Advice for Women: What to Do When You Discover He's an Atheist
Friendly Atheist found the answer on YouTube.
Tuesday, March 31, 2009
Sean Eddy on "Open Education"
I've been thinking a lot lately about how to get my textbook online without asking everyone involved to work for free. It's not an easy problem.
There's a myth out there that some places like MIT are putting up all kinds of useful information for free. The Open Courseware project sounds really exciting until you realize that they can't publish any of the slides they use in their powerpoint presentations because they're all copyrighted. It also doesn't take much perusal to realize that many MIT professors don't know as much about their subjects as you might imagine.
There's a new book advocating the concept of "Open Education" ("Opening Up Education" T. IIyoshi and M.S.V. Kumar eds. MIT Press). The book is reviewed by Sean Eddy on PLoS Biology [Open Revolution].
Sean Eddy used to be an active participant on the talk.origins newsgroup back when he was a graduate student so I eagerly followed the link to his review. I wasn't disappointed. It's the same Sean Eddy that I knew 12 years ago. He can still recognize bullshit when he sees it.
So, while I like storming the establishment with pitchforks and torches as much as anyone, when I picked up Opening Up Education (or rather, when I downloaded the PDF to my Kindle), I was looking for pragmatism, not utopianism. After 500 pages of “the silos we all know about in higher education are under assault in the new world,” the “hated textbook publishers,” the “epistemological hegemony of higher education,” and the “noble philosophy” of making everything free—“traitors” and “patriots” and “communists,” oh my!—my hopes were beaten down. Many of the 30 essays in this collection are more manifesto than explanation, and many of the 38 authors are writing more for their fellow revolutionary comrades than for us.Life is never as simple as the Web 2.0 fans make out. Somebody is going to have to do a lot of work before the quality of a website matches what's in the best introductory textbooks. And it's extremely naive to think that all that work is just going to be given away for free.
I'm not just talking about authors. There's a whole team of people involved in publishing my textbooks. This includes editors who correct my spelling and grammar—an onerous task in my case. It includes artists who make the figures and editors who obtain permissions and copyrights for photographs. Then there's the staff at the publishers who receive and mail out manuscripts for review and editing and who handle all the paperwork/electrons associated with a major project.
Are we going to ask all of them to work for free by putting everything on the web? Of course not.
Sean does an excellent job of bursting the bubble.“Remix,” “collective wisdom,” “Web 2.0”—many of these essays ride a bubble of popular digital punditry enthusiastically but too uncritically. Many technologists today are infected with an idea that “community is king,” that high-quality content will rain down freely merely because we connect digital communities openly. This confuses ways of sharing ideas with ways of creating ideas. It is a kind of magical thinking that has much in common with the cargo cults that cut landing strips in the jungle and carved radios from sticks in hope that more sophisticated beings would parachute technological artifacts down upon them. With all respect to the passionate and pioneering initiatives described in this collection, building landing strips to receive open educational content will not be enough. More attention must be paid to the fact that someone still needs to spend time painstakingly developing artful ways to make difficult concepts understandable—to teach!—and that it will take even more time (thus money) to render these hard-won ideas using multimedia web technology compared with writing textbooks. Success hinges on the adoption of open licensing by the professionals who make digital educational resources, and on finding ways to finance their work.I have some ideas. I'd like to put my book on the web so that everyone can read it but nobody can download it or print out the figures and text. If you need a printed version you can sign on to the server and print out a chapter for $3. The pages would come with your name and email address printed in the header and footer—or perhaps as a watermark. The idea is to make the material available at minimal cost to an individual user while inhibiting the distribution of photocopies.
No matter how easy it is to read something online, I think there's still a market for a printed version of the material. I know from personal experience that highlighting and scribbling in the margins on my computer monitor doesn't work.
Online textbooks have several advantages such as hyperlinks, frequent revisions and updates, and interactive learning. But we need to find a way to pay for it. If you think the work is going to be given away for free then you are living in a dream world. Check out the MIT Open Courseware site under Biology to see what the cargo cult version of Web 2.0 gets you.
[Photo Credit: Nature]
[Hat Tip: Jonathan Eisen at The Tree of Life]
Religion and Child Abuse
I don't think that religious indoctrination is always an example of child abuse. However, there are other ways that count as clear examples of abuse [Taliban blocks UN polio treatment in Pakistan].
Militants had reportedly agreed to allow the [polio] vaccination program to take place as part of the peace agreements.
However, the militants had reneged on their word and despite assiduous efforts made by the increasingly irrelevant local administration, no vaccinations have taken place.
“It’s a US tool to cut the population of the Muslims. It is against Islam that you take a medicine before the disease”, said, Muslim Khan, Swat’s Taliban spokesman, speaking by telephone.
[Photo Credit: daylife/Reuters: "A man holds his twins as he waits for them to receive polio vaccines in the southern province of Kandahar September 21, 2007. Afghan health officials said on Friday they had brokered a deal with Taliban leaders to allow the immunization of children against polio in rebel-held areas in a rare sign of cooperation between the warring sides."]
[Hat Tip: RichardDawkins.net]
Way too Sensitive?
The techniques for detecting DNA and RNA are extremely sensitive. This sensitivity often leads to misinterpretations because it become difficult to separate signal from noise. The idea that 90% of our genome may be transcribed into functional RNA, for example, may be due to the sensitivity of an assay that can easily detect tiny amounts of accidental transcription.
Similarly, the often proclaimed ubiquity of alternative splicing may be due to the easy detection of splicing mistakes. Other examples of problems with noise might be the presumed abundance of small regulatory RNAs and the frequency of transcription factor binding sites.
The problem is acute when it comes to analyzing DNA from fossils. There, tiny amounts of contamination can really screw things up. That's why John Hawks is also interested in this problem of over-sensitive DNA assays.
Just how sensitive is the technology? Hawks has found a very interesting and informative example [The trouble with contamination]. This example is about contamination but keep in mind that it also applies to the detection of noise in transcription, DNA binding, and splicing.
Here's the original report from the BBC ['DNA bungle' haunts German police]. Over the past few years German police have been on the lookout for a mysterious woman who was linked to several murders. Her DNA was found at over 40 different crime scenes. This woman became one of the most wanted people in Europe but nothing was known about her aside from her DNA.
Finally someone became suspicious and started to look closely at the way they were collecting and analyzing DNA. To make a long story short, the alleged murderer is a factory worker in Bavaria who works in a factory that manufactures cotton swabs. The same swabs that are used to collect samples at a crime scene. Those swabs were contaminated with her DNA.
There's a lesson here. Any technology that can detect the DNA from a factory worker on a cotton swap is quite capable of detecting tiny insignificant amounts of nucleic acids inside a cell.
1,2,3 ... What Are We Fighting for?
President Obama wants to sacrifice more American in Afghanistan and Canada's Prime Minister, Stephen Harper, is suggesting that this might be something that Canada should support. This is in spite of the fact that there are times when he seems to know the right answer to the question; Can We Win in Afghanistan?.
Let's make sure everyone knows what we're fighting for: 'Worse than the Taliban' - new law rolls back rights for Afghan women.
Hamid Karzai has been accused of trying to win votes in Afghanistan's presidential election by backing a law the UN says legalises rape within marriage and bans wives from stepping outside their homes without their husbands' permission.
The Afghan president signed the law earlier this month, despite condemnation by human rights activists and some MPs that it flouts the constitution's equal rights provisions.
The final document has not been published, but the law is believed to contain articles that rule women cannot leave the house without their husbands' permission, that they can only seek work, education or visit the doctor with their husbands' permission, and that they cannot refuse their husband sex.
Glass Knives
One of the best labs I ever took as an undergraduate was an advanced cytology lab where we learned to use the electron microscope.1 Part of the process was preparing thin sectioned material and that involved making our own glass knife that would cut very thin slices from wax-embedded tissue.
Here's a video from Leica showing how it's done today.2
I was reminded of this recently when I had occasion to refer to an electron micrograph taken by Harrison Latta. Latta invented the glass knife back in 1949. You can read about his discovery in this tribute to him on the University of California, Los Angeles, website.
This is one of those simple technological innovations that made a huge difference but would never have been recognized by the Nobel Prize committee.
1. Yes, they had electron microscopes back in those days!
2. You can also buy diamond knives but that's a lot less fun.
Monday, March 30, 2009
YouTube Suspends the Account of the James Randi Education Foundation
If you have a YouTube account, follow these instructions.
To complain to youtube follow this link;
http://www.google.com/support/youtube...
Scroll to the very bottom and click on "new issue"
Select "suspended account" from the options and express your opinion.
The mediafire link is;
http://www.mediafire.com/?sharekey=4d...
UPDATE: I was astonished to learn that some readers don't know who James Randi is or what the James Randi educational foundation is all about.Randi is a former magician ("The Amazing Randi") from Toronto, Ontario (Canada). He is best known for investigating claims of the paranormal and for his one million dollar challenge. He has appeared on television many times and often writes columns and article debunking paranormal claims.
The goal of the James Randi Educational Foundation is ...
The James Randi Educational Foundation is a not-for-profit organization founded in 1996. Its aim is to promote critical thinking by reaching out to the public and media with reliable information about paranormal and supernatural ideas so widespread in our society today.The current President of the foundation is Phil Plait of Bad Astronomy.
The Foundation's goals include:
* Creating a new generation of critical thinkers through lively classroom demonstrations and by reaching out to the next generation in the form of scholarships and awards.
* Demonstrating to the public and the media, through educational seminars, the consequences of accepting paranormal and supernatural claims without questioning.
* Supporting and conducting research into paranormal claims through well-designed experiments utilizing "the scientific method" and by publishing the findings in the JREF official newsletter, Swift, and other periodicals. Also providing reliable information on paranormal and pseudoscientific claims by maintaining a comprehensive library of books, videos, journals, and archival resources open to the public.
* Assisting those who are being attacked as a result of their investigations and criticism of people who make paranormal claims, by maintaining a legal defense fund available to assist these individuals.
To raise public awareness of these issues, the Foundation offers a $1,000,000 prize to any person or persons who can demonstrate any psychic, supernatural or paranormal ability of any kind under mutually agreed upon scientific conditions. This prize money is held in a special account which cannot be accessed for any purpose other than the awarding of the prize.
Located in Fort Lauderdale, Florida, the Foundation is funded through member contributions, grants, sales of books and videos, seminars, and conferences.
Monday's Molecule #115
Identify this molecule and explain why it is useful. You must supply the common name and the formal IUPAC name.
I'm looking for the Nobel Laureate whose name is associated with this molecule.
The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.
There are seven ineligible candidates for this week's reward: Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, and Elvis Cela from the University of Toronto.
Dima and Bill have donated their free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.
THEME:
Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.
Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.
Comments will be blocked for 24 hours.
Ethical Framing
The bad news is that Matt Nisbet has published some guidelines for proper framing. You won't be surprised to learn that Richard Dawkins and PZ Myers are engaging in "unethical" framing [The Ethics of Framing Science: Four Guiding Principles]. You will be surprised to learn that fellow framer Chris Mooney is also unethical.
Although Matt doesn't mention it, I assume that scientists like Ken Miller and Francis Collins are "ethical" framers.
The good news is in the comments section of Nisbet's blog. Hardly anyone agrees with him any more. It looks like his 15 minutes of fame are just about over, proving that Andy Warhol knew more about framing than Matt Nisbet.
[Photo Credit: Andy Warhol, DeVorzon Gallery]
God Won't Allow Climate Catastrophe
You'll be pleased to know that global climate change isn't going to end in catastrophe. Rep. John Shimkus from Illinois says as much during a hearing of the U.S. House Subcommittee on Energy and Environment in Washington.
He quotes directly from the Bible concluding, "The Earth will end only when God declares it’s time to be over. Man will not destroy this Earth. This Earth will not be destroyed by a flood."
It's comforting to know that church and state are separated in America and free speech is sacrosanct.
In Canada we just had a major kerfuffle in the press over a science minister who hinted that he might not believe in evolution. I wonder if Rep. John Shimkus is going to get into trouble for not believing in global warming because it conflicts with the Bible?
[Hat Tip: Friendly Atheist]
Scientific Breakthroughs for March 30, 2009
I was reading the list of press releases on ScienceDaily Headlines and I thought you might be interested to learn about some of the most important discoveries in the past 24 hours. For the most part, these are press releases from universities and research institutes.
None of them are real breakthroughs. Some of them are interesting, incremental advances in our understanding of the natural world. Some of them are trivial results that have been elevated to importance by a press release and a headline. Some of them are silly. Some of them are probably wrong.
- New Breakthrough In Global Warming Plant Production
- Optimal Running Speed Associated With Evolution Of Early Human Hunting Strategies
- Fish Oils Reduce Greenhouse Gas Emissions From Flatulent Cows
- Food Choices Evolve Through Information Overload
- Psychiatric Disorders Are Common In Adults Who Have Had Anorexia
- Genetic Changes Outside Nuclear DNA Suspected To Trigger More Than Half Of All Cancers
- Why Parachutists Die
- Brain Building: Brain Growth Tied To Cell Division In Mouse Embryos
- New Theory On Largest Known Mass Extinction In Earth's History
- Team Approach Appears To Work Best For Insect Colonies
Free Speech in Oklahoma
The Oklahoma legislature is trying to intimidate the University of Oklahoma for inviting Richard Dawkins to speak last month. The Tulsa World publishes an article today that covers both sides of the controversy. After reading that article, the only logical conclusion is that free speech in Oklahoma is being threatened by elected politicians [Dispute evolves on OU speech by scientist].
This is outrageous. How can you have State Representatives advocating laws that violate the American Constitution and the Bill of Rights? Isn't that treasonous?
Oklahoma is one of those states that still has the death penalty and it still carries out executions. According to US Federal Law, the penalty for treason can be death [Capital punishment in the United States]. That raises an interesting possibility when it comes to dealing with creationists. 
[Hat Tip: RichardDawkins.net]
Sunday, March 29, 2009
Don McLeroy, Creationist Dentist
This has already been posted on Panda's Thumb and elsewhere but it deserves to be seen by everyone. It's Don McLeroy, the creationist dentist who is chair of the Texas Board of Education. He has somehow gotten the idea that he knows more about evolution than the experts.
That makes him very dangerous.
Friday, March 27, 2009
Media distortion damages both science and journalism
New Scientist has just published an article on the dangers of bad science journalism. Irony noted.
Simon Baron-Cohen explains how Media distortion damages both science and journalism .
WHEN media reports state that scientist X of Y university has discovered that A is linked to B, we ought to be able to trust them. Sadly, as many researchers know, we can't.
This has three serious consequences. For starters, every time the media misreports science, it chips away at the credibility of both enterprises. Misreporting can also engender panic, as people start to fear the adverse consequences of the supposed new link between A and B. Lastly, there can be a damaging effect on researchers' behaviour. Funding agencies and science institutions rightly encourage scientists to communicate with the media, to keep the public informed about their research and so foster trust. If their work is misrepresented, they may withdraw into the lab rather than risk having to spend hours setting the record straight.
I work in one of those sensitive areas of research, autism, in which the facts are liable to be misreported or - sometimes worse - misinterpreted.
[Photo Credit: Simon Baron-Cohen: by Brian Harris (GNU Free Documentation License).]
Thursday, March 26, 2009
Carl Zimmer on Science Jounralism
Carl Zimmer has written a lengthy blog posting about the troubles with science journalism [Visions of the Crash]. You should read all of it but I want to comment on one small part.
The rise of blogs about science has brought me many pleasures. I’ve particularly liked the astringent criticism of bad science journalism. As soon as a piece is published, scientists who know the lot about the subject can, if necessary, rip a journalist a new one. I personally have been very influenced by Mark Liberman, a linguist at Penn, who has time and again shown how important it is for reporters to pay attention to the statistics in science. What seems at first like stark results–like the difference between the male and female brain–can melt away if you look at the actual data.I'm not an expert in everything. Most of the science articles I read are explaining things that are way outside my area of expertise. They may be good articles or they may not be. I'm usually skeptical.
But some bloggers go a step further. They claim that these individual cases of journalistic misconduct add up to an indictment of the whole business. Hence, as Moran declares, we can live without science journalists.
It’s odd that many of the people making these pronouncements are scientists themselves–people, in other words, who know that you don’t do science by anecdote. If a blogger sits down in the morning and reads ten stories in a newspaper’s science section and notices that one that makes a howler of a mistake, you know what that blogger will be writing about. Blogs are an outlet for righteous fury. Bloggers are much less likely to write a post that begins, “I read nine articles this morning about science that were fairly accurate and pretty well written.” Ho hum.
However, the majority of articles I read that fall within my areas of expertise—biochemistry, molecular biology, genomes, evolution—do not impress me. It's not just a case of picking out the worst article out of ten to criticize. It's more like every second article has a problem.
When I talk to people in other fields there report the same statistics. It's looks like the average quality of science journalism, even in popular science magazines like SEED, Discovery, New Scientist, and National Georgraphic, leaves a lot to be desired.
I'm not very happy with most scientific papers either.
Darwin's two-for-one deal
Three cheers for Ryan Gregory! He has published an article in todays Globe and Mail explaining why evolution is both a fact and a theory: Darwin's two-for-one deal.
Go to his blog [Evolution Commentary] and congratulate him.
How Does Streptomycin Work?
Streptomycin is a powerful antibiotic that inhibits growth of bacteria while having very little effect on eukaryotes. It blocks protein synthesis by binding to the bacterial ribosome.
Let's review the steps of protein synthesis. The three steps are initiation, where the ribosome and factors are assembled at the start codon on the messenger RNA (mRNA); elongation, where the polypeptide chain elongates as the translation machinery moves along the mRNA; and termination, where the assembly falls apart and the completed polypeptide chain is release.
During the elongation phase there are three sites at the interface between the ribosome and the mRNA where transfer RNAs (tRNAs) can bind. The P site holds the peptidyl-tRNA molecule. The growing polypeptide chain is bound to the tRNA molecule that contributed the last amino acid. The A site binds the incoming aminoacylated tRNA molecule. The anticodon of this aa-tRNA is complementary to the mRNA codon located in the A site. Insertion of the correct aa-tRNA is mediated by elongation factor Tu (in bacteria)..
Formation of the peptide bond then occurs in a reaction catalyzed by peptidyl transferase—an enzymatic activity of the ribosomal RNA in the ribosome. When this happens the growing peptide chain (grey balls) is transferred to the tRNA that was in the A site.
The next step is to shift the ribosome relative to the mRNA bringing the peptidyl-tRNA molecule into position in the P site and freeing up the A site for a new amimoacyl tRNA to bind. This step is called translocation and it is mediated by elongation factor G (EF-G). During the translocation the uncharged tRNA is temporarily moved to the exit site (E site) before being released.
Streptomycin inhibits the translocation step by binding to the small subunit ribosomal RNA and blocking the activity of EF-G.
Here's a picture (below) of what the bacterial ribosome looks like. Most of it is RNA (yellow chain) folded into a complex conformation. The three dimensional structure is stabilized by a number of small proteins (orange + blue) bound to the outer surface of the RNA. One of these proteins is S12, located in the grove where mRNA binds to the ribosome. S12 stabilizes the RNA three-dimensional structure to which streptomycin binds.
Bacteria rapidly develop resistance to streptomycin, which explains why it isn't as effective today as it was when it was first introduced in the 1940s. One of the common resistance mutations affects ribosomal protein S12. The mutant protein is able to maintain the proper RNA conformation in the presence of streptomycin and this allow translocation to proceed.
Thesis Defense - 35th Anniversary
Today is the 35th anniversary of my Ph.D. oral defense. The event took place in the Department of Biochemical Sciences at Princeton University back in 1974.
It began with a departmental seminar. When the seminar was over I retired with my committee to a small classroom for the oral exam.
I don't remember everyone who was on my committee. My Ph.D. supervisor (Bruce Alberts) was there, as was my second reader, Abe Worcel. I know Uli Laemmli was there and so was Arnie Levine. I'm pretty sure the external member of the committee was Nancy Nossal from NIH in Bethesda, MD (USA). It's a bit of a blur after all these years.
I remember being fairly confident about the exam. After five and a half years I was pretty sure that everyone on my committee wanted to get rid of me and the easiest way to do that was to let me pass. Bruce stood to gain $3000 per year of research money and Uli was going to get back the basement of his house where Ms. Sandwalk and I had been living for the past month.
The toughest questions were from Uli Laemmli, which should not come as a surprise to anyone who knows him. He has this annoying habit of expecting people to understand the basic physics and chemistry behind the biochemical sciences. Fortunately, my inability to answer most of his questions didn't deter him from voting to pass me. 
This photograph was taken at a party that evening. I look pretty calm at that point but this may have had a lot to do with the various refreshments that were being served.
The amazing thing about the photograph—as I'm sure you all agree—is how little I've changed since then—apart from a haircut.
Back in those days we didn't spend a lot of time writing a thesis. I started in the middle of January and the entire process of writing and defending took nine weeks. My thesis was bound and delivered to the library about one week after the Ph.D. oral.
The second page of my thesis has only three words on it. It says, "To Leslie Jane." This is Ms. Sandwalk. She really should have her name on the cover 'cause I couldn't have graduated without her. Typing my thesis was only one of her many contributions. There are 257 pages in my thesis and she typed every one. As a matter of fact, she typed them twice, one draft and then the final version.
The figures in my thesis were all hand drawn. I've included one (below) to illustrate what I was doing during those five and a half years.
The Alberts lab was interested in DNA replication during bacteriophage T4 infections of E. coli. We knew that replication was carried out by a complex protein machine that assembled at a replication fork but we didn't know all the players or what they did.
The T4 proteins required for DNA replication were known from genetic studies. The most important genes were genes 30 (ligase), 32 (single-stand DNA binding protein), 41, 43 (DNA polymerase), 44, 45, and 62. The products of the unknown genes were called 41P, 44P, 45P and 62P.
We wanted to purify and characterize those proteins; my target was the product of gene 41, or 41P.
We had a cool assay, developed mostly by a postdoc in the lab named Jack Berry. What we did was to prepare a cell lysate from cells that had been infected by bacteriophage carrying an amber mutation in one of the genes. This lysate could not support DNA synthesis, as measured by incorporation of 32P nucleotides, unless we added back the missing component. This is the basis of an in vitro complementation assay that worked for each of the unknown proteins.
In my case, I used traditional protein purification methods to isolate fractions of proteins and them tested them for activity in the complementation assay. The figure below shows the elution profile of proteins bound to a hydroxylapatite column. The peak centered on fraction 61 is the activity of the complementation assay. It indicates that 41P elutes early as a sharp peak in the elution profile. 
The complementation assay doesn't tell us anything about the function of 41-protein, only that it complements an extract that's deficient in 41P. Strictly speaking, it doesn't even tell us that the activity is due to the product of gene 41 since it could be something else that complements in vitro.
Fortunately we had another way of identifying 41P. I started my purification with extracts from 17 liters of infected cells. To this I added extracts from cells that had been labeled with radiaoctive amino acids. One batch was from a wild-type infection where all T4 proteins are labeled with 14C amino acids. The other batch is from an infection with an amber mutation in gene 41. In this case every protein except 41P is labeled with 3H amino acids.
You can adjust the settings on a scintillation counter so they distinguish between 14C and 3H but there's some overlap. The equations for calculating the contribution of each isotope in each window are relatively simple. All you need are good standards to get the distribution. One of the most fun things I did as a graduate student was to write a computer program (in Fortran) that did these calculations automatically and plotted them on a plotter. This was back in the time when computers were housed in large separate buildings and required dozens of people to look after them.
If you look of the elution profile in the figure you'll see there's an excess of 14C over 3H in the same fractions where the complementation activity is located. What this means is that the wild-type extract has a protein at that position that's not found in the am41 extract. It's another way of identifying the product of gene 41.
The double label technique was useful 35 years ago but nobody does it anymore. It was fun while it lasted.
(I never did figure out what 41P did during DNA replication but a few years after I left a postdoc identified 41P as a helicase—an enzyme that unwinds DNA ahead of the replication fork. The enzyme is now called gp41 for "gene product.")
Wednesday, March 25, 2009
What's the best way to describe a graduate student?
The controversy over the 1952 Nobel Prize reminds me that we haven't had a poll in a long time. Check out the poll in the left-hand sidebar. How would you describe a graduate student?
You must answer by April Fool's Day.
Nobel Laureate: Selman Waksman
The Nobel Prize in Physiology or Medicine 1952
"for his discovery of streptomycin, the first antibiotic effective against tuberculosis"
Selman Abraham Waksman (1888 - 1973) won the Noble Prize in 1952. The award was for discovering streptomycin.Waksman was a soil microbiologist at Rutgers University in New Jersey (USA). In the 1930s, after the success of penicillin, he decided to change the focus of his research and look for more antibiotics. He reasoned that soil microorganisms should be a good source of novel anti-bacterial drugs.
Streptomycin was the most famous of the many antibiotics discovered in Waksman's lab. It was largely due to the dedicated work of a graduate student, Albert Schatz, who first identified streptomycin's potent effect on gram negative bacteria in October 1943. Over the next few years, Waksman became famous for discovering streptomycin and Schatz was all but forgotten.
In 1950, Schatz sued his former supervisor for recognition, and a share of the royalties. The case was settled out of court with Rutgers agreeing that Schatz and Waksman would be identified as co-discoverers of streptomycin. Schatz received a share of the royalties.In spite of this settlement, the Nobel Prize committee awarded the prize to Wakesman and not to Waksman and Schatz. This was mildly controversial at the time but didn't qualify as a major scandal. It seems more egregious today.
The issue is part of a continuing controversy about how to attribute recognition when graduate students are working under the direction of their supervisors. There's no better way to start a fight than to bring this up with a group of graduate students. Are they apprentices, slaves, or collaborators?
I am indebted to Philip Johnson of York University (Toronto, Canada) for alerting me to the controversy and for sending along this excellent article about Albert Schatz.
Waksman does not specifically mention Schatz's contribution in his Nobel lecture but he is mentioned in the presentation speech (see below) in an obvious attempt to minimize his contribution. Knowing what we know now, should the Nobel Prize website be modified to include a discussion of the controversy? I think it should.
THEME:
Nobel Laureates
In 1940 Dr.Waksman and his collaborator had succeeded in isolating the first antibiotic, which was called «actinomycin» and it was very toxic. In 1942 another antibiotic was detected and studied, called «streptothricin». This had a high degree of activity against many bacteria and also against the tubercle bacillus. Further studies revealed that streptothricin was too toxic. During the streptothricin studies Dr. Waksman and his collaborators developed a series of test-methods, which turned out to be very useful in the isolation of streptomycin in 1943.
Encouraged by the discovery of streptothricin and stimulated by the triumphal development of penicillin treatment, the research team headed by Dr.Waksman continued their untiring search for new antibiotic-producing microbes. Before the discovery of streptomycin no less than 10,000 different soil microbes had been studied for their antibiotic activity. Dr. Waksman directed this work and distributed the various lines of research among his young assistants. One of these was Albert Schatz, who had previously worked with Dr. Waksman for 2 months and in June 1943 returned to the laboratory. Dr. Waksman gave him the task of isolating new species of Actinomyces. After a few months he isolated two strains of Actinomyces which were shown to be identical with Streptomyces griseus, discovered by Dr. Waksman in 1915. In contrast to the previous one the rediscovered microbe was shown to have antibiotic activity. To this antibiotic Dr. Waksman gave the name «streptomycin». He studied the antibiotic effect of streptomycin with Schatz and Bugie and found that it was active against several bacteria including the tubercle bacillus. These preliminary studies were completed in a relatively short time, thanks to the clear principles which had been set out previously by Dr. Waksman for the study of streptothricin.
The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.
Making Tracks
Look at the photo on the right. Do you know why this is an important discovery? Did you know you could win a case of beer for discoveries like this?
Find the answer on Catalogue of Organisms: More Crunchy Scleritome Goodness. Find out more about the little "problematic" animal in the photo.
Stasis Is Data, says Don McLeroy
Don McLeroy is a creationist dentist from Texas. His claim to fame is that he is the current chair of Texas State Board of Education. That board is trying to insert creationist-friendly standards into the state curriculum.
Today, the Austin American Statesman published an op-ed piece by McLeroy in which he defends creationism: Enlisting in the culture war.
It makes for amusing reading. I want to address one particular issue that illustrates how creationists misunderstand the science they criticize. It vividly points out what we are up against. The opponents of science don't even take the time to understand what they oppose.
Let's start by looking at the chart (right). It illustrates the now-famous pattern of punctuated equilibria as detected in the fossil record. What it shows is that speciation by cladogenesis (splitting) is associated with morphological change. When a new species evolves from a parent species it does so quite rapidly. After the speciation event (horizontal lines on the chart) the two species exist side-by-side in the same environment for millions of years without significant morphological change. Eventually they becomes extinct as shown by the termination of the vertical lines.
Species exist for 5-10 million years. During most of that time they do not change very much. This is what Eldredge and Gould called "stasis." The entire pattern is one of stasis interrupted by short periods of evolution at the time of speciation, or "punctuated equilibria."
The patterns in the fossil record raise interesting questions. One of the most important is whether it represents the normal pattern of evolution or whether it is confined to a minority of clades. What causes stasis? Why is change associated with cladogenesis? Why do species go extinct? All of these are widely discussed in the scientific literature.
None of the questions is a challenge to evolution. Punctuated equilibria is a pattern that might lead to an extension of evolutionary theory.
Now let's look at what McLeroy writes in his op-ed piece.
It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that).
Richard Dawkins
The next step in resolving this controversy is simply to use the scientific method to weigh in on the issue of evolution. Consider the fossil record. What do we actually observe? What are the data?I don't see a problem with explaining punctuated equilibria to high school students, assuming, of course, that Texas has competent science teachers. It would teach students about critical thinking and reinforce some of the fundamental concepts of evolution.
Stephen Jay Gould stated: "The great majority of species do not show any appreciable evolutionary change at all. [This is called 'stasis.'] These species appear ... without obvious ancestors in the underlying beds, are stable once established and disappear higher up without leaving any descendants."
"...but stasis is data..."
Once we have our observations, we can make a hypothesis. The controversial evolution hypothesis is that all life is descended from a common ancestor by unguided natural processes. How well does this hypothesis explain the data? A new curriculum standard asks Texas students to look into this question. It states: "The student is expected to analyze and evaluate the sufficiency or insufficiency of common ancestry to explain the sudden appearance, stasis, and sequential nature of groups in the fossil record." It should not raise any objections from those who say evolution has no weaknesses; they claim it is unquestionably true.
This isn't what McLeroy has in mind. I think it's very clear what he thinks about punctuated equilibria. He thinks it supports some (unstated) version of creationism. The point of his op-ed piece is to convince his supporters that scientists are trying to hide important evidence for creationism.
I'm assuming that McLeroy simply doesn't understand the science behind punctuated equlibria, or evolution, and that's why he misrepresents it in his article. This means that McLeroy is ignorant, stupid, or insane. There's another possibility but we won't consider that.
Here's something I found on the Wikipedia website for Don McLeroy.
In 2009, McLeroy spoke at a board meeting with several quotes from scientists in an attempt to discredit evolution. The quotes were later revealed by a biology teacher to be incomplete, out of context, or incorrect taken from a creationist website.[10][11] McLeroy said that while "some of the material was taken from the creationist site, he added: “A lot of the quotes I did get on my own.”You may be wondering if these out-of-context quotations include anything on punctuated equilibria or stasis. It would be embarrassing to find out that McLeroy repeated those misleading quotations only a few weeks after learning that they were wrong. Here's the list: Collapse of a Texas Quote Mine.
Pray for Texas. The decision on education standards will be made any day now.
[Image Credit: Punctuated Equilibrium and Patterns from the Fossil Record]
Tuesday, March 24, 2009
I'm Beginning to Really Like Jerry Coyne
That's because he writes things like Must we always cater to the faithful when teaching science?.
As long as I have been a scientist, I have lived with my colleagues’ view that one cannot promote the acceptance of evolution in this country without catering to the faithful. This comes from the idea that many religious people who would otherwise accept evolution won’t do so if they think it undermines their faith, promoting atheism or immoral behavior. Thus various organizations promoting the teaching of evolution, including the National Academy of Sciences and the National Center for Science Education, have published booklets or websites that explicitly say that faith and science are compatible. In other words, that is their official position. The view of many other scientists that faith and science (or reason) are incompatible is ignored or disparaged. As evidence for the compatibility, the most frequent reason cited is that many scientists are religious and many of the faithful accept evolution. While this proves compatibility in the trivial sense, it doesn’t show, as I’ve pointed out elsewhere, that the two views are philosophically compatible.I agree. Organizations like NCSE, AAAS, and the National Academies should just talk about science. As soon as they start to say that science and religion are compatible they are misrepresenting a huge number of scientists and stepping outside their mandates.
....
Because of this, I think that organizations promoting the teaching of evolution should do that, and do that alone. Leave religion and its compatibility with faith to the theologians. That’s not our job. Our job is to show that evolution is true and creationism and ID aren’t. End of story.
Monday's Molecule #114: Winners
UPDATE: The molecule is streptomycin, 5-(2,4-diguanidino-3,5,6-trihydroxy-cyclohexoxy)- 4-[4,5-dihydroxy-6-(hydroxymethyl) -3-methylamino-tetrahydropyran-2-yl] oxy-3-hydroxy-2-methyl-tetrahydrofuran-3-carbaldehyde. Streptomycin inhibits protein synthesis in bacteria. The Nobel Laureate is Selman Waxman.
This week's winners are Bill Chaney of the University of Nebraska and Elvis Cela of the University of Toronto.
Identify this molecule and briefly describe its function. You must supply the common name and one of the the formal IUPAC names. I'm looking for the Nobel Laureate who discovered this molecule.
The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.
There are seven ineligible candidates for this week's reward: Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto, Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, and Alex Ling from the University of Toronto.
Dima has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.
THEME:
Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.
Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.
Let the Physicists Fix the Economy.
Chad Orzel at Uncertain Principles has an interesting idea on how to fix the current economic crisis. He thinks all traders and financial wizards should be fired because Physics Can Fix This.
And, seriously, do you really think that these transactions are too complicated for physicists to figure out? We're talking about people who have spent the last several years thinking about folding and twisting strings in eleven dimensions. Unless the transaction records are all encrypted in some private cipher, they'll have no trouble figuring it out. And even if they are encrypted, that will only slow things down a little-- given what we know about the rocket scientists on Wall Street, the cipher key is probably written on a Post-It stuck to the computer. With a magnet.Sounds good to me. It can't possibly be any worse.
Better yet, they'll be cheap. We're talking about theoretical physics grad students and post-docs-- most of them are currently working for less than Vikram Pandit spends on shoes. The pre-bonus salary given to a typical financial executive is more money than they can reasonably expect to make in their current line of work. It'll be a major blow to the over-priced restaurant industry in lower Manhattan, but they'll rebound once they learn to mark up Ramen noodles a thousand percent.
And best of all, we don't have to worry about them getting greedy and wrecking the entire global economy in order to make some short-term gains. We're talking about people who, to this point, have completely sacrificed their financial well-being in pursuit of higher mathematical truth. They're used to working toward the long-term success of abstract goods.
Medical Care? - Canada Bad, America Great
OldFart is an American doctor who sometimes posts on M.D.O.D.. Here's what (s)he wrote last Friday [Natasha Richardson R.I.P.].
How do you think Natasha Richardson's family likes that socialized medicine in Canada??Every civilized country has socialized medicine because they think it's a fundamental right to get medical care without having to worry about how to pay for it. What is it about American doctors that they are so opposed to this concept?
Any 3rd year med student or an EMT worth his salt would know she was a set-up for an epidural hematoma. It is an incredibly classic story for it. And so easy to diagnose with an 8 second CT of the brain.
But in Canada I bet she was "put in queue" for a CT scan next week and had to fly to the US in order to get one in a real hospital's ED. But by then she was brain dead.
Still want Hussein's version of medicine here you fuckin' brain dead liberals?? Could save a lot of tax payor's dollars, huh? Everybody could get the "same access" to health care huh?
Just not when it's your family..
My prayers to Ms Richardson's family.
M.D.O.D. is a group blog. Another American doctor, 911doc, has added this update ...
EDITOR'S NOTE: OLDFART POSTED BELOW A FEW HOURS AGO AND SITTING HERE IN BED WITH THE WIFE I LEARNED, IN THAT REPUTABLE MEDICAL JOURNAL 'PEOPLE MAGAZINE', THAT MRS. RICHARDSON HAD INDEED REFUSED TRANSPORT AND MEDICAL CARE AFTER WHAT WAS A MINOR FALL ON A 'BUNNY SLOPE' (ON WHICH SHE WAS NOT WEARING A HELMET).I'm also curious. How easy is it to get a CT scan in the first aid station at the bottom of a ski slope in either country? How often are CT scans performed in the small town local hospitals? In the USA does it matter whether you have insurance or would everyone be given a CT scan after banging their head? Do celebrity actresses get treated differently than single mothers earning $35,000 per year with no health insurance?
THOUGH I TOO WONDERED IF THE 'QUEUE UP' PROBLEM WAS AT PLAY HERE IT EVIDENTLY WAS NOT, AND SO WHILE WE WILL NO DOUBT HAVE OTHER OPPORTUNITY TO COMPARE THE ACCESS TO EMERGENCY CARE IN SOCIALIZED COUNTRIES TO THE ACCESS TO EMERGENCY CARE HERE, THIS IS NOT THE CASE TO DO IT WITH.
I WILL ASK THIS QUESTION OF ANY CANADIAN PHYSICIANS WHO HAPPEN BY HOWEVER. HOW QUICKLY CAN ONE GET A CT OF THE BRAIN IN A CASE SUCH AS THIS WHERE THERE APPARENTLY WAS NO OBVIOUS TRAUMA AND THE ONLY COMPLAINT ONE HOUR AFTER THE FACT WAS A WORSENING HEADACHE? HOW ABOUT FOR A INTERNATIONAL CELEBRITY?
And what does Hussein have to do with medical care in Canada?
[Hat Tip: Pure Pedantry]
Signals of Positive Selection in Humans?
Signals of recent positive selection in a worldwide sample of human populations is the title of a paper that has just been published in Genome Research (Pickrell et al. 2009).
These workers looked for signs of positive selection using techniques similar to those employed by Hawks et al. in their 2007 paper. That 2007 paper serves as one of the important bits of evidence in the recently published book, The 10,000 Year Explosion.
The idea is to pick out regions of the genome that have linked clusters of polymorphisms (SNPs = single nucleotide polymorphisms). These cluster are called haplotypes and they indicate that a region of the genome has not undergone much recombination in the recent past, because recombination tends to shuffle polymorphisms. One way this linkage could be preserved is when a part of the genome is under positive selection so its increase in frequency is rapid. This is called a selective sweep.
Pickrell et al. (2009) examined a database of 657,143 SNPs called the Human Genome Diversity-CEPH Panel (HGDP). These polymorphisms come from a global sample of 53 populations. The Hawks et al. (2007) paper examined the HapMap database of 3.1 million SNPs from three populations.
Pickrell et al. (2009) also detect a large number of regions that are candidates for positive selection. Their sites overlap those of the earlier study—about half of their sites were also identified by Hawks et al. (2007).
A number of candidates for positive selection are discussed in the paper but the authors note that many of the potential sites are not near any genes that have been well-characterized. It's important to look at individual cases in order to get a feel for the data, especially since the possibility of false positives is a concern.
Specific Examples
Here are a few of the single genes that were identified in one or more groups (e.g. Bantu, Europeans, native American etc.) They are from the top ten strongest signals so they presumably represent some of the best cases for selection.
Heat Shock Transcription Factor 2 (HSF2): This is one of two genes for the major heat shock transcription factor. The heat shock genes are highly conserved and so is their regulation. It's very unlikely that a mutation in the native North American population would be beneficial relative to the allele in all other populations.
succinate-CoA ligase, GDP-forming, β-subunit (SUCLG2) This is the gene for succinyl-CoA synthetase, one of the enzymes of the Krebbs cycle. The data suggest that an allele of this gene was positively selected in the population of Oceania (Pacific Ocean). This doesn't seem very likely.
oxoacyl-ACP synthase, mitochondrial (OXSM) This is the mitochondrial version of a β-ketoacyl synthetase, a standard enzyme required for fatty acid synthesis. An allele shows signs of positive selection in Eurasian populations but not in any other population. It doesn't seem likely that there's an allele conferring a beneficial effect that hasn't already become fixed in mammals over 100 million years ago.
mannosidase, alpha, class 2A, member 1 (MAN2A1) This is a mannosidase located in the Golgi. It's required for one of the last stages in the oligosaccharide maturation pathway—a pathway that's found in all eukaryotes. Pickrell et al. (2009) suggest that an allele of this gene has been selected in the pygmy and Bantu populations. Again, it isn't likely that a standard metabolic gene would be selected in this way.
False Positives?
The patterns of potential selective sweeps strongly suggest local and/or regional sweeps. Since this is the pattern you might expect from random genetic drift, it raises a question about false positives. The authors of the 2009 paper say, ...
Further exploration of the geographic patterns in these data and their implications is warranted, but from the point of view of identifying candidate loci for functional verification, the fact that putatively selected loci often conform to the geographic patterns characteristic of neutral loci is somewhat worrying. This suggests that distinguishing true cases of selection from the tails of the neutral distribution may be more difficult than sometimes assumed, and raises the possibility that many loci identified as being under selection in genome scans of this kind may be false positives. Reports of ubiquitous strong (s = 1-5%) positive selection in the human genome (Hawks et al. 2007) may be considerably overstated. [My emphasis-LAM]It should come as no surprise that John Hawks disagrees. He has posted a rebuttal on his blog at: Overstating the obvious.
It's an interesting debate but let's not lose sight of the most important point—it is a scientific debate. The case for massive amounts of accelerated human evolution has not been proven in spite of what you might read in The 10,000 Year Explosion and in articles in the popular press.
UPDATE: See Razib's posting: Signals of recent positive selection in a worldwide sample of human populations...maybe
Hawks, J., Wang, E.T., Cochran, G.M., Harpending, H.C., and Moyzis, R.K. (2007) Recent acceleration of human adaptive evolution. Proc. Natl. Acad. Sci. (USA) 104:20753-20758. Epub 2007 [PubMed] [DOI:10.1073/pnas.0707650104]
Pickrell, J.K., Coop, G., Novembre, J., Kudaravalli, S., Li, J.Z., Absher, D., Srinivasan, B.S., Barsh, G.S., Myers, R.M., Feldman, M.W., and Pritchard, J.K. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Research 23 published in advance March 23, 2009 [DOI: 10.1101/gr.087577.108]
Monday, March 23, 2009
Fox News host apologizes
From the CTV website: Fox News host apologizes in face of Canadian outrage. [See the video at: Here's What Fox News Thinks of Canada's Military.]
The host of a Fox News program has apologized for a segment on the Canadian military that Defence Minister Peter MacKay called "disgusting" and "crass."I wonder if they've ever treated 9/11 in a "lighthearted, humorous and ridiculous" manner? What about the USA? Have they ever mocked their own country on this show?
A group of pundits on "Red Eye with Greg Gutfeld," which airs weekdays at 3 a.m. on Fox News, each took turns trashing Canada and its military during an episode that aired on March 17.
...
Gutfeld issued an apology Monday afternoon saying, "I realize that my words may have been misunderstood. It was not my intent to disrespect the brave men, women and families of the Canadian military, and for that I apologize."
But the host also seemed to defend his program, adding "Red Eye is a satirical take on the news, in which all topics are addressed in a lighthearted, humorous and ridiculous manner."
Monday's Molecule #113
Identify this molecule and briefly describe its function. You must supply the common name and one of the the formal IUPAC names.
I'm looking for the Nobel Laureate who discovered this molecule.
The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.
There are seven ineligible candidates for this week's reward: Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto, Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, and Alex Ling from the University of Toronto.
Dima has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.
THEME:
Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.
Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.
Comments will be blocked for 24 hours.
Dropping Courses
Chad Orzel of Uncertain Principles has started a discussion about when students should be allowed to drop courses [Academic Poll: Drop It Like It's Hot?].
Why not visit his blog and share your thoughts? I think this is an important issue. Universities may need to make changes.
Astrology in The Toronto Star
I read The Toronto Star every day but I missed this article published last Friday [The vernal equinox: Science and mysticism].
Staff reporter Nick Aveling thought it would be fun to contrast the words of a scientist (Astronomer Randy Attwood) and an astrologer (Michael Barwick). The title of the article implies that this might be an attempt at humor but I'm not sure.
What are the implications of today's equinox?Phil Plait of Bad Astronomy didn't think it was funny: Canada slips further into goofiness. Neither did any of the people who posted comments on the newspaper's website.
Attwood: As the earth goes around the sun it appears that the overhead sun seems to be creeping towards the north. For the next three months it will continue to creep north until the first day of summer, when it's at its farthest point north. As the sun gets higher that means it's able to concentrate more heat on the ground.
Barwick: Somebody who's born at 0 degrees Aries – that's a particularly strong Aries person ... William Shatner, Captain Kirk, has kind of the ultimate Aries energy in a way: going forth, boldly going where no one has gone before, pioneering, being in command, leading intuitively. This is Aries.
Sunday, March 22, 2009
Gene Genie #44
The 44th edition of Gene Genie has been posted at Mary Meets Dolly [Gene Genie #44].
My first Gene Genie! For my Catholic readers, Gene Genie is the "blog carnival of genes and genetic conditions." (No rubbing of ancient oil lamp necessary.) I hope I shall do it justice.The beautiful logo was created by Ricardo at My Biotech Life.
The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.
Here are all the previous editions .....
- Scienceroll
- Sciencesque
- Genetics and Health
- Sandwalk
- Neurophilosophy
- Scienceroll
- Gene Sherpa
- Eye on DNA
- DNA Direct Talk
- Genomicron
- Med Journal Watch
- My Biotech Life
- The Genetic Genealogist
- MicrobiologyBytes
- Cancer Genetics
- Neurophilosophy
- The Gene Sherpa
- Eye on DNA
- Scienceroll
- Bitesize Bio
- BabyLab
- Sandwalk
- Scienceroll
- biomarker-driven mental health 2.0
- The Gene Sherpa
- Sciencebase
- DNA Direct Talk
- Greg Laden’s Blog
- My Biotech Life
- Gene Expression
- Adaptive Complexity
- Highlight Health
- Neurophilosophy
- ScienceRoll
- Microbiology Bytes
- Human Genetic Disordrs
- The Genetic Genealogist
- ScienceRoll
- Genetics & Health
- Human Genetics Disorders
- ScienceRoll
- Genetic Future
- Pharmamotion
- Mary Meets Dolly
SEED Reviews The 10,000 Year Explosion
The latest issue of SEED praises US President Obama's emphasis on science and offers a list of ideas "for revising the role of science in America." The number one recommendation is "Make Scientific Literacy a National Priority."
What's needed is better ways of fostering critical thinking and imagination not only in the nation's schools but among its citizenry.Good advice, although I wish they'd mentioned the importance of skepticism along with critical thinking. Scientifically literate citizens should not blindly accept every new breakthrough that appears in the scientific literature.
Scientific literacy is not just about being able to weigh in on scientific debates of the day by parsing climate change or understanding the difference between a theory and a guess. The ability to empirically test one's ideas about the world and discard beliefs in light of new evidence is fundamental to the ideals of a just and democratic society; it brings people to the table to debate issues reasonably and with minimum rhetoric.
We must rely on good science journalism to inform the general public. Good science journalists will analyze and distill the latest scientific information and help put it in context. They will explain things that are controversial, but exciting, and avoid being swept up by the inevitable rhetoric that accompanies every new discovery.
T.J. Kelleher is a senior editor at SEED. In this same issue, Kelleher reviews The 10,000 Year Explosion a book by Gregory Cochran and Henry Harpending. Let's see whether the review is an example of critical thinking.
This is a trade book, not a scientific publication. The main thesis of the book is that humans are evolving rapidly. This thesis is supported by several lines of evidence.
- A number of just-so stories from anthropology [see Examples of Accelerated Human Evolution]. Some of them are reasonable, many aren't.
- A paper published in Dec. 2007 claiming there are thousands of human genes being selected in various populations (Hawks et al. 2007). To the best of my knowledge this analysis has not been independently replicated in the scientific literature and the technology is not without critics.
- A paper by Hawks et al. (2008) claiming that human adaptive evolution has recently accelerated by acquiring genes from Neanderthals.
- A claim that within the past 1,000 years the IQ of Ashkanazi Jews has increased relative to the general European population because medieval Ashkanazi Jews engaged in occupations that required high intelligence (Cochran et al. 2006). [See Race and Intelligence, Evolution in the Ashkenazi Jewish Population.]
Let's see what T.J. Kelleher thinks of all this. Here's the first two paragraphs of the review.
"The 10,000 Year Explosion" would be important even if it were only about population genetics and evolutionary biology, but Gregory Cochran and Henry Harpending, a physicist turned biologist and a biological anthropologist, respectively, at the University of Utah, have written something more. This book is a manifesto for and an example of a new kind of history, a biological history and not just of the prehistoric era. Covering broad ground over human history and prehistory, the authors argue for the singular importance of genes in human history, not just as markers but also as makers.Is this an example of critical thinking? Is this the best way to enhance scientific literacy?
The first four of the book's seven chapters serve as something of a preamble to the final three. Cochran and Harpending first present the evidence for recent, accelerated human evolution after the invention of agriculture. In its own right that argument is a fairly revolutionary proposition, bit one with clear data, both skeletal and genetic, to back it up: investigations of the human genome undertaken as part of the International Hap Map Project and elsewhere have clearly demonstrated that selection has been ongoing and has accelerated over time. This has been a landmark finding in human biology, and Cochran and Harpending, building on their own work and that of others, including John Hawks of the University of Wisconsin-Madison, convincingly tie the advent of architecture—and the stresses resulting from the new diets. new modes of habitation, new animal neighbors, and new modes of living that agriculture made possible—to this accelerated evolution. It is work destined to launch a thousand careers.[My emphasis-LAM]
Cochran, G., Hardy, J., and Harpending, H. (2006) Natural history of Ashkenazi intelligence. J. Biosoc. Sci. 38:659-93.
Hawks, J., Cochran, G., Harpending, H.C., and Lahn, B.T. (2008) A genetic legacy from archaic Homo. Trends Genet. 24:19-23. Epub 2007 Dec 3. [PubMed] [DOI: 10.1016/j.tig.2007.10.003 ]
Hawks, J., Wang, E.T., Cochran, G.M., Harpending, H.C., and Moyzis, R.K. (2007) Recent acceleration of human adaptive evolution. Proc. Natl. Acad. Sci. (USA) 104:20753-20758. Epub 2007 [PubMed] [DOI:10.1073/pnas.0707650104]
New Scientist Sheds its Last Ounce of Credibility
Many of us were upset last month when New Scientists published some old news about the early tree of life and sensationalized it on their cover [Darwin Was Wrong?]. They claimed that "Darwin Was Wrong" when, in fact, Charles Darwin didn't even know about molecular evolution or the relationships of bacterial species.
The New Scientist editors admitted that the cover was designed to sell magazines and they seemed to be aware of the problem [Explaining the New Scientist Cover].
They even published a critical letter from Daniel Dennett, Richard Dawkins, Jerry Coyne, and PZ Myers [Blunt Talk from Four Evolutionists].
New Scientists has now begun an ad campaign to attract new subscribers and guess which cover they choose? Jerry Coyne and PZ Myers are advocating a scientific (Coyne) or personal (PZ) boycott of New Scientist. I'm conflicted about that. In spite of its recent errors, New Scientist is far superior to SEED and Discover as a science magazine. If we really want to punish the worst of the popular science magazines then SEED is a much better target.1 
1. The monthly column by PZ Myers in SEED is the exception, not the rule.
Here's What Fox News Thinks of Canada's Military
The ignorance in this segment makes me very angry. Can anyone tell me what the US military is protecting Canada from? The Iraqis? Cubans? The people of Granada or Panama? Kosovo? Afghanistan? Lebanon? Maybe the Somalis, or the Vietnamese?
Canada has only been invaded once in its history (1812) and it wasn't by any of those countries.
Does this embarrass any of my American friends, especially those who like to defend the American media?
[Hat Tip: Canadian Cynic]
Saturday, March 21, 2009
Canada Has Been Saved from George Galloway
George Galloway is a Scottish MP who speaks out on behalf of Palestinians and expresses support for Hamas. He was recently invited to Canada to give a speech in Toronto but Canada's Immigration Minister, Jason Kenney, immediately recognized that Canada can't tolerate that. Kenney determined that a member of the British parliament is a threat to our national security and Galloway was banned from entering Canada.
Jennifer Smith is embarrassed by her country's behavior [Jason Kenney's Personal War on Terror]. So am I.
"Science journalists? Don't make me laugh"
"Science journalists? Don't make me laugh" is the title of an article by Ben Goldacre appearing in The Guardian. Goldacre discusses how British health and science journalists covered the recent papers on testing for prostate cancer.
The bottom line is ...
Journalists insist that we need professionals to mediate and explain science. From today's story, their self-belief seems truly laughable.Note to science journalists; people are beginning to catch on to your scam. Matt Nisbet helped a lot by making it obvious.
I want science journalists to start policing themselves. It's time to take off the blinders and recognize that many science journalists are not very good at accurately reporting about science. The good ones need to speak out instead of issuing motherhood statements about how good they all are.
Friday, March 20, 2009
Get a Job in Newfoundland
Memorial University of Newfoundland
Tenure-track Positions in Gene Expression and Metabolic Biochemistry
The Department of Biochemistry at Memorial University invites applications for two tenure-track positions at the level of Assistant Professor, one in each of the targeted areas listed below. Applicants should have a PhD or equivalent degree with a minimum of two years post-doctoral research experience and should possess a strong research record with significant future promise. The successful applicants will be expected to develop externally funded research programmes with relevance to one of the research foci of the department: 1) Development and health, and 2) Membranes and molecular interactions. They will also be expected to show a commitment to effective teaching at the undergraduate and graduate levels. The new faculty members will be encouraged to collaborate with the faculty in the department and elsewhere in the university.
1) Gene Expression (ref # VPA-BIOC-2008-001). The successful applicant for this position will be expected to develop a research programme focused on some area of gene regulation such as, but not limited to, transcriptional regulation by DNA-protein interactions, chromatin structure/remodeling, or gene expression profiling.
2) Metabolic Biochemistry (ref # VPA-BIOC-2008-002). The successful applicant will be expected to develop a research programme focused on some area of metabolic biochemistry such as, but not limited to, metabolomics, gene-nutrient interactions, or metabolic regulation including signaling pathways.
Applicants should submit a curriculum vitae, a summary of past research, a statement of proposed research and reprints of 3 publications. The application must be accompanied by the names, affiliations and contact information of three referees.
Memorial University is the largest university in Atlantic Canada offering diverse undergraduate, graduate and medical school programmes to almost 18,000 students. As the Province’s only university, Memorial plays an integral role in the educational and cultural life of the Province of Newfoundland and Labrador. The Biochemistry Department consists of 18 faculty with expertise in a wide range of biochemical areas. For information about the Department of Biochemistry please see the departmental webpage. St. John’s is a safe, friendly city with great historic charm, a vibrant cultural life, affordable housing and easy access to a wide range of outdoor activities. For more information about St. John’s please see the municipal website.
Memorial University is committed to employment equity and encourages applications from qualified women and men, visible minorities, aboriginal people and persons with disabilities. All qualified candidates are encouraged to apply; however, Canadian Citizens and Permanent Residents will be given priority. Partners of candidates for positions are invited to include their resumes for possible matching with other job opportunities.
Applications should be received by the Department of Biochemistry by May 15, 2009.
Applications should be addressed to: Dr. Martin Mulligan, Head, Department of Biochemistry, Memorial University, St. John’s, NL, Canada, A1B 3X9. Applications may also be submitted electronically to biochead@mun.ca or by fax: (709) 737-2422. Please quote the appropriate job reference number on all correspondence.
Happy Vernal Equinox!
Today at 11:44 UT (= 7:44 AM Eastern Time) the sun appeared to cross the celestial equator in its northward movement. (See Movement of Our Star for the real explanation.)
Most people in the Northern Hemisphere think of this as the first day of Spring. I prefer to think of it as the end of Winter. Springlike days are still a few weeks off in Toronto.
Here's a brief explanation from Wikipedia.
An equinox in astronomy is the moment in time (not a whole day) when the centre of the Sun can be observed to be directly above the Earth's equator, occurring around March 20 and September 23 each year.
More technically, at an equinox, the Sun is at one of two opposite points on the celestial sphere where the celestial equator (i.e., declination 0) and ecliptic intersect. These points of intersection are called equinoctial points—the vernal point and the autumnal point. By extension, the term equinox may be used to denote an equinoctial point.
[Photo Credit: The photograph shows the position of the sun at various times throughout the year at 12h (UT) over the Temple of Aphaia (490-480 BC), Athens (Anthony AYIOMAMITIS). The image is called the solar analemma. See here for an explanation. The celestial equator is perpendicular to the long axis of the image and half way between the top and bottom. The crossover point of the figure eight depends on your distance from the equator. I'd love to see one taken on the equator or in the southern hemisphere.]
[Image Credit: eSky]
"Science is my job - faith is my rock"
"Science is my job - faith is my rock" is the title of an article in today's Globe and Mail. Zosia Bielski is a journalist who writes on a wide range of topics with an emphasis on social issues. She was prompted to write about the conflict between science and religion because of the controversy surrounding Canada's Science Minister, Gary Goodyear.
As usual, there's no mention of the fact that most active scientists are non-religious. The proportion of atheist scientists is much higher than the proportion of atheists in the general public. Apparently this fact has little to do with a conflict between science and religion.
Zosia Bielski takes the standard approach to this issue. She interviews three religious scientists and discovers that they can reconcile their faith and science. What a surprise!
She does not interview anyone who thinks there's a serious conflict between science and religion. If she had written an article about the lack of faith among scientists and had only interviewed atheist scientists, she would have been accused (rightly) of biased journalism. The lack of balance would have been recognized by any competent editor and she would have been told to go out and get statements from religious scientists. It seems like "balance" only works one way.
What's interesting about the article is that she interview Rev. Ambury Stuart, a climatologist who is also a United Church minister. What Stuart has to say about the conflict between science and religion is very interesting.
"I struggled with this all my life. I grew up in the United Church, I always attended. You say, 'Well, can you believe in God if you believe in Newton's laws?' And the short answer is yes, you can, but it takes a while," Mr. Stuart said.This is about as honest as you get. Stuart is telling us that the conflict between religion and science is real and challenging. You have to work really hard at reconciling science and religion. Many religious beliefs don't survive the challenge.
"You have to think through a lot of stuff. It's not simplistic. You try and divide your brain into two bits: One bit you'll use on Sunday and the rest of it you'll use the rest of the week, and it doesn't work. It doesn't have to."
Evolutionary evangelist Michael Dowd's book "Thank God For Evolution" helped Mr. Stuart smooth out his own message at Glebe Road United Church in Toronto. He weaves his scientific passions into his sermons.
"You can look at scripture and say this means a whole lot more than we ever thought it meant before, because it applies to everything," Mr. Stuart said. "The idea that we are related, that we are kin with the rest of life, is essential for Christianity to do anything constructive in the ecological crisis."
That's an important lesson for people like Gary Goodyear. Any religion that denies evolution is incompatible with science. You have to choose one or the other. You can't be a Young Earth Creationist without being anti-science. If that kind of faith is your "rock" then science can't be your job.
Thursday, March 19, 2009
Nobel Laureate: Willard Libby
The Nobel Prize in Chemistry 1960.
"for his method to use carbon-14 for age determination in archaeology, geology, geophysics, and other branches of science"
Willard Frank Libby (1908 - 1980) won the Nobel Prize in Chemistry for using 14C decay to date organic material. Libby set out to study cosmic rays. He, and others, determined that one of the effects of cosmic ray is to produce carbon-14 atoms from nitrogen-14 atoms in the upper atmosphere.
He determined that the rate of production of carbon-14 and its rate of disintegration (half-life ~5600 years1) has reached an equilibrium. No matter where you find carbon, in the ocean, the atmosphere, or the biosphere, its radioactivity corresponds to about 14 disintegrations per minute per gram.
Living things incorporate this equilibrium mixture of 14C and 12C. Thus, we, like all other living things, are radioactive and this level of radioactivity can be measured using techniques that Willard Libby developed. When living things die, they stop incorporating carbon and the existing 14C continues to decay. As time goes on, the level of radioactivity declines with a half-life of ~5600 years. The age of organic material can be determined directly by measuring the remaining radioactivity of extracted carbon.
That's the basis of radiocarbon dating. Libby confirmed the feasibility of the technique by dating Egyptian artifacts, tree rings of known age, and the dead sea scrolls (labeled "Bible" in the figure). The results confirmed that radiocarbon dating works.
The results were published in the late 1940's. Since then, the technology has improved considerably. Today, scientists measure 14C directly using mass spectrometry so they don't have to wait for it to decay. Detailed calibration curves have been worked out to take account of the fact that cosmic ray intensity has varied somewhat over the past few thousand years.
With current technology, reliable dates back as far as 60,000 years can be obtained. This is about the limit of radiocarbon dating because the half-life of Carbon-14 is so short compared to more long-lived isotopes.
The presentation speech highlights the importance of radiocarbon dating in a number of disciplines.
THEME:
Nobel Laureates
Libby's dating method soon attracted attention from the scientific world, and it was not long before carbon-14 laboratories were set up in many countries. Today, some forty institutions carry on investigations in this field, nearly half of them in America. Also here, in Sweden, we have such institutions, and their investigations have given results of great value. All age determinations - nowadays several thousand every year - are published in a general review, and thus made rapidly available throughout the world. The literature in this field has grown from year to year, and at present covers an impressive area.One of the scientists who suggested Libby as a candidate for the Nobel Prize has characterized his work in the following way: "Seldom has a single discovery in chemistry had such an impact on the thinking in so many fields of human endeavour. Seldom has a single discovery generated such wide public interest".
Professor Libby. The idea you had 13 years ago of trying to determine the age of biological materials by measuring their carbon-14 activity was a brilliant impulse. Thanks to your great experimental skill, acquired during many years devoted to the study of weakly radioactive substances, you have succeeded in developing a method that is indispensible for research work in many fields and in many institutes throughout the world. Archaeologists, geologists, geophysicists, and other scientists are greatly indebted to you for the valuable support you have given them in their work. The Swedish Academy of Sciences desires to join those who offer you grateful thanks for what you have done for the benefit of so many sciences, and has decided to award you this year's Nobel Prize for Chemistry. May I congratulate you on behalf of the Academy, and ask you to receive the prize from the hands of His Majesty the King.
1. The modern value is 5730±40 years.
[Photo Credit: University of California History Digital Archives, Copyright © 2006 The Regents of the University of California.]
The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.
Science Journalism in Decline
There's an editorial in Nature this week on science journalism [Filling the Void]. It's not very interesting.
There's an article by Geoff Brumfiel that's much more interesting [Science journalism: Supplanting the old media?]. Since I'm mentioned in that article, and since I can't comment on their site, I thought I'd make a few comments here.
First, I posted a comment on Chris Mooney's blog where I said, "Most of what passes for science journalism is so bad we will be better of without it." What I meant to say was, "Most of what passes for science journalism is so bad we will be better off without it". I just want there to be a correct version that everyone can quote.
The article correctly points to a trend ...
Traditional journalists are increasingly looking to such sites to find story ideas (see 'Rise of the blogs'). At the same time, they rely heavily on the public-relations departments of scientific organizations. As newspapers employ fewer people with science-writing backgrounds, these press offices are employing more. Whether directly or indirectly, scientists and the institutions at which they work are having more influence than ever over what the public reads about their work.Over the past decade it has been the "professional" science journalists themselves who were the gullible victims of scientific hype and PR. The scientific accuracy of press releases leaves a great deal to be desired. They are, after all, intended to promote the researcher and the institution. They are heavily biased.
It is not a good thing that individual scientists and their institutions are managing the science news. It's a disaster.
The amount of material being made available to the public by scientists and their institutions means that "from the pure standpoint of communicating science to the general public, we're in a kind of golden age", says Robert Lee Hotz, a science journalist for The Wall Street Journal. But that pure standpoint is not, or should not be, all that there is to media coverage of science. Hotz doubts that blogs can fulfil the additional roles of watchdog and critic that the traditional media at their best aim to fulfil. That sort of work seems to be on its way out. "Independent science coverage is not just endangered, it's dying," he says.I hear this a lot. Science journalists seem to think that they have served as watchdogs and science critics by tempering the hype and propaganda spewed out by institutional PR departments.
I wish it were true. If science journalists really did their job of separating the wheat from the chaff then I would be their biggest cheerleader. Instead, for the most part they have been completely seduced by the lure of scientific breakthroughs and revolutions promoted by self-serving scientists and their institutions. There are notable exceptions, but the majority of science journalists have failed at the one job they are supposed to do better than non-science journalists.
That's why we would be better off without them.
Coincidentally, Ryan Gregory has just posted an article about Scitable, "A Collaborative Learning Space for Science" hosted by Nature magazine. I'm pretty sure that Nature is proud of this site. They think the articles are good examples of science writing.
Ryan highlights an article by Leslie Pray, a free-lance science writer. The title is: Transposons, or Jumping Genes: Not Junk DNA?. Read what Ryan Gregory has to say at Scitable Again. He thinks the article is "total nonsense." I agree with him.
If this is an indication of the ability of science journalists to cut to the chase and give us the straight dope, then it's no wonder that scientists are skeptical.
Regulatin' Genes
Some of us old fuddy-duddies have been learning about the regulation of transcription for over forty years. When you've been teaching about regulatory proteins, like HOX proteins, for twenty-five years, the novelty sort of wears off.
It's fun to see the enthusiasm of students who have just recently been "turned on" by gene regulation, especially when one of them is also a Toronto Blue Jays fan! Strange that the university looks a lot more like Stanford than the University of Toronto [HumBio instructor, students rap about science on YouTube].
Time to Change the Channel
My local Liberal candidate is Omar Alghabra, who lost the last election to one of Harper's Conservatives. Omar sent me a link to this video. He though I might get a kick out of it.
I did.
Don't Leave Canada Behind
This is a letter sent to Prime Minister Stephen Harper and Leader of the Opposition Michael Ignatieff. It is signed by hundreds of Canadian scientists. I don't expect it to have any effect on Harper but it will be interesting to see if the Liberal Party decides to support science.
March 16, 2009
The Right Honourable Stephen Harper Prime Minister of Canada The Right Honourable Michael Ignatieff, Leader of the Opposition Ottawa
Subject: Don't leave Canada behind
Dear Prime Minister, Dear Leader of the Opposition
U.S. President Barack Obama is taking advantage of the current financial crisis to push his country forward in new directions by greatly boosting funding to scientific research and education as a means to jump start innovation in a new economy. The scope of his vision is stunning, including an increase of more than $15 billion in scientific research, and a promise to double the funding for education in the next 10 years. For more details, see http://www.sciencedebate2008.com.
Our government has also tried to stimulate the research / university sector in Canada, wishing to take important initiatives. At the heart of the plan is a $2 billion dollars infrastructure fund for shovel-ready renovation projects in post-secondary institutions, a fund that was actively solicited by university presidents. There is also an additional $750 million for the Canadian Foundation for Innovation (CFI), and $87.5 million over three years for doctoral scholarships. While these funding announcements are surely welcome, we would like to share our concerns as to the potential effect of some of these decisions, in particular in view of the bold and visionary course taken by the Obama administration south of the border.
1. When the U.S. government is proposing to boost the funding of the National Science Foundation (NSF) by 40% ($3 billion on top of its current $6.9 billion), we see Canada’s "stimulus budget" cutting NSERC's by 5%. When the U.S. administration is proposing to boost the funding of the National Institute of Health (NIH) by 30% ($8.5 billion in addition to its current $29 billion), our "stimulus budget" is cutting CIHR's by 5%, while essentially ignoring the needs of Genome Canada. When US researchers are being actively approached for ideas to use the stimulus money to think big and to hire and retain their researchers, their Canadian counterparts are now scrambling to identify budget cuts for their Labs, while worrying about the future of their graduating students. Recent Tri-council grants competitions, which were post stimulus budget, are already pointing towards sharply lower success rates (by more than 20% in some disciplines), lower start-up grants for young researchers, and negligible research funding for smaller institutions and provinces. These cuts are huge steps backward for Canadian Science and we ask the government to immediately develop a multi-year plan to significantly increase this country’s R&D investment through our granting councils.
2. The infrastructure support for Canada's post-secondary institutions is surely beneficial for their depleted budgets for deferred maintenance. However, the federal support requires 50% in matching funds which few institutions currently have. The net effect of this decision will be to dictate priorities for universities and provincial governments too eager to get the federal funds, and as such to divert further funds from teaching, training and research. We therefore ask government to drop the requirement of matching funds.
3. The CFI has provided a tremendous boost to certain aspects of Canada's research infrastructure over the last 10 years. However, the constraints of the program have left many important research disciplines out of its potential beneficial impact. Moreover, similar matching rules continue to apply to CFI projects, and as a consequence of the present lack of available support from the private sector and from provincial governments, even some of the already approved projects are being postponed and cancelled. At this point in time, we believe that removing the matching requirements for current and future CFI projects would be extremely beneficial for Canada and its research infrastructure.
4. The funding of an additional 500 doctoral scholarships is great news for a country that is committed to have ``the best educated, most skilled and most flexible workforce in the world". However, it seems this funding is coming at the expense of the highly qualified personnel (HQP’s) that could have been recruited more efficiently by our senior researchers through their Tri-Council grants. We believe that a more efficient strategy for ensuring a successful HQP policy is to give our leading researchers the flexibility to manage the selection, recruitment, and support of their own graduate students through their peer-reviewed research grants, and via well-established leveraging procedures with the universities and the private sector. We also regret that the $17.5-million assigned to SSHRC for graduate scholarships have been earmarked towards students in business and finance. As Alain Dubuc writes in La Presse: ``En boudant certains domaines de recherche, nos universités vont perdre leur pouvoir d'attraction. Et bien des jeunes talentueux iront ailleurs.
(See http://www.cyberpresse.ca/)
5. President Obama is proposing to double federal funding for education over the next 10 years, and pledging to “restore science to its rightful place” with billions in new investments. To advise his government, he has appointed leading scientists to his cabinet and as his advisors (including a Nobel laureate as energy Secretary). The Obama administration has also involved the directors of NIH and NSF in federal budget discussions about the future of research. We need a similar approach in Canada, where top research scientists and humanists can help shape directions in Ottawa for research funding.
A new economy is coming out of this crisis and research and development will be the lifeblood to that new economy. We call upon you not to let Canada be left behind.
Sincerely,
Margaret Ann Armour, Chemistry, Order of Canada (University of Alberta) Tom Archibald, Chair of Mathematics (Simon Fraser University) Alejandro Adem, Mathematics (University of British Columbia) Tom Allison (University of British Columbia) Ali Arya, Information Technology (Carleton University) Peter Abrams, Ecology and Evolutionary Biology (University of Toronto) Jim Arthur, Mathematics (University of Toronto) Marshall Agueh, Mathematics (University of Victoria) John Beamish, Chair, Physics (University of Alberta) Edward Bierstone, Mathematics (University of Toronto) Yaacov Ben-David, Biophysics (University of Toronto) Herman Brunner, Mathematics (Memorial University) Margaret Beattie, Mathematics (Mount Allison University) Peter Borwein, Mathematics (Simon Fraser University) Anne Bourlioux, Mathematics (Universite de Montreal) Hans U. Boden, Chair, Math and Statistics (McMaster University) David Brydges, Mathematics (University of British Columbia) Martin Barlow, Mathematics (University of British Columbia) Michael Bennett, Mathematics (University of British Columbia) Kai Behrendt, Mathematics (University of British Columbia) Mark Bauer (University of Calgary) Vijay Bhargava, Electrical Engineering (University of British Columbia) Hichem Ben-El-Mechaiekh,Chair, Mathematics (Brock University) Sydney Bulman-Fleming, Chair, Mathematics (Wilfred Laurier University) Sandra Barr, Acting Head, Earth and Environmental Science (Acadia University) W. Kendal Bushe, Mechanical Engineering (University of British Columbia) Sherryl Bisgrove, Biological Sciences (Simon Fraser University) Mary Berbee, Botany, (University of British Columbia) Jeff Babb, Chair, Mathematics and Statistics (University of Winnipeg) Maxim R. Burke, Chair, Mathematics and Statistics (University of PEI) Susan Baldwin (University of British Columbia) Chris Bose, Mathematics (University of Victoria) Patrick Brosnan, Mathematics (University of British Columbia) Michelle Boue (Trent University) John Bowman, Mathematics (University of Alberta) Walter Craig, Mathematics (McMaster University) John Carter, Applied Science and Engineering (University of Toronto) Rustum Choksi, Mathematics (Simon Fraser University) Dan Coombs, Mathematics (University of British Columbia) Clifton Cunningham, Mathematics (University of Calgary) Mohamed Cheriet, Engineering (École de technologie supérieure, Montreal) Marilyn Chapman (University of British Columbia) Eric Cytrynbaum, Mathematics (University of British Columbia) Jingyi Chen, Mathematics (University of British Columbia) K. Carriere Cough, Statistics, (University of Alberta) Richard Craster, Mathematics (University of Alberta) Vladimir Chernousov, Mathematics (University of Alberta) James Colliander, Mathematics (University of Toronto) Christina C. Christara, Computer Science (University of Toronto) John Clague, Earth Sciences (Simon Fraser University) Laura Cowen, Mathematics (University of Victoria) Paul Deguire directeur, mathématiques et de statistique (Université de Moncton) Karl Dilcher, Chair, Math. and Stats. (Dalhousie) Lawrence M. Dill (Simon Fraser University) Henri Darmon, Mathematics (McGill University) Rob DeWreede, Botany, (University of British Columbia) Gregory Dudek, Chair, Computer Science (McGill University) Dan Dumont, Director, Molecular and Cellular Biology (University of Toronto) David Dunlop, Physics (University of Toronto) Ivar Ekeland, Math Economics (University of British Columbia) George Elliott, Mathematics (University of Toronto) Kadriye Ercikan, Education (University of British Columbia) Yousry Elsabrouty (The University of Calgary) Neil Emery, Director, Environmental & Life Sciences (Trent University) Roderick Edwards (University of Victoria) Ian Frigaard, Math and Mech. Engineering (University of British Columbia) Don Fraser, Statistics (University of Toronto) Richard Froese, Mathematics (University of British Columbia) Don Fisher (University of British Columbia) Eugene Fiume, Computer Science (University of Toronto) John Friedlander, Mathematics (University of Toronto) Jorge Filmus, Molecular and Cellular Biology (University of Toronto) Nassif Ghoussoub, Mathematics (University of British Columbia) Randy Goebel, Computing Science (University of Alberta) Dan Gibson, Earth Sciences (Simon Fraser University) Andrew Granville, Mathematics (Universite de Montreal) Pengfei Guan, Mathematics (McGill University) Ling Guan, Electrical Engineering (Ryerson) Sean Graham, Botany (University of British Columbia) Dmitri Goussev (Gusev), Chair, Chemistry (Wilfrid Laurier University) Stephen Gustafson, Mathematics (University of British Columbia) Terry Gannon, Mathematics (University of Alberta) Veronique Godin, Mathematics (University of Calgary) J. Scott Goble, Education (University of British Columbia) Charles Gale, Chair, Physics (McGill University) Ed Grant, Head,Chemistry (University of British Columbia) Ian Graham, Mathematics (University of Toronto) Jacques Hurtubise, Chair, Mathematics & Statistics (McGill University) Hedley David, Medecine (University of Toronto) Viqar Husain, Chair, Mathematics (U.New Brunswick) Stephen B. Heard Chair, Biology (University of New Brunswick, Fredericton) François Huard, Head, Mathematics (Bishop's University) Nicola J Hodges, School of Human Kinetics (University of British Columbia) Felix Herrmann, Earth and Ocean Science (University of British Columbia) Dr. Holger Hintelmann, Chair, Department of Chemistry (Trent University) Craig Heinke, Physics (University of Alberta) Anita Hubley, Education (The University of British Columbia) Alexander Holroyd, Mathematics (University of British Columbia) Reinhard Illner, Mathematics (University of Victoria) Victor Ivrii, Mathematics (University of Toronto) Andrew Irvine (University of British Columbia) Slim Ibrahim (University of Victoria) Sebastian Jaimungal, Statistics (University of Toronto) Lisa Jeffrey, Mathematics (University of Toronto) Daniel James, Physics (University of Toronto) Robert Jerrard, Mathematics (University of Toronto) Rachel Kuske, Head, Mathematics (University of British Columbia) Young-June Kim, Physics (University of Toronto) Young-Heon Kim, Mathematics (University of British Columbia) Niky Kamran, Mathematics (McGill University) Kalpdrum Passi, Chair, Mathematics & Computer Science (Laurentian University) Boualem Khouider, Mathematics ( University of Victoria) Kalle Karu, Mathematics (University of British Columbia) Maria Klawe, Computer Science (President of Harvey Mudd) Patrick Keeling, Botany, (University of British Columbia) Jennifer Klenz, Botany, (University of British Columbia) Leslie R. Kerr, Biology/Psychology (Trent University) Faqir Khanna, Physics (University of Alberta) Don Krug, Education (University of British Columbia) Raymond Kapral, Chemistry (University of Toronto) Anthony Lau, Mathematics (University of Alberta) Robert K. Logan, Physics (University of Toronto) Michael Lamoureux, Mathematics (University of Calgary) Yue Xian Li, Mathematics (University of British Columbia) Victor Leung, Electrical Engineering (University of British Columbia) Victor G. LeBlanc, Directeur, Chair, Mathematics (University of Ottawa) Wenyuan Liao (University of Calgary) Mark Lewis, Mathematics (University of Alberta) James Lewis, Mathematics (University of Alberta) Aaron Levin (University of Alberta) Alexander Litvak, Mathematics (University of Alberta) Paul Lasko, Chair, Biology (McGill University) Sheldon Lin, Statistics (University of Toronto) Hoi-Kwong Lo, Electrical and Computer Engineering (University of Toronto) Wendy Lou, Biostatistics (University of Toronto) Ben Liang, Electrical and Computer Engineering (University of Toronto) Bill Langford, Mathematics (Guelph University) Marcelo Laca (University of Victoria) Alan Mackworth, Computer Science (University of British Columbia) Bojan Mohar, Mathematics (Simon Fraser University) Richard G. Miller, Biophysics and Immunology (University of Toronto) Greg Martin, Mathematics (University of British Columbia) Robert McCann, Mathematics (University of Toronto) Franklin Mendivil (Acadia University) Akos Magyar, Mathematics (University of British Columbia) Brian Marcus, Mathematics (University of British Columbia) Barrie McCullough (University of British Columbia, Okanagan) Robert Moody, Mathematics (University of Alberta) Patrick Martone, Botany, (University of British Columbia) Peter Minev, Mathematics (University of Alberta) Amy Metcalfe, Education (University of British Columbia) Jim Mattsson (Simon Fraser University) Bill Milsom, Head, Zoology (University of British Columbia) Eckhard Meinrenken, Mathematics (University of Toronto) Sharon Morsink, Physics (University of Alberta) Bonny Norton, Education (University of British Columbia) Raymond Ng, Computer sc. (University of British Columbia) Adrian Nachman, Electrical and Computer Engineering (University of Toronto) Carl Ollivier-Gooch, P.Eng. (University of British Columbia) Fergal O'Hagan (Trent University) Peter Ottensmeyer, Medical Biophysics (University of Toronto) Don Page, Physics (University of Alberta) Anthony Peirce, Mathematics (University of British Columbia),Ed Perkins, Mathematics (University of British Columbia), Marion Porath (University of British Columbia) Roger Pierre, Directeur, Mathematiques et de statistique (Universite Laval) Cindy Prescott, Forestry (University of British Columbia) Arturo Pianzola, Mathematics (University of Alberta) Royann Petrell (University of British Columbia) Peter Pivovarov (University of Alberta) Daniel D. Pratt, Education (University of British Columbia) Erich Poppitz, Physics (University of Toronto) Ue-Li Pen, Astrophysics (University of Toronto) Toniann Pitassi, Computer Science (University of Toronto) Ian Putnam, Mathematics (University of Victoria) Jeremy Quastel, Mathematics and Statistics (University of Toronto) Christiane Rousseau (Universite de Montreal) David J. Rowe, Physics (University of Toronto) Andrew Rechnitzer, Mathematics (University of British Columbia) Cristian Rios, Mathematics (University of Calgary) Chris Radford, Head Mathematics and Statistics (Memorial University) Loren Rieseberg, Botany (University of British Columbia), Dale Rolfsen, Mathematics (University of British Columbia), Reinhard Jetter, Botany (University of British Columbia) Volker Runde, Mathematics (University of Alberta) Omar Rivasplata (University of Alberta) Peter C. Ruben, Director Kinesiology (Simon Fraser University) Steven Rogak, Mech. Eng. (University of British Columbia) Jeffrey Rosenthal, Mathematics (University of Toronto) Jonathan Rose, Chair of Electrical and Computer Engineering (University of Toronto) Nancy Reid, Statistics (University of Toronto) Joe Repka, Mathematics (University of Toronto) William Reed, Mathematics (University of Victoria) Gordon Slade, Mathematics (University of British Columbia) Stephen Strother, Medical Biophysics (University of Toronto) Gordon Semenoff, Physics (University of British Columbia) Mohamad Sawan, Engineering (Polytechnique, University of Montreal) Viena Stastna (University of Calgary) Fred Sack, Head of Botany (University of British Columbia) Paul Stephenson, Head, Mathematics and Statistics (Acadia University) Raj Srinivasan, Chair, Mathematics (University of Saskatchewan),Brian Seymour, Mathematics (University of British Columbia),Anne Scholefield, Education (University of British Columbia) Jedrzej Sniatycki, Mathematics (University of Calgary) K D Srivastava, Engineering (University of British Columbia) Philip Stamp, Physics (University of British Columbia) Dominik Schoetzau, Mathematics (University of British Columbia) Paul L. Smith, Head, Earth and Ocean Sciences (University of British Columbia) Sudarshan Sehgal, Mathematics (University of Alberta) Catherine Sulem, Mathematics (University of Toronto) Theodore Shepherd, Physics (University of Toronto) Vuk Stambolic, Medical Biophysics (University of Toronto) Nicole Tomczak-Jaegermann (University of Alberta) Peter Tiidus, Acting Dean, Science (Wilfrid Laurier University) Phillippe Tortell, Botany, (University of British Columbia) John R. Topic (Trent University) Elisabeth Tillier, Genomics (University of Toronto) Tai-Peng Tsai, Mathematics (University of British Columbia) Derek J. Thorkelson, Chair, Earth Sciences (Simon Fraser University) Mak Trifkovic (University of Victoria) Bill Unruh, Physics (University of British Columbia) Jennifer A. Vadeboncoeur, Education (University of British Columbia) Stephanie van Willigenburg, , Mathematics (University of British Columbia) Andrew Vreugdenhil, Director, Materials Science (Trent University) Frank Weichman, Physics (University of Alberta) Rabab Ward, Electrical Engineering (University of British Columbia) Brent Ward, Earth Sciences (Simon Fraser University) Michael Ward, Mathematics (University of British Columbia) Jason Waywitka (University of Alberta) Doug Wiens (University of Alberta) Eric Woolgar, Physics (University of Alberta) Tony Ware, Mathematics (University of Calgary) Shoshana Wodak, Biochemistry, and Molecular Genetics (University of Toronto) Margaret Wyeth (University of Victoria) Glyn Williams-Jones, Earth Sciences (Simon Fraser University) Reem Yassawi, Head, Math (Trent University) Vlad Yaskin (university of Alberta) Janet Ye, Mathematics (University of Victoria) Nora Znotinas, Chair, Physics & Computer Science (Wilfrid Laurier University) Richard Zemel, Computer Science (University of Toronto) Julie Zhou, Mathematics (University of Victoria)
[Hat Tip: Genomicron]
John Moore Gets It Right
Believe it or not, there are columnists at The National Post who actually understand the issue concerning Gary Goodyear's beliefs. John Moore tells it like it is when he says, ignorance is not a civil right.
Of course it matters whether the Science Minister acknowledges or contests evolution. This isn't a case of a politician who likes to read the Bible and pray -- it's a Cabinet Minister who holds philosophical beliefs that are antithetical to his portfolio. Jonathan Kay insists Christian-hating lefties would never raise similar alarm over a Cabinet minister of another faith. Well this leftie, who holds faith in considerably high regard, would have very serious concerns about an aboriginal justice minister who declined to comment on the efficacy of Western legal systems, and would be even more up in arms if a Scientologist health minister refused to discuss mental illness. And I'm pretty sure the National Post editorial board would have some pretty pointed questions for a Muslim MP given the status of women portfolio.I wish I'd written that!
The first problem with Goodyear is that he fronts the science portfolio in a government that has demonstrated through its most recent budget that it doesn't value the sector. The man delegated to argue the vital importance of science at the Cabinet table doesn't actually know what it is. More significantly, Goodyear's insistence that religion should come to bear on science provides comfort to those who teach their children the falsehood that to follow God you must reject science.
This is the willful dissemination of scientific illiteracy. More frankly put, it is the promotion of stupidity.
Gary Goodyear "Clarifies" Some More
Minister of State for Science and Technology, Gary Goodyear, is being asked of clarify his position on science. Is he, or is he not, anti-science? Specifically, does he reject the scientific fact of evolution? Yesterday, newspapers reported on his wishy-washy definition of evolution. Most people concluded that he is, indeed, a creationist of the sort that rejects science.
Today's National Post documents the evolving strategy of the Conservative Party and their friends. They are trying to make this into an issue about freedom of religion rather than a simple question of scientific literacy [My beliefs not relevant: Goodyear].
In light of those responses, critics were still wondering yesterday whether someone who believes the Earth is just thousands of years old is heading Canada's science and technology sector.Hmmm ... let's think about this for a minute. How many people think it's relevant that a Minister of Science and Technology is anti-science?
Mr. Goodyear bucked at requests to clarify his point of view yesterday, cutting short a question into whether he defined evolution in the popular Darwinian sense.
"My entire background has been in science, and my personal beliefs are not important," Mr. Goodyear repeated. "What I'm doing and what the government is doing to move this country forward -- that's important."
When pressed, Mr. Goodyear added that there would be no conflict of interest for a minister heading the science and technology industry to hold a belief in creationism.
"Absolutely not. How ridiculous. It's absolutely ridiculous. That's why I didn't answer the question, because it has no relevance," he said.
David Asper Doesn't Get It
David Asper1 writes about The Liberal War on Faith in today's issue of The National Post.
Throughout the growth of the current Conservative party, starting with the establishment of Reform, the Alliance and then the merger with the Progressive Conservatives, there has been a festering undercurrent of anti-religious bigotry in the methods of attack used by left-wing critics.We need to put a stop to this moving of goalposts. The issue is NOT religious faith. Nobody objects to a Minister of Science who accepts the basic tenets of science and is religious. As Asper points out in his article, it's almost certain that previous ministers of science believed in a God that created the Earth billions of years ago. They also accepted the scientific fact of evolution.
Now, we have a reporter from the Globe following the same script. The essence of the newspaper's front-page slag on Tuesday was that if you have a religious faith that includes the idea of a God who created the heavens and the earth billions of years ago, it must mean you entirely reject the evolutionary process that shaped the life forms that subsequently developed -- and are therefore unfit to be the Minister of Science and Technology.
What we can't accept is a Minister of Science who is anti-science. If your religion forces you to reject fundamental facts of science in order to cling to the idea that the Earth in only 10,000 years old then that's a problem. If you believe in such nonsense then you can be a newspaper columnist—or maybe even the owner of a major newspaper—but you can't be in charge of science policy in Canada. It makes us the laughing stock of civilized nations. Even the USA is laughing at us this time, and that's saying a lot.
David Asper is trying to make this into an attack on all religious beliefs but it's not. He should be ashamed of himself for distorting the truth and avoiding the real issue.
On the other hand, anyone who writes this (below) isn't going to listen to reason.
It's also worth noting that the Charter of Rights -- created under a Liberal government --begins with an acknowledgement of the supremacy of God. Our national anthem also calls on God to keep our land glorious and free. So please, enough with the facade of outing people who believe in a higher power.
1. David Asper is the Chairman of the National Post newspaper and Executive Vice President of CanWest Global Communications Corp. He is a former trustee of the Fraser Institute, a conservative propaganda machine that masquerades as a research institute. He is a supporter of Conservative Party candidates.
[Photo Credit: University of Toronto]
Wednesday, March 18, 2009
Goodyear's Bad Day
Here's a link to Chris Selley's article on The National Post website [Chris Selley's Full Pundit: Goodyear's bad day].
The article has links to several Canadian journalists. I'm pleased to see that many of them recognize the problem. We can't have a creationist Minister in charge of science.
The Future of Science Blogging
Daniel Brown of Biochemical Soul is looking for feedback on the future of science blogging [Science Blogging: The Future of Science Communication & Why You Should be a Part of it].
Personally I don't think the science blogosphere is going to attract more than a few percent of scientists and science students. Most of them don't have the time or the interest. Most of my colleagues are completely turned off by blogs. They see blogs as a negative influence on science.
The science blogosphere is a fun and interesting playground for those of us who have eclectic interests and are willing to invest the time and effort to read a few dozen blogs a day, but that's not going to appeal to the average scientist. Daniel does a good job of listing all the benefits of blogging and reading blogs but, in my experience, none of these benefits are convincing for the average scientist.
Frankly I think that's a good thing. My experience with newsgroups over the past twenty years indicates that it's much better to have a small number of really dedicated and interested participants than to try and expand to cover everyone. Besides, the more science blogs there are out there, the most difficult it is to read them all.
Four Solar Eclipses on Saturn
The inhabitants of Saturn were recently treated to four solar eclipses on the same day. In the video below you can see the four moons and their shadows crossing Saturn. The photos were taken by the Hubble Space Telescope and the video was prepared by National Geographic.
It's exciting to be living at a time when such images are quickly available to the general public. This video would have seemed like magic only a century ago. A century from now it might seem trivial since we may have our own satellites orbiting Saturn.
Liberal Science Critic Marc Garneau Says that Believing in Evolution Is not a Job Requirement for the Science Minister
Marc Garneau (right) is the Liberal science critic in Canada's House of Commons. The same Globe and Mail article that mentioned Goodyear's "clarification" of his position on evolution has the following quotation from Marc Garneau [Minister clarifies stand on evolution].
On Tuesday, Liberal science critic Marc Garneau said that believing in evolution is not a job requirement for the science minister.Garneau is dead wrong. If you reject evolution you are anti-science. There's no two ways about it. You cannot deny evolution without attacking the very core of scientific reasoning and evidence-based conclusions. What Garneau is saying is that it's OK for a science minister to be anti-science.
“It is a personal matter. It is a matter of faith.… I don't think it prevents someone from being a good minister,” said the former astronaut, who has been a vocal critic of the government for its cuts to the three granting councils that fund university-based research in Canada.
But Jim Maloway, the New Democratic Party science critic, said that if the minister did not believe in evolution that could influence government policy. “I don't see a commitment to a really broad approach if you are encumbered by the denial of evolution,” he said.
That would be like putting a witch doctor (or a chiropractor) in charge of health care, or a soothsayer in charge of finances.
There may be a place for anti-science creationists in the Federal Cabinet but not in charge of science. Acceptance of the core principles of science is a job requirement because part of the job is gaining the confidence of the scientific community. You can't have a science minister who questions the honesty and integrity of Canadian scientists. Make no mistake about it, that's exactly what creationists do.
We need a new minister of science and we need a new Liberal science critic.1
1. What do other scientists think about this? See Science minister's coyness on evolution worries researchers. Note that the scientists are worried about a creationist in charge of science while the non-scientists don't see it as a big problem.
Gary Goodyear "Clarifies" His Stance on Evolution
Today's Globe and Mail reports that Canada's Minister of State (Science and Technology) has "clarified" his position on the validity of evolution [Minister clarifies stand on evolution].
OTTAWA — Science minister Gary Goodyear now says he believes in evolution.Those of us who have been dealing with creationists for several decades will recognize those words. That's a creationist speaking. They're willing to admit to microevolution within kinds but unwilling to admit to common descent.
“Of course I do,” he told guest host Jane Taber during an appearance on the CTV program Power Play. “But it is an irrelevant question.”
....
On Tuesday, Mr. Goodyear said twice during the CTV interview that he did believe in evolution.
“We are evolving every year, every decade. That's a fact, whether it is to the intensity of the sun, whether it is to, as a chiropractor, walking on cement versus anything else, whether it is running shoes or high heels, of course we are evolving to our environment. But that's not relevant and that is why I refused to answer the question. The interview was about our science and tech strategy, which is strong.”
Goodyear could have easily said that he accepts common descent and the idea that modern species, including humans, evolved over billions of years from more primitive organisms. That's what "believing" in evolution means to most people. He did not say that.
That pretty much settles it for me. Goodyear is a creationist. He rejects one of the fundamental concepts of biology. That makes him anti-science.
The man in charge of science in Canada is anti-science. Heaven help us.
Tuesday, March 17, 2009
Monday's Molecule #112: Winners
UPDATE:The equation shows beta decay of 14C from Wikipedia. The Nobel Prize went to Willard Libby for developing 14C dating technology.
This week's winner is Dima Klenchin from the university of Wisconsin (again) by two minutes over Ollie Nanyes. The undergraduate winner is Alex Ling of the University of Toronto.
You may have noticed that today's molecule isn't a molecule. Your task is to identify what this equation is describing.
There's only one Nobel Laureate whose discovery is relevant. The first person to identify the equation and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.
There are six ineligible candidates for this week's reward: James Fraser of the University of California, Berkeley, Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto, Maria Altshuler of the University of Toronto, David Schuller of Cornell University and Adam Santoro of the University of Toronto
A previous winner has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.
THEME:
Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.
Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.
Happy St. Patrick's Day!
Niall Nóigiallach is a very famous man (Nóigiallach is Gaelic for "having Nine Hostages"). He was an Irish King who lived from about 350 to 405 AD. The "nine hostages" refers to hostages that he kept from each of the places that owed him allegiance.
Niall was fond of raiding the coast of Roman Britain and on one of those raids he captured a man named Maewyn Succat, who became a slave in Ireland. Succat eventually escaped, returned to Britain, and became a Christian missionary. He then went back to Ireland to convert the Irish heathens to Christianity. We know Maewyn Succat by his Christian name, Patrick, or Saint Patrick.
Aside from converting the Irish heathens to Christianity, St. Patrick is famous for his skill as a magician. One of his most famous tricks was removing all the snakes from Ireland. At least that's what the legend says.
Connie Barlow describes A St. Patrick's Day Parable.(This is the same Connie Barlow I met last summer—the one who edited Evolution Extended.)
Ireland is a land of no snakes. It has no slithering serpents. There are no rat snakes in Ireland; there are no rattlesnakes; there are no garter snakes. There are no snakes at all.She goes on to explain why there are no snakes in Ireland but I prefer to swtich to the website of the Smithsonian National Zoological Park for their explanation of Why Ireland Has No Snakes.
The absence of snakes in Ireland seems to cry out for an explanation — but only if one regards or ventures to the island from outside: from England, say, or from continental Europe. To the indigenous Celts, there would, of course, have been nothing to explain. The Gaelic peoples no more needed to explain an absence of snakes on their island home than they needed to explain an absence of kangaroos. To those who came to Ireland from abroad, however, a dearth of serpents was a striking anomaly in need of an answer.
We humans must have answers. And so arose the legend of St. Patrick and the snakes. The reason Ireland has no snakes, the story goes, is that Patrick charmed all snakes on the island to come down to the seashore, slither into the water, and drown. So Ireland did once have snakes, but it has them no more. Patrick charmed them all into the sea.
Now snakes are found in deserts, grasslands, forests, mountains, and even oceans virtually everywhere around the world. Everywhere except Ireland, New Zealand, Iceland, Greenland, and Antarctica, that is.
One thing these few snake-less parts of the world have in common is that they are surrounded by water. New Zealand, for instance, split off from Australia and Asia before snakes ever evolved. So far, no serpent has successfully migrated across the open ocean to a new terrestrial home. As the world's oceans have risen and fallen over the millennia, land bridges have come and gone between Ireland, other parts of Great Britain, and the European mainland, allowing animals and early humans to cross. However, any snake that may have slithered it's way to Ireland would have turned into a popsicle when the ice ages hit.
The most recent ice age began about three million years ago and continues into the present. Between warm periods like the current climate, glaciers have advanced and retreated more than 20 times, often completely blanketing Ireland with ice. Snakes, being cold-blooded animals, simply aren't able to survive in areas where the ground is frozen year round. Ireland thawed out for the last time only 15,000 years ago. Since then, 12 miles of icy-cold water in the Northern Channel have separated Ireland from neighboring Scotland, which does harbor a few species of snakes. There are no snakes in Ireland for the simple reason that they can't get there.
[The book cover is from a book by Sheila MacGill Callahan (Author) and Will Hillenbrand (Illustrator). You can buy it on Amazon.com.]
Reposted from St. Patrick Banished Snakes from Ireland with a snippet from Niall Nóigiallach - Niall of the Nine Hostages. You find out how Irish I am by clicking here.
You Can Be Good Without God
I spotted this ad at the Queen's Park subway station in Toronto.
Kudos to the Humanist Association of Canada.
NSERC President Praises Gary Goodyear
Gary Goodyear is Canada's Minister of State (Science and Technology). His government has just cut funding of basic research grants by $148 million over the next three years. Gary Goodyear is a chiropractor and he may be a creationist.
So, what does the President of NSERC think of this? See the [press release].
OTTAWA — Prime Minister Stephen Harper ventured into the lion's den Monday, defending his government's record on science funding before some of the country's top researchers.I know some people who would disagree with Suzanne Fortier. Two representatives of the Canadian Association of University Teachers (CAUT) didn't have such a favorable impression [When Chiropractors Get Angry ....].
He emerged without a scratch.
Indeed, he actually basked in praise for Gary Goodyear, his minister of state for science and technology.
Goodyear has been much maligned by some scientists who maintain research was shortchanged in the Jan. 27 federal budget. But there was no criticism Monday at an awards ceremony for the winners of prestigious research prizes handed out by the federally funded Natural Sciences and Engineering Research Council.
"It has been a real pleasure for us to work with the Hon. Gary Goodyear," said NSERC president Suzanne Fortier.
"He has already proven himself a champion of the science and technology community."
Some people would argue that. as a kind of public servant, the President of NSERC should not criticize government policy. Perhaps, but that doesn't mean she has to suck up to the executioner.
[Photo Credit: NSERC]
Does Canada's Science Minister Accept Evolution?
You might think that's a silly question. How could anyone in Canada become Minister of State (Science and Technology) and not accept the most important scientific fact in biology? Yes, it's true that Gary Goodyear is a chiropractor but he can't also be a creationist, can he?
Apparently he can, according to The Globe and Mail [Minister won't confirm belief in evolution].
Researchers aghast that key figure in funding controversy invokes religion in science discussionWe are in far worse trouble than I thought. No wonder the Stephen Harper party is cutting back on basic research. They must think most researchers are really stupid for believing in all those silly theories like evolution.
Canada's science minister, the man at the centre of the controversy over federal funding cuts to researchers, won't say if he believes in evolution.
“I'm not going to answer that question. I am a Christian, and I don't think anybody asking a question about my religion is appropriate,” Gary Goodyear, the federal Minister of State for Science and Technology, said in an interview with The Globe and Mail.
A funding crunch, exacerbated by cuts in the January budget, has left many senior researchers across the county scrambling to find the money to continue their experiments.
Some have expressed concern that Mr. Goodyear, a chiropractor from Cambridge, Ont., is suspicious of science, perhaps because he is a creationist.
Monday, March 16, 2009
Monday's Molecule #112
You may have noticed that today's molecule isn't a molecule. Your task is to identify what this equation is describing.There's only one Nobel Laureate whose discovery is relevant.
The first person to identify the equation and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.
There are six ineligible candidates for this week's reward: James Fraser of the University of California, Berkeley, Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto, Maria Altshuler of the University of Toronto, David Schuller of Cornell University and Adam Santoro of the University of Toronto
A previous winner has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.
THEME:
Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.
Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.
Comments will be blocked for 24 hours.
Casey Luskin on Junk DNA and Junk RNA
Intelligent Design Creationists can't abide junk DNA. Its very existence refutes the idea that living things are designed by some intelligent being. This is why the IDiots go out of their way to make up stories "disproving" junk DNA.
The latest attempt is by Casey Luskin [Nature Paper Shows "Junk-RNA" Going the Same Direction as "Junk-DNA"]. Having failed to explain why half of the human genome is composed of defective transposons, he now pins his hope on the idea that most of the genome is transcribed. Luskin seems particularly upset by my statement that most of these transcripts are junk [Junk RNA].
Luskin thinks that a recent paper in Nature supports his view that a large fraction of the genome isn't junk. The paper by Guttman et al. (2009) says no such thing. Here's the important part ...
Genomic projects over the past decade have used shotgun sequencing and microarray hybridization1, 2, 3, 4 to obtain evidence for many thousands of additional non-coding transcripts in mammals. Although the number of transcripts has grown, so too have the doubts as to whether most are biologically functional5, 6, 13. The main concern was raised by the observation that most of the intergenic transcripts show little to no evolutionary conservation5, 13. Strictly speaking, the absence of evolutionary conservation cannot prove the absence of function. But, the markedly low rate of conservation seen in the current catalogues of large non-coding transcripts (<5% of cases) is unprecedented and would require that each mammalian clade evolves its own distinct repertoire of non-coding transcripts. Instead, the data suggest that the current catalogues may consist largely of transcriptional noise, with a minority of bona fide functional lincRNAs hidden amid this background. Thus, to expand our understanding of functional lincRNAs, we are faced with two important challenges: (1) identifying lincRNAs that are most likely to be functional; and (2) inferring putative functions for these lincRNAs that can be tested in hypothesis-driven experiments.In other words, most of the transcripts are probably transcriptional noise, or junk, just as I said. This is the consensus opinion among informed1 molecular biologists.
Guttman et al. wanted to identify the small subset that might be functional. They identified 1,675 transcripts that show evidence of conservation. The average transcript has six exons averaging 250 bp. Thus, each transcript has about 1500 bp. of conserved exon sequence.
Even if every single one of these lincRNAs have a biological function they will only account for 1675 × 1500 = 2.5 million bp. This represents less than 0.1% of the genome. Casey Luskin ain't gonna disprove junk DNA using this paper.
Luskin ends his article with ...
As an ID proponent, I'm still waiting for Darwinists to let go of their precious "junk" arguments for blind evolution and common descent and learn the lesson that you can't assume that if we don't yet see function for a biomolecule, then it's probably just "junk."This is a point of view that creationists share with many scientists who haven't studied the subject. They assume that the only reason for labeling most of our DNA junk is because we don't know what it does. That's just not true. There's plenty of good evidence that most of our genome can't be functional. We know a lot about the part that consists of transposons and defective transposons, for example [Junk in Your Genome: SINES and Junk in your Genome: LINEs]. That's 44% of our genome.
1. I added the qualifier "informed" after a commenter pointed out that most molecular biologists probably don't know enough about the topic to have an opinion. Thus, according to this commenter, the consensus opinion would be "I don't know."
Science Cannot Fully Describe Reality, Says Templeton Prize Winner
Shocking news: the winner of this year's Templeton Prize says that science isn't everything. He proposes a way to reconcile science and religion [Science Cannot Fully Describe Reality, Says Templeton Prize Winner].
The only shocking thing about this is that Science magazine treats it seriously. Don't they know what the Templeton Prize is for? It's for people who advocate reconciliation between science and religion.
Sunday, March 15, 2009
Censorship at Uncommon Descent
Barry Arrington posted this message on Uncommon Descent.
The moderation policy does not apply to you; you are held to a higher standard. I expect your posts to have at least some tangential relationship to Darwinism, ID, or the metaphysical or moral implications of each. The purpose of this site is not to provide a place for you to jump up and rant on one of your pet peeves. DaveScot will no longer be posting at UD.What in the world did DaveScot do to deserve this?
He posted an article pointing out that religious people were often racist. He challenged the current dogma on Uncommon Descent that was trying to link Darwin to racism. You can read it here but you won't find it at Racism Sans Darwin - other inspirations on Uncommon Descent. Here's an excerpt ...
Since we now seem to be focused on racism instead of design detection and my motto is “When in Rome do as the Romans do” in order to balance the picture of the theory of evolution’s role in racist movements let’s look at some of the other modern history where evolution isn’t the banner around which racists rally.I guess the IDiots at Uncommon Descent don't want anyone to distract from their "Darwin was a racist" campaign.
Selected bits from Religious Tolerance on Christian Identity Movements . Timothy McVeigh, for instance, was a card carrying CIM member.History:
The Christian Identity movement is a movement of many extremely conservative Christian churches and religious organizations, extreme right wing political groups and survival groups. Some are independent; others are loosely interconnected. According to Professor Michael Barkun, one of the leading experts in the Christian Identity movement, “This virulent racist and anti-Semitic theology, which is practiced by over 50,000 people in the United States alone, is prevalent among many right wing extremist groups and has been called the ‘glue’ of the racist right.”
The largest Christian Identity movement has traditionally been the Ku Klux Klan which was reorganized in 1915 by William Simmons, a Christian pastor. He had been inspired by the film The Birth of a Nation which portrayed the KKK as a champion of white civilization. The KKK slid into obscurity by the second World War, but was revitalized in the mid 1950’s as a reaction to enforced racial integration in the southern US.
DaveScot was a big fan of Expelled I wonder if he'll complain to Ben Stein?
[Hat Tip: Afarensis]
What's Up with New Scientist?
Amanda Gefter wrote a nice article in New Scientist pointing out the sneaky tricks that creationists use to discredit science. You can read the article here.
As a book reviews editor at New Scientist, I often come across so-called science books which after a few pages reveal themselves to be harbouring ulterior motives. I have learned to recognise clues that the author is pushing a religious agenda. As creationists in the US continue to lose court battles over attempts to have intelligent design taught as science in federally funded schools, their strategy has been forced to... well, evolve. That means ensuring that references to pseudoscientific concepts like ID are more heavily veiled. So I thought I'd share a few tips for spotting what may be religion in science's clothing.Unfortunately, you can't read this article on the New Scientist website because it has been removed. If you click on How to spot a hidden religious agenda you'll find the following message ....
Red flag number one: the term "scientific materialism". "Materialism" is most often used in contrast to something else - something non-material, or supernatural. Proponents of ID frequently lament the scientific claim that humans are the product of purely material forces. At the same time, they never define how non-material forces might work. I have yet to find a definition that characterises non-materialism by what it is, rather than by what it is not.
New Scientist has received a complaint about the contents of this story. It has temporarily been removed while we investigate. Apologies for any inconvenience.I can't imagine a complaint that would cause a respectable magazine to withdraw that article. It sounds like New Scientist isn't standing behind its writers.
[Hat Tip: PZ Myers]
Friday, March 13, 2009
Shepherd's Pie
John Wilkins knows about Real Meat Pies.
Janet Stemwedel has a recipe for Vegetarian Shepherd's Pie.
VEGETARIAN SHEPHERD'S PIE!!!! Gimme a break.
Janet, what do you think those sheps are herding out there in the fields? Tofu?
The Profzi Scheme
This cartoon is making the rounds. It's from PHD Comics.
I've been associated with four universities in my career and I've never seen anything that even remotely resembles this. In my experience, departments recruit outstanding junior faculty who may, or may not, work in a field similar to current faculty members. Usually not. No single Professor makes the decision to recruit new scholars to the department.
In my experience, when funding gets tight it is often the senior faculty members who lose and the productive junior faculty survive. Is my experience that unusual?
Is the Media Being Responsible about Health Issues?
Ben Goldacre is a physician and he doesn't think the media is being responsible. In fact, he thinks they may be complicit in the needless deaths of children. Visit his blog Bad Science and read why he says ... Christ I need a haircut. Then watch this video.
We have a problem with health literacy and science literacy. Professional health journalists and professional science journalists have a choice. They can continue to do nothing and blame the marketplace—in which case they become part of the problem—or they can speak out on behalf of good science—in which case they can become part of the solution.
[Thanks to Chris Nedin for the link.]
The Taste of Gouda
Dutch Gouda cheese has a unique taste (pronounced HOW-dah in the Netherlands but Goo-dah everywhere else). Most of the chemicals that make up this unique taste have been identified. The bitter taste is due to CaCl2 and MgCl
Combinations of all these compounds at the appropriate concentrations mimicked the taste of Gouda cheese but something was missing. The "mouthfulness," and the complexity of the mature cheese was not present in the artificial concoctions. The missing taste is called the kokumi sensation.
Theme
A Sense of Smell
Toelstede et al. (2009) have found the missing chemicals. They mostly consist of various γ-L-glutamyl dipetides such as γ-Glu-Glu, γ-Glu-Gly, γ-Glu-Gln, γ-Glu-Met, γ-Glu-Leu, and γ-Glu-His. The structure of γ-Glu-Glu is shown below.
Most people don't realize that peptides and amino acids can impart very powerful tastes. Monosodiun glutamate (MSG) is an obvious example. So is aspartame, a powerful sweetener that's a modified tripeptide (Asp-Phe-Ala methyl ester).
Isn't biochemistry wonderful?
Here's a tough question. Let's say you could identify, with absolute certainty, all the chemicals that make up the taste of Gouda cheese. Let's say you make them in a lab and mix them with tofu and get something that tastes exactly like Gouda cheese. Would there be some people who want to ban that artificial Gouda cheese because it has chemicals? Would those same people be happy to eat the "natural" cheese because it doesn't have chemicals?Toelstede, S., Dunkel, A., and Hofmann. T. (2009) A Series of Kokumi Peptides Impart the Long-Lasting Mouthfulness of Matured Gouda Cheese. J. Agric. Food Chem., 2009, 57 (4), pp 1440–1448. [DOI: 10.1021/jf803376d]
Mitotic Recombination
It is widely believed that recombination, or crossing over, only occurs at meiosis in diploid eukaryotes. Most textbooks reinforce this belief by associating crossovers with chiasmata, which are only seen at meiosis.
In spite of the textbook claims, most people are well aware of the fact that recombination takes place in somatic cells. After all, it's the basis of most recombinant DNA technology and underlies many of the mechanisms that cause cancer. Furthermore, some developmental processes, such as immunoglobulin gene rearrangements require recombination in somatic cells.
Mitotic recombination has been known to occur since the 1930s when it was used for fate mapping in Drosophila so it's somewhat surprising that crossing over is so intimately connected with meiosis in the textbooks. The frequency of mitotic crossing over may be lower than that seen during meiosis, although the differences may not be great in most species.
In yeast, the frequency of recombination during meiosis can be 10,000 times greater than the frequency of crossing over in somatic cells but that's partly because meiotic recombination is very high in yeast cells. Perhaps they have been selected in vitro for high rates of recombination.
Why does recombination occur in mitotic cells? Probably for the same reason it occurs during meiosis—it's a form of DNA repair.
There's a short review of mitotic recombination in the lastest issue of PLoS Genetics [Mitotic Recombination: Why? When? How? Where?]. Let's try and put an end to the false idea that recombination and crossing over only takes place during meiosis.
Thursday, March 12, 2009
Levels of Selection
There's an interesting article in the latest issue of New Scientist. Bob Holmes writes about The selfless gene: Rethinking Dawkins's doctrine.
Evolutionary success is all about looking out for number one - or so most biologists would tell you. The genes that do the best job of passing themselves along to the next generation, whether by brute selfishness or canny cooperation, are the ones that flourish - a view most memorably championed by Richard Dawkins more than 30 years ago in his bestselling book The Selfish Gene.The article is better than most. It gives an adequate overview of group selection and species selection (sorting).
This relentless focus on the gene may not tell the whole story, however. A small but growing coterie of evolutionary biologists argue that it leaves us blind to crucial evolutionary processes at higher scales - among groups, species and even whole ecosystem. If they are right, the popular view of evolution and the biological world needs a radical shake-up.
Almost everyone agrees that the gene's-eye view works perfectly well most of the time. "It's dominated the field, and dominated for a long time," says Michael Ruse, a philosopher of science at Florida State University in Tallahassee. Indeed, many biologists think the selfish-gene concept can explain all the intricacies thrown up by evolution, and not just the obviously selfish ones.
However, before reading on you should be aware of two false notions that are being perpetuated. First, there's more to evolution than adaptation and selfish genes. Not all genes are selfish and even at higher levels species sorting may occur in the absence of species selection.
Second, the concept of the selfish gene has been very important in evolutionary theory. Far more important, I think, than most people realize. But it is not correct to say that it has dominated the field, or that it's the current dogma. If you consult any evolutionary biology textbook you'll find that "selfish gene" barely gets mentioned. Almost everything is explained by considering the individual organism as the unit of selection. Dawkins has failed to convince any but a handful of evolutionary biologists that the gene perspective is a better way of looking at evolution.
The article closes with ....
It is still too early to know whether group, species and ecosystem-level selection are major evolutionary forces or merely minor curiosities - baroque ornaments on the central edifice of individual or gene-level selection. But the dominance of the "selfish gene" in evolutionary thought is facing its strongest challenge in many years.This is a good way of putting it. Hierarchical theory is an interesting development and it is making some headway but it's fair to say that most evolutionary biologists don't think of group selection and species selection as major players.
However, the dominant thinking is that it's the individual and not the gene that forms the proper unit of selection. And the greatest challenge to the dominance of selection at the level of the either the gene or the individual is neither group selection or species selection, it's random genetic drift.
Note: People get confused about the meaning of The Selfish Gene. Just because we talk about population genetics and changing frequencies of alleles does not mean that we are adopting Dawkins' perspective. He explains what he means by "selfish gene" in the opening chapter of The Extended Phenotype.
The thesis that I shall support is this. It is legitimate to speak of adaptations as being "for the benefit of" something, but that something is best not seen as the individual organism. It is a smaller unit which I call the active germ-line replicator. The most important kind of replicator is the "gene" or small genetic fragment. Replicators are not, of course, selected directly, but by proxy; they are judged by their phenotypic effects. Although for some purposes it is convenient to think of those phenotypic effects as being packaged together in discrete "vehicles" such as individual organisms, this is not fundamentally necessary. Rather, the replicator should be thought of as having extended phenotypic effects, consisting of all its effects on the world at large, not just its effects on the individual body in which it happens to be sitting.
Examples of Accelerated Human Evolution
Gregory Cochran and Henry Harpending claim that human evolution has accelerated in the last 10,000 years. In one sense this has to be correct since the number of humans is increasing exponentially and that means far more mutations are occurring every generation. Many of those new mutations are contributing to a significant increase in variation.
But that's not what they mean. They claim that adaptations have increased. When they talk about accelerated human evolution they are mostly talking about an increase in natural selection.
For those of you who have not read the book, I thought I'd give you some of the examples that feature prominently in the opening chapter.
... when humans hunted big game 100,000 years ago, they relied on close-in attacks with thrusting spears. Such attacks were highly dangerous and physically taxing, so in those days, hunters had to be heavily muscled and have thick bones. That kind of body had its disadvantages—if nothing else, it required more food—but on the whole, it was the best solution in that situation. But new weapons like the atlatl (a spearthrower) and the bow effectively stored muscle-generated energy, which meant that hunters could kill big game without big biceps and robust skeletons. Once that happened, lightly built people, who were better runners and did not need as much food, became competitively superior. A heavy build was yesterday's solution: expensive, but no longer necessary. (p. 3)
With the invention of nets and harpoons, fish became a more important part of the diet in many parts of the world., and metabolic changes that better suited humans to that diet were favored. (p. 4)
Close-fitting clothing provided better protection against cold, allowing people to venture farther north. In cool areas, people needed fewer physiological defenses against low temperatures, while in the newly settled colder regions they needed more such defenses, such as shorter arms and legs, higher basal metabolism, and smaller noses. (p. 4)
With the advent of new methods of food preparation, such as the use of fire for cooking, teeth began to shrink, and they continued to do so over many generations. Pottery, which allowed storage of liquid foods, accelerated that shrinkage. (p. 4)
As the complexity of human speech approached modern levels, there must have been selection for changes in hearing (both changes in the ear and in how the brain processes sounds) that allowed better discrimination of speech sounds. Think of the potential advantages in being just a bit better at deciphering a hard-to-understand verbal message than other people: Eavesdropping can be a life-or-death affair. (p. 4)
... we believe that the obvious difference between racial groups are linked to gene variants that have recently increased in fitness and had major fitness effects. Blue eyes, found only in Europeans and their near neighbors, are a result of a new version of the DNA that controls the expression of OCA2 that has undergone strong selection, at least in Europe. (p. 18)
Dry earwax is common in China and Korea, rare in Europe, unknown in Africa: The gene variant underlying dry earwax is the product of strong recent selection. (p. 18)
We can confidently predict that many (perhaps most) as yet unexplained racial differences are also the product of recent selection. For example, we argue that the epicanthic eyelid found in the populations of northern Asia is most likely the product of strong and recent selection. (p. 18)
Atheist Buses Will Run in Ottawa
Ottawa city council voted last month to ban the atheist ads from OC Transpo buses.1 Last night they voted 13-7 to allow the ads after city solicitor Rick O'Connor told them the ban is an unreasonable infringement of free speech [City blesses atheist ads].
Transit officials made the decision after receiving four complaints from the public, but O'Connor said in the end the city's argument may not hold up in court.Thanks to the Humanist Association of Ottawa for standing up for freedom of expression.
"Based on the information available at this time, it appears that the city may not be able to justify its refusal of the proposed advertising on the basis that it is offensive, and consequently, it may be found to be an unreasonable infringement of the association's freedom of expression under Section 2(b) of the Charter," the memo says.
"If the decision to refuse the ads was based solely on the four complaints received from the public, it is likely that this decision will be found to be unreasonable and lacking in proportionality, and therefore not justifiable under Section 1 of the Charter."
1. Technically, they did not ban the ads. Instead, they failed, in a tie vote, to overturn the decision of OC Transpo. That decision has now been overturned in a second vote and the ads will run.
Teach Your Children Well
Chelsea Juman is one of the Intel Baby Nobelist Finalists on the Scientific American website.
According to her study, if you drank underage as a teenager you should never tell your children 'cause, if you do, they'll think it's OK.
Well, it's too late for me but all you young people out there better pay attention. You need to start lying to your children from a very young age. Whatever you do, pretend you never touched a glass of wine or a bottle of beer before you were 21 years old.1 Don't even think about drugs. Lie through your teeth. That'll make 'em respect you.
As soon as they turn 21 you can take them out to a bar and have a long talk about responsible drinking.
Better not tell them about sex either. Abstinence is the only answer.
1. If you're an American. If you live in any other country you can tell them you drank when you were much younger—16 in Italy, Germany, or France, for example.
In the Quality of Heatlh Care Journalism
A survey of members of the Association of Health Care Journalists (AHCJ) reaches the following conclusions [U of Minnesota professor authors report the state of health care journalism] ....
So, the quality of health care journalism has declined. This isn't earth shattering news.
- Ninety-four percent of survey respondents say the bottom line pressure in media organizations is seriously hurting the quality of news coverage of health care issues
- Forty percent of staff reporters in the survey say the number of health reporters at their organization has gone down since they've been there, and 11 percent say they personally have been laid off over the past few years due to downsizing.
- Thirty-nine percent of respondents who are still in the business believe it is at least somewhat likely that their position will be eliminated in the next few years
- Nearly nine in ten (88 percent) survey respondents think health care coverage leans too much toward short "quick hit" stories, and two-thirds (64 percent) say the trend toward shorter stories has gotten worse in the past few years
- A majority of respondents (52 percent) say there is too much coverage of consumer or lifestyle health, and too little of health policy (70 percent), health care quality (70 percent) and health disparities (69 percent)
I bet that 100% of health care journalists will say that it's not their fault.1
"Real" science journalists are different. Most of them say they are doing a terrific job and the bad science reporting is all due to other journalists writing about science.
1. Of course it's not all their fault but when a bad health care article gets published you can't blame it all on the editors.
On the Demise of Religion
Michael Spencer writes about The coming evangelical collapse in The Christian Science Monitor.
We are on the verge – within 10 years – of a major collapse of evangelical Christianity. This breakdown will follow the deterioration of the mainline Protestant world and it will fundamentally alter the religious and cultural environment in the West.I agree with him but I think he's mistaken if he thinks that belief in God will survive the collapse of the evangelical right.
Within two generations, evangelicalism will be a house deserted of half its occupants. (Between 25 and 35 percent of Americans today are Evangelicals.) In the "Protestant" 20th century, Evangelicals flourished. But they will soon be living in a very secular and religiously antagonistic 21st century.
This collapse will herald the arrival of an anti-Christian chapter of the post-Christian West. Intolerance of Christianity will rise to levels many of us have not believed possible in our lifetimes, and public policy will become hostile toward evangelical Christianity, seeing it as the opponent of the common good.
Millions of Evangelicals will quit. Thousands of ministries will end. Christian media will be reduced, if not eliminated. Many Christian schools will go into rapid decline. I'm convinced the grace and mission of God will reach to the ends of the earth. But the end of evangelicalism as we know it is close.
Evangelical Christianity is in trouble because its very core is being challenged, not because of its association with old-fashioned morality.
[Hat Tip: RichardDawkins.net]
Wednesday, March 11, 2009
Darwin First Day Cover
Heather sent me a package of stuff from the Royal Mail, including a complete set of Darwin stamps and various brochures. She included a magazine on Darwin and a first day cover (see below).
I bet there aren't any other bloggers who have a first day cover. Eat your hearts out.
Thanks Heather, I owe you one.
Nobel Laureate: Fred Sanger
The Nobel Prize in Chemistry 1958.
"for his work on the structure of proteins, especially that of insulin"
Frederick Sanger (1918 - ) won the Nobel Prize in Chemistry for developing techniques to sequence proteins and for determining the amino acid sequence of insulin. This was Sanger's first Nobel Prize. The second was for developing the chain termination method of DNA sequencing.
From today's perspective it's difficult to appreciate the importance of Sanger's work on protein sequencing. His work confirmed that the functions of proteins depended on the sequence of amino acid residues in a polypeptide chain and it confirmed that every molecule of a protein had the same amino acid sequence. Recall that in 1958 the relationship between the nucleotide sequence of a gene and the amino acid sequence of a protein was still being worked out and the genetic code had not been discovered.
Sanger's work led to the widespread use of sequencing technology which, in turn, led to the discovery of differences between species. It wasn't long before phylogenetic trees based on amino acid sequences were being published.
Some Nobel Prizes are given for quick discoveries but this isn't one of those. Sanger worked on his project for ten years making only small advances each year. The presentation speech specifically mentions this.
THEME:
Nobel Laureates
Doctor Frederick Sanger. It sometimes happens that an important scientific discovery is made so to say "overnight" - if the time is ripe and the necessary background is there. Yours is not of that kind. The first successful determination of the structure of a protein is the result of many years of persistent and zealous work, in which the final solution of the problem has been approached step by step. You knew when you began to look into the structure of the insulin molecule 15 years ago that the problem was a formidable one. So did the whole scientific world. Those who knew you, were confident, however, that you would ultimately succeed, and each successive publication from your laboratory strengthened our confidence. Intelligence, knowledge and skill in the mastering of the methods required - we know you have them all - but in such a venture these are not enough. Without your wholehearted devotion to the task you had set before you, many obstacles on your way would have appeared insurmountable. Now that many years of work have been crowned with success you may look back and rejoice. You can also enjoy the satisfaction of seeing the roads you have broken and paved being used by many in their search for the building principles of the key substances of Life. However, very likely you are more apt to look ahead. It was Alfred Nobel's intention that his prizes should not only be considered as awards for achievements done but that they should also serve as encouragement for future work. We are confident that you are a worthy recipient of the Nobel award also in this sense.
The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.
Why Is Science Important?
The short answer is that science is important because knowledge is always better than ignorance and science teaches you how to distinguish between them.
The long answer is ... [Why Is Science Important?]
Why is Science Important? from Alom Shaha on Vimeo
[Hat Tip: Bad Astronomy]
Putting the Atheist Bus Campaign in Context
You can skip to the two minute mark after watching for one minute.
[Hat Tip: Friendly Atheist]
Shopping Is a Throwback to the Days of Cavewomen
David Holmes is a Fellow in the Division of Psychology and Social Change at Manchester Metropolitan University in Manchester (UK). His latest "research" results were reported in the Telegraph: Shopping is 'throwback to days of cavewomen'.
Shoppers are using instincts they learnt from their Neanderthal ancestors, researchers have found.1Now, assuming that women did all the gathering (they probably didn't), and assuming everyone lived in caves (they didn't), it still seems improbable that you could gather much food by strolling around the inside of a cave.
Dr David Holmes, of Manchester Metropolitan University, said skills that were learnt as cavemen and women were now being used in shops.
He said: "Gatherers sifted the useful from things that offered them no sustenance, warmth or comfort with a skill that would eventually lead to comfortable shopping malls and credit cards.
"In our evolutionary past, we gathered in caves with fires at the entrance.
"We repeat this in warm shopping centres where we can flit from store to store without braving the icy winds."
The study was commissioned by Manchester Arndale shopping centre in response to a rise in January visitors, according to the Daily Express.
Amanda Marcotte at Pandagon hits the nail on the head [The next evolutionary step for evo psych].
I’m curious to know what kind of study they commissioned with what kind of data collection, because right now it appears that they just paid someone with a PhD to make shit up. Of course, evo psych has been on about that for forever, so it was just a matter of time before marketers saw the potential---if you can make something up and call it science because of the sexist content and the thin veneer of authority granted by doctorate degrees, why not go whole hog?Making shit up is NOT science. It's closer to stand-up comedy.
Here's an example of comedy/satire by MissPrism.
When cave-ladies ground up roots and seeds to make pies for their cave-husbands, a white colour indicated the food was free of toxic contaminants. Cave-ladies accordingly evolved to value white above all other colours, which is why women today all long for a white wedding dress!In spite of the fact that I like the conclusion, this isn't science. MissPrism's story is just as credible as the stories made up by evolutionary psychologists and that's a damning conclusion. It suggests that the entire field of evolutionary psychology is practically worthless as a science—maybe when we kick all the the evolutionary psychologists out of the universities, they can make a living by writing comedy.
However, cave-ladies also needed to be able to tell when their cave-pie was cooked to a delicious golden brown. Women's visual systems therefore make a far more acute distinction between white and brown than those of men, who in our evolutionary past only saw the pies in their cooked state. For this reason, men can't see dirt and should never do laundry.
1. All available scientific evidence indicates that Neanderthals were not our ancestors.
[Hat Tip: Hopeful Monster at Chance and Necessity: Malls, caves, and evolutionary psychology]
Tuesday, March 10, 2009
Salmon with Peas on Toast
When my kids were growing up I used to make them one of my favorite meals—Mom's Creamed Salmon on Toast. We usually enjoyed it when Ms. Sandwalk was away from home.
Now that they are adults, my children never lose an opportunity to make fun of Dad's cooking and how they were forced to eat salmon when Mom was away.
Now the joke's on them ... or at least on my son, because ...
Teenage boys who eat fish at least once a week achieve higher intelligence scores. Looks like boys get smart by eating salmon. It explains why my son is so smart. It also explains why my daughter never appreciated salmon and peas on toast. It doesn't work on girls.1
1. I don't believe the study. It's ridiculous to think that eating fish is all it takes to make you smarter. If that were true then Newfoundlanders would be smarter than cowboys or vegetarians ... hmmmmm, come to think of it ....
P.S. Just in case there is someone out there who doesn't get my sense of humor, here's a link to a posting about my daughter [Another Dr. Moran]. And just so he doesn't feel left out, here's a link to my son's website [Gordon Moran].
Richard Dawkins on "Purpose"
One of the most astonishing discoveries of modern science is that the universe does not exhibit any signs of "purpose" or "goals." This single conclusion is probably more responsible for the profound conflict between science and religion than any other. The attractiveness of religion was that it seemed to answer the "why" questions that science, presumably, could not answer. Now, modern science tells us that the question was meaningless.
That evolution is a blind, purposeless process is difficult to grasp, yet it is a fundamental part of understanding biology. The concept is explicitly mentioned in college level textbooks, although some introductory biology textbooks place less emphasis on it than you will find in more advanced courses.
Here's how Douglas Futuyma describes purpose in Evolution (2005) (p. 12).
Above all, Darwin's theory of random, purposeless variation acted on by blind, purposeless natural selection provided a revolutionary new kind of answer to almost all questions that begin with "Why?" Before Darwin, both philosophers and people in general answered "Why?" questions by citing purpose. Since only an intelligent mind, with the capacity for forethought, can have purpose, questions such as "Why do plants have flowers?" or "Why are there apple trees?"—or diseases, or earthquakes—were answered by imagining the possible purpose that God could have had in creating them. This kind of explanation was made completely superfluous by Darwin's theory of natural selection. The adaptations of organisms—long cited as the most conspicuous evidence of intelligent design in the universe—could be explained by purely mechanistic causes. For evolutionary biologists, the flower of the magnolia has a function but not a purpose. It was not designed in order to propagate the species, much less to delight us with its beauty, but instead came into existence because magnolias with brightly colored flowers reproduced more prolifically than magnolias with less brightly colored flowers. The unsettling implication of this purely material explanation is that, except in the case of human behavior, we need not invoke, nor can we find any evidence for, any design, goal, or purpose anywhere in the natural world.Richard Dawkins made the same point in his book River Out of Eden (1995) (pp. 96-98). Here he is reading those pages.
It must be emphasized that all of science has come to adopt the way of thought that Darwin applied to biology. Astronomers do not seek the purpose of comets or supernovas, not chemists the purpose of hydrogen bonds. The concept of purpose plays no part in scientific explanations.
The concept of purposeless, or accidental, evolution comes naturally to those evolutionary biologists who are used to thinking about random genetic drift. Those biologists tend to be comfortable with the idea that the tape of life will never be replayed.
But, as Richard Dawkins notes at the end of his reading, there are other biologists for whom "the illusion of purpose is so powerful that [they] use the assumption of good design as a working tool." Many of these biologists are not completely comfortable with the idea that the tape of life may not play out the same. They tend to see convergence, and other things, as evidence of some sort of inevitable purpose (design) in the history of life. This is, of course, materialistic design, not supernatural design.
This point of view crops up in terms such as "the evolution of evolvability," "facilitated variation," and even "self-organization."
In addition to this subtle form of "purpose" we see clear evidence of true purpose in animals with sophisticated brains. Those animals clearly develop goal-oriented behaviors.
Dawkins addresses these points in his current lecture tour by making a distinction between different definitions of purpose.
The Purpose of PurposeWesley Elsberry was at the Dawkins lecture in Michigan on March 2nd and he has posted a lengthy summary on The Panda's Thumb: Richard Dawkins and “The Purpose of Purpose”. It's very helpful for those of us who couldn't attend one of these lectures.
"We humans are obsessed with purpose. The question, “What is it for?” comes naturally to a species surrounded by tools, utensils and machines. For such artifacts it is appropriate, but then we go too far. We apply the “What is it for?” question to rocks, mountains, stars or the universe, where it has no place.
How about living things? Unlike rocks and mountains, animals and plants, wings and eyes, webbed feet and leaves, all present a powerful illusion of design. Since Darwin, we have understood that this, too, is an illusion. Nevertheless, it is such a powerful illusion that the language of purpose is almost irresistible. Huge numbers of people are seriously misled by it, and biologists in practice use it as a shorthand.I shall develop two meanings of “purpose”. Archi-purpose is the ancient illusion of purpose, a pseudo-purpose fashioned by natural selection over billions of years. Neo-purpose is true, deliberate, intentional purpose, which is a product of brains. My thesis is that neo-purpose, or the capacity to set up deliberate purposes or goals, is itself a Darwinian adaptation with an archi-purpose.
Neo-purpose really comes into its own in the human brain, but brains capable of neo-purposes have been evolving for a long time. Rudiments of neo-purpose can even be seen in insects. In humans, the capacity to set up neo-purposes has evolved to such an extent that the original archi-purpose can be eclipsed and even reversed. The subversion of purpose can be a curse, but there is some reason to hope that it might become a blessing."
Monday's Molecule #111: Winners
UPDATE: I guess the hint was too much of a giveaway. The molecule is insulin from pig (Sus scrofa). Pig pancreas was the major source of insulin for diabetics before recombinant DNA. It is very similar to human insulin.
The Nobel Laureate is Fred Sanger who won in 1958 for determining the sequence of insulin. It was his first of two Noble Prizes.
The winners are David Schuller of Cornell University by one minute over Dima Klenchin, and Adam Santoro of the University of Toronto.
Identify this molecule. Be as specific as possible, including the species. Explain why that species was chosen. Here's a hint: 1b17.
There's are several possible Noble Prizes associated with this molecule. I'm looking for the prize that was awarded for determining the primary structure.
The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.
There are six ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin. Alex Ling of the University of Toronto, James Fraser of the University of California, Berkeley, Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto and Maria Altshuler of the University of Toronto.
Dima has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.
THEME:
Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.
Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.
A Letter from the President of CIHR
There's a crisis in science funding in Canada. The budgets of the main granting councils are being cut by $148 million over the next three years.
Laura Frost is the President of the Canadian Society of Biochemistry, Molecular & Cellular Biology (CSBMCB). She recently wrote to Prime Minister Harper to draw his attention to the seriousness of this decision.
Dear Mr. Harper;CSBMCB has also published a letter from the President of the Canadian Institutes of Health Research (CIHR). Read this letter ... comments below.
On behalf of the Canadian Society of Biochemistry, Molecular & Cellular Biology (CSBMCB), I would like to congratulate the Government of Canada for a number of measures in the 2009 Budget, including the more than $1.5 billion investment in science and technology. The CSBMCB is pleased to see in the budget $750 million for the Canada Foundation for Innovation (CFI) in support of research infrastructure and $87.5 million for the temporary expansion of the Canada Graduate Scholarship Program as well as continued funding for Genome Canada.
However, the lack of additional new investment in Canada’s granting agencies Canadian Institutes of Health Research (CIHR), NSERC and SSHRC is of great concern. Without increased investments in operating funds to support doing research, Canada could lose the competitive edge that previous investments in students, scientists and infrastructure have achieved. Operating monies are the funds that allow our gifted students and other trainees to become competitive at an international level and leaders in the next generation of scientists. Without these crucial increases, fewer labs will be funded and fewer students, scholarships notwithstanding, will be trained in the diverse areas of science that define “interdisciplinary research”. Targeted research is one essential component of the funding process, but as a country, we need a strong background in basic research that feeds into technological development and planning for crises ranging from SARS to mountain pine beetles to environmental concerns in the oil sands.
Over the past several years, many leaders and national and provincial partners dedicated to advancing research in Canada have advocated for increased investments in discovery research through the granting councils to match the growth in infrastructure and research capacity through the CFI and the Canada Research Chairs Program respectively. Failure to align these funding streams at the federal level has created a serious imbalance in the supply and demand in health research and research generally, which will, in turn, increasingly affect our capacity to retain and recruit the best scientists.
The biotechnology sector is also suffering from a lack of investment capital. This industry serves as a primary receptor for much of Canadian research related to health, agriculture, manufacturing, environmental and resource-based emerging technologies. Fifty percent of Canadian companies indicate they will be closing or selling off their operations to international partners by the end of this year. Canada cannot afford to ignore the competitive environment other nationals will be adopting to help grow and stimulate their knowledge-based industries.
The economic impact of Canadian health research is significant. On an annual basis our industry generates $12 billion in economic activity and provides employment and training for over 10,000 people across Canada. The sector also supports more than 20,000 scientists, clinical investigators and other researchers and staff.
Canada has many of the right ingredients to succeed in the knowledge-based economy including a highly skilled workforce and some of the best research facilities in the world. The CSBMCB looks forward to working with the Government of Canada in laying the foundation for a stronger and more sustainable economy of the future in which research and development in the health and life sciences are a top national priority.
Sincerely,
Laura Frost, Ph.D.
President, CSBMCB
MESSAGE FROM THE PRESIDENT OF CIHRThis is unacceptable. It sounds like a letter from a political lackey and not from someone who is really concerned about scientific research in Canada. Why can't Alain Beaudet mention that he is fighting on behalf of all Canadian scientists to increase CIHR funding in order to better support basic research? Is it because he isn't fighting?
Following the January 26, 2009 Speech from the Throne, the Government of Canada tabled its 2009 Budget, Canada’s Economic Action Plan in the House of Commons on January 27. The Budget outlined the Government’s economic stimulus package designed to bolster the Canadian economy and provide support for Canadians as the world’s economies work through the current economic crisis. The Budget 2009 speech and documents can be found on the Finance Canada website at: http://www.fin.gc.ca.
Research plays a key role in improving the health of Canadians. That’s why, over the past three years, the Government has increased the annual base budget of the Canadian Institutes of Health Research (CIHR) by over $142 million. This year CIHR plans to spend approximately $917 million on peer-reviewed health research projects conducted at universities, hospitals and research centres across Canada.
I have summarized below the details of Budget 2009 as it relates to CIHR.
First, CIHR will receive $35M over the next three years for Canada Graduate Scholarships (CGS) to fund an additional 200 doctoral scholarships, valued at $35, 000 each per year for three years beginning in 2009-10, and an additional 400 master’s scholarships, valued at $17, 500 each for one year, in both 2009-10 and 2010-11.
Second, Budget 2009 also provided the results of the Government’s Strategic Review process. CIHR was one of the 21 Government Departments and Agencies that undertook a Strategic Review of its programs and services. The objective of the process was to assess whether programs:
• are effective and efficient;
• meet the priorities of Canadians; and
• are aligned with federal responsibilities.
The results of the process are as follows:
• CIHR funding of the Open Team Grant program will be discontinued. To respect current commitments, reductions will be phased in over the next three years with $1.5M in 2009-10, $5.5M in 2010-11, and $27.6M in 2011-12 and thereafter; and
• Funding for the Intellectual Property Mobilization (IPM) program will be discontinued. To respect CIHR’s current commitments, the annual reductions of $2M will commence in 2010-11 and end in 2011-12.
In addition, funding under the Indirect Costs Program will be reduced in proportion to reductions in the above direct cost programs. The relative ratio of funding for the direct and indirect costs will therefore remain essentially the same as prior to the Strategic Review.
In summary, taking into account the new investments for the Canada Graduate Scholarships and the strategic reallocations, CIHR’s budget for 2009-10 will increase by $12.5M, bringing our total budget to $978.8M.
Sincerely,
Alain Beaudet, MD, PhD
President
Canadian Institutes of Health Research
We need someone who will stand up and oppose government underfunding, not someone who will make excuses for it. If the current President does not have the confidence of the scientists who are supported by CIHR then perhaps we should find a new CIHR President who does have their confidence.
Monday, March 09, 2009
Happy Birthday PZ!
Today is PZ Meirirz birthday.
So far he's not having a good one [No More Birthday] so don't bother to send him an email message.
Wait until tomorrow.
Monday's Molecule #111
Identify this molecule. Be as specific as possible, including the species. Explain why that species was chosen.
Here's a hint: 1b17.
There's are several possible Noble Prizes associated with this molecule. I'm looking for the prize that was awarded for determining the primary structure.
The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.
There are six ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin. Alex Ling of the University of Toronto, James Fraser of the University of California, Berkeley, Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto and Maria Altshuler of the University of Toronto.
Dima has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.
THEME:
Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.
Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.
Comments will be blocked for 24 hours.
Good Quality Journalism Sells Newspapers
On Saturday night we celebrated my nephew's birthday at Pic Nic on Queen St. East. I won't tell you how many years we were celebrating ... let's just say that I remember babysitting Mark when I was 18 years old. He's old enough to fend for himself (on most days).
We got to discussing science journalism—he reads my blog. Mark was defending (poorly 
) the idea that newspapers, TV, etc. are profit-making companies and, consequently, it is unreasonable to expect them to be truthful and accurate. Sensationalism sells. I was defending the idea that telling the truth about science isn't necessarily going to hurt profits. Accurate science can be just as exciting as gross distortions of the truth. Maybe even more exciting.
We had a really fun time discussing the topic, aided, perhaps, by the excellent wine list at the restaurant. I wish I could remember all the points I made. I think some of them were brilliant.
Along comes André Picard of The Globe and Mail to back up my case better than I was able to do on Saturday night. (You lose again, Mark! ) Here's his bio.
André Picard is the public health reporter at The Globe and Mail, where he has been a staff writer since 1987.I think we can assume he's an expert on health journalism in the same way that we have experts in science writing.
He has received much acclaim for his writing, including the Michener Award for Meritorious Public Service Journalism, the Canadian Policy Research Award, the Atkinson Fellowship for Public Policy Research and the Award for Excellence in Women’s Health Reporting. In 2002, he received the Centennial Prize of the Pan-American Health Organization as the top public health reporter in the Americas.
Does André Picard try and sell papers by sensationalizing topics like vaccination, prescription drugs, complementary medicines and "health" foods?
Let's check out his article in last Thursday's paper: The Internet has changed the nature of scientific debate.
If you read scientific literature and health research with an open mind and still conclude that vaccines are not poisons, that chelation therapy will not cure heart disease, that realigning someone's chakra is not going to clear up a bladder infection, or that strange concoctions of vitamins and minerals cannot cure bipolar disorder - all theories that have pretty broad followings on the Web - then you are dismissed as an agent of an evil empire.This is an example of honest, skeptical reporting and I think the general public will be just as interested in reading about the exposure of quacks as in reading articles that promote their claims.
Those who promote these bogus therapies - and often profit from them - will, paradoxically, dismiss you as a paid shill for Big Pharma, oppressive government or some other branch of the devilish military-industrial complex.
Doctors, nurses, pharmacists, pharmacologists, biochemists, immunologists, geneticists and journalists are not to be trusted. They are all on the take.
Medical journals that publish peer-reviews research: They are nothing but promotional tools for Big Pharma and researchers are their puppets and profiteers.
So who do you trust?
Well, you depend on chiropractors and Hollywood stars to give you advice about vaccinating your baby; you trust the guy at the health-food store to offer up a sure-fire cure for arthritis; and you take as gospel the e-mail that warns ominously that if new food safety rules are adopted by government, storm troopers will soon be busting down your front door to seize the chamomile tea.
In the world of cyberspace science, the best evidence is anecdote and the more fantastical the claims, the larger the following they seem to garner.
In other words, accuracy and the truth can sell newspapers. And the public benefits.
Let's have more of it in the science section.
[Photo Credit: Dr. Louise Nadeau and Mr. André Picard as masters of ceremonies at the 2006 Fifth Annual Canadian Health Research Awards celebration.]
[Hat Tip: Propter hoc: The most sensible thing I’ve read in months and RichardDawkins.net]
Did biologists really think that human evolution stopped?
John Hawks has responded to my posting on the Discover article. In that posting [Are Humans Still Evolving?] I criticized Hawks and his colleagues for claiming that the consensus view among scientists is that human evolution is over.
Recall that the opening sentence of the article is ...
For decades the consensus view—among the public as well as the world’s preeminent biologists—has been that human evolution is over.John replies with: Did biologists really think that human evolution stopped?.
Yet despite the abundant evidence that human biologists have opposed the idea of recent human evolution, I still think that McAuliffe's opening sentence does construct a "straw man" argument. Many prominent examples don't prove that there has been a decades-long consensus that human evolution stopped. And our research is not about human evolution merely continuing -- we think it actually accelerated. Evidence that some biologists thought that human evolution stopped is interesting. But the reality is that almost no one has thought that human evolution accelerated.So, John and I agree that McAuliffe's article was misleading when she suggested that the consensus view was that human evolution had stopped. It was misleading in spite of the fact that one can find quotations from some prominent scientists who might have held this view.
My position is that the consensus view is often that found in the leading textbooks. The textbooks on evolution always discuss recent examples of human evolution; such as lactose tolerance, skin color, and shifts in the frequency of blood type alleles. Most of them spend time discussing races and diversity—usually with the goal of dispelling false concepts of race, but always with the assumption that humans have, and are, evolving.
Take Evolution by Barton et al. (2007), for example. They have sections on the evolution of humans by random genetic drift and natural selection. One section on page 775 is headed: Natural Selection Has Shaped, and Is Shaping, Human Evolution. The standard examples are explained. Barton et al. discuss what happens when negative selection is relaxed due to medical advances and they point out, correctly, that this will lead to the accumulation of formerly deleterious alleles by drift. They even address the very issue that Hawks writes about (p. 775).
It is unclear how effective natural selection has been in our recent history. On the one hand, our relatively low effective population size (Ne ~ 104) makes it impossible for us to avoid accumulating mildly deleterious mutations, and there is evidence that more such mutations have accumulated along our lineage than along that of our sister species, the chimpanzee. However, it could be that our low effective population size actually reflects the effects of a large number of selective sweeps, and therefore the success of natural selection. (Recall that Ne is really a measure of the inverse rate of genetic drift. It can be reduced by both low population size and selective sweeps.) When a favorable mutation is swept to fixation, it may carry with it more weakly deleterious alleles that happen to be tightly linked to the original mutation. Thus, we can make two radically different interpretations of the observed low genetic diversity within our species: on the one hand, that it reflects a low population size in the past, implying inefficient selection, or on the other, that it is a side effect of intense adaptive selection.Since this is what evolutionary biologists are teaching undergraduates, I think it's fair to say that the consensus among evolutionary biologists is that humans are evolving. Indeed, most evolutionary biologists know that it is impossible to stop evolution.
I guess we can conclude that the author of the Discover article didn't get her straw man version of human evolution from John Hawks. Where, then, did she get it? Maybe it was from Henry Harpending, John's former postdoc advisor and collaborator.
Harpending has just published a book with Gregory Cochran, another collaborator on the "acceleration" paper. The opening chapter of The 10,000 Year Explosion is Overview: Conventional Wisdom.Scientists have long believed that the "great leap forward," some 40,000 t0 50,000 years ago in Europe, marked the advent of cultural evolution and the end of significant biological evolution in humans. At this time, the theory goes, humans developed culture, as shown by the sophisticated new tools, art, and forms of personal decoration that emerged in the Upper Paleolithic. Culture then freed the human race from the pressures of natural selection: We made clothes rather than growing fur and built better weapons rather than becoming stronger.I assume John Hawks will agree that this "conventional wisdom" is a straw man. Perhaps Gregory Cochran and Henry Harpending are referring to a subset of scientists when they talk about arrested human evolution. Perhaps they are only referring to adaptationists, or maybe just adaptationist anthropologists?
The argument that the advent of behavioral modernity somehow froze human evolution is dependent on the notion of a static environment. In other words, if a population—of humans, wolves, crabgrass, you name it—experiences a stable environment for a long time, it will eventually become genetically well matched to that environment. Simple genetic changes then do little to improve individual fitness, because the species is close to an optimum.
My own view is that humans are evolving (duh!) and that the evidence for accelerated evolution is unconvincing at this time, but intriguing. I think this is the consensus view among evolutionary biologists. If I were trying to educate the general public that's what I would tell them.
I would not tell them that a revolution in our thinking about human evolution is in progress.
Epigenetics, Lamarck, and Darwin.
Ryan Gregory at Genomicron educates us about Jean-Baptiste Pierre Antoine de Monet, Chevalier de la Marck and Charles Darwin [Lamarck didn't say it, Darwin did.
What people insist on dubbing "Lamarckian inheritance" in the context of epigenetics is actually closer to the view held by Darwin than by Lamarck....
International Women's Day
Yesterday (Sunday) was International Women's Day.
Ms. Sandwalk and I celebrated by buying a new monitor for her computer. The monitor was designed and marketed by an American company and assembled in Asia (probably by women) using parts that were produced in five or six other countries.
Hey, don't knock it! What did you do to celebrate international women yesterday?
Apparently men in Russia celebrate a little differently.
The Value of Science in Canada
Canadian Girl Postdoc in America writes about The Value of Science in Canada. Here's a teaser ... read it all.
Stephen Harper (the Prime Minister of Canada) is, as far as I'm concerned, has an underlying ideology that he weasels into every policy. While I may be a granola eating birkie-wearing tree hugger, Harper is a neo-con who lives and dies by the market. He won't listen to hard-done-by stories of the 'little people' and his natural inclination is toward rigid conservative policies. Stephen Harper's closest advisor (Tom Flanagan) believes in the teachings of Leo Strauss, a man who taught that people "are too stupid to make informed decisions about their political affairs. Elite philosophers must decide on affairs of state for us." Strauss also believed that the ruling elite should hide the truth from the public -- Strauss's "noble lie" -- in order to protect the citizens from themselves.
The comparison between Harper and Bush is stark and explains why Canadian scientists are fearful about