Molecular Evolution Exam - April 2015

Here's the final exam in my course. Students have to answer the first two questions and three of the next five questions. How would you do?

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1. Choose a subtopic from your essay and explain it better than you did in your essay and/or rebut the comments and criticisms made by the marker/grader.


2. Michael Lynch says in The Origins of Genome Architecture ....
   

   Nothing in Evolution Makes Sense Except in the Light of Population Genetics
   Evolution is a population genetic process governed by four fundamental forces, which jointly dictate the relative abilities of genotype variants to expand through a species. Darwin articulated a clear but informal description of one of those forces, selection (including natural and sexual selection), whose central role in the evolution of complex phenotypic traits is universally accepted, and for which an elaborate formal theory in terms of changing genotype frequencies now exists. The remaining three evolutionary forces, however, are non-adaptive in the sense that they are not the function of the fitness properties of individuals: mutation (broadly including insertions, deletions, and duplications) is the fundamental source of variation on which natural selection acts; recombination (including crossing-over and gene conversion) assorts variation within and among chromosomes; and random genetic drift insures that gene frequencies deviate a bit from generation to generation independently of other forces. Given the century of theoretical and empirical work devoted to the study of evolution, the only logical conclusion is that these four broad classes of mechanisms are, in fact, the only fundamental forces of evolution. Their relative intensity, directionality, and variation over time define the way in which evolution proceeds in a particular context.

   Do you agree with Lynch that “Nothing in Evolution Makes Sense Except in the Light of Population Genetics”? If so, why isn’t population genetics taught in introductory biology courses? If not, why not?


3. Imagine that identical female twins were born to a woman in 1000 AD. Imagine that you could find a direct descendant of each twin in 2015. If you sequence the complete genomes of the descendants, approximately how many differences would you expect to find? How do these compare to the differences between any two randomly selected individuals from the same part of the world? Explain your reasoning and describe any assumptions you make. Think carefully before you answer. The second question is the most important one. (Human mutation rate = 130 mutations per generation. Haploid genome size = 3.2 × 10⁹ bp.)


4. Why do some scientists think that there is no unique tree of life?


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?


6. What is “evolvability ”and why could it be important in evolution? Why are some scientists skeptical of this claim?


7. Richard Dawkins once wrote,
   

   Even the most ardent neutralist is quite happy to agree that natural selection is responsible for all adaptation. All he is saying is that most evolutionary change is not adaptation. He may well be right, although one school of geneticists would not agree. From the sidelines, my own hope is that the neutralists will win, because this will make it so much easier to work out evolutionary relationships and rates of evolution. Everybody on both sides agrees that neutral evolution cannot lead to adaptive improvement, for the simple reason that neutral evolution is, by definition, random, and adaptive improvement is, by definition, non-random. Once again, we have failed to find any alternative to Darwinian selection, as an explanation for the feature of life that distinguishes it from non-life, namely adaptive complexity.
   
   Richard Dawkins (1986) The Blind Watchmaker. p. 304

   Can you describe situations in Richard Lenski’s ongoing evolution experiment where neutral or deleterious alleles were essential for adaptive change?

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Nature reviews Nessa Carey's book on junk DNA

Read it at" Genetics: We are the 98%. Here's the important bit ...

Finally, Junk DNA, like the genome, is crammed with repetitious elements and superfluous text. Bite-sized chapters parade gee-whizz moments of genomics. Carey's The Epigenetics Revolution (Columbia University Press, 2012) offered lucid science writing and vivid imagery. Here the metaphors have been deregulated: they metastasize through an otherwise knowledgeable survey of non-coding DNA. At one point, the reader must run a gauntlet of baseball bats, iron discs, Velcro and “pretty fabric flowers” to understand “what happens when women make eggs”. The genome seems to provoke overheated prose, unbridled speculation and Panglossian optimism. Junk DNA produces a lot of DNA junk.

The idea that the many functions of non-coding DNA make the concept of junk DNA obsolete oversells a body of research that is exciting enough. ENCODE's claim of 80% functionality strikes many in the genome community as better marketing than science.

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Nessa Carey doesn't understand junk DNA

Nessa Carey is a science writer with a Ph.D. in virology and she is a former Senior Lecturer in Molecular Biology at Imperial College, London.

She has written a book on junk DNA but it's not available yet (in Canada). Judging by her background, she should be able to sort through the controversy and make a valuable contribution to informing the public but, as we've already noted Nessa Carey and New Scientist don't understand the junk DNA debate.

Casey Luskin has a copy of the book so he wrote a blog post on Evolution News & Views. He's thrilled to find someone else who dismisses junk DNA and "confirms" the predictions of Intelligent Design Creationism. I hope Nessa Carey is happy that the IDiots are pleased with her book [New Book on "Junk DNA" Surveys the Functions of Non-Coding DNA].

Human mutation rates - what's the right number?

There's some controversy over the rate of mutations in humans. The latest summary comes from science journalist Ewen Callaway, a Senior Reporter for Nature, writing on March 10, 2015: DNA mutation clock proves tough to set.

Theme

Mutation

-definition
-mutation types
-mutation rates
-phylogeny
-controversies
Let's review what we know. The first thing we have to do is define "mutation" [What Is a Mutation?]. A mutation is any alteration of the nucleotide sequence of a genome. It includes substitutions, insertions, and deletions.

The mutation rate can be described and defined in many ways. For most purposes, we can assume that it's equivalent to the error rate of DNA replication since that accounts for the vast majority of substitutions. Substitutions are far more numerous than most insertions and deletions. (But see, Arlin Stoltzfus on The range of rates for different genetic types of mutations).

Does natural selection constrain neutral diversity?

Razib Khan is an adaptationist and he's discovered a paper that gets him very excited: Selectionism Strikes Back!.

Here's the paper and the abstract.

Corbett-Detig, R.B., Hartl, D.L., Sackton, T.B. (2015) Natural Selection Constrains Neutral Diversity across A Wide Range of Species. PLoS Biology Published: April 10, 2015 doi: 10.1371/journal.pbio.1002112

The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.

It is impossible for someone like me to evaluate this paper. Can someone take a look to see if it's valid?

How many selective sweeps must there every 50,000 years in order to remove substantial amounts of neutral diversity from junk DNA?

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Story-telling and the origin of eukaryotes

Austin Booth and Ford Doolittle have just published a paper that discusses the origin of eukaryotes (Austin and Doolittle, 2015). They point out that many of the stories about this event are not grounded in fact. Read the paper.

Writing for public audiences, and often even for themselves, biologists are not loath to make simplifying claims about uniqueness and importance that are rhetoric disguised as fact. Such generalizations serve purposes in the doing of science, but are often not themselves testable scientific claims and are subject to biases. Evolutionary biology may be especially vulnerable to hype, as suggested by the frequency with which revolutionary evolutionary claims in top-notch journals are debunked. Additionally, anthropocentrism, as it grades into "zoocentrism" and then "eukaryocentrism," surely remains a subtle distorter of objectivity.

Our aim here is to critique general claims about the uniqueness and special importance of eukaryogenesis, with an aim to making them more open to question and conceptual and empirical analysis. We ask (i) whether eukaryogenesis entailed such a "genuinely unlikely sequence of events" as to justify belief in its uniqueness as a process, (ii) if, as is often claimed, eukaryogenesis has a problematic or unique theoretical status in evolutionary biology, (iii) what intrinsic features might have conferred on eukaryotes their presumed "richer evolutionary potential," and (iv) if this greater potential might be just a presumption, an illusion reflecting eukaryocentric bias.

There are many useful ways of understanding evolution, and their articulations can be intellectually valuable and experimentally fruitful. We advocate a more self-conscious pluralism that would require not that we stop telling eukaryogenesis stories but that we do recognize them for what they are. We do not claim to know whether there is any best story, any theory by which the apparent differential success of eukaryotes can be objectively probed and causally rationalized. What we have questioned here is whether premises of existing theories have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was "special," any such notion has more than rhetorical value.

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Booth, A. and Doolittle, W.F. (2015) Eukaryogenesis, how special really? Proc. Natl. Acad. Sci. (USA) Published online before print April 16, 2015 [doi: 10.1073/pnas.1421376112]

James Lunney doesn't get no respect - does he deserve it?

James Lunney has quit the Conservative Party of Canada and decided not to run in the next federal election. He's upset because he doesn't believe in evolution and lots of people, including me, are pointing out the stupidity of his views. Because those views are based on religion, he interprets this to be an attack on his faith.

Here's what he says on his website [Evolution Controversy].

Maybe it’s because I am tired of seeing my faith community mocked and belittled. To not respond is to validate my accusers and worse yet, imply that I lack the courage of my convictions to stand–up for what I believe. This is not a legacy I wish to leave behind. Many of you colleagues represent constituencies beyond the ones who elected you; I hope that no member of any faith community in Canada is compelled to defend the beliefs of their community in the future.

Freedom of Religion and conscience are fundamental freedoms in Canada. Bigotry cloaked in defense of "science" is as intolerable and repugnant as bigotry from any other source.

It is contrary to our multi-racial, multicultural and multi-faith character and the tolerance for diversity that defines us as Canadians.

I know members on all sides of the house are concerned about bullying in general and cyber-bullying in particular. The government has brought in new legislative measures to address some aspects of this brutal phenomenon and there are many social actions like the pink shirt initiative that seek to shield the vulnerable.

We are living in an era where knowledge is increasing at an astounding pace; there are so many technical advances it is hard to keep up and what we refer to in general as "science" has been parsed into more and more diverse pursuits of knowledge.

I urge you to read the entire article that he posted on April 1st 2015. See if you think he deserves the respect he craves. He sounds like a kook to me.

How many times have we heard this stuff before? And how many times have we seen this style of writing?

So is "Evolution Theory or Fact?

The late Stephen Jay Gould stated: "a fact is something that is proven to the extent that to not believe it is perverse"!

That translates to: a fact is something that my friends and I believe, AKA eminence-based science. There’s a lot of that in health-care, where it’s known as eminence-based medicine as opposed to evidence- based medicine. There are people in the medical world expressing concern about the immense influence of KOLs (Key Opinion Leaders) with influencing public policy and decision making in directing scientific inquiry

Darwin’s brilliant and convincing construct that defined a century and a half of scientific belief, is in crisis because of astounding advances in molecular biology and it’s all about THE CELL.

You have 80-100 trillion cells, 200 cell types, all reading the same genetic library, but as different as they are, working together in specialized communities to perform astonishing synchronized manufacturing, recycling, transport, packaging and delivery functions. Twenty-five thousand miles of blood vessels if you strung them end to end; that is a trip around the world at the surface.

Every cell is worlds within worlds of nanotechnology finely tuned and regulated.

Darwin’s elaborate construct is stalled at the cell; even the simplest prokaryotic cell is infinitely beyond the odds of ever coming together by random, undirected process.

Jame Lunney is attacking evolutionary biologists and their acceptance of the scientific evidence for evolution, which happens to be their area of expertise. It seems ironic that he accuses others of bigotry and bullying.

James Lunney is a chiropractor and he has a B.Sc. (science). He says, "I have a background in Science: my credentials modest as they are, are superior on this file to many in this chamber and most of my critics."

That explains a lot.

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Physiologists fall for the Third Way

I looked forward to this "conversation" because I was already familiar with Denis Noble and his strange views of evolution [A physiologist thinks about evolution]. Noble reiterated his view of modern evolutionary theory at the meeting. He thinks that modern evolutionary theory (The Modern Synthesis or Neo-Darwinism) is all about random mutation and natural selection. He thinks it is based on the views of Richard Dawkins in The Selfish Gene. Neither he nor Michael Joyner (an anaethesiologist at the Mayo Clinic) have learned about random genetic drift or Neutral Theory and neither of them have much knowledge of population genetics. In other words, they are pretty ignorant about evolution even though they feel entitled to attack it.

Plant biologists are confused about the meanings of junk DNA and genes

A recent issue of Nature contains a report on plant micro-RNAs (Lauressergues et al., 2015). The authors found that certain genes for plant micro-RNAs encoded short peptides in the micro-RNA precursors and those peptides seemed to have a biological function. What this means is that part of the longer precursor RNA that is cleaved to produce the final micro-RNA may have a function that wasn't recognized. If you thought that the part of the precursor that was thought to be discarded as useless junk was, in fact, junk, then you were wrong—at least for some genes.

This is not a big deal and the authors of the paper don't even mention junk DNA.

The paper was reviewed by Peter M. Waterhouse and Roger P. Hellens in the same issue (Waterhouse and Hellens, 2015). They think it's a big deal. Here's what they say,

Student essays about evolution

Students in my molecular evolution course have to write an essay. They can pick any topic they like as long as it's related to evolution and some controversy in the scientific literature. I have to approve the topic. The idea is that the students have to critically evaluate both sides of an issue and pick a side that they can defend.

The essays tell me a lot about what things are interesting in the course and how well the students understand the topics. Here are this year's topics.

• Education: Misconceptions in Evolutionary Biology
• Are Transposable Elements Junk?
• RNA World Hypothesis
• Evolutionary Psychology and Biology: A Comparison
• The End for the Alternative Search for Complexity
• C-Value Paradox: Why Junk DNA Looks So Good
• Will Humans Ever Be Perfectly Evolved?
• Epigenetic Inheritance: A Turning Point in Evolution?
• Back to Basics (about evolutinary biology eduaction)
• The Relationship between Natural Selection and Artificial Selection
• Foreign Gene Incorporation in Agriculture and in the wild: Debunking Anti-GMO Rhetoric and the "Unnatural" Fallacy
• Enhancers: An Evo-Devo Perspective
• Will humans stop evolving?
• Genomic Screening: Currently Not Worth the Trouble
• The Decade Long Argument Over Junk
• What Is a Gene?
• Sex: Is It Really Advantageous?
• A Critical Analysis of Stephen Meyer's Darwin's Doubt; The Explosive origin of Animal Life and the Case for Intelligent Design
• The Role of Natural Selection in the Process of Biological Human Evolution
• The Struggle Between Humans and Bacterial Evolution
• Drifting Away: Perspectives on Modern Evolution
• The Continuing Struggle Against Junk DNA
• The Evolution of Influenza A: Antigenic Drift at Work?

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Junk DNA comments in the New York Times Magazine

It's always fun to be quoted in The New York Times Magazine but there's a more serious issue to discuss. I'm referring to a brief article about online comments after Carl Zimmer published a piece on "Is Most of Our DNA Garbage?" a few weeks ago. If you read the comments under that article you'll discover that we have a lot of work to do if we are going to convince the general public that our genome is full of junk.

Richard Lenski answers questions about the long-term evolution experiment (LTEE)

Richard Lenski has a blog called Telliamed Revisited. He's been answering questions about his long-term evolution experiment and the latest answers are at: Questions from Jeremy Fox about the LTEE, part 2.

"Did the LTEE have any hypotheses initially, and if so, how were you going to test them?

Short answer: Yes, the LTEE had many hypotheses, some pretty clear and explicit, some less so. (What, did you think I was swimming completely naked?)"

Well worth reading ....

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Apparently it really is impossible to teach Intelligent Design Creationists about evolutionary theory

Last week I asked an important question, "Is it impossible to educate Intelligent Design Creationists on evolutionary theory?.

The reason I asked is because in spite of our best efforts over several decades, the Intelligent Design Creationists still don't understand modern evolutionary theory. We see this all the time whenever they start criticizing evolution. It gets them into all sorts of trouble, especially when we debate junk DNA.

Many of their objections to evolution would be easily answered if they only understood that there's more to evolution than natural selection and the appearance of design. They would understand why Michael Behe is wrong about the edge of evolution, for example, and why their pseudoscientific probability calculations are nonsense. They can't possibly understand molecular evolution and phylogenetic trees based on sequences unless they understand that it has almost nothing to do with "Darwinism" and the appearance of design.

IDiots say that evolution violates the Second Law of Thermodynamics

Over on the main "science" blog of the Intelligent Design Creationists, that famous scientist, kairosfocus, says on Piotr (and KS, DNA_Jock, VS, Z et al) and “compensation” arguments vs the energy audit police ..., quoting that other famous scientist Granville Sewell,

The discovery that life on Earth developed through evolutionary "steps," coupled with the observation that mutations and natural selection -- like other natural forces -- can cause (minor) change, is widely accepted in the scientific world as proof that natural selection -- alone among all natural forces -- can create order out of disorder, and even design human brains, with human consciousness. Only the layman seems to see the problem with this logic. In a recent Mathematical Intelligencer article ["A Mathematician's View of Evolution," The Mathematical Intelligencer 22, number 4, 5-7, 2000] I asserted that the idea that the four fundamental forces of physics alone could rearrange the fundamental particles of Nature into spaceships, nuclear power plants, and computers, connected to laser printers, CRTs, keyboards and the Internet, appears to violate the second law of thermodynamics in a spectacular way.

There's obviously a problem. The IDiots have to believe and trust one set of scientists and not another.

Since the evidence for evolution is overwhelming, the Second Law of Thermodynamics must be wrong.

Stupid chemists.

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Photo credit: Aubrey Hirsch

Is it impossible to educate Intelligent Design Creationists on evolutionary theory?

We all know how much creationists like to label their opponents as "Darwinists." What you don't know is that many of us have spent decades trying to teach creationists about modern evolutionary theory and why is is much more than just mutation plus natural selection. Some Intelligent Design Creationists seem to get it but then they quickly revert to the old rhetoric.

So, the question is whether the Intelligent Design Creationists really understand modern evolutionary theory or not. If they do, then they must be lying when they claim that it's just natural selection and "Darwinism." It can't be excused as ignorance in that case. Alternatively, if they don't understand modern evolutionary theory then they must be stupid.

Which is it?

A physicist tries to understand junk DNA: Part II

Yesterday I posted some comments on a blog post by physicist Rob Sheldon [A physicist tries to understand junk DNA ]. My comments were based on what I had seen on Uncommon Descent but it turns out that was only a summary of a longer post that appeared on Evolution News & Views (sic): More on Junk DNA and the "Onion Test".

The longer post doesn't add very much to the argument but it does have something interesting at the bottom. Here's what Rob Sheldon says about the Onion Test and junk DNA.

Don't misuse the word "homology"

Here's the latest science news from The Allium": Evolutionist Loses It As Colleague Conflates Homology and Similarity Yet Again.

Evolutionary biologist Dr. Constance Noring shot and killed her microbiology colleague and formerly good friend, Dr. Dan Deline when, for the umpteenth time he used the word homology when he really should have said similarity.

Read the rest. I sympathize with Professor Noring. This could have been me if Canadians were allowed to buy handguns.

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C0nc0rdance reads from Dobzhansky defending accommondationism

Here's how COncOrdance explains his latest YouTube video.

To celebrate Darwin Day, Feb 12th, 2015, I offer the words of Dobzhansky, who was a central figure in the modern evolutionary synthesis with his 1937 book, "Genetics and the Origin of Species". Dobzhansky was also a deeply religious man who believed that God had a hand in the process of evolution, a view I don't share, but try to understand.

Dobzhansky cites Teilhard de Chardin, who was a biologist, a theistic evolutionist, and a controversial figure who described evolution as cosmic attainment of perfection, a concept I also strongly disagree with.

This is an excerpt from the original work:
The American Biology Teacher, Vol. 35, No. 3 (Mar., 1973), pp. 125-129. [Nothing in Biology Makes Sense except in the Light of Evolution]

I'm not sure what purpose is served by reading from Dobzhansky's book where he praises Pierre Teilhard de Chardin. Keep in mind that Teilhard's most famous book was reviewed by Peter Medawar who described it like this: "... the greater part of it, I shall show, is nonsense, tricked out with a variety of metaphysical conceits, and its author can be excused of dishonesty only on the grounds that before deceiving others he has taken great pains to deceive himself."

That's pretty much the consensus view of Teilhard these days. It's also pretty common to point out that science as a way of knowing conflicts with religion as a way of knowing in spite of what Dobzhansky said 46 years ago.

Here's the video ....

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Is most of our DNA garbage?

Carl Zimmer's article on junk DNA has appeared in the online edition of the New York Times magazine at: Is Most of Our DNA Garbage?.

Carl was in Toronto and Guelph last December gathering information for his article. You can see that Ryan Gregory is featured and my colleague Alex Palazzo gets quoted.

Here's a picture of us having dinner. That's Alex on the left, second from left is some old dude who everyone ignores, Ryan is next and Carl Zimmer is on the right.

Carl is still the best science journalist on the planet and I appreciate that he has alerted the public to a serious problem in genome studies. The general public has been snowed by the ENCODE publicity campaign and by naive journalists who have enthusiastically reported that junk DNA is dead.

It is not. The most knowledgeable scientists recognize that the issue is not settled. The very best ones () know that 90% of our genome is junk.

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Bacterial resistance to antibiotics has nothing to do with evolution according to Michael Egnor MD

Sorry, I couldn't resist. Here's what Michael Egnor says on Evolution News & Views (sic): No, Despite Often-Heard Claims, Antibiotic Resistance in Bacteria Is Not Evolution.

This notion, however, is mistaken. Bacterial resistance to antibiotics has nothing to do with evolution. Evolution, in the Darwinian sense of undirected (unintelligent) process of random heritable variation and natural selection, is the process by which populations of living things change over time without intelligent agency causing or guiding the process. When the process of change in populations is guided by intelligence, it is called artificial selection -- breeding.

Of course I'm not the first to point this out. Charles Darwin, in the Origin of Species, made exactly the same argument. In his first chapter, he discussed artificial selection -- animal husbandry and breeding of plants. In subsequent chapters he developed an argument that in nature, changes in population are accomplished by natural selection, without intelligent agency. Darwin distinguished artificial selection from natural selection -- he distinguished breeding from evolution, and of course his theory of evolution is a theory of natural selection, not a theory of animal husbandry or plant breeding, which had been practiced for thousands of years and to which Darwin contributed nothing.

Bacterial resistance to antibiotics is artificial selection. Antibiotics are intelligently designed by medical researchers, deliberately administered to patients by doctors, who understand that there are some bacteria that are not sensitive to the antibiotic and that have the potential to proliferate. Actually, the administration of antibiotics that kill some but not all of the bacteria in the patient is quite deliberate, because there are huge populations of beneficial bacteria (e.g. in the gut) that should not be killed since they are necessary for health.

Shhhh. Don't tell Michael Behe who wrote a whole book based on resistance to antimalarial drugs.

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