Mutation-Driven Evolution

Back in the late 1980's, I read Molecular Evolutionary Genetics by Masatoshi Nei. He introduced me to the concept that the history of life is driven by mutation and that the old-fashioned view of mutationism needs to be looked at more carefully. A decade later, Arlin Stoltzfus took up the cause and he has published a number of papers on the topic.

If you want to read more about mutationism then you can't find a better source than the series of posts by Arlin on Sandwalk from 2010. The last one, The Mutationism Myth VI: Back to the Future, contains links to all of the others. Be warned, it will be hard to resist the idea of mutationism after you read Arlin's explanation. It will hurt your brain.

I just learned that Masatoshi Nei is about to publish a new book called Mutation-Driven Evolution. Here's the description on Amazon ...
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Mutation

The purpose of this book is to present a new mechanistic theory of mutation-driven evolution based on recent advances in genomics and evolutionary developmental biology. The theory asserts, perhaps somewhat controversially, that the driving force behind evolution is mutation, with natural selection being of only secondary importance. The word 'mutation' is used to describe any kind of change in DNA such as nucleotide substitution, gene duplication/deletion, chromosomal change, and genome duplication. A brief history of the principal evolutionary theories (Darwinism, mutationism, neo-Darwinism, and neo-mutationism) that preceded the theory of mutation-driven evolution is also presented in the context of the last 150 years of research. However, the core of the book is concerned with recent studies of genomics and the molecular basis of phenotypic evolution, and their relevance to mutation-driven evolution. In contrast to neo-Darwinism, mutation-driven evolution is capable of explaining real examples of evolution such as the evolution of olfactory receptors, sex-determination in animals, and the general scheme of hybrid sterility. In this sense the theory proposed is more realistic than its predecessors, and gives a more logical explanation of various evolutionary events.

Mutation-Driven Evolution is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of molecular evolution and population genetics. It assumes that the readers are acquainted with basic knowledge of genetics and molecular biology.

I can't wait to get my hands on a copy of this book. Look for a review in a few months.

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Freedom to Follow the Evidence without Philosophical Restrictions.

Let's look at a recent post on Evolutin News * Views (sic): From Discovering Intelligent Design: Opposition from the Scientific Establishment. As the title suggests, this is an excerpt from one of the books being heavily promoted by the IDiots.

They have a problem. How do the IDiots explain why 99.9% of biologists oppose Intelligent Design Creationism? It's because they all have a materialistic bias that prevents them from following the evidence wherever it may lead. Read this bit ...

ID challenges a reigning scientific paradigm. But as sociologist Steve Fuller says, ID is not anti-science, but rather anti-establishment. ID theorists want more scientific investigation, not less. They simply want the freedom to follow the evidence without harassment or philosophical restrictions.

An ID-based view of science promises to open new avenues of scientific investigation. Without materialist paradigms governing science, perhaps more scientists would have sought function for structures like "junk" DNA and vestigial organs, rather than assuming they were non-functional evolutionary relics.

Let me remind you that the presence of junk DNA in our genome was not anticipated by those who believed in the importance of natural selection. What happened was that the evidence became too substantive to ignore so scientists had to accept the presence of junk DNA in spite of the fact that most of them expected selection to eliminate it.

Now if you insist on believing in an intelligent design paradigm then you simply can't follow the evidence wherever it may lead because junk DNA isn't part of your worldview. In other words, the example used by the IDiots in this post is the exact opposite of the point they are making.

Oops!

Now you know why we call them IDiots.

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Teaching Biochemistry from a Canadian Perspective

I've always been a bit embarrassed to admit that my own department doesn't adopt my textbook in their introductory biochemistry courses. The honors course uses the 4th edition of Voet & Voet but it's only "recommended," not required. The large introductory course for non-specialists recommends several textbooks, including mine.

The arguments against having a required textbook have often focused on the idea that none of the current textbooks covers the material that's being taught—especially in the large course. Our large (1300 students) course tended to emphasize human physiology from a biochemical perspective. Many of the lectures in the metabolism section involved specific case studies.

"The Best Science Book Ever Written"

Some economist named George Gilder has read Darwin's Doubt, the latest IDiot book. Gilder says ...

I spend my life reading science books. I've read many hundreds of them over the years, and in my judgment Darwin's Doubt is the best science book ever written. It is a magnificent work, a true masterpiece that will be read for hundreds of years.

See David Klinghoffer gloat about this at: George Gilder: Darwin's Doubt Is "Best Science Book Ever Written," "Will Be Read for Hundreds of Years".

Are you still wondering why I call them IDiots?

UPDATE: George Gilder is one of the co-founders of the Discovery Institute and the author of the book (Stephen Meyer) works for the Discovery Institute. Just saying .. I'm sure the relationship has no bearing on Gilder's review and I'm sure it's completely above board for someone like George Gilder to be quoted in a blurb on the cover. If there was anything wrong then surely David Klinghoffer would have mentioned it in his blog post. (This is one of those cases where "IDiots" might be too kind.)

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My Visit to High School Biology Classes

Last Monday I went back to my old high school (Nepean High School in Ottawa, Canada) to visit with students in various biology classes. My host was Susanne Gerards who teaches grade 11 biology and grade 12 biology. She's also the lead author on the biology textbook [Biology 12] that the students use in the grade 12 courses.

I was "guest lecturer" in two grade 12 biology classes and one grade 11 biology class. The grade 12 students had just finished the sections on biochemistry and molecular genetics (information flow) so they were up on most things that I blog about. I was surprised at the amount of information they had just leaned—it's comparable to what we teach in our introductory biochemistry course except that there's less emphasis on structures and nothing on enzyme kinetics.

The students were wonderful. Many of them are going to take science courses in university. (They all had their university acceptances.) Only a few of them are interested in medicine.¹

The grade 11 students had finished their section on evolution. Most of them thought that evolution was driven by changes in the environment but they had at least been exposed to random genetic drift. It took a little prompting to that get that out of them. (I think Susanne was a bit embarrassed!). My impression was that the students understood quite a bit about evolution and this was a pleasant surprise.

One of the classes had just finished a discussion about junk DNA when a student raised it in class. He claimed that recent evidence proved that most of our genome has a function. I think the students were still a bit confused about genomes but at least they talked about it. (We didn't talk about it much when I was there.)

I'm pretty sure that the most important thing the students learned was that you actually get paid to be a graduate student! They were also surprised about the relatively high salaries that professors earn when they're hired. I'm hoping that some of them will pursue a career in science.

Susanne Gerards and I had an excellent lunch in Westboro where the restaurants and shops are quite a bit more upscale than they were in the 1960s when I lived there. We also had a lot of fun talking about science after class. With teachers like that I'm confident that Ontario high school students are getting a good science education.

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1. Hardly any of them were going to the University of Toronto in spite of the fact that it's the best university in Canada. I'm not sure why they were avoiding it. The most popular universities were Queen's, McGill, and Waterloo.

What Does the Bladderwort Genome Tell Us about Junk DNA?

The so-called "C-Value Paradox" was described over thirty years ago. Here's how Benjamin Lewin explained it in Genes II (1983).

The C value paradox takes its name from our inability to account for the content of the genome in terms of known function. One puzzling feature is the existence of huge variations in C values between species whose apparent complexity does not vary correspondingly. An extraordinary range of C values is found in amphibians where the smallest genomes are just below 10⁹bp while the largest are almost 10¹¹. It is hard to believe that this could reflect a 100-fold variation in the number of genes needed to specify different amphibians.

Since then we have dozens and dozens of examples of very similar looking species with vastly different genome sizes. These observations require an explanation and the best explanation by far is that most of the genomes of multicellular species is junk. In fact, it's the data on genome sizes that provide the best evidence for junk DNA.

How Do IDiots Define Evolution?

It's not difficult to find a proper definition of evolution. All you have to do is check your basic introductory textbooks on evolution. Google is not your friend in this case 'cause there's a lot of misinformation out there. If you're really interested in a scientific definition of evolution why not go right to the primary source?

Most textbooks use some version of the following for the minimal DEFINITION of evolution [see What IS Evolution?].

Evolution is a process that results in heritable changes in a population spread over many generations.

Now, we all know that Intelligent Design Creationists are keen on real science. They certainly don't want to mislead their flock. Let's see how they define evolution in the latest book they are promoting [From Discovering Intelligent Design: Define Your Terms].

A Concept-Driven Graduate Education

Like most graduate departments, we are constantly evaluating and modifying our graduate program but rarely do we step back and look at the big picture. What are we trying to accomplish?

Graduate education, like undergraduate education, has been subjected to serious study over the past few decades. Guttlerner and Van Vactor (2013) have just published a brief review in Cell that summarizes the goals and how they are trying to achieve them at Havard.

The authors begin by pointing out the importance of a concept-driven curriculum.

The modernization of science education requires a shift from a content-driven curriculum to an interdisciplinary, concept-driven curriculum (Association of American Medical Colleges and Howard Hughes Medical Institute, 2009; American Association for the Advancement of Science, 2009; National Research Council, 2003, 2009). Such a curriculum organizes information around unifying concepts and frees educators from the insurmountable task of presenting the complete breadth of an ever-expanding scientific knowledge base (D’Avanzo, 2008). Concept-driven education is increasingly seen as fundamental for contemporary research scientists and physicians (Association of American Medical Colleges and Howard Hughes Medical Institute, 2009).

Inside Higher Ed Weighs in on the Ball State Academic Freedom Controversy

This is getting more and more interesting. Now there's an article in Inside Higher Ed discussing the controversy over whether Eric Hedin of Ball State University should be teaching a science course that emphasizes Intelligent Design Creationism. [see Science or Religion?]

The article discusses the difference of opinion between Jerry Coyne, on the one hand, and PZ Myers and me, on the other. It's very interesting to read the comments. Jerry Coyne has posted on the Inside Higher Ed article at: Ball State agrees to investigate science course infected with Christianity. His readers have lots to say on the issue of academic freedom.

Let's be clear about one thing. I'm not an American so I'm not terribly concerned about the American Constitution. If Eric Hedin were teaching in Canada, the legal issue would never come up. The part of this that I don't like is outsiders threatening departmental chairs to get them to take action against one of their faculty members. Four Creationists have tried to get the administration of my university to shut down Sandwalk and in all cases my university simply filed the letters in the waste basket.¹ I ban people from Sandwalk if I ever hear of them trying to intimidate someone by complaining to their employer. That's unacceptable behavior in my book.

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1. After sending me a copy.

Earthquake!

Epicentre near Ottawa. Two quakes: 5.2 magnitude at 9:43 am and a 4.1 magnitude aftershock 10 minutes later. I didn't feel either of them. Earthquakes like this happen about 30,000 time a year. We feel one of them every few years in this part of Canada. They are mostly harmless, but exciting.

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[Photo credit: CBC News]

On Teaching Genetics Using Students' and Parents' ABO Blood Types

There are some schools that think it's cool to show examples of simple Mendelian inheritance by collecting and analyzing the blood types of their students and their parents. What could possibly go wrong?

Let me tell you why this is a bad idea. It's true that 99% of the time the blood type of a student is going to be consistent with that of their presumed biological parents. But what if it's not? That could mean that a child is adopted and the child may not know or not want that information to be public. It could also mean that the child's biological father (or mother) is not the same person they call "Mommy" or "Daddy." Is the trauma associated with that discovery worth the benefits of the experiment?

I have a blog post on The Genetics of ABO Blood Types. It's quite popular and every few weeks I get a letter from a distraught parent who has just discovered that the blood type of their children doesn't match the blood type of the parents. Here's the latest example (posted with permission) ...

Dear Professor Moran: I hope you don't mind my writing to you, but I just came across your blog, Sandwalk after doing some research about blood types and wondered if you might have an opinion....

My daughter, in 7th grade is working on a blood type project at school and came home quite upset yesterday after telling the teacher that she was type A+ and both her Dad and I are O+. The teacher (whom I have not yet dragged over hot, burning coals....) told her that that was impossible - that she would either have to have been adopted or have a genetic defect.... It got me thinking that perhaps I had made a mistake somewhere along the way and we spent some time last night digging through info to try to figure it out. I checked with our doctors this morning and our daughter's pediatrician and all blood types have been confirmed. Both my husband and I are O+ and our daughter is A+ She is definitely not adopted and unless she was switched at birth, then there is no doubt as to parentage -- should I be concerned? I do recall that when she was born she had mild jaundice which one doc explained was due to blood type incompatibility.

If high school teachers aren't knowledgeable enough to handle these situations then they should avoid these "experiments."

These "anomalies" are quite frequent and they have simple explanations once you know the real genotype. For example, one parent could be heterozygous for two different O alleles. One with a mutation near the beginning of the gene and the other with a mutation near the end of the gene. Any germ cell recombination event between the two alleles could generate an A allele or a B allele depending on the origin of the O allele.

I think it's also possible for one of the parents to actually be AO or BO but the functional allele is expressed at a very low level giving an O-type phenotype. The A or B allele could, by chance, be much more active in the child. There could be epistatic effects such that splicing or transcription is defective in the parent but compensated for by enhanced activity in the child due to unlinked mutations. (These are known as "suppressors" in bacterial genetics.)

There are many other possibilities. They're rare but it's certain that they will show up in some school class somewhere. It's usually not a good idea to investigate the personal genomics of students because of these problems.

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Jerry Coyne Is at it Again!

Jerry Coyne has discovered that some obscure Professor in some American college is teaching from a Christian viewpoint in his class on "The Boundaries of Science." Jerry thinks that he can stop this Professor from teaching things that he (Coyne) disagrees with by threatening the university with a lawsuit. PZ Myers and I disagreed, pointing out that academic freedom in the universities is an important principle that should not be ignored [see Is It Illegal to Teach Intelligent Design Creationism in American Universities?].

Jerry stands by his position: The Freedom from Religion Foundation to Ball State University: cease and desist your religious indoctrination. Nobody is arguing that Professors shouldn't be criticized for bad teaching and nobody is arguing that the instructor's colleagues and department can't reassign courses to keep a bad teacher away from students. That's not the situation here. The Chair of the department is aware of the situation and doesn't object.

It's dangerous for outsiders to start dictating what a Professor can and can't teach and it's especially dangerous to use legal threats to enforce your own perspective on another university. I strongly disagree with the letter that the Freedom from Religion Foundation sent to the President of Ball State University [see Coyne's blog website]. If this were my university I would expect it to fight such a demand with all the resources at their disposal and I'm certain that my union and the Canadian Association of University Teachers (CAUT) would support my university. So would I.

CAUT actively defends academic freedom as the the right to teach, learn, study and publish free of orthodoxy or threat of reprisal and discrimination. Academic freedom includes the right to criticize the university and the right to participate in its governance. Tenure provides a foundation for academic freedom by ensuring that academic staff cannot be dismissed without just cause and rigorous due process.

I have defended the academic freedom of racists and holocaust deniers in the past. I've even defended the right of an extreme free-market capitalist to indoctrinate business students. In the name of academic freedom, I will even tolerate adaptationists who teach evolution incorrectly.

The purpose of academic freedom is to protect the rights of those who disagree with the majority. Those rights must be protected for everyone, including those who you think are wrong. Otherwise it's not academic freedom.

I teach a course where I promote an atheist view of evolution and the idea that science and religion are incompatible. If the Freedom from Religion Foundation ever wrote a letter to my President demanding that I cease and desist they would be be ignored except, perhaps, for a few laughs over coffee.

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Michael Denton on Junk DNA

I was reading the latest spiel from Sal Cordova (scordova) when I noticed a reference to Michael Denton. Cordova was ranting about how Taxonomic nested hierarchies don’t support Darwinism and he began with ...

Taxonomic nested hierarchies don’t support Darwinism or common descent, actually the opposite. Michael Denton convincingly argued that nested hierarchies can be used to argue against macro evolution. If the fish are always fish, then they will never be birds, reptiles, apes, or humans.

I knew that this was a misrepresentation of Denton's views since he (Denton) supports the idea that nested hierarchies represent the true history of common descent.

Michael Denton thinks that evolution was directed and that explains why fish and mammals are so different even though they contain a common ancestor. He accepts common descent but rejects spontaneous mutation and mechanistic fixation of alleles as the explanation. I checked his latest book Nature's Destiny (1998) to confirm that I was right.

Denton supports a teleological view where God created conditions (first cause) that would lead to humans (final cause) but that the process included evolution from common ancestors. In Denton's case the "design" was inherent in the laws of physics and chemistry and the rules of mutation and gene expression.

While refreshing my memory, I came across this paragraph that I had highlighted in his book fifteen years ago.

If it is true that a vast amount of the DNA in higher organisms is in fact junk, then this would indeed pose a very serious challenge to the idea of directed evolution or any teleological model of evolution. Junk DNA and directed evolution are in the end incompatible concepts. Only if the junk DNA contained information specifying for future evolutionary events, when it would not in a strict sense be junk in any case, could the finding be reconciled with a teleological model of evolution. Indeed, if it were true that the genomes of higher organisms contained vast quantities of junk, then the whole argument of this book would collapse. Teleology would be entirely discredited. On any teleological model of evolution, most, perhaps all, the DNA in a genome of higher organisms should have some function. (pp. 289-290

I wonder what Intelligent Design Creationists think of this argument?

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The Positive Values of a Roman Catholic Education?

The Ontario government funds Roman Catholic Schools but not schools of any other religion. I've just returned from a high school reunion at one of the "public" schools (nonreligious) so I've been thinking about the education I received in an environment that was free of religious indoctrination.

My friends all seem to be pretty moral and they seem to be at least as good at practicing the Golden Rule as any other citizens. When we were students we organized contributions to charity and helped the needy. We made lifelong friends in the public schools.

Most of my high school friends are pretty secular in their outlook and a large percentage are nonbelievers. The percentages aren't much different among my friends who went to Roman Catholic schools.

Here's a bit of propaganda from one who supports government funding of Roman Catholic schools. They need all the support they can get because Roman Catholic values are coming under heavy criticism lately. Roman Catholic students have been bussed to anti-abortion protests and school clubs for gays and lesbians have been banned in the Roman Catholic schools system. "Sex education" is a joke.

What do you think? Does this make you want to continue sending your tax dollars to the Roman Catholic schools?

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Scientific Authority and the Role of Small RNAs

A few weeks ago I criticized Philip Ball for an article he published in Nature: DNA: Nature Celebrates Ignorance. Phil has responded to my comments and he has given me permission to quote from his response. I think this is going to stimulate discussion on some very interesting topics.

The role of small RNAs is one of those topics. There are four types of RNA inside cells: tRNA, ribosomal RNA (rRNA), messenger RNA (mRNA), and a broad category that I call “small RNAs.”

The small RNAs include those required for splicing and those involved in catalyzing specific reactions. Many of them play a role in regulating genes expression. These roles have been known for at least three decades so there haven’t been any conceptual advances in the big picture for at least that long.

What’s new is an emphasis on the abundance and importance of small regulatory RNAs. Some workers believe that the human genomes contains thousands of genes for small RNAs that play an important role in regulating gene expression. That’s a main theme for those interpreting the ENCODE results. Several prominent scientists have written extensively about the importance of this “new information” on the abundance of small RNAs and how it assigns function to most of our genome.