May 2013 Archives

Died in committee


According to NCSE’s scorecard, that is what happened to most of 10 anti-science bills introduced in state legislatures. Most of the bills used the now traditional “strengths and weaknesses” or “academic freedom” ploys, but some would have allowed “teachers to ‘intelligently explore’ controversies and help wayward students ‘develop critical thinking skills,’” as NCSE puts it. Four bills attacked climate change in addition to evolution. None of the bills was enacted into law. Unfortunately, a bill to repeal the “notorious” Louisiana Science Education Act also failed.

Three years ago I became a chimera. Again. I am also geneticist. Surprisingly, the two are unrelated.

Evolution and climate change in NCSE’s mission


As most PT readers probably know, the National Center for Science Education (NCSE) has added climate change education to the core issues it is concerned with. I was originally dubious of that move, feeling that the focus on evolution education was enough to handle without adding another issue on which there’s public/political debate, though (as is also the case with evolution) considerably less scientific debate.

I’ve come around, though, for a couple of reasons. One, of course, is the increasing trend on the part of anti-evolutionists to lump climate change in with evolution in their “controversial issues” and so-called “academic freedom” legislation. These are part of the more general anti-science movement that Kenneth Miller warned against in Only a Theory, and I share Miller’s apprehensions in that respect. I do not think Miller exaggerates the threat to science literacy and support in the U.S.

Brilliant blunders


Mario Livio definitely does not pick on someone smaller than he. Indeed, when he decided to write about what he considers scientific blunders, he went after Darwin, Kelvin, Pauling, Hoyle, and Einstein.

The full title of his latest book is Brilliant Blunders: From Darwin to Einstein – Colossal Mistakes by Great Scientists That Changed Our Understanding of Life and the Universe, which is more of an abstract than a title. It would be incorrect to claim that Livio has not laid a glove on any of his subjects, but neither, it seems to me, are all of the errors “colossal.” Still, the book was well worth reading and contains excellent introductory material for those who are not experts in the subjects and even for those who are. The organization of the book is also interesting in that every chapter relates in some way to evolution, whether of life or the earth or the universe, and the transitions from scientist to scientist are relatively seamless.

Ardea herodias


Ardea herodias – great blue heron, Walden Ponds, Boulder, Colorado, May, 2013.

Not stated is whether they manage to lose weight, nor whether they still get cavities or develop diabetes. But a recent article in Science shows that cockroaches evolved an aversion to glucose after glucose was used for a number of years as a poisoned bait. That is, the cockroaches developed an aversion to the bait rather than a resistance to the poison. The Science article is kind of written in Greek

In response to the anthropogenic assault of toxic baits, populations of the German cockroach have rapidly evolved an adaptive behavioral aversion to glucose (a phagostimulant component of baits).

but The New York Times has a nice summary and notes, almost as a throw-away, that the result might have application to diseases, such as malaria, that are spread by mosquitoes.

Memo to potential trolls: Yes, yes, we know—they are still cockroaches!!

Yesterday, I received a letter and a booklet from an organization called Day Star Research. The booklet was written by the president of Day Star, Fred Heeren, who writes, among other things,

Day Star Research is committed to

* Promoting healthy dialogue between the religious and non-religious.

* Fighting irrational extremism with rationality.…

* Encouraging Christians to reverse their reputation for anti-intellectualism, insensitivity, and judgmentalism.…

The world’s rarest birds


Photograph by Huajin Sun.


Grus japonensis – red-crowned crane. This photograph, which adorns the dust jacket of The World’s Rarest Birds, earned second prize in the “endangered or data-deficient” category of a worldwide photo contest. I will review the book briefly, below the fold.

Note added May 21, 11:00 a.m., MDT: You may see the contest winners here and the winners of a second contest here.

My breasts. My genes.


Angelina Jolie wrote about her decision to have a double mastectomy after learning that she carries a version of the BRCA1 gene with mutations that are significantly associated with developing breast cancer, speaking with her doctor, and considering the risks and benefits to herself, and for her family.

Es Baluard Mallorca Spain 2008 14
By ILA-boy

Many people have reacted, but I particularly like this response from Judith Soal that introduces the complexity of understanding the genetic component of diseases. We still have quite a lot to learn about the relationship between genes, environment, and disease, but we do know that some genetic mutations increase susceptibility to disease, but also that people without known genetic mutants are often affected by diseases due to environment, to novel mutations, or, by chance.  Moreover, rarely is the culprit of a disease a single gene. But, for now, we’ll leave this to others.

I want to focus on something else. Something that is relevant to every person. Something that both of these articles touch on.

The genome from a species of bladderwort (Utricularia gibba) was recently published. Ed Yong has a wonderful summary about the bladderwort genome paper and its relationship with current debates regarding what is functional (introduction to the ENCODE project). Here’s my accessible research introduction:

The bladderwort is a carnivorous plant with beautiful yellow flowers on top:

Horned Bladderwort (4959623968)
This is a captivating “horned bladderwort” (Utricularia cornuta), by Jacopo Werther

And curious “bladders” on its roots that it uses to trap its prey.

John Searle’s homunculus announces phased retirement


Those who know John Searle’s “Chinese Room” critique of the possibility of genuine consciousness in artificial/machine intelligences will enjoy this:

John Searle’s homunculus announces phased retirement

After 54 years of teaching at Berkeley, the man inside John Searle’s head has announced he will be entering a three-year phased retirement after the end of the current semester. The diminutive Zhu Tao made the announcement at a press conference Monday in a rare out-of-costume appearance.

At the conference Zhu said he is retiring from his current position in order to spend more time with Searle’s family. “I have become quite attached to these people,” Zhu said through a translator. “Although, admittedly, not being able to understand a word they say has limited the intimacy of our relationships.”

While he expressed sadness at the end of an era, Zhu looked back with pride at his time inside John Searle’s head. Zhu is popularly credited with sparking the shift away from brain-based cognition. Today that shift continues apace, with figures such as Andy Clark and David Chalmers outsourcing their thinking to call centers in India as part of a growing movement of philosophers who believe cognition can extend beyond the boundaries of one’s skull.

Drosera rotundifolia


Photograph by Dennis Venema.

Photography contest, Honorable Mention.


Drosera rotundifolia – round-leaved sundew, Fort Langley Bog, British Columbia.

Mark Perakh dies


I was very saddened to receive the following a few minutes ago:

It is with great sorrow that Talk Reason announces the death of TR co-founder and major contributor Mark Perakh on May 7, 2013, following a brief illness. He was 88 years old.

Mark Perakh was a professor emeritus of mathematics and statistical mechanics at California State University in Fullerton, CA. Perakh taught physics and wrote some 300 scientific papers. His work in physics focused on superconductivity and his book on thin films was translated into eight languages. He also wrote and published the novel Man in a Wire Cage.

Perakh’s fame particularly comes from writing about science and religion on Talk Reason (a website he helped found) and from his regular contributions to the blog The Panda’s Thumb. He also wrote a book critical of pseudo-science, Unintelligent Design.

His death is a great loss to the scientific blogging community.

Mark also contributed considerably to Why Intelligent Design Fails (which I edited with Taner Edis) and was available any time I needed advice. I will miss him greatly.

Introgression or genetic exchange between crops and their wild relatives is of broad interest due to concern regarding the escape of transgenes from genetically engineered crops. Many fear the potential deleterious effects of such introgression including decreased fitness or diversity of wild relatives and/or the creation of “superweeds” that are resistant to the current arsenal of herbicides. But there is another side to crop-wild gene exchange. A paper published in the open-access journal PLoS Genetics this week reveals that crop-wild introgression is likely a longstanding and potentially beneficial phenomenon in some agroecosystems. Matthew Hufford, Jeffrey Ross-Ibarra and colleagues describe how introgression from wild relatives has shaped the genome of corn, potentially providing essential adaptations as it spread from a narrow center of domestication into novel environments.

Corn was domesticated in the lowlands of southwest Mexico ~10,000 years ago from a wild grass known as teosinte. A few thousand years later corn colonized the high altitudes of the Mexican Central Plateau. There, it came into contact with a different wild teosinte, one presumably well adapted to the new environment. Both corn and teosinte in the highlands have characteristics such as purple pigmentation and hairy stalks and leaves that are believed to help these plants tolerate the lower temperatures and higher ultra-violet radiation of the highlands. For some time, biologists have been stumped as to whether corn and teosinte obtained these highland adaptations independently or through introgression, with some arguing that the shared characteristics were a good example of maize genes escaping into the wild.

The National Center for Science Education announced that its executive director, Eugenie Scott, will retire at the end of the year:

NCSE’s executive director Eugenie C. Scott announced on May 6, 2013, that she was planning to retire by the end of the year, after more than twenty-six years at NCSE’s helm. “It’s a good time to retire, with our new climate change initiative off to a strong start and with the staff energized and excited by the new challenges ahead,” she commented. “The person who replaces me will find a strong staff, a strong set of programs, and a strong board of directors.”

I was going to update a previous post about sperm stem cell transplants in boars, when I came across a very recent paper with a similar technique in the Rhesus monkey, and I couldn’t pass it up. So a little of the background content here is duplicated from that previous post.

Loxodonta africana

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Photograph by Paul Ruggeri.

Photography contest, Honorable Mention.


Loxodonta africana – African elephant. Mud dries on the back of the elephant. The mud in the furrows between the folds remains moist, helping the elephant to keep cool in the heat. The dried mud on the folds helps protect against sunburn.

My old friend, the Alert Reader, sent me a cartoon that he claimed had appeared on Ken Ham’s Facebook page. Captioned “Famous sayings of Ken Ham,” the cartoon shows a caricature of Ham and three balloons, including this one:

It’s designed to do what it does do.

What it does do it does do well.

Doesn’t it?

Yes, it does.

I think it does.

Do you? I do.

Hope you do, too. Do you?

I found it hard to believe that the cartoon was not a parody and wondered why it is found on Ham’s own Facebook page. The Alert Reader responded with the following, also reportedly from Ham’s Facebook page:

Here is a list of the 1000 most commonly used words in the English language.

Check it out. See if you can explain your research in these 1000 words.

My try:

I study how things that are different between men and women change over time.

Please add the description of your research in the comments!

Stephen Dilley’s new book, Darwinian Evolution And Classical Liberalism: Theories in Tension, is now available, at least on Kindle. Chapter 12 is by me; it’s entitled, somehwat dully, “Classical Liberalism And Evolution.” In it, I argue that evolution, far from undercutting the premises of classical liberalism, is at least compatible with them, and, as I think, provides a stronger foundation for them than any variety of creationism. But, as I contend at the outset, it doesn’t much matter, because evolution is true. So if it’s incompatible with libertarianism, then so much the worse for libertarianism.

Chapter 11 is by my friend Shawn Klein; it’s called, somewhat more interestingly, “Volitional Consciousness and Evolution.” Other contributors include Roger Masters and Michael J. White.

I opened my mailbox last week, and what should appear before my wondering eyes, but the new issue of Molecular Biology and Evolution. Inside is our recent (and open access!!) paper: Gene survival and evolution on the human Y chromosome. Here’s my summary of our work. (Editorial Note: it is so, so much easier to distill down research articles that I haven’t spent years of my life on.)

Whale hands


Reposted a portion from here.

While touring the Museum of Vertebrate Zoology at UC Berkeley’s Cal Day, my daughter made a comment that I am so very proud of. We were looking at the fossils of several marine mammals. I was describing the anatomy of the whale, and she interrupted me to point at this part and tell me that it was the “hand”. Yes! What a very clever observation, dear little person! 

Whale “hand” yesterday verified that a “science” test (below the fold) given to 4th graders at a sectarian school is in fact real. Answers in Genesis, meanwhile, vilifies anyone who objects to such nonsense being taught as science, calling them “intolerant atheists” who “viciously attack [a] Christian school.”

World’s first WWW page …


… has been posted here in honor of the twentieth anniversary of the Web.

Thanks to David Young of Free Range Geeks for the tip.

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