Wednesday, May 27, 2009

A new online collaborative learning space, and a scholarship opportunity

Via email from the Nature Publishing Group I just got word of a new online resource they've developed to help students learn genetics, and perhaps for teachers to teach the subject as well. Scitable is the NPG's new collaborative learning space for science, bringing together a library of scientific overviews with a worldwide community of scientists, researchers, teachers, and students. What's more, Scitable is even (for the moment, I hope forever) free! The first topic area with substantial content now online there is Genetics. Given how much time I spend on population genetics in my Evolution class, this promises to be a good resource for students needing a refresher to keep up with the class. And perhaps my colleagues teaching Genetics will find it useful as well.


And for students checking it out right now, there is also a scholarship being offered:



As a way of introducing students to Scitable, we are running a "Portrait of My DNA" contest that allows students to compete for one of three scholarships. ...



If the first place student is referred by you, your department will receive an additional scholarship of equal value to give to the student of your choice. You can learn more about the contest at http://www.nature.com/scitable/study-center.



So students, if you are still reading this blog even though the semester is over (for you anyway, although I'm still grading!), check the website out, and throw your hat in for the scholarship.



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Friday, May 8, 2009

Scifri Videos: Hobbit Bones Hold Clues To Its Origin


[via Scifri Videos: Hobbit Bones Hold Clues To Its Origin]


There is also a NYT story about this, based on several paper out in Nature yesterday reporting the first detailed analyses of this hominid's foot bones. Here's an excerpt from the Nature News&Views article:


Fossils of tiny ancient humans, found on the island of Flores, have provoked much debate and speculation. Evidence that they are a real species comes from analyses of the foot and also — more surprisingly — of dwarf hippos.


Good science requires a healthy dose of tempered scepticism — at its heart, the process involves trying to reject proposed hypotheses. So it was understandable that the announcement (1, 2) in 2004 of the discovery of a species of dwarfed hominin, Homo floresiensis, from the island of Flores, Indonesia, stimulated a range of opinions, many of them sceptical, that the fossils constituted a new species and were not the consequence of some pathological condition.


Two papers in this issue, by Jungers and colleagues3 and by Weston and Lister4, together with contributions to a special online issue of the Journal of Human Evolution, will go a long way towards addressing the sceptics' concerns. The studies provide considerable evidence — literally from head to toe — that H. floresiensis is a true species of hominin (that is, a species more closely related to humans than to chimpanzees and other apes). More importantly, the analyses prompt hypotheses about the human family tree that will require more fossil evidence to test.


I'll have more on this after class, once I've got my hands on the actual papers!


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Thursday, May 7, 2009

Your term papers better not have cited papers from these "journals" from Elsevier!

I expect it is unlikely that any of the evolution term papers just turned in may have cited from these "biomedical journals" published by Elsevier - but this breaking scandal in the world of scientific publishing highlights the need for good critical evaluation and thinking skills so you can separate the scientific wheat from the drug companies' (and other vested interests') chaff. If you haven't heard about this scandal, it started with the discovery that the big pharma company Merck had paid Elsevier to publish fake journals made to look like they were peer-reviewed! (quick, how many of their journals have you read/cited in the recent past?) Now it turns out, they published at least SIX such "journals":



Scientific publishing giant Elsevier put out a total of six publications between 2000 and 2005 that were sponsored by unnamed pharmaceutical companies and looked like peer reviewed medical journals, but did not disclose sponsorship, the company has admitted.



Elsevier is conducting an "internal review" of its publishing practices after allegations came to light that the company produced a pharmaceutical company-funded publication in the early 2000s without disclosing that the "journal" was corporate sponsored.



The allegations involve the Australasian Journal of Bone and Joint Medicine, a publication paid for by pharmaceutical company Merck that amounted to a compendium of reprinted scientific articles and one-source reviews, most of which presented data favorable to Merck's products. The Scientist obtained two 2003 issues of the journal -- which bore the imprint of Elsevier's Excerpta Medica -- neither of which carried a statement obviating Merck's sponsorship of the publication.

[via Elsevier published 6 fake journals :The Scientist [7th May 2009]]

If some of our students already had trouble telling if a particular journal is peer-reviewed - Elsevier just made it harder. And while students citing something from one of these fake journals for a term paper may not seem like such a big deal, the real problem here is, of course, the intended target readership for these "journals": doctors and other practitioners in the biomedical fields! How much time does your doctor have to look behind the curtain of such publications to decide if a paper about some drug trial is trustworthy? Do medical (and related professional) schools emphasize critical thinking skills enough to safeguard against such fraud? (I have some doubts about that given how many doctors are creationists - but that's another story).


What's even more unfortunate is that this scandal is breaking at a time when the anti-vaccination movement seems to be reaching a peak in the US (and increasing the casualty count of children around the world) - with Oprah jumping on that anti-science bandwagon last week! These purveyors of anti-science woo would probably eat up a story like this as further evidence that all of science is untrustworthy and how you cannot believe anything they say in any scientific journals! Why, oh why did Elsevier have to go and muddy the bathwater so much more when there's already a growing mob straining to tip over the tub, and toss out the baby (science) as well?!



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Wednesday, May 6, 2009

What does Open-mindedness really mean?

Many of us scientists are often accused of not being "open-minded" about a variety of "explanations" that others have come up with for a range of phenomena, real and imagined: from creationism to intelligent design, homeopathy to anti-vaccinationism, astrology to psychic phenomena... the list goes on! Its a real stumper, this accusation, because how can we be conducting science at all if our minds are closed to alternative hypotheses? It is more often the case that the accusers, whether purveyors of woo or merely gullible to it, haven't really thought through this notion of open-mindedness. This video should help clarify what it actually means, and why some of us practicing scientists are likely to dismiss some of these "alternatives" rather readily!

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Adaptationist hypotheses are sexy, but don't forget the null hypothesis!

Just because a trait exists, or some process happens, and I can come up with an adaptationist just-so-story to explain its significance, doesn't necessarily mean that that trait or process actually has any functional, adaptive significance! That old lesson, hammered into behavioral ecologists like me by Gould and Lewontin's classic paper from 30 years ago, it seems, must be learned all over again by a new generation of genomic biologists! So argues Michael White in this must-read essay on the fascinating phenomenon of Genomic Junk and Transcriptional Noise:



With hot, new technologies, biologists are taking higher-resolution snapshots of what's going on inside the cell, but the results are stirring up controversy. One of the most interesting recent discoveries is that transcription is everywhere: DNA is transcribed into RNA all over the genome, even DNA that has long been thought to have a non-functional role. What is all of this transcription for? Does the 'dark matter' of the genome have some cryptic, undiscovered function?



Unfortunately, in all of the excitement over possible new functions, many biologists have forgotten how to frame a null hypothesis - the default scenario that you expect to see if there is no function to this transcribed DNA. As a result, the literature is teeming with wild, implausible speculation about how our excess DNA might be beneficial to us.



So here, let's step back and look at what we expect from DNA when it's playing absolutely no functional role; in other words, let's look at the null hypothesis of genomic junk and transcriptional noise. We can then take our null hypothesis and use it to look at a fascinating new study of how genomic parasites sculpt transcription in our cells.



There is no such thing as inert DNA

What bothers me most about the recent hullaballoo over pervasive transcription is the tacit assumption that non-functional DNA has to be inert. This is a terrible assumption from both a biochemical and an evolutionary viewpoint. We have every reason to expect non-functional DNA to be noisy.

...

[via Genomic Junk and Transcriptional Noise]

Now, I don't know a whole lot about what goes on inside cells and the intricacies of DNA transcription - so it is still news to me that there is so much more transcription going on than is actually "needed", a whole lot of transcriptional noise from non-coding regions of our genomes! But, as White argues so well, just because this non-coding DNA is getting transcribed doesn't mean it is no longer "junk" - all this transcription may simply be a result of basic biochemistry. Throw together a whole bunch of DNA and RNA polymerases, within the confined quarters of, say, a typical mammalian cell, and some of this stuff is bound to happen. So my genome-studying friends - excited as you are about the huge volumes of data you are drowning in and all these new discoveries, pause a moment to reflect on what it all means, and stop seeing function everywhere. Remember the NULL hypothesis, which, in this case, predicts transcriptional noise to occur all the time.



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Just little bit of G, T, C, A ...

An ass-shaking jam, indeed, from Bio-Rad, courtesy of Dr. Isis the Scientist!

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Tuesday, May 5, 2009

Hmm... you want a study guide for the final exams?

Any questions?


song chart memes


see more Funny Graphs


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Monday, May 4, 2009

The forensics of investigating meth labs at tonight's Café Scientifique!

Tonight we — i.e., the Central Valley Café Scientifique — present what appears to be (barring some last minute surprise) the final talk of the academic year - on methamphetamine labs. Before we go on our summer hiatus, Dr. Eric Person, my colleague in the Chemistry Department here who had law enforcement experience up in the Washington area prior to joining academia, will tell us about the forensics of pursuing meth labs in answering the question "Why is it so hard to buy Sudafed?". The Café will be at the usual time (6:30-8:30 PM) and place (Lucy's Lair), and you can get all the details, including map and directions, at our website.



And no, we did not deliberately time this talk about meth labs just days before finals week!!

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Sunday, May 3, 2009

The Life and Times of Australopithecus - a colloquium @CSUF this Monday

As the semester winds down, we have a special treat on campus this Monday, when the Biology colloquium series winds down for the semester with a lecture by paleoanthropologist Dr. Kaye Reed, of the Institute of Human Origin at Arizona State University, on "The Life and Times of Australopithecus" . This lecture is co-sponsored by the Tri-Beta Biological Honors Society and the Consortium for Evolutionary Studies at CSU-Fresno, and is part of our ongoing series celebrating Darwin Bicentennial year. Dr. Reed has been working in Ethiopia and other parts of Africa, places where some of the most important and exciting hominin fossils (such as the famous Australopithecine, Lucy seen in the reconstructed portrait here) have been discovered. Her specialization is paleoecology with a focus on reconstructing the ecological communities within which our own lineage evolved. So it should be a very exciting lecture - I hope to see you there (especially if you are taking one of my classes!)!


Spatiotemporal coordinates: Monday, May 4, 2009 @3:00PM in Room 109 of Science II building, CSU-Fresno (of course!).


Website for additional details: Darwin's Bulldogs.


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A perfect storm for viruses

According to Nathan Wolfe, a virus hunter interviewed last week in another TED Q&A, "We've created a perfect storm for viruses". An excerpt:


SARS, avian flu, swine flu ... what's going on here? Why are we suddenly seeing so many more outbreaks of viruses from animals?


Viruses have always passed from humans to animals. In fact, the vast majority of human diseases have animal origins. But the human population is different from what it once was. For most of our history, we lived in geographically disparate populations. So viruses could enter from animals into humans, spread locally and go extinct. But the human population has gone through a connectivity explosion. All humans on the planet are now connected to each other spatially and temporally in a way that's unprecedented in the history of vertebrate biology. Humans -- as well as our domestic animals and wild animals we trade -- move around the planet at biological warp speed. This provides new opportunities for viruses that would have gone extinct locally to have the population density fuel they need to establish themselves and spread globally.


We've created a "perfect storm" for viruses. And we'll continue to see -- as we have in the past few years -- a whole range of new animal diseases as outbreaks in human populations. But we have to stop being surprised by them. Right now, global public health is like cardiology in the '50s -- just waiting for the heart attack, without understanding why they occur or the many ways to monitor for them, detect them early and ultimately prevent them. Swine flu is not an anomaly. We know that swine flu -- like the vast majority of new outbreaks -- comes from animals. We should be monitoring those animals and the humans that come into contact with them, so we can catch these viruses early, before they infect major cities and spread throughout the world.


And here's Wolfe's TED talk:



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