La Brea Tar Pits

The La Brea tar pits are in the middle of greater Los Angeles on Wilshire Boulevard. The area is now a single large city block that contains the remaining tar pits and the Page Museum.

The tar pits are composed of thick black asphalt and usually there are bubbles of methane forming on the surface. The largest pit was mined for the asphalt in the early 1900's and now it's a dirty-looking lake with methane bubbles.

The Page Museum contains some of the fossils that have been removed from the pits. (You can see an evacuation in progress at Pit 23.) These plants, insects, and animals date from about 40,000 years ago to about 11,000 years ago. The panorama below show the main species: mastodons, juniper trees, saber-toothed cats, camels, Dire wolves, ground sloths, horses, bisons, and a variety of currently extant small animals.

The museum is well worth a visit if you are in the Los Angeles area and you are interested in evolution. Creationists will not like it.

There are millions of fossils and this allows paleontologists to look at variation within a species. There's a nice display of 404 Dire wolf skulls to illustrate the point.

Here's an example of a small tar pit.

Granddaughter Zoë liked the museum but the grassy hills outside the building were an even bigger hit with all the young children. They could climb to the top and roll down to the bottom. Zoë did this several hundred times before we had to get in the car. She was sad to leave the La Brea Tar Pits.

---

Cirque du Soleil on Santa Monica Beach

 

Yesterday we went to see the Cirque du Soleil's production of Ovo. Here's the description from Wikipedia.

Ovo (Portuguese for "egg"), was created and directed by Brazilian dancer/choreographer Deborah Colker – the first woman to create a Cirque production—that heavily relies on Brazilian music and some dance performances mixed in with the traditional circus arts; premiered in Montreal in 2009 and is currently touring North America. The show looks at the world of insects and its biodiversity where they go about their daily lives until a mysterious egg appears in their midst, as the insects become awestruck about this iconic object that represents the enigma and cycles of their lives.

The show was in a large tent set up by a pier on Santa Monica beach (Los Angeles, United States). It was magic and granddaughter Zoë loved it.

---

Disneyland 2012

 
On Friday we visited Disneyland with our granddaughter Zoё. It was fantastic, much better than my previous visit; Disneyland 1967.

---

Disneyland 1967

 
In May 1967 I decided to drive from Ottawa to California with my friends Paul Young and Brian McManus. We arrived in Los Angeles on a Saturday and spend all day Sunday trying to surf at Malibu. Monday was the day we set aside to visit Disneyland before driving to San Fransisco on Tuesday.

Little did we know that Disneyland was closed on Mondays and Tuesdays. That was a sad day.

---

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?

---

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?”

---

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.

---

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.

---

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]

---

[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.

---

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

---

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.

---

[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?

---

[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.

---

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".

---

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.