Sunday, January 31, 2010

Performance Feedback Revision - a peer-reviewed hip-hop definition of Evolution!

Last year, we enjoyed Baba Brinkman's performance of The Rap Guide to Evolution on our campus when he was in Fresno for the Rogue Festival. His show has gone on to a larger world stage since, as you can see in the above video, from the Hammersmith Apollo in the UK. He was there as a part of Nerdstock: Nine Lessons and Carols for Godless People, which was recently broadcast on television by the BBC! You can watch the whole show on YouTube (if you're outside the UK and therefore not able to use BBC's iPlayer). I thought I should share Performance, Feedback, Revision here for my students since I am going over the basic conceptual framework of evolution in several classes these days - and Brinkman provides a fun restatement of some of the concepts, in rap (and peer-reviewd rap, no less!)! If you haven't done so yet, you really ought to go listen to the whole rap album, available via his website.

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Iron in the oceans and past climate change - @ Valley Café Sci this Monday night!

Central Valley Café Scientifique presents:

The Role of Iron Fertilization and Past Climate Change: Where Does All That Dirt Come From?
Dr. Jennifer Latimer
Indiana State University & Consortium for Ocean Leadership

At Lucy’s Lair on Maple and Behymer
Monday, February 1, 2010, 6:30-8:30 PM

Do join us, if you can, for some fine Ethiopian fare with a hearty helping of marine science!

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Saturday, January 30, 2010

Now that's one fairly odd parent...


Three piglets rests next to their adoptive mother, Sai Mai, an eight-year-old tiger, at the Sriracha Tiger Zoo in Thailand's Chonburi Province

What an incongrously touching image! And I wonder whoever thought of making this happen! What became of the piglet's biological mother? More importantly (in the larger rarity scale of things), what became of the tigress' cubs? She's surely had some recently if she's able to nurse...

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Friday, January 29, 2010

Seminar today: Step-by-step evolution of the vertebrate blood coagulation system

Friday, January 29, 2010

3:00-4:00 PM in Science II, Room 109


Dept. of Chemistry & Biochemistry and Molecular Biology

University of California, San Diego

La Jolla, CA

The availability of whole genome sequences for a variety of vertebrates is making it possible to reconstruct the step-by-step evolution of complex phenomena like blood coagulation, an event that in mammals involves the interplay of more than two dozen genetically encoded factors. Gene inventories for different organisms are revealing when during vertebrate evolution certain factors first made their appearance or, on occasion, disappeared from some lineages. The whole genome sequence databases of two protochordates and seven non-mammalian vertebrates were examined in search of some 20 genes known to be associated with blood clotting in mammals. No genuine orthologs were found in the protochordate genomes (sea squirt and amphioxus). As for vertebrates, although the jawless fish have genes for generating the thrombin-catalyzed conversion of fibrinogen to fibrin, they lack several clotting factors, including two thought to be essential for the activation of thrombin in mammals. Fish in general lack genes for the “contact factor” proteases, the predecessor forms of which make their first appearance in tetrapods. The full complement of factors known to be operating in humans doesn’t occur until pouched marsupials (opossum), at least one key factor still being absent in egg-laying mammals like the platypus.

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Wednesday, January 27, 2010

Genie Scott on Evolution Versus Creationism

This is the second lecture of the course on Darwin's Legacy offered at Stanford in 2008. I posted the first lecture earlier today.

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Darwin's Legacy: introduction to a course from Stanford University

On NCSE's Facebook page this morning I discovered a link to this wonderful series of lectures on Darwin's Legacy put together as a continuing education course by Stanford University in fall 2008. I will post the whole series here, since it has recently become available online. Or you can get a jump start and go to the source: watch the whole thing in YouTube videos like the one above on Academic Earth or download it to your favorite portable device by downloading it from iTunes U.

While we don't have Stanford's resources or reach, as you may know, we are nevertheless also hosting our own modest Evolutionary Biology Lecture Series under the umbrella of the Consortium for Evolutionary Studies at California State University, Fresno this year. And as some of you may remember, we had NCSE's Dr. Eugenie Scott speaking on campus last month; she's also featured as the second talk in the Stanford course. This friday we'll learn about the evolution of the vertebrate blood coagulation system from Dr. Russell Doolittle of UC San Diego. Join us if you can, or come back here for videos/podcasts - I will try to record and post as many as I can.

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NOVA | Darwin's Darkest Hour

While the big cinema treatment of Darwin's great pause in publishing "On the Origin of Species" may never make it down to theatres in our neck of the woods, out here in California's Central Valley (not a big market for stories about Darwin, it seems!), the above version on PBS' Nova was actually quite compelling. Having read some mixed reviews of Creation (although most reviews have been positive), I wonder if this televisual treatment may actually be superior in capturing the remarkable intellectual ferment behind Darwin's work. Rather than the movie's dramatic emphasis (from what I've read) on the emotional drama of Darwin's life after the death of little Annie, this Nova biopic choses to focus more on the intellectual turmoil (without downplaying the emotional turmoil at all), and even has Charles and Emma going back and forth in a very compelling way as he develops his arguments. If you're fortunate to be living in a place where Creation was released in theatres (or have managed to score a copy to view somehow), I'd love to know what you think: how does this compare?

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Tuesday, January 26, 2010

Step-by-Step Evolution of Vertebrate Blood Coagulation


Friday, January 22, 2010

Brain Matters | The Human Spark | PBS Video

The final, and perhaps the most fascinating, part of the series anchored by Alan Alda. Go to the show's website for a lot more information and supporting material.

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Wednesday, January 20, 2010

Memo to my students: I will get it done ASAP!


Sunday, January 17, 2010

Astonishing image of a bird and the recent solar eclipse!


Friday, January 15, 2010

Did the Pier 39 Sea Lions disappear because of 20th anniversary blues?

Perhaps they skipped town because they got wind of a party being thrown to mark the 20th anniversary of their taking over San Francisco's Pier 39. I imagine it could be depressing for these wonderful creatures of the open sea to realize that they've spent almost 20 years hanging out in an urban tourist trap! And not merely hang out, but actually become the bait in that tourist trap... yikes! Surely that's reason enough to hightail it out of there?!

All kidding aside, back on shore, someone over at the Marine Mammal Center has got to be wondering why on earth no one thought of tagging some of these beasts! You know, with one of them GPS transponder things so they could have kept track of them at times like these. Did no one ever think the animals might just take off some day, as abruptly as they had appeared?

Meanwhile, they had to postpone the anniversary party to a later date when, hopefully, the guests of honor will actually deign to be present! I sure hope they do return...

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Thursday, January 14, 2010

Got a creationist in your face about evolution? There's an app for that!

If you ever argue with creationists, you know that the Index to Creationist Claims is an incredibly useful site, as is the book version, The Counter Creationism Handbook. Life just got a little sweeter: it is now available as a smartphone app for the blackberry and iPhone (just get into the App Store and search for 'creationist'). Well, sweeter for us; creationists will find themselves a little more readily refuted now.

Here's an iTunes link to the Creationist Claims Index app, which at 99 cents might just be the thing I should recommend to my students as I begin teaching Intro Bio (Bio 1B) next week. I just hope I don't have to keep turning to it myself too often. I also wonder if this might have helped last year when I had a creationist grad student in my very lab?! I do have and recommend the paperback version, but having it handy one a phone might have helped others in the lab who got into head-scratchingly odd conversations with that student.

Thanks PZ, and the creators of this app!

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So Human, So Chimp | The Human Spark | PBS Video

This is what had our girls riveted to the television last night - something about all the young 'uns (of various primate species) featured in this episode. What is it about young primates (human and non-human) that fascinates us so much?

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Wednesday, January 13, 2010

EclipseWatch: documenting animal behavior oddities during this week's solar eclipse

This Friday (Jan 15, 2010) some parts of the old world will experience a solar eclipse - even an annular one if you are in the right place! Now you may have heard stories of wild animals behaving strangely during eclipses, getting disoriented perhaps, showing unusual movement patterns, or just plain going nuts (heck, we humans probably behave most strangely of all!). A new citizen science project in India (parts of which will see the eclipse) seeks to document instances of such behavioral changes in animals through crowdsourcing! So if you happen to be in the path of the eclipse, and see something intriguing, go to EclipseWatch and share your observation! Here's the deal:

Have you wondered how animals and birds respond during a solar eclipse?

Here is a chance for you to contribute information based on your own observations during the solar eclipse on 15 January 2010! It’s very easy: just sign up using a simple form and map to indicate your intention to participate. Then download a data collection form (available on 14 Jan) with easy instructions, and fill it in with your observations.

EclipseWatch collects information about the flight of crows, kites, pigeons and bats; and the sounds of crows, sparrows, house lizards (geckoes) and dogs before, during, and after the eclipse. Please participate no matter where you are in the country, and no matter what the intensity of the eclipse will be in your area. The idea is to compare the reaction of animals across regions of different coverage of the eclipse.

Anyone can participate, so please join us in this unique India-wide effort to observe the natural world!

And if won't be in the eclipse's shadow, you can still help by spreading the word, so please retweet this / share it via Facebook / email anyone you know living in that region. It'll be cool to generate a good database of anecdotes from which interesting patterns may emerge!

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Hummingbirds: Magic in the Air (full video)

We didn't make it back to Fresno in time to watch this air last Sunday, on PBS' Nature. How wonderful that the entire video is available for viewing online! Enjoy the magic...


Saturday, January 9, 2010

Fast food waste management, a la Burgerville

What every restaurant should (be required to) have!

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Thursday, January 7, 2010

Becoming Us | The Human Spark | PBS Video

And lo - PBS does have it available online (and posterous is nifty again in sucking up the embed code via bookmarklet). Enjoy!

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Alan Alda searches for the Human Spark on PBS, and does it rivetingly

Just watched the first episode, Becoming Us, of this new PBS series tonight (after skipping out on SICB social events as I was too tired after a long day at talks). Even our 9-yr-old (and 4-yr-old - for the most part) was absorbed. Quite an edutaining episode, which I hope PBS shares in full via their website like they do their NOVA shows. If so, I'll share them here. Meanwhile, enjoy these excerpts - and visit the show's website for a lot more information and discussion.

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Tuesday, January 5, 2010

Hummingbirds: Magic in the Air - this Sunday on Nature (PBS)

Now this looks like something worth setting up your DVR to record this sunday: PBS Nature's upcoming episode (premiering Sunday, Jan 10, 2010) on Hummingbirds. Here are a few excerpts of stunning footage that'll wow you:

Hummingbird babies:

Incredible agility - featuring biologist Doug Altshuler (whom we tried to hire in our department at Fresno State a few years ago... when we were still able to hire anyone at all!):

Expert hunters:

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Monday, January 4, 2010

Carnival of Evolution #19 is up... Observations of a Nerd, who kicks off the new year thus:

Well, it's 2010, and it's time for another edition of the Carnival of Evolution! Without further ado...

Go check it out!

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Café Scientifique tonight: Epidemiology of Lung Cancer in the Central Valley

Each year 160,000 Americans die from lung cancer and another 220,000 are diagnosed with the disease. About 85-90% of lung cancer is attributable to cigarette smoking and other tobacco related exposures; however, one in five American adults continue to smoke. Although there has been a decline in smoking during the last several decades, recent national data suggest the decline has leveled off, especially among young adults. In this presentation, the worldwide distribution of lung cancer, state and local patterns of lung cancer will be presented, as well as data on smoking habits and other risk factors for this deadly disease.

For those of you in Fresno tonight - a reminder: the above is the topic for tonight's talk at the Central Valley Café Scientifique by Dr. Paul Mills of the UCSF-Fresno Medical Education Program. And note that we meet at a new venue tonight. Enjoy - even if some of us regulars have to miss it!

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Education for the future and the future of education

I'm preparing for what ay be the biggest teaching challenge of my hitherto untenured professorial career: Biology 1B, or Intro Bio (the diversity and evolution edition), the large lower division undergraduate course which (for pre-meds and other non-bio-majors) may be the only time that many of the students encounter the diversity of life on this planet and the mechanism that produced that diversity - Evolution. Teaching evolution in the San Joaquin Valley of California is a challenge, as I have noted before, but I've only done so at the other end of our majors' core sequence - the upper division Evolution class. Students taking that class have, by that time, generally come to terms with evolution, or at least become good at hiding their trouble with it (and don't ask me which I prefer!). I will now experience what its like to teach the E-subject at the lower division level, especially for many students who won't be taking the course to get a biology degree. Should be fun, eh?

Should I tone it down, perhaps even skirt around the E-word as some in this region suggest, to avoid creating conflicts for some students that may impair their learning? Or should I hammer it in, so that those who object to it are "weeded out" to alternative career choices - and perhaps turned more hostile towards evolution? How about, instead, I try to really light a fire of curiosity in their minds so that more of them actually want to learn evolutionary biology in all its glory? Ah... that last is the ideal I'd like to shoot for, but am also most apprehensive about being able to pull off without falling into the second category: appearing to be hammering it in too strongly! But surely, I have to try to excite them about evolution, don't I? For these students are the future pillars of this state and country, so isn't it my duty as a science professor to make sure they get a proper understanding of and appreciation for science, even if - especially if - it pushes them outside their cultural comfort zones and forces them to acknowledge and push beyond the boundaries of their ignorance? More selfishly - some of these kids will become doctors who may treat me in my old age, while others will sit on school boards that determine what my daughters can learn - or not - in their classroom! How can I forgo my one chance of making sure they have the right scientific foundation?

These would be questions keeping me up even ordinarily, but this year they hold a sharper edge, owing to our current circumstances: Caifornia's higher education system is in crisis along with the state's economy, putting a college degree farther out of reach for many; I teach in the California State University system, which is the worst affected among the triumvirate leading the state's higher education; our campus serves one of the poorest regions in the state (perhaps the country) with a high proportion of "minority" students; and I'm told that bad economic times can make people more cautious and conservative - even fundamentalist if you ask at least one evolutionary biologist who recently argued that the ecologically sound way to address the problem of terrorism is to increase existential security for people (I don't buy that - but will defer that argument to another post to avoid a lengthy detour here). Giving students a sound foundation in science - including evolution - therefore becomes more important than ever if we are to collectively pull ourselves up by our bootstraps.

This Sunday's Los Angeles Times had a couple of thought-provoking articles that are pertinent to this discussion and well worth your while, especially if you live in California. First, Professor William Tierney, director of the Center for Higher Education Policy Analysis at the University of Southern California, calls for a brand new master plan for higher education in California since the old master plan (which put the triad of UC-CSU-Community Colleges in charge of public higher education) is outdated and probably past its use-by date. Many points worth thinking about in the article, but one that particularly resonates with me right now is this:

* High school and higher education must be linked to ensure that when students graduate from high school, they are prepared for college.

Tens of millions of dollars are spent each year bringing more than 50% of Cal State students up to speed in math and English, with often negligible results. That kind of waste could be significantly reduced if high schools and colleges agree on what entering freshmen should know and then work together to bring it about. That means, at a minimum, requiring four years of English and three years of math, including algebra.

High schoolers also should be tested to prove they can do college-level work -- not simply to meet high school requirements. If they can't, corrective steps should be taken in high school to overcome their deficiencies. This demands collaborative relationships between high schools and colleges that don't exist now.

This seems like such a no-brainer to me that I'm surprised its been overlooked thus far. So much of what we find ourselves doing in university these days is remedial education that its not funny! My life would be so much easier if the K-12 system didn't just kick the problem upstairs and "graduate" students lacking in basic skills, especially in critical thinking and other fundamentals of science - not just math and English! How much farther would I be able to take these kids if they only came better prepared... oh I can dream!

Second, Dr. Irving Epstein, HHMI Professor of Chemistry at Brandeis University raises broader questions about the science of science education:

At most universities, freshman chemistry, a class I've taught for nearly 40 years, is the first course students take on the road to a career in the health professions or the biological or physical sciences. It's a tough course, and for many students it's the obstacle that keeps them from majoring in science. This is particularly true for minority students.

My intro bio course is another such obstacle, made acute by the "majority minority" nature of our student body.

In 2005, more than two-thirds of the American scientific workforce was composed of white males. But by 2050, white males will make up less than one-fourth of the population. If the pipeline fails to produce qualified nonwhite scientists, we will, in effect, be competing against the rest of the world with one hand tied behind our backs.

We've been able to survive for the last several decades in large measure because of the "brain drain" -- the fact that the most able students from other countries, particularly China and India, have come here to study science at our best universities and, in many cases, have stayed to become key players in our scientific endeavors.

At many top schools, including my own, international students constitute from 30% to 70% of the doctoral candidates in math, physics and chemistry.

This resonates too, for I am an exemplar of this very "brain drain": a non-white immigrant from India who came to this country for graduate school because I was starving for evolutionary biology back in India!

The situation might be tolerable, if embarrassing, were it not for recent changes in world economies and attitudes toward science and education. As a result of dramatically increased investment by other countries in science, the brain drain is not just slowing, it appears to be changing direction.

International students and post-docs are returning to their home countries in much greater numbers after reaping the benefits of an American education, and many who have worked for years at U.S. companies and universities are being lured home by offers of new labs, easy access to research funding and the comforts of their native culture.

And this last part hits even closer to home, as I too experience greater pressure these days to return home to new institutions of higher learning in India. Many colleagues there (and my own spouse here) wonder (aloud) why I have chosen to remain at an institution such as this one where I teach more classes each semester than they have to during a whole year (or two), where research is a "required hobby" that I have to constantly scrape up time for, and where the student body is such a problematic one. How much longer can I stave off these questions and fight the tide of the reverse brain drain? Interesting to be pondering this even as my tenure file makes its way up my university's hierarchy this year, giving me that shot at existential security: what price such personal existential security against an increasingly insecure future? I guess the answer for me will depend on how California handles this crisis (no good omens thus far) - but in the meantime, I still have to address this challenge: 

We need to ensure that American science draws on all of our population, not just selected, and shrinking, segments of it. But how?

Read the rest of Epstein's article, and Abel Pharmboy's commentary on the same at ScienceBlogs for some potential answers. And if you have a better solution, please do share, won't you? Meanwhile, I better get back to writing that syllabus, and preparing my talk for the SICB meeting which just got underway tonight!

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Sunday, January 3, 2010

An evolutionary retrospective on 2009 from rapper Baba Brinkman

Our favorite evolved rapper, Baba Brinkman, who had us rapt in Fresno last February with his Rap Guide to Evolution, offers his retrospective of the just concluded year when we celebrated Charles Darwin's Bicentennial, and the sesquicentennial of a little book he wrote:


In the final hours of 2009, let us take a moment to reflect on this: up until 150 years ago, no one had the faintest idea why we look like we do, why we act like we do, or where we came from. Now we know, and we have Charles Darwin to thank. Three cheers!

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