The Ugliness of the Leaf-Nosed Bat

 

Here's a photo of the head of a leaf-nosed bat. I was posted on Jerry Coyne's blog website today [A new leaf-nosed bat]. Jerry is discussing an article in National Geographic: Strange New Leaf-Nosed Bat Found in Vietnam. You'll probably be curious about the strange appearance of this bat's face. How did that happen?

Well, there are several possibilities that account for the evolution of ugly bats. I wonder what Coyne says ....?

Leaf-nosed bats are found in both the New and Old World, and the New World ones are the most numerous group in the order Chiroptera (bats), which itself is one of the most diverse order of mammals, second only to rodents (40% of mammal species are rodents; 20% are bats). A probably aprocryphal story relates evolutionist J. B. S. Haldane’s answer when asked what one could infer about the Creator from surveying his creation. ”An inordinate fondness for beetles,” Haldane supposedly said. (Of the roughly 1.7 million described species on Earth, 300,000-400,000 are in the order Coleoptera—beetles.) If that question were asked about mammals, one could reply that God showed an inordinate fondness for rodents and bats, and a notable distaste for primates.

The function of the “leaf” isn’t fully known, but it’s suspected to be important in receiving the echolocation signals emitted by bats.

You may find this beast ugly, but that’s speciesism! I find all animals beautiful because they’re products of evolution, embodying all the mechanisms that drive the process. The ugliness, in this case, is probably a byproduct of natural selection.

Why should we assume that the ugliness is a byproduct of natural selection? Lot's of humans are ugly, is that also a byproduct of natural selection? :-)

Seriously, we don't know why these bats have such faces. Why couldn't it just be an accident of evolution? I'm not saying that this is necessarily true. What I AM saying is that it's wrong to just ASSUME, without evidence, that such an appearance is probably due to natural selection. I bet I would get lots of flak if I said that it was probably due to random genetic drift.

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American Roman Catholics and "Religious Liberty"

 

There's a major kerfluffle going on in the United States. It's exacerbated by the year-and-a-half long campaign for President.

Most outsiders are puzzled by the complaint of the American Roman Catholic churches so here's a bit of background as I understand it. In most civilized countries, universal health care provides all services to all citizens regardless of their personal beliefs. Thus, everyone can get "free" blood transfusions paid for by your taxes. Jehovah's Witnesses are under no obligation to get a blood transfusion if they prefer to die instead.

Similarly, birth control pills are covered by basic health insurance in most (all?) civilized states, as are abortions under a variety of circumstances. Nobody is forced to use contraceptives and nobody is forced to have an abortion but your taxes support these options, as they should.

Things are different in America because the cost of health insurance has to be paid, in part, by employers. This creates a conflict. Let's consider the hypothetical case of a group of employees working for the Jehovah's Witnesses. The church wants to remove blood transfusions from the coverage because blood transfusions are against their religious beliefs. Apparently, forcing the Jehovah's Witnesses to fund blood transfusions for their atheist, Catholic, and Muslim employees is a violation of religious freedom!

That's a hypothetical case. The real case involves funding contraception and abortion coverage for employees of Roman Catholic churches. Here's a copy of the letter that was read in many Roman Catholic churches last Sunday. This sort of convoluted logic could only make sense in America.

The solution is obvious: universal single-payer health care is the best way to enforce tolerance. You can't count on tolerance from the Roman Catholic Church. (The irony is that a majority Roman Catholic employees would make use of health care coverage that included abortion and contraception, in spite of what the church says.)

Dear Brothers and Sisters in Christ:

I write to you concerning an alarming and serious matter that negatively impacts the Church in the United States directly, and that strikes at the fundamental right to religious liberty for all citizens of any faith. The federal government, which claims to be "of, by, and for the people," has just been dealt a heavy blow to almost a quarter of those people -- the Catholic population -- and to the millions more who are served by the Catholic faithful.

The U.S. Department of Health and Human Services announced last week that almost all employers, including Catholic employers, will be forced to offer their employees' health coverage that includes sterilization, abortion-inducing drugs, and contraception. Almost all health insurers will be forced to include those "services" in the health policies they write. And almost all individuals will be forced to buy that coverage as a part of their policies.

In so ruling, the Obama Administration has cast aside the First Amendment to the Constitution of the United States, denying to Catholics our Nation's first and most fundamental freedom, that of religious liberty. And as a result, unless the rule is overturned, we Catholics will be compelled to either violate our consciences, or to drop health coverage for our employees (and suffer the penalties for doing so). The Obama Administration's sole concession was to give our institutions one year to comply.

We cannot--we will not--comply with this unjust law. People of faith cannot be made second class citizens. We are already joined by our brothers and sisters of all faiths and many others of good will in this important effort to regain our religious freedom. Our parents and grandparents did not come to these shores to help build America's cities and towns, its infrastructure and institutions, its enterprise and culture, only to have their posterity stripped of their God given rights. In generations past, the Church has always been able to count on the faithful to stand up and protect her sacred rights and duties. I hope and trust she can count on this generation of Catholics to do the same. Our children and grandchildren deserve nothing less.

And therefore, I would ask of you two things. First, as a community of faith we must commit ourselves to prayer and fasting that wisdom and justice may prevail, and religious liberty may be restored. Without God, we can do nothing; with God, nothing is impossible. Second, I would also recommend visiting www.usccb.org/conscience, to learn more about this severe assault on religious liberty, and how to contact Congress in support of legislation that would reverse the Obama Administration's decision.

Sincerely yours in Christ,

+Alexander K. Sample
Most Reverend Alexander K. Sample
Bishop of Marquette

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[Hat Tip: RichardDawkins.net: Catholics hear anti-Obama letter in church]

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.

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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.

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Disneyland 2012

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

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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.

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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.]