Monday's Molecule #131: Winner

 
The reaction pathway depicts the formation of the chromophore of green fluorescent protein (GFP). The light fluorescence is due to light that is absorbed by this chromophore and re-emitted at a longer wavelength.

Roger Tsein analyzed the pathway and created variants that would increase the efficiently and change the color of the light. For this he shared the 2008 Nobel Prize.

A surprising number of you found this easy and responded quickly with the correct answer. Some of you actually knew what it was without resorting to Google! The winner is Alex Ling of the University of Toronto.

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This week we have an entire pathway to help you out. The goal is to identify the final product on the right and explain its significance. There are several possible Nobel Laureates who might be associated with this molecule but I'm looking for the one who worked on the pathway and presents it in the Nobel lecture. The Nobel Prize was awarded, in part, for the creation of mutant with a threonine substitution at position 65.

The first person to identify the molecule and the Nobel Laureate, 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: Ian Clarke of New England Biolabs Canada in Pickering ON, Canada. Dima Klenchin of the University of Wisconsin at Madison, Dara Gilbert of the University of Waterloo, Anne Johnson of Ryerson University, and Cody Cobb, soon to be a graduate student at Rutgers University in New Jersey.

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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The Dutch are p*ssed as well

 
You just can't make this stuff up, ... oh, wait a minute, it's Fox News. Carry on.

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[Hat Tip: Pharyngula

Your polite neighbours to the North are p*ssed off

 
From DAILY KOS ...

Oh yes indeedy.

The Shona Holmes thing? You know, the one whose story changes depending on her audience?

In the commercial she was DYING! In her testimony, not so much.

Most people here are aware of who is funding this Shona dog and pony show, that would be the good ol' Koch industry-John Bircher related Americans for Prosperity. The same astroturf factory that brought you teabagging (Branding FAIL) and Joe teh Plumber.

They are using the name Patients United Now. The only united Patients seem to be those with a huge stake in the Healthcare insurance industry and their other think tank friends. Their language and talking points are directly from Frank Luntz, Cunning Linguist part 2: framing healthcare (My co blogger has an interesting way with words too!)

Some of us have gone beyond being angry at the way Canada is being portrayed. My current thinking is that Americans deserve exactly the kind of health care system they wish for.

Why should Canadians care if Americans are dying or going bankrupt because they can't afford health care? While the rest of the civilized world sees universal health care as a basic human right, the USA is allowed to have a different opinion if they choose. After all, they have different opinions on many other important social issues.

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Evolution and (lack of) design

 
The recurrent laryngeal nerve in humans begins in the brain then travels down into the the thorax, loops around the aorta, and travels back up the neck where it innervates the larynx.

This pathway doesn't makes much sense. A better design would be to innervate the larynx directly without looping around the aorta.

This isn't much of a problem in humans but in giraffes the recurrent laryngeal nerve has to travel several extra meters in order to get to its final destination. Those who advocate that evidence of design is evidence of God prefer to ignore examples such as these.

But can it be explained by evolution? Of course it can. This branch of the vagus nerve is present in fish were it is the fourth vagus nerve innervating one of the posterior gills. You can trace its evolution as the modern blood vessels evolved in the mammal lineage. Mark Ridley describes it, with diagrams, in his textbook Evolution.

You can also see what the region looks like during development on the Critical Biomass blog.

The point is that this is another example of something that makes sense in the light of evolution but otherwise seems quite senseless. The other point is that Intelligent Design Creationism fails to provide any explanation of phenomena such as the path of the recurrent laryngeal nerve.

This is a well-known example of something that looks like "bad design" and that's why it is often used to refute the main message of the Intelligent Design Creationists. Jerry Coyne uses several examples like this in his book Why Evolution Is True.

Have you ever wondered how the creationists respond to these examples of evolution? Here's an example from Darwin's God by Cornelius Hunter: Are Evolutionists Delusional (or just in denial)?.

Coyne inverts the message to say that imperfect designs make sense in evolution. Of course, but so what? So do perfect designs, and everything in between. All these make sense in evolution just as my bad day yesterday makes sense in astrology and warp drive makes sense in science fiction movies. When you can make up whatever just-so stories come to mind, then everything "makes sense."

The bottom line is that it is precisely from theology and metaphysics that evolution derives its power. Evolution is proclaimed to be a fact by Dobzhansky, Coyne and the evolutionists not on the basis of speculative science. As Elliott Sober has pointed out, evolution's truth status comes from the assumed unlikeliness of design, and all the theology entailed therein. It is, as Sober put it, Darwin's Principle.

Evolutionists like to make factual claims. One fact that is incontrovertible is that evolution is driven by theological claims--that is a matter of public record. Evolution is a religious theory. What is interesting is that the evolutionist denies any such thing. He may as well be denying the nose on his own face. This is truly a fascinating mythology.

Whether evolutionists are liars, delusional or in denial is difficult to say. What is obvious is that evolutionary thought is bankrupt. Religion drives science, and it matters.

Are you having trouble following the logic of this argument? Let me help you out with the short version ....

Intelligent Design Creationism is a religious theory that fails to explain most of what we observe in biology. But that's OK since evolution is also a religious theory. Nyah, nyah!

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[Image Credit: Critical Biomass]

How Many M&M's in a Jar?

 
I just had to copy this from GrrlScientist 'cause my favorite¹ daughter loves M&M's and physics.

Here's the Science paper that calculates the packing fraction of M&M's.

Donev, A., Cisse, I., Sachs, D., Variano, E.A., Stillinger, F.H., Connelly, R., Torquato, S., Chaikin, P.M. (2004) Improving the density of jammed disordered packings using ellipsoids. Science 303:990-993. [PubMed] [doi: 10.1126/science.1093010]

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1. and only

Sam Harris vs Francis Collins

 
Sam Harris has published an op-ed piece in The New York Times where he questions whether the religious beliefs of Francis Collins are compatible with science [Science Is in the Details].

Dr. Collins has written that “science offers no answers to the most pressing questions of human existence” and that “the claims of atheistic materialism must be steadfastly resisted.”

One can only hope that these convictions will not affect his judgment at the institutes of health. After all, understanding human well-being at the level of the brain might very well offer some “answers to the most pressing questions of human existence” — questions like, Why do we suffer? Or, indeed, is it possible to love one’s neighbor as oneself? And wouldn’t any effort to explain human nature without reference to a soul, and to explain morality without reference to God, necessarily constitute “atheistic materialism”?

Francis Collins is an accomplished scientist and a man who is sincere in his beliefs. And that is precisely what makes me so uncomfortable about his nomination. Must we really entrust the future of biomedical research in the United States to a man who sincerely believes that a scientific understanding of human nature is impossible?

I'm not particularly worried about the possibility that Collins' beliefs will influence his decisions at NIH. I'm worried about the mixing of science and religion that occurs when a well-known Christian apologist is appointed to such a prominent scientific position.

It would have been far better to choose someone who was not publicly engaged in the science vs religion debate. NIH should be strictly neutral on this issue.

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Monday's Molecule #131

 

This week we have an entire pathway to help you out. The goal is to identify the final product on the right and explain its significance. There are several possible Nobel Laureates who might be associated with this molecule but I'm looking for the one who worked on the pathway and presents it in the Nobel lecture. The Nobel Prize was awarded, in part, for the creation of mutant with a threonine substitution at position 65.

The first person to identify the molecule and the Nobel Laureate, 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: Ian Clarke of New England Biolabs Canada in Pickering ON, Canada. Dima Klenchin of the University of Wisconsin at Madison, Dara Gilbert of the University of Waterloo, Anne Johnson of Ryerson University, and Cody Cobb, soon to be a graduate student at Rutgers University in New Jersey.

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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What Does the Roman Catholic Church Believe about Evolution?

 
As I'm sure you all know by now, the "official" position of the Roman Catholic Church is theistic evolution. Humans evolved over billion of years from primitive single-cell organisms. God intervened near the end of the process to add a soul and some other religious goodies but the important idea is that a literal interpretation of Genesis is not part of Roman Catholic dogma.

Or so I thought until I saw this. Here's a Roman Catholic priest, Father Jonathan Morris, stumped by a question about Adam and Eve and their children. I guess he must have forgotten what he learned in seminary? (We can't blame this one on FOX News.)

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[Hat Tip: Friendly Atheist]

Marriage Commissioner Can't Refuse to Marry Gays because of his Religon

 
Orville Nichols is a marriage commissioner in the Province of Saskatchewan in Canada. Some years ago he refused to marry a gay couple because it was against his religion.

The couple was married by another commissioner but one of the partners (M.J.) filed a complaint with the Saskatchewan Human Rights Commission who ruled that Nichols did not have the right to refuse to marry people on the grounds that it was against his religion. M.J. was awarded $2500.

But that wasn't the end of it. Orville Nichols thought that his rights were being violated. According to CBCNews ...

Nichols appealed that ruling, arguing that his religious beliefs should be protected under the Charter of Rights and Freedoms.

But in a 39-page decision dated July 17, Court of Queen's Bench Justice Janet McMurty dismissed Nichols' argument, concluding that the human rights tribunal was "correct in its finding that the commission had established discrimination and that accommodation of Mr. Nichols' religious beliefs was not required."

This makes perfect sense. It you are an employee of the government then you have to do your job, part of which, in this case, was marrying gay couples. You can't refuse to do your job because it conflicts with your personal prejudices. If that conflict makes it impossible to carry out your duties then you must resign your position.

This is not the first time that Nichols has been warned.

He launched his own human rights complaint in 2005, months before he even met M.J., alleging that his religious freedoms would be violated should he be asked to marry same-sex couples. That complaint was dismissed by the Saskatchewan Human Rights Commission in 2006.

In those countries that currently ban gay marriage there's a fear that legalizing gay marriage will lead to situations just like this among those who perform civil ceremonies. That fear is fully justified. Once gay marriage becomes illegal legal, discrimination against gays becomes illegal.

Religious beliefs can never be used to justify discrimination and religious beliefs do not not qualify as "humans rights" when they are used as excuses to violate the civil rights of others.

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Oenothera californica subsp. eurekensis

 

This is a photo of the rare, endangered, Eureka Dunes evening primrose. Read about it on Botany Photo of the Day.

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Nobel Laureate: Peyton Rous

 

The Nobel Prize in Physiology or Medicine 1966

"for his discovery of tumour-inducing viruses"

Peyton Rous (1879 - 1970) won the Noble Prize in 1966 for his discovery and characterization of several viruses that cause cancer in birds and mammals. He is best known for his work on Rous Sarcom Virus (RSV), a retrovirus that infects chickens and causes cancer.

The original work was done many years earlier as he describes in his Nobel lecture.

In 1910 I described a malignant chicken sarcoma which could be propagated by transplanting its cells, these multiplying in their new hosts and forming new tumors of the same sort. In other ways the growth showed itself to be a neoplasm of a classical sort, yet, as reported in 1911, its cells yielded a causative virus. Numerous workers had already tried by then to get extraneous causes from transplanted mouse and rat tumors but the transferred cells had held their secret close. Hence the findings with the sarcoma were met with down-right disbelief, though soon several other, morphologically different, "spontaneous" chicken tumors were propagated by transplantation and from each a virus was got causing growths of its kind. Not until after some 15 years of disputation amongst oncologists were the findings with chickens deemed valid, and then they were relegated to a category distinct from that of mammals because from them no viruses could be obtained. Only in 1925, through the efforts of a British worker, W.E. Gye, was much attention given them by scientists.

The virus causing the chicken sarcoma first studied, now generally termed the RSV, has been maintained for more than fifty-five years and is still studied in many countries. Throughout most of this time it would engender growths only in chickens and closely related fowls; but of late several extraneous, non-neoplastic viruses have become associated with it, during its passage in unusual avian hosts; and its scope has thus been so enlarged that now not at few mammals, including monkeys, have been found to develop tumors after inoculation with the enhanced material

For many years the idea that a virus could cause cancer was not part of mainstream oncology. It took a number of other advances to make the idea acceptable. Part of the problem was due to a lack of understanding about the various modes of viral infection. Work on bacterial viruses (bacteriophage) showed clearly that a virus genome could integrate into the normal cellular chromosome and be carried along in all the offspring of those cells.

Fifty years after the initial discovery of a cancer-causing virus, scientists could finally begin to formulate a mechanism based on the results of the phage ground and bacterial geneticists. It's interesting to see the state of knowledge in 1966 as seen in the presentation speech.
THEME:
Nobel Laureates

The situation changed radically in the 1950's. The study of tumour viruses is a central area of modern cancer research. Two developments are responsible for this remarkable change. Recent developments in microbial genetics have lead to reinterpretation of the virus concept itself. It turns out that certain types of virus can introduce parts of their own genetic material into a cell without killing it or inhibiting its multiplication. The virus material thus introduced may become actually integrated with the gene material of the recipient cell and behave as a new hereditary factor. Virus infection can thus lead to a permanent change in some cellular characteristics. This re-evaluation of the virus concept made it possible to understand how a tumour virus might change the regulated behaviour of normal cells to the malignant proliferation characteristic of cancer cells. In the same period many new viruses capable of inducing malignant tumours in mammals were discovered. In 1981 Gross found a virus that induces leukemia in mice. A few years later he and two women scientists, Stewart and Eddy, isolated a remarkable new virus, called polyoma, capable of inducing an array of tumours in many different mammalian species. Since 1960 more than a dozen new tumour virus types have been isolated. It was established, furthermore, that tumour viruses could change normal to cancer cells in the test tube after a very short time of contact. This opened the way for direct studies on cancerous transformation of human cells, an approach previously hidden behind the walls of the living organism. Remarkably enough, it could be shown that Rous' own virus, previously regarded as lacking any importance for mammals, induces cancer under certain conditions in many different mammalian species and may even transform human cells in test tube cultures. Swedish scientists in Lund and Uppsala have made important contributions in this regard. It is not yet clear in which way viruses induce cancer but there is much to indicate that the virus does not behave like a little boy setting fire to a hayrick and running away; part of the viruses' own genetic material seems to be directly responsible for the malignant behaviour of the virus transformed tumour cell.

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The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

How to deal with scientists who cheat

 
What do you do when a scientists (PI, post-doc, graduate student) is caught falsifying data? Should they be expelled from the community, fired from their job, or given a slap on the wrist and rehabilitated?

This isn't an easy question as Janet Stemwedel demonstrates in Tempering justice with mercy: the question of youthful offenders in the tribe of science. I hate it when she does that. It would be so easy to conclude that cheating scientists should be drummed out of the profession but then along comes Janet to confuse me.

She's right, of course. There ought to be a range of punishments that fit the wide range of crimes and motives.

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Cody Cobb's Visit

 
We had a fun visit with Cody Cobb the other day when he flew up to Toronto for a free lunch [Lunch with a winner].

I mentioned that Cody was a blogger but I didn't link to his blog because I wasn't sure if he wanted to be identified as the author of 90% True. Well, apparently he doesn't care, 'cause he's posted two articles about his visit to Toronto.

In Canadian Lunch he reviews a lot of the things we talked about, including our lunch debates with Alex Palazzo. In Science Blogging he covers the discussion about the value and purpose of science blogging. They're both excellent reads—pay him a visit.

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The Richard Dawkins Award Goes to Bill Maher

 
Atheist Alliance International is an organization that gives out The Richard Dawkins Award each year. The criteria, according to Wikipedia are ...

The Richard Dawkins Award will be given every year to honor an outstanding atheist whose contributions raise public awareness of the nontheist life stance; who through writings, media, the arts, film, and/or the stage advocates increased scientific knowledge; who through work or by example teaches acceptance of the nontheist philosophy; and whose public posture mirrors the uncompromising nontheist life stance of Dr. Richard Dawkins.

This year the award goes to Bill Maher. One assumes that he is the man who best exemplifies the criteria for the award.

Does Bill Maher advocate increased scientific knowledge and does his public posture resemble that of Richard Dawkins?

Not bloody likely. As Orac and others have pointed out, Maher believes in all sorts of kooky ideas including the idea that vaccinations don't work [Bill Maher gets the Richard Dawkins Award? That's like Jenny McCarthy getting an award for public health].

Bill Maher may be a good atheist but he sure ain't a good scientist.

So what does PZ Myers think of this? [Put Maher in the hot seat]

However, let's be clear about the obvious. He is being given this award for making a movie this year that clearly promotes atheism and mocks religion, and that's all that is being endorsed.

Nope, sorry PZ but you seem to be wrong about that. Unless, of course, the criteria for the award as described in the Wikipedia article are wrong.

You need to be much more that a good little religion-bashing atheist to meet the criteria and it's as plain as the nose on your face that Bill Maher doesn't qualify.

BTW, like PZ, I was not a big fan of Religulous. Thus, I don't even agree that Bill Maher was in the same league as Richard Dawkins and his Root of all Evil series.

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Dawkins, Tyson, Druyan, Stenger

 
This panel discussion took place recently in November 2007 at the Center of Inquiry in New York. The participants are Richard Dawkins, Neil Degrasse Tyson, Ann Druyan and Victor Stenger. I'm becoming a fan of Victor Strenger and you can see why by watching this video. I'm not a fan of Ann Druyan, and Neil Degrasse Tyson doesn't impress me as much as he impresses everyone else (including himself).

The thing that troubles me most about this discussion is the general agreement that "science" is nothing more than learning about physics, astronomy, chemistry, geology and biology. I think "science" is a way of knowing that includes absolutely everything; english, history, music, sociology and whatever. Real knowledge ("truth") in any of these subjects can only come from applying scientific methodology based on evidence and rationality coupled to a healthy degree of skepticism.

The discussion about whether science should confront religion is particularly interesting. Ann Druyan was the wife of Carl Sagan and she helped produce Cosmos. She claims that science has a wonderful story of its own to tell and there's no need to criticize religion. In fact, it's counter-productive to do so.

Ms. Druyan suggests that Sagan's description of science in Cosmos is the best way to sell science to the general public. She says that the TV series is still being shown frequently on television even though it was made in 1980.

To me that raises an obvious question. Thinking scientifically, I can't help but ask the obvious question. If this was such an effective way to communicate science how come after 29 years it hasn't had much effect on science literacy in the USA? Shouldn't we be basing our claims about science education on evidence and not on wishful thinking?

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