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, June 13, 2008
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.
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
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).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.
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.
Larry MoranSurprising 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.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.
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.”
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.
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 ...
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.
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