Saturday, March 08, 2008
Polymerase Chain Reaction
The other day I was talking with several colleagues about PCR, or the polymerase chain reaction. We first started to hear about it in the mid-1980's and I was not very impressed. It was a cool reaction but what the heck was it good for? I didn't think I would ever have a need to learn about PCR.
Today's citation classic on The Evilutionary Biologist proves just how wrong I was about PCR [This Week's Citation Classic]. John Dennehy talks about it's inventor Kary Mullis, an "interesting guy" (one of the understatements of the year). Mullis is by far the most embarrassing Noble Laureate.
Uncommon Descent holds that...
The mission of Uncommon Descent is clearly stated at the top of the sidebar on the blog. It says ...
Materialistic ideology has subverted the study of biological and cosmological origins so that the actual content of these sciences has become corrupted. The problem, therefore, is not merely that science is being used illegitimately to promote a materialistic worldview, but that this worldview is actively undermining scientific inquiry, leading to incorrect and unsupported conclusions about biological and cosmological origins. At the same time, intelligent design (ID) offers a promising scientific alternative to materialistic theories of biological and cosmological evolution -- an alternative that is finding increasing theoretical and empirical support. Hence, ID needs to be vigorously developed as a scientific, intellectual, and cultural project.The Intelligent Design Creationists make a big deal of this whenever they get around to defending their worldview. They claim that Intelligent Design Creationism is a "promising scientific alternative" that deserves respect. They say that Intelligent Design Creationism is not just anti-evolutionism.
There're lying, of course, but what else is new. Here's the latest posting on Uncommon Deescent as posted by that well-known scientist and intellectual DaveScot [Speaking of T-Shirts - this is reputedly by the same designer].
DARWIN: The Evolution Revolution
Today is the opening day of the Darwin exhibit at the Royal Ontario Museum in Toronto (Canada). The exhibit runs from now to Aug. 4, 2008 [The Evolution Revolution].
Discover the extraordinary story of Charles Darwin in Darwin: The Evolution Revolution, the most comprehensive exhibition ever mounted on the man whose revolutionary theory changed the world. This extraordinary exhibition traces Darwin’s life from his early years of curious observation and scientific study to his uninspired days at boarding school. Relive his five-year voyage aboard the HMS Beagle that brought him to the Galapagos Islands, and discover some of the unique animals he encountered, including African spur-thighed tortoises, an iguana and live frogs.Walk through his historic study where he developed his ground-breaking Theory of Evolution. Intimate letters, photographs and personal artifacts give insight into aspects of Darwin’s life that are rarely seen. Discover why it took so long for Darwin to publish his findings, and how his daughter’s untimely death in 1851 may have contributed to his decision to eventually publish On The Origin of Species.
Interactive media and videos help bring Darwin and his ideas to life, and contemporary scientists explain how Darwin’s theories have held their relevance in so many areas of modern biology and science.
Darwin is organized by the American Museum of Natural History, New York in collaboration with The Field Museum, Chicago; the Museum of Science, Boston; the Royal Ontario Museum, Toronto, Canada; and the Natural History Museum, London, United Kingdom.
[Photo Credit: David McKay, ©ROM: A first edition of Charles Darwin’s On the Origin of Species, published in 1859, on loan to the ROM from the Thomas Fisher Rare Book Library, University of Toronto. (The Origin of Species)]
Is it cheating to discuss an assignment in a Facebook study group?
A student at Ryerson University in Toronto faces expulsion from the university for setting up a Facebook study group that discussed chemistry assignments. This is a complicated issue that's made the newspapers here in Toronto. One of the undergraduate bloggers at the University of Toronto explains the situation and offers an opinion. Check out Expelled for cheating on Facebook?.
Unethical conduct in general, and cheating in particular, has become a major problem at universities around the world. Part of the problem is due to the availability of resources and contacts on the internet. This opens up new possibilities for circumventing the intent of assignments and essays—possibilities that weren't available a decade ago. Nobody knows how to deal with the new realities.
In this particular case, the Professor explicitly required that students complete the assignment individually without help from anyone else. That's a very reasonable requirement, in my opinion, and there probably were times the past when almost all students were honorable enough to obey this rule. Today, that sense of "honor" seems horribly old-fashioned. To most students it will not seem like cheating if they ask their friends for help with the assignments and share information. That's what happened on the Facebook study group.
Ironically, the public nature of Facebook is what brings the chemistry students together in the first place but it is also what revealed that they are violating the rules.
[Photo Credit: The Toronto Star: Student faces Facebook consequences]
Friday, March 07, 2008
Science, Religion, and Framing
There was a conference on framing at the AAAS meeting last month [How Matt Nisbet Conned AAAS]. When the meeting was first being organized I wrote to the moderator, David Goldston, to complian about the lack of balance and fairness. He replied that he had nothing to do with inviting the speakers. He told me that, as moderator, he intended to play "devil's advocate" to ensure fairness.Goldston has written up a summary of the meeting for Nature (Goldston, 2008). In that article he cautions us that the public may not be as hostile to science as we think. With that in mind, it is wise, acording to Goldston, to develop ways to make science more appealing to a religious public.
Recognizing the complexity of public attitudes, a number of scientists and other scholars are trying to develop language to discuss evolution in ways that might build bridges to the religious. These efforts were the subject of a well-attended panel I moderated at last month's annual meeting of the American Association for the Advancement of Science in Boston, Massachusetts. Some panellists, in effect, advocated co-opting the language of religion. For example, Kenneth Miller of Brown University in Providence, Rhode Island, the author of a leading textbook on evolution and a practising Catholic, talked about embracing the notion of life having a design, but explaining it as the result and embodiment of evolution. Others, such as Matthew Nisbet, a communications scholar at American University in Washington DC who organized the panel, suggested moving the discussion away from scientific theory and talking about the medical and other benefits that have resulted from understanding evolution.What are those two facets? The first is the fact that the fight is not about science alone. It's about a whole range of social issues that upset the religious right.
No doubt all these approaches are worth trying, and the general message of the panel — that scientists should address the public with respect rather than contempt — is well taken. But the panel failed to grapple with two important facets of the way science and religious attitudes intersect.
The second point is more interesting ...
Second, the panellists tiptoed around the fact that scientific discovery can genuinely undermine religious beliefs. The focus of the panel was on teaching evolution, but discoveries in genetics and neuroscience are likely to be far more problematic in the long run. The two fields are verging on drawing the ultimate materialist picture of human nature — humans as nothing more than proteins and electrical impulses, all machine and no ghost, to play off Descartes' formulation. This view will challenge not only fundamentalist views about the soul, but more widely held notions about what it means to be a person. That will further complicate age-old questions about the nature of individual responsibility and morality.That's a good point. What does it have to do with the conference and with the views advocated by people like Miller and Nisbet? Would using the language of religion and talking about design—as Miller suggests—make believers more comfortable about becoming materialists? Will advertising the medical benefits of science—as Nisbet sugggests— relieve the angst of learning that God has no role to play in the universe? I don't think so. Framing science isn't going to hide the fact that it is antithetical to many of the core beliefs of the religious.
So far, so good. At least Goldston dropped a little hint to suggest that he wasn't completely taken in by the Nisbet propaganda.
But wait. In his last paragraph Goldston goes completely off the rails revealing why he was chosen as moderator.
Responding to these issues will be difficult for scientists and non-scientists alike. New discoveries about the human genome and neuroscience will no doubt be clearly linked to potential medical advances, but they may also raise new questions about what kinds of interventions are appropriate. The conundrums may leave even atheists longing for some theological guidance on how to decide what is moral. And wandering about this uncharted territory may make the well-rehearsed battles over evolution seem like the good old days.What nonsense. Atheists don't need "theological guidance" to work through these problems. As a matter of fact, atheists are well placed to deal with the issues once the stranglehold of religion is broken. That's because atheists have long been deciding what's "moral" in the absence of God. We're good at it.
Goldston, D. (2008) The Scientist Delusion. Nature 462:17. [Nature] [doi:10.1038/452017a]
[HatTip: Pete Dunkelberg]
Name This Building
How many of you can identify this Parisian building? I know I couldn't before I came across it two weeks ago. Michael Egnor Is an IDiot
Michael Egnor rises to the defense of Jonathan Wells. Readers may recall that Wells made a really stupid claim that studying antibiotic resistance in bacteria had nothing to do with evolution. When the authors of the paper in question rejected this silly claim, Wells bent over backwards to justify his stupidity. Now Michael Egnor joins him [Dr. Wells’ Observation about the King’s Clothes].
There's one small part of that posting that really caught my eye.
The viscous personal attacks on Dr. Wells are an example. If you were a scientist, how candid about questioning the relevance of Darwinism would you be if your livelihood depended on Darwinist professors like Dr. Myers and Dr. Moran?Anyone with an IQ above 50 knows that neither PZ or I are Darwinists [Why I'm Not a Darwinist]. We have both posted numerous articles attacking adaptationism and the emphasis on natural selection as the only mechanism of evolution. We have questioned all kinds of things about the modern orthodoxy from punctuated equilibria to evo-devo.
In other words, both of us have as much of a reputation for questioning fellow evolutionists as for challenging IDiots like Wells and Egnor.
The fact that Michael Egnor cannot see this speaks volumes.
John Doesn't Like Richard
John Wilkins went to hear Richard Dawkins last night in Pheonix, Arizona. I'll leave it to you readers to figure out why John and Richard were together in such a strange place. (Hint: It's not because John got lost.)I'm sure it will come as a surprise to no one that Wilkins took exception to some of the things Dawkins said [Dawkins' Lecture in Poenix]. As you might imagine, Wilkins really got annoyed when Dawkins talked about those who choose to overlook the silliness of belief in the supernatural. Here's what John writes ...
In particular I was annoyed that those of us who do not condemn someone for holding religious beliefs were caricatured as "feeling good that someone has religion somewhere". Bullshit. That is not why we dislike the Us'n'Themism of TGD. We dislike it because no matter what other beliefs an intelligent person may hold, so long as they accept the importance of science and the need for a secular society, we simply do not care if they also like the taste of ear wax, having sex with trees, or believing in a deity or two. Way to go, Richard. Good bit of framing and parodying the opposition. Real rational.John, it's you who aren't being rational about this topic. Somewhere on this planet there may be a true believer in God who resembles your hypothetical caricature but they are very rare.
Most people who are willing to believe in imaginary deities are willing to believe all sorts of other things as well. They do NOT accept science with all of it's implications, You need only think of Ken Miller, Francis Collins, Michael Denton, and Simon Conway Morris to see how religious beliefs corrupt science. It's also a bit of a stretch to imply that their version of a "secular society" is the same as that of atheists.
Wake up and smell the roses. I don't care if some people like the taste of ear wax because that preference does not impinge on their understanding of science. You just can't make a similar valid claim about believers in the supernatural no matter how many times you say it. Your logic fails because there are very few believers whose faith doesn't conflict with science in one way or another.
Do You Trust Homeopathic Medicine?
tkindoll at Skeptchick analyzes an international poll were respondents were asked whether they trust homeopathic medicne [Hot Off the Press - New Data on Homeopathy Usage Around the World]. Read her comments. Here's the bottom line—citizens of India are the most ignorant of science on this issue but the French are way up there as well. This is something I observed while I was in France a few weeks ago. There are frequent favorable references to pseudoscientific medicine on French television.
Vaccines Don't Cause Autism
David Kirby is one of the most prominent proponents of the claim that autism is really mercury poisoning and it's caused by childhood vaccines. This isn't my field but I can recognize woo when I see it. Fortunately for the side of rationality, there are some smart people who know how to deal with the purveyors of ignorance. One of these is Orac at Respectful Insolence.
The US government recently settled a court case that appears to concede a role for vaccines in autism. Orac dissects that claim in a really excellent posting, David Kirby and the government "concession that vaccines cause autism": The incredible shrinking causation claim. Here's the bottom line ...
Orac is the nom de blog of a humble pseudonymous surgeon/scientist with an ego just big enough to delude himself that someone, somewhere might actually give a rodent's posterior about his miscellaneous verbal meanderings, but just barely small enough to admit to himself that few will. (Continued here, along with a DISCLAIMER that you should read before reading any medical discussions here.)1
One thing that you should remember about Kirby's pretty rhetorical flourishes and speculation. It's all there to distract you from the utter failure of science to support the original claims of the mercury militia, namely that mercury in vaccines was the cause for most cases of autism, or, as Generation Rescue puts it, that autism is a "misdiagnosis for mercury poisoning." Multiple large and well-designed epidemiological studies have utterly failed to find a link between mercury in vaccines or vaccines in general and autism. Indeed, the idea that vaccines cause autism is the incredible shrinking hypothesis. It's gone from confident claims that mercury or vaccines cause nearly all cases of autism to a lot of handwaving based on one case conceded by the government in which the plaintiff had a rare mitochondrial disease which may have been aggravated by vaccines plus multiple bouts of inflammation due to otitis media, a far cry from previous cries blaming vaccines for an "autism tsunami." Is it possible that in rare cases vaccines can aggravate a preexisting condition and lead to injury that resembles autism or ASD? Despite all the studies cited by Kirby in is speculations, what we really have is one documented case of a child in which childhood vaccines probably exacerbated a preexisting mitochondrial disease who later went on to meet the diagnostic criteria for mild autism; so it's possible. It's also a far cry from the original claims of the mercury militia. Don't forget that. Also don't forget that, no matter what new physiologic alterations or abnormalities are found in autistic children, antivaccinationists always--and I mean always--manage to find a rationale to link it to vaccines, no matter how tortured that rationale is.This is a serious issue. It's part of a much bigger picture including the attack on science by creationists. The issue is not only science vs. religion: it's rationalism vs. superstition. David Kirby is just as dangerous to the cause of science as Jonathan Wells of any or the other creationists.
Other Links: Rebecca on Skepchick: Vaccines don’t cause autism. Okay?
1. This is one of those times when I refer to an anonymous blogger because, as Orac himself admits, his identity is an open secret.
Thursday, March 06, 2008
Hybrid Plants Colonize New Environments
Today's Botany Photo of the Day shows Helianthus anomalus, a hybrid species of sunflower that grows in the sand dunes of Utah. This species arose about 50,000 years ago as a hybrid of Helianthus annuus and Helianthus petiolaris. The Botany Photo of the Day website describes experiments that reproduced this hybridization event showing that hybrids can be more fit—in certain environments—than either parent. [see Jane Harris Zsovan Doesn't Understand Speciation]
To My American Friends
Be careful. here's a great deal at stake here.The world can't afford another eight years of the Bush doctrine.
Lunch with the Winners
I just got back from lunch with the winners of the Monday Molecule/Nobel Laureate quiz. The two winners were Alex Ling and Dave Schuller. Alex is a student at the University of Toronto. Unfortunately he had to rush off to a class before I could get my camera ready. Maybe I can borrow the photo that Dave took and post it later on.Dave Schuller is an X-ray crystallographer from Cornell working in the group that manages the synchrotron [MacCHESS]. He decided to drive up from Cornell this morning to have lunch with us. Right now he's on his way back with a stop at McMaster University in Hamilton. Maybe that's why he looks a little dazed in the picture.
Dave brought me a mastodon from the Natural History Museum at Cornell. He also brought me some Bible Flash Cards so I can practice memorizing my Bible Stories. Here's an example ....Q: Where did God ask Abraham to go?
A: Isreal, but it took 25 years of traveling to get there.
Some of the other questions were much more difficult. How many of you can remember how Ruth cared for Naomi or where the Last Supper was held? I didn't know the answer to those ones but thanks to Dave Schuller I do now.
Tangled Bank #100
The latest issue of Tangled Bank is #100. It's hosted at AECHAEOPORN [Tangled Bank #100, Bad Flu Edition].
PZ Myers, in his link to this clears up a numbering error, and it turns out this is the 100th edition of Tangled Bank. Congratulation to Dr. Myers in such a long term and well run blog carnival, and thanks to all the other hosts who put time and energy to 1 through 99!
I’ve come down with a terrible flu right in time for Tangled Bank #100. This is making it quite difficult to even sit at my computer and type. Luckily, we have a volunteer to put together this issue in my absence. A famous movie star and producer and great mind of evolutionary biology. His most recent work will include the likes of Dr. Richard Dawkins and Dr. PZ Myers.
Because of various publicity concerns, he wishes to remain nameless. However, he promised that his work will be fair an unbiased, offering no cherry picking or quote mining at all.
If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.
The Humanist Globe
I just found a new website called the The Humanist Globe. It was created by Mark Robinson who I met at the opening of the Centre for Inquiry (Toronto) last year. Check it out. It's full of all kinds of interesting things.
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