), Ph.D. at MIT.



Saturday, May 20, 2017

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,

Thursday, May 18, 2017

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.

Tuesday, May 16, 2017

"The Perils of Public Outreach"

Julia Shaw is a forensic psychologist. She is currently a senior lecturer in criminology at the London South Bank University (London, UK). Shaw is concerned that we are creating a culture where public outreach is being unfairly attacked. Read her Scientific American post at: The Perils of Public Outreach.

Shaw's point is rather interesting. She believes that scientists who participate in public outreach are being unfairly criticized. Let's look closely at her argument.
What scientists write in academic publications is generally intended for a scientific community, full of nuance and precise language. Instead, what scientists say and write in public forums is intended for lay audiences, almost invariably losing nuance but gaining impact and social relevance. This makes statements made in public forums particularly ripe for attack.

Wednesday, May 10, 2017

Debating philosophers: Pierrick Bourrat responds to my criticism of his paper

I recently criticized a paper by Lu and Bourrat on the extended evolutionary synthesis [Debating philosophers: The Lu and Bourrat paper]. Pierrick Bourrat responds in this guest post.


by Pierrick Bourrat
Research Fellow, Department of Philosophy
Macquarie University
Sydney, Australia

Both Qiaoying Lu and I are grateful to Professor Moran for the copious attention he has bestowed on our paper. We are early career researchers and didn’t expect our paper to receive so much attention from a senior academic in a public forum. Moran claims that our work is out of touch with science (and more generally works in philosophy of biology), that the paper is weakly argued and that some of what we write is false. But in the end, he puts forward a similar position to ours.

Saturday, May 06, 2017

Debating philosophers: Epigenetics

Qiaoying Lu and Pierrick Bourrat are philosophers in Australia.1 Their research interests include evolutionary theory and they have taken an interest in the current debate over extending evolutionary theory. That debate has been promoted by a small group of scientists who, by and large, are not experts in evolution. They claim that current evolutionary theory—which they define incorrectly as the 1960s version of the Modern Synthesis—needs to be overthrown or extended by including things like epigenetics, niche construction, developmental biology, and plasticity [New Trends in Evolutionary Biology: The Program].

Lu and Bourrat have focused on epigenetics in their recent paper [Debating philosophers: The Lu and Bourrat paper]. They hope to reach an accommodation by re-defining the evolutionary gene as: "any physical structure that causes a heritable variation." Then they go on to say that, "we define the phenotype of an evolutionary gene as everything that the gene makes a difference to when compared to another gene."

By doing this, they claim that epigenetic changes (e.g. transient methylation) fall with the new definition. Therefore, epigenetics doesn't really represent a challenge to evolutionary theory. They explain it like this ....

Thursday, May 04, 2017

Debating philosophers: The molecular gene

This is my fifth post on the Lu and Bourrat paper [Debating philosophers: The Lu and Bourrat paper]. The authors are attempting to justify the inclusion of epigenetics into current evolutionary theory by re-defining the concept of "gene," specifically the evolutionary gene concept. So far, I've discussed their understanding of current evolutionary theory and why I think it is flawed [Debating philosophers: The Modern Synthesis]. I described their view of "genes" and pointed out the confusion between "genes" and "alleles" and why I think "alleles" is the better term [Debating philosophers: The difference between genes and alleles]. In my last post I discussed their definition of the evolutionary gene and why it is too adaptationist to serve a useful function [Debating philosophers: The evolutionary gene].

Wednesday, May 03, 2017

Debating philosophers: The evolutionary gene

This is the forth post on the Lu and Bourrat paper [Debating philosophers: The Lu and Bourrat paper]. The philosophers are attempting to redefine the word "gene" in order to make epigenetics compatible with current evolutionary theory.

I define a gene in the following way: "A gene is a DNA sequence that is transcribed to produce a functional product" [What Is a Gene?]. This is a biochemical/molecular definition and it's not the same as the definition used in traditional evolution.

Lu and Bourrat discuss the history of the evolutionary gene and conclude,

Debating philosophers: The difference between genes and alleles

This is my third post on the Lu and Bourrat (2017) paper [Debating philosophers: The Lu and Bourrat paper]. Part of their argument is to establish that modern evolutionary theory is a gene-centric theory. They need to make this connection because they are about to re-define the word "gene" in order to accommodate epigenetics.

In my last post I referred to their defense of the Modern Synthesis and quoted them as saying that the major tenets of the Modern Synthesis (MS) are still the basis of modern evolutionary theory. They go on to say,

Tuesday, May 02, 2017

Debating philosophers: The Modern Synthesis

I'm discussing a paper by Lu and Bourrat (2017) [Debating philosophers: The Lu and Bourrat paper]. They begin by describing current evolutionary theory, known (to them) as the Modern Synthesis. The paper is about challenges to current evolutionary theory from those who advocate an extended evolutionary synthesis or from those who would replace, rather than extend, current evolutionary theory. It is reasonable to begin with a description of the theory that's being challenged.

Here's what Lu & Bourrat say,

Debating philosophers: The Lu and Bourrat paper

John Wilkins posted a link on Facebook to a recent paper by his colleagues in Australia. The authors are Qiaoying Lu of the Department of Philosophy at Macquarie University in Sidney Australia and Pierrick Bourat of the Department of Philosophy at The University of Sydney in Sidney Australia.

Lu, Q., and Bourrat, P. (2017) The evolutionary gene and the extended evolutionary synthesis. The British Journal for the Philosophy of Science, (advanced article) April 20, 2017. [doi: 10.1093/bjps/axw035] [PhilSci Archive]

Abstract: Advocates of an ‘extended evolutionary synthesis’ have claimed that standard evolutionary theory fails to accommodate epigenetic inheritance. The opponents of the extended synthesis argue that the evidence for epigenetic inheritance causing adaptive evolution in nature is insufficient. We suggest that the ambiguity surrounding the conception of the gene represents a background semantic issue in the debate. Starting from Haig’s gene-selectionist framework and Griffiths and Neumann-Held’s notion of the evolutionary gene, we define senses of ‘gene’, ‘environment’, and ‘phenotype’ in a way that makes them consistent with gene-centric evolutionary theory. We argue that the evolutionary gene, when being materialized, need not be restricted to nucleic acids but can encompass other heritable units such as epialleles. If the evolutionary gene is understood more broadly, and the notions of environment and phenotype are defined accordingly, current evolutionary theory does not require a major conceptual change in order to incorporate the mechanisms of epigenetic inheritance.

1 Introduction
2 The Gene-centric Evolutionary Theory and the ‘Evolutionary Gene’
      2.1 The evolutionary gene
      2.2 Genes, phenotypes, and environments
3 Epigenetic Inheritance and the Gene-Centred Framework
      3.1 Treating the gene as the sole heritable material?
      3.2 Epigenetics and phenotypic plasticity
4 Conclusion

The selfish gene vs the lucky allele

The Selfish Gene was published forty-one years ago (1976) and last year there was a bit of a celebration. I think we can all appreciate the impact that the book had at the time but I'm not sure it's as profound and lasting as most people believe ["The Selfish Gene" turns 40] [The "selfish gene" is not a good metaphor to describe evolution] [Die, selfish gene, die!].

The main criticisms fall into two categories: (1) the primary unit of selection is the individual organism, not the gene, and (2) the book placed too much emphasis on adaptation (Darwinism). I think modern evolutionary theory is based on 21st century population genetics and that view puts a great deal of emphasis on the power of random genetic drift. The evolution of a population involves the survival of individuals within the population and that, in turn, depends on the variation that exists in the population. Thus, evolution is characterized by changes in the frequencies of alleles in a population.

Friday, April 28, 2017

Professor, please can I have more marks?

I submitted my grades on Thursday morning and they were approved by the Department of Biochemistry in short order. Once the final grades have been approved and submitted to the Faculty they can't be changed unless the change is approved by the Departmental Chair. Students may appeal their grade by paying a fee to re-read their final exam but, even then, I do not have the authority on my own to change a grade. I have to justify any change in writing. This is a good thing.

A few hours after the grades were posted I received an email message from a student [It's that time of year, again]. Here's part of what the student said,
I just saw my final mark ... which was an 76, and was very surprised. I thought I'd done well on the final exam, and had studied hard. My performance on the Midterm was good, and I had expected this to be just as well. As such, I wanted to humbly inquire whether it'd be possible to move me a 77 (a 1% increase) or even an 80. This small difference could make a very big impact on my GPA as I apply for positions to pursue a master or other professional degrees. With the mark as it is now, I fall below the GPA requirement for a program I wish to enroll in next year and will have to do another few courses or a full year to make up for it.

Friday, April 21, 2017

Thursday, April 20, 2017

Bill Martin is coming to town!!!

Contact me by email if you'd like to meet him on Sunday, April 30th.




The last molecular evolution exam: Question #6

How can alleles be fixed in a population by positive natural selection (i.e. adaptation) if the environment remains constant for thousands of years?

Question #1, Question #2, Question #3, Question #4, Question #5, Question #6


The last molecular evolution exam: Question #5

Many people believe that recombination evolved because it increases genetic variation in a population and this provided a selective advantage over species that didn’t have recombination. Do you agree with this explanation for the evolution of recombination? Why, or why not? What are the other possibilities?

Question #1, Question #2, Question #3, Question #4, Question #5, Question #6


The last molecular evolution exam: Question #4

More than 90% of our genome is transcribed when you add up all the transcripts from various cell types and various times of development (= pervasive transcription). Many biologists take this as evidence that most of the DNA in our genome is functional. What are the counter-arguments? Who do you believe and why?

Question #1, Question #2, Question #3, Question #4, Question #5, Question #6


The last molecular evolution exam: Question #3

The Three Domain Hypothesis has eukaryotes and archaea branching off from eubacteria. It shows eukaryotes more closely related to archaea than to eubacteria. However, many scientific studies indicate that a majority of our genes are more similar to eubacterial genes than to archaeal genes. How do you explain this apparent conflict?

Question #1, Question #2, Question #3, Question #4, Question #5, Question #6


The last molecular evolution exam: Question #2

The paper by Andrews et al. (2011) lists a number of common misconceptions held by their students. One of them is the idea that, “Evolution is a process that will never stop, even in the human species.” Why do they think this is a misconception? Do you agree?

Andrews, T.M., Kalinowski, S.T., and Leonard, M.J. (2011). “Are humans evolving?” A classroom discussion to change student misconceptions regarding natural selection. Evolution: Education and Outreach, 4:456-466. [doi: 10.1007/s12052-011-0343-4]
Question #1, Question #2, Question #3, Question #4, Question #5, Question #6


The last molecular evolution exam: Question #1

Eugene Koonin described his view of the proper null hypothesis for evolutionary questions. One of the examples he used concerns the evolution of recent gene duplications (Koonin, 2016 p.5). Describe how one possible fate of these genes relates to constructive neutral evolution. What are the other possible fates of these genes? Which one is most likely?

Koonin, E.V. (2016) Splendor and misery of adaptation, or the importance of neutral null for understanding evolution. BMC biology, 14:114 [doi: 10.1186/s12915-016-0338-2]

... in eukaryotes, duplicates of individual genes cannot be effectively eliminated by selection and thus often persist and diverge. The typical result is subfunctionalization, whereby the gene duplicates undergo differential mutational deterioration, losing subsets of ancestral functions. As a result, the evolving organisms become locked into maintaining the pair of paralogs. Subfunctionalization underlies a more general phenomenon, denoted constructive neutral evolution (CNE).

Question #1, Question #2, Question #3, Question #4, Question #5, Question #6


Sunday, April 09, 2017

Vimy Ridge

Today marks the 100th anniversary of the beginning of the Battle of Vimy Ridge. The battle invovled four divisions of the Canadian Corps and it has become a symbol for Canada of the sacrifices made during World War I. The symbol is remarkable for the beautiful Canadian National Vimy Ridge Memorial designed by Walter Seymour Allward. He intended it to be a "sermon against the futility of war."

It is remarkably successful as such a symbol since, among other things, it contains the names of more than 11,000 Canadians who died in World War I and whose bodies were never recovered. We visited the memorial in 2011 with my granddaughter Zoë [Canadian National Vimy Memorial] and found the name of Lance Corporal Robert Alexander Hood, a cousin of Leslie's grandfather and Zoë's great-great-grandfather.



Saturday, April 08, 2017

Somatic cell mutation rate in humans

A few years ago, Tomasetti and Vogelstein (2015) published a paper where they noted a correlation between rates of cancer and the number of cell divisions. They concluded that a lot of cancers could be attributed to bad luck. This conclusion didn't sit well with most people for two reasons. (1) There are many well-known environmental effects that increase cancer rates (e.g. smoking, radiation), and (2) there's a widespread belief that you can significantly reduce your chances of getting cancer by "healthy living" (whatever that is). The first objection is based on solid scientific evidence but the second one is not as scientific.

Some of the objections to the original Tomasetti and Vogelstein paper were based on the mathematical models they used to reach their conclusions. The authors have now followed up on their original study with more data. The paper appears in the March 24, 2017 issue of Science (Tomasetti and Vogelstein, 2017). If you're interested in the debate over "bad luck" you should read the accompanying review by Nowak and Waclaw (2017). They conclude that the math is sound and many cancer-causing mutations are, in fact, due to chance mutations in somatic cells. They point out something that should be obvious but bears repeating.