Monday's Molecule #40

 

Name this molecule. There's a short common name but it's not sufficient. You have to supply the complete IUPAC name in order to win the prize. There's a direct connection between this Monday's Molecule and Wednesday's Nobel Laureate(s).

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this Wednesday's reward. Both of them are waiting to collect their prize when September rolls around. The prize is a free lunch at the Faculty Club.

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 the Nobel Laureate. Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.


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

Francis Collin on CBC Radio

 
CBC Radio recently interviewed Francis Collins. The interview was conducted by Mary Hynes a woman who shows herself to be completely ignorant of atheism [Tapestry: Interview with Francis Collins].

You can listen to the entire interview if you dare but there's nothing new here. For the most part, Collins repeats the same old tired arguments we saw in his book The Language of God [Theistic Evolution According to Francis Collins]. One of the things he says is that when he was an atheist he began to question his lack of belief. All of his questions about God were answered on reading the first few pages of Mere Christianity by C.S. Lewis! I bet you didn't realize how easy it is to become a Christian! Neither did PZ Myers so he posted the first chapter of Mere Christianity on his blog [Get Ready fo Become a Christian]. Atheists beware, read it at your peril. You might fall down on your knees and be converted to Christianity.

Collins believes that one of the strongest arguments for the existence of God is our sense of what's right and wrong. He calls this the Moral Law. Somehow we seem to know the difference between good and evil. Collins also thinks that the concept of altruism is a major stumbling block for atheists. Here's how he puts it in the radio interview.

... because if you pursue the socio-biological explanation of altruism to its ultimate conclusion, and you say that it's really just evolution that is responsible for this sense of right and wrong, you can't get away from what that means, That means that good and evil have no absolute significance at all. They're purely arbitrary. They're evolutionary contrivances. The idea that we have in our head about something being right or wrong is just a complete illusion. And for people who want to adopt that view you have to go all the way there and embrace that. And something about that, in people I talk to, even those who .. consider themselves to be atheists or agnostics, that really troubles them. And it should.

Now many people seem to think that C.S. Lewis and Francis Collins have a very sophisticated view of religion—one that Dawkins fails to grasp when he criticizes religion. But as far as I'm concerned, if this is the best they can do then theists deserve all the criticism they get.

Evolution has given us brains and we have learned how to use them. Over thousands of years we have developed rules of behavior designed to improve our security and well-being and promote an orderly society. Accordingly, it is "bad" to take something that doesn't belong to you and it is "good" to help your neighbor. It is "bad" to lie and it is "good" to tell the truth. In the long run, if everyone does "good" things your society will be better off. Nobody like thieves and liars. They can't be trusted.

"Good" and "bad" are not arbitrary and they are not the direct product of evolution. They have "absolute signficance"—they promote social interactions and humans can achieve much more collectively than they can as individuals. Collins is way off base here. I don't know of any atheists who are troubled by this. I can't imagine who he's talking to.

Denyse O'Leary and the Blogosphere

 
Denyse certainly got my attention when she announced on her blog that she had some nice things to say about me and some "almost-nice" things about PZ Myers [Podcast: Why I think the blogosphere beats legacy media cold, plus heartfelt regards to Larry Moran and PZ Myers]. Listen to Casey Luskin interviewing Denyse O'Leary and decide for yourselves. The relevant questions come at 12 minutes and 45 seconds into the podcast when she's asked about PZ Myers and me [Blogophile: Denyse O'Leary and the Blogosphere]. If you don't want to follow the link to a podcast where you can skip to the end then listen to the whole thing below.


Click here to get your own player.

The Purpose of Graduate Education

 
There has been considerable debate about the real purpose of a graduate education. Is it just a way of training students to become university Professors? [Job Propsects for Graduate Students]. Is it true that graduate students are just indentured labour as a recent article in Nature implied?

These are interesting questions. One of the issues that often comes up in these debates is the "pressure" to publish. Supervisors will often try to persuade their graduate students to publish papers. Is this a good thing or a bad thing?

It's a good thing, in spite of what most people believe. Here's how Ryan Gregory sets up the question ...

At the base of this discussion is the assumption that most advisors actually do encourage/pressure their students to publish -- an assumption with which I will not disagree here. What remains open is the interpretation of why this might occur. There are several possibilities:

Read his blog to see why graduate students should publish papers and why this doesn't necessarily mean that the advisor is treating them like slave labor [Why would advisors encourage students to publish?].

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[Photo Credit: Graduate students in the Dept. of Biochemistry, University of Toronto.]

Gene Genie #14

 

The 14th edition of Gene Genie has just been published on Microbiology Bytes [Gene Genie #14: Bugs and Beyond].

Top Five Dead Scientists

 
Robin Ince lists his top five scientists in the video. It's obviously intended to be a farce since he doesn't mention Charles Darwin. Some bloggers have asked for serious submissions. For example Peter Mc at The Beagle Project Blog wants to know who you would name for the other four spots [Top five dead scientists: list 'em]. So does James Randerson at the Guardian [Top five dead scientists].

So who would I choose besides Charles Darwin at #1? How about Isaac Newton (#2) and Albert Einstein (#3). They seem pretty obvious. I'm tempted to go with Ibn al-Haytham (965-1039) for the #4 position although I don't know as much about him as I should. At #5 I'll pick Thomas Hunt Morgan (1866 - 1945) the first geneticist to win a Nobel Prize and the founder of modern genetics. (And because nobody else has named him yet.)

Honorable mentions to Max Planck, Niels Bohr, Francis Crick and Louis Pasteur. Some of those mentioned by others don't even make the top 100 on my list.



[Hat Tip: Coturnix]

Six Days 'Till the Poll Closes

 
Get on over to the left-hand margin and vote for your view of evolution. The poll closes at the end of August. When it does, I'll explain the errors of your ways!

Sam Harris Gets It Right (Again)

 
Sam Harris has a letter in this week's Natrue where he takes the editors to task for their accommodationist approach to the fight between rationalism and superstition [Scientists should unite against threat from religion].

The immediate object of Harris' letter is a recent commentary praising Islam as an "intrinsically rational world view" that is "perfectly in harmony with scientific naturalism." Harris points out the fallacy of such a position then goes on to raise questions about a review of Francis Collin's book The Language of God. According to Harris, the review, entitled "Building Bridges," ...

... represents another instance of high-minded squeamishness in addressing the incompatibility of faith and reason. Nature praises Collins, a devout Christian, for engaging "with people of faith to explore how science — both in its mode of thought and its results — is consistent with their religious beliefs".

I agree with Harris that the Theistic Evolution version of Christianity promoted by Collins is not compatible with reason and science. I agree with Harris that Nature should be ashamed of itself for suggesting otherwise. This is an area where the editors of Nature should either avoid comment or, preferably, defend science.

Harris closes his letter with a nice jab.

There are bridges and there are gangplanks, and it is the business of journals such as Nature to know the difference.

People Living Today Outnumber all Those Who Have Died in the Past

 
Friday's Urban Legend: DEFINITELY FALSE

This month's issue of Scientific American addresses this popular myth [Fact or Fiction?: Living People Outnumber the Dead].

The human population has swelled so much that people alive today outnumber all those who have ever lived, says a factoid whose roots stretch back to the 1970s. Some versions of this widely circulating rumor claim that 75 percent of all people ever born are currently alive. Yet, despite a quadrupling of the population in the past century, the number of people alive today is still dwarfed by the number of people who have ever lived.

The data is supplied by Carl Haub, an expect on world demographics at the Population Reference Bureau in Washington DC (USA) [How Many People Have Ever Lived on Earth?].

The myth isn't as outlandish as it seems. If you look at the chart above it's not difficult to imagine that the area under the curve from 1950 - 1998 might be close to the area under the rest of the curve. (The start point—Adam & Eve in 5,000 BC is meant as a joke.) Nevertheless, Carl Haub points out that it just doesn't make sense once you start to think about it seriously. But, and this is a serious "but", nobody really knows how many people were alive in the past.

Any such exercise can be only a highly speculative enterprise, to be undertaken with far less seriousness than most demographic inquiries. Nonetheless, it is a somewhat intriguing idea that can be approached on at least a semi-scientific basis.

And semi-scientific it must be, because there are, of course, absolutely no demographic data available for 99 percent of the span of the human stay on Earth. Still, with some speculation concerning prehistoric populations, we can at least approach a guesstimate of this elusive number.

The guesstimate begins with a decision about when to start counting. Haub picks 50,000 BC as a somewhat arbitrary beginning of the human population. As it turns out, the exact start point may not matter very much since the human population was probably small for many tens of thousands of years.

The growth in human population can only be estimated by making guesses about the average life expectancy and birth rate at different points in time. Carl Haub is about as knowledgeable in this field as anyone so we can assume that his guesstimate is as good as it gets. Remember that we are interested in how many people have ever lived and this has to include children who died young as well as adults who lived to be 40 or 50 years old.

There are estimates of the number of people alive in 1AD based on the population of the Roman Empire and China. The consensus is about 300 million (45 million in the Roman Empire). By 1650 the world's population may have been close to 500 million even when you take into account the ravages of the Black Death.

Here's the bottom line. The people alive today represent about 6% of all the people who have ever lived.

The Rings of Uranus Viewed Edge-on

 
The photograph and caption from SciencDaily says it all [Astronomers Get First Look At Uranus's Rings As They Swing Edge-on To Earth].

This series of images from NASA's Hubble Space Telescope shows how the ring system around the distant planet Uranus appears at ever more oblique (shallower) tilts as viewed from Earth - culminating in the rings being seen edge-on in three observing opportunities in 2007. The best of these events appears in the far right image taken with Hubble's Wide Field Planetary Camera 2 on August 14, 2007. (Credit: NASA, ESA, and M. Showalter (SETI Institute))

As expected, Phil Plait of Bad Astronomy has much more information and lots of spectacular photographs [Yes, yes, rings around Uranus, haha]. Where does he get them?

Do You Support Our Troops?

 
A. Whitney Brown explains why he supports the brave American troops fighting in Iraq. His talk applies to my support of brave Canadian troops fighting in Afghanistan—or at least it raises the same questions.



[Hat Tip: Canadian Cynic]

Job Prospects for Graduate Students

 

This week's issue of Nature has two short articles on the future of science in the USA. The first one refers to Indentured Labour. It talks about the fact that the number of life science researchers in the universities (tenure and tenure-track) has leveled off at about 30,000 while the number of students earning degrees in the life sciences has doubled. The pejorative reference to graduate students as indentured labour is quite unnecessary. It declares a bias and prevents rational discussion.

The second article makes a similar point [More biologists but tenure stays static] about the job prospects of Ph.D. students.

Both Nature articles are based on statistics compiled by the Federation of American Societies for Experimental Biology (FASED). The original study can be found at [Education and Employment of Biological and Medical Scientists: Data from National Surveys]. The Nature articles have stimulated considerable debate on the blogosphere, See PZ's posting and the comments [The most daunting numbers I've seen yet].

Most of the postings have failed to ask the really hard questions so that's what I'm going to do. But first, let's look at the data from the powerpoint presentation on the FASEB site.

The first graph shows the number of Ph.D. graduates in life sciences over the past 40 years. The rate was about 4,000 per year throughout most of the 1980's then jumped up to about 6,000 per year in the late 1990's. Lately there has been a further increase to about 7,000 per year. Much of the increase is due to foreign students.


The second graph shows the increase in positions for researchers with a Ph.D. in life sciences. The number of jobs has almost tripled from 1973 to 2003. Most of the increase has been in industry as a result of the expansion of biotech firms. Most of the fuss is because the number of academic jobs seems to have flattened out at about 60,000. Of these, only 30,000 are tenure or tenure-stream positions. At our university the number of positions in hospital research institutes (non-tenured) has vastly outpaced the number on the campus (tenured) so this isn't a surprise to me.


One of the questions being debated is whether we should continue to graduate far more Ph.D's than the number of academic positions that need to be filled. The answer is yes and here's why.

Assuming (incorrectly) that our primary purpose in graduate education is to train our replacements and assuming (incorrectly) that all graduates want an academic position, we should still graduate more candidates than there are positions because we will want to choose the best candidates for a position and this means that there has to be a larger supply than the demand. How large should this supply be if we were to treat graduate students as a commodity? I don't know, maybe five or ten times the number of jobs?

Now, don't get me wrong. I'm not advocating that we behave this way. I'm simply pointing out to those who do want us to adopt this point of view that there should be many more Ph.D.'s than jobs. That's something that most people don't seem to understand. They seem to think that the number of Ph.D. graduate should approximate the number of jobs available. What this would mean in practice is that the selection for tenure-stream Professors would take place mostly on admission to graduate school and whatever happens afterwards is hardly relevant (i.e., no weeding out). (Some people even think that the candidates for tenure-stream positions are chosen from graduates of their own institutions. Those people are really out of touch.)

Is the "crisis" as serious as most people think? I don't believe it is for several reasons. First, many of the foreign students will return to their native countries. This means that the graduate students who are getting Ph.D.'s in America won't all be looking for jobs in America. Second, many students want to take jobs in industry because they pay better. They won't be competing for academic positions. Third, there's a considerable lag between the expansion of student numbers and the expansions of faculty. Many universities have plans for faculty expansion in the near future. Fourth, the steady-state level of faculty positions disguises the fact that faculty hired in the 1970's expansions are now retiring. Thus, for the short term there will be more new hiring than the graphs indicate.

But behind all this debate and discussion is a more serious issue. Why do students go to graduate school? Is it only because they want to be trained for a future job? Should Professors look upon every graduate student as a job trainee and behave accordingly? I'd like to think that there are still students out there who go to graduate school for the love of science. I did.

The graduate school experience is an end all by itself and not always a means to an end. Sure, it would be nice if things work out and the student gets a nice post-doc and an academic position—if that's what they want—but there's other things to do after graduate school. I've known lots of students who went into teaching, medicine, or law for example. I've known students who choose to be full-time parents even though they did well in graduate school and enjoyed the experience.

I'm very reluctant to fall into the mindset where I view every graduate student as a trainee for a job in industry and academia and not as a young inquisitive scientist. If Professors adopt the former mindset, and some do, then the goal of graduate research is not to answer important scientific questions but to churn out enough papers in respectable journals to ensure you get a good post-doc. The fact that this goal is sometimes compatible with the ambitions of the P.I. (more papers) makes for a deadly combination.

Hugh McLachlan on Cloning Humans

 
Last week I posted an article on cloning humans. It was a reference to a piece in New Scientist by Hugh McLachlan, a Professor of ethics at Glasgow Caledonian University in Scotland (UK). McLachlan does not oppose the cloning of humans and neither do I.

Here are some other articles on the same topic [Ignore The Boys from Brazil - say Yes to human cloning], [Poor reasons for making human cloning illegal].

McLachlan sent me the following message in response to some of his critics. It addresses some of the issues that have come up in the comments on Sandwalk. He has given me permission to post it.

I think that the risks to the embryos are irrelevant to the issue of whether or not human cloning should be illegal. (Whether public money should be spent on human cloning if it is a very inefficient technique is another matter.) The potential mothers should be informed about the known risks and they must, of course, give their consent. The risk to the mothers is not a justification for making the technique illegal in my view.

Consider an analogy. Imagine that 100 people were trapped, unconscious in a building. They might, for instance, be hostages. A bomb might be primed to explode shortly. If they are not rescued fairly soon they will die. Suppose that the only way they could be rescued is if they were snatched by SAS. The snatch might kill them all. It might result in some being injured, impaired and disabled. It might even result in some living a life that was not worth living. However, there is a chance that one or more might survive to live a normal life. Should we take the chance and snatch them? If we are thinking only about the interests of those 100 people, we must do it even if the chances are remote that any will be saved.

To say that it should be illegal to make the snatch because of the risk to the hostages would be absurd. It is similarly absurd to say that, because of the risks to the embryos involved, human cloning should be illegal.

There is a risk to the soldiers. However, since people volunteer to be soldiers and might even volunteer for particular dangerous missions it is generally judged acceptable that soldiers are exposed to such risks. I can see no reason why we should not allow potential mothers to accept the risks of delivering clones if that is what they want to do.

The objection about the risks to the embryos/clones involved looks at the issue of risk and uncertainly the wrong way round. Suppose that some technique or other were devised to reduce the suffering of those people who had some particular relatively minor ailment. The question of the risk of the technique to these potential patients might be relevant particularly if we assume that to live with the ailment is still pleasant and worthwhile even if not as pleasant and worthwhile as life without the ailment. Suppose that, with the technique, the likelihood is that X% of the patients will be cured completely of the ailment, Y% will end up with a worse case of the condition and that Z% will die in the course of treatment.

In a situation such as this, it is important to know what numbers X, Y and Z stand for to try to judge whether the risk involved in worth taking. Ideally, we would tell the patients and let them decide for themselves. However, human cloning is quite different from this imagined scenario. For the people who might be born as a result of cloning - whether, in the event, they actually are born - cloning is their only chance of birth and life. In the absence of cloning, they will not be born. Hence, cloning is not a risk for them but an opportunity - their only opportunity. To make cloning illegal in their interests on the grounds that, in the course of the technique, not all implanted embryos will become healthy mature human bodies is absurd.

Fool me once .... shame on you ...

 
See Can You Hear the Drums Beating?, Bush Flubs the Message and A Prelude to War.

There's an old saying in Tennessee — I know it's in Texas, probably in Tennessee — that says, fool me once, shame on — shame on you. Fool me — you can't get fooled again.
                                                   George W. Bush 2002

[Hat Tip: John Lynch]

Rationalism vs. Superstition: The Enemies of Reason (Part 2)

 
Here's part 2 of Enemies of Reason, Richard Dawkins' attack on superstition. This episode focuses on medical quacks and kooks. It's very entertaining. You'll certainly like the segment on how to increase the number of strands in your DNA!

Read Orac's review at Respectful Insolence. The point to remember is that the battle is between rationalism and superstition and the atheism vs. religion controversy is only a subset of the bigger battle. And evolution vs. creationism is an even smaller subset. You are missing the point when you ask people like Richard Dawkins to align themselves with moderate theists in order to combat the extreme versions of creationism.