Exam Question #3

 
Now that you've tried Exam Question #1 and Exam Question #2, let's see how you do with this one.

There are hardly any pseudogenes in bacterial genomes. Why haven’t pseudogenes been eliminated from our genome?

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Exam Question #2

 
Most of you wouldn't have passed Exam Question #1. Let's see how you do with this one.

Here’s a quotation from an article published by Kathleen McAuliffe in Discover magazine in 2009 [They Don't Make Homo Sapiens Like They Used To].

For decades the consensus view—among the public as well as the world’s preeminent biologists—has been that human evolution is over. Since modern Homo sapiens emerged 50,000 years ago, “natural selection has almost become irrelevant” to us, the influential Harvard paleontologist Stephen Jay Gould proclaimed. “There have been no biological changes. Everything we’ve called culture and civilization we’ve built with the same body and brain.” This view has become so entrenched that it is practically doctrine.

Is it true that the consensus view among “the world’s preeminent biologists” is that human evolution has stopped? Do you agree with this “doctrine?”

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My Moderation Policy

 

Barry Arrington¹ at Uncommon Descent has banned many defenders of evolution. This is not the first time that this has happened but for the first time the moderator at Uncommon Descent tries to offer a defense of the policy ... [Why is Barry Arrington Stifling Dissent at UD?].

If you visit some of our more vociferous opponents’ websites that is the question being asked. The answer, of course, is that I am not stifling rational argument on this site. In fact, just the opposite is true; my purpose has been to weed out those who refuse to engage in rational argument so that rational argument can be pursued by those who remain.

My moderation policy is very different. I allow comments from creationists in spite of the fact that they are incapable of engaging in rational argument.

Creationists, by definition, are incapable of being rational in this debate. Isn't it ironic that they set themselves up as the arbitrators of rational argument?

There's a good reason why we refer to this controversy as a contest between rationalism and superstition.

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1. Barry Arrington is a lawyer from Colorado

We're Not in Toronto Anymore

 
These are views from the back and front yards of my daughter's house in Los Angeles. It definitely gives us the feeling that we're not in Toronto (or Kansas) anymore.

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Exam Question #1

It's that time of year again. My students have a mid-tern test on Feb. 28th so I giving out a list of questions that will be on the exam. Here's one.

Here are two different trees depicting the evolutionary relationship of various classes of animals. Which one is better? Why?

The question is based on the following assigned paper:

Meisel, R.P. (2010) Teaching Tree-Thinking to Undergraduate Biology Students. Evo. Edu. Outreach 3:621-628. [doi: 10.1007/s12052-010-0254-9]

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[Image Credit: The tree on the left is from Campbell Biology Chapter 32 Activities Quiz (2002)]

The Cost of Introns

Michael Lynch estimates that the cost of adding an intron to an intronless gene is equivalent to adding about 31 bp of essential target (Lynch, 2010). This is roughly the number of base pairs in an average intron that have to be preserved in order for the intron to be properly spliced. Adding an intron increases the chances that a gene will be inactivated by mutation.

In spite of this deleterious cost, introns have spread in certain genomes; notably, in mammals and flowering plants. How do we explain the spread of introns? Is it consistent with the null hypothesis of random genetic drift?

According to Lynch the answer could be, yes. Here's what he says in his book The origins of genome architecture.

For newly arisen introns having no functional significance for the products of their host genes, the primary force opposing their ability to spread throughout a population is their excess mutation rate to defective allele(s), and because this force is expected to be quite weak, selection will be ineffective in preventing intron colonization in populations experiencing substantial levels of random genetic drift.

The selection coefficient for intron deletion has to be above a certain threshold in order to prevent introns from spreading. This threshold depends on the population size: in large populations the deleterious effect of introns is sufficient to ensure that they will be kept to a minimum, or eliminated entirely.

For species with small populations there will be a cutoff where the selection coefficient cannot overcome the effect of random genetic drift and intron insertion is effectively neutral.

Lynch calculates the cost of the extra target nucleotides as a function of the mutation rate (μ) and explains why the cutoff is 2N_gμ = 0.04 (N_g is the effective number of genes ~ 2N_e). You can estimate 2N_gμ by counting the nucleotide diversity at silent sites in protein-encoding genes (π_s). Thus, a plot of number of introns vs π_s [2N_gμ] is a test of the hypothesis.

Here's the figure from Lynch's book.

The data indicates that species with small values of π_s the spread of introns cannot be prevented even though introns may be deleterious. The cutoff is about 0.04 as predicted.

This does not prove that intron proliferation in some species is due to random genetic drift but it does show that the hypothesis cannot be ruled out. There's no need to invoke adaptive explanations for the initial spread of introns in vertebrate and plants genomes.

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Lynch, M. (2010) Rate, molecular spectrrum, and consequences of human mutation. Proc. Natl. Acad. Sci. USA 107:961-968. [doi: 10.1073/pnas.0912629107]

Monday's Molecule #159

 

This is a very important molecule for many reasons. Versions of it are found in all living species. Its function is essential in most (all?) species.

Pieces of this molecule are found in many viruses. The molecule also plays a prominent role in the debate about junk DNA.

Identify the molecule—the common name will do. You don't have to specify the species but anyone who does will get an honorable mention if the winner doesn't. Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch. I'm about to leave for Los Angeles for a couple of weeks but I promise to organize lunch dates as soon as I get back at the end of February.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: It's 7SL RNA from humans. The winner is Joseph C. Somody.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi

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Is "Out-of-Africa" Dead or Just Severely Wounded?

 

Here's a good summary from the New York Times [DNA Turning Human Story Into a Tell-All]. The story is written by Alanna Mitchell. John Hawks links to it [Denisova in the news], suggesting that he thinks it's pretty accurate.

The opening paragraphs of the New York Times story emphasize the controversy ...

The tip of a girl’s 40,000-year-old pinky finger found in a cold Siberian cave, paired with faster and cheaper genetic sequencing technology, is helping scientists draw a surprisingly complex new picture of human origins.

The new view is fast supplanting the traditional idea that modern humans triumphantly marched out of Africa about 50,000 years ago, replacing all other types that had gone before.

Instead, the genetic analysis shows, modern humans encountered and bred with at least two groups of ancient humans in relatively recent times: the Neanderthals, who lived in Europe and Asia, dying out roughly 30,000 years ago, and a mysterious group known as the Denisovans, who lived in Asia and most likely vanished around the same time.

Their DNA lives on in us even though they are extinct. “In a sense, we are a hybrid species,” Chris Stringer, a paleoanthropologist who is the research leader in human origins at the Natural History Museum in London, said in an interview.

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[Image Credit: The map is from The Human Journey.]

Is Neanderthal Your Distant Cousin or Your Ancestor?

 

The answer to the question is "mostly cousin" or "both," depending on whether you are African, Asian, or European. Lots of evidence suggests that people who migrated out of Africa in the past few hundred thousand years met and mated with indigenous populations of other humans who were already living in Asia and Europe.

The availability of many genome sequences coupled with our sophisticated understanding of population genetics allows workers to estimate how much Neanderthal DNA entered the modern European and Asian populations. It won't be long before similar studies are done with the Densovan genome.

There's lots of discussion about whether the strict "Out-of-Africa" scenario is still valid [Out of who knows where] [The scientists behind Mitochondrial Eve tell us about the "lucky mother" who changed human evolution forever]. There's little doubt that some version of the multiregional hypothesis is correct although it may not be as thorough as the original proponents argued.

John Hawks is an expert on this sort of thing and he's just posted some of his work on his blog [Which population in the 1000 Genomes Project samples has the most Neandertal similarity?]. He doesn't allow comments so you can ask questions here—he's been known to read Sandwalk when he gets bored doing real science.

I'll ask the first questions. John, what percentage of the genomes of Africans, Europeans, and Chinese are derived from the Neanderthal population? Your figure shows the amount of Neanderthal (Vi33.16) intrusion as something called "shared derived variants" but how much of the total genome does that represent? Is any of it in parts of the genome where there are genes?

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[Image Credit: I don't know where this picture came from. I got it on Just Another Brooklyn Blog.]

Happy Birthday Charles Darwin

[Reposted from 2008.]

Charles Robert Darwin was born on this day in 1809. Darwin was the greatest scientist who ever lived.

In honor of his birthday, and given that this is a year of politics in America, I thought it would be fun to post something about Darwin's interactions with politicians. The historical account is from Janet Browne's excellent biography (Brown 2002).

William Gladstone (photo below) was an orthodox Christian. He was not a fan of evolution. In March 1877 Gladstone was leader of the Liberal party and a former Prime Minister of the most powerful country in the world. He was spending the weekend with John Lunnock—a well-known liberal—and a few other friends, including Thomas Huxley.

They decided to walk over to Darwin's House in Downe. This was 18 years after the publication of Origins and Darwin was a famous guy. The guests were cordially received by Darwin and his wife Emma. Darwin and Emma were life-long liberals and they were honored by Gladstone's visit. A few days later, Darwin wrote a note to his friend saying,

Our quiet, however, was broken a couple of days ago by Gladstone calling here.—I never saw him before & was much pleased with him: I expected a stern, overwhelming sort of man, but found him as soft & smooth as butter, & very pleasant. He asked me whether I thought that the United States would hereafter play a much greater part in the history of the world than Europe. I said that I thought it would, but why he asked me, I cannot conceive & I said that he ought to be able to form a far better opinion,—but what that was he did not at all let out.

A few years later Gladstone sent Darwin one of his essays on Homer. Darwin gratefully acknowledged the gesture.

In 1881, when Gladstone was Prime Minister again, Darwin and some of his friends petitioned Gladstone to award a pension to Alfred Russel Wallace, who was in dire financial straits at the time. Gladstone granted the request. Two months later Gladstone offered Darwin a position as trustee of the British Museum but Darwin declined. (Remember, Gladstone did not agree with Darwin about evolution, or religion.)

When Darwin died, Gladstone was instrumental in arranging for him to be buried in Westminster Abbey. The funeral was held on April 26, 1882. William Gladstone was too busy to attend. He went to a dinner at Windsor.

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Brown, J. (2002) Charles Darwin: The Power of Place (Vol. II). Alfred A. Knopf, New York (USA)

If I was in L.A. ...

 

It's windy, snowy, and -14°C. Ms. Sandwalk gets it exactly right on her blog [If I was in L.A.].

We'll soon be in Los Angeles for a couple of weeks visiting our granddaughter (and her parents). I hope to meet up with some of you while I'm there. Leave a comment or email me. My email address is "l" period "moran" and the domain name is "utoronto" period "ca".

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Note to grammar police. I know the proper use of subjunctive mood. I suspect John Phillips does as well. Denny Doherty was Canadian and was almost certainly taught proper grammar in school. Mama Cass attended university so it's likely she too knew about subjunctives. As for Michelle ... well, three out of four ain't bad.

How to Turn a University Into a Glorified High School

 

Ian D. Clark is Professor of Public Policy and Governance here at the University of Toronto. He has attracted a lot of attention lately because he and his colleagues advocate the creation of Teaching-only Universities in Ontario. The scary part of this ridiculous idea is that it might soon become official policy of the Ontario government as described in a recent article by Louise Brown in The Toronto Star [Teaching-only universities would cut education costs, author says].

Undergraduate universities that focus on teaching only would create cosier classes, cut salary costs and boost student satisfaction, argues Ian Clark, the former head of the Council of Ontario Universities.

Moreover, he says professors at these new universities should be required to teach twice as many courses as usual — a full 80 per cent of their time with 10 per cent left for research and 10 per cent for administration.

Clark and professor David Trick are co-authors of a controversial new book that calls for new teaching-oriented universities where profs would have much higher course-loads. Simply by doubling the number of courses a professor teaches each semester to four from two could cut the operating cost of educating a student to $9,800 from $14,300 at a campus of 10,000, Clark noted Tuesday at a conference sponsored by the University of Toronto’s Ontario Institute for Studies in Education.

Having profs teach more courses is one cost-saving tip rumoured to be part of economist Don Drummond’s report next week to Premier Dalton McGuinty.

How Did the Zebra Get Its Stripes?

We've been discussing the adaptationist approach to biology on another thread and this is a good example to illustrate the issues. If I were to ask you how the zebra got its stripes, what would you think?

Would you immediately assume that it could be an evolutionary accident with no adaptive significance then start to wonder if you could rule out such an explanation? Can random genetic drift of neutral alleles explain the zebra's stripes?

Or would you immediately start thinking of adaptive explanations for why all three extant species of zebras have stripes but no other large mammals in the same environment are striped. Most other horses don't have prominent stripes but many have faint stripes on some parts of their bodies (Darwin, 1859).

I argue that you have to rule out the null hypothesis (drift) before invoking adaptationist explanations. In other words, the first question you need to ask is whether zebra stripes are adaptive. But that's not the adaptationist approach. Adaptationists begin with the assumption that stripes are adaptive, then they start looking for adaptive explanations.

What if the favorite adaptive explanation is refuted? What does an adaptationist do next? Gould and Lewontin (1978) provide the answer ...

Remember Chris Mooney?

 

Chris Mooney has achieved some remarkable goals in the past ten years or so. He's an atheist accommodationist who doesn't understand atheism or accommodation. He's a science journalist who doesn't understand science or the important elements of science journalism (it's all about spin framing). He's a supporter of evolution but he's only interested in American politics—he doesn't actually understand evolution.

Nisbet & Mooney Reveal Their True Colors
Matthew Nisbet and Chris Mooney Video on Framing Science
Changing Minds Through Science Communication
For Once, Chris Mooney Talks Sense
The Future of Science Journalism
Science Journalism in Decline
Some scientists are astrologers, therefore science and astrology are compatible
Chris Mooney Changed His Mind
The Doctrine of Joint Belief
Chris Mooney and Sheril Kirshenbaum in Newsweek
Boring ....
The Difference between Truth and Framing
Chris Mooney vs Atheists: Part XXXIV
Chris Mooney Asks a Hard Question
The Great Accommodationist Dud

Chris is about to publish a new book called The Republican Brain: The Science of Why They Deny Science--and Reality. Like most professional writers he knows that he has to hype the book in order to get people to buy it so he's started the campaign with an article on HuffPost under their new "Science" category [Want to Understand Republicans? First Understand Evolution].

The main theme is that Republicans are genetically different from Democrats and that difference is due to evolution. No, I'm not kidding ....

Jerry Coyne says "huh?" [Chris Mooney, evolution, and politics]. Get on over to Coyne's blog website and join the fun.¹ Can Mooney, the science journalist, screw up evolution? ... let's count the ways.

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1. What would we do for fun if we didn't have Chris Mooney? We'd have to pick of the creationists all the time and thatgets boring.

Was Newton the Greatest Scientist Who Ever Lived?

Most of us know that Charles Darwin was the greatest scientist who ever lived but one still finds the occasional misguided physicist/mathematician who thinks that the honor should go to an eighteenth century Englishman named Isaac Newton (1642-1727) [Top Five Dead Scientists] [Westminster Abbey: Darwin vs Newton] [Books by Charles Darwin] [Why I'm Not a Darwinist].

Now we have more direct evidence.¹ The Israel National Library has just put a pile of Newton's writings on line [Israel National Library uploads trove of Newton's theological tracts ]. We get to see direct example of how Newton thinks like a scientist.

My favorite is Newton's predictions about when the apocalypse will take place. He starts his calculation with the crowning of Charlemagne as Holy Roman Emperor in 800 AD and goes downhill from there [Newton on the date 2060 (early 18th century)].

In the instance displayed on this manuscript folio, Newton calculates a tentative date using the 1260 days (taken to be years) from Daniel in part to counter the claims of some of his contemporaries, who claimed that the end would come in the seventeenth or eighteenth century. Newton stood apart from contemporary interpreters who were predicting the imminent restoration of the Jews, the fall of the Catholic Church and the Second Coming of Christ. Nevertheless, Newton’s own fervent belief in these prophetic events is not in doubt. The abbreviation “A.C.” stands for Anno Christi (“the year of Christ”).

So then the time times and half a time are 42 months or 1260 days or three years and an half, reckoning twelve months to a year and 30 days to a month as was done in the Calendar of the primitive year. And the days of short lived Beasts being put for the years of lived [sic] kingdoms, the period of 1260 days, if dated from the complete conquest of the three kings A.C. 800, will end A.C. 2060. It may end later, but I see no reason for its ending sooner. This I mention not to assert when the time of the end shall be, but to put a stop to the rash conjectures of fanciful men who are frequently predicting the time of the end, and by doing so bring the sacred prophesies into discredit as often as their predictions fail. Christ comes as a thief in the night, and it is not for us to know the times and seasons which God hath put into his own breast.

There's lots more where this came from but I don't want to embarrass the Newton supporters any further.

By way of contrast, the real greatest scientist who ever lived was a non-believer who never would have treated the Bible as a scientific authority.

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1. The information isn't new. It's just that we can now see for ourselves that Isaac Newton was remarkably unscientific in most of his writings.

P.S. Some losers are going to argue that Newton was still the greatest scientist and we should ignore the fact that his religious beliefs made him write many stupid anti-science treatises. That's like saying that Young Earth Creationists (like Newton) can be good scientists even though they believe the Earth is only 6000 years old.