January 2014 Archives

Dan Phelps, president of the Kentucky Paleontological Society, will participate in an “extended interview” with Terry Mortenson of Answers in Genesis. The participants will discuss the question, “Is teaching creationism harmful to children, society?” at 11:00 a.m., Eastern Standard Time, Thursday, January 30, on WEKU of Richmond, Kentucky. It looks like you can get it streaming. I will refrain from noting that modern journalism thinks there are two sides to every question, even when there are not.

Does any reader know of any other, similar warm-ups or “extended interviews”?

Panthera pardus


Photograph by Ed Neubaum.

Photography contest, Honorable Mention.

Neubaum_Leporad in tree Kruger Park SA.jpg

Panthera pardus – African leopard, Kruger park, South Africa.

Brief background:

We have two copies of each non-sex gene. Each version of the gene is called an allele: one inherited from your genetic mother, one from your genetic father. It is generally thought that each allele is expressed (turned out) at the same intensity. But, there are some examples where this isn’t true. The most notable occurs on the X chromosome. Females with two X chromosomes inherited one X chromosome from each parent, but one of these X chromosomes is almost completely inactivated. That means that instead of having biallelic expression (expression from both the maternal and paternal allele), most genes on the X chromosome exhibit monoallelic expression.

In recent work, Deng et al (2014) isolated single cells from two different stains of mice, where they could detect maternal-alleles and paternal-alleles for over 82% of assayed genes (in the other genes, there were not unique variants that allowed deciphering between the two alleles). For each gene, the authors characterized whether they could detect expression from both the maternal and paternal alleles, or from only the maternal or paternal allele. Although the title says, “mammalian,” all of the experiments and analysis were conducted in mouse cells and tissues, so far as I can tell.

My notes and thoughts on the paper:

That is the title of a Slate article by Zack Kopplin. But actually it is much worse (see also NCSE’s take here). Here are the first 3 paragraphs of Kopplin’s article.

By David MacMillan. The author has a B.S. in physics from the University of North Alabama and once wrote a very positive review of the Creation Museum.

It’s rare to see a prominent scientist or educator agree to a public debate with someone from the creation science movement. Giving equal time to both sides might be a foundational principle of American dialogue, but it paints the issue as more of a controversy than it actually is. That’s why it surprised a lot of people when Bill Nye, science educator and TV personality, agreed to debate the president of Cincinnati’s Creation Museum, Ken Ham.

Freshwater: Reconsideration denied


The Ohio Supreme Court today denied John Freshwater’s motion to reconsider his appeal of the decision to terminate him as a middle school science teacher in the Mt. Vernon City Schools. This brings to an end the involvement of the state courts in the affair. (I’m on a mobile and can’t post a link to the case page-someone can do so in a comment.)

Freshwater’s only remaining possibility is to convince the U.S. Supreme Court to grant cert. It’s not known whether he or the Rutherford Institute will attempt that.

Cancer Genomics Symposium


I attended the Cancer Genomics Symposium, hosted at UC Berkeley ( http://qb3.berkeley.edu/ccb/cancer-[…]s-symposium/).

A lot of great research was discussed, but it really struck me that every talk highlighted the importance of understanding evolution if we are going to tackle cancer.

My general take-home messages from the Symposium are:

- Cancers evolve, so treatments need to keep up.

- Next-generation sequencing is a sensitive diagnostic tool and allows for earlier detection.

- Therapies can be fine-tuned as we understand patient-specific and tumor-specific signals.

You can read the Storify here:

Agkistrodon contortrix


Photograph by Nicholas Plummer.

Photography contest, Honorable Mention.


Agkistrodon contortrix – juvenile copperhead snake.

We just had a paper published over at PLoS Genetics entitled, “Natural selection reduced diversity on human Y chromosomes.” But, as you may recall, it has been available on the arXiv for quite some time.

Others have already summarized the work (Razib Khan nails the punchline, and Ian Sample has a summary for the popular press).

Below are answers to many of the questions I received about this work.

Cyanocitta stelleri


Cyanocitta stelleri – Steller’s jay, Chautauqua Park, Boulder, Colorado, 2013.

Oooh, do I smell a book deal! NPR today ran an interview with a Christian pastor who supposedly made a New Year’s resolution to live for a year without God. Ryan Bell was the pastor of a Seventh-Day Adventist congregation but was asked to resign when he expressed doubts about God.

Robert Asher is a Cambridge mammal paleontologist, zoologist, phylogeneticist, author of Evolution and Belief, and generally really smart guy. He has just published a commentary at HuffPo on one aspect of Stephen Meyer’s arguments, namely, Meyer’s argument about “uniformitarianism.”

Evolution Weekend


The Clergy Letter Project has announced the ninth annual Evolution Weekend, February 7-9, 2014. Their theme this year is Different Ways of Knowing/Asking Different Questions, and they say,

Evolution Weekend is an opportunity for serious discussion and reflection on the relationship between religion and science. An ongoing goal has been to elevate the quality of the discussion on this critical topic, and to show that religion and science are not adversaries. Rather, they look at the natural world from quite different perspectives and ask, and answer, different questions.

They go on to note that many religious people recognize evolution as “sound science” and furthermore that “mischaracteriz[ing] evolution for partisan gain” has real (and I would add, uniformly negative) “consequences for society.” Read their statement for yourself, and by all means bug your clergyperson to address evolution from the pulpit or to develop some special program for that weekend – even if you have to prepare that program yourself! I certainly intend to bug my rabbi, who last year very graciously helped me put together a program on the trolley problem, and see what we can do this year.

Science word clouds


Today I broke down and made a word cloud. But, it’s a pretty awesome word cloud. It shows the top 75 words used in my research publications in 2013 (excluding common words).

M. Wilson Sayres’ 2013 research publication word cloud.

I used http://www.wordle.net, which is nice because it also has code you can modify yourself. I was also directed to http://www.tagxedo.com, which has the advantage of making word clouds in fun shapes.

de_Queiroz_2014_Monkeys_Voyage.pngNote: this is an off-the-cuff review that I wrote while experiencing jet-lag induced insomnia (I am in Canberra, Australia, to give a workshop on BioGeoBEARS at the 2014 meeting of the International Biogeography Society at Australia National University). I have a more formal review in preparation for the Reports of the National Center for Science Education.

Review of: de Queiroz, Alan (2014). The Monkey’s Voyage: How Improbable Journeys Shaped the History of Life. Basic Books: New York, pp. 1-348. http://themonkeysvoyage.com/ - Amazon Link

Today, a book is coming out that is destined to become a classic of science writing. Normally, popular science books popularize well-established science. The research being popularized may be decades or centuries old. Certainly popularization of such material is important, but I found that for me, the appeal of such works dropped off as I matured as a scientist. There are only so many times you can read about Darwin and the Beagle, or Laplace and the hypothesis he had no need of, or the sequence from Mendel to Watson and Crick, before you feel like you’ve heard it all before and it ceases to become interesting.

Alan de Queiroz is doing something different. He is popularizing an active scientific controversy in biogeography. Biogeography is the science of where species live and how they got there. The biogeographical controversy is termed “dispersal versus vicariance,” and it runs long and deep. Understanding what the controversy is about, and why anyone would care, takes a little bit of background.



Stone courtesy of Toby Shannon.

I think that it would be useful or me to take notes on the papers I’m reading, and I figured it might be useful to share them online because, open science and all. These papers will be in my area of study: sex chromosome evolution and sex-biased processes. If you’re interested, please go read the paper, and we can have a discussion in the comments. The link to the paper and full citation are found at the bottom. Let’s jump right in!

Jangravi et al. (2013) introduce the Chromosome-centric Human Proteome Project (C-HPP), focusing on the Y chromosome (Y-HPP). Their project is scheduled to run over the next 10 years, and they state that “the objective of Y-HPP is to map and annotate all proteins encoded by genes on the MSY sequences.” In this, Jangravi et al. (2013) give an excellent overview of the Y chromosome, contribute new synthesis of previous work, and describe the plans for their group’s project.

Bill Nye to debate Ken Ham?!


Let us hope not, but a reader just sent me the following from Mr. Ham’s Facebook page:

Well the big news for 2014 as we begin this new year is that in February, at the Creation Museum, I will be debating the well known Bill Nye The Science Guy! In the next day or so we will post more details including how you can buy tickets to this event. It’s quite rare these days for such a well known evolutionist to publicly debate a creationist–so we do expect a lot of media interest. For now, I just wanted to let you know about this–keep watch for details!

If it is true, I sincerely hope Mr. Nye will reconsider. There is nothing to debate, and a “debate” with Mr. Nye will only give Mr. Ham credibility that he does not deserve and increase not only his visibility but also his ability to attract investors. May I suggest that Mr. Nye take his cue from the noted Holocaust scholar, Deborah Lipstadt, who told the magazine Limmud,

If Limmud’s organisers invited Lipstadt to participate in a panel discussion with [Holocaust denier David] Irving, she would refuse point blank. “I don’t debate Holocaust deniers. Putting him on a panel would mean someone lost their mind. He’s a liar – why give a liar a platform?”

I sometimes bowdlerize that to “I do not debate liars,” and it is a policy I recommend to anyone who is tempted to “debate” a creationist. Whether you win or lose, you will convince no one and will only add to the prominence of your opponent, who can now say, “See, I debated a prominent scientist; I must be taken seriously now.”

Please, Mr. Nye, do not “debate” with Ken Ham or any other charlatan. No good will come of it – no good can come of it.

Update, January 2, 9:30 MST: February 4, at the Creation “Museum,” $25.00. See here.

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