Green T4 Bacteriophage Earrings

Ms. Sandwalk's birthday is coming up in a few weeks and I'm getting nervous. I always seem to choose the wrong present. Turns out that a telephoto lens for her camera isn't very romantic. Who knew?

This year it's a sure thing. I worked on bacteriophage T4 as a graduate student and she helped me type my thesis. It's the perfect gift. [NEW - Green T4 Bacteriophage Earrings]

Right?

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A Question for Anthropologists

This year's special issue of Scientific American is "Beyond the Limits of Science." One of the articles is about human evolution. The title is Super Humanity in the print issue but the online title is Aspiration Makes Us Human.

The author is Robert M. Sapolsky, a professor of biology and neurology at Stanford University in California (USA). Stanford is a pretty good school so he probably knows his stuff.

Here's how Sapolsky starts off ...

Sit down with an anthropologist to talk about the nature of humans, and you are likely to hear this chestnut: “Well, you have to remember that 99 percent of human history was spent on the open savanna in small hunter-gatherer bands.” It's a classic cliché of science, and it's true. Indeed, those millions of ancestral years produced many of our hallmark traits—upright walking and big brains, for instance.

This doesn't make sense.

Let's assume that our ancestors left Africa only 50,000 years ago. If that represents 1% of our evolutionary history then it means that our species and it's immediate direct ancestors lived on the African open savannah for 4,950,000 years.

Could that possibly be true even if you only count the main line of descent? What is the evidence that supports these claims? How much of the early history of Homo sapiens was influenced by adaptation to open savannah? Does anyone have a scientific answer to this question?

Setting aside the "main line," we now have good evidence that modern Homo sapiens acquired alleles from Neanderthals, Denisovans, and, perhaps more ancient Homo erectus. All three spent substantial time evolving in places that looked nothing like the open savannah in Africa. The proportion of the "invading" alleles may be only 10% or less but that's still significant.

Do we know for sure that all of the important features of modern humans came from alleles that were fixed by adaptation on the savannah? What if some of the more important behavioral alleles came from Neanderthals and became fixed because they were so much fitter than the savannah alleles?

Take the alleles that make women like to shop, for example. Maybe they arose in the Denisovans because they have access to better trade routes in central China? Maybe the women on the savannah preferred to store their cash in elephant tusks?

The evolutionary psychologists have developed awesome explanations for human behavior based on their detailed understanding of the social structure of hunter-gatherer groups living on the savannah for millions of years. What if our genetic ancestors lived elsewhere? The bad news is that all those just-so stories will be wrong. The good news is that they can publish a completely different set of stories and get twice as many publications.

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Atheists Have to Address the Social and Emotional Needs of People (or the Church Wins)

I stole this title from the Friendly Atheist, Hemant Mehta [Atheists Have to Address the Social and Emotional Needs of People (or the Church Wins)].

Watch the video. Hemant makes the point that large churches in the USA provide a number of social services that, apparently, aren't available anywhere else. He points out that asking someone to give up their religion is asking them to give up all kinds of other things like volunteer groups, daycare, and support groups. Hemant thinks that atheists need to create "churches" that will fill these needs.

This is the same argument made by another prominent American atheist, Dan Dennett [What Should Replace Religion?].

I don't get it. Why should atheists have to form their own "churches"? In Canada these services are provided by local community centres—there are four within a short drive of were I live. The one within walking distance is called South Common Community Centre. It has a swimming pool (see photo above), a public library, many gyms and exercise rooms, and meeting rooms. There's daycare and classes of various sorts, dozens of volunteer organizations and support groups, swimming lessons for adults and children and lots more. The community centres are funded by civic government and paid for by taxes. They are open to everybody.

Some of them rent out space for church services on Sundays but they are definitely secular. They are not atheist centres.

The best way to provide the services that people need has already been invented. It's called socialism. It's wrong to assume that the only solution is competing services supplied by various religious churches plus one non-religious church.

Is it impossible to work in America toward the goal of secular social services for all? Is that why the only solution seems to be for atheists/humanists to form their own competing religion to provide those services for nonbelievers?

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What Would Disprove Jerry Coyne's Version of Evolution?

Jerry Coyne has a particular view of evolution—one that conflates fact, theory, and history [What would disprove evolution?].

Based on his version of evolution, he then offers some examples of what it would take to disprove evolution.

I was tempted last month to challenge his views but I kept putting it off. Now, Ryan Gregory has done the job, and it's an admirable job.

I agree with everything Gregory says at: An example of why it is important to distinguish evolution as fact, theory, and path.

Please leave comments on Ryan's site.

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Disproving Evolution

Elsewhere on the internet there's a discussion about whether evolution can be disproved by simply finding a fossil out of order.

Here's what I said on Facebook ...

The statement is untrue. If we discover that a given species is older than we thought then we will just revise our view of the history of life on Earth. It will not disprove the fact of evolution and it will have no effect on evolutionary theory. It is a mistake to link the truth of evolution to our current understanding of the history of life. That history can be easily changed without threatening evolution.

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R. Elsiabeth Cornwell Talks About Social Networks

R. Elisabeth Cornwell is Executive Director of the Richard Dawkins Foundation (US). She has a Ph.D. in psychology and her day job is Professor at the University of Colorado at Colorado Springs.

Here's Cornwell giving a talk at TAM2012. It makes me cringe but is it just me? Apparently not if you read the comments at YouTube.


She talks a lot about bullies and their presumed psychiatric problems but she doesn't give any examples. Who is she thinking about? Jonathan Wells? PZ Myers? Margaret Thatcher? Rush Limaugh? Stephen Jay Gould? Jerry Falwell? Ken Miller? Ann Coulter? Christopher Hitchens? Thomas Huxley? Rachel Maddow? Richard Dawkins?

It would have been nice to see the difference between pre-internet "bullies" and those on the internet. Are there any example of people who were "civilized" before they got on the internet but became bullies once they started a blog?

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Stipends for Graduate Students

Here's what we pay our slaves graduate students while they are working toward their degrees. How does it compare with other biochemistry departments?

Biochemistry Graduate Student Stipends for 2012-2013

M.Sc. students

Domestic Students
$17,000 living allowance plus tuition ($7,160.00) and incidental fees ($1,241.52) = $25,401.52

International Students
$17,000 living allowance plus tuition ($16,886.00) and incidental fees ($1,241.52) AND UHIP ($684.00) = $35,811.52

Ph.D. students

Domestic Students
$19,000 living allowance plus tuition ($7,160.00) and incidental fees ($1,241.52) = $27,401.52

International Students
$19,000 living allowance plus tuition ($16,886.00) and incidental fees ($1,241.52) AND UHIP ($684.00) = $37,811.52

(UHIP is the University Health Insurance Plan)

My graduate student stipend in 1968 was $3000, which is $19,500 in 2012 dollars. I don't remember how much tuition and the health plan cost. We lived in subsidized housing, The rent was $56 per month.

We have about 140 graduate students in our department. Many of them are in the photo along with several much older "students" who earn a lot more money.

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Donald E. Nicholson (1916 - 2012)

Donald Nicholson died last May. He was 96 years old.

Nicholson was a professor of biochemistry at the University of Leeds in the United Kingdom. He started drawing metabolic charts back in 1955 and they gradually evolved into the works of art that you have seen in all the textbooks and on the walls of labs in offices in biochemistry departments around the world. I doubt that there's a single biochemist that hasn't studied these charts at some time during their undergraduate experience.

Lately his metabolic charts have been the property of the International Union of Biochemistry and Molecular Biology (IUBMB) but many of them have been marketed by Sigma-Aldrich [Metabolic Pathways].

Recent additions have included several minimaps of specific pathways such as those involved in lipid metabolism, glycolysis, the urea cycle etc. It's sad that we won't see any additions to this collection or any updates.

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A Sophisticated Theologian Explains Why You Should Believe in God

Modern atheists are often accused of being ignorant of the most up-to-date arguments for the existence of god(s).¹ We are told that there's a very sophisticated group of theologians out there who shouldn't be ignored.

Whenever we ask for those "sophisticated" arguments for the existence of god(s) we are directed to various Courtier's Replies discussing how to rationalize the properties of various gods. They all begin with the assumption that god(s) exist. As I pointed out earlier, there's no reason why an atheist should care about things like the problem of evil. It makes about as much sense as debating the cut of the Emperor's new clothes or the stylishness of his new hat.

Alvin Plantinga is one of these "sophisticated" theologians. Listen to him explain why atheists should believe in god(s). Is this really the best they can do?

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1. The second most common complaint is that we don't even have good arguments for atheism—at least not as good as those thinkers of the 20th century who were full of angst over not having a god to believe in. Apparently modern atheists aren't very sophisticated unless they are contemplating suicide.

[Hat Tip: Jerry Coyne: Plantinga on why he believes in God, dislikes the New Atheists, and finds naturalism and evolution incompatible.]

Monday's Molecule #181

Last week's molecule was an intermediate in some amino acid biosynthesis pathways and the enzyme that makes it is the target of Roundup®. Replacing this enzyme with a Roundup® resistant version yields genetically modified food plants [Monday's Molecule #180].

This week's molecule is a lot more complicated. You need to identify the specific type of molecule. Defective metabolism of this molecule is associated with a famous disease. Name the disease.

Post your answers as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is ganglioside G_M2. Defects in ganglioside synthesis are responsible for a number of genetic diseases in humans including Tay-Sachs disease. This is the same molecule featured in Monday's Molecule #162 back on March 19, 2012. There was no winner that time.

This week's winner is Matt McFarlane, an undergraduate. He lives in Canada but he's quite far away and probably won't make it for lunch.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa
Aug. 7: Raul A. Félix de Sousa
Aug. 13: Matt McFarlane

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An Example of "Directed" Mutation and an Idiotic "Gotcha"

There's nothing in modern evolutionary theory that allows for mutations that arise specifically because they will produce a future benefit. That's why we say that mutations are "random" with respect to outcome.

There's nothing in the known history of life that suggests it has a purpose or direction. In particular, there's nothing to suggest that 3.5 billion years of evolution were just advanced preparation for the appearance of Home sapiens. That's why we say that evolution appears unguided and purposeless [Is "Unguided" Part of Modern Evolutionary Theory?]. And that's why anyone who says that life shows evidence of purpose is not being scientific.

Creationists aren't happy about this so they will go to extraordinary lengths to wiggle out of the inescapable conclusion based on solid evidence. The usual excuse is to postulate that god is very sneaky. He/she/it makes a huge effort to hide his/her/its manipulations so that it only appears that evolution is unguided and purposeless. The clever creationists aren't fooled by this sneaky god; they can detect its deception, but scientists can't.

Humanities Aren't Science? More's the Pity

Science is a way of knowing that is evidence based and requires rational thinking and healthy skepticism. It's the only successful way of knowing that has ever been invented.

Whenever investigators in the humanities discover new knowledge it turns out that they have been using a scientific approach. They've been thinking like a scientist. What else could they be doing?

Maria Konnikova is a graduate student in psychology at Columbia University. She writes in Scientific American that Humanities aren’t a science. Stop treating them like one.

Well, it's certainly true that many disciplines in the humanities are very unscientific—evolutionary psychology comes to mind—but this is one of the first times I've ever heard someone be proud of the fact that they don't think scientifically. Why in the world would she say that?

Turns out she's confused about what science is and what it isn't. She thinks that science requires lots of quantitative data and lots of mathematics and statistics.

Sometimes, there is no easy approach to studying the intricate vagaries that are the human mind and human behavior. Sometimes, we have to be okay with qualitative questions and approaches that, while reliable and valid and experimentally sound, do not lend themselves to an easy linear narrative—or a narrative that has a base in hard science or concrete math and statistics. Psychology is not a natural science. It’s a social science. And it shouldn’t try to be what it’s not.

Hmmmm ... that might explain a lot. I guess if you are seeking knowledge in the social sciences it's okay to use a non-scientific approach to gain knowledge. I wonder what approach they follow? Do they pray for guidance? Use a Ouija board? Or do they just make stuff up?

Maybe Konnikova is just saying that humanities disciplines are not chemistry, physics, biology or geology? Nah, that's too obvious. It doesn't merit an article in "Scientific" American. Maybe we'll find out what she really means when her book comes out in January. It's title is: Mastermind: How to Think Like Sherlock Holmes. Did Sherlock Holmes think like a scientist or did he think like someone in the humanities?

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[Hat Tip: Mike the Mad Biologist]

Science and Christianity—Different Ways of Finding Truth?

Chris Mulherin is an Anglican Minister who studies the relationship of science and religion. In this video he claims that science and religion are compatible. Specifically, science and Christianity are compatible.

UPDATE: Eric MacDonald does an excellent job of taking down Chris Mulherin in Science and Religion Again!. MacDonald is a former Anglican priest. (Hat Tip: Jerry Coyne.

He doesn't explain how rising from the dead, miracles, souls, heaven, and a Bible full of lies are compatible with science. Instead, he concentrates on the old saw of different magisteria. Christianity answers different questions than science and discovers different truths.


Id' like to echo the challenge I made some years ago and the one Jerry Coyne issues today [Do both science and faith produce truth?]. Can anyone give us an example of a "truth" discovered by religion—one that we all recognize as genuine knowledge? Name a "why" question that religion answers in a way that we all accept as meaningful and true.¹

Those who think that science and religion are compatible like to accuse us of not understanding the serious philosophical issues. I don't think that's correct but, if it is, here's a chance for the serious courtier theologian to set us straight.

Waiting .....

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1. It's not good enough to say that if only Christians accept the answer as true, then Christianity has discovered truth. If that were the case then astrology and homeopathy are also valid ways of finding truth even if astologers and homeopaths are the only ones who believe the answers. I'm guessing that no serious philosopher would defend such a ridiculous position.

Is "Unguided" Part of Modern Evolutionary Theory?

Creationists are unhappy with the claim that the evolution of life on Earth appears unguided and purposeless. Casey Luskin would like to think that it's a fundamental part of "the theory of Darwinian evolution" [Unguided or Not? How Do Darwinian Evolutionists Define Their Theory?].

An argument we are increasingly hearing from theistic evolutionists is that the "unguided" or "random" aspects of Darwinian evolution are merely "philosophical gloss" or an "add-on" promoted by new atheists who use bad philosophy. Jay Richards covered this question in his recent dialogue with Alvin Plantinga--see here, here, here, and here for the series. While many new atheists undoubtedly make poor philosophers, the "unguided" nature of Darwinian evolution is not a mere metaphysical "add on." Rather, it's a core part of how the theory of Darwinian evolution has been defined by its leading proponents. Unfortunately, even some eminent theistic and intelligent design-friendly philosophers appear unaware of the history and scientific development of neo-Darwinian theory.

This is wrong in many ways.

Here's the simple explanation ... so simple that even an IDiot should be able to understand it.

Modern evolutionary theory consists of many parts including the mechanisms of evolution. The main mechanisms are natural selection and random genetic drift and those two mechanisms act on populations containing variation. The variation is due to the presence of mutations and mutations arise "randomly" with respect to ultimate purpose or goal.

There are tons of experiments proving that mutations are essentially random. (Let's not get into quibbling about the meaning of "random.")

Now let's look at the history of life on Earth. This is a completely separate subject from evolutionary theory. It's like the difference between the theory of gravity and how and when our particular solar system formed.

Looking all the evidence used to reconstruct the probable history of life we see no evidence whatsoever that it was guided in any particular direction or that there was any underlying purpose. That's why we conclude that the evolution of life on Earth appears unguided. It's a tentative conclusion based on fact and observation and not on "the theory of Darwinian evolution."

While it is true that evolutionary theory doesn't allow for a "guided" mechanism, it isn't true that the history of life has to be devoid of purpose or guidance. There could well be evidence that god intervened or that particular organisms were preferred over others and the history was tilted in one direction. But there's no evidence that this is the case—with the possible exception of beetles.

The history of life looks exactly like it should if it were the result of accident, contingency, and evolution. There's no evidence of god(s). That's what makes the creationists upset, not evolutionary theory.

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Only Young Scientists Overthrow Old Concepts?

Max Planck once said ...

A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.

This does not conform to my experience in the biological sciences.

I think that what usually what happens is that a new way of thinking is promoted by well-established investigators. Gradually other scientists are convinced by the evidence to change their minds and the new scientific truth spreads within the community.

When a substantial number of scientists are converted, they start teaching the new concept in graduate and undergraduate courses. This produces a young generation who never heard of the old "truth."

If I'm correct then a new generation of scientists grows up familiar with the new scientific truth but only because the established scientists converted and started training the next generation properly.

When it comes to challenging old established concepts in a discipline I find that initially the younger scientists are often quite conservative unless they just happen to be working on that problem. This shouldn't be a surprise since our young investigators have their hands full just establishing themselves in their field. They don't have time to think about what's going on in the rest of the discipline. In fact, it might be detrimental to their careers to challenge most established concepts.

As I'm writing this I'm having trouble coming up with examples in biology. Most of the conceptual shifts that come to mind are ongoing controversies where it still isn't clear that the new scientific truth will replace the old one. I'm thinking of evo-devo, challenges to evolutionary theory, junk DNA, chemiosmotic theory, metabolism & thermodynamics, the tree of life, photosynthesis, and even new ways of teaching.

Can anyone think of examples were the shift has been completed so we can test the Max Planck hypothesis?

How about the shift from thinking that genes were proteins to genes are DNA?

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