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Tuesday, February 28, 2012

Exam Question #7

 
Today is the day of the midterm test in my course on molecular evolution. Here's one of the possible question on the test. Almost every student should get full marks on this one.
Imagine that a new mutation gives rise to a beneficial allele with a selection coefficient of 0.1 (s = 0.1) . What is the normal fate of this allele in a population of 10,000 individuals? Explain your answer.
Sandwalk readers should try and put this selection coefficient into perspective. It's probably at the high end for new beneficial alleles. What this means is that most adaptive explanations need to postulate a significant benefit to each individual in order to make the probability of fixation come out to some reasonable number.

Exam Question #1
Exam Question #2
Exam Question #3
Exam Question #4
Exam Question #5
Exam Question #6


Exam Question #6

 
This is an easy question. Here are the others: Exam Question #1, Exam Question #2, Exam Question #3, Exam Question #4, Exam Question #5.
To a first approximation, the rate of fixation of neutral alleles in a population is independent of effective population size. Why?


Exam Question #5

 
Did you try and answer Exam Question #1, Exam Question #2, Exam Question #3 or Exam Question #4? Were they too hard? Try this one.
Steven Pinker is an evolutionary psychologist at Harvard. He wrote ...
Are we still evolving? Biologically, probably not much. Evolution has no momentum, so we will not turn into the creepy bloat-heads of science fiction. The modern human condition is not conducive to real evolution either. We infest the whole habitable and not-so-habitable earth, migrate at will, and zigzag from lifestyle to lifestyle. This makes us a nebulous, moving target for natural selection.
What definition of evolution do you think he has in mind? Is he correct?


Exam Question #4

 
Now that you've tried Exam Question #1, Exam Question #2, and Exam Question #3, let's see how you do with this one.
Many evolutionary biologists think that population genetics is the key concept in understanding evolution but biology students often complete several years of courses without ever learning about effective population sizes, mutations rates and the importance of random genetic drift. Why? Is it because population genetics is not a necessary key concept in evolution?


Sunday, February 26, 2012

A "Simple" Argument for Intelligent Design Creationism

 
Once again, it's time to remind people of a famous quotation by Isaac Asimov—a biochemist— from his 1981 essay, The “Threat” of Creationism [see Bill Dembski, Isaac Asimov, and The Second Law of Thermodynamics].
Creationists have learned enough scientific terminology to use it in their attempts to disprove evolution. They do this in numerous ways, but the most common example, at least in the mail I receive is the repeated assertion that the second law of thermodynamics demonstrates the evolutionary process to be impossible.

In kindergarten terms, the second law of thermodynamics says that all spontaneous change is in the direction of increasing disorder—that is, in a "downhill" direction. There can be no spontaneous buildup of the complex from the simple, therefore, because that would be moving "uphill." According to the creationists argument, since, by the evolutionary process, complex forms of life evolve from simple forms, that process defies the second law, so creationism must be true.

Such an argument implies that this clearly visible fallacy is somehow invisible to scientists, who must therefore be flying in the face of the second law through sheer perversity. Scientists, however, do know about the second law and they are not blind. It's just that an argument based on kindergarten terms is suitable only for kindergartens. [my emphasis - LAM]
Now, let's look at this video from: Are You Looking for the Simplest and Clearest Argument for Intelligent Design?]. Keep in mind that one definition of a "simple" argument is one that is suitable for kindergarten students (and IDiots).



This video was posted on the leading IDiot blog Evolution News & Views. It tells us a lot about the quality of their science and their commitment to truth.


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.


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

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

Wednesday, February 22, 2012

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.



Monday, February 20, 2012

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.







Sunday, February 19, 2012

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.







Saturday, February 18, 2012

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?”


Thursday, February 16, 2012

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.