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Tuesday, June 17, 2008

Wordle

 
Eva Amsen is writing her thesis. It is very easy to get distracted when you are writing your thesis—everyone needs a break from time to time. Eva found a fabulous website while she was surfing the net looking for references to put in her thesis and she blogged about it on [Expression Patterns].

The website is called Wordle. Here's what it does ...
Wordle is a toy for generating “word clouds” from text that you provide. The clouds give greater prominence to words that appear more frequently in the source text. You can tweak your clouds with different fonts, layouts, and color schemes. The images you create with Wordle are yours to use however you like. You can print them out, or save them to the Wordle gallery to share with your friends.
I fed it my essay on What Is a Gene? and here's what it gave me ...

Each time you try you get a different configuration of words so it's worthwhile to experiment a bit in order to get a pleasing layout. You can change fonts, colors, background and other things afterwards. Isn't this great?

Here's how Wordle handles another essay Evolution by Accident.



Here's another example with Theistic Evolution: The Fallacy of the Middle Ground.


This is so much fun. It must be bad for you. Send me your favorite Wordles, they must be created from something you wrote.


With or Without God

 
Come to the Centre for Inquiry's lecture by Gretta Vosper.

With or Without God: Why the Way We Live is More Important than What We Believe

Starts: Friday, June 20th at 7:30 pm
Ends: Friday, June 20th at 9:30 pm
Location: Centre for Inquiry Ontario, 216 Beverley St, Toronto ON (1 minute south of College St at St. George St)

Lecture and Book Launch:
Gretta Vosper, United Church Minister at West Hill United Church, Toronto, and founder and Chair of the Canadian Centre for Progressive Christianity

In Gretta Vosper's church there are no prayers, no miracles-performing magic Jesus and no omnipotent God at all. Vosper's book argues that the Christian church, in the form in which it exists today, has outlived its viability and either it sheds its no-longer credible myths, doctrines and dogmas, or it's toast. With a humanist worldview, Vosper proposes a radical change at the heart of faith. The new church she envisions will play a viable and transformative role in the shaping of a future society. What will save the church from certain demise, Vosper argues, is a new emphasis on just and compassionate living.

A catered receptions shall precede the talk at 6pm exclusively for Friends of the Centre.

Canadian Centre for Progressive Christianity:

MacLeans Magazine coverage "The Jesus Problem":

Globe and Mail coverage "Taking Christ Out of Christianity"

Cost: $6 general, $4 students, FREE for Friends of the Centre


Monday, June 16, 2008

Monday's Molecule #76

 
Name this molecule, being as specific as you can.

There's a direct connection between today's molecule and a Nobel Prize. The prize was awarded for discovering the basic structure of the molecule, although not at the level of detail depicted here. That came later.

The first person 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 four ineligible candidates for this week's reward. You know who you are.

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 may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: The molecule is immunoglobulin G (IgG) and the Nobel Laureates are Gerald Edelman and Rodney Porter (1972). The first correct answer was from Jon Turnbull who beat everyone else by more than one hour! Honorable mention (and a free lunch) goes to Haruhiko Ishii of UCSD. Not only did he identify the molecule as IgG, he also showed that it was very likely to be Mab231, a mouse monoclonal anti-canine lymphoma antibody composed of IGg2a heavy chains and κ light chains [PDB 1IGT].


Café Scientifique and Nature Network Pub Night

 
CAFÉ SCIENTIFIQUE PRESENTS
The future of medicine: help, hope or hype? (download the poster)

What lies in the future for medicine and health care? Over the next 50-100 years, how will we conquer illnesses and stay healthy? Join the discussion and debate at the next Café Scientifique, The future of medicine: help, hope or hype?, where experts will peek at the potential for robotics, genomics, alternative therapies and personalized medicine to cure our ills.

Experts:
  • Dr. Tony Pawson – Distinguished Investigator, Samuel Lunenfeld Research Institute of Mount Sinai Hospital
  • Karl Schroeder – Science fiction author and futurist
  • Dr. Calvin Gutkin – Executive Director and CEO, The College of Family Physicians of Canada


Wednesday, June 18, 2008, from 6 to 8pm
Duke of York Pub – ground floor
39 Prince Arthur Avenue -Close to the St. George subway (Bedford exit)

FREE

Presented by the Samuel Lunenfeld Research Institute of Mount Sinai Hospital and Ontario Science Centre, with generous support from Canadian Institutes of Health Research.

Café Scientifique is a place where, for the price of a cup of coffee or a pint of beer, anyone can join discussions that explore the latest ideas in science and technology.

The members of the Toronto hub of Nature Network will meet afterwards in the Duke of York (same place as Café Scientifique) [see Eva Amsen's posting on easternblot]. You get two stimulating meetings for the price of one (i.e. free!).

If you haven't yet joined the Toronto hub of Nature Network you should sign up here. Current members of the Toronto hub are here.


Kansas vs Darwin

 
Jeff Tamblyn, the director of Kansas vs Darwin will be in town this week for the ReelHeART International Film Festival. The film will be shown on Thursday evening. Here's the trailer, details below ...


Kansas vs. Darwin screening Thursday, June 19, 7:00 PM
ReelHeART International Film Festival
RHIFF MAIN PROGRAM B Tickets $8
INNIS THEATER 222
Innis College, University of Toronto
2 Sussex Avenue [1 block south of Bloor Street, on St. George Street]
Toronto, ON M5S 1J5
Advance Sales on line April 21, 2008 at www.reelheart.com

Kansas vs. Darwin
Director, Jeff Tamblyn, USA

Kansas vs. Darwin is a smart, funny, feature-length documentary about the Kansas state school board hearings on evolution. Features intimate revealing interviews with all major players on both sides, and exclusive, multi-camera footage of the hearings. Far more than a political film, Kansas vs. Darwin skillfully weaves multiple themes into a gripping dialectic, putting you face to face with, and inside the heads of, those who oppose your most closely held beliefs. Challenging and entertaining, it’s packed with fascinating characters who will leave you in admiration and astonishment, embarrassment and exasperation, as they feverishly pursue their goals, sometimes stumbling over their own eagerness in the attempt to win the most important battle of their lives.
I'm going. Contact me if you plan to attend and you want to meet up for dinner before the show.


Sunday, June 15, 2008

Fernando

 
Fernando was one of ABBA's biggest hits. There's a lot of debate about which war it refers to. The song mentions crossing the Rio Grande and that prompts many people in America to think of the Mexican revolution of 1910-1920. However, there aren't many examples of fighting that took place near the Rio Grande and there aren't too many examples of revolutionaries who crossed into Mexico from the USA.

Most people assume the song is about the Spanish civil war and the reference to the Rio Grande is just a generic reference to a river. Keep in mind that ABBA is a European group and the Spanish Civil War is still fresh in the memories of many europeans. For many it was glorious, but losing, fight against fascism.

The song refers to Fernando, a man who fought on the losing side against tyranny and fascism. Fernando was a revolutionary and a guerrilla fighter. He is now old and gray like many of the freedom fighters from all over Europe who went to Spain in the 1930's.

John McCain likes ABBA. I hope he appreciates that this song is about people who fought to defend their country from foreign domination. (Franco was supported by Hitler and Mussolini.)




Friday, June 13, 2008

Bias Against Female First-Author Papers

 
This is a follow-up to a posting back in January where I mentioned a recently published article by Budden et al. (2008) [see Bias Against Women?]. That article claimed to show evidence of a systematic bias against papers with women as first authors. The bias was mitigated when a particular journal switched to a double-blind reviewing system. This resulted in a significant increase in the number of published papers with women as first authors.

I was first alerted to the problem when GrrlScientist posted a favorable review of the paper, agreeing with the conclusion that journal reviewers were biased against papers with female first authors [Women, Science and Writing].

My first reaction was skeptical. These are biology papers and it didn't seem plausible that reviewers would be biased against papers with female first authors. There might possibly be a bias against papers from a lab run by women but that's not the same thing. In the biological sciences the principle investigator is often the last author and not the first. Furthermore, in my experience there wasn't any discrimination against female scientists at this level (publication). Half of our graduate students are women—why would we be biased against papers with one of them as first author? The study just didn't make sense.

Many Sandwalk readers interpreted my skepticism as an attempt to dismiss all forms of sexism in science. That was not my intent. Far from it, in fact, because I was very much aware of a particular case of sexism that greatly troubled me. What makes me angry is that I know of overtly sexist behaviors that are not challenged by scientists in the same department who are, themselves, not sexist. The subject of sexism came up at SciBarCamp in February where there was a session organized by physics professors to discuss sexism in physics departments. There seems to be a major problem in physics.

If you read the comments in my January posting you'll see how difficult it was to separate out the issue of whether the particular study on double-blind reviews was a legitimate scientific study, and whether sexism is common in science.

At the risk of encountering the same problem again, let's look at some recent events. A re-analysis of the original publication data has been published by Webb et al. (2008). They looked more carefully at the data from journals with double-blind review and from comparable journals that identify the authors. They found that the number of papers with women as first authors showed a general increase in most journals. The trend in the journal that initiated double-blind review back in 2001 was not significantly different. Thus, they conclude that there's no evidence of systemic bias against female first authors.

This is one of the points that I mentioned in the comments to my January posting but several other readers dismissed it. They implied that any attempt to question the data in the original paper was, itself, sexist.

The following correction appeared in the last week's (June 4th) issue of Nature.
The Editorial 'Working double-blind' (Nature 451, 605–606; 2008) referred to a study(1) that found more female first-author papers were published using a double-blind, rather than a single-blind, peer-review system. The data reported in ref. 1 have now been re-examined (2). The conclusion of ref. 1, that Behavioral Ecology published more papers with female first authors after switching to a double-blind peer-review system, is not in dispute. However, ref. 2 reports that other similar ecology journals that have single-blind peer-review systems also increased in female first-author papers over the same time period. After re-examining the analyses, Nature has concluded that ref. 1 can no longer be said to offer compelling evidence of a role for gender bias in single-blind peer review. In addition, upon closer examination of the papers listed in PubMed on gender bias and peer review, we cannot find other strong studies that support this claim. Thus, we no longer stand by the statement in the fourth paragraph of the Editorial, that double-blind peer review reduces bias against authors with female first names.
I believe that Nature has done the right thing in retracting their earlier claim. The problem of sexism in science is serious and needs to be addressed. But it doesn't do anyone any good if one side is supporting their claims with sloppy science. It would be good if we could get beyond that.

It may not be easy. The authors of the original paper have published a critique of the re-analysis (Budden et al. 2008b). They dispute the re-interpretation although they admit that their analysis is subject to different interpretations.

If the original paper was any other kind of scientific paper the criticism would be harsh. It will be interesting to see if any of the original strong supporters of the claim of sexist bias against female first authors are willing to reconsider their position on that particular issue.


[Hat Tip: R. Ford Dennison]

Budden, A., Tregenza, T., Aarssen, L., Koricheva, J., Leimu, R. and Lortie, C. (2008a) Women, Science and Writing. Trends in Ecology & Evolution, 23(1), 4-6. [PubMed] [doi:10.1016/j.tree.2007.07.008] (ref 1.)

Budden, A.E., Lortie, C.J., Tregenza, T., Aarssen, L., Koricheva, J., and Leimu, R. (2008b) Response to Webb et al.: Double-blind review: accept with minor revisions. Trends in Ecology and Evolution [doi:10.1016/j.tree.2008.04.001]

Webb, T. J., O'Hara, B. and Freckleton, R. P. (2008) Does double-blind review benefit female authors? Trends in Ecology and Evolution [doi:10.1016/j.tree.2008.03.003] (ref 2.)

Alex Palazzo in Toronto

 
Alex Palazzo of The Daily Transcript has been in Toronto for the past few days. We were able to get together for lunch on Wednesday and for some light liquid refreshments on Wednesday evening. It should come as no surprise that we were able to find several things we agree on and several more that we don't. It was a lot of fun. (I made a bet with Alex on Wednesday evening. He'll reveal it on his blog. He will lose.)

Yesterday's departmental seminar was very impressive. Alex has a nice story to tell about targeting mRNA to the endoplasmic reticulum. He has also discovered an unusual pathway for exporting certain mRNAs from the nucleus. This pathway seems to be specific for those mRNAs that encode secreted proteins.

I think everyone in the department was impressed. Maybe he'll be my colleague next year.


Alex Meets Toronto Bloggers

 
Alex Palazzo of The Daily Transcript met with Eva Amsen of easternblot, John Dupuis of Confessions of a Science Librarian, and Phillip Johnson of Biocurious.

Eva posted photos and a description of what they talked about [Science Bloggers].


Friday the 13th in Port Dover

 
It's Friday the 13th and the bikers are gathering in Port Dover. This year they're hoping to set a new Guinness record for the most bikes (>10,000).




Friday the 13th

 
Friday's Urban Legend: FALSE

[reposted from April 13, 2007]

Having a morbid fear of Friday the 13th—paraskevidekatriaphobics—is one of the most widespread superstitious beliefs in western industrialized nations. Believe it or not, there are many people who refuse to leave their house on Friday the 13th because they fear that bad luck will befall them if they venture outside. (Apparently, the bad luck doesn't find them in their homes.)

Personally, I like the attitude of the "eccentric" (rational?) men in the photo.
Members of the Eccentric Club of London at their annual Friday the 13th lunch in 1936 – surrounded by objects that are connected with superstitions. Picture: Getty Images [Unlucky roots of Friday the 13th].
There is no evidence to support the irrational fear of Friday the 13th, with the single exception of a study published 14 years ago in the British Medical Journal [Is Friday the 13th bad for your health?]. That study showed an increase in accidents on Friday the 13th compared to Friday the 6th.

According to scholars, the fear of Friday the 13th is a recent invention. There is no mention of it before 1900 [Why Friday the 13th Is Unlucky]. It seems that people simply combined a fear of the number 13—triskaidekaphobia—with an obscure dead of Fridays. Nobody knows for sure why the number 13 is considered unlucky but there are several popular myths. The most common are a Norse myth about having 13 people at dinner and a Christian myth about the Last Supper.

There is no significant historical record documenting a widespread irrational fear of Fridays although there are plenty of minor examples of Friday avoidance. Some people thought it was bad luck to be married on a Friday or to set sail on a ship. In Christian cultures the day is associated with the fact that Jesus was crucified on a Friday and Friday is the day that Adam was tempted by Eve to eat the forbidden fruit.


Thursday, June 12, 2008

Tangled Bank #107

 
The latest issue of Tangled Bank is #107. It's hosted at Syaffolee [Tangled Bank #107: The CYOA Edition].
You're trapped on a cruise ship in the South Pacific, bored out of your mind. The swimming pool holds no appeal. Gambling is pointless because the advantage is on the house. The books you brought with you have long been finished. You've even resorted to registering for a cha-cha class to relieve your ennui. But that's no fun, because the instructor is always yelling at you for having two left feet.

Then on a Wednesday morning, the ship docks on a small island. Travelers are allowed to go on land for the day. You debark and after wandering past the marketplace filled with locals hawking loud jewelry and ceremonial masks (probably manufactured in Taiwan), you find yourself in a small clearing with several paths meandering off into the undergrowth. There's a sign nearby saying:

"Welcome to the one hundred and seventh edition of Tangled Bank."

At the foot of the sign is a machete.

If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

Religulous

 
Coming to theaters near you in October [Religulous].




[Hat Tip: Brian Larnder at Primordial Blog]

Graduation

 
With 72,000 students, you can appreciate that graduation ceremonies need to be spread out over several weeks at the University of Toronto. At this time of year we have graduations every day and sometimes twice a day.

Today it was the turn of St. Michael's College. It was such a beautiful day that I couldn't resist taking a picture of the graduating class as they walked across the front campus to Simcoe Hall. There were about 500 students in this line.

How many of you went to your graduation? I did.


Charles McVety Visits the ROM

 
I was taking Bryant Ing1 to lunch today when we decided to check out what was happening at the Royal Ontario Museum. There was supposed to be a big anti-racism rally led by "Dr." Charles McVety. He's the man who claims that Charles Darwin was a racist [Canadian Creationist: Charles McVety].

Here he is (left) speaking to his supporters right in front of the museum where the Charles Darwin exhibit is housed. One of his supporters handed us a leaflet explaining why Darwin was a racist. (I'm sure you all know the quotes and I'm sure you all know that Darwin was very enlightened for a man of his time.)

We didn't stay long. McVety was going on about the title of Darwin's famous book. He was making the point that the book is about the preservation of favoured races.2 There were at least three or four people nodding their heads in agreement.

Toronto's finest were there in full riot gear to keep the huge crowd under control. You can see from the photo that they were very suspicious of Bryant and me. Some of them seem to be reaching for their weapons. You can click on the photo to see a larger version where their facial expression tells all.

The last photograph (below) is a view of the entire crowd. I figure there were about ten McVety sycophants supporters present and about ten passers-by who were curious about what was going on. There were almost as many reporters and camera crews. It was a non-event. We went to the Faculty Club for a nice lunch. Mmmmmm, fish and chips!




1. Winner of Monday's Molecule #66.

2. The actual title is On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.

Canadian Creationist: Charles McVety

 
"Dr."1 Charles McVety is President of Canada Christian College in Toronto.

McVety is currently promoting the movie Expelled in Canada. He claims that it exposes the racism behind "Darwinism" as well as revealing how universities repress academic freedom by firing creationists.

I presume that Canada's Christian College is one of the last bastions of academic freedom where academics are allowed to say and think whatever they believe without fear of reprisal or dismissal. I assume this must be true because McVety feels so strongly about the importance of academic freedom. Evolutionists must be welcome at McVety's college.

The protection of academic freedom is probably behind this statement from the Canada Christian College website on college standards ...
Canada Christian College strives to maintain a distinctly Christian living and learning environment conducive to a rigorous study of God’s Word. Membership in Canada Christian College is obtained through application and invitation. Those who accept an invitation to join the College agree to uphold its standards of conduct. In return, they gain the privilege of enjoying the benefits of college membership and undertake to work for the best interests of the whole community (Phil. 2:4).

Compliance with these standards is simply one aspect of a larger commitment by students, staff, and faculty to live as responsible citizens, to pursue biblical holiness, and to follow an ethic of mutual support, Christian love in relationships, and to serve the best interests of each other and the entire community. Individuals who are invited to become members of this community but cannot with integrity pledge to uphold the application of these standards are advised not to accept the invitation and to seek instead a living-learning situation more acceptable to them.
In an effort to be much more respectful of creationists, no matter how stupid they might be, I will refrain from calling them names, like IDiot. This posting adheres to this new policy. I hope it pleases my atheist friends who favor accommodation.

Larry Moran
Surprising as it might seem, there are some people who don't like Charles McVety and his activities. A recent posting from Kady O'Malley on Macleans.ca blogs isn't all that complimentary [The opposite of YPF?]. (Macleans is a Canadian newsmagazine similar to Time and Newsweek.)
Perhaps he was inspired by the turnout for Young People Fucking, or maybe he misses all that media attention he got after taking credit for getting C-10 through the House with nary a peep over the controversial changes to the film tax rebate. Whatever the reason, Reverend Charles McVety is headed back to the capital to co-host a private screening of a very different kind of film: Expelled: The Movie, the controversial anti-Darwin documentary that purports to expose a sinister anti-creationism bias within the mainstream scientific community.

Interestingly, in his come-one-come-all invite to the film - which was forwarded to all MPs and staffers via parliamentary email by Conservative MP Maurice Vellacott - McVety doesn’t even mention the religious aspect of the debate; instead, he accuses Darwin of “overt racism”, and calls on Canadians to “blot out out this terrible scourge in our society.”
McVety and his friend(s) are holding an anti-racism rally today at 12:30 outside the Darwin exhibit at the Royal Ontario Museum, Toronto. You'd better get there early if you want to be at the front of the crowd where you can touch the great man. I assume traffic on Bloor Street will be tied up for hours.

Canadian Cynic might be there. (Warning! If you follow the link to Canadian Cynic you might be disappointed 'cause Canadian Cynic doesn't adhere to my new policy of accommodating accommodationists. Neither does PZ Myers who uses a rude word in referring to McVety and his somewhat misleading interpretation of Charles Darwin.


1. Here's a description of Charles McVety's degree Degree or Not Degree?.

Spring in Nova Scotia

 
One of my colleagues, David Tinker, has retired and moved to the Annapolis valley in Nova Scotia (Canada). He sent me a picture of a woodland path and it's so beautiful that I thought I'd share it with Sandwalk readers. Another one of my colleagues, Michael Paul, just retired and left yesterday to live near David in the Annapolis Valley. I can see why.




Wednesday, June 11, 2008

Nobel Laureates: Stanford Moore and William Stein

 

The Nobel Prize in Chemistry 1972.

"for their contribution to the understanding of the connection between chemical structure and catalytic activity of the active centre of the ribonuclease molecule"


Stanford Moore (1913 - 1983) and William Stein (1911 - 1980) were awarded the 1972 Nobel Prize in Chemistry for working out the role of amino acid side chains in the mechanism of catalysis by bovine ribonuclease A [see How Enzymes Work].

This is one of the most important achievements in biochemistry although it could hardly have been considered a breakthrough since the result was widely anticipated and predicted. Many other enzymes were being studied at the time and the award was, in a sense, a recognition of the general concept and not the particular contributions of Moore and Stein. Moore and Stein also developed the technique of automated amino acid analysis of proteins and peptides.

Moore and Stein shared their Nobel Prize with Christian Anfinsen.

The presentation speech was delivered by Professor Bo Malmström of the Royal Academy of Science.THEME: Nobel Laureates
Your Royal Highnesses, Ladies and Gentlemen,

The key substances of life are called enzymes. Everything we humans undertake - if we sit here enjoying the splendour of a Nobel ceremony, if we perform work, or even if we simply feel joy or sorrow - occurs by means of enzyme reactions. The phenomenon described as life is a network of coupled enzymatic processes. In chemical terminology the enzymes are catalysts, i.e. substances which accelerate chemical reactions without being consumed themselves. The concept of catalysis was introduced about 150 years ago by the great Swedish chemist Jöns Jacob Berzelius, who also, with astonishing intuition, suggested that the tissues of a living organism have catalytic activity. Around the turn of the century scientists started to associate this catalytic effect with specific substances, enzymes. This year's three Nobel Prize winners in Chemistry, Christian B. Anfinsen, Stanford Moore and William H. Stein, have performed fundamental studies with the enzyme ribonuclease making it possible for us now to approach the problem of enzymatic activity on a molecular level.

From a chemical point of view enzymes are proteins. These are built up of 20 different amino acids which are linked together into long chains. Despite the fact that proteins have only 20 building blocks, there are thousands of enzymes, each with its specific properties. This large degree of variation becomes possible because the number and sequence of the amino acids in the chain can be varied. Ribonuclease was the first enzyme for which the complete amino acid sequence was determined thanks to contributions from Anfinsen and from Moore and Stein.

Every living organism has its own characteristic pattern of enzymes. It can also produce a copy of itself, and this progeny has the same enzymes. An important question concerns the source of the information which has to be passed on from generation to generation for the enzyme pattern to be preserved. We know, thanks to contributions which have led to earlier Nobel Prize awards, that a specific molecule, called DNA, serves as the carrier of the traits of inheritance. These traits are expressed by DNA controlling the synthesis of enzymes. DNA accomplishes this by determining the sequence of the amino acids making up a particular protein molecule. An active enzyme does not, however, consist just of a long chain of amino acids linked together, but the chain is folded in space in a way which gives the molecule a globular form. What is the source of the information responsible for this specific folding of the peptide chain? It is this question in particular which has been the concern of Anfinsen's investigations. In a series of elegant experiments he showed that the necessary information is inherent in the linear sequence of amino acids in the peptide chain, so that no further genetic information than that found in DNA is necessary.

The contributions of Moore and Stein concern another fundamental question regarding ribonuclease, namely the basis for its catalytic activity. The reacting substances, the substrates, are bound to an enzyme in what is generally called its active site. In the complex so formed there is an interaction between enzyme and substrate leading to a changed reactivity of the substrate. Knowledge about the structure of an enzyme is of little help in understanding this interaction if it is not possible to find the active site and to determine the chemical groups in it. Moore and Stein discovered as an important principle that the active site contains amino acids with an anomalously high reactivity compared to the same amino acids in free form. This high reactivity is of direct importance for the catalytic activity of the enzyme, but Moore and Stein also found it possible to utilize it to label two amino acids in the active site by chemical modification. In this way the position of these amino acids in the long peptide chain could be unambigously determined. Through these investigations Moore and Stein were able to provide a detailed picture of the active site of ribonuclease long before the three-dimensional structure of the enzyme had been determined.

Dr. Anfinsen,

I have tried to explain your pioneering investigations showing that the linear sequence of amino acids in the enzyme ribonuclease determines the biologically active conformation of this enzyme. This finding has profound implications for our understanding of the way in which active enzyme molecules are formed in living cells.

Drs. Moore and Stein,

I have attempted to summarize your fundamental contributions to our understanding of the relationship between chemical structure and catalytic activity in the enzyme ribonuclease. In particular, I have stressed your studies leading to the localization of two specific histidine residues in the active site of the enzyme. It is for these pioneering experiments that the Royal Academy of Sciences has decided to award this year's Nobel Prize in Chemistry to you together with Dr. Anfinsen.

Drs. Anfinsen, Moore and Stein,

On behalf of the Royal Academy of Sciences I wish to convey to you our warmest congratulations, and I now ask you to receive your Prizes from the hands of His Royal Highness the Crown Prince.


How Enzymes Work

Enzymes are protein catalysts that speed up reactions. In the most extreme cases the catalyzed reaction will take place 1023 times faster than the rate of the uncatalyzed reaction. Typical values are about 1014. What this means is that a reaction that would normally take years can occur within a second inside the cell because the reaction is catalyzed by an enzyme.

How do enzymes do this? The answer is surprisingly complicated. Let's look at a simple reaction forming part of the glycolysis pathway.


In this reaction, one molecule of DHAP is converted to one molecule of G3P, and vice versa (the reaction is readily reversible). The reaction is catalyzed by a famous enzyme called triose phosphate isomerase or TPI.

As the reaction proceeds, there will be a point when neither DHAP or G3P exist. Instead, there will be a transition state whose structure is somewhere in between that of the product and the substrate. This transition state only exists for a nanosecond or less. One of the things that enzymes do is to create a pocket where the binding of the transition state intermediate1 is favored. What this does is to lower the activation energy between the reactant and product making the transition from one to the other much easier. The net effect is to speed up the process by many order of magnitude.

Transition state stabilization is one of the most important mechanisms of enzyme catalysis. There are very few direct proofs of this in the scientific literature because the hypothetical transition state is so unstable and transient. However, there is a huge number of indirect experiments that confirm the importance of this mechanism. They include the binding of more stable transition state analogues and the modeling of hypothetical transition states into the active site of an enzyme.

Another important mechanism of catalysis is substrate binding. The role of an enzyme is to recruit reactants such as DHAP into the active site of the enzyme where it is precisely positioned for the subsequent reaction. In the example show here, the reactant has bound to the active site of trisose phosphate isomerase where it aligned with two important amino acid side chains: histidine (His, dark blue) and glutamate (Glu, red). In this case, a single reactant is oriented correctly for the subsequent reaction. In other cases the role of binding is more obvious since two different reactions are correctly positioned to react with each other.

The enzyme serves as a stable platform for aligning the substrates in the correct orientation. The arrangement of the active site pocket and the surrounding channel can greatly increase the probability that the reaction will take place. In solution, without enzyme, many collisions between molecules will be nonproductive.

In addition to transition state stabilization, and substrate binding effects, enzymes also exhibit catalytic effects on acceleration of reactions. There are many different kinds of catalytic effects but the main ones are ionization effects, acid-base catalysis, and covalent catalysis. In all cases, the effect is mediated by the side chains of amino acid at the active site.

An example of acid-base catalysis in triose phosphate isomerase is shown in the diagram on the right. You don't need to follow the specifics of the reaction. The idea is that a histidine side chain (His-95) forms a hydrogen bond with the substrate while a glutamate residue (Glu-165) acts as an acid-base catalyst to extract a proton from DHAP.

The role of amino acid side chains in catalysis and substrate binding was mostly worked out the 1970's when the first enzyme structures were being solved. One of the first examples was ribonuclease A [Monday's Molecule #75]. Stanford Moore and William Stein received the Nobel Prize in 1972 for being among the very first biochemists to demonstrate how enzyme work at the molecular level.


1. A transition state is not an intermediate. The difference is too technical for this posting. I just want to make sure we don't get any quibbles in the comments section.

Tuesday, June 10, 2008

God Is Not Winning

 
John Brockman runs a website called The Edge. Most (all?) of the contributers are authors and many of them are clients of Brockman. He is, among other things, a literary agent for prominent authors (Richard Dawkins, Daniel Dennett, Jared Diamond). If you want to understand what The Edge is all about, read Brockman's essay on The Third Culture.

Gregory Paul and Phil Zuckerman have just published an article on The Edge titled WHY THE GODS ARE NOT WINNING. They make some important points that are often overlooked and frequently misrepresented. Here are some quotes ...


It is well documented that Christianity has withered dramatically in Europe, Canada, Australia, New Zealand and Japan. The failure of the faith in the west is regularly denounced by Popes and Protestant leaders. Churches are being converted into libraries, laundromats and pubs. Those who disbelieve in deities typically make up large portions of the population, according to some surveys they make up the majority of citizens in Scandinavia, France and Japan. Evolution is accepted by the majority in all secular nations, up to four in five in some.

......

Nor is it all that surprising that faith has imploded in most of the west. Every single 1st world nation that is irreligious shares a set of distinctive attributes. These include handgun control, anti-corporal punishment and anti-bullying policies, rehabilitative rather than punitive incarceration, intensive sex education that emphasizes condom use, reduced socio-economic disparity via tax and welfare systems combined with comprehensive health care, increased leisure time that can be dedicated to family needs and stress reduction, and so forth.

As a result the great majority enjoy long, safe, comfortable, middle class lives that they can be confident will not be lost due to factors beyond their control. It is hard to lose one's middle class status in Europe, Canada and so forth, and modern medicine is always accessible regardless of income. Nor do these egalitarians culture emphasize the attainment of immense wealth and luxury, so most folks are reasonably satisfied with what they have got. Such circumstances dramatically reduces peoples' need to believe in supernatural forces that protect them from life's calamities, help them get what they don't have, or at least make up for them with the ultimate Club Med of heaven. One of us (Zuckerman) interviewed secular Europeans and verified that the process of secularization is casual; most hardly think about the issue of God, not finding the concept relevant to their contented lives.

The result is plain to see. Not a single advanced democracy that enjoys benign, progressive socio-economic conditions retains a high level of popular religiosity. They all go material.


[Hat Tip: Brian Larnder at Primordial Blog]
 

The 3rd issue of the Molecular and Cell Biology Carnival has been posted by Bertalan Meskó at ScienceRoll [Molecular and Cell Biology Carnival #3: Animations].
It’s my pleasure to host the 3rd edition of the Molecular and Cell Biology Carnival. This is the first time I host a non medicine-related carnival, so I really hope you will like the posts I found.
Submit your articles here.

The previous editions are ...
  1. the skeptical alchemist
  2. Cotch.net
  3. ScienceRoll



Come to This Seminar!

 
Alex Palazzo of The Daily Transcript is giving a talk in our Department ....

Department of Biochemistry Special Seminar

"Beyond The Signal Sequence Hypothesis: Nuclear Export and Endoplasmic
Reticulum Targeting of mRNAs."


Dr. Alexander Palazzo Ph.D.
Department of Cell Biology
Harvard Medical School

Thursday, June 12th

Room 4171 MSB
11:00 a.m.

Dr. Palazzo is a candidate for a Faculty position in the Department
of Biochemistry.


Contact me by email if you want to meet Alex for lunch tomorrow.


One Million!!!

 
I'm fascinated by the statistics of blogging. Who reads blogs? Why do they read blogs? Do blogs serve a useful purpose or are they just for fun? What's the future of blogging?

Part of the fascination is looking at the data to see which postings attract the most attention and how many people regularly check in each day. Are some blogs better than others? Are some blogs more popular? Why?1

A few minutes ago somebody logged on to Sandwalk to view a page and registered the one millionth page view since this blog began collecting data. That's pretty interesting. It means that Sandwalk is an average science blog in terms of popularity, far behind the best ones that have one million views per month.



One of the interesting things about science blogging is that there's a 25% dropoff in readers during the months of May, June, July, and August. (Other bloggers see this too.) I assume this is mostly students who don't read blogs during the summer. Is it because they only have high speed internet access when they're at school or is it because they're not interested in blogs during the summer?


1. I wonder if there's a direct correlation between the number of readers and the number of postings per day? Some blogs put up lots of articles every day even though many of those articles don't take much effort. Does this build readership so that when you post something important it's more likely to get attention? That doesn't work for me as a reader. There are quite a few excellent blogs that I scan every day even though the postings are infrequent. On the other hand, when I've tried posting several times a day over a period of a few weeks, the number of visits does increase significantly.

Monday, June 09, 2008

Monday's Molecule #75

 
Some readers have been complaining that Monday's Molecule is too easy.1 That's why I've chosen a more difficult task for you today.

You have to examine the structure and figure out what's going on. The molecule you have to identify isn't even shown in the figure—only small fragments are depicted. You need to identify the invisible molecule and explain why this figure is so important. Its importance is mostly historical. The elucidation of what's happening is a defining moment in biochemistry and helped open up a whole new field of study.

There's a direct connection between today's molecule and a Nobel Prize. The prize was awarded for discovering exactly what the figure depicts. The first person to correctly identify the molecule, describe what the figure shows, 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 three ineligible candidates for this week's reward.

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. [Hint: A co-recipient of this week's Nobel Laureates is already on the list.]

Correct responses will be posted tomorrow. I may select multiple winners if several people get it right. (Like that's going to happen this week!)

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: Turns out it wasn't as difficult as I thought. The winning answer arrived within one hour, followed shortly by several other correct answers. The image shows a small piece of RNA about to be cleaved in the active site of Ribonuclease A. The key residues are His12, His119, and Lys 41 and their interactions with the substrate are shown. Note how they form weak interactions with the phosphodiester linkage. This causes destabilization of the bonds in preparation for cleavage. The Nobel Laureates are Stanford Moore and William Stein who received the Nobel Prize in 1972 for working out the mechanism of Ribonuclease A. This was the first detailed demonstration of how enzymes worked at the molecular level.

The winner is Michael Clarkson. Congratulations Michael.


1. Okay, maybe not "some" readers. Maybe it's only one reader. In fact, maybe I'm the reader.

Gene Genie #33

 
The 33rd edition of Gene Genie has been posted at Neurophilosophy [Gene Genie 33].
Welcome to the 33rd edition of Gene Genie, the blog carnival devoted to genes and genetic diseases.

In this edition, there is a strong emphasis on cancer. There's also a focus on leukodystrophy, and a special section on personalized genetics.
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



Sunday, June 08, 2008

America: The Greatest Experiment in the History of Mankind

 
Here's one of the men who could be "leader of the free world." There's no doubt in his mind that Christianity is the superior religion. I wonder if the other candidate thinks differently?



BTW, how's that experiment working out?

See Jim Lippard's comment at McCain thinks the Constitution establishes a Christian nation. I don't think Jim is going to vote for this man!


[Hat Tip: Canadian Cynic]

Saturday, June 07, 2008

 
Stephen Jay Gould is one of my heroes. This video in six parts was made back in 1984 but most of it is as true and accurate today as it was back then. Thanks to Laelaps for finding it on YouTube.















How to Activate Your Junk DNA!

 
I suppose it was inevitable. Sooner or later a private company would figure out how to activate your junk DNA and turn you into a super being. At a price, of course.

A company called Mastery Life A.C. and/or DNA Perfection has learned the trick [Unleash Your Genetic Potential NOW!]. What you need to do is establish a mental connection to someone named Toby Alexander—this is done by mental telepathy. Your brainwave frequency will "entrain" to his and that's all it takes. Naturally it takes more than one session to achieve the best results. Four at least. The cost is $100 per session for a total minimum cost of only $400. (You can use PayPal.)

How does it work? Well, I must confess that the biology is too complicated for me so let me just quote from the website.
Most people know that DNA is the 'blueprint of life' and is located in every cell of the body. In addition to each chromosome's 2 strand double helix of DNA, there are an additional 10 etheric strands of DNA available to each human, which have been dormant since the beginning of recorded history. Each additional strand possesses attributes that permit the individual to perform greater human accomplishments. Scientists acknowledge that we currently only use 3% of our current 2 strand DNA. Thus we live in a society where people are sick, unhappy, stressed out, create wars, have difficulty experiencing love, and are totally disconnected with the universe. Most people have to meditate for many years just to have a so-called 'mystical' experience, that's how disconnected we are now. Imagine activating 100% of your 2 strand DNA, PLUS 10 additional strands! You will go from using 10% of your brain to becoming a multi-dimensional being with psychic, telepathic, and manifestation abilities beyond anything you've ever dreamed of. Plus, you will stop the aging process and actually start to rejuvenate to look and feel YOUNGER. This is the Original Divine Blueprint, what man USED to be. It has been written that Jesus had 12 strands of DNA activated. There have been children born throughout the history of humanity to raise the frequency of the planet that have more than 2 strands of DNA active - they are known as Indigo children. These are the incredibly intelligent, loving, and amazing children that are being mistakenly diagnosed as having A.D.D. because they are too smart to pay attention in class. Your DNA is your blueprint of life and is what controls every single function inside each of your cells. If you change your DNA, you really will change your life.
I strongly believe that George Hull David Hannum, in his famous comment to P.T. Barnum, grossly underestimated the number of suckers born every minute.


[Hat Tip: New Scientist, Feedback, My 17-23, 2008 p. 64]

Friday, June 06, 2008

D-Day

 
Today marks the 64th anniversary of the invasion of Normandy on June 6, 1944. British, Canadian and American forces opened the second front against Germany. On the eve of the invasion, General Dwight D. Eisenhower issued the following Order of the Day.

Soldiers, Sailors and Airmen of the Allied Expeditionary Force!

You are about to embark upon the Great Crusade, toward which we have striven these many months. The eyes of liberty loving people everywhere march with you. In company with our brave Allies and brothers in arms on other Fronts, you will bring about the destruction of the German war machine, the elimination of Nazi tyranny over the oppressed peoples of Europe, and security for ourselves in a free world.

Your task will not be an easy one. Your enemy is well trained, well equipped and battle hardened. He will fight savagely.

But this is the year 1944! Much has happened since the Nazi triumphs of 1940-41. The United Nations have inflicted upon the Germans great defeats, in open battle, man to man. Our air offensive has seriously reduced their strength in the air and their capacity to wage war on the ground. Our Home Fronts have given us an overwhelming superiority in weapons and munitions of war, and placed at our disposal great reserves of trained fighting men. The tide has turned! The free men of the world are marching together to Victory!

I have full confidence in your courage and devotion to duty and skill in battle. We will accept nothing less than full Victory! Good luck! And let us beseech the blessing of Almighty God upon this great and noble undertaking.

For baby boomers it means a day of special significance for our parents. In my case, it was my father who took part in the invasions. He was an RAF pilot flying rocket firing typhoons in close support of the ground troops. During the initial days his missions were limited to quick strikes and reconnaissance since Normandy was at the limit of their range from southern England. During the second week of the invasion his squadron landed in Normandy and things became very hectic from then on with several close support missions every day.

The photograph above shows a crew loading rockets onto a typhoon based just a few kilometers from the landing beaches in Normandy. Here's an example of the effectiveness of rocket-firing typhoons [Air Power Over the Normandy Beaches and Beyond].

Intelligence information from ULTRA set up a particularly effective air strike on June 10. German message traffic had given away the location of the headquarters of Panzergruppe West on June 9, and the next evening a mixed force of forty rocket-armed Typhoons and sixty-one Mitchells from 2 TAF struck at the headquarters, located in the Chateau of La Caine, killing the unit's chief of staff and many of its personnel and destroying fully 75 percent of its communications equipment as well as numerous vehicles. At a most critical point in the Normandy battle, then, the Panzer group, which served as a vital nexus between operating armored forces, was knocked out of the command, control, and communications loop; indeed, it had to return to Paris to be reconstituted before resuming its duties a month later.






A Little Learning Is a Dangerous Thing

 
A little learning is a dangerous thing; drink deep, or taste not the Pierian spring: there shallow draughts intoxicate the brain, and drinking largely sobers us again.

Alexander Pope
An Essay on Criticism, 1709
Philip G. Altbach is Monan professor of higher education and director of the Center for International Higher Education at Boston College (USA). He has just published an article on Open Access in THE (Times Higher Education) [Hidden cost of open access].

Professor Altbach complains that the problem with Open Access is the absence of peer review.
Profit, competition and excess have spawned the open-access movement. Academics, librarians and administrators think it is the answer to monopolistic journals. But there are several problems with it. Chief among them is that peer review is eliminated - all knowledge becomes equal. There is no quality control on the internet, and a Wikipedia article has the same value as an essay by a distinguished researcher....

Essentially, open access means there is no objective way of measuring research quality. If the traditional journals and their peer-review systems are no longer operating, anarchy rules. Researchers will have no accurate way of assessing quality in a scholarly publication.
This is dead wrong, of course, and the comments on the website make it very clear that Professor Altbach has goofed.

I like this comment ...
Ah, sweet irony. If this article had undergone "peer review", or some other accuracy or quality checking critera, then it would never had seen the light of day...
Bora Zivkovic at A Blog Around the Clock is all over it 'cause he's the Online Community Manager at PLoS-ONE (Public Library of Science) [A really, truly bad article about Open Access]. The question is ... why would a Professor of higher education at Boston University write an article about Open Access without doing a little bit of investigation to find out about it?


Blacks Have Rhythm, Asians Aren't Creative, Whites Rule the World

 
Friday's Urban Legends

From time to time on Friday morning I post some examples of urban myths/legends. Today I've copied a comment from an old thread on Race and Intelligence. Someone named E.A. posted this comment two days ago and I thought it might be fun to pick out all the factual and logical errors in his/her comment. (Hint: there are more than three.) Most of them are due to bigotry of some sort or another, coupled to an excessive dose of political correctness. (E.A. provided a link to the blog True Newspaper).

It's appropriate to examine these false ideas today since this is an historic week in the USA. American Democrats have just nominated their first black man for President and no doubt there will be much discussion about race over the next six months.

First,
Jewish people are the most intelligent. They win almost 40% of the Nobel Prize's and they have a small population of only 14 million. So by far they exceed the other races in intelligence. The other races having huge numbers and such small contributions.

Second,
IQ tests, test intellectual conformity, not creativity and originality. This would explain the Asian high IQ's. They as a people are the ultimate conformists.

In IQ tests there is typically only one answer to the problem. That problem being a social conformity to reason. But everyone knows that Genius's and all of the greatest developments in the world are not the product of conformity. Conformity never breeds creativity. We can see this in the lack of influence the Asian population has had on Science. China used to be called the "sick man" of Asia. Their population is massive and their contribution to innovation is almost nil. We can see this lack of originality in their adoptation of European philosophies, I.e. Communism.

Friedrich Nietzsche and other Philosophers have critized Asians. Nietsche used the words "Pallid osification" to describe Orientals.

Pallid: lacking sparkle or liveliness.

Osification: The process of becoming set and inflexible in behavior, attitudes, and actions. Inflexible conformity, rigid unthinking acceptance of social conventions.

The reality is Asian people have yet to understand that laws and rules are arbitrary. Europeans make the rules and Asian's follow them.

It also doesn't make sense that Asian's are considered smart because of the fact that they have destroyed their own countries. This is due to over-population and their basic lack of enviromental understanding.

It is also common scientific fact that women who have many children are ignorant, and those who have less children are more intelligent. This has already been proven in studies. So it seems strange to say that Asians are smart when the obviousness of their backwards countries, and medieval lifestyle makes them contrary to that premise.

Europeans have the most advanced civilizations and every other race has yet to meet these levels other than the Japanese. The Japanese only being good at copying other people's inventions and making them better. Other than that their original creativity is lacking as well. They took American cars and made them better. They took the German camera and made it better. And they took German steel and made it better. Otherwise the greatest advances still come from Europeans and Jews. Other than that the Orientals have yet to produce an Einstein or a Thomas Edison.

When it comes to Black people. It makes sense that they have low intellectual comformity, I.e. IQ tests. They are far too creative to be trapped in this unoriginal form of conditioning. You can tell their creative capacity in their athletics, music, dance, and the way they talk. They by far exceed the Asiatic races in these areas. Being better singers, musicians ect. Blacks far exceed Asians in emotive expression. In all of North America there is only one or two famous high-paid Asian actors.

Reality, Europeans rule the world and they have allowed others to exist only out of desire for economic bennifet. They, (Europeans) are also the physically strongest, winning the Strongest Man competitions again and again.

The greater the conformity, the weaker the race. Thus we see the races as they are today. The wild animal being bred out of man, and the physically impotent, conformist thriving.

Otherwise "Group psychology" is the most destructive thing in the world. All these stereotypes are false when it comes to the individual. Individualism is the most important thing for this time. All countries, Religions, groups need to dissolve for man to live in peace.



Thursday, June 05, 2008

Our Galaxy Loses Two Arms

 
This is what the Milky Way actually looks like as shown on the Astronomy Picture of the Day for October 20, 2007.

Most of us have rarely never seen it like this because we live in light polluted areas where most stars have become invisible. We are seeing our galaxy from one of the spiral arms looking toward the central cluster of stars. Much of the center is obscured by dust clouds.

The model below shows what the Milky Way galaxy was supposed to look like when I was growing up [from Astronomical Adventures]. It has four large spiral arms and a large central blob of stars. The model is based on our view of other spiral galaxies and on observations that were made from Earth-based telescopes.

Our solar system is located in the Cruz arm. Other models were similar although the names of the arms were different. The basic plan was a spiral with four large arms (Norma, Scutum-Centaurus, Sagittarius and Perseus) projecting outward from a dense circular mass of stars at the center of the galaxy.

This view has been substantially altered over the past few decades. Astronomers now recognize that the Milky Way is a bar galaxy whose central mass of stars forms a bar shape with arms trailing off the ends of the bar.

Typical bar galaxies have only two main arms and recent results indicate that our galaxy conforms to this pattern [Two Of The Milky Way's Spiral Arms Go Missing]. The most recent model is shown below. As you can see, two of the four major arms have now disappeared or have been greatly reduced in size and importance.

The galaxy looks very different from the one I learned about as a child. Does anyone know where our solar system is located on the new model?

UPDATE: I replaced the old image (below) with one from Astronomy Picture of the Day from June 6, 2008. It shows where we are in the galaxy.