Book Review: Supernatural Selection

So far, it’s been about three months since Sci’s dissertation. During that time, she has:
– defended her dissertation
– moved to New Huge City
– started a post-doc(!)
– been sending out paper to beef up her little CV
– been learning large numbers of new, difficult, cool techniques
– been awesome
– completely failed to take a vacation.
Sci has ALSO, during this time, accrued yet another tidy little pile of books for review. In fact, there was a tidy little pile waiting on the doorstep of her new apartment ON THE DAY SHE MOVED IN. Sci was simultaneously excited (presents!) and dismayed (AUGH MORE SCIENCE TO READ) by the gifts. And so it has taken her a little bit of time to get started. I did get through “your brain on food“, but other than that it’s been slow going. And Sci admits that she paused a bit for some fiction on the way (delicious, delicious fantasy fiction. OM NOM NOM), and may pause for a bit more before she keeps going.
Anyway, the latest one the arrive in the mail was Supernatural Selection, by Matt J Rossano. And though it took me a while, due to various factors, Sci’s through it. And here is her review.
Supernatural Selection, by Matt J. Rossano

WHAT…is your favorite color?

Palmer and Schloss. “An ecological valence theory of human color preference” PNAS, 2010.
Sci will admit that she didn’t really know all that much about color preference theory until she read this paper. And that until she read this paper…she thought a lot of it was silly.
Also, she doesn’t have a favorite color. That might have something to do with it. Can someone have a favorite color palette instead?
Anyway, let’s talk color preference theory.

Book Review: The Tangled Bank

A few months ago, Sci had a secret shame. A secret, secret shame. For Sci is a science blogger, and blogs on Scienceblogs and…
…didn’t know ANYTHING about evolution.
Ok, perhaps that wasn’t exactly true. But Sci’s a physiologist, not an evolutionary biologist. I studied neuroanatomy, not HOW that neuroanatomy evolved. In my day to day life, I could care less how it GOT that way, what I’m concerned with is what goes wrong with it, and how I can go about fixing the problems to improve the lives of people. Let’s just say they don’t force us grad students to take classes in evolution, and while the basic ideas were covered in Bio 101, I hadn’t had much exposure to them since. It’s not that I don’t WANT to know about evolution. But if you’re going to give me a choice between, say, a book by Stephen Jay Gould and a book by Oliver Sacks, well…
And Sci’s always been a little ashamed of herself over this. I mean, I’m a SCIENTIST! Evolution is one of those things I’m…supposed to know about. For cocktail parties (cause, y’know, grad students go to a LOT of cocktail parties). Like stem cells and vaccines, there are things that people who aren’t scientists just kind of expect scientists to be versed in, or at least to have a relatively well-founded opinion on. Sci hates to disappoint.
And so, when, in the deep, dark night of a relatively early Wednesday morning before her first cup of coffee, Sci expressed her shame to Laelaps, Brian immediately had a solution. “Carl Zimmer just wrote a book on it!” quoth Brian, “you should ask to review a copy!”
Hmmm…learning about evolution (check). Learning about it from a blogger I totally respect (check! His tattoo gallery is wicked!). Free book (BONUS!).
I emailed Carl. I was TOTALLY TOTALLY thrilled when I realized he had actually HEARD OF ME!!! *squee!*
And a few days later, I got a TOME in the mail. A tome of SCIENCE!!!

(DUDE! Is that Tiktallik on the cover!? SWEET!)

The Tangled Bank: an Introduction to Evolution by Carl Zimmer.
Unfortunately, Sci got a galley copy of the book. For those unfamiliar with the publishing world, that means a GIGANTIC PILE of xeroxed pages, as yet unbound. I ended up being very sad about this, which I will get into. SciCat, on the other hand, approves of the galley copy, and is in favor of all books being in this format. She’s sitting on it now.

Alliance for Science Announces Winners of National High School Essay Contest

FOR IMMEDIATE RELEASE
Mary Detweiler,
The Alliance for Science
info@allianceforscience.org
Falls Church, VA — May 17, 2008. The non-profit Alliance for Science announced the results this week of its second annual National High School Essay Contest. Students were asked to write a 1,000 word essay on either “Agriculture and Evolution” or “Climate and Evolution”. Neal Desai, a 10th grader at the Pembroke Hill School in Kansas City, Missouri won the top prize. Neal’s insightful essay addressed the tradeoffs between the benefits obtained from genetically modified crops and the potential risks. For example, he noted the benefits of “Golden rice”, which produces beta-carotene which our bodies convert into vitamin A. “In my trips to foreign countries, I have personally seen the form of blindness and weakened immune system described as symptoms of vitamin A deficiency,” he wrote. But he also acknowledged that the money spent on bioengineering might have been better spent distributing vitamin A capsules to those in need. The essay also voiced concerns about developments in sterile-seed technology, which requires farmers to buy fresh seed from the manufacturer every year, and could adversely affect biodiversity if the trait were to escape into the wild.
Second place winner Frances Ellerbe of Columbia, South Carolina, addressed the issue of whether natural evolutionary adaptation could keep pace with rapid climate change. She noted that in the case of the American Beech, it could not, owing to the narrow climate band in which it grows, the slow migration rate, and the fact that this species takes 40 years to produce seeds.
Third place winner David Martorana of Honolulu, Hawaii, gave his personal account of receding beaches and shrinking coral reefs, both linked to global warming. He noted the grave impact on commercial agriculture and the fishing industry that could result from rapid climate change.
Fourth place winner Marleigh Higgins of Brookline, Massachusetts, provided a personal viewpoint that came from a summer spent on a tree nursery in rural Madagascar. She observed how the traditional slash-and-burn agriculture, called Tavy, was leading to rapid deforestation and the destruction of habitats. She lamented the rapid loss of biodiversity, particularly given that scientists have recently learned of the potential medical use of native plant species.
The Alliance for Science awarded a total of $1,000 dollars in cash prizes, with a top prize of $300 going to the top student. The sponsoring teachers received an assortment of books, DVDs, and educational software. These included author-signed works provided by Brown University biology professor Dr. Kenneth Miller, a textbook author who gave expert testimony critical of intelligent design at the 2005 Kitzmiller, et al vs. Dover Area School District trial.
The Alliance’s contest director Dick Lessard said “We were impressed by how seriously the top students took this contest. They probed beyond the obvious and their essays reflected a genuine appreciation for how a detailed understanding of science can help inform public policy debates”.
Full text of the winning essays can be found at the Alliance’s website, http://www.allianceforscience.org/essay. The website also describes plans for the 2009 essay contest, designed to coincide with the 200th anniversary of the birth of British naturalist Charles Darwin. The essay theme is titled “In Darwin’s Footsteps”, and asks students to write an essay about a modern-day scientist or group of scientists whose work exhibits the same qualities and virtues as Darwin demonstrated during his career.
The mission of the Alliance for Science is to heighten public understanding and support for science and to preserve the distinctions between science and religion in the public sphere.
###

For more information, please visit The Alliance for Science. From there you can find out more details about the winning essays, download the press release, learn about next year’s topic, and how to donate to the prize fund.

Convergent evolution of a gene that blocks HIV in monkeys

Here we have yet another example of evolution cobbling together new proteins from existing structures. And what do you know, it kinda matters:

The TRIM5-CypA gene found in Asian macaques is a hybrid of two existing proteins, TRIM5 and CypA. This combination creates a single protein that blocks infections by lentiviruses.
This is the second time a TRIM5-CypA hybrid gene has been identified in monkeys. The other one — TRIMCyp — was found in South American owl monkeys in 2004. But it’s not likely that these two gene combinations arose from a single common ancestor, the Harvard researchers said.

Didn’t arise from a single common ancestor? But how can we know that? Only if the gene isn’t present in other Old World monkeys or other New World monkeys.

TRIM5-CypA wasn’t found in monkey closely related to the Asian macaques and TRIMCyp wasn’t found in any other South American primate species. This suggests that the two combination genes evolved separately, once in the macaques and once in the owl monkeys.

Ooops.
That’s pretty telling. These two populations of primate are separated by many millions of years of evolutionary processes. Likely this mutation is fixed in both species because it provides some sort of evolutionary advantage outside of HIV infections. It will be interesting to see what that might advantage might be.
I’d like to see the full paper, but PLoS Pathology is down for maintenance right now. Oh well. In the meantime, we’ll all just reflect on how useless Intelligent Design is.

Darwin Day redux and link to Massimo Pigliucci interview

They put on a fantastic Darwin Day celebration in Iowa City. Excellent camaraderie, good times good people good beer and whatnot, and the turnout for all the events was exceptional.
Massimo Pigliucci gave a nice interview for the local NPR station which you can find here.

Darwin Day with evolutionary biologist
Massimo Pigliucci
In an event co-sponsored the University of Iowa Department of Biological Sciences to celebrate Darwin Day in Iowa City featuring renowned evolutionary biologist, philosopher, and professor at SUNY Stonybrook, Dr Massimo Pigliucci. His book Denying Evolution has been praised for its clear and wise advocacy of the Darwinian view of life.

Just scroll down to the archives. The direct link is here. Massimo’s a really great, good-natured guy, and if you get a chance you should check out his blog.

Nice Evolution Primer Site

If you’re looking for a website that gives a nice intro to the nature of science and evolution, but doesn’t use lots of jargon, you should check out This View of Life. From the About page:

The aim of this project is to present the topic of evolution in a scientifically accurate manner that avoids technical language, but that also avoids potentially misleading colloquial language. It strives to be accessible to the non-scientist and so it represents a general outline, merely scratching the surface of the large body of research in the many facets of this topic. For more detailed information, see the references.
As an instructor for a college freshman-level biology course, I became aware that the theory of evolution is widely misunderstood by the general public. As many have noted, this is not because the theory is a conceptually difficult one. Indeed, it would be difficult to find a simpler one with such broad explanatory power. However, researchers often use highly technical language that is lost on many readers. In addition, in attempting to explain how evolution works, scientists and journalists alike often use colloquial language that can be misread as asserting (for example) that evolution is under the conscious control of individuals, that individuals can evolve, that evolution is goal-oriented, or that it results in perfection. This, coupled with deliberate attempts at obfuscation by anti-evolution groups using popular media, has created much confusion and even disdain for this extremely well-supported explanation of biological diversity.

The site is organized into sections dealing with genes and heredity, the mechanisms of evo, the evidences for evo, and also a nice focus on ecology and energetics to explain niches and why no “ultimate species” evolves. The author does a really nice job of creating an accessible package. There’s not a lot of tangential information to confuse the reader, the site is simply and pleasantly designed, lay examples are given, and the distraction of the creation/evolution “argument” is left for other sites to deal with. We’re left with a tidy discussion of what science is and how it works, and where evolution fits within that framework. If you don’t know where to start and are intimidated by larger information warehouses like TalkOrigins, start with This View of Life instead.

Nice Evolution Primer Site

If you’re looking for a website that gives a nice intro to the nature of science and evolution, but doesn’t use lots of jargon, you should check out This View of Life. From the About page:

The aim of this project is to present the topic of evolution in a scientifically accurate manner that avoids technical language, but that also avoids potentially misleading colloquial language. It strives to be accessible to the non-scientist and so it represents a general outline, merely scratching the surface of the large body of research in the many facets of this topic. For more detailed information, see the references.
As an instructor for a college freshman-level biology course, I became aware that the theory of evolution is widely misunderstood by the general public. As many have noted, this is not because the theory is a conceptually difficult one. Indeed, it would be difficult to find a simpler one with such broad explanatory power. However, researchers often use highly technical language that is lost on many readers. In addition, in attempting to explain how evolution works, scientists and journalists alike often use colloquial language that can be misread as asserting (for example) that evolution is under the conscious control of individuals, that individuals can evolve, that evolution is goal-oriented, or that it results in perfection. This, coupled with deliberate attempts at obfuscation by anti-evolution groups using popular media, has created much confusion and even disdain for this extremely well-supported explanation of biological diversity.

The site is organized into sections dealing with genes and heredity, the mechanisms of evo, the evidences for evo, and also a nice focus on ecology and energetics to explain niches and why no “ultimate species” evolves. The author does a really nice job of creating an accessible package. There’s not a lot of tangential information to confuse the reader, the site is simply and pleasantly designed, lay examples are given, and the distraction of the creation/evolution “argument” is left for other sites to deal with. We’re left with a tidy discussion of what science is and how it works, and where evolution fits within that framework. If you don’t know where to start and are intimidated by larger information warehouses like TalkOrigins, start with This View of Life instead.

The 2nd Annual Alliance for Science Essay Contest

Those crazy folks over at the Alliance for Science are putting up the notice for their 2nd Annual Evolution Essay contest!!! The first contest, while thrown together at the very last minute, turned out to be a success. Five high school students received cash prizes and a slew of autographed science books, plus a year’s subscription to Seed Magazine. The first place winner’s science teacher also received a cash prize to spend on classroom supplies, and additional teaching materials.
This year, they’re getting a jump on things early. The contest doesn’t happen until February, but start thinking about your essay now. Tell your teachers so they can get their classrooms involved. This year’s topics are rather timely: Climate, Agriculture, and Evolution.
The Alliance is also looking for a little help on the judging side of things, so please contact them if you’re interested. And as always, if you wish to donate a copy of a book or contribute financially to the prizes, all donations are tax-deductible.

BREAKING: Christian University Censors Science!!!!!

Ha ha, fooled you!
The Discovery Institute has just issued this on their blog, the inaccurately named Evolution News and Views:

According to CSC senior fellow and leading ID theorist William Dembski, what follows is:

“[A] big story, perhaps the biggest story yet of academic suppression relating to ID. Robert Marks is a world-class expert in the field of evolutionary computing, and yet the Baylor administration, without any consideration of the actual content of Marks’s work at the Evolutionary Informatics Lab, decided to shut it down simply because there were anonymous complaints linking the lab to intelligent design.”

Read on if you care at all about academic freedom and protecting the right of scientists to freedom of scientific inquiry.

So Dembski takes a step down in status, returning to the place that canned him once already. He comes crawling back as a postdoc, and is somehow surprised when the University doesn’t want to see him around anymore? Shocking. Who does that??? When you’re a professor and you want to do research, you do it in your lab. If you can’t do it in your lab, you go on sabbatical so you can bring it to your lab someday. Then you get grants to fund said work in your lab. If your institution won’t support said work, you find one that will hire you. But stepping back into a postdoc is like going back to trade school for something you’re already certified to do. And there but for the grace of God go I.
Is this really about academic freedom, or is it about the University not wanting to deal with some flunky they already pink-slipped? Because if it’s the former, the DI is basically admitting that even devoutly Christian schools, like the esteemed Baylor University, don’t find Intelligent Design stealth creationism to be very compelling. Methinks if the DI’s strategy is actually to win people over, throwing the egomaniacal Dembski under the bus on this one might be a better option.
I mean really. Can you say “I’m hell bent on using you for the affiliation” any more clearly?