Sunday, November 30, 2008

Greg Laden on "Race" (Again)

 
Greg Laden is one of those people who want to abolish use of the word "race" to define genetic subpopulations. He claims that there is no such thing in humans (or in other species). But even if it were biologically correct we shouldn't use the word because is has been misused by non-scientists.

Here's an example of his reasoning from The Scientific, Political, Social, and Pedagogical Context for the claim that "Race does not exist.".

The race concept has been very successful in its many nefarious applications, but this is not what I wish to speak about here. Rather, I want to acknowledge that a concept that divides humans into a particular set of groups in a useful way might be, well, useful and not such a bad thing. The fact that medical researchers use race to divide subjects, and find differences between races, and that these differences are important to know about, is important, even if it does not validate the races. What it means is that an unworkable race concept works sometimes, even if the races themselves don't exist. Nonetheless, it is reasonable to acknowledge that even though races don't really exist and many, if not most, applications of the race concept are obnoxious, it may be that its use is not entirely inappropriate all the time.

I will argue, however, that the down side of the use of race requires its abolition among scientists. Since race is usually not a biologically useful concept for humans (or many other species), and is never a truly valid concept, it is difficult to justify its use given the negative political and social consequences it carries.
Greg and I have been over this ground before. It think it's silly to pretend that races don't exist. That's carrying the anti-racist agenda too far.


Best Canadian Sci/Tech Blog: Round Two

 
The first round of voting for the best Canadian Sci/Tech Blog is over.

As I said earlier, I voted for Bad Astronomy in the first round [Best Canadian Sci/Tech Blog]. I know Phil Plait isn't a Canadian, but he should be.

Here are the five finalists. I'm voting for Post Darwinist in order to make this contest look as silly as possible.


The Conservative Party Will Help You Write a Letter to the Editor

 
If you go to the Conservative Party website at Harper Leadership 08 you can get help in writing a letter to the editor. If you enter some sort of name and address you will eventually end up on a page that gives you the latest Conservative version of framing spin.

This is how Harper is going to avoid defeat when he faces the House of Commons. (Click on the image to see a larger version.)

The idea that the opposition parties don't have a mandate to from a coalition is particularly ironic given Stephen Harper's own position just a few years ago. Here's what is reported prominently on the front page of today's Toronto Star

But opposition MPs are accusing the Prime Minister of hypocrisy, charging that Harper is overlooking his own efforts to forge a coalition to replace Paul Martin’s minority Liberal government in 2004.

Harper, then Conservative leader, even joined with NDP Leader Jack Layton and Bloc Québécois Leader Gilles Duceppe to write then-governor general Adrienne Clarkson, urging her to look at "options" if Martin's government fell in the fall of 2004, mere months after it won a minority mandate on June 28.

"We respectfully point out that the opposition parties, who together constitute a majority in the House, have been in close consultation," read the Sept. 9, 2004, letter from the three leaders.

"We believe that, should a request for dissolution arise this should give you cause, as constitutional practice has determined, to consult the opposition leaders and consider all of your options before exercising your constitutional authority."

That message is in stark contrast to the one Harper delivered Friday night, when he charged that Liberals don't "have the right to take power without an election."

"The opposition has been working on a backroom deal to overturn the results of the last election without seeking the consent of voters. They want to take power, not earn it," he said in a statement.

Now Conservative MPs are being instructed to take that message to Canadians.



[Hat Tip: Canadian Cynic: Because they really do need babysitting, that's why]

Is Superstition the Default Belief?

 
Are you getting tired of the modern mantra about religion—you know, the one that says it's wired into our genes and therefore probably correct or at least beneficial? I am.

So, apparently, is A.C. Graying who writes in Friday's Guardian (UK) [Children of God].
Earlier this week I had occasion to debate – if the soundbite culture of radio news permits that description – with a member of Oxford University's Centre for Anthropology and Mind the "findings" of its cognition, religion and theology project, to the effect that children are hardwired to believe in a "supreme being". The research is funded by the Templeton Foundation, an organisation keen to find, or to insert, religion into science and to promote belief in their compatibility – which, note, comes down to spending money on "showing" in the end that the beliefs of ancient goatherds are as good as modern physics.

Justin Barrett, a Christian and member of the centre's research team (whether it is research or propaganda is the moot question here) says with his colleagues on the centre's website:
"Why is belief in supernatural beings so common? Because of the design of human minds. Human minds, under normal developmental conditions, have a strong receptivity to belief in gods, in the afterlife, in moral absolutes, and in other ideas commonly associated with 'religion' … In a real sense, religiousness is the natural state of affairs. Unbelief is relatively unusual and unnatural."
This claim was the subject of Barrett's lecture at Cambridge, in which he exhibited his reasons for thinking that children are innately disposed to believe in intelligent design/creationism and a supreme being. His real reasons for thinking this, of course, are that he is a man of faith funded by a faith-based organisation; but the reasons he professed were that children have an innate tendency when small to interpret what happens in the world to be the outcome of purposive agency.

Now on this point he and I, an atheist funded by no organisation keen on promoting atheism, agree. Children's earliest experiences are of purposive agency in the adults and other people around them – these being the entities of most interest to them in their first months – and for good evolutionary reasons they are extremely credulous, not only believing that things must be acting as their parents do in being self-moving and intentional, but also believing in tooth fairies, Father Christmas, and a host of other things beside, almost all of which they give up believing before puberty, unless the beliefs are socially reinforced – as with religious and, to a lesser extent, certain other superstitious beliefs. Intellectual maturation is the process in important part of weaning oneself from the assumption that trees and shadows behave as they do for the same reason that one's parents, other humans, and dogs and cats do; it is every bit as natural a fact about children that they cease to apply intentionalistic explanations to everything as that they give them to everything, on the model of their parents' behaviour, in the earliest phases of development.

...


[Hat Tip: RichardDawkins.net

Kill Him, Kill Him Dead

 
These are interesting times in Canada. We recently re-elected the Conservative Party as the party with the most seats in Parliament—but not a majority. That means Stephen Harper becomes Prime Minister of a minority government.

What this normally means is that the government has to craft legislation that will receive the support of a majority of the house. But that's not what Harper proposes to do. Instead he has come up with a proposal that promotes a hard-core right-wing agenda. He did this because he assumed that the Liberal party would be forced to support the government in spite of the fact that they are ideologically opposed to many of the items in the legislation. Harper thought that the Liberal party was in such desperate shape to avoid an election that they would vote for the devil.

Turns out he was wrong. In an extraordinary development, the three opposition parties—Liberals, New Democratic Party, Bloc Quebecois—have forged a coalition and announced they will vote against the government bill.1 This will bring down the government. Stephen Harper will not be Prime Minister but there will not be an election. Instead, the coalition will form a new government.

Scott Reid of The Globe and Mail has a column in yesterday's paper that illustrates the seriousness of the crisis. It's unusual to see such language in a Canadian newspaper—especially The Globe and Mail—so I thought I'd reproduce part of his column here to show the world what is going on. I agree with Scott Reid. For the good of Canada Stephen Harper must be stopped before he does serious harm to the country.
First things first: take him out.

After all, Stephen Harper is the most dangerous animal lurking in the jungles of Parliament. He is a threat to the future viability of the Liberals. A blood simple opponent of the NDP and the only serious contemporary challenge to the Bloc Quebecois. Without him, his party is an unlikely combination of Reform Party leftovers, Harris refugees and Red Tory desperates. They don't matter or even exist without Mr. Harper. So before you think a moment longer, opposition leaders, think on that.

And if that's not compelling enough, remember: He doesn't play to win. He plays to conquer. Under his guidance, the public interest is always subjugated to his personal political advancement. And he poisons Parliament with an extreme, bare-fanged breed of partisanship that has no hope of repair until he is banished.

This becomes relevant because suddenly, he is weak. In fact, at this particular moment, he is almost unable to defend himself. Owing to a ridiculously ill-considered act of hubris, he has laid himself vulnerable to his opponents. Their imperative could not be more clear: kill him. Kill him dead. Do not, whatever you do, provide him with an opportunity to extend his hold on power. Because you can be damn certain he will never again be so reckless as to give you a chance to finish him off.

Fate tends to be grudging with gifts of this significance. To ignore it would be an error every bit as historic as the one Mr. Harper himself has made.

So don't get fancy. Don't get confused. And don't get weak in the knees. If you don't put Mr. Harper in his grave, he'll put you in yours.


1. They will also vote in favor of a non-confidence motion put forward by the Liberal party.

Friday, November 28, 2008

Biochemistry on the Web: The Citric Acid Cycle

Here are some websites that discuss the Citric Acid Cycle [Krebs animation][Wikipedia].

This is one of the fundamental biochemical pathways yet both of these sites contain errors. This is the time of the year when I challenge the students in my introductory biochemistry class to find one single website that correctly shows the reactions of the citric acid cycle with all the correct substrates and products (including water and protons). There are two sites that don't count: ones with images from my book (Horton et al.) and ones that are direct copies of the International Biochemistry and Molecular Biology (IUBMB) website. In five years my students have not succeeded. Can any Sandwalk reader find one?

Here are the links to the IUBMB reactions. They all have the correct reaction at some location. You may have to follow one or more of the links to the reaction to see the complete, correct version.

Enzymes of the Citric Acid Cycle

citrate synthase [EC 2.3.3.1]
aconitase [EC 4.2.1.3]
isocitrate dehydrogenase [EC 1.1.1.41][EC 1.1.1.42]
α-ketoglutarate dehydrogenase [EC 1.2.4.2]
succinyl-CoA synthetase [EC 6.2.1.4][EC 6.2.1.5]
succinate dehydrogenase [EC 1.3.5.1]
fumarase [EC 4.2.1.2]
malate dehydrogenase [1.1.1.37]


The Yale Experience with Alternative Medicine

 
Do you think that modern medical schools at major universities will never be advocates of quackery? Wrong!

The experience of Yale University's School of Medicine should be a warning that those who believe in evidence-based medicine have to be vigilant. Yale recently held an "Integrative Medicine Scientific Symposium." One of the speaker was David L. Katz, MD, MPH, FACPM, FACP. Katz is associate professor, adjunct, of Public Health and director of the Prevention Research Center (PRC) at the Yale University School of Medicine. He is a proponent of almost every form of non-evidence based medicine that you can imagine.

A short video of his presentation is included below. It's from the blog DC's Improbable Science: Integrative baloney @ Yale. I'm including it because it illustrates the length to which these quacks will go in order to make their point. Note that the quack is introduced by the Dean of Education at Yale—listen to how easily he may have been bamboozled into thinking that this is about legitimate science.

The most important points in the video are the ones where Dr. Katz explains away evidence-based medicine. You see, the problem isn't so much with the lack of "evidence" as with the concept of "evidence" itself. The practitioners of alternative medicine advocate changing the very concept of "evidence" to a "more fluid concept of evidence." What this means is that if a large-scale, double-blind experiment shows no effect it's not the end of the story. There are other kinds of evidence that may show the effectiveness of alternative medicine. (One of them seems to be anecdote.)



I hope that the University of Toronto is not going in this direction.


Snopes Warns Against Embedded Tracker Programs - Pass It on

 
Friday's Urban Legend: False

Have you ever received an email messgage like this?

Snopes Warning

Pass this one on to all your e-mail buddies and take the time to read the Snopes.com article listed below. It is full of good advice especially about the "cookies."

To whom it may concern:

Just a word to the wise. E-mail petitions are NOT acceptable to Congress or any other municipality. To be acceptable petitions must have a signed signature and full address.

Almost all e-mails that ask you to add your name and forward on to others are similar to that mass letter years ago that asked people to send business cards to the little kid in Florida who wanted to break the Guinness Book of Records for the most cards. All it was, and all this type of e-mail is, to get names and "cookie" tracking info for tele-marketers and spammers to validate active e-mail accounts for their own purposes.

Any time you see an e-mail that says forward this on to "10" of your friends, sign this petition, or you'll get good luck, or whatever, it has either an e- mail tracker program attached that tracks the cookies and e mails of those folks you forward to, or the host sender is getting a copy each time it gets forwarded and then is able to get lists of "active" e mails to use in spam e-mails, or sell to others that do.

Please forward this notice to others and you will be providing a good service to your friends, and will be rewarded by not getting 30,000 spam e-mails in the future.

(If you have been sending out the above kinds of email, now you know why you get so much spam!)
According to snopes.com they have never warned against "tracking programs" embedded in email messages [False Advice]. It may be good advice to not spam your friends but nothing in this email message is directly from the snopes.com website and nobody at snopes.com have authorized it.

If there was such a thing as an embedded email tracking program then passing on this message would be an excellent way to spread it!


Thursday, November 27, 2008

So Many Turkeys

 
This is almost as much fun as curling! Ms. Sandwalk will love this game [Turkey Shoot].



[Hat Tip: Chaotic Utopia]

Online Curling

 
Even if you don't like computer games, you won't be able to resist this one. It's an online curling game on the Little Mosque on the Prairie website.

Ms. Sandwalk, Jane and Gordon are going to be so excited about this. I can hardly wait to get a tournament going with my children and their American partners, Michael, and Rachel. Such an easy way to teach them the best things about Canadian culture!!




[Hat Tip: The Unexamined Life]

Thanksgiving Day in the USA

 
Some people give thanks for turkey or pumpkin pie. Some people give thanks for football. Others are truly thankful that they have been blessed with good fortune.

Sean Carroll gives thanks for the spin-statistics theorem.

Most people wouldn't understand but I do. I've hung out with physicists and astronomers. This really is how they think.



Complimentary and Alternative Medicine at the University of Toronto

 
The Faculty of Arts & Science at the University of Toronto offers a program called "Human Biology." Students who complete the program will graduate with an Honours B.Sc. degree. One of the courses is HMB434H1: Complementary and Alternative Medicine.

The textbook for the course is Fundamentals of Complementary and Integrative Medicine by Marc S. Micozzi.

Here's the course description.
Complementary/ alternative medicine (“CAM”) is used in health care systems not only in North America, but also in countries such as China, India, and Vietnam (WHO, 2002). It involves the use of non-biomedical, “holistic” and/or culturally-specific health services and practices in the treatment of illness and disease (such as Chinese acupuncture), and an expanded concept of health, illness, and wellness. This course provides an introduction to the concepts, theoretical basis, evidence-based analysis, and pressing challenges and issues in CAM today. Specific topics include introductions to: complementary/ alternative medicine in industrialized countries and commonly used modalities such as homeopathy and naturopathic medicine; traditional medicine (TM) and primary health care (PHC); traditional Chinese Medicine (TCM) and China; Ayurvedic medicine in India; Canada’s First Nations; and integrative health systems and models. Course format includes lectures, guest-presentations, films/documentaries, and inter-active class discussions/exercises. Students will also have the opportunity to analyze CAM systems and modalities.
I've been pretty nervous about this course ever since one of our students blogged about it last year [U of T has a course in complementary and alternative medicine]. I was hoping that the course would present both sides of the story.

That idea was just blown out of the water at a meeting that I just returned from. I got a chance to talk to one of the instructors, Daniel Hollenberg. What I was hearing was not good so I steered to conversation around to homeopathy thinking that this might relieve my fears. It didn't.

Here, without comment, is what I was told by a man who teaches science students at my university.
  • Philosphers of science recognize that there are several different kinds of evidence—not just the reductionist evidence of traditional medicine. In particular, epistemologists talk about holistic evidence. Alternative medicine is supported by holistic evidence not reductionist evidence.

  • Evidence in support of homeopathy has been published in Lancet, and he teaches that to his students.

  • While there may be examples of some homeopathic medicines that don't work, the theory of homeopathic medicine is understood and supported by physicists who have published papers explaining how water retains the memory of molecules that used to be dissolved in it. He mentioned Ursala Franklin as a supporter of homeopathy.


Nobel Laureates: George Hitchings and Gertrude Elion

 

The Nobel Prize in Physiology or Medicine 1988.
"for their discoveries of important principles for drug treatment"


Gertrude B. Elion (1918 - 1995) and George H. Hitchings (1905 - 1998) won the Noble Prize for their work on the treatment of disease and organ transplantation. They developed a number of drugs that interfered with nucleic acid synthesis leading to effective treatment of malaria as well as bacterial and viral infections. They are especially noted for the development of drugs that inhibit the body's ability to reject the transplant. One of the most famous of these immunosuppression drugs is azathioprine, a drug that is still used in some cases to suppress the immune response.

Elion and Hitchings worked together at the Wellcome Research Laboratories in Research Triangle Park, NC, USA. They are among a select group of Nobel Prize winners who did their prize winning research outside of academia. Elion and Hitchings shared the Nobel Prize with Sir James W. Black.

Here's what the press release said about Elion and Hitchings

THEME:
Nobel Laureates
Studies of Nucleic Acid Synthesis Result in the Discovery of New Drugs

Gertrude Elion and George Hitchings have collaborated since 1945. Their original research idea was to look for differences in nucleic acid metabolism between normal human cells, cancer cells, protozoa, bacteria and virus, which could be utilized to develop drugs that selectively block the growth of cancer cells and of noxious organisms. Over the years this research philosophy has formed the basis for the development of drugs against a variety of disorders including leukemia, malaria, virus infections and gout.

When Elion and Hitchings presented their ideas at the end of the 1940s the knowledge about nucleic acid metabolism was very limited. It was known, however, that purines and pyrimidines are incorporated into nucleic acids. Elion and Hitchings studied the growth of the Lactobacillus casei, a bacterium dependent on folic acid or a combination of purines (hypoxanthine, guanine) and pyrimidines (thymine). The purpose was twofold, to characterize the metabolic pathways involved in the biosynthesis of nucleic acids and to identify antimetabolites in the nucleic acid metabolism (Figure 3).
Figure 3.

Figure 3. Purine bases (adenine, guanine and hypoxanthine) are synthesized from simple precursors. Nucleosides are then formed by the addition of sugar moieties (deoxyribose or ribose) and subsequently converted into nucleotides by the addition of phosphate (mono-, di- and triphosphate). Nucleotides take part in cellular metabolism and are the building blocks in the synthesis of RNA and DNA. Structural analogues of the natural substances can specifically block the different metabolic steps. Some examples are given in the figure.
Already in 1948 Elion and Hitchings discovered a substance, diaminopurine, an adenine antagonist, which inhibited the growth of L. casei (Figure 3). It was also found to have an effect on experimentally induced leukemia. Clinical trials in patients were initially promising but had to be interrupted due to toxic side effects. Stimulated by this finding Elion and Hitchings continued their research which soon resulted in two new chemotherapeutic drugs, thioguanine (1950) and 6-mercaptopurine (1951). In collaboration with the Sloan-Kettering Institute 6-mercaptopurine was tried in leukemic patients who were resistant to methotrexate. About one third of the patients responded with complete remission (1953). The finding was soon confirmed, and 6-mercaptopurine (as well as thioguanine) are still used in the treatment of leukemia (Table II).

Elion and Hitchings tried to improve the therapeutic properties of 6-mercaptopurine by using sulphur-substituted compounds. The result was azathioprine (1957) which replaced mercaptopurine as an inhibitor of the immune response. For a long time azathioprine was the only drug available to prevent rejection of transplanted organs. It is still used for that purpose but also for the treatment of autoimmune diseases.

Attempts were also made to prolong the effect of 6-mercaptopurine by blocking its metabolism by xanthine oxidase which is involved in the endogenous production of uric acid (Figure 3). In 1963 this research resulted in another new drug, allopurinol, which blocks the formation of uric acid and therefore is used in the treatment of primary and secondary gout.

Hitchings and collaborators also developed pyrimethamine (1950) and trimethoprim (1956) which were found to be effective in the treatment of malara and bacterial infections, respectively. Both drugs have a strong affinity to the enzyme dihydrofolate reductase, but pyrimethamine is 2000 times more toxic to the enzyme system in the malaria parasite than in the host. Trimethoprim has 100 000 times higher affinity to the bacterial compared to the human enzyme. An important discovery was that the chemotherapeutic effects of these two compounds were markedly enhanced by sulphonamides, drugs which inhibit the synthesis of folic acid. This pharmacotherapeutic principle is used in the combination drugs trimethoprim-sulfa and pyrimethamine-sulfa which are used in the treatment of bacterial infections and malaria, respectively.

A more recent application of Elion's and Hitchings' research philosophy is acyclovir, a drug used in the treatment of infections with herpes virus. Already in the 1950s they had shown that antipurines had to be transformed into nucleotides in order to become active in the cell. The herpes virus carries information which leads to the production of a new enzyme which transforms nucleosides to nucleotides (thymidine kinase) in the infected cell. This enzyme has considerably less substrate specificity than the cell's normal enzyme. Therefore, acyclovir is transformed into its corresponding nucleotide which is the active antimetabolite and the growth of the virus is inhibited (Figure 3).

Acyclovir was described by Elion and coworkers in 1977 and is a modern example of the realization of the basic ideas from 1950. An even more recent application of these ideas is the development of azidothymidine (AZT) which was described in 1985 by other scientists from the same institute, and which is the hitherto best documented drug in the treatment of AIDS. It can be added that trimethoprim-sulfa is used in the treatment of Pneumocystis carinii, a relatively common complication to AIDS.

The clinical use of the drugs discovered by Elion and Hitchings is summarized in Table II.
Table 2.



References

G. Gahrton, B. Lundh: Blodsjukdomar. Lärobok i hematologi. Natur och Kultur, Stockholm, 1983.

Läkemedelsboken 1987/88, Apoteksbolaget, Stockholm, sid, 87-88, 150-151, 249, 625.

J.H. Shelley: Creativity in Drug Research. Trends in Pharmacological Sciences. 1983, vol. 4.

L. Stryer: Biochemistry, 3rd edition. W.H. Freeman and Company, San Francisco, 1988, chapter 25, 601-625.


[Photo Credit: George Hitchings and Gertrude Elion (top) from Welcome Images]

The IDiot Version of Reality

 
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
Check out this posting by Barry Arrington on Uncommon Descent [Peppered Moth Idolatry].
The venerable peppered moth (Biston betularia) has popped up a couple of times in recent posts. It seems that some of our Darwinian commenters (see, e.g., qwerty017 in comment [2] here) have not gotten the memo – the peppered moth myth has been completely exploded. Don’t take our word for it. Uber-Darwinist Jerry Coyne says in the November 1998 edition of Nature: “For the time being we must discard Biston as a well-understood example of natural selection in action.” Why else would the popular school text Biology pull its discussion of Biston as an example of “evolution in action”?
Here are some examples of scientists who have not heard message from the IDiot's.

Douglas Futuyma in his textbook Evolution published in 2005 (p. 293).
Until the 1930s, most evolutionary biologists followed Darwin in assuming that the intensity of natural selection is usually very slight. By the 1930s, however, examples of very strong selection came to light. One of the first examples was INDUSTRIAL MELANISM in the peppered moth (Biston betularia). ...
There are many scientific papers on the "myth" as well. Here's the abstract from Saccheri et al. (2008).
Historical datasets documenting changes to gene frequency clines are extremely rare but provide a powerful means of assessing the strength and relative roles of natural selection and gene flow. In 19th century Britain, blackening of the environment by the coal-fired manufacturing industry gave rise to a steep cline in the frequency of the black (carbonaria) morph of the peppered moth (Biston betularia) across northwest England and north Wales. The carbonaria morph has declined across the region following 1960s legislation to improve air quality, but the cline had not been comprehensively described since the early 1970s. We have quantified changes to the cline as of 2002, equivalent to an interval of 30 generations, and find that a cline still exists but that it is much shallower and shifted eastward. Joint estimation of the dominant fitness cost of carbonaria and dispersal parameters consistent with the observed cline change indicate that selection against carbonaria is very strong across the landscape (s approximately 0.2), and that dispersal is much greater than previously assumed. The high dispersal estimate is further supported by the weak pattern of genetic isolation by distance at microsatellite loci, and it implies that in addition to adult dispersal, wind-dispersed first instar larvae also contribute to lifetime dispersal. The historical perspective afforded by this study of cline reversal provides new insight into the factors contributing to gene frequency change in this species, and it serves to illustrate that, even under conditions of high dispersal and strong reverse selection acting against it, complete erosion of an established cline requires many generations.
Wow, this is a tough call. Who are you going to believe, evolutionary biologists like Futuyma and Sacheri et al., or an IDiot like Barry Arrington?

There's no rush. Take a microsecond or two to make up your mind.

See Revenge of the Peppered Moth. Ohmygod! These photographs are faked!, and Peppered Moths and the Confused IDiots for some insight into why one textbook got cold feet in 2000.


Saccheri, I.J., Rousset, F., Watts, P.C., Brakefield, P.M. and Cook, L.M. (2008) Selection and gene flow on a diminishing cline of melanic peppered moths. Proc. Natl. Acad. Sci. USA 105:16212-16217. [doi:10.1073/pnas.0803785105]

Tuesday, November 25, 2008

On the Origin of Species

 
Yesterday (Nov. 24, 2008) marked the 149th anniversary of the publication of On the Origin of Species by Charles Darwin. Ms. Sandwalk just bought me an illustrated edition by David Quammen and I highly recommend it. The text is from the first edition of Darwin's work and the illustrations cover a wide range of topics including copies of Darwin's letters and letters from his friends. This is an excellent way to get people interested in one of the most important books ever published.

I was prompted to re-read Origin and I discovered some things I had long forgotten. Most importantly, the style of Darwin's writing is impressive. He takes the time to argue his point by highlighting the most relevant objections to his ideas. While we all recognize that this is the appropriate style for a scientific work, we also recognize (unfortunately) that it may be a lost art. There are too many papers these days that ignore anything that weakens one's case.
In the four succeeding chapters, the most important and gravest difficulties on the theory will be given: namely, first, the difficulties of transitions, or in understanding how a simple being or a simple organ can be changed and perfected into a highly developed being or elaborately constructed organ; secondly, the subject of Instinct, or the mental powers of animals; thirdly, Hybridism, or the infertility of species and the fertility of varieties when intercrossed; and fourthly, the imperfection of the Geological Record.
The second thing I re-discovered is the clarity and forcefulness of Darwin's writing, given the style of the Victorian era. Also his foresight and originality.
Although much remains obscure, and will long remain obscure, I can entertain no doubt, after the most deliberate study and dispassionate judgment of which I am capable, that the view which most naturalists entertain, and which I formerly entertained—namely, that each species has been independently created—is erroneous. I am fully convinced that species are not immutable, but that those belonging to what are called the same genera are lineal descendants of some other and generally extinct species, in the same manner as the acknowledged varieties of any one species are the descendants of that species. Furthermore, I am convinced that Natural Selection has been the main but not the exclusive means of modification.
Thomas H. Huxley read an advance copy of On the Origin of Species and sent a letter to Darwin, which he received on the day before the book went public. Huxley knew what was coming ...
I trust you will not allow yourself to be in any way disgusted or annoyed by the considerable abuse and misrepresentation which, unless I greatly mistake, is in store for you. Depend upon it you have earned the lasting gratitude of all thoughtful men. And as to the curs which will bark and yelp, you must recollect that some of your friends, at any rate, are endowed with an amount of combativeness which (though you have often justly rebuked it) may stand you in good stead.

I am sharpening my claws and beak in readiness.
The letter is published in the illustrated edition by David Quammen.


Deceptive Science?

 
I was recently taken in by a paper where the authors implied that they were the first to identify one of Gregor Mendel's original genes [see Identity of the Product of Mendel's Green Cotyledon Gene (Update)].

The reason I was sensitized to this issue is because of a similar incident involving a paper published in Cell. Here's an outline of the issue as reported in The Times Higher Education.

It appears that the Cell paper is very misleading. It does not give appropriate credit to the work of other labs.

Peter Lawrence asked if he could publish a letter in Cell but he was told to post comments on the website instead. This is not appropriate. Nobody reads those comments. The author of the suspect Cell paper, Jeffrey Axelrod of Stanford School of Medicine (Palo Alto, CA USA) stands by his publication. The editors of Cell use the common excuse when a journal is caught with it's pants down.
After being sent four of the letters of complaint, Professor Axelrod added on the 6 November: "Our paper (Chen et al, June 2008) underwent a strict process of peer review prior to publication. Concerns about the review process should be directed to Cell. We stand by our conclusions as stated in the paper, as well as by our use of citations."

Cell declined to respond to questions put by Times Higher Education. However, in a response to the complaint from Professor Lawrence, Cell's senior scientific editor Connie Lee said: "I can only assure you that the reviewers were experts in planar cell polarity and the consensus decision was that the model presented by Chen et al was thought-provoking, well supported and provided a sufficient conceptual advance beyond the existing literature."
The incident raises a serious question. Is the pressure to publish so great that authors are tempted to deceive editors and reviewers by making their work seem more original and novel than it really is?

This is not a new problem. A few years ago Nature was pressured into publishing an editorial defending its policies against the charge that they were publishing bad science in order to be the first journal to publish "breakthroughs" (Adam and Knight, 2002). The Nature editorial denies that the popular journals are promoting sensationalism.
Editors of leading journals reject the suggestion that standards are slipping in the face of heightened competition. "Nature has nothing to gain by the pursuit of glamour at the expense of scientific quality, considering, not least, the criticisms, corrections and retractions we would then habitually be forced to publish," argued this journal in an editorial comment earlier this month5. And many researchers who were interviewed for this article agree that the system is still working tolerably. If it ain't broke, they say, don't try to fix it.
Speaking of the pursuit of glamour, Nature continues its policy of hiring science writers to promote and hype papers that have recently been published in its journal [Human genes are multitaskers].


Adam, D. and Knight, J. (2002) Journals under pressure: Publish, and be damned... Nature 419: 772-774. [doi:10.1038/419772a]

Identity of the Product of Mendel's Green Cotyledon Gene (Update)

Last year I drew your attention to the identification of one of Gregor Mendel's original seven mutants [Identity of the Product of Mendel's Green Cotyledon Gene]. At the time, I thought that a recent 2007 paper by Sato et al. was the first publication to make this identification. Now I realize that I slighted the original discoverers Armstead et al. (2007) and earlier publications. The Armstead et al. paper is referenced in the later Sato et al. paper but the reference does not give appropriate credit to the work done by Armstead et al. in identifying the Mendelian gene. It was easy to get the impression that the Japanese group was the first to make the definite connection between Mendel's gene and work done in other species. I suspect that this was deliberate.

Here's a revised version of my original posting. Thanks to a reader who alerted me to the proper credit.




Another of Mendel's seven genes has been identified. This one is described in his 1865 paper Experiments in Plant Hybridization [MendelWeb] as character number 2.
2. To the difference in the color of the seed albumen (endosperm). The albumen of the ripe seeds is either pale yellow, bright yellow and orange colored, or it possesses a more or less intense green tint. This difference of color is easily seen in the seeds as their coats are transparent.
Mendel's reference to the color of albumin, or endosperm, is inaccurate. He was actually observing the color of the cotyledons—the "seed leaves" that surround the embryo in the pea seed. These tiny leaves are covered by a seed coat that is partially transparent.

In wild-type peas the seeds turn yellow as they mature (I) but certain mutants exhibit a "stay-green" phenotype where the peas retain their green color (i). The figure shows seeds from a plant with the II genotype (top) and the ii genotype (bottom). The seed coat has been removed from the lower pair of each group of four peas.

A paper published in Science identifies the "stay-green" gene that Mendel worked with (Armstead et al. 2007). This work is based on several decades of study of the "stay-green" phenotype by Howard Thomas and his colleagues at the Institute of Grassland and Environmental Research, Aberystwyth, UK (Armstead et al. 2006; Thomas, 1987; Thomas et al. 1996; Thomas and Stoddart, 1975).

It turns out that the gene, called sgr (stay-green), encodes an enzyme that is localized to chloroplasts and plays a role in the degradation of chlorophyll during senescence and maturation of seeds. When the enzyme is defective chlorophyll isn't broken down and the tissue stays green.

This brings to three the number of Mendel's genes that have a known function. The wrinkled pea phenotype is caused by a defect in the gene for starch branching enzyme (Bhattacharya et al., 1990) [Biochemist Gregor Mendel Studied Starch Synthesis]. The tall/short phenotypes are caused by defects in the gene for gibberellin 3β-hydroxylase (Martin et al., 1997). Gibberellins are plant growth hormones.


[Photo Credit: The photograph of mutant and wild-type pea seeds is taken from Figure 1 of Sato et al. (2007)]

Armstead, I., Donnison, I., Aubry, S., Harper, J., Hörtensteiner, S., James, C., Mani, J., Moffet, M., Ougham, H., Roberts, L., Thomas, A., Weeden, N., Thomas, H., and King, I. (2007) Cross-species identification of Mendel's I locus. Science 315: 73. [DOI: 10.1126/science.1132912]

Armstead, I., Donnison, I., Aubry, S., Harper, J., Hörtensteiner, S., James, C., Mani, J., Moffet, M., Ougham, H., Roberts, L., Thomas, A., Weeden, N., Thomas, H., and King, I. (2006) From crop to model to crop: identifying the genetic basis of the staygreen mutation in the Lolium/Festuca forage and amenity grasses. New Phytologist 172: 592-597.

Bhattacharyya, M. K., Smith, A. M., Ellis, T. H., Hedley, C., and Martin, C. (1990) The wrinkled-seed character of a pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme. Cell 60:115-122.

Martin D.N., Proebsting W.M., Hedden P. (1997) Mendel's dwarfing gene: cDNAs from the Le alleles and function of the expressed proteins. Proc. Natl. Acad. Sci. (USA) 94:8907–8911.

Sato Y., Morita R., Nishimura M., Yamaguchi H., and Kusaba M. (2007) Mendel’s green cotyledon gene encodes a positive regulator of the chlorophyll-degrading pathway. Proc. Natl. Acad. Sci. (USA) 104: 14169-14174. [doi: 10.1073/pnas.0705521104].

Thomas, H. (1987) Sid: a Mendelian locus controlling thylakoid membrane disassembly in senescing leaves of Festuca pratensis. Theoretical and Applied Genetics 73: 551 555.

Thomas, H., Schellenberg, M., Vicentini, F., Matile, P. (1996) Gregor Mendel's green and yellow pea seeds. Botanica Acta 109: 3-4.

Thomas, H., and Stoddart, J.L. (1975) Separation of chlorophyll degradation from other senescence processes in leaves of a mutant genotype of meadow fescue (Festuca pratensis). Plant Physiology 56: 438-441.

Monday, November 24, 2008

Monday's Molecule #98

 
Name this molecule. This time we need the common name and the systematic (IUPAC) name. A Nobel Prize was awarded for discovering this molecule and showing how it is involved in cell metabolism.

The first one to correctly identify the molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are only three ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin, Dale Hoyt from Athens, Georgia and Ms. Sandwalk from Mississauga, Ontario, Canada. Dale and Ms. Sandwalk have offered to donate the free lunch to a deserving undergraduate so the first two undergraduates to win and collect a free lunch can also invite a friend.

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 Laureate(s) 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. Comments are now open.

UPDATE: The molecule is azathioprine [6-(3-methyl-5-nitroimidazol-4-yl)sulfanyl-7H-purine]. The Nobel Laureates are Gertrude B. Elion and George H. Hitchings. Alex Ling of the University of Toronto beat everyone else so he gets another free lunch only this time he can invite a friend. There were a dozen people who got this one—that's a surprise to me since I had never even heard of the Nobel Laureates unitil last week.


A Fondness for Beetles

 
By now everyone has heard the story. There are almost as many species of beetle as all the rest of the insects put together. This is what prompted J.B.S. Haldane to say that God has "an inordinate fondness for beetles."

Now that's fine if you're an ordinary person, but if you're into taxonomy the huge diversity of beetles presents some really tough problems. Christopher Taylor describes one of the problems of classifying beetles in The Diversity of Ground Beetles.

Apparently God isn't the only one who likes beetles.


Best Canadian Sci/Tech Blog

 
The Canadian Blog Awards are for "Celebrating the best in the Canadian blogosphere." Here are the nominees for Best Sci/Tech Blog.
I'm not sure why Bad Astronomy is on a list of blogs that celebrate the best in the Canadian blogosphere but that's who I voted for. I'm hoping that Phil Plait is NOT a Canadian 'cause that would point out how silly these awards really are.

Wouldn't it be funny if Mindful Hack or Post Darwinist won? That would say a lot about the people who vote for these things.

I support Canadian Cynic who refuses to participate ...
Another year, another incarnation of the Canadian Blog Awards, and another request to please delete CC HQ from any and all categories in which we've been nominated for a fairly simple reason -- we're not interested in any popularity contest in which voters seriously have to choose between CC HQ and batshit crazy, racist, white supremacist, Nazi sympathizer loons like Kate McMillan and Kathy Shaidle for "best blog."
I wish I could take the same stance but nobody nominated me for anything. Damn, I don't even get to withdraw my nomination.

BTW, I'm not familiar with most of these blogs. Can anyone point me to the wheat among all the chaff?


Saturday, November 22, 2008

Canada's New Minister of State (Science and Technology) Is a Chiropractor

 
It's true. Checkout the Stephen Harper website, which incidentally, is supposed to be the Prime Minister's website.
The Honourable Gary Goodyear
Minister of State (Science and Technology)

Cambridge (Ontario)

Gary Goodyear was first elected to the House of Commons in 2004 and re-elected in 2006 and 2008.

Prior to entering federal politics, Dr. Goodyear practised chiropractic medicine and worked as an advisor to investment firms in the biomedical industry.

Dr. Goodyear was a co-designer of a three-year post-graduate sports fellowship program. He also co-authored “Practice Guidelines” and was Public Relations Director and Past President for the College of Chiropractic Sports Sciences in Toronto. Dr. Goodyear has taught at the Canadian Memorial Chiropractic College and the University of Waterloo. He has worked with many athletes, both amateur and professional, including serving as medical services chair for the Ontario Special Olympics.

Dr. Goodyear is a graduate of the University of Waterloo and the Canadian Memorial Chiropractic College.
It's bad enough that we have a chiropractor advising the government about science but this particular one seem especially unqualified. He also practiced acupuncture when he was actively seeing patients. Dr. (sic) Goodyear is strongly supported by evangelical christians (e.g. Christian Conservatives). That may not have anything to do with his ability to understand modern science. Gary Goodyear was endorsed by Vote Marriage Canada, a group that opposes gay marriage.

The website of the Canadian Memorial Chiropractic College has a lengthy article praising the 4 MPs who are chiropractors (3 Conservatives, 1 Liberal) [Chiros on the Hill].
“The single biggest criticism of politicians,” explains Dr. Colin Carrie, Class of ’89 and Member of Parliament for the electoral district of Oshawa, Ontario, “is that they don’t listen.” Chiropractors, he says, are educated to be exceptional listeners. “Regardless of our political stripes, we want to do what’s right for our patients and our constituents.”
It’s people skills, agrees his colleague and fellow Conservative Dr. Gary Goodyear (MP for Cambridge, Ontario). “Every chiropractor has to be a people person, that’s what we were taught at CMCC.”

Goodyear, Class of ’83, and Chair of the Committee of Procedure and House Affairs, adds with a laugh that his advisors have had occasion to remind him not to be quite so hands-on when dealing with his constituents. “My election team has actually told me to stop touching people so much, but I can’t help it. It’s just natural to me. As a chiropractor, you automatically love people. Chiropractic is a touchy-feely profession—that transfers.”

Interestingly, all four chiropractic MPs tell similar stories about how—for each in his or her own way—they have come to view their constituents in much the same light as chiropractors perceive their patients: “You can’t be a successful chiropractor without good interpersonal skills,” explains Dr. James Lunney, (Class of ’83, Nanaimo-Alberni, BC). “Our job as chiropractors is taking complicated issues, and finding ways of explaining them—interpreting X-rays, for example—you have to be able to communicate to your patient what needs to be communicated.” The job requirements are strikingly similar, he says, on Parliament Hill. “Any chiropractor who deals with patient issues successfully has the skills to make the transition into politics. If you can manage a practice, you have an aptitude for politics.”
I'm beginning to see the parallels between being a politician and a chiropractor. This is not complimentary to politicians.


Good IDEA?

 
The Discovery Institute is promoting the IDEA Center.
As part of our efforts to support academic freedom on evolution, we are teaming up with the IDEA Center (Intelligent Design and Evolution Awareness) to help students in starting an IDEA chapter on their campus. Such campus clubs are a fun and educational way for students to examine all sides of the debate over evolution.

IDEA Clubs are student-initiated clubs that foster academic freedom as students learn about scientific evidence that supports intelligent design and also learn about modern evolutionary theory. IDEA Clubs are a growing network of student-led clubs on university and high school campuses around the United States with thirty new chapters formed to date.
(my emphasis)
Here's a challenge for everybody no matter which side you are on. Finding anti-evolution articles on the IDEA Center website is trivial. All the standard lies are there, sometimes in multiple articles. But can anyone find a single bit of evidence that supports Intelligent Design Creationism?

What about modern evolutionary theory? Is there anything on the website that comes remotely close to explaining modern evolutionary theory?

I didn't think so? How many campus have clubs of IDiots like this?


Friday, November 21, 2008

Riding in the Car to Get Cherries

 
Riding in the Car to Get Cherries is a painting by Kanzi who also gave it the title. The painting is part of Apes Helping Apes.




Were Neanderthals stoned to death by modern humans?

 
Were Neanderthals stoned to death by modern humans? is the provocative title of a press release reported in New Scientist. The author of the study is interviewed,
Human aerial bombardments might have pushed Neanderthals to extinction, suggests new research. Changes in bone shape left by a life of overhand throwing hint that Stone Age humans regularly threw heavy objects, such as stones or spears, while Neanderthals did not.

"The anatomically modern humans would have this more effective and efficient form of hunting," says Jill Rhodes, a biological anthropologist at Bryn Mawr College in Pennsylvania, who led the new study. A warmer Europe would have opened up forests, enabling longer range hunting, she says.

Rhodes and a colleague studied changes to the arm bone that connects the shoulder to the elbow – the humerus – to determine when humans may have begun using projectile weapons.

"If we're trying to understand whether anatomically modern humans had projectiles, then why not read the signature that it can imprint in the skeleton," Rhodes says.
The paper by Jill Rhodes of the Department of Anthropology, Bryn Mawr College and Steven E. Churchill of the Department of Evolutionary Anthropology, Duke University appears in The Journal of Human Evolution under Article in Press.
Rhodesa, J.A. and Churchill, S.A. (2008) Throwing in the Middle and Upper Paleolithic: inferences from an analysis of humeral retroversion. [doi:10.1016/j.jhevol.2008.08.022M]
Here's the complete text of the conclusiosn from that paper.
Clinical evidence from professional and college-level throwing athletes reveal differences in the humeral retroversion angle both between athletes and comparative (non-throwing) samples and between the dominant (throwing) and non-dominant limbs in the athletes. Comparative analysis of humeral architecture, specifically the humeral retroversion angle, in Pleistocene fossil humans has the ability to contribute new insights into the origins of projectile weaponry by examining the individuals who would have wielded those weapons. While the data is equivocal (in part because of confounding variables that affect humeral retroversion and in part because of small fossil sample sizes), we can reach two conclusions. First, while Neandertals tend to have high amounts of humeral retroversion, the overall pattern between limbs and between sexes strongly suggests that it is not due to habitual throwing behavior. The humeral retroversion data is largely consistent with other lines of evidence pertaining to projectile weaponry; the preponderance of evidence, ranging from fossil spears and Mousterian lithics to the articular and diaphyseal morphology of upper limb bones, suggests that Neandertals did not habitually employ long-range projectile weapons ([Churchill et al., 1996], [Schmitt et al., 2003], [Shea, 2003a], Shea, 2006 J.J. Shea, The origins of lithic projectile point technology: evidence from Africa, the Levant, and Europe, J. Archaeol. Sci. 33 (2006), pp. 823–846. Article | PDF (774 K) | View Record in Scopus | Cited By in Scopus (15)[Shea, 2006] and [Churchill and Rhodes, in press]). It is worth noting that earlier hominins also lack humeral torsion, further demonstrating that the increased retroversion found in Neandertals is unlikely to be linked to throwing. Second, we cannot reject the suggestion of projectile weapon use in the European Upper Paleolithic. The patterns seen in bilateral asymmetry in humeral retroversion angle suggest a variable use of throwing in the middle Upper Paleolithic (and thus great inter-individual variation in asymmetry), perhaps related to regional differences in hunting practices or the importance of projectile-based hunting. The levels of asymmetry seen in late Upper Paleolithic males are consistent with the regular use of projectile technology by this time.
Is it just me, or does there seem to be a disconnect between what's in the paper and what's in the press release? Why would the author allow the press release to say something that cannot be found anywhere in the paper?


Thursday, November 20, 2008

Creationists Fight Dirty, Scientists Don't

 
Martin at The Atheist Experience has been posting about the Texas State Board of Education hearings on science standards. Several members of the board want to "teach the controversy," which means teaching the creationist lies about evolution in an attempt to discredit it. His latest posting (Crippled dogs and one-trick ponies) is quite interesting.

Martin points out that when creationist board members use the standard lies and misconceptions to make their point about flaws in evolution, the pro-science witnesses should be prepared to hit back just as hard. They lose credibility if they waffle.

This is not a scientific dispute. Creationists don't care about science.


This Is Ridiculous

 
The New York Times has an article by Nicholas Wade on Regenerating a Mammoth for $10 Million. It outlines a possible method for re-creating extinct organisms from a knowledge of their DNA sequence. The idea is to produce a mammoth.

I suppose there's nothing wrong with this kind of speculation. After all, we all did it back when Jurassic Park first came out. But there's a time to be serious as well. Why in the world would we want to spend $10 million of valuable research money to bring back the mammoth? I can see the importance of resurrecting the dodo or the sabre tooth tiger, but mammoths? Who need them? Do they even taste good?

Wait a minute ... there's even more exciting news in the New York Times article. George Church, a "genome tecchnologist" at Harvard Medical School was interviewed. He describes out a way to resurrect Neanderthals.

The full genome of the Neanderthal, an ancient human species probably driven to extinction by the first modern humans that entered Europe some 45,000 years ago, is expected to be recovered shortly. If the mammoth can be resurrected, the same would be technically possible for Neanderthals.

But the process of genetically engineering a human genome into the Neanderthal version would probably raise many objections, as would several other aspects of such a project. “Catholic teaching opposes all human cloning, and all production of human beings in the laboratory, so I do not see how any of this could be ethically acceptable in humans,” said Richard Doerflinger, an official with the United States Conference of Catholic Bishops.

Dr. Church said there might be an alternative approach that would “alarm a minimal number of people.” The workaround would be to modify not a human genome but that of the chimpanzee, which is some 98 percent similar to that of people. The chimp’s genome would be progressively modified until close enough to that of Neanderthals, and the embryo brought to term in a chimpanzee.

“The big issue would be whether enough people felt that a chimp-Neanderthal hybrid would be acceptable, and that would be broadly discussed before anyone started to work on it,” Dr. Church said.
What a clever way to get around all the ethical issues (not)! However, aren't we missing the point here? Why would we want to clone a Neanderthal in the first place? (BTW, you need two of them.)

What if the Neanderthals turn out to be smarter than us—a distinct possibility? Wouldn't they take over all the good jobs, like university professors? And what if they turn out to be stupider than the average human? Don't we already have enough creationists?


[Hat Tip: john hawks weblog: Clone your own Neanderchimp baby?]

Closed for the Winter

 
We've just had our first significant snowfall in Toronto and the campus maintenance people have sprung into action. The main ramp leading into my building from the subway station has been closed for the winter. You may recall that this is the entrance where the expensive stone walkway is useless [If you build it, will they follow?].

Toronto is in Canada. In Canada we have real winters, with snow and ice. You may be asking yourself why anyone would build an entrance that has to be shut down for five months of the year. That's a very good question.

This entrance was constructed a few years ago when the Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR) was built. The ramp consists of wood slats with about one centimeter spaces between them. I'm told that a special kind of wood was used and it's very expensive.

Here's the problem as it was explained to me. First, it is difficult to clean ice and snow from a wooden walkway without damaging it. Second, when this kind of wood gets wet it becomes very slippery. That means you can't use salt to get rid of the ice without creating dangerous conditions in the winter.

I'm told that the university and the architects have been unable to reach agreement on who should fix this problem.

CCBR was designed by the architectural firms of Alliance & Behnisch Architekten. The architects won the Royal Institute of British Architects Awards (RIBA) in 2006 for this building [RIBA 2006]. They also won the Governor General's Medal in Architecture for 2008 for this building.

Here's part of the press release from the University of Toronto.

The Governor General's Medals in Architecture recognize outstanding achievement in recently built projects by Canadian architects. These awards are administered jointly with the Canada Council for the Arts, which is responsible for the adjudication process and contributes to the publication highlighting the medal winners. The recipients of the 2008 Governor General's Medals in Architecture were selected by a jury of distinguished architects.

Elizabeth Sisam, assistant vice-president (campus and facilities planning), said buildings like the Donnelly CCBR are very complex and boast many notable features.

"The CCBR is a very clever design that knits the Medical Science Building to the CCBR while being respectful of the heritage buildings and at the same time maintains and enhances pedestrian routes and entrances through to the campus," Sisam said. "Below grade, there are research laboratories that extend all the way to the sidewalk. The inside of the building in the area of the laboratories is a flexible design allowing the research teams to expand and contract. The exterior has a very unique treatment, a 'double façade' which is an excellent example of sustainable design."
The original design did not "knit the Medical Science Building to the CCBR." That was only added after many of us complained about the original design and the Dean of Medicine (David Naylor) intervened to provide extra funding to build the proper connection. In the original plan the buildings would have been quite separate.

The end product does not "maintain and enhance pedestrian routes and entrances through to the campus." The entrance off College St. requires that you climb up an annoying two flights of steps inside the building before gaining access to the lobby where the cafeteria is located. The direct entrance to this lobby from the other side (see photo above) could only be considered an "enhancement" by someone with a wicked sense of humour.


Wednesday, November 19, 2008

Science 2.0

 
You may have heard of Science 2.0. It's the latest "revolution" in science. You can read a nice summary from the Howard Hughes Medical Institute [Science 2.0 You Say You Want a Revolution?].


Personally, I think blogging is going the become part of the culture in the same way that newsgroups did in the past except that more people are going to read the blogs. I don't think it's going to be a revolution. I don't think the majority of scientists and students are going to become regular readers of blogs. The blogosphere culture is not for everyone. Many of my colleagues are completely turned off. Blogging is going to be just one more way of communicating science and sharing ideas.

I'm skeptical of OpenWetWare (OWW) and other software that allows you to put all your notes and protocols on the web. Right now, most labs don't make shared electronic versions of protocols and notes even though we've been able to do that for 25 years. I don't see why that's going to change. My notebooks have lots of comments that I've scribbled in the margins (F**k - forgot to add magnesium!). I don't know why I'd want to share that with everyone on the planet.

I've done lots of "secret" experiments in my lifetime just to check out some crazy idea. So have the graduate students and post-docs in my lab. Does this sort of thing never go on in the labs that have adopted open access lab books? That doesn't sound like any kind of lab that I'd like to be in. Too much control for my liking. (According to the article it's "where the cool people are." I don't think so.)

Open-Access Journals are here to stay and will only increase in popularity.


[Hat Tip: A Blog Around the Clock]

Reprogenetics and Genetic Variants

 
Reprogenetics is a company that offers the following service.
Preimplantation Genetic Diagnosis consists of the biopsy of a single cell per embryo, followed by its genetic diagnosis through different techniques (FISH, PCR, or CGH), and the subsequent replacement to the patient of those embryos classified by genetic diagnosis as normal.

Reprogenetics provides PGD analysis to IVF centers, including diagnosis of aneuploidy for advanced maternal age (such as Down's syndrome), repeated IVF failure, recurrent spontaneous abortions, chromosome translocations and inversions, as well as for gene defects such as Cystic fibrosis, fragile X, Myotonic Dystrophy, Thalasaemia, Tay Sachs, and others. We can also provide an experienced embryologist to perform embryo biopsy and cell processing.
Other tests may be offered soon including predisposition for diabetes and other genetic diseases.

The research director of Reprogenetics was interviewed for an article that appeared today on the Nature website [Gene testing of embryos needs guiding]
Last week, at a meeting of the American Society for Reproductive Medicine in San Francisco, California, researchers cautioned that they do not yet advocate this use of genetic tests. But as the technology advances, consumer demand is likely to overwhelm societal ethical qualms. "If people think they can make their babies healthier at year one, year two, or in utero, they will do it," says Jacques Cohen, research director at Reprogenetics, a genetic-testing company in West Orange, New Jersey.

...

Cohen says that as the understanding of disease genetics progresses, use of tests that seem controversial now may become more acceptable in the future: "If you had the chance to decrease your child's risk of a disease like diabetes and you didn't, society would blame you."
I assume this is a profit-making company. I wonder why Nature chooses to rely on the opinion of someone who has a vested interest in the technology? Especially someone who has an opinion like that?

What can he be thinking? Does he think that the average American in the future will be forced to undergo in vitro fertilization to avoid being sued by their children?


[Hat Tip: The Sciphu Weblog: This pisses me off a little]

Nobel Laureate: Sinclair Lewis

 


The Nobel Prize in Literature 1930.
"for his vigorous and graphic art of description and his ability to create, with wit and humour, new types of characters"




Sinclair Lewis (1885 - 1951) won the Noble Prize in Literature for his novels about average Americans doing non-average things. The prize committee specifically mentions Main Street, Babbitt, Arrowsmith, Elmer Gantry, and Dodsworth.

Sinclair Lewis was the first American to win a Nobel Prize in Literature.

Arrowsmith is a novel about a scientist. It is one of the first works of the 20th century to describe the realities of being a scientist and really should be required reading for all science students. Lewis relied heavily on his scientific adviser, the microbiologist Paul de Kruif, and the novel is based loosely on Félix d'Herelle. Here's how the novel is described in the presentation speech on the Nobel Prize website.

THEME:
Nobel Laureates
Arrowsmith (1925) is a work of a more serious nature. Lewis has there attempted to represent the medical profession and science in all its manifestations. As is well known, American research in the natural sciences, physics, chemistry, and medicine ranks with the best of our age, and it has several times been recognized as such from this very platform. Tremendous resources have been placed at its command. Richly endowed institutions work unceasingly on its development.

That even here some speculative persons want to take advantage of their opportunities may be regarded as inevitable. Private industries are on the alert for scientific discoveries and want to profit from them before they have been tested and finally established. The bacteriologist, for instance, searches with infinite care for vaccines to cure widespread diseases, and the manufacturing chemist wants to snatch them prematurely from his hand for mass production.

Under the guidance of a gifted and conscientious teacher, Martin Arrowsmith develops into one of the idealists of science. The tragedy of his life as research worker is that, after making an important discovery, he delays its announcement for constantly renewed tests until he is anticipated by a Frenchman in the Pasteur Institute.

The book contains a rich gallery of different medical types. We have the hum of the medical schools with their quarrelling and intriguing professors. Then there is the unpretentious country doctor, recalled from Main Street, who regards it as an honour to merge with his clientele and become their support and solace. Then we have the shrewd organizer of public health and general welfare, who works himself into popular favour and political power. Next we have the large institutes with their apparently royally independent investigators, under a management which to a certain extent must take into consideration the commercial interests of the donors and drive the staff to forced work for the honour of the institutes.

Above these types rises Arrowsmith's teacher, the exiled German Jew, Gottlieb, who is drawn with a warmth and admiration that seem to suggest a living model. He is an incorruptibly honest servant of science, but at the same time a resentful anarchist and a stand-offish misanthrope, who doubts whether the humanity whose benefactor he is amounts to as much as the animals he kills with his experiments. Further we meet the Swedish doctor, Gustaf Sondelius, a radiant Titan, who with singing and courage pursues pests in their lairs throughout the world, exterminates poisonous rats and burns infected villages, drinks and preaches his gospel that hygiene is destined to kill the medical art.

Alongside all of this runs the personal history of Martin Arrowsmith. Lewis is much too clever to make his characters without blemish, and Martin suffers from faults which at times seem obstructive to his development, both as a man and as a scientist. As a restless and irresolute young man he gets his best help from a little woman he encountered at a hospital where she was an insignificant nurse. When he begins to drift about the country as an unsuccessful medical student, he looks her up in a little village in the Far West, and there she becomes his wife. She is a devoted and simple soul, who demands nothing and who patiently waits in her solitude when, bewitched by the siren of science, her husband loses himself in the labyrinths of his work.

Later she accompanies him and Sondelius to the plague-infected island where Arrowsmith wants to test his serum. Her death in the abandoned hut, while her husband listens distractedly to another and more earthy siren than that of science, seems like a poetically crowning final act to a life of primitive self-sacrificing femininity.

The book is full of admirable learning, certified by experts as being accurate. Though a master of light-winged words, Lewis is never superficial when it comes to the foundations of his art. His study of details is always as careful and thorough as that of such a scientist as Arrowsmith or Gottlieb. In this work he has built a monument to the profession of his own father, that of the physician, which certainly is not represented by a charlatan or a faker.


Gene Genie #40

 
The 40th edition of Gene Genie has been posted at Human Genetics Disorders [Gene Genie Edition 40].
NSGC Conference exibit and MBA thesis poster presentation videos from the October 24-28 2008 AEC Conference by Chavonne Jones
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 .....
  1. Scienceroll
  2. Sciencesque
  3. Genetics and Health
  4. Sandwalk
  5. Neurophilosophy
  6. Scienceroll
  7. Gene Sherpa
  8. Eye on DNA
  9. DNA Direct Talk
  10. Genomicron
  11. Med Journal Watch
  12. My Biotech Life
  13. The Genetic Genealogist
  14. MicrobiologyBytes
  15. Cancer Genetics
  16. Neurophilosophy
  17. The Gene Sherpa
  18. Eye on DNA
  19. Scienceroll
  20. Bitesize Bio
  21. BabyLab
  22. Sandwalk
  23. Scienceroll
  24. biomarker-driven mental health 2.0
  25. The Gene Sherpa
  26. Sciencebase
  27. DNA Direct Talk
  28. Greg Laden’s Blog
  29. My Biotech Life
  30. Gene Expression
  31. Adaptive Complexity
  32. Highlight Health
  33. Neurophilosophy
  34. ScienceRoll
  35. Microbiology Bytes
  36. Human Genetic Disordrs
  37. The Genetic Genealogist
  38. ScienceRoll
  39. Genetics & Health
  40. Human Genetics Disorders