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Wednesday, January 07, 2009

Nobel Laureate: Elias Corey

 

The Nobel Prize in Chemistry 1990.

"for his development of the theory and methodology of organic synthesis"



Elias James Corey (1928 - ) was awarded the Nobel Prize for his contributions to the synthesis of organic molecules. Here's the Press Release describing his achievements.

Prize for masterly development of organic synthesis

The development of the art of organic synthesis during little over a hundred years has afforded efficient methods of manufacturing products such as plastics and other artificial fibres, paints and dyes, biocides and pharmaceutical products, all of which have contributed to the high standards of living and health, and the longevity, enjoyed at least in the Western world.

This year's Nobel Prize in Chemistry has been awarded to Professor Elias J. Corey, USA, for his important contributions to synthetic organic chemistry. He has developed theories and methods that have made it possible to produce a large variety of biologically highly active, complicated natural products, thereby making, among other things, certain pharmaceuticals commercially available. Corey's work has also led to new general methods of producing, synthesising, compounds in simpler ways.

The background to Elias J. Corey's successes lies in the fact that he has in a strictly logical way developed the principles of what is termed retrosynthetic analysis. This involves starting from the planned structure of the molecule one wishes to produce, the target molecule, and analysing what bonds must be broken, thus simplifying the structure step by step. One then finds that certain fragments are already known and their structure and synthesis already described. After working backwards in this way from the complex to the already known, it is possible to start building, synthesising, the molecule. This method has proved very amenable to data processing, which has entailed rapid developments in synthesis planning. Combining this synthesis planning with singular creativity, Corey has developed new methods of synthesis. He has produced some hundred important natural products, for example the active substance in an extract from the ginkgo tree, used in folk medicine in China.

Background information

Organic synthesis, that is, the production of complicated organic compounds using simple and cheap starting material, is one of the prerequisites of our civilisation. It is understandable that contributions in this field have often been rewarded with the Nobel Prize in Chemistry. Thus in 1902, only the second year that Nobel Prizes were awarded, the Chemistry Prize went to Emil Fischer for his work on synthesis within sugar and purine chemistry. In 1905 Adolf von Baeyer received the prize in recognition of contributions to the development of the chemical industry through his work on organic dyestuffs. Otto Wallach received the 1910 Prize for contributions to the development of the chemical industry. The 1912 prize went to Victor Grignard for his development of organic magnesium compounds, also termed Grignard reagents, into important intermediates in organic synthesis. In 1950 Otto Diels and Kurt Alder shared the Nobel Prize for discovering the preparatively very useful diene synthesis. Robert B. Woodward received the 1965 prize for his brilliant contributions to the development of the art of organic synthesis. In 1979 Herbert C. Brown and Georg Wittig were rewarded for developing boron compounds and phosphorus compounds, respectively, into important reagents in organic synthesis.

The synthesis of complicated organic compounds often shows elements of artistic creation, as for example architecture. Many earlier syntheses were performed more or less intuitively, so that their planning was difficult to perceive. Asking a chemist how he came upon precisely the starting materials and reactions that so elegantly led to the desired result would probably be as meaningless as asking Picasso why he painted as he did. The process of synthetic planning has been likened to a game of three-dimensional chess using 40 pieces on each side. But the problem may be even harder than this. Over 35,000 usable methods of synthesis are described in chemical literature, each with its possibilities and its limitations. During the synthesis, moreover, new methods appear which can modify the strategy.

Beginning in the 1960's, Corey coined the term, and developed the concept of, retrosynthetic analysis. Starting from the structure of the molecule he was to produce, the target molecule, he established rules for how it should be dissected into smaller parts, and what strategic bonds should be broken. In this way, less complicated building blocks were obtained, which could later be assembled in the process of synthesis. These building blocks were then analysed in the same way until simple compounds had been reached, whose synthesis was already described in the literature, or which are commercially available. Corey showed that strictly logical retrosynthetic analysis was amenable to computer programming. At present, synthesis planning with the help of computers is developing rapidly.

Through his brilliant analysis of the theory of organic synthesis, Corey has contributed in high degree to his own and other researchers' being able, during the last few decades, to complete total syntheses, hitherto impossible, of complicated, naturally-occurring, biologically active compounds, according to simple logical principles.


Elias J. Corey has himself synthesised about a hundred important natural products, of which only a few will be mentioned here. In 1978 he produced gibberellic acid (1), which belongs to a class of very important plant hormones of complicated structure. Recently, he has also synthesised (+)-ginkgolid (2), which owing to its complicated structure is a formidable challenge to anyone working in synthetic chemistry. (+)-ginkgolid is the active substance in an extract from the ginkgo tree, used as a folk medicine in China. The sales value of this natural product is believed to amount to $500 million annually. It is used in treatment of blood circulation disturbances in the elderly, and in asthma. Corey's most important total syntheses concern the medically very important eicosanoids such as prostaglandins, prostacyclins, thromboxanes and leucotrienes, which occur naturally in extremely small quantities. These frequently very unstable compounds answer for multifarious and vital regulatory functions of significance for reproduction, blood coagulation, normal and pathological processes in the immune system, etc. Their importance is witnessed by the award of the 1982 Nobel Prize in Physiology or Medicine to Sune Bergstrom, Bengt Samuelsson and Sir John Vane for the discovery of prostaglandins and closely related biologically active substances. Corey has with enormous skill carried out structural determination and total syntheses of a large number of compounds of many different types of eicosanoids such as prostaglandins and leucotrienes such as lipoxin A (3). It is thanks to Corey's contributions that many of these important pharmaceuticals are commercially available.

To perform the total syntheses successfully, Corey was also obliged to develop some fifty entirely new or considerably improved synthesis reactions or reagents. It is probable that no other chemist has developed such a comprehensive and varied assortment of methods which, often showing the simplicity of genius, have become commonplace in the synthesising laboratory. His systematic use of different types of organometallic reagent has revolutionised recent techniques of synthesis in many respects. He has also in recent years introduced a number of very effective enzyme-like catalysts. These chiral catalysts give only one mirror isomer of the target product, in certain types of synthetically important reaction. The chiral catalysts are simple and easy to recover, and can in some cases be used in their own production.


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.

[Photo Credit: NIH.]

A Primer on Skepticism

 
What more could you ask for than A Primer on Skepticism from Mike's Weekly Skeptic Rant? Here are some quotations from that posting to tempt you into reading the whole thing ....
If anyone can show me, and prove to me, that I am wrong in thought or deed, I will gladly change. I seek the truth, which never yet hurt anybody. It is only persistence in self-delusion and ignorance which does harm.
                                                Marcus Aurelius

The invisible and the non-existent look very much alike.
                                                Delos B. McKown

The statistics on sanity are that one out of every four Americans are suffering from some form of mental illness. Think of your three best friends. If they're ok, then it's you.
                                                Rita Mae Brown


Democracy and Lawyers

 
In Canada we vote by marking a "X" on the ballot and putting it in a box. The person with the most "X's" wins.

If the vote is close, we count the ballots again and declare a winner.

It doesn't work that way in America as we learned in 2000. It took several truckloads of lawyers and many judges to count the ballots in Florida. Ultimately it was the US Supreme Court who decided that George Bush would be President.

Now they're doing it again, only this time it's a Senate race in Minnesota [Funny Business in Minnesota]. The lawyers and the judges will decide who actually won. Meanwhile, politicians in Washington will fight over which candidate they will put into the Senate while the court cases are being decided. Apparently the Senate doesn't have to accept the recount as long as the loser is unhappy.

This must be why they call America "the greatest democracy on Earth." It's because America has so many lawyers.


Probably?

 
In Britain there are 800 buses with the sign, "There’s probably no God. Now stop worrying and enjoy your life." [Atheists Send a Message, on 800 Buses]

Apparently the British atheists wanted to leave out the word "probably" but that wouldn't conform to British advertising guidelines. I wonder if the guidelines apply across the board?

Are there bus and billboard signs that say, "Jesus probably loves you?"

Has the British anthem been changed to, "God probably saves the Queen?"

And what about the coins? Will they be changed to read, "Queen, probably by the grace of God" (D.P.G.) in order to conform to advertising standards?

The best remark comes from an American tourist who spotted the sign on a bus. America is the bastion of free speech (according to some Americans) but only if it's speech that doesn't offend.
Spotting one of the buses on display at a news conference in Kensington, passers-by were struck by the unusual message.

Not always positively. "I think it’s dreadful," said Sandra Lafaire, 76, a tourist from Los Angeles, who said she believed in God and still enjoyed her life, thank you very much. "Everyone is entitled to their opinion, but I don’t like it in my face."


Denyse O'Leary and a Lesson on Irony

 
I was going to blog about this last weekend but I put it off until Monday, then I didn't get around to it yesterday. Now Canadian Cynic has used the exact same quotation that I was planning to highlight. His posting is funnier than anything I could have written. Read it at ... If the irony were any thicker ...


Tuesday, January 06, 2009

Mendel's Garden #27

 
The 27th edition of Mendel's Garden has just been posted on Another Blasted Weblog [Mendel’s Garden No. 27].
Happy Befana from a freezing Rome. Got myself in a bit of a tizz with all this Blog Carnivalia stuff. I thought I was hosting Mendel’s Garden over at the Agricultural Biodiversity Weblog, but it seems I agreed to do it here instead. Not sure why, especially after my recent idleness. P’raps I’ll cross-post. Anyway, on with the show.


Hot Talks - Fact or Friction: The Continuous Tension Between Science and Religion

 
University of Toronto
Hart House, The Arbor Room
Wednesday, January 21st, 6:30 PM


Join us for an evening of open discussion on the topic of the tension between science and religion. There will be a reception following the event at 8:30pm. Speakers for the evening include:

Professor Jan Sapp

Professor Sapp is a professor of Biology and History at York University. His research is focused on the fields of cell and molecular biology, microbial phylogeny, symbiosis, genetics, evolution and ecology – all from an historical perspective. His historical research on evolutionary biology aims to enlarge the boundaries of that history from focusing solely on Mendelian genetics and the development of neo-Darwinian evolutionary theory.

Professor Yiftach Fehige

Professor Fehige is an assistant professor at St. Michael’s College and the Department of History and Philosophy of Science. His research focuses on Christianity and science, thought experiments, revelation, and research ethics. Professor Fehige is currently working elaborating a pragmatic account of thought experiments in terms of a naturalistic theory of intuition.

Professor Amanda Peet

Professor Peet is a fellow of Trinity College and teaches both within the college and across other disciplines including the Department of physics. She is a member of the Canadian Association of Physicists, the Canadian Institute for Particle Physics and the American Physical Society. She focuses on understanding the fundamental dynamics of all forces and particles seen so far in Nature, especially gravity.

Professor Michael Bourgeois

Professor Bourgoeis is an associate theology professor at Emanuel college. He focuses on constructive, historical, and contextual theologies — including both formative and alternative theological traditions. His particular interests include the relation of theology to the natural sciences, especially on questions of the origin and destiny of the universe and divine action; and expressions of religious ideas in popular culture.


Get a Job in Newfoundland

 
Memorial University: Departments of Computer Science and Biology

MEMORIAL UNIVERSITY
Tenure-Track Faculty Position in Bioinformatics


The Departments of Computer Science and Biology at Memorial University have each embarked on multi-year renewal programs. Each department currently has more than 20 tenure-stream faculty members, and supports M.Sc., Ph.D. and collaborative graduate programs. For more details, see http://www.mun.ca/biology/Home/ and http://www.mun.ca/computerscience/. Both departments invite applications for a tenure-track position in Bioinformatics, starting no later than September 1, 2009. This will be a joint appointment between the departments. The appointment will be made at the level of Assistant Professor, with the primary appointment in Computer Science, and equal responsibility in both departments, in accordance with the terms of Memorial’s Collective Agreement.

A Ph.D. in Computer Science, Computational Science, Biology, or related fields is required and postdoctoral or equivalent experience is desirable. Applicants should have experience in Bioinformatics, and be keen to do interdisciplinary work between the departments. Applicants should possess a strong research record with outstanding promise for future research, and be able to demonstrate the potential for excellent undergraduate and graduate teaching in Bioinformatics.

Applicants should submit a Curriculum Vitae, statements of research interests, teaching interests and philosophy, and up to three reprints of publications. The application should be accompanied by names of at least three referees of international standing, who are willing to provide letters of recommendation (include details on affiliations, plus phone numbers and email addresses). All material must be received by January 15, 2009; refer to position VPA-COSC-2007-001 in all correspondence, and submit materials to:

Dr. Wolfgang Banzhaf, Head
Department of Computer Science
Memorial University
St. John’s, NL, Canada, A1B 3X5
Email: chair@cs.mun.ca

Memorial University is the largest university in Atlantic Canada. As the Province’s only university, Memorial plays an integral role in the educational and cultural life of the Province of Newfoundland and Labrador. Offering diverse undergraduate and graduate programs to almost 18,000 students, Memorial provides a distinctive and stimulating environment for learning. St. John’s is a very safe and friendly city with great historic charm, a vibrant cultural life, and easy access to a wide range of outdoor activities.

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.


Get Several Jobs in British Columbia

 
University of British Columbia: Departments of Botany and Zoology

Tenure track biology instructor positions

Closing date: January 15, 2009 at 5pm

The Departments of Botany and Zoology at the University of British Columbia (Vancouver, Canada) are seeking candidates to fill at least four tenure-track Instructor positions to teach in the Biology Undergraduate Program. At least two positions will be in cellular and molecular biology, with the remaining positions open to biologists in any area. Candidates must hold a PhD in Biology, have a broadly integrative perspective on the biological sciences, and be committed to the improvement of biology undergraduate teaching. Postdoctoral teaching and/or research experience is preferred.

Successful candidates will demonstrate 1) evidence of outstanding teaching, and 2) the ability to contribute to ongoing curriculum and course redevelopment.

Duties of the positions vary, but may include lecturing in introductory and advanced courses, teaching and administration of a large third-year undergraduate laboratory course in the area of specialty, participation in course and curriculum development, and the training and supervision of graduate student teaching assistants. There are also opportunities to work in collaboration with the Carl Wieman Science Education Initiative (www.cwsei.ubc.ca).

Interested candidates should submit a letter of application, a curriculum vitae, a statement of teaching philosophy, an outline of teaching interests, evidence of teaching effectiveness, and the names and contact information for at least three individuals who would be willing to provide letters of references to jobs@zoology.ubc.ca. Candidates are particularly encouraged to highlight previous experience in fostering the education of students from diverse backgrounds.

Review of applications will begin January 15, 2009 and continue until the positions are filled, with appointments anticipated to begin by July 1, 2009.

The University of British Columbia hires on the basis of merit and is committed to employment equity. All qualified persons are encouraged to apply; however, priority will be given to Canadian citizens and permanent residents of Canada.


Get a Job in Ontario

 
University of Western Ontario: Department of Biology
The University of Western Ontario
Faculty of Science
Department of Biology

Applications are invited for a 3-year Limited Term position in Biology commencing July 1, 2009. As a minimum, the preferred applicant will have a Ph.D. in Biology or a related field, and appropriate training in University level teaching. The successful applicant will be expected to contribute to the department’s commitment to excellence in teaching and provide evidence of his/her ability to teach at the undergraduate level. The successful candidate will be responsible for participating in the teaching of courses in cell and developmental biology as well as general biology.

Applications, including a curriculum vitae and names and addresses of three referees whom we may contact, should be submitted to:

Dr. M. Brock Fenton, Acting Chair
Department of Biology
The University of Western Ontario
London, Ontario
N6A 5B7

Applications for this position will be accepted until January 31, 2009 or until a suitable candidate is found.

Positions are subject to budget approval. Applicants should have fluent written and oral communication skills in English. All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority. The University of Western Ontario is committed to employment equity and welcomes applications from all qualified women and men, including visible minorities, aboriginal people and persons with disabilities.



Mendel's Stem Length Gene (Le)

The seven traits that Gregor Mendel worked with were: seed shape (R/r), cotyledon color (I/i), seed and flower color (A/a), pod shape (V/v), pod color (Gp/gp), flower position (Fa/fa), and stem length (Le/le). The last trait is also known as Tall (T) and short (t).

The gene responsible for cotyledon color has been identified. It encodes an enzyme that degrades chlorophyll [Identity of the Product of Mendel's Green Cotyledon Gene (Update)]. The gene giving rise to the wrinkled phenotype (r) encodes the starch branching enzyme [Biochemist Gregor Mendel Studied Starch Synthesis].

The gene responsible for stem length has also been identified and cloned (Lester et al., 1997). It encodes an enzyme called 3β-hydroxylase. This enzyme is responsible for one of the last steps in the synthesis of the gibberallin GA1. See Monday's Molecule #102 for the structure of a similar gibberellin.

Gibberellins are plant growth hormones and GA1 is required to stimulate the grown of the stem in pea plants. The wild-type enzyme synthesizes GA1 from its substrate GA20. The pea gene (Le) is related to a similar gene in other flowering plants. Defects in those genes produce dwarf plants.

Lester et al. (1997) cloned the pea gene and identified a restriction length polymorphism that was associated with a mutant version of the gene (le). In the mutant, a single alanine residue was replaced by a threonine residue and this resulted in a 3β-hydoxylase activity that was 20-fold less than the wild type level. The reduced amount of gibberellin GA1 could account for the smaller plants.

The restriction length polymorphism was used as a genetic marker in crosses between Le/Le plants and le/le plants. It segregated with the le genotype as expected. This experiment establishes that the gene for 3β-hydoxylase is the Le gene that Mendel studied and the phenotype is due to differing levels of the plant hormone gibberellin GA1.


Lester, D.R., Ross, J.J., Davies, P.J., and Reid, J. (1997) Mendel’s Stem Length Gene (Le) Encodes a Gibberellin 3β-Hydroxylase. The Plant Cell 9:1435-1443. [PDF]

Monday, January 05, 2009

Darwin Celebrations at the University of Toronto

 
The University of Toronto is hosting a celebration of Darwin next Novermber [Origin of Species at 150: a celebratory conference].
150 Years after Origin: Biological, Historical, and Philosophical Perspectives

Victoria College, University of Toronto, November 21-24, 2009
Darwin wrote in his autobiography, “In July [1837] I opened my first notebook for facts in relation to the Origin of Species, about which I had long reflected, and never ceased working for the next twenty years.” In 1842, he wrote a “very brief abstract” of his theory (35 pages), which in the summer of 1844 he expanded to 230 pages. Beginning in September 1858, after receiving an essay from Alfred Russell Wallace, “On the Tendency of Varieties to Depart Indefinitely from the Original Type,” which outlined the central mechanism of evolution on which Darwin had been working, he began work on completing the manuscript of The Origin of Species by Means of Natural Selection. John Murray, the publisher, launched the book on November 24, 1859 by releasing 1,250 copies. The impact of The Origin of Species has equalled the impact of Newton’s Philosophiæ Naturalis Principia Mathematica. It is the unifying theoretical framework for all modern biology.

November 24, 2009 marks the 150th anniversary of the publication of The Origin and The Institute for the History and Philosophy of Science and Technology, the Department of Ecology and Evolutionary Biology, and the Department of Philosophy at University of Toronto are mounting a Gala Celebratory Conference. The conference will culminate in a gala dinner on November 24 at which participants will toast the tremendous achievement of Charles Robert Darwin.

Five multi-disciplinary symposia have been organized. For each symposium, the panel consists of a biologist, a historian of biology and a philosopher of biology.

The Institute for the History and Philosophy of Science and Technology is located on the elegant, historic Victoria University campus (one of the University of Toronto’s federated universities) and the conference will be held in that location
The emphasis is on history and philosophy. It would be a perfect opportunity to put Darwin into the context of the modern world. It would be a crying shame if the conference was wasted on promoting natural selection and misrepresenting modern evolutionary theory. Do the conference organizers really mean it when they say that a 150 year old book, Origin of Species, is, "the unifying theoretical framework for all modern biology?

Here's the preliminary program.
Saturday November 21, 2009

6-7 pm: Keynote Address: to be announced

7-9pm: Reception

Sunday November 22, 2009

9-10 am: Keynote Address
Evelyn Fox Keller (Massachusetts Institute of Technology)

10 am-12 pm: Symposium:
Gender, Evolution, and Sexual Selection
Lisa Lloyd (Indiana University)
Marlene Zuk (University of California)
Erika Milam (Clemson University)

12-2 pm: Lunch Break

2-3 pm: Keynote Address
Michael Ruse (Florida State University)

3-4 pm: Contributed Papers Session
to be announced

4-5 pm: Contributed Papers Session
to be announced

5-6 pm: Keynote Address
James Moore (University of Cambridge)

Monday November 23, 2009

9-11 am: Symposium:
Evolution and Development
Manfred Laubichler (Arizona State University)
Jane Maienschein (Arizona State University)
Michael Dietrich (Dartmouth College)

11am-12pm: Contributed Papers Session
to be announced

12-2 pm: Lunch Break

2-4 pm: Symposium:
Species
John Beatty (University of British Columbia)
Kevin de Queiroz (National Museum of Natural History)
Marc Ereshefsky (University of Calgary)

4-5 pm: Contributed Papers Session
to be announced

5-6 pm: Keynote Address
Alison Pearn (Darwin Correspondence Project)

6-7 pm: Special Presentation
A Play: "Re: Design (A Dramatisation of the Correspondence of Charles Darwin and Asa Gray)"

Tuesday November 24, 2009

9-11 am: Symposium:
Taxonomy
Mary Winsor (University of Toronto)
Kevin Padian (Berkeley)
Richard Richards (University of Alabama)

11am-12pm

Contributed Papers Session
to be announced

12-2 pm: Lunch Break

2-4 pm: Symposium:
Ecology
Joan Roughgarden (Stanford University)
Gregg Mitman (University of Wisconsin-Madison)
Gregory Cooper (Washington and Lee University)

4-5 pm: Contributed Papers Session
to be announced

5-6 pm: Keynote Address
Sean Carroll (University of Wisconsin-Madison)

6-7 pm: Break

7-8 pm: Keynote Address
Spencer Barrett (University of Toronto)

8-10:30 pm: Origin at 150 Gala Dinner
Most of the speakers are strangers to me. I have no idea where they might be coming from in terms of their understanding of evolutionary theory.

Of the ones I do know, Sean Carroll is a fan of natural selection and Spencer Barrett is a classic adaptationist. It's worrisome that the organizers invited Michael Ruse to give a keynote address. As I've mentioned before, Ruse does not seem to have a very good handle on modern evolutionary theory. I fear that the conference participants will be subjected to a particular point of view that will not be a fair description of how Darwin contributed to modern biology.

If The Institute for the History and Philosophy of Science thinks Michael Ruse is going to give a good overview of Darwin's contribution then this does not bode well for the conference. They should have learned from his appearance at the Royal Ontario Museum last June [Darwinism at the ROM].

At that symposium Ruse asked, "Is Darwin's Theory Past Its "Sell By" Date." I think Michael Ruse has passed his "best before" date. It's time for him to retire.


Darwin Week Activity at CFI

 
I attended a lecture by Carl Zimmer last summer at the Chautauqua Institute [Carl Zimmer at Chautauqua]. He posted the text on his blog at: Darwin, Linnaeus, and One Sleepy Guy.

Here's one of the important bits ...
I’d like to thank the Chautauqua Institution for inviting me to speak during this week’s series. I’m particularly grateful that the Chautauqua Institute saw fit to make this week’s theme Darwin *and* Linnaeus. We are now descending into a frenzy of Darwin celebrations, and you’re not going to escape it until the end of 2009. We’ve got his 200th birthday in February, and the 150th anniversary of the publication of the Origin of Species in November. The spotlight is going to be on Darwin, and Darwin alone.

I think this is a mistake. Darwin deserves celebrating, but that doesn’t mean we should fall prey to a cult of personality. Darwin did not invent biology. Darwin did not even find most of the evidence that he used to back up his theory of evolution. And he certainly did not discover all there was to know about evolution. Biologists have discovered many new things about evolution since his time. In some cases, they’ve challenged some of his most important arguments. And that’s fine. That’s the great strength of science.

So today I’m going to take advantage of our dual celebration of Linnaeus and Darwin. I’m going to talk about the process of science, how great thinkers challenge the thinkers of the past, how their own great ideas are altered by future generations. I’m going to talk about why Linnaeus was so important, and how Darwin shattered some of Linnaeus’s most cherished claims. I’m also going to talk about modern biologists have done the same to Darwin.

The best way to convey how drastically biology has changed since Darwin’s day is to focus on one group of living things. It’s a group about which Darwin–and Linnaeus–had little to say. I’m going to talk about microbes.
Carl was pointing out the obvious. Science has not stood still since 1859, the year that Origin of Species was published. As we approach the celebrations in February and November it's important to keep this in mind. That's why I'm giving a talk about the modern view of evolution and how it builds upon, but differs from, the views of Charles Darwin in 1859.

Come listen ...
Darwin Week Activity: Pre and Post Darwinian Science with Larry Moran

Starts: Friday, February 13th at 7:00 pm

Ends: Friday, February 13th at 9:30 pm

Location: Centre for Inquiry Ontario, 216 Beverley St, Toronto ON (1 minute south of College St at St. George St)

What was science like before Darwin, and how did it change after Darwin?

Larry Moran will be discussing our modern scientific world in light of the impact Darwin and his theory of evolution due to natural selection has had on it.

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto.

$5, $3 for students and FREE for Friends of the Centre


How Does Your Blood Clot?



Some of you have been following the smackdown of Casey Luskin over his attempt to revive the irreducible complexity of the blood clotting cascade. This is a complicated pathway so I wrote a bunch of postings last year to try and explain the pathway at the molecular level.

Theme

Blood Clotting
Here's the complete list in case anyone wants more information in order to follow the discussion.

March 26, 2007
Monday's Molecule #19. Warfarin—an anticoagulant and a rat poison.

March 27, 2007
Vitamin K. Vitamin K plays an important role in blood clotting.

March 28, 2007
Nobel Laureates: Dam and Doisy. Dam: "for his discovery of vitamin K" Doisy: "for his discovery of the chemical nature of vitamin K".

April 2, 2007
Monday's Molecule #20. Heparin—an anticoagulant.

April 2, 2007
Blood Clotting: The Basics. Fibrinogen and how it forms clots.

April 4, 2007
Nobel Laureate: Arne Tiselius. "for his research on electrophoresis and adsorption analysis, especially for his discoveries concerning the complex nature of the serum proteins".

April 4, 2007
Blood Clotting: Platelets. What are platelets and how do they form blood clots?

April 4, 2007
Blood Clotting: Extrinsic Activity and Platelet Activation. Description of the activity of thrombin and the activation of blood platelets.

April 5, 2007
Blood Clotting: Intrinsic Activity. The role of factors VIII and IX. Deficiencies in Factor VIII cause hemophilia A an X-linked form of hemophilia that was common in European royal families descending from Queen Victoria.

April 8, 2007
Genes for Hemophilia A & B and von Willebrand disease. Locations of the F8, F9 and vWF genes on human chromosomes X and 12.

April 12, 2007
Inhibiting Blood Clots: Anticoagulants. How does heparin inhibit blood clotting?

April 15, 2007
Human Anticoagulant Genes. Mapping the genes for anticoagulant factors.

April 16, 2007
Dicumarol and Warfarin Inhibit Blood Clotting. The role of vitamin K in blood clotting.

September 26, 2007
A Synthetic Anticoagulant Related to Heparin. Synthesis of a new anticoagulant to replace heparin.

April 26, 2008
Fibrin and Blood Clots.
What does a blog clot look like?

May 10, 2008
On the Evolution of the Blood Clotting Pathway.
Ian Musgrave explains Russel Doolittle's latest results.


George Johnson Revists His Defense of Scienc Journalism

 
John Horgan and George Johnson are at it again. They clarify some important points in a followup to their earlier discussion about science journalism (see Who the Heck Is George Johnson?).


John Horgan asks the key question when he says, "Where do we get informed criticism of science these days?"

George Johnson points out that there's a lot of junk on the internet and this includes most science blogs. He does go out of his way to mention the best science blogs but he seems to be surprised and upset at the amount of junk masquerading as legitimate science.

He's right, of course, but that's not the point. What Johnson still seems to ignore is the criticism of traditional print science journalism. I'm not saying that science blogs are perfect—far from it—what I'm saying is that the hubris of science journalists is unjustified. They're not nearly as good as they think they are. As a matter of fact, in my opinion the quality of science on science blogs is superior to the quality of science described by science journalists in the print media.

As a general rule, science journalists are better writers but they are not necessarily better at describing the correct science. It's the content of articles by science journalists that I'm criticizing, not their literary style. I don't think George Johnson gets this. He seems to put all of his emphasis on the literary aspect of science journalism and not enough on the scientific accuracy part of science journalism. Johnson admires good writing.

John Horgan gets it. His main complaint is that it's the scientists, and not the science journalists who are hyping their discoveries and misrepresenting the importance of their work. Horgan points out that scientists are often too deeply immersed in their work to see the big picture. George Johnson is happy to agree with him. I agree too—it's scientists who are behind bad science.1

However, both Horgan and Johnson see themselves as writers who are able to rise above this self-interest on the part of scientists and put things in proper context. According to them, the role of a science journalist is to pick out the real breakthroughs and to present an accurate view of the science, unencumbered by the prejudices and biases of those scientists who are down in the trenches.

I agree that this should be the goal of science journalism. What I expect of good science journalism is that it avoid the hype and put the science in context. In that sense, Horgan and Johnson are correct—they have identified an important role for science journalism.

So, how's it working out? Badly, I'm afraid. Most science journalists who write about the things I know are failing miserably at this important task. Their prose may be good but they are completely taken in by the scientists who exploit them. This would be unacceptable if we were talking about political reporting or the writings of an art critic. It's just as unacceptable when we're talking about science reporting. That's the issue.

While scientists are responsible for bad science in the first place, it also seems to be scientists who recognize bad science. I don't see too many examples of science journalists who recognize bad science. As a group they seem to be very gullible.

Here's the excerpt where Horgan and Johnson discuss the future of science journalism. Horgan is pessimistic and Johnson is more of an optimist. The first part of this excerpt is where Johnson defends the effort that science journalists put into their work. Science journalists may work hard but you don't get "A's" just for effort.


It's interesting to hear Johnson defend Scientific American and Discovery as good examples of science journalism. It's more evidence that he doesn't know the difference between good science and bad science.


1. Listen to the exchange when John Horgan describes evolutionary psychology. Horgan knows that a lot of it is garbage. Johnson doesn't. I think this is part of Johnson's problem. He doesn't seem to have a good feel for the difference between good science and bad science in spite of the fact that he (Johnson) brags about the amount of work that goes into good science journalism and how important it is to have good sources. Johnson seems to think that most articles written by science journalists must be accurate because science journalists are supposed to do their homework. That's a bad assumption.