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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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 ...

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 His criticism is based on a naive and outdated view of modern evolutionary biology.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.

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).

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.

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.

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].

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.

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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?

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

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

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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.

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,

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.

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.

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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.

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,

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

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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

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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

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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

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