The Tree of Life

I'm off to a meeting on Perspectives on the Tree of Life.¹ (See Perspectives on the Tree of Life: Day One, Day Two, Day Three.)


If you want to follow the real scientific debate on the tree of life then read my earlier posting on The Three Domain Hypothesis especially the one on "The Web of Life."

The basic idea is that there is no strict branching tree of life that accounts for the data during the early stages of life on Earth. The first group of single-cell organisms exchanged genes so frequently that the gene phylogeny looks much more like a jumbled web that a traditional tree.

You should also listen to Ford Doolittle's talk on The Tree of Life. If you have any questions you'd like to ask, post them here and I'll bring them up at the meeting.

This part isn't very controversial. There really are good evolutionary biologists who are questioning the tree of life. It's just part of the gradual undoing of the Three Domain Hypothesis in light of the enormous amount of data refuting it.

What's controversial is the rejection of the very concept of trees in evolutionary biology and that's where the philosophers come in. This meeting has a 50:50 mixture of philosophers and scientists. It's gonna be fun.

Do you remember what was wrong with the New Scientist story last winter? It wasn't that scientists were questioning the tree of life 'cause that part of the story is quite accurate. What upset me was the fact that New Scientist exploited Charles Darwin by tying him to the idea that early bacterial evolution was treelike when, in fact, he knew nothing at all about the subject.

How could he have been wrong when he never wrote a thing about the relationship between various divisions of bacteria and archaebacteria and their affinities with eukaryotes?

The other thing that bugged me was that this story wasn't new but New Scientist played it up as a new discovery.

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1. The original title of the meeting was "Questioning the Tree of Life" but it's been changed to more closely reflect the divergent opinions of the participants.

What is NIH up to?

 
We've been debating the appointment of a new NIH Director (Francis Collins) but ignoring the role that NIH's Office of Science Education plays.

On Wednesday night (tomorrow) they're showing Inherit the Wind and that puts them right smack in the thick of the discussion about science and religion.

I think this is a mistake—NIH should keep their nose out of that debate—but that's not the worst of it. Following the movie they've asked Matt Nisbet to lead a discussion about evolution. Here's how he describes it on his blog.

Following the film, I have been invited to make a few remarks on the evolution debate as it plays out in contemporary culture and the enduring themes from the classic movie. The event and film series is designed to facilitate active audience participation and debate, so I expect there will be some very interesting discussion. For more on the relevant themes related to science and public engagement, see this forthcoming article on "What's Next for Science Communication?"

Matt Nisbet? Were all the real scientists too busy? Why didn't they fly in Jerry Coyne for the evening? Or Richard Lewontin? Or Niles Eldredge? Even better, PZ Myers. These are scientists who know and understand science.

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P.S. I don't think Clarence Darrow was an accommodationist. I wonder how Matt is going to frame that?

Good Food, Bad Food

Most of us are all too familiar with the food police. The food police are a group of self-appointed “experts" on nutrition. Not only do they know what to eat and what to avoid, they also feel duty bound to tell everyone else. You may be a victim ... or you may be one of them.

We've all heard the standard dogmas: whole wheat bread is good, white bread is bad; spinach is good, pork is bad; saturated fats are bad, unsaturated fats are good.. And we’ve been told hundreds of times to load up on various vitamins and supplements. You can't keep them straight. One year it's vitamin E that will make you smarter and the next year its vitamin A. At least the food police are consistent on a few things; for example, they all love omega-3 fatty acids.

Most reasonable people have learned to be skeptical about nutritional claims. We've been through several cycles of wine being good for you, then bad for you, and good for you again. We've listened to so many claims about the wonders of this diet or that one that we've given up trying to make sense of it all. About the only thing we agree on is that the diet kooks are probably wrong in spite of the fact that Larry King and Oprah Winfrey believe in them.

Who is to blame for all this mess? Is nutrition science really a science or is the field really in as much trouble as it seems from the outside? Is the media to blame for misrepresenting the science?

Reynold Specter is a clinical professor of medicine whose areas of expertise include vitamins and the effect of diet on kidney functions. He discusses the problem in the May/June issue of Skeptical Inquirer: Science and Pseudoscience in Adult Nutrition Research and Practice.

Here’s the take-home message ....

Human nutrition research and practice is plagued by pseudoscience and unsupported opinions. A scientific analysis separates reliable nutrition facts from nutritional pseudoscience and false opinion.

According to Specter, most nutrition claims are based on bad science. Many of them are unproven and a surprising number have actually been disproven by well-controlled, double-blind clinical studies.

So, what do we know for certain? We know that the average adult needs vitamins, essential amino acids, essential fatty acids, high quality protein (animal or vegetable), minerals, and a source of fuel calories. The fuel can come from carbohydrates, fat, or protein or some combination of these.

We know that carbohydrates, fats, and proteins can be inter-converted once they have been digested. We know that the levels of most metabolites are maintained at steady state levels (homeostasis) in healthy adults. And finally, we know that nutritional requirements change as you get older.

Just about everything else is either wrong or debatable according to Reynold Specter. The majority of people are neither too fat nor too thin. They have a body mass index (BMI) less than 30—usually in the optimal range of 20 to 25. For normal healthy people we can ask whether food supplements are necessary and whether there are particular supplements that will prevent disease.

The answer, notwithstanding thousands of positive EOS [epidemiology observation studies] and, in some cases, small inadequate clinical trials is there is no rigorous scientific evidence for the utility of dietary supplements, including megavitamins in normal weight (nonpregnant) adults with a stable BMI of 20 to 25 eating a diet containing adequate amounts of nutrients in Table 1.

Specter says that many common claims have been shown to be false by scientific studies. They include claims that fibre will prevent bowel cancer, that megadoses of vitamin D will prevent dementia, and that a low-fat diet will reduce your risk of a heart attack

Why then, have so many papers been published in the medical literature claiming benefits for food supplements and certain diets? Part of the problem is that these preliminary studies are just that—they were never intended to be the last word on the subject. Part of the problem is what's called “healthy person bias." Health conscious people tend to exercise and take supplements. This group is going to have fewer medical problems regardless of whether they take supplements or not but small scale studies don't control for that so it looks like there's a causal relationship between taking supplements and good health.

But most of the problem is due to how the system works. There are too many people who benefit from the status quo in nutritional science and hardly anyone who benefits if the quality of publications were to be improved.

Under the current system, authors find it easy to publish preliminary work; journal editors are happy to make larger profits; commercial enterprises enjoy increases in the sales of food supplementals and fad diets; and the news media have lots to write about. Don't expect this to change in favor of good science.

The bottom line is that the food supplement industry is dominated by poor science at best and outright quackery at worst. One could argue that this situation is harmless. After all, if P.T. Barnum's favorite group¹ of people want to waste their money, then why should the rest of us care? Reynold Specter tells us why our society needs to be concerned.

As I noted earlier, even widely used supplements such as vitamins E, C, and carotene in ‘standard megadoses’ (greater than five times the RDA) may indeed be harmful. The potential for harm for many other types of supplements is not been systematically studied, although there are convincing data that certain supplements may damage the liver, kidney, or heart or alter drug metabolism. For example, the amino acid tryptophan (used to induce sleep) and ephedrine-containing herbs (for asthma) were removed from the over-the-counter market because of severe toxicity, including deaths in some people.

What about diets? There is no scientific evidence to support the claims that certain common foods are better than others. For the average person, saturated fats are no better or worse than unsaturated fats and potatoes or white rice aren't any worse for you than whole-wheat. And there's nothing magical about eating five daily servings of fruit and vegetables. Everything works as long as you don't eat too much.

If you are obese you need to eat more moderately in order to cut back on fuel intake. Everybody knows this. It is not rocket science. But do weight loss diets actually work?

None work well. On average, over the long term, obese humans do not lose much weight on voluntary low-calorie diets of any kind. (There are of course a few obese individuals who have ‘self discipline’ and can lose weight and keep the weight off. Their secret is obscure.)

Many people profit from weight loss diets but unfortunately the patients aren't among them.

Be skeptical of the claims of so-called nutritionists. Don't be fooled into thinking that "nutrition science" is any more scientific than creation science.

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1. I know it was really David Hannum, and not P.T. Barnum, who said "There's a sucker born every minute."

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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