The importance of Neutral Theory and Nearly-Neutral Theory cannot be exaggerated. It has radically transformed the way experts think about evolution, especially at the molecular level. Unfor… Read More

DNA Is Not Destiny: The Remarkable Completely Misunderstood Relationship between You and Your Genesby Steven J. HeineW.W. Norton & Company, New York/London (2017)ISBN: 978-0-393-24408-3S… Read More

I highly recommend this brief editorial by Naruya Saitou: "Chance, Finiteness, and History" (Saitou, 2018). Saitou is a strong proponent of Neutral Theory and the importance of random geneti… Read More

John Mattick is the most prominent defender of the idea that the human genome is full of functional sequences. In fact, he is just about the only scientist of any prominence who's on that si… Read More

I've been talking to philosophers lately about the true state of the junk DNA controversy. I imagine what it would be like to stage a great debate on the topic. It's easy to come up with nam… Read More

I just learned about a workshop scheduled for the end of this month. The topic is: Evolutionary Roles of Transposable Elements and Non-coding DNA: The Science and the Philosophy. I'd love to… Read More

A friend has a neighbor who's in possession of a pamphlet from 1863 on the Owen vs Huxley debate. The text of the pamphlet is here: A Report of A SAD CASE, Recently tried before the Lord May… Read More

The three main human databases (GENCODE/Ensembl, RefSeq, UniProtKB) contain a total of 22,210 protein-coding genes but only 19,446 of these genes are found in all three databases. That leave… Read More

Nature is arguably the most prestigious science journal. Articles published in Nature are widely perceived to be correct, unbiased, and factual. This perception is certainly true of articles… Read More

Several readers alerted me to a paper that was posted on bioRxiv a few weeks ago (May 28, 2018). The paper claimed that the human genome contains 43,162 genes consisting of 21,306 protein-co… Read More

Press releases have become a serious problem. I'm frequently upset whenever I read a press release covering a field I'm familiar with. They rarely do a good job of explaining what's actually… Read More

There's an interesting discussion going on about lateral gene transfer (LGT) in eukaryotes. LGT is the process by which DNA from one species invades the genome of another species. It was app… Read More

The citric acid cycle1 is usually taught as depicted in the diagram on the right.2 A four-carbon compound called oxaloaceate is joined to a two-carbon compound called acetyl-CoA to produce a… Read More

It's important to define what you mean when you use the word "gene." I use the molecular definition since most of what I write refers to DNA sequences. There's no perfect definition but, for… Read More

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 paper… Read More

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 Bir… Read More

Dan Riskin: The Good, Bad, & Natural: What Mother Nature says about morality?Thursday, April 12, 20187:30 - 10:00 pmThe Franklin House263 Queen Street SStreetsville (Mississauga), Ontari… Read More

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 (Lakh… Read More

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 se… Read More

Here's my latest compilation of the composition of the human genome. It's depicted in the form of a pie chart.1There are several ways of estimating the amount of functional DNA and the amoun… Read More

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… Read More

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… Read More

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… Read More

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 knowledge… Read More

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 ge… Read More

ThemeGenomes& Junk DNAI'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 so… Read More

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 b… Read More

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… Read More

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… Read More

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… Read More

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 al… Read More

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 pre… Read More

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 Kum… Read More

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 protei… Read More

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 Var… Read More

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 [Funct… Read More

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 se… Read More

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: Introduci… Read More

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… Read More

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… Read More

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… Read More

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… Read More

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… Read More

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 co… Read More

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… Read More

ThemeMutation-definition-mutation types-mutation rates-phylogeny-controversiesMutations are mostly due to errors in DNA replication. We have a pretty good idea of the accuracy of DNA replica… Read More

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 techniq… Read More

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 m… Read More

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 pseudogen… Read More

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 evo… Read More

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… Read More

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… Read More

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: Introduci… Read More

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 j… Read More

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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 whethe… Read More

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 Evolutionar… Read More

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 diffe… Read More

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

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 Thin… Read More

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 Phil… Read More

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 thr… Read More

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 bee… Read More

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 Royalis… Read More

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. Halda… Read More

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… Read More

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. Franc… Read More

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 co… Read More

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 a… Read More

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 tra… Read More

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 p… Read More

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 d… Read More

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 produ… Read More

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… Read More

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 g… Read More

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? Read More

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

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

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

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 h… Read More

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 polymorphi… Read More

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… Read More

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 a… Read More

Today is anniversary of D-Day—the day British, Canadian, and American troops landed on the beaches of Normandy.1For baby boomers it means a day of special significance for our parents… Read More

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 Me… Read More

We had a great time last night discussing Can You Tell Real Science News from Fake News? Read More

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

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… Read More

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 stu… Read More

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 accompl… Read More

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… Read More

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 w… Read More

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 Pier… Read More

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 evo… Read More

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 evolution… Read More

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… Read More

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-c… Read More

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 Synthes… Read More

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 Austral… Read More

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 s… Read More