Thursday, March 27, 2008

In other news...

If only things were the other way around...







glumbert - Gay scientists isolate Christian gene

[Hat-tip: Onegoodmove]


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No one was being expelled here...

... even though corrupting young minds like this should be a punishable offense, not a profitable business venture! Yes, BC Tours is a real business, which, apart from conducting these tours, also sells videos and more at their website.

A question to my students (esp. those who were asking me recently about my views on religion and science): what would you do if one of these kids showed up in your class? I wouldn't be surprised if there are people here on our campus who have been subjected to such a tour - and I am really curious what they think. Of course, the guide here has a very particular notion of how children should learn to think, doesn't he? Always ask "how do you know" - which is great thing for science students to learn - but then completely dismiss any real scientific explanation because it strays from a literal interpretation of a self-contradictory 2000 year-old collection of stories! What a recipe for life-long learning! One part that really got my goat was where the smarmy guide goes "now fossils are usually rather boring because they are piles of dead things"!! What a horrible way to close off a child's mind to the true wonders of the real world!


Several years ago when we visited the American Museum of Natural History, our (then) kindergardener daughter couldn't get enough of fossils after spending 3 entire days wandering among the exhibits, much of it in the Darwin exhibit. So fascinated and thrilled was she by all of it that she's been a fossil nut ever since - to the extent of demanding a fossil-themed birthday party last year (we obliged, and her friends had a lot of fun digging up and taking home real fossils as party favors)! Tell me - shouldn't I do everything I can to keep her away from these pious charlatans?


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A beginner's guide to making a phylogenetic tree

By courtesy of Sandra Porter's blog Discovering Biology in a Digital World comes this neat beginner's guide to making a phylogenetic tree. Here's the video:



A beginner's guide to making a phylogenetic tree from Sandra Porter on Vimeo.

Go to the original post for a brief description.


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Monday, March 24, 2008

On being expelled from Expelled

Richard Dawkins and PZ Myers set the record straight on how the latter got expelled from Expelled!!

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Sunday, March 23, 2008

'Lying for Jesus?' - Richard Dawkins on getting expelled from Expelled

Much of the internets (at least the reality-based, rational, irony-rich segments) have been rolling with laughter over the kerfuffle on good friday in Minneapolis when PZ Myers was expelled from the audience of the IDiotic documentary Expelled despite being featured - and thanked - in the film itself, and even as his companion Richard Dawkins, Darwin's rottweiler, was allowed in. You have probably caught the story somewhere by now for even the New York Times picked it up. Now we have Dawkins' own account of the incident as well as a trenchant critique of the film itself. Not to be missed!


I have to say that, once I'd picked myself up from the floor after all that ROFL-ing friday night upon reading PZ's comic account, I was inclined to chuckle and move on. Until, that is, a couple of Pharyngula's sciblings (fellow scienceblogs writers) started trying to throw PZ and Dawkins under the bus over this silly business! While I am not surprised that those master "framers" of science, Matt Nisbet and Chris Mooney are upset at these two atheist gadflies kicking up such a ruckus without even actually misbehaving - I am puzzled that they want PZ and Dawkins to shut up even in the face of such blatant (if incompetent) targeting by the ID goons! Surely, at least in this incident, N&B ought to be telling their religious friends that they shouldn't be overreacting to mild-mannered atheists (who, in this case, had bent over backward in consenting to be interviewed under false pretenses by the producers of this film), rather than trying to shove the atheists into a closet?


I therefore have to now share the following videos with you. Watch and tell me - how threatened are you by these two science geeks?



And this, from their interviews in the film itself, where they were apparently so rude, as spun through the IDiot perspective:



So I have to ask, once again, why can't these master framers try to actually "frame" atheists like Dawkins and PZ in better humanistic light to their religious pals? Why not tell the religious that they really have little to fear from these atheists, other than gaining some sound scientific knowledge, and even getting an occasional guffaw out of their irreverent wit, rather than tell scientists to shut up for fear of offending the pious? And how much duller our lives would be if people like Dawkins and PZ shut up?


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Evolution: Education and Outreach - a new journal

This new journal, just launched this year by the National Evolutionary Synthesis Center, the UC Berkeley Museum of Paleontology, and Global Education Outreach, should be a good source of review articles on evolutionary topics. Here's a description:

Evolution: Education and Outreach promotes accurate understanding and comprehensive teaching of evolutionary theory for a wide audience. Targeting K-16 students, teachers and scientists alike, the journal presents articles to aid members of these communities in the teaching of evolutionary theory.

The journal addresses the question of why we should care about evolution by exploring the practical applications of evolutionary principles in daily life and the impact of evolutionary theory on culture and society throughout history.

Evolution: Education and Outreach connects teachers with scientists by adapting cutting-edge, peer reviewed articles for classroom use on varied instructional levels. Teachers and scientists will collaborate on multi-authored papers and offer teaching tools such as unit and lesson plans and classroom activities, as well as additional online content such as podcasts and powerpoint presentations.

[From SpringerLink - Journal]

It is edited by a powerful father-and-son team: Dr. Niles Eldredge, Curator of the Division of Paleontology at the American Museum of Natural History, and George Eldredge, Special Education teacher at the John F. Kennedy High School in the Bronx, New York. And the best thing is - the journal is freely accessible online (at least for now)! So check it out - and don't be surprised if you find me using papers from here for some extra reading once in a while.

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Friday, March 21, 2008

Friday photo: ponder the evolutionary ecology of this job...

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Seems somehow apropos towards the end of spring break week, no?


(Click on image for larger version - captured at McKenzie Preserve; © Madhusudan Katti, 2007)



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Thursday, March 20, 2008

Funniest story I've read in a while from the frontiers of creationism...

Two atheist evolutionists (and I mean two of the biggest gadflies) walk into a movie theater for a preview screening of a film about how "smart" creationist ideas are "expelled" from public school science classrooms run by the "neo-Darwinist" establishment. One of the gadflies is recognized as a local pillar of said "establishment", and - you guessed it - expelled from the theater by some uniformed men at the behest of the film's producer. He leaves, struggling only to control his giggles, and rushes to the nearest internet portal to blog the incident. For the producers appear blissfully unaware who the other gadfly is whom they have let in along with a number of acolytes... read the story to find out who it is!

Made my evening... :-))



(and if any of you students don't know who the main characters in this story are, you better go spend some serious time here and, especially, here!)

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Wednesday, March 19, 2008

Is stem cell therapy ok if it comes from the East?

Here's something to ponder in the wake of Jason Bush's talk, as we await the next lecture (on April 23rd) in the Ethics Center Seminar series where theologian Ted Peters (author of The Stem Cell Debate) will take up some of the more sticky moral controversies that Jason punted on last week! While a lot of the opposition to stem cell research in the US comes from the religious right, especially over the issue of embryonic stem cell research, there is opposition from the left as well - especially the "alternative medicine" left which sees everything in western medicine as being somehow tainted and unnatural. And then, by (illogical) extension, that any other "alternative" to western medicine is therefore much better for you, even if practitioners of said alternative don't have a clue about how their medicine works, if it works at all! But what if "eastern" medicine starts offering therapies based on stem cell research (and other products of "western" science)? And start doing so when such therapies are not available here in the west? Skeptico raises this question in an interesting commentary on an NPR story about how some Americans are heading to China seeking stem cell therapies not available in the US. In addition to the welcome and enjoyable bashing of irrational "skeptics" like Bill Maher, Skeptico makes this important point:



The truth is, ancient people, who did not understand how the body works or what really made people ill, just made stuff up about these things. The ancient Chinese made up stuff about meridians and chi. Ancient Indians made up stuff about chakras. Ancient Europeans made up stuff about humors. We now know better, and so have abandoned humors and bloodletting. The only mystery is why people still insist that chi and chakras are real. But whatever you believe is real, the distinction clearly is not between “western” and “eastern” (fill in your preferred country) therapies. The distinction is between therapies that work and those that don’t. Scientists in China are researching real medicine, and trying to find out what works and what doesn’t, just like scientists in the west. Maybe some have oversold their results, but scientific procedures, not ancient myth, will ultimately decide what works and what doesn’t.


So can we now please abandon this pretence that doctors in the west practice something called “western medicine”, while the Chinese have access to some secret knowledge that “western science” still hasn’t yet caught up with? There is only medicine that works – or at least, is backed by reliable evidence that it does – and pre-scientific superstitious quackery that doesn’t. The East/West labels mean nothing. And the next time some twit like Maher intones gravely against “western medicine”, just say, “yeah, I don’t fancy bloodletting either” - and advise him to go visit Doctor Hu in Hangzhou. Preferably on a one-way ticket.



I've always thought that the main criterion in medicine is whether it works. Even if we don't fully understand underlying mechanisms! Any good medicine should aim to cure the afflicted, without getting caught up in its own dogmas about how the human body is supposed to work. Figuring out the "how" and "why" of any successful medicine - well that's the job of science. That's why you can have many "alternative" medicines, but only one science - for there is no western or eastern science once we understand how any particular disease and its cure works, is there? And on the flip side (and this may raise some of your hackles), that's why medicine (even in the west) isn't always necessarily a science either!


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Monday, March 17, 2008

Algorithmic Ants


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(photo taken by Madhu Katti @ McKenzie Preserve near Fresno, California)

An interesting interview in Edge that you can also watch on video. Here's an excerpt that should tantalize:



A fundamental question in biology is how the functioning of collective systems works—whether you are dealing with the function of a tissue and how the cells within a tissue interact, or whether you're dealing with ecologies or even ecosystems. We really need to build a new understanding and new tools that allow us to integrate across these scales. People refer to top-down and bottom-up; in some sense we have to take both approaches to try to understand these systems.



There is no characteristic scale that is the right scale to observe a system—one of the reasons I studied animal groups is that the systems can be taken apart and put together very easily. Some of the models and the understanding that we get from how these groups function—we are all familiar with the dramatic collective patterns exhibited by schools of fish or flocks of birds—and the way we can take these systems—like an ant colony—apart to see how they really function gives us deep insights.



So one line of research is to do specific testable ideas on specific systems. But another line of research is to try to find the fundamental principles that underlie, for example, collective decision-making in biological systems. And what we find remarkable is, when we actually look at the algorithms used by, say, an ant colony, or used by a school of fish, when making collective decisions, at a certain level of description, the types of algorithms they use are also the types of algorithms we now know humans use in the visual system, for example, to make decisions about what we are seeing.



Natural selection has found these same principles time and time again and included them in different systems in different ways, but fundamentally the principles are the same. I think this is a growing new area of research; we are really trying to build across these different systems.



Ants have algorithms. If you think about an ant colony, it's a computing device; there's some wonderful work by Jean-Louis Deneubourg in Brussels and his collaborators that really started this field in a way with Ilya Prigogine and later on Jean Louis Deneubourg looking at the ways in which social insect colonies can interact. One example would be—it sounds trivial, but if you think about it, it is quite difficult—how can a colony decide between two food sources, one of which is slightly closer than the other? Do they have to measure this? Do they have to perform these computations?

[Read the rest at Edge: ANTS HAVE ALGORITHMS: A Talk with Iain Couzin]

[Hat-tip: 3 Quarks Daily]



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Friday, March 14, 2008

Evolution Schmevolution - Overview



[From Evolution Schmevolution - Overview | The Daily Show | Comedy Central]



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Wednesday, March 12, 2008

Time to Fight HIV in Our Genes

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A lot of scientists are aware of the CCR5 gene and the mutant form of this gene that has a base pair deletion at position 32. The normal CCR5 gene codes for a receptor protein that gets HIV into the cell and people with the mutant form are resistant to HIV because the virus is unable to enter into the cell. It is an exciting time in the medical community because researchers have discovered a new promising gene that could potentially prevent the virus from forming. HIV is a rapidly mutating virus that is hard to stop with vaccines and cocktail drugs. It has been scientists’ objective to find new ways of fighting HIV despite its constant evolution, and they might have discovered a way to fight it naturally.


So what is this magical gene that is located in every cell of our body? It is called the TRIM22 gene and it has the amazing ability to prevent the assembly of the virus in our cells. A team of Canadian researchers at the University of Alberta discovered this gene and are excited to continue doing experiments to see how it works exactly. When the gene was placed into cells it actually prevents the virus from forming and intern prevents the onset of AIDS. In another experiment, the research team prevented cells from turning on the TRIM22 gene which caused the coordinating interferon to become ineffective at blocking the HIV infection. Under normal conditions this interferon coordinates attacks by the TRIM22 gene against infections. This means the TRIM22 gene is a crucial part of our defense against HIV. These research findings can be found in the public library of science pathogens.


Further research is necessary to answer more questions about this gene and its ability. For instance, the TRIM22 gene does not work in people who are already infected with HIV. Reasons for this are still unknown and mind boggling to scientists. Other studies are being done to see what other viruses the TRIM22 gene can fight. The tests done here were conducted using computer analysis and cell cultures, so it will be interesting to see what happens when they test the genes on model organisms.


The prospects of this research are promising and scientist hope to use this natural means for fighting the HIV virus to synthesize drugs that mimic the TRIM22 gene. Science and technology are allowing medicine to go in directions that it has never gone before. With dedicated scientists and proper funding it is possible that we will find a cure to HIV in the next few decades.


[contributed by Sheena Edmonds]



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Let the Training Begin (reflections on Bush's lecture)

Stem+cell+research_670_18006666_0_0_10474_300.jpg Dr. Bush gave a fascinating lecture today on stem cell research; how far we have come and how far we have left to go. The first mouse embryonic stem cells were cultured in 1981, and the first human embryonic stem cell was cultured in 1998. Just a decade later, scientists are able to transform these and other stem cells into any tissue in the body. A technique done regularly among researchers is somatic cell nuclear transfer. This is when the nucleus is removed from an unfertilized egg cell and replaced with the nucleus from a patients somatic cell (heart cell, liver cell, etc.). This ultimately puts the genetic material of the patient into cells that can become any part of their body. This is exciting because whenever tissue is transplanted into a human being there is always the risk of rejection, but this method minimizes that risk because the cell contains instructions for life, unique to the donor.

Some might ask how the undifferentiated stem cells become destine for specific tissue types. One way scientists are doing this is by treating stem cells with different “cocktails” of growth factors that will determine their final destination. One example Dr. Bush gave was the experiment where mouse cells were treated with two different growth factors which caused them to become cardiac muscle cells. He showed a brief video of these cells and they were actually beating! He said they are now even able to take cells that are already at there terminal state, like skin cells, and make them into stem cells. We saw an example of this in class when Dr. Katti showed us how they took skin cells, turned them into stem cells, which became red blood cells that were placed in a mouse with sickle cell anemia and ultimately cured the mouse of this disease.

It is truly amazing what these cells and this research is capable of. There are some set backs for those doing stem cell research. For example, the federal government will only provide funding for research done on 21 cell lines that have been approved. However, this does not stop private funding from taking place. Dr. Bush believes that we are about five to ten years away from seeing stem cells used in medicine. In July of this summer, Dr. Bush is going to have a workshop for university professors showing them how to culture stem cells so that, in the future, college courses can be designed to teach students these methods.

From the stand point of evolution, will stem cells and their potential in medicine ultimately have adverse effects on the human population? Futuristically speaking, if we eliminate disease are we eliminating natural selection on our species? Will this cause the human population to rapidly overshoot its carrying capacity because everyone is living healthy lives without terminal illnesses? Or on the other hand, will new diseases arise from strains of mutant stem cells? As much as it is exciting to find cures to Parkinson’s, liver disease, and sickle cell anemia; it is equally frightening to ponder the repercussions of this new wisdom.

Check out these websites for additional news regarding stem cells:


Somatic Cell Nuclear Transfer (Therapeutic Cloning)

California Institute for Regenerative Medicine

Chemical Turns Stem Cells Into Beating Heart Cells


[contributed by Sheena Edmonds]

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Tuesday, March 11, 2008

Bush to speak on the ethics of stem cell culture - Mar 12 noon @ Fresno State


No... not that Bush / Shrub! Rather, its our own department's Jason Bush, who actually knows a little something about stem cell research as a scientist, and who happens to be from north of the border - the northern border of the US, that is. Our Bush will be speaking as part of the CSU-Fresno Center For Ethics spring lecture series:

March 12
Jason A. Bush: “The Art, Mystery, and Controversy of Stem Cell Culture”
As stem cell research has exploded in the past 5 years, fundamental concepts have changed and we have made technical advancements. Scientists see the potential and opponents see the slippery slope. This lecture will discuss the complex issues that engulf stem cell research.
Jason Bush has a Ph.D. in Experimental Medicine from the University of British Columbia. He did post-doc work in Cancer Biology at The Burnham Institute. He is Assistant Professor in the Biology Department at Fresno State.
[From Upcoming Ethics Center Events and Lectures]
The lecture will be in the Alice Peters Auditorium at 12:00 PM on March 12, 2008. Should be fun, so try to be there!

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Monday, March 10, 2008

The Birds of Pantanal, Brazil - a talk @ Fresno Audubon tomorrow night

DSC_2751.JPGHere's a promising event for a fun evening tomorrow, not too far from campus here:

MARCH MEETING: March 11, 2008. The Birds of Pantanal, Brazil
Dr. Monique Franca, a native of Brazil, will talk about the “Birds of Pantanal, Brazil.” Pantanal is a paradise for wildlife and a paradise for bird watchers! Meetings are held in the Calaveras Room on the first floor of the UC Center at 7:30 PM (550 E. Shaw Ave).
There's more about Pantanal and the speaker in the Yellowbill, Fresno Audubon's newsletter.

[From Fresno Audubon Society]

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Wednesday, March 5, 2008

Superbug Nightmare - on Nightline tonight

I don't know how many of you students watch ABC's Nightline (after all, it competes with Leno and Letterman!), but even if you are not in the habit - and especially if you are thinking about writing your term paper on this or a related topic - you might want to watch/TiVo it tonight (11:35 Pm on our local Channel 30), because it promises a segment on antibiotic resistant bacteria! A highly relevant evolutionary topic in the mainstream media can't really be missed now, can it? Well, let's see how much evolution they talk about... at least the accompanying article on their website contains the e-word twice! Here's a blurb about what's on for tonight:

Killer "Superbug"

MRSA is a million-year-old bacterium that kills 19,000 Americans a year, claiming more lives in the US than even AIDS. Though once confined mainly to hospitals, the bacterial infection is now increasingly common outside of medical facilities. Once contracted, MRSA is hard to treat because it's resistant to most antibiotics. ABC's Vicki Mabrey reports on the fight against this "superbug."
And you can also watch a somewhat cheesy "promotional" video if you like.
[From ABC News: 'It's Everywhere': Superbug Nightmare]

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Monday, March 3, 2008

Evolution of Human Morality

An interesting report in the Economist on a panel discussion among some eminent biologists about human morality at the recent AAAS meeting. And the author seems surprised that biologists are "invading" a field that was supposedly safe in the hands of "philosophers"! If evolutionary biology can explain so much about the evolution and functioning of our own bodies and minds, why should a supposedly complex behavior such as "morality" be off limits to biologists? The article only touches on some of the intriguing ideas, but you should dig up other writings of some of the people mentioned.
Particularly intriguing is the research by David Sloan Wilson and Ingrid Storm of SUNY, Binghamton on conservative vs. liberal teenagers:

He and his colleague Ingrid Storm looked at liberals and conservatives (in the American senses of the words). Each group has a package of values it sees as moral, while viewing many of the beliefs of the other side as immoral. Dr Wilson and Dr Storm restricted their study to white, Protestant teenagers, in order to eliminate confounding variables. However, their volunteers came from two different traditions—Pentecostal, which tends to the conservative, and Episcopalian, which tends to the liberal.

The researchers conducted the study by giving each volunteer a beeper that went off every two hours or so. When it beeped, the volunteer answered a questionnaire about what he was doing at that moment, and how he felt about it.

Dr Wilson and Dr Storm found several unexpected differences between the groups. Liberal teenagers always felt more stress than conservatives, but were particularly stressed if they could not decide for themselves whom they spent time with. Such choice, or the lack of it, did not change conservative stress levels. Liberals were also loners, spending a quarter of their time on their own. Conservatives were alone for a sixth of the time. That may have been related to the fact that liberals were equally bored by their own company and that of others. Conservatives were far less bored when with other people. They also preferred the company of relatives to non-relatives. Liberals were indifferent. Perhaps most intriguingly, the more religious a liberal teenager claimed to be, the more he was willing to confront his parents with dissenting beliefs. The opposite was true for conservatives.

Dr Wilson suspects that the liberal package of individualism and confrontation is the appropriate response to survival in a stable environment in which there is leisure for learning and reflection, and the consequences for a group's stability of such dissent are low. The conservative package of collectivism and conformity, by contrast, works in an unstable environment where joint action, and thus obedience to their group, are at a premium. It is an interesting suggestion, and it is one that plays into the question of how morality actually evolved.
Intrigued? Read the rest of the article here.

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