How Does Your Blood Clot?

Some of you have been following the smackdown of Casey Luskin over his attempt to revive the irreducible complexity of the blood clotting cascade. This is a complicated pathway so I wrote a bunch of postings last year to try and explain the pathway at the molecular level.

Theme

Blood Clotting
Here's the complete list in case anyone wants more information in order to follow the discussion.

March 26, 2007
Monday's Molecule #19. Warfarin—an anticoagulant and a rat poison.

March 27, 2007
Vitamin K. Vitamin K plays an important role in blood clotting.

March 28, 2007
Nobel Laureates: Dam and Doisy. Dam: "for his discovery of vitamin K" Doisy: "for his discovery of the chemical nature of vitamin K".

April 2, 2007
Monday's Molecule #20. Heparin—an anticoagulant.

April 2, 2007
Blood Clotting: The Basics. Fibrinogen and how it forms clots.

April 4, 2007
Nobel Laureate: Arne Tiselius. "for his research on electrophoresis and adsorption analysis, especially for his discoveries concerning the complex nature of the serum proteins".

April 4, 2007
Blood Clotting: Platelets. What are platelets and how do they form blood clots?

April 4, 2007
Blood Clotting: Extrinsic Activity and Platelet Activation. Description of the activity of thrombin and the activation of blood platelets.

April 5, 2007
Blood Clotting: Intrinsic Activity. The role of factors VIII and IX. Deficiencies in Factor VIII cause hemophilia A an X-linked form of hemophilia that was common in European royal families descending from Queen Victoria.

April 8, 2007
Genes for Hemophilia A & B and von Willebrand disease. Locations of the F8, F9 and vWF genes on human chromosomes X and 12.

April 12, 2007
Inhibiting Blood Clots: Anticoagulants. How does heparin inhibit blood clotting?

April 15, 2007
Human Anticoagulant Genes. Mapping the genes for anticoagulant factors.

April 16, 2007
Dicumarol and Warfarin Inhibit Blood Clotting. The role of vitamin K in blood clotting.

September 26, 2007
A Synthetic Anticoagulant Related to Heparin. Synthesis of a new anticoagulant to replace heparin.

April 26, 2008
Fibrin and Blood Clots.
What does a blog clot look like?

May 10, 2008
On the Evolution of the Blood Clotting Pathway.
Ian Musgrave explains Russel Doolittle's latest results.

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George Johnson Revists His Defense of Scienc Journalism

 
John Horgan and George Johnson are at it again. They clarify some important points in a followup to their earlier discussion about science journalism (see Who the Heck Is George Johnson?).


John Horgan asks the key question when he says, "Where do we get informed criticism of science these days?"

George Johnson points out that there's a lot of junk on the internet and this includes most science blogs. He does go out of his way to mention the best science blogs but he seems to be surprised and upset at the amount of junk masquerading as legitimate science.

He's right, of course, but that's not the point. What Johnson still seems to ignore is the criticism of traditional print science journalism. I'm not saying that science blogs are perfect—far from it—what I'm saying is that the hubris of science journalists is unjustified. They're not nearly as good as they think they are. As a matter of fact, in my opinion the quality of science on science blogs is superior to the quality of science described by science journalists in the print media.

As a general rule, science journalists are better writers but they are not necessarily better at describing the correct science. It's the content of articles by science journalists that I'm criticizing, not their literary style. I don't think George Johnson gets this. He seems to put all of his emphasis on the literary aspect of science journalism and not enough on the scientific accuracy part of science journalism. Johnson admires good writing.

John Horgan gets it. His main complaint is that it's the scientists, and not the science journalists who are hyping their discoveries and misrepresenting the importance of their work. Horgan points out that scientists are often too deeply immersed in their work to see the big picture. George Johnson is happy to agree with him. I agree too—it's scientists who are behind bad science.¹

However, both Horgan and Johnson see themselves as writers who are able to rise above this self-interest on the part of scientists and put things in proper context. According to them, the role of a science journalist is to pick out the real breakthroughs and to present an accurate view of the science, unencumbered by the prejudices and biases of those scientists who are down in the trenches.

I agree that this should be the goal of science journalism. What I expect of good science journalism is that it avoid the hype and put the science in context. In that sense, Horgan and Johnson are correct—they have identified an important role for science journalism.

So, how's it working out? Badly, I'm afraid. Most science journalists who write about the things I know are failing miserably at this important task. Their prose may be good but they are completely taken in by the scientists who exploit them. This would be unacceptable if we were talking about political reporting or the writings of an art critic. It's just as unacceptable when we're talking about science reporting. That's the issue.

While scientists are responsible for bad science in the first place, it also seems to be scientists who recognize bad science. I don't see too many examples of science journalists who recognize bad science. As a group they seem to be very gullible.

Here's the excerpt where Horgan and Johnson discuss the future of science journalism. Horgan is pessimistic and Johnson is more of an optimist. The first part of this excerpt is where Johnson defends the effort that science journalists put into their work. Science journalists may work hard but you don't get "A's" just for effort.


It's interesting to hear Johnson defend Scientific American and Discovery as good examples of science journalism. It's more evidence that he doesn't know the difference between good science and bad science.

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1. Listen to the exchange when John Horgan describes evolutionary psychology. Horgan knows that a lot of it is garbage. Johnson doesn't. I think this is part of Johnson's problem. He doesn't seem to have a good feel for the difference between good science and bad science in spite of the fact that he (Johnson) brags about the amount of work that goes into good science journalism and how important it is to have good sources. Johnson seems to think that most articles written by science journalists must be accurate because science journalists are supposed to do their homework. That's a bad assumption.

Monday's Molecule #102

 
Name this molecule. Your task is to identify the molecule and give it a biochemically accurate name (the IUPAC name would be perfect, but it's not required). A Nobel Laureate is associated with this molecule, and similar molecules, because the prize was awarded, in part, for synthesizing them in the laboratory.

The first one to correctly identify the molecule and name the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize.

There are three ineligible candidates for this week's reward: Alex Ling of the University of Toronto, Timothy Evans of the University of Pennsylvania, and John Bothwell of the Marine Biological Association of the UK in Plymouth, UK. John, Dale, and a previous winner (Ms. Sandwalk) have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Alex got the first one.

THEME:

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

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

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

UPDATE: The molecule is gibberellin A3 (GA3), a plant hormone. The Nobel Laureate is Elias Corey. The winner is, once again, Dima Klenchin of the University of Wisconsin. Congratulations Dima.

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The Open Laboratory 2009

 
The best science postings have been selected for the 3rd edition of The Open Laboratory. See the results: The Open Laboratory 2008 - and the Winners are......

There are 50 articles. This year the number of postings from the SEED consortium is only 20% of the total, indicating that there are a lot of other science blogs out there.

Out of the eclectic mix I picked the few that discussed evolutionary biology or the molecular biological sciences. Here they are.

Important new flu paper in Cell: part I

Detecting natural selection: a pika's tale

Space Invader DNA jumped across mammalian genomes

Finches, bah! What about Darwin's tomatoes?

Biochemistry of Halloween: Installment 1

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What Does Your Genome Sequence Reveal?

 
John Hawks has some interesting comments about your DNA. What does it actually tell you about your risk of dying or inheriting some nasty symptoms? What would a third party do with your genome scan? Will newspapers publish the results of secretly obtained genetic information from politicians and other famous people?

Would that be an invasion of privacy? Of course it would.

Read Privacy, politicians, and genetic testing.

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Top Ten Evolution Articles from New Scientist

 
In my opinion, New Scientist is the best of the current crop of science magazines for the general public, although, in all honesty, the competition is not very challenging.

New Scientist has published Darwin's dangerous idea: Top 10 evolution articles. Most of them are fairly respectable. The main exception is an article on epigenetics [Rewriting Darwin: The new non-genetic inheritance]. That article is an embarrassment.

One of the best articles is Evolution: 24 myths and misconceptions. I've already posted my kudos at: Evolution: 24 myths and misconceptions. One of the nicest things about the series of articles is their description of random genetic drift as an important player in evolution; for example, Evolution myths: Natural selection is the only means of evolution.

Which brings me to the last article in the top ten list: Freedom from selection lets genes get creative. Here's what it says about random genetic drift.

Natural selection, first identified by Charles Darwin in On the Origin of Species, occurs when genetic mutations cause changes in the body and behaviour of an animal that affect its ability to survive and pass on its genes. Some mutations will have positive effects, others may kill an animal outright or somehow affect its offspring's ability to survive and reproduce. Harsh climates, sparse food and relentless predators destroy many individuals, leaving only those that survive best under exactly those pressures. As a result, the more intense the pressure of natural selection, the tighter the fit between a species and its niche.

So, what happens when the pressure is off? You might think there would be little impetus to adapt, so that species would pretty much stay the same. Not so, says Deacon. Animals still change because genes mutate all the time. The constant rewriting of DNA supplies the raw material from which natural selection picks its winners and losers, and when selection is relaxed, the process of weeding out is less ferocious. Instead, a process called genetic drift kicks in as mutations proliferate and animals with a much wider variety of traits are able to survive and reproduce. Some of the classic traits of a species may be lost, while others can arise for no reason other than that it simply doesn't matter if they do.

Close, but it doesn't quite merit a cigar. Drift does not "kick in" when selection pressure is lifted. Drift occurs all the time. It even competes with natural selection.

And while it's partially true that, "the more intense the pressure of natural selection, the tighter the fit between a species and its niche" it's also true that intense "pressure" increases the chance of extinction.

It seems strange that popular journals can publish articles about evolution that disagree with each other and nobody (editors?) seems to notice.

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Happy New Year

 
This is a year to celebrate Charles Darwin and evolution. In order to start off on the right foot here are some simple¹ thoughts from our Intelligent Design Creationist friends over at Uncommon Descent [TEN THOUGHTS DARWINISTS NEED TO PONDER BEFORE BREAKFAST].

As we head into the new year and the impending Darwin bi-centennial on February 12th, we’re sure to be regaled with story after story of the wondrous things that Darwinian evolution hath wrought. A friend e-mailed the following to me, and with his permission, I reproduce it here below the fold. Perhaps pondering some of these questions might bring some balance to what is otherwise sure to be a lopsided Darwin love-fest for the next couple of months. The original of this can be found at the University of California Santa Barbara Veritas Forum website.

1. Evolution by natural selection is more plausible in a theistic world than an atheistic world.
2. Darwin never accounted for the arrival of the fittest. Naturalism’s god-of-chance is always called upon to do the job.
3. Science rules out the possibility that natural processes might prevent major evolutionary change simply by definition because biological stability and conservation would imply that creation events had taken place since the creation of the universe.
4. Creation preceded Evolution anyway.
5. Edward Blyth described the process of natural selection well before Darwin and Wallace. He concluded that it acted as a force of conservation eliminating deterimental variations from populations.
6. Darwin admitted that based upon the data published in his Origin of Species, one could come to “directly opposite” conclusions. For example, natural selection can prevent major evolutionary change from occurring on a gradual step-by-step basis by eliminating useless transitional stages thus explaining the lack of transitional sequences leading to all of the major body plans (phyla) in the fossil record.
7. Natural selection better describes biology’s “ordinary rules of stability” than major evolutionary change.
8. Darwinian theory predicts a pervasive pattern of natural history that is upside-down from the pattern found in the fossil record.
9. Natural history is more compatible with progressive creation than Darwinian evolution.
10. The ultimate origin of Nature itself cannot be natural. Either Nature or a Natural Law Giver has always existed. Nature has not always existed. What do you conclude?

All these questions, and more, will be answered at the Darwin 2009 Festival in Cambridge, July 5-10, 2009. Speakers include Sir David Attenborough, Dr. Matt Ridley, Lord John Krebs, Professor Steve Jones, Dame Gillian Beer, Lord Robert May, Richard Dawkins, Professor Dan Dennett, Ian McEwan and AS Byatt.

Is anyone from North America interested in going?

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1. I use the term very literally.

Another Way of Knowing?

Thanks to one of our favorite IDiots, Michael Egnor, we now have an answer to an important question. The question is whether there are ways of knowing other than science (evidence + rationalism). Egnor's answer is .... wait for it .... subjective experience! [My Challenge to Dr. Novella: The Materialist Color Tutor’s Dilemma].

Imagine a tutor who specializes in teaching children about color. He’s a materialist, named…Steve. He knows all that is known about color. He knows the physics, the optics, the chemistry, the neurobiology, everything. A family retains him to teach their child, a prodigy, all that can be known about color.

Tudor Steve goes to work. He teaches the little genius about quantum mechanics with relevant application of string theory to flesh out the more subtle issues, then goes on to teach the precocious child chemistry, optics, neurobiology, all of the material and physical facts about color. The child excels in color class in school, acing all of the exams on the physics and the chemistry and the neurobiology.

Then, one day, the boy confides in tutor Steve: the child is color-blind. He has learned all of the physical facts about color, but he has no idea what color looks like. He knows that tutor Steve is a materialist, so he assumes that all there is to know about color can be explained from a materialistic standpoint, including what color looks like. That’s why the child’s parents hired Steve the materialistic color tutor.

So the boy asks tutor Steve:

"Please explain to me what color looks like."

Materialist color tutor Steve has a dilemma. Material facts about color can, of course, be taught. But can ‘what it is like to see color,’ the subjective experience of color, be taught? If it can’t, then there is knowledge of color that is not material knowledge. Therefore materialism cannot completely explain the subjective experience (the qualia) of color. Therefore subjective experience is something in addition to matter. And therefore dualism is necessary to explain the mind.

How would materialist tutor Steve explain what color looks like to a person who is color blind?

That's a tough question all right. But it's only one of many difficult questions of this type. Here are some others that Michael Egnor might want to ponder.

• How do you explain intelligence to someone who is stupid?
• How do you explain what it's like to be abducted by UFO's if you've never been kidnapped by aliens?
• How does a bat explain echolocation to a human?
• How do you explain astrology to someone who doesn't know their birthday?
• How do you explain love, or anger, to someone who has never been angry or in love?
• How do you explain homeopathy to someone who has never been cured by drinking water?
• How do you explain Canada to someone who has never been there?
• Where are the weapons of mass destruction?
• Does Michael Egnor exist?

Hands up, all those who think these questions reveal non-scientific ways of knowing about the truth? How many think that human feelings and emotions cannot be explained by science and scientific reasoning? Has Michael Egnor proved that UFOs astrology homeopathy God exists?

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Religion may have evolved because of its ability to help people exercise self-control

 
Here's an example of evolutionary thinking by a psychologist at the University of Miami. Read the press release (below) and watch the video. It's only when you watch the video that you realize where Professor McCullough is coming from on this issue. He uses the word "evolution" to talk about cultural phenomena without necessarily including genetic changes. In other words, he is not talking about biological evolution.

This can be very confusing and I recommend that evolutionary psychologists change their practice. They should refer to "cultural evolution" and distinguish it from "biological evolution" whenever possible.

Religion may have evolved because of its ability to help people exercise self-control

A study by a University of Miami psychologist reveals that religion facilitates the exercise of self-control and attainment of long-term goals

CORAL GABLES, FL (December 30, 2008)—Self-control is critical for success in life, and a new study by University of Miami professor of Psychology Michael McCullough finds that religious people have more self-control than do their less religious counterparts. These findings imply that religious people may be better at pursuing and achieving long-term goals that are important to them and their religious groups. This, in turn, might help explain why religious people tend to have lower rates of substance abuse, better school achievement, less delinquency, better health behaviors, less depression, and longer lives.

In this research project, McCullough evaluated 8 decades worth of research on religion, which has been conducted in diverse samples of people from around the world. He found persuasive evidence from a variety of domains within the social sciences, including neuroscience, economics, psychology, and sociology, that religious beliefs and religious behaviors are capable of encouraging people to exercise self-control and to more effectively regulate their emotions and behaviors, so that they can pursue valued goals. The research paper, which summarizes the results of their review of the existing science, will be published in the January 2009 issue of Psychological Bulletin.

"The importance of self-control and self-regulation for understanding human behavior are well known to social scientists, but the possibility that the links of religiosity to self-control might explain the links of religiosity to health and behavior has not received much explicit attention," said McCullough. "We hope our paper will correct this oversight in the scientific literature." Among the most interesting conclusions that the research team drew were the following:

• Religious rituals such as prayer and meditation affect the parts of the human brain that are most important for self-regulation and self-control;
• When people view their goals as "sacred," they put more energy and effort into pursuing those goals, and therefore, are probably more effective at attaining them;
• Religious lifestyles may contribute to self-control by providing people with clear standards for their behavior, by causing people to monitor their own behavior more closely, and by giving people the sense that God is watching their behavior;
• The fact that religious people tend to be higher in self-control helps explain why religious people are less likely to misuse drugs and alcohol and experience problems with crime and delinquency.

McCullough's review of the research on religion and self-control contributes to a better understanding of "how the same social force that motivates acts of charity and generosity can also motivate people to strap bomb belts around their waists and then blow themselves up in crowded city buses," he explained. "By thinking of religion as a social force that provides people with resources for controlling their impulses (including the impulse for self-preservation, in some cases) in the service of higher goals, religion can motivate people to do just about anything."

Among the study's more practical implications is that religious people may have at their disposal a set of unique psychological resources for adhering to their New Year's Resolutions in the year to come.

I leave it up to you, dear readers, to decide whether non-religious people (atheists) tend to have higher rates of substance abuse, worse school achievement, more delinquency, worse health behaviors, more depression, and shorter lives. It would imply that countries like Sweden, where half the population is non-religious, are in much worse shape than America, where more than 80% is religious. It would imply that extremely religious countries like Saudi Arabia must be near-perfect societies full of very old people.

Incidentally, the idea of "self-control" is not well explained. If you behave in a certain way because you fear punishment from your god or your priests, then this isn't exactly what I think of when I use the term "self-control."

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What Is the New Atheism?

Andrew Brown blogs at Helmintholog and also at AndrewBrown's Blog, part of the Guardian website. Andrew and I met in London a few years ago. We had an interesting discussion.

Yesterday Andrew posted a provocative article where he attempts to define the New Atheism [The New Atheism, a definition and a quiz]. He is not a fan, to put it mildly.

So, who does he rely on to construct a definition of the New Atheists?

The ideas I claim are distinctive of the new atheists have been collected from Richard Dawkins, Sam Harris, Christopher Hitchens, Jerry Coyne, the American physicist Robert L. Park, and a couple of blogging biologists, P Z Myers and Larry Moran. They have two things in common. They are none of them philosophers and, though most are scientists, none study psychology, history, the sociology of religion, or any other discipline which might cast light on the objects of their execration. All of them make claims about religion and about believers which go far beyond the mere disbelief in God which I take to be the distinguishing mark of an atheist.

That's very distinguished company. I'm flattered. I guess it means I'll have to take the quiz!

Quiz? Yes, that's right, Andrew proposes that we atheists 'fess up to six propositions that represent the New Atheist position, or at least the Andrew Brown version of New Atheism.

All of these propositions will be found in the authors I have cited as well as in the comments to religious articles here. I sometimes think that only the last two are unique to the new atheists: you can certainly find the others in earlier authors. But those are the six doctrines which I would reject when saying rude things about the new atheists.

What would be interesting in comments is if people would score themselves out of six. I expect that one of the most common forms of disagreement would be to claim that you are a three or a four, but none the less the believers are so repulsive and dangerous that the other two points just don't matter. That's how politics works, after all, and the new atheism is interesting as a political or social movement, not an intellectual one.

Challenge accepted.

Here are the six propositions and my position on each of them.

1. There is something called "Faith" which can be defined as unjustified belief held in the teeth of the evidence. Faith is primarily a matter of false propositional belief.

I agree.

2. The cure for faith is science: The existence of God is a scientific question: either he exists or he doesn't. "Science is the only way of knowing – everything else is just superstition" [Robert L. Park]

I agree, as long as we understand that science is a way of knowing that relies on evidence and rationality. The other, undefined, ways of "knowing" will reject either evidence or rationality.

The question before us is whether supernatural beings exist or not. I fail to see why a scientist isn't as competent to answer that question as those who study "psychology, history, the sociology of religion, or any other discipline which might cast light on the objects of their execration." The object of my attention (not execration) is supernatural beings. Why would a psychologist or a sociologist know more about their possible existence than I do?

3. Science is the opposite of religion, and will lead people into the clear sunlit uplands of reason. "The real war is between rationalism and superstition. Science is but one form of rationalism, while religion is the most common form of superstition" [Jerry Coyne] "I am not attacking any particular version of God or gods. I am attacking God, all gods, anything and everything supernatural, wherever and whenever they have been or will be invented." [Dawkins]

I agree, except for the minor quibble that science is not the opposite of religion. Religion is a set of beliefs based almost exclusively on the worship of supernatural beings. I think that religion is silly because these supernatural beings do not exist. Belief in such beings is not the opposite of the scientific way of knowing: it is outside of the scientific way of knowing. Such beliefs are based on some other, undefined, way of knowing that we may refer to as superstition for want of a better term.¹ The battle is between rationalism and superstition.

4. In this great struggle, religion is doomed. Enlightened common sense is gradually triumphing and at the end of the process, humanity will assume a new and better character, free from the shackles of religion. Without faith, we would be better as well as wiser. Conflict is primarily a result of misunderstanding, of which Faith is the paradigm. (Looking for links, I just came across a lovely example of this in the endnotes to the Selfish Gene, where lawyers are dismissed as "solving man-made problems that should never have existed in the first place".)

I agree.

5. Religion exists. It is essentially something like American fundamentalist protestantism, or Islam. More moderate forms are false and treacherous: if anything even more dangerous, because they conceal the raging, homicidal lunacy that is religion's true nature. [Sam Harris]

I don't agree with all of this. While it's true that even moderate forms of religion are based on the irrational belief in non-existent beings, that only makes them false—not treacherous, and certainly not homicidal. Most modern religions are trying to promote good things that I support. The mistake theists make is in assuming that you have to believe in non-existent beings in order to be good.

6. Faith, as defined above, is the most dangerous and wicked force on earth today and the struggle against it and especially against Islam will define the future of humanity. [Everyone]

Nonsense. We will be better off when people abandon their belief in supernatural beings but that's a far cry from saying that such superstitious beliefs are the most dangerous and wicked force on Earth.²

I have never singled out Islam for special attention. As a matter of fact, I am very much opposed to characterizing the current struggles as a war between Islam and Christianity. I may not be an historian but I know enough history to understand that Islam has a solid track record of tolerance and understanding. Probably a better record than Christianity.

What's my score? I agree with the first four propositions and disagree with the last two. I guess that means I'm not a true New Atheist. I should have known that those other guys were too good for me.

Oops, PZ only gives himself 2 out of 6 [Oh, no! The New Atheists are getting attacked again!]. I guess I'm more of a New Atheist than he is. Go figure.

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1. I anxiously await Andrew Brown's next essay when he defines the New Theism and reveals to us these other ways of thinking.

2. Earth, the planet, begins with an upper-case letter, just as the names of all the other planets do.

[Hat Tip: Richard Dawkins.net]

On Darwin and Atheism, by Richard Dawkins

 
Richard Dawkins posts a comment about an article written by Madeleine Bunting [Darwin shouldn't be hijacked by New Atheists - he is an ethical inspiration]. She repeats the rather boring complaint that the "New Atheists" are about to hijack the 2009 celebrations.

She says,

In particular, what would have baffled Darwin is his recruitment as standard bearer for atheism in the 21st century. Darwin kept his pronouncements on religion to a minimum, partly out of respect for his Christian wife. Despite continuing claims that he was an atheist, most scholars acknowledge that he never went further than agnosticism.

Richard Dawkins replied ...

It is true that Darwin declined to call himself an atheist. But his motive, clearly expressed to the atheist intellectual Edward Aveling (incidentally the common-law husband of Karl Marx's daughter) was that Darwin didn't want to upset people. Atheism, in Darwin's view, was all well and good for the intelligentsia, but ordinary people were not yet "ripe" for atheism. So he called himself an agnostic, largely for diplomatic reasons..

In any case, what Darwin chose to call himself, as a pillar of his local parish in the nineteenth century, is of less interest than the cogency of the arguments themselves. Before Darwin came along, it was pretty difficult to be an atheist, at least to be an atheist free of nagging doubts. Darwin triumphantly made it EASY to be an intellectually fulfilled and satisfied atheist. That doesn't mean that understanding Darwin drives you inevitably to atheism. But it certainly constitutes a giant step in that direction.

I stand with Dawkins¹ except that I would include all of the modern scientific advances as additional facts that make it easy to be an atheist and difficult to believe in supernatural beings.

Science doesn't turn you into an atheist but it sure as heck poses a severe challenge to most established religions. That's why religions fear science.

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1. On the issue of superstition vs. rationality, I'm in (almost) complete agreement with Richard Dawkins and I admire him greatly for writing The God Delusion. On the issue of evolutionary theory, I'm not in complete agreement.

An Adaptationist View of Stephen Jay Gould

In last week's issue of Nature, Steve Jones reviews Stephen Jay Gould: Reflections on His View of Life. Jones is part of the British school of Darwinism, along with Richard Dawkins, the late John Maynard Smith, and others.¹ This group shares many perspectives on evolutionary theory including an emphasis on natural selection. They are also united in their dislike of, and misunderstanding of, Stephen Jay Gould.

The misunderstanding shows up in several places in the Jones review [A wonderful life by leaps and bounds].

Being part of the anti-Gould school means that Jones is obliged to trot out the famous quotation by Maynard Smith (it's part of their oath of allegiance).

Gould held fast to Darwin's maxim that "All observation must be for or against some view if it is to be of any service", and was among that band who felt that those not for him must be against him — which was not much help in keeping friends. The great biologist John Maynard Smith wrote that most evolutionists saw Gould as "a man whose ideas are so confused as to be hardly worth bothering with, but as one who should not be publicly criticized because at least he is on our side against the creationists".

Gould was hurt by that acidulous statement, which was without doubt unfair.

Of course it was unfair—so why repeat it? The statement says more about the British Darwinists than about Gould. The fact that they find Gould's ideas "confusing" isn't something to be proud of.

One of Gould's major contributions to evolutionary theory was punctuated equilbiria, with Niles Eldredge. The basic idea is that the fossil record shows millions of years of stasis (no change) and when change occurs it takes place relatively quickly during speciation by cladogenesis (splitting). After that, the two species (parent and daughter) continue to exist together in the same environment.

The morphological changes that occur when a new species is formed are not dramatic. They are similar to the differences between closely related modern species. In many cases it takes an expert to even recognize the new species in the fossil record.

Punctuated equilibrium is a theory of speciation and stasis. The changes during speciation may be due to natural selection or some form of random genetic drift. That's not what's important about punctuated equilbria—what's important is that change is coupled to speciation and nothing happens for most of the life of a species.

Here's what Steve Jones has to say about it.

Whatever the importance of sudden leaps in the fossil record, his notorious idea of punctuated equilibria, nicknamed 'punk eek' and referred to as 'evolution by jerks' by some of its critics — their own views characterized by Gould as "evolution by creeps" — gave the fossilized field of palaeontology a much-needed kick in the pants. Gould saw punk eek as a "coordinating centrepiece" that "congealed into a coherent critique" of evolutionary theory. Many biologists, by contrast, insist that what look like palaeontological leaps can be explained by simple Darwinism. To them, an instant in geology may represent almost an infinity in biology, leaving plenty of time for evolution by natural selection to do its normal job.

He just doesn't get it, does he? The speciation event takes place over a period of about one hundred thousand years as Gould and Eldredge explained. That's plenty of time for selection, or drift, or founder effect, or whatever. Punctuated equilibria is not a challenge to natural selection, it's a challenge to gradualism.

Furthermore, anyone who refers to punctuated equilibria as "sudden leaps" is revealing an understanding of the theory that's no better than that of the creationists. As is anyone who thinks that "Darwinism" explains speciation.

His other great passion, contingency — the notion that evolution goes on with sudden bangs rather than protracted whimpers — has also not held up particularly well. Wonderful Life, Gould's 1989 book on the Burgess Shale, suggests that the obscure fauna of the late pre-Cambrian represents a lost universe wiped out by some unknown disaster, but now we know that they have descendants among modern animals. Even so, scientific ideas often change, and that volume, like most of his others, remains a rattling good read. The fact that nature must build on what it has, and not on what it wants, is still at the centre of evolutionary thinking.

Talk about confused thinking! When did Gould ever say that contingency is "the notion that evolution goes on with sudden bangs"?

Gould and Lewontin made great play with the parallels between the Spandrel School and the many evolutionists who say that every character in every animal is there for an adaptive reason and if you look hard enough you'll find it.

There's some truth in their argument, but to accept it as the only truth is basically to give up and walk away, to stop being an ornithologist and turn into a bird-watcher. You become somebody who observes rather than analyzes. What they're saying to lots of biologists is, "Abandon hope, go home, and become a liberal-arts graduate!" I may be overcriticizing the Lewontin and Gould view; both of them like to poke people with their sharp pitchforks. The spandrels were a particularly successful poke. But what happened as a result of the famous spandrel paper? The answer is, not much.

Steve Jones in
The Third CultureAs for Wonderful Life, it is, indeed, a book about contingency—just like the movie from which it takes its title. One wonders whether Steve Jones has actually read the book, or seen the movie.

While it's true that some of the unusual Cambrian species that Gould once thought were separate phyla have now been lumped into modern phyla, it's also true that there are many that haven't. Gould's point is that some of those enigmatic Burgess Shale species have left no descendants and, if you could have observed them back then, you would not have been able to pick out the eventual winners and losers. In other words, if you re-wind and replay the tape of life it will come out differently.

Jones is not referring to these species however. He's talking about the "pre-Cambrian" fauna—presumably the Ediacara biota. It's not an important part of Gould's book. As far as I know the relationship between Ediacaran species and modern species is still very controversial. Perhaps Jones has studied this in more detail that I have.

One of the ideas to come out of punctuated equilibria is the idea of species sorting. This makes sense when you think about it. If most speciation occurs by cladogenesis and not by gradual transformation, then over time the number of species in a clade doubles every five to ten million years. Eventually there will be hundreds of similar species. The reason this doesn't happen is that species go extinct. They die.

If species within a clade are "born" and "die" then this looks an awful lot like evolution at a different scale than the birth and death of individuals within a population. The idea of species sorting, where the species in a clade are treated like the individuals within a population, is part of Gould's hierarchical theory of evolution. He claims that it is an extension of the Modern Synthesis.

Whether he's right or wrong doesn't matter. What matters is whether his critics have the intelligence to understand hierarchical theory in general, or species sorting in particular. I don't have much respect for evolutionists who refuse make a modest attempt to understand; it's not rocket science.

Here's what Steve Jones says.

Backwards ran his sentences, and some of his ideas were equally opaque. In support of punk eek, for example, he wrote that "species are individuals ... by all vernacular criteria", which is at best obscure, and at worst obscurantist.

No, Professor Jones, it is not obscure and it is not obscurantist. Gould explains it very well to those who can read his works with an open and intelligent mind. He's talking about species sorting and treating species as "individuals" that are selected within a clade.

As Reflections portrays, its hero showed an increasing regard for style over content, and was resistant to the notion that anyone should dare to edit his writings. The pinnacle — the very summit, crown and peak — of his great Olympus of orotundity was his last voluminous volume, The Structure of Evolutionary Theory, published in the year of his death. All the authors agree that this is not a book to be lightly tossed aside, but their motives for saying so vary. Its reviews are quoted with a certain relish: "an elephantine opus"; "pathological logorrhea"; "billowing clouds of verbal flatulence" — but Gould had no doubt of its value. In it he came out with the idea of life as a series of interlocking hierarchies and of a grand unification of its sciences into some post-Darwinian consilience, comprehensible only to the chosen.

The Structure of Evolutionary Theory is long and tedious but those who criticize its ideas are the ones who confuse style over content. I don't agree with many of Gould's ideas about species sorting and hierarchical theory and therefore I stand as the exception to Steve Jone's claim. It was comprehensible to this unchosen one so it must also be comprehensible to others who disagree with Gould. You just have to make the effort.

If you don't make the effort to understand Gould then you should refrain from criticizing him. It doesn't make you look good.

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1. For examples of the Steve Jones perspective on evolution see Have Humans Stopped Evolving? and Steve Jones Says Human Evolution Is Over.

[Image Credit: The Cheltenham Ladies' College]

"Monkey Girl" and False Icons

 
Monkey Girl: Evolution, Education, Religion, and the Battle for America's Soul is a book about the Dover trial. It's written by Edward Humes, an ex-newspaper journalist turned author.

The cover of the book shows one of the common, but false, icons of human evolution. This series of skeletons depicts a steady upward march of human evolution from a chimpanzee to modern humans. The image is false in two ways: (1) humans did not evolve from something that looks like modern chimpanzees, and (2) the "progress" was not a linear transformation as depicted, instead, there where many side branches and lineages that went extinct.

This is the icon that Stephen Jay Gould attacked in Wonderful Life and elsewhere in his essays. Even the Intelligent Design Creationists recognize that this is a bad way to depict evolution. Casey Luskin writes in A Partisan Affair (Part 2): False Attacks Upon Discovery Institute in Edward Humes’ Pseudo-History of Kitzmiller, "Monkey Girl".

Any book with an icon of evolution on its cover — in this case, the fanciful diagram of ape-like skeletons transitioning into a human skeleton — is bound to be unfriendly towards intelligent design (ID).

For once I agree with Casey Luskin!!!! The diagram is a fanciful "icon" and the book is unfriendly towards creationists.

I realize that trade book authors don't get much say in cover design but that has to change. I urge all authors to insert a clause in their contracts that requires approval of the cover design and title. Let's try and prevent future embarrassments of this sort.

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If Spiders Are Arthropods then Where Are the Segments?

 
Christopher Taylor of Catalogue of Organisms has the answer [Attercop].

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[Image Credit: Commonwealth Scientific and Industrial Research Organisation (CSIRO)]

Trouble with Blogger

 
I'm pretty happy with Blogger, most of the time.¹ However, every now and then the powers that be meddle with the code and screw up a feature that we've come to rely on. I don't understand why this happens—you'd think they would test all their changes before implementing them.

A few weeks ago Blogger decided to mess with the RSS feeds and other things. The changes had two obvious effects: I can no longer detect links to my blog via Technorati, and recent comments are stuck on old comments (June 20, 2007).

Blogger has a "Help Group" forum where you can post about problems with Blogger. There are hundreds of postings—most of them concern mistakes made by the users, many of whom don't read instructions very well. The thread concerning the RSS feed [Problem with the comments feed] was begun on December 19th, shortly after the problem first appeared. On December 21 the Blogger team indicated that they were aware of the problem.

Thanks for the heads up folks! We're looking into this right now and hope to have this sorted out shortly.

We'll make sure to update this thread when we have some news to pass along. Thanks for your patience,

Gatsby
The Blogger Team

As of today (Dec. 30) it still hasn't been fixed.

Why is it taking so long to fix a problem that they created in the first place?

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1. After all, it's free. I shouldn't complain about such an excellent service at such a low price. (But I will anyway.)

Recreational Mathematics

 
Ms. Sandwalk has discovered a new game called Blokus. I recommend it highly.

She has a description of the game on her blog and an explanation of "polyominoes"—a term used in recreational mathematics. What she didn't put on her blog is her reaction on discovering that some people think that mathematics can be recreational!!

Incidentally, she hasn't yet won a game of Blokus. This makes up for all the times when she beats me at word games.

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Philosophers and the Existence of God

 
The existence of God is one of the exciting questions in philosophy. I firmly believe that all undergraduates should take a course in philosophy where they address issues like this and learn how to argue logically and rationally. Philosophy is the most important subject in university.

However, sometimes philosophers seem to get so badly off track that they fail to see the forest for the trees. The debate over the ontological argument for the existence of God falls into this category. I can't believe that modern philosophers would waste more than a microsecond on such a stupid argument.^1.

Here's one version of the argument from Wikipedia.

1. God is, by definition, a being greater than anything that can be imagined and is the cause of all things, but is not bound causally by anything (otherwise God would be ontologically dependent on something else which would in turn undermine "its" greatness).
2. Existence both in reality and in imagination is greater than existence solely in one's imagination.
3. Therefore, God must exist in reality: if God did not, God would not be a being greater than anything which can be imagined.

Alex Byrne wastes far more than a microsecond in the latest issue of Boston Review [God: Philosophers weigh in]. Check it out if you want to wade through some mind-numbing examples of tree-gazing. (There are other interesting bits in the article that might make it worth your while.)

Part way through that article, Byrne decides that philosophical arguments in general, and arguments for the existence of God in particular, are often not very significant. He says the following ...

A better complaint is that sound philosophical arguments with significant conclusions are as rare as atheists in foxholes: the track record of philosophical “proofs” is not exactly impressive, unlike the mathematical variety.

What the heck?

There have been millions of atheists in (metaphorical) foxholes throughout history. Does this mean there are millions of sound philosophical arguments with significant conclusions? Or does it mean that Alex Byrne is one of these people who think that atheists becomes believers whenever they're under stress, in spite of the fact that there are no sound arguments for the existence of God?

What a strange thing for a philosopher to say.

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1. It's fun to debate the logic of the ontological argument and to try and construct proofs that it is false. That's not what I mean when I say that it's a stupid argument. What I mean is that it is stupid to actually think that such a clever twisting of words would actually cause someone to believe that a perfect supernatural exists.

[Hat Tip: RichardDawkins.net]

On the Origin of Eukaryotes

 
Theme

The Three Domain Hypothesis
If all you do is read the textbooks, you would think that the origin of eukaryotic cells has been discovered. Most textbooks describe the Three Domain Hypothesis as a done deal. Eukaryotes and archaebacteria share a more recent common ancestor than either group does with the remaining groups of bacteria. Thus, eukaryotes arose from archaebacteria.

The scientific literature does not reflect this confidence. In fact, there is general agreement that the classic Three Domain Hypothesis is no longer viable as a complete explanation for the origin of eukaryotic cells. The current consensus favors a more confused picture of early life with lots of gene swapping—the so-called web of life. It is not clear that eukaryotes as a group arose from any particular prokaryotic clade. It is likely that in addition to horizontal gene transfer, there were probably one or more fusion events where the cells from two separate lineages united to form a hybrid.¹

This week's issue of the Proceedings of the National Acedemy of Sciences (USA) has a paper that addresses the problem, one more time. Cox et al. (2008) ask whether there is phylogenetic support for the Three Domain Hypothesis by analyzing 53 well conserved genes. The answer is no. But is there support for one of the alternatives, the Eocyte Hypothesis? The answer is, maybe.²

The commentary by John Archibald is worth reading. Here's an excerpt.

Evolving Views on the Tree of Life

Next to life itself, the origin of complex cells is one of the most fundamental, and intractable, problems in evolutionary biology. Progress in this area relies heavily on an understanding of the relationships between present-day organisms, yet despite tremendous advances over the last half-century scientists remain firmly divided on how to best classify cellular life. Many adhere to the textbook concept of 2 basic types of cells, prokaryotes and eukaryotes, as championed by Stanier and van Niel (7). Others posit that at its deepest level life is not a dichotomy but a trichotomy comprised of cells belonging to the domains Bacteria, Archaea, and Eukarya, each monophyletic and sufficiently distinct from one another to warrant equal status (5, 8). The conceptual and practical challenges associated with establishing a genealogy-based classification scheme for microbes have been fiercely debated for decades (see ref. 9 for recent review), and the literature is rich in philosophy and rhetoric.

The genomics revolution of the 1990s brought tremendous optimism to the field of microbial systematics: if enough genomes from diverse organisms could be sequenced and compared, definitive answers to questions about evolutionary relationships within and between eubacteria, archaebacteria, and eukaryotes would surely emerge. More specifically, it should be possible to discern how eukaryotes evolved from prokaryotes (if indeed that is what happened), and perhaps even who among modern-day prokaryotic lineages is our closest ancestor. Unfortunately, with the sequences of hundreds of eubacterial, archaebacterial, and eukaryotic genomes has come the realization that the number of universally distributed genes suitable for global phylogenetic analysis is frustratingly small (10). Lateral (or horizontal) gene transfer has shown itself to be a pervasive force in the evolution of both prokaryotic and eukaryotic genomes, and even if a “core” set of genes can be identified (and there is much debate on this issue), how confident are we that the phylogenetic signal in these genes reflects the vertical history of cells? How meaningful are sequence alignment-independent, gene content-based approaches to resolving the “tree of life” (11)? To what extent is a “net of life” a more accurate and useful metaphor for describing the full spectrum of life on Earth (10, 12–14)?

The bottom line is that the earliest stages of evolution are still very much open questions. It is wrong to assume that the Three Domain Hypothesis is correct and scientists, as well as textbooks writers, should stop making this assumption.

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1. Most workers make the unstated assumption that eukaryotic cells are more recent than prokaryotic cells. The idea that archaebacteria could have arisen by a fusion of an early eukaryote with an early prokaryote is just as consistent with most of the data yet this possibility is almost never discussed.

2. Cox et al. use very "sophisticated" techniques for analyzing their sequence data. Much of the controversy in this field involves disputes over which computer programs give the most accurate results. What's really going on, in my opinion, is that the data isn't good enough to justify the kinds of manipulations that are being done. The trees give you a good approximation of the true phylogeny but subjecting the data to over-analysis isn't helpful.

Archibald, J.M. (2008) The eocyte hypothesis and the origin of eukaryotic cells. Proc. Natl. Acad. Sci. (USA) 105:20049-20050. [doi:10.1073/pnas.0811118106]

Cox, C.J., Foster, P.G., Hirt, R.P., Harris, S.R., and Embley, T.M. (2008) The archaebacterial origin of eukaryotes. Proc. Natl. Acad. Sci. (USA) 105:20356-20361. [doi:10.1073/pnas.0810647105].

My Christmas Jigsaw Puzzle

 
According to Wikipedia, the first commercial jigsaw puzzles were marketed in England by John Spilsbury in 1760.

I haven't been putting them together for nearly that long. Every Christmas we buy a jigsaw puzzle and try to assemble it before the end of the holidays. Ms. Sandwalk usually gives up after the first day.

Do you know what "tessellation" means?

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Pop Evolutionary Psychology

 
David J. Buller is a Professor of Philosophy at Northern Illinois University (USA). He is an expert in his field, He is not a professional science journalist although he has written a book and many articles.

This is relevant because many science journalists have written favorable articles about popular evolutionary psychology. This is the field that promotes evolutionary explanations for many human behaviors. They are the classic examples of adaptationist just-so stories.

Buller has just published an article in Scientific American where he argues against these popular stories [Evolution of the Mind: 4 Fallacies of Psychology].

Here's part of what he says ...

Some evolutionary psychologists have made widely popularized claims about how the human mind evolved, but other scholars argue that the grand claims lack solid evidence

...

The most notable representatives of Pop EP are psychologists David M. Buss (a professor at the University of Texas at Austin and author of The Evolution of Desire and The Dangerous Passion) and Steven Pinker (a professor at Harvard University whose books include How the Mind Works and The Blank Slate). Their popular accounts are built on the pioneering theoretical work of what is sometimes referred to as the Santa Barbara school of evolutionary psychology, led by anthropologists Donald Symons and John Tooby and psychologist Leda Cosmides, all at the University of California, Santa Barbara.

According to Pop EP, “the human brain consists of a large collection of functionally specialized computational devices that evolved to solve the adaptive problems regularly encountered by our hunter-gatherer ancestors” (from the Web site of the Center for Evolutionary Psychology at U.C.S.B.). Just as evolution by natural and sexual selection has endowed all humans with morphological adaptations such as hearts and kidneys, Pop EP says, so it has endowed all humans with a set of psychological adaptations, or “mental organs.” These include psychological mechanisms, or “functionally specialized computational devices,” for language, face recognition, spatial perception, tool use, mate attraction and retention, parental care and a wide variety of social relations, among other things. Collectively, these psychological adaptations constitute a “universal human nature.” Individual and cultural differences are, by this account, the result of our common nature responding to variable local circumstances, much as a computer program’s outputs vary as a function of its inputs. The notable exceptions to this rule involve sex differences, which evolved because males and females sometimes faced distinct adaptive problems.

Moreover, because complex adaptation is a very slow process, human nature is designed for the hunter-gatherer lifestyle led by our ancestors in the Pleistocene (the period from 1.8 million to 10,000 years ago). As Cosmides and Tooby colorfully say, “our modern skulls house a Stone Age mind.” Pop EP proposes to discover our universal human nature by analyzing the adaptive problems our ancestors faced, hypothesizing the psychological mechanisms that evolved to solve them and then testing those hypotheses using standard-fare psychological evidence, such as paper-and-pencil questionnaires. Pop EP claims that a number of psychological adaptations have been discovered in this way, including evolved sex differences in mate preferences (males prefer nubility; females prefer nobility) and jealousy (men are more distressed by a mate’s sexual infidelity, women by emotional infidelity).

I believe that Pop EP is misguided. The ideas suffer not so much from one fundamental flaw as from many small mistakes. Nevertheless, recent critiques of evolutionary psychology point to some general problems of Pop EP.

There's nothing remarkable about this article. The majority of evolutionary biologists know full well that pop evolutionary psychology is a farce. For most biologists, it's an embarrassment.

The real puzzle is why most science journalists seem to be completely unaware of the controversy. They haven't been doing their job. Next time you see an article promoting the "latest discoveries" of pop evolutionary psychology look for the balance. Do you see the disclaimers questioning the relevance of the entire field? If those points aren't mentioned then you know that science journalists have not done their homework.

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Top Ten Intelligent Design Creationist Stories

 
Denyse O'Leary is one of the best of an excellent group of science journalists.¹ When she selects her top ten science stories of 2008 it's time to pay attention, especially since these are stories about Intelligent Design Creationism [The top ten Darwin and Design stories of the year.

Here's the list ...

The Altenberg 16
Atheists and Agnostics Defend ID
Expelled #1 Political Documentary of 2008
Louisiana Academic Freedom Act
Biologic Institute Releases Stylus: A System for Evolutionary Experimentation
A Molecular Clutch Discovered in the Flagella
Royal Society Expels Director of Education
Leading Biologists Marvel at the "Irreducible Complexity" of the Ribosome
Have Cosmologists Lost Their Brains?
Design-based Biomimetics Yields Tangible Results

What a sad list.

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1. Not. I wonder what George Johnson thinks of science journalists like Denyse O'Leary?

The "Best" of Genetics Science Writing from New Scientist

 
The blogosphere is discussing the conflict between scientists and science journalists. The issue is not whether science journalists can write for the general public—I take that as a given—it's whether what they write is scientifically accurate. Do articles by science journalists fairly represent the state of science?

New Scientist has risen to the challenge by listing it's top ten article on genetics [Genetics: Top 10 articles from 2008.

Here's the list of titles. Judge for yourselves.

Me and my genome
DNA dating: Can genes help you pick a mate?
Genes make mice squeal during sex
Are political leanings in the genes?
Cloning 'resurrects' long-dead mice
Genetically modified humans: Here and more coming soon
MicroRNAs: The cell's little emperors
Solar-powered sea slug harnesses stolen plant genes
Cancer special: Living with the enemy
Goldmine bug DNA may be key to alien life

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Webpages as Graphics for Sandwalk

 
Here's the Webpages as Graphics for this blog. I have no idea what this means.

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Who the Heck Is George Johnson?

 
A few weeks ago I wrote about Epigenetics at SEED. The article in SEED was written by a scientist who wants to change evolutionary theory in order to accommodate epigenetics. I pointed out that this was a poorly written article. One of the worst problems was the definition of epigenetics, which was broad enough to include the kitchen sink.

Abbie Smith picked up on this on her blog ERV. She agreed that the SEED article was not helpful [ew... epigenetics in SEED...].

Along comes someone named George Johnson. He interprets Abbie's criticism of the science, and mine, as a rant against science journalism. Well, he's right, even though in this case it's science journalism being written by a scientist. Apparently science journalists (I assume George Johnson is one) are very sensitive about criticism from scientists. Apparently science journalists are very good at what they do ... how dare scientists criticize what they write about science!!!

Watch George Johnson make a fool of himself on this bloggingheads video with John Horgan. Johnson reads my name from the ERV posting but it seems he didn't bother to read my posting. If George Johnson has the courage to show up here I'll be happy to explain to him why this particular SEED article is bad. He's welcome to read all my other criticisms of science journalism and and attempt to defend the science journalists.

Pay close attention to Johnson's comments when he reads the passage from Abbie's blog. It's clear that he doesn't know what chromatin is and he doesn't know what epigenetics is. On the other hand, he is certain that Nicholas Wade, who writes about molecular biology, is a great science writer. How would George Johnson know this? Johnson may be able to tell whether Nicholas Wade is a good writer but he sure isn't in a position to judge whether he's a good science writer since the most important thing about science writing is accuracy and Johnson knows nothing about molecular biology.

This may be one of the biggest problems with science writers. They can't tell the difference between science and writing. And they don't like it when scientists point this out to them.

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Name That Research Scientist

 
I'd love to know the name of this "research scientist" and the name of the pharmaceutical company he works for.

From DonaldM at Uncommon Desent:

Today, I had the privilege to have lunch with a research scientist who works in the area of bio-pharmaceuticals for a pharmaceutical company. He told me about their research with proteins and genes that enable them to develop products that alleviate or cure a wide range of diseases at the cellular level. Of great value to the research they do was the Human Genome Project because it made available the entire database to whoever needed it. That information enabled them to move several projects forward.

He knew from our conversation that I had been involved in the Intelligent Design/Evolution debate, so I asked him what role evolution played in all thier research. Now, this is a research facility that is carrying on a huge number of projects across a number of areas in cellular biology, bio-chemistry, hemotology, oncology and other related areas. He said that evolution plays no role whatsoever in their research and that evolutionary theory doesn’t make one whit of difference to the outcome of any of their research projects and never has. To clarify, I said, "so the heuristic value of evolutionary theory to your biological research is…." and he answered "Nil!".

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Center for Inquiry World Congress 2009

 

The Center for Inquiry's 12th World Congress:
Science, Public Policy, and the Planetary Community
April 9-12, 2009
Bethesda, MD Hyatt Hotel (just outside of Washington, DC)

2009 marks the bicentennial of both Charles Darwin's and Abraham Lincoln's birth and the 150th anniversary of the publication of On the Origin of Species. There can be no more fitting opportunity to discuss and consider the appropriate relationship between science and public policy. Please join us as scientists and scholars from around the world analyze the role of science, explain how it works, explore its connection to public policy, and examine its significance for the global community.

Speakers
Norm Allen
Mona Abousenna
Tom Beauchamp
Roger Bonnet
David Contosta
Austin Dacey
Tarek Fatah
Barbara Forrest
Ren Fujun
Christopher Hitchens
Pervez Hoodbhoy
Leo Igwe
Philip Kitcher
Lawrence Krauss
Paul Kurtz
Ronald A. Lindsay
Elizabeth Loftus
John C. Mather
Joe Nickell
James Randi
Michael Ruse
Armadeo Sarma
Patricia Scott Schroeder
Drew Shindell
Eleanor Smeal
Eddie Tabash
Floris van der Berg
Toni Van Pelt
Ibn Warraq
Mourad Wahba
Richard Wiseman

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Student Perceptions of "The Spandrels of San Marco"

 
Hopeful Monster asked his senior biology majors to read "The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme." [Student perceptions of San Marco].

I think he was disappointed.

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How Women Got Their Menopause

The December 13 issue of New Scientist has an article about the evolution of menopause in humans [Are daughters-in-law to blame for the menopause? ]. The author is Alison Motluk, the Toronto corresponent for New Scientist.

She begins with ..

IT FLIES in the face of natural selection, yet in humans it seems fixed and universal: at around age 50, not far past the midpoint of life, normal healthy women lose their capacity to bear children. Following a decade of gentle winding down, the whole reproductive system screeches to a halt. It is as though, after a few years of wearing bifocals, all women suddenly went blind.

Menopause is a mystery. It leaves women with 20, 30, perhaps even 50 years of life - squandered time in evolutionary terms, because no further genes can be passed on. Yet the selection pressure for menopause must have been strong: there are no known pockets of women around the world who do not go through it. All the evidence suggests menopause has been around a long time, and that the age at which it hits has changed little. Increased longevity seems not to have budged our closing hours. Nor, apparently, has lifestyle; it hits hunter-gatherers at pretty much the same age as hip New Yorkers.

The search for an adaptive explanation for menopause has been going on for over fifty years.

The most common just-so story is called the "Grandmother Hypothesis." It imagines a time in the distant past when humans females were fertile until the day they died, which for 75% of women who survived childhood was before the age of 30 according to a recent study. A mutation arose in one individual and the effect was to induce menopause, or sterility, at about age 50. This new mutation proved to be so beneficial that it spread throughout the species. Today every woman undergoes the pain and frustration of menopause.

Why was it so beneficial? Because post-menopausal women whose partners were still alive could invest their time in looking after their grandchildren instead of having more children of their own.

To its credit, the New Scientist article reviews the latest work on the Grandmother Hypothesis and concludes, correctly, that the effect on ancient hunter-gather societies could not possibly have been significant enough to be adaptive.

The same reasoning applies to the "Mother Hypothesis," which claims that by going through menopause a mother will avoid the risks of future childbirths enabling her to concentrate on raising her existing children. Both of these hypotheses assume that "just saying no" was not a reasonable strategy in ancient societies and that's why menopause was necessary.

So what's the alternative if you are committed to an adaptive just-so story? You are going to be shocked ... menopause evolved to benefit daughters-in-law!!! (Our daughter-in-law will be so pleased.)

I'm not even going to dignify such a stupid idea by pointing out the obvious flaws.

In case you haven't clued in by now, the bottom line is that all these hypotheses are flawed from the get-go because they all make the unnecessary assumption that the pain and suffering of menopause are adaptive. What if they aren't? What if menopause is neutral with respect to evolution or even maladaptive? What's the point of making up irrational just-so stories when there's no evidence to suggest that menopause has any positive effect of fitness?

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Get a Job

 

Assistant Professor, Tenure Stream
Dept. of Cell & Systems Biology
University of Toronto

The Department of Cell & Systems Biology at the University of Toronto invites applications for a tenure track faculty position to be appointed at the Assistant Professor level in the field of Systems Biology to begin July 1, 2009.

We particularly encourage applications from candidates who have demonstrated excellence in addressing fundamental questions in biology using high-throughput approaches or gene/protein network analyses with bioinformatic, genomic, proteomic, or imaging tools. Our vision is to advance systems biology-based research, with a specific interests in developing expertise in systems neurobiology, but we welcome applicants from all others areas of systems biology which complement existing strengths in the department (www.csb.utoronto.ca).

Candidates should have at least two years of research experience beyond their doctoral degree. In addition to pursuing a vigorous, internationally-recognized research program, the successful candidate will contribute to undergraduate and graduate teaching in the molecular life sciences. The successful candidate would also be expected to network with researchers university-wide to take advantage of the extensive resources in systems biology at the University of Toronto and its affiliated institutions. A generous start-up package will be provided. Salary will be commensurate with qualifications and experience.

We encourage qualified applicants to submit their applications online at: www.jobs.utoronto.ca/faculty.htm. Applicants should submit their curriculum vitae, copies of significant publications, and statements of research and teaching interests. Applicants should also arrange for three confidential letters of recommendation to be sent directly to: Professor Daphne Goring, Chair, Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada; or by email to search@csb.utoronto.ca by January 31, 2009.

The University of Toronto offers the opportunity to teach, conduct research and live in one of the most diverse cities in the world, and is responsive to the needs of dual career couples. The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, members of sexual minority groups, and others who may contribute to the further diversification of ideas.

All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority.

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Poinsettias Are Poisonous

 
Friday's Urban Legend: False

From 6 Medical Myths Debunked For Christmas.

Dr. Vreeman and Dr. Carroll found that the largest study of poinsettia "toxicity" to date involved an analysis of 849,575 plant exposures reported to the American Association of Poison Control Centers. None of the 22,793 poinsettia cases revealed significant poisoning. No one died from poinsettia exposures or ingestions, and more than 96 percent did not even require treatment in a health care facility. Another study, looking at poinsettia ingestion by rats, could not find a toxic amount of poinsettia, even at doses which would be the human equivalent of consuming 500-600 poinsettia leaves or a pound and a half of the plant's sap. Dr. Vreeman cautions, though, that you should always call a poison control center if someone eats a plant not intended for consumption.

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Suicides Increase Over the Holidays

 
Friday's Urban Legend: False

From 6 Medical Myths Debunked For Christmas.

The holidays can bring out the worst in people, and the stresses of family get-togethers, loneliness, and the cold, dark winter months are commonly thought to increase the number of suicides at Yule time. But studies conducted around the globe show that, while the holidays may be a difficult time for some, there is no scientific evidence to suggest a holiday peak in suicides, according to Dr. Vreeman and Dr. Carroll. Furthermore, suicides are actually more common during warm and sunny times of the year.

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Sugar Makes Kids Hyperactive

 
Friday's Urban Legend: False

From 6 Medical Myths Debunked For Christmas.

This is without a doubt false, report Dr. Vreeman and Dr. Carroll, who are both pediatricians at Riley Hospital for Children. They write that "in at least 12 double-blinded, randomized, controlled trials, scientists have examined how children react to diets containing different levels of sugar. None of these studies, not even studies looking specifically at children with attention deficit-hyperactivity disorder, could detect any differences in behavior between the children who had sugar and those who did not." This includes sugar from candy, chocolate and natural sources. Even in studies of children who were considered "sensitive" to sugar, children did not behave differently after eating sugar-full or sugar-free diets.

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Let's Count the Ways a Creationist Can Go Wrong

 
The latest posting on Uncommon Descent tries to undermine the concept of a natural origin of life [Life From Chiral Crystals . . . Really?]. Maybe one of these days they'll actually put up some evidence to support Intelligent Design Creationism instead of always attacking science.¹

Patrick is worried about the chirality problem, which can be pretty well explained by just applying a bit of common sense [Amino Acids and the Racemization "Problem"]. Unfortunately, it's not just the IDiots who are confused about the chirality problem. Many chemists and biologist also seem to have weird ideas about the requirement for 20 L-amino acids when life began.

Patrick quotes Timothy Standish who says,

Much as the Miller-Urey experiment demonstrated that it is possible to produce insignificant yields of a very few biologically important monomers in a laboratory device, Noorduin et al. demonstrated that chemists are capable of producing enantiomerically pure crystals under laboratory conditions. This laboratory technique fails to show a mechanism by which enatiomerically pure solutions of all 20 amino acids used in protein construction may have existed before the advent of life, not to mention the other chiral molecules found in living things. As a consequence, the chirality problem for chemical evolution remains unresolved by this technique.

How many things are wrong with this paragraph?

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1. Not holding my breath.