12:34:56 07/08/09

 
Sometime around midday you could write the exact time and date as 12:34:56 07/08/09 and if you were up early you could have witnessed 04:05:06 07/08/09.

But only in Europe—and a few other countries [Date and time notation by country].

In America you celebrated the big day last month and if your country is unlucky enough to have adopted the international standard notation then you've missed the big day by two years.

In Canada we use all three notations and this leads to a great deal of confusion. The good news is that we get to celebrate the sequential date three times. Tonight there will be a huge celebration in downtown Toronto with parades and fireworks and speeches by famous people.

How many more sequential time/dates will we celebrate in Canada this millennium?

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On this Day in 1945

(reposted from August 6, 2007)

At 8:15 AM on August 6, 1945 an atomic bomb was detonated over Hiroshima, Japan. Approximately 78,000 civilians were killed on that day. Six months later the death toll had risen to about 140,000 people.

There are many arguments in favor of dropping the bomb just as there are many arguments against it. What's clear is that in the context of 2007 we are not in a good position to judge the actions of countries that had been at war for many years.

The most important lesson of Hiroshima is that war is hell and many innocent people die. It's all very well to enter into a war with the best of intentions—as the Japanese did on December 7, 1941—but it's foolish to pretend that when you start a war there won't be any suffering. When you do that you can really say that the victims of Hiroshima died in vain.

The killing and maiming of civilians is an inevitable outcome of war, no matter how hard you might try to restrict your targets to military objectives. Before going to war you need to take the consequences into account and decide whether the cost is worth it.

One of the many mistakes in Iraq was the naive assumption that it would be a clean war with few casualties and no long-term consequences for the Iraqi people. Yet today, the numbers of innocent lives lost in Iraq is comparable to the numbers lost in Hiroshima and Nagasaki. And what is the benefit for Iraq that outweighs the cost in human lives? Is it "freedom" and "democracy"?

Hiroshima was not a glorious victory. It was ugly, heartbreaking, and avoidable. War is not an end in itself, it is the failure of peace. War is not an instrument of your foreign policy—it is an admission that you don't have a foreign policy.

[The top photograph shows the mushroom cloud over Hiroshima on the morning of August 6, 1945 (Photo from Encyclopedia Britanica: Hiroshima: mushroom cloud over Hiroshima, 1945. [Photograph]. Retrieved August 7, 2007, from Encyclopædia Britannica Online. The bottom image is taken from a Japanese postcard (Horoshima and Nagassaki 1945). It shows victims of the attack on Hiroshima.]

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Are Miracles Compatible with Science?

 
This is a common question in the debates about science and religion. My answer is "no." A miracle, by definition, must be miraculous, which means it is not explicable by the process we use in science (evidence and rationality).

Philosophers love this kind of question because it gives them loads of opportunities to talk about dead philosophers and how they interpreted the word "miracle." If they can find logical inconsistencies, or slight subtleties of meaning, then they can declare victory for belief in miracles.

Watch Hugh McLachlan perform this "miracle" in an article written for New Scientist: Opinion: Do you believe in miracles?.

THESE days most people think it unscientific to believe in "miracles", and irreligious not to believe in them. But would the occurrence of miracles really violate the principles of science? And would their non-occurrence really undermine religion? David Hume and Richard Dawkins have attempted to answer these questions in their different ways, but I am not convinced by their arguments, and for me they remain open questions.

So, it's an open question whether miracles are compatible with science, eh? I wish Hugh McLachlan had given us some examples of miracles that he thinks would be compatible with science.

He's been known to read Sandwalk [Hugh McLachlan on Cloning Humans] so maybe he'll give us an examples in the comments.

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Ten Unexplained Human Characteristics

 
New Scientist is at it again. This time they've come up with Ten things we don't understand about humans.

1. Blushing
2. Laughter
3. Pubic Hair
4. Teenagers
5. Dreams
6. Altruism
7. Art
8. Superstition
9. Kissing
10. Nose-picking

It goes without saying that these "problems" are much more of a concern for adaptationists than for pluralists.

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Decoding the Structure of the HIV Genome

 
The title of the press release on Biology News Net caught my eye: UNC researchers decode structure of an entire HIV genome. I clicked the link on my aggregator and read the first two paragraphs.

The structure of an entire HIV genome has been decoded for the first time by researchers at the University of North Carolina at Chapel Hill. The results have widespread implications for understanding the strategies that viruses, like the one that causes AIDS, use to infect humans.

The study, the cover story in the Aug. 6, 2009, issue of the journal Nature, also opens the door for further research which could accelerate the development of antiviral drugs.

By the time I finished the article I thought I had a pretty good idea of what they were talking about but, just to be sure, I visited the Nature website to read the actual scientific paper.

Watts, J.M., Dang, K.K., Gorelick, R.J., Leonard, C.W., Bess Jr., J.W., Swanstrom, R., Burch, C.L. and Weeks, K.M. (2009) Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 460:705-710 [doi: 10.1038/nature08237]

Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS and other serious health threats. Viral replication is regulated at many levels, including the use of conserved genomic RNA structures. Most potential regulatory elements in viral RNA genomes are uncharacterized. Here we report the structure of an entire HIV-1 genome at single nucleotide resolution using SHAPE, a high-throughput RNA analysis technology. The genome encodes protein structure at two levels. In addition to the correspondence between RNA and protein primary sequences, a correlation exists between high levels of RNA structure and sequences that encode inter-domain loops in HIV proteins. This correlation suggests that RNA structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger RNA motifs. We also identify organizational principles for unstructured RNA regions, including splice site acceptors and hypervariable regions. These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by previously unrecognized regulatory motifs and that extensive RNA structure constitutes an important component of the genetic code.

The authors determined the two- and in some cases the three-dimensional structure of the HIV RNA genome. In other words, they figured out the way RNA folds to form regions of secondary structure (double-stranded RNA). This RNA molecule functions as a complex messenger RNA and the secondary structure plays a role in regulating how the molecule is translated.

The press release doesn't really convey this result very well, especially in the opening paragraph. Part of the problem is misue of the word "decode." We're familiar with journalists who use "decode" to mean "nucleotide sequence" as in "Scientists decoded the human genome." This elevates "decode" to an entirely new meaning.

In fairness, this confusion over the word "decode" is exacerbated by the language used by the authors in the paper.

Our discovery that the peptide loops that link independently folded protein domains are encoded by highly structured RNA indicates that these and probably other mRNAs encode protein structure at a second level beyond specifying the amino acid sequence. In this view, higher-order RNA structure directly encodes protein structure, especially at domain junctions. The extraordinary density of information encoded in the structure of large RNA molecules (Figs 1, 2 and 4d) represents another level of the genetic code, one which we understand the least at present. This work makes clear that there is much to be discovered by broad structural analyses of RNA genomes and intact mRNAs.

I'm not sure this language is helpful.

UPDATE: The press release from Scientific American is different: HIV genome structure decoded.

It might not be super high-res, but researchers at the University of North Carolina at Chapel Hill have described the first full structure of the HIV-1 genome.

The paper, published online today in Nature, maps out the virus' genome down to a one-nucleotide resolution with the help of a technique call SHAPE—selective 2'-hydroxyl acylation analyzed by primer extension—to paint the full, previously unknown picture of the virus (Scientific American is part of Nature Publishing Group).

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Censorship in the Scientific Community

 
Richard Dawkins interviews Wendy Wright of Concerned Women for America. You really have to watch this if you want to understand what science is up against in some parts of the world.

Richard tries very hard to be patient and respectful. I would not have been so kind in the face of such massive stupidity and ad hominem attacks by Wendy Wright. I find it absolutely astonishing that she attacks scientists and accuses them of stupidity and conspiracy then complains about ad hominem attacks when Richard asks why she rejects evolution.








I don't know how much of this you can stand. Parts 5, 6, and 7 are here.

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Monday's Molecule #132: Winner!

 
This is a complex between parts of the T-cell receptor (green and blue) and the major histocompatibility complex class II molecule (MHC class II) shown in orange and yellow. There's a peptide bound in the presentation site of the class molecule (red).

When a cell becomes infected with a virus, various viral proteins are broken down into peptides and bound to a site on class II molecules. These molecules are then presented on the surface of the cell when they can be recognized by the T-cell receptor. Since the viral peptide will be seen as a foreign antigen, the infected cell will be destroyed.

The Nobel Laureates are Rolf Zinkernagel and Peter Doherty.

There weren't very many correct answers this week¹ but Markus-Frederik Bohn thought it was very easy. He's a graduate student at the Lehrstuhl für Biotechnik in Erlangen, Germany. He has a Canadian connection but I'll let him reveal it in the comments if he wishes.

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This is a very famous molecular complex. You need to identify this complex by naming all the major components. You will not win if you skip this part. (Don't forget the red bit.)

There is a Nobel Prize associated with the discover of this complex although the work was done long before the structure was solved. The first person to identify the molecules and the Nobel Laureate(s), wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only five ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin at Madison, Dara Gilbert of the University of Waterloo, Anne Johnson of Ryerson University, Cody Cobb, soon to be a graduate student at Rutgers University in New Jersey, and Alex Ling of the University of Toronto.

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

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1. Because immunology isn't biochemistry and possibly not even a real science.

The figure is from Reinherz et al. (1999).

Reinherz, E.L., Tan, K., Tang, L., Kern, P., Liu, J., Xiong, Y., Hussey, R.E., Smolyar, A., Hare, B., Zhang, R., Joachimiak, A., Chang, H.C., Wagner, G., and Wang, J. (1999) Science 286:1913-1921. [PubMed] [doi: 10.1126/science.286.5446.1913]

Lateral Gene Transfer and the Return of Lamarckian Evolution

 
Mark Buchanan believes that physics has entered a new era where it has gone beyond the fundamental forces into the realm of "collective phenomena". He claims that biology is about to do the same as he explains in an article that was just published in Nature Physics: "Collectivist Revolution in Evolution."

It now seems clear that biology may also have a second act linked to the widespread importance of collective phenomena. The explosion of genetic and genomic data, of course, has ushered in the era of systems biology, as biologists have come to recognize the need to gain a more holistic understanding of the functioning of organisms. But this may not be the most radical transformation in store for biological science. A coming revolution in biology, some suggest, may go so far as to unseat Darwinian evolution (ran in its modern form) from its position as the key explanatory process in biology, and may just bring back some form of Lamarckian evolution—that old idea of the inheritance of acquired characteristics.

No, it's not epigenetics, it's lateral gene transfer (LGT) that's going to unseat Darwinian evolution and bring back Lamarck.

Much of what he writes about LGT is correct. It does, indeed, make interpretation of molecular evolution more difficult, especially at the root. But some of his ideas do not represent the consensus view in biology: for example, the role of lateral gene transfer in the evolution of the genetic code.

The conjecture is that horizontal gene transfer was indeed required for the present genetic code to take the form it has, and that the emergence of life most likely went through a series of stages, with the early stage more Lamarckian in character, and only the latter stages becoming more Darwinian.

Exploring that point in greater detail will be a task for a new kind of biology, one that breaks with many of the presuppositions of traditional evolutionary thinking, and explores the potential for rich and surprising dynamics in a collective setting. It will almost surely benefit from the ideas and experience of physics, which has already experienced its own collectivist revolution.

This kind of hyperbole is not helpful. Shame on Nature Physics for publishing it.¹

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1. I wonder if Nature Genetics publishes opinion pieces by evolutionary biologists on the overthrow of quantum mechanics?

NIH and Francis Collins

 
I wish that Obama had picked someone else as his nominee for Director of NIH. I'm not opposed to Collins simply because he is religious. I'm opposed to him because he has taken a very public and vocal position on the roles of science and religion. Here's how I've expressed my viewpoint in comments on my own blog and elsewhere.

I'm not opposed to Collins just because he is an evangelical Christian. And I would not be opposed to someone from another faith, nor to an atheist.

But when a person becomes an outspoken advocate of a particular religious belief and establishes a foundation and a website to promote that belief (e.g. BioLogos) then that's a different story.

The banner on the BioLogos site reads, "We believe that faith and science both lead to truth about God and creation." Collins has gone beyond merely holding a belief that may or may not be compatible with science. He is now actively identified with a particular position; namely, that science and evangelical Christianity are compatible.

Not only that, Collins is on record favoring the use of his office to promote his personal religious beliefs [Mixing Science, Religion, and Politics].

It would be far better to appoint someone who could maintain a decent separation between religion and science. The Director of a major government funding agency should not be openly advocating a religious perspective on science.

It would be just as unwise to appoint a vocal atheist or a vocal Muslim.

This seems to be a difficult position for most people to grasp. PZ Myers shares my perspective on the appointment [Is it really that hard to understand?] but no matter how many times he tries to explain it, there's always someone who tries to turn it into an attack on all Christians. The latest is Matt Springer.

Religion should be kept out of scientific organizations whether they they are government run, like NIH, or collections of scientists like AAAS and NAS [What Should Scientific Organizations Say about Religion?, Theistic Evolution: How Does God Do It?]. By nominating someone with a strong, vocal, religious perspective, Obama is sending the wrong message.

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UCSC Official Mascot

 
Fred Zlotnick took this picture of a banana slug in his back yard.

Believe it or not, the banana slug is the official mascot of the University of California Santa Cruz.

The Banana Slug, a bright yellow, slimy, shell-less mollusk found in the campus's redwood forest, was the unofficial mascot for UC Santa Cruz's coed teams since the university's early years. The students' adoption of such a lowly creature for a team mascot was their reaction to the fierce athletic competition fostered at most American universities. UCSC has always offered a wide-ranging physical education and recreation program designed to appeal to the greatest number of students, but it has based its approach on some unusual ideas: that athletics are for all students, not just team members of major sports; that the most important goal of a collegiate physical education department should be to introduce as many students as possible to lifelong physical activities; and that the joy of participating is more important than winning.

In 1980, when some campus teams wanted more organized yet still low-key participation in extramural competition, UCSC joined Division III of the NCAA in five sports. Since the application required an official team name, UCSC's then chancellor polled the student players, and out of this small group emerged a consensus for a new moniker--the sea lions. It was a choice that the chancellor considered more dignified and suitable to serious play than the Banana Slugs. But the new name did not find favor with the majority of students, who continued to root for the Slugs even after a sea lion was painted in the middle of the basketball floor.

After five years of dealing with the two-mascot problem, an overwhelming proslug straw vote by students in 1986 convinced the chancellor to make the lowly but beloved Banana Slug UCSC's official mascot. By the time the chancellor had left office, he was won over to the proslug camp, even to the point of featuring the Slug on his personal holiday card.

In May 2004, Reader's Digest named the Banana Slug the best college mascot. The Banana Slug even figured in a court case involving campus mascots. Judge Terence Evans, writing the opinion for the Seventh Circuit Court of Appeals, stated the following: "We give the best college nickname nod to the University of California, Santa Cruz. Imagine the fear in the hearts of opponents who travel there to face the imaginatively named 'Banana Slugs'?" (Crue et al. v. Aiken, June 1, 2004)

Our Sammy the Slug mascot has been appearing around campus at sports events and other functions. And, when the men's tennis team played in the NCAA championships, their T-shirts read: "Banana Slugs-No Known Predators."

UC Santa Cruz Foundation trustee Anne Neufeld Levin wrote a children's book, Sally Slug, illustrated by UCSC alumna and former Foundation trustee Patricia Rebele. The book, published in 2002, is available at slugstore.ucsc.edu. Proceeds from sales of the book benefit the UCSC Foundation and provide for art history purchases and exhibits in the library.

Sounds like my kind of school. I wonder if they need a biochemistry Prof?

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Is "Organic" Food Better for You than "Conventionally" Produced Food?

 
The London School of Hygiene and Tropical Medicine has just completed a study of the scientific literature commissioned by the Food Standards Agency in the UK [Comparison of composition (nutrients and other substances) of organically and conventionally produced foodstuffs: a systematic review of the available literature].

According to the press release ...

An independent review commissioned by the Food Standards Agency (FSA) shows that there are no important differences in the nutrition content, or any additional health benefits, of organic food when compared with conventionally produced food. The focus of the review was the nutritional content of foodstuffs.

Gill Fine, FSA Director of Consumer Choice and Dietary Health, said: ‘Ensuring people have accurate information is absolutely essential in allowing us all to make informed choices about the food we eat. This study does not mean that people should not eat organic food. What it shows is that there is little, if any, nutritional difference between organic and conventionally produced food and that there is no evidence of additional health benefits from eating organic food.

'The Agency supports consumer choice and is neither pro nor anti organic food. We recognise that there are many reasons why people choose to eat organic, such as animal welfare or environmental concerns. The Agency will continue to give consumers accurate information about their food based on the best available scientific evidence.’

This makes a lot of sense. There was never a good reason for assuming that organically grown foods would be more healthy than conventionally grown food and now we have scientific evidence to support that assumption. From now on, whenever you hear someone say that "organic" foods are more healthy you can inform them that what they are saying is contrary to scientific evidence.

There may be other reasons for wanting to eat organically grown food. It may be better for the environment and it may contain fewer traces of pesticides and herbicides. Those claims haven't been refuted by this study. (Although, as far as I know, there's no scientific reason to believe that treating food with herbicides and pesticides is dangerous to the consumer. Besides, organic food is also treated.)

You may wonder why this is such a big deal. Maybe you never thought that organic food was more nutritious than conventionally grown food. If so, you are one of the more rational consumers. Most other consumers are more inclined to believe what the image above shows and what they think are scientific studies proving that organic food is better. That image is from this report in the Daily Mail from 2007: Organic food really IS better for you, claims study.

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[Image Credit: The top image is from Green Expander where they say, "Organic food is becoming more and more popular. This is the healthy food, without any additives, with higher levels of vitamin C and essential minerals. Organic food comes from trusted farms and food companies, that are inspected at least once a year."]

Land Snails and Slugs

 
Most of us don't know very much about slugs and land snails but Christopher Taylor at Catalogue of Organisms is doing his best to educate us (and himself): Wild Slug Chases (Taxon of the Week: Gastrodontoidea).

I need to warn you that his posting isn't suitable for all audiences. Some of these animals are capable of having sex with themselves and that's not something you want your children to know. Also, some of these animals aren't as pretty as warm fuzzy animals like cats. I find it helps to think of snails and slugs as dinner rather than pets.¹

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1. For some people, this works for cats too.

Monday's Molecule #132

 
This is a very famous molecular complex. You need to identify this complex by naming all the major components. You will not win if you skip this part. (Don't forget the red bit.)

There is a Nobel Prize associated with the discover of this complex although the work was done long before the structure was solved. The first person to identify the molecules and the Nobel Laureate(s), wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only five ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin at Madison, Dara Gilbert of the University of Waterloo, Anne Johnson of Ryerson University, Cody Cobb, soon to be a graduate student at Rutgers University in New Jersey, and Alex Ling of the University of Toronto.

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

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

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The figure is from Reinherz et al. (1999).

Reinherz, E.L., Tan, K., Tang, L., Kern, P., Liu, J., Xiong, Y., Hussey, R.E., Smolyar, A., Hare, B., Zhang, R., Joachimiak, A., Chang, H.C., Wagner, G., and Wang, J. (1999) Science 286:1913-1921. [PubMed] [doi: 10.1126/science.286.5446.1913]

Breakthrough!! The Third Replicator Is Discovered

 
The editors at New Scientist have become completely incapable of distinguishing between science and things that pretend to be science. The latest evidence of this failing is an article by Susan Blackmore titled: Evolution's third replicator: Genes, memes, and now what?.

WE HUMANS have let loose something extraordinary on our planet - a third replicator - the consequences of which are unpredictable and possibly dangerous.

What do I mean by "third replicator"? The first replicator was the gene - the basis of biological evolution. The second was memes - the basis of cultural evolution. I believe that what we are now seeing, in a vast technological explosion, is the birth of a third evolutionary process. We are Earth's Pandoran species, yet we are blissfully oblivious to what we have let out of the box.

This might sound apocalyptic, but it is how the world looks when we realise that Darwin's principle of evolution by natural selection need not apply just to biology. Given some kind of copying machinery that makes lots of slightly different copies of the same information, and given that only a few of those copies survive to be copied again, an evolutionary process must occur and design will appear out of destruction.

But all is not lost. One of the benefits arising out of the self-destruction of New Scientist is that it gives us all a chance to watch a train wreck in action.

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[Photo Credit: Train Wreck at Gare Montparnasse, Paris, France, 1895 from Answers.com]

Happy Simcoe Day!!

 

Today is Simcoe Day in Toronto, a holiday named after John Graves Simcoe, the first Lieutenant Governor of Upper Canada (1791-1796).

According to Wikipedia ...

He founded York (now Toronto) and was instrumental in introducing institutions such as the courts, trial by jury, English common law, freehold land tenure, and for abolishing slavery in Upper Canada long before it was abolished in the British Empire as a whole (it had disappeared from Upper Canada by 1810, but was not abolished throughout the Empire until 1834).

The holiday is known by many other names in other parts of Canada including the term "Civic Holiday," a name that brings tears to your eyes.

I think the entire country should name this holiday "Simcoe Day" in honor of John Graves Simcoe, the founder of Toronto, which is, after all, the greatest city in Canada. If Canada were to officially recognize the superiority of Toronto (and Torontonians) it would go a long way toward unifying the country.

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