The evolution of the citric acid cycle

I just realized that I don't have a post devoted to the evolution of the citric acid cycle. This need to be remedied since I often talk about it. It's a good example of how an apparently irreducibly complex pathway can arise by evolution. It's also a good example to get students to think outside of the box. Undergraduate biochemistry courses usually concentrate on human physiology and too often students transfer that bias to all other species. They assume that what happens in humans is what happens in plants, fungi, protozoa, and bacteria.¹

Here's what the standard citric acid cycle looks like (Moran et al., 2011 p. 393).

Once again, the IDiots don't understand evolution

This is so frustrating. I've been debating creationists for almost 30 years. My colleagues and I have tried time and time again over those three decades to educate them about real evolutionary theory. We've also tried to teach them about the difference between evolution and the history of life. In order to explain the history of life on Earth you need to account for mass extinctions and other chance events that have nothing to do with evolution. They refuse to listen.

The latest evidence is a recent post by David Klinghoffer [Theory of Evolution? Call It a "Narrative" Instead]. He says,

The theory of evolution by natural selection operating on random mutations, as a sweeping explanation for life and how it got there, is a "narrative." It presents a very smooth story, persuasive to most scientists. The facts may all be true, but the conclusion: BS.

No knowledgeable scientist thinks that natural selection is the only mechanism of evolution so no knowledgeable scientist thinks that mutation + selection explains the history of life. That's just BS. Not only are scientists aware of what modern evolutionary theory actually says but they're also aware of other factors that determined the history of life.

Now you know why we call them IDiots. What is it that makes them so resistant to learning about the ideas they so adamantly oppose? They can still oppose correct ideas if they want. Isn't that better than fighting strawmen?

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Why does the human population carry an allele that increases the risk of Alzheimer's?

The human apolipoprotein E gene (ApoE) has several alleles segregating in the human population. One of them, E4, is associated with increased risk of Alzheimer's. Ed Yong, writing for The Atlantic, asks "Why Do Humans Still Have a Gene That Increases the Risk of Alzheimer's?

I can think of several answers off the top of my head. The most important one is that Alzheimer's has very little effect on your ability to have children. The disease may not even have developed in most of our ancestors who tended to die younger. In order to be subject to negative selection the allele has to affect adults before they reproduce.

The second reason is that the slight deleterious effect, if there is one from an evolution perspective, may not have been significant enough in small populations. I know, and I hope my students know, that neutral and deleterious alleles can reach significant frequency in a population by chance. The general public doesn't know this.

Check out Ed Yong's article to see his explanation.

“It doesn’t make sense,” says Ben Trumble, from Arizona State University. “You’d have thought that natural selection would have weeded out ApoE4 a long time ago. The fact that we have it at all is a little bizarre.”

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The pervasive transcription controversy: 2002

I'm working on a chapter about pervasive transcription and how it relates to the junk DNA debate. I found a short review in Nature from 2002 so I decided to see how much progress we've made in the past 15 years.

Most of our genome is transcribed at some time or another in some tissue. That's a fact we've known about since the late 1960s (King and Jukes, 1969). We didn't know it back then, but it turns out that a lot of that transcription is introns. In fact, the observation of abundant transcription led to the discovery of introns. We have about 20,000 protein-coding genes and the average gene is 37.2 kb in length. Thus, the total amount of the genome devoted to these genes is about 23%. That's the amount that's transcribed to produce primary transcripts and mRNA. There are about 5000 noncoding genes that contribute another 2% so genes occupy about 25% of our genome.

Pyruvate dehydrogenase astonishes Ann Gauger

Ann Gauger was reading a cell paper the other day [Digging Deep in Biology: "Things Get Even More Complicated When You Look Closer"]. The subject was the localization of citric acid cycle enzymes and pyruvate dehydrogenase (PDH). She did a little digging and this is what astonished her ...

... so I looked up pyruvate dehydrogenase and found to my astonishment that it is not one enzyme but an enormous complex of three different enzymatic activities clustered together on a cube-shaped core of 24 units, or alternatively a dodecahedral core of 60 units. The enzymes work together to turn pyruvate into acetyl CoA in a three-step process, handing off to each other as the reaction proceeds.

Why are most biologists adaptationists?

I enjoyed listening to Michael Lynch's talk on Friday. Much of what he said has been covered in Sandwalk over the past few years. His main point was that nothing in biology makes sense except in the light of population genetics. He laments the fact that most biologists, and even most evolutionary biologists, don't have a firm grasp of population genetics and the importance of random genetic drift.

I asked him why he thought this was true. He said he didn't know why. I think he was being polite. If you read his book, "The Origins of Genome Architecture," you'll see that he attributes this phenomeon to ignorance of modern evolutionary theory.

The dynamic duo tell us about five problems with evolution

Here's a link to a remarkable radio interview with Stephen Meyer and Doug Axe. The subject is the Royal Society meeting last November on New trends in evolutionary biology: biological, philosophical and social science perspectives. The theme is not Intelligent Design Creationism, instead it's all about so-called problems with evolutionary theory. That's really what ID is all about in spite of what the IDiots may claim. [see A Royal Pain: Stephen Meyer and Douglas Axe on Five Problems for Evolution.]

Here are the five problems according to IDiots.

1. Fossil record (Cambrian explosion)
2. The origin of information (no known natural source of information)
3. The necessity of early mutations (you can't mutate regulatory genes that act early in development because all mutations in those genes are lethal)
4. Epigenetic information (you can't evolve new body plans by mutating DNA because development is controlled by non-DNA epigenetic information)
5. The universal design intuition that we all have (everybody thinks that people are created by a god-like designer, even atheists, so it must be true)

What the heck is epigenetics?

"Epigenetics" is the (relatively) new buzzword. Old-fashioned genetics is boring so if you want to convince people (and grant agencies) that you're on the frontlines of research you have to say you're working on epigenetics. Even better, you can tell them that you are on the verge of overthrowing Darwinism and bringing back Jean-Baptiste Lamarck.

But you need to be careful if you adopt this strategy. Don't let anyone pin you down by defining "epigenetics." It's best to leave it as ambiguous as possible so you can adopt the Humpty-Dumpty strategy.¹ Sarah C.P. Williams made that mistake a few years ago and incurred the wrath of Mark Ptashne [Core Misconcept: Epigenetics].

Genetic variation in the human population

With a current population size of over 7 billion, the human population should contain a huge amount of genetic variation. Most of it resides in junk DNA so it's of little consequence. We would like to know more about the amount of variation in functional regions of the genome because it tells us something about population genetics and evolutionary theory.

A recent paper in Nature (Aug. 2016) looked at a large dataset of 60,706 individuals. They sequenced the protein-coding regions of all these people to see what kind of variation existed (Lek et al., 2016) (ExAC). The group included representatives from all parts of the world although it was heavily weighted toward Europeans. The authors used a procedure called "principal component analysis" (PCA) to cluster the individuals according to their genetic characteristics. The analysis led to the typical clustering by "population clusters." (That term is used to avoid the words "race" and/or "subspecies.")

Birth and death of genes in a hybrid frog genome

De novo genes¹ are quite rare but genome duplications are quite common. Sometimes the duplicated regions contain genes so the new genome contains two copies of a gene that was formerly present in only one copy. "Common" in this sense means on a scale of millions of years. Michael Lynch and his colleague have calculated that the rate of fixed gene duplication is about 0.01 per gene per million years (Lynch and Conery, 2003 a,b; Lynch 2007). Since a typical vertebrate has more than 20,000 genes, this means that 200 genes will be duplicated and fixed every million years.

The initial duplication event is likely to be deleterious since there will now be redundant DNA in the genome. The slightly deleterious allele (duplication) can be purged by negative selection in species with large population sizes (e.g. bacteria). But in species with smaller populations, natural selection is not powerful enough to eliminate slightly deleterious alleles so the duplication persists and may become fixed in the population.

Do seahorses evolve faster?

Genome sequencing is becoming so routine that it's difficult to publish your new genome sequence in a top journal. The trick is to find something unique and exciting about your genome so you can attract the attention of the leading journals. The latest success is the seahorse genome published in the Dec. 15, 2016 issue of Nature (Lin et al., 2016.

The species is the tiger tail seahorse Hippocampus comes. The assembled genome is 502Mb or about 1/6th the size of the human genome. The seahorse has 23,458 genes (protein-coding?) or about the same number as most other vertebrates. About 25% of the genome is junk (transposon-related).¹

Save the date!!! Michael Lynch is coming to Toronto

Michael Lynch is giving a seminar next week on Friday, January 13, 2017 in the Dept. of Ecology and Evolutionary Biology at the University of Toronto. The title is: Mutation, Drift, and the Origin of Subcellular Features. The talk is at 3PM in the Earth Sciences Centre rm B142.

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The exit exam for biochemistry and molecular biology students

I'm a big fan of teaching fundamental concepts and principles and a big fan of teaching critical thinking. I think the most effective way of accomplishing these objectives is some form of student-centered learning. As I near the end of my teaching career, I wonder how we can tell if we succeed? It should be relatively easy to develop an exit exam for our biochemistry/molecular biology students to see if they grasp the basic concepts and can demonstrate an ability to think critically.

Here are some of the questions we could have on that exam. Each one requires a short answer with an explanation. The explanation doesn't have to be detailed or full of facts, just the basic idea. Students are graded on their ability to think critically about the answers. Many of the questions don't have a simple answer. Can you think of any other questions?

You MUST read this paper if you are interested in evolution

A reader alerted me to a paper that was just published in BMC Biology.¹ The author is Eugene Koonin. He makes the case for neutral evolution (random genetic drift) and against adaptationism. You may not agree with his take on evolutionary theory but you better be aware of it if you claim to be knowledgeable about evolution.

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]

The study of any biological features, including genomic sequences, typically revolves around the question: what is this for? However, population genetic theory, combined with the data of comparative genomics, clearly indicates that such a “pan-adaptationist” approach is a fallacy. The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified. The adaptationist fallacy can be costly, inducing biologists to relentlessly seek function where there is none.

The Edge question 2017

Every year John Brockman asks his stable of friends an interesting question. Brockman is a literary agent and most of the people who respond are clients of his. (I want to be one.) The question and responses are posted on his website Edge. This year's question is, "What scientific term or concept ought to be more widely known?"

This year, the introduction is more interesting than the responses. Here's part of what Brokman wrote,