The last Monday's Molecule was α-linolenate [Monday's Molecule #203]. It is an omega-3 essential fatty acid. The winner was Anders Ehrnberg.
Today's molecule is actually three different molecules (1,2 and 3). Give the common names for the terminal part of each molecule—the names used in most textbooks. Identify E2 (enzyme name) and briefly explain what's going on.
Email your answers to me at: Monday's Molecule #204. I'll hold off posting your answers 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 email message.)
The Centre for Inquiry logo (above) is from the CFI Canada Facebook page. It's an amazing piece of work because it embodies one of the key features of CFI as an umbrella organization that brings together a number of different groups to unite around common goals.
This is a lot harder than you might think. I think of myself as a skeptic and an atheist but I am not a Humanist. If an organization like CFI were to be taken over by Humanists, I could not be a member. Other people are worried that CFI might be dominated by atheists and an atheist agenda. Some of them have left the organization because they think of themselves as skeptics who are not anti-religion.
Lately the conflict between (some) skeptics and atheists has claimed another victim. PZ Myers is so upset with the narrow view of skepticism promoted by Jamy Ian Swiss [see Skeptics have the amazing superpower of being simultaneously fierce and timid] that he now declares, "I officially divorce myself from the skeptic movement."
What's the problem? It's that some skeptic movements want to concentrate on pseduoscience and pseudomedicine and leave religion alone. They are atheists and accommodationists. Not content with just ignoring vocal atheists, they criticize their tactics as being offensive and inimical to the important skeptical causes. I don't agree with that version of skepticism and neither does PZ Myers. However, unlike PZ, I think the solution is to make it clear that people like Jamy Ian Swiss are wrong to exclude atheism from the skeptical movement.
If the skeptical movement becomes officially accommodationist and anti-atheist then I will have to abandon it just like PZ Myers did.
The advantage of CFI is that it can "accommodate" all these points of view, if we are careful. It can promote an "Extraordinary Claims" campaign that links skepticism about religion and skepticism about pseudoscience and quackery. It can launch a campaign against religion in the schools without antagonizing believers. It can promote charitable causes that bring together freethinkers, humanists, and atheists. It can sponsor Humanist officiants who can preside at weddings and funerals. It can do much to promote what all those groups have in common. All we have to do is tolerate the occasional cause that we might not completely agree with.
It's a bit ironic that PZ Myers is offended by the direction that skepticism is taking yet seems blind to the re-branding of "freethought" that he supports. I'm hoping that in Canada we can avoid the competing conferences that pit freethoughters against skeptics and atheists against humanists. So far, we seem to be on the right track with the Committee for Advancement of Scientific Skepticism (CASS) and CFI events celebrating Dawkins & Krauss and "The Unbelievers" as well as Eschaton 2012, and the upcoming Imagine No Religion.
UPDATE: Jack Scanlan of Young Australian Skeptics says, "A person can be a skeptic and believe in a god." [PZ’s Problem: Does Skepticism Makes An Exemption For Religion?]. I disagree.
Let's ignore for a minute the people who comment on Sandwalk because it's clear that the most uncivil group is the creationists. Let's also ignore the people who comment on the creationist blogs because there it's also the supporters of religion who are the most uncivil. Oh hell, let's just ignore reality altogether and assume, for the sake of argument, that supporters of evolution are more uncivil than creationists.
Stephen A. Batzer speculates, very civilly, why this imaginary assumption might be true [Why Darwinism and Incivility Seem to Go Together].
- They're human. That says a lot that's negative about them and of course about us, too.
- They're typing, probably anonymously, on the Internet. I'm sure you have noticed the level of discourse on the Internet. The Lincoln-Douglas debates it isn't. On any topic.
- You are challenging their religious beliefs, which they know, just know, to be true.
- Thought leaders in the Darwinian movement, such as Dawkins, Prothero, Shermer and so on, inculcate and advocate incivility by their own example. Look at the way biologist James Shapiro and philosopher Jerry Fodor have been treated. It's ugly.
- "A little knowledge is a dangerous thing." That Darwinism is a FACT has been proclaimed since before all of us were born. Saying that the Darwinian mechanism of speciation is not a fact strikes many folks as if you're intimating that there is no Japan. It's just a made up country. When I try to measure the level of personal knowledge that Internet advocates have of evolutionary theory, it is almost universally superficial. This includes biologists.
- They have not taken the time to understand what the issues are or what evidence is convincing to those who disagree with them. They are ignorant in a nearly comprehensive way about why thoughtful, educated people find the "generate and filter" paradigm causally insufficient.
Isn't that amusing?
Now for the next bit ...
WARNING!!! Turn off your irony meter. It doesn't matter whether you have the updated Mark VIII with the extra power pack or not. Turn it off, NOW!!!
Here's how Stephen A. Batzer ends his post on Evolution News & Views (sic).
One thing that draws me to the ID movement is that it has the polite and understated ethic that science is supposed to have -- but does not have when the subject is evolution.
This month's Carnival of Evolution is hosted by Dirk Steinke at DNA Barcoding. He's another one of those nasty Canadian bloggers who seem to be everywhere these days. Read: Carnival of Evolution #59: A letter from the Doctor
Dear Wilfred,
Are you still watching the stars with your new telescope? I bet you can see what I see outside the windows of my TARDIS. The star you're searching for is still there, it just tends to fall out of view occasionally.
Do you remember how you always said how you'd love to be travelling with me again through the skies? I envy you right now, living on this wonderful planet in your lovely little house treating yourself to a flask of tea on your porch while you look at the stars. They're beautiful, I would know, I live amongst them and I've traveled to so many. I’ve seen galaxies born and fading away.
If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission.
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Steven Novella blogs at Science-Based Medicine. Yesterday he was upset about American politicians who want to restrict research grants to projects that "advance the national health, prosperity, or welfare, and to secure the national defense" [Politics of Public Research Funding]. The goal is to put a stop to silly basic science research like studying sex in snails.
Here's the quote of the day from Steven Novella.
I have noticed, however, that researchers have become reflexively good at making up plausible-sounding possible applications for their basic science research – as if they have to constantly justify their research. Every basic-science study that looks at viruses, therefore, may one day cure the common cold. Anything dealing with cell replication may be a cure for cancer. Any materials advance will lead to supercomputers or superlight vehicles. All brain research, apparently, might one day cure Alzheimer’s disease.
I would love for a scientist to say something to the effect of “I have no idea what, if any, practical use this research might lead to, but the knowledge is really cool”. I guess you just don’t say that to a grant committee, however.
The students in my Molecular Evolution course have written the final exam. I finished grading the exams yesterday and the final course marks have been submitted. Now I don't have to think about teaching until August.
Just for fun, I'm posting the final exam questions. How do you think you'd do? I gave the students a list of all possible questions on the last day of class. The only one they hadn't seen was question #2. They knew that the first question would definitely be on the exam.
Students had to answer questions 1 & 2 and choose any three of the other questions.
- Choose a subtopic from your essay and explain it better than you did in your essay and/or rebut the comments and criticisms made by the marker/grader.
- Imagine that identical female twins were born to a woman in 1000 AD. Imagine that you could find a direct descendant of each twin in 2013. If you sequence the complete genomes of the descendants, approximately how many differences would you expect to find? How do these compare to the differences between any two randomly selected individuals from the same part of the world? Explain your reasoning and describe any assumptions you make. Think carefully before you answer. The second question is the most important one. (Human mutation rate = 130 mutations per generation. Haploid genome size = 3.2 × 109 bp.)
- There are hardly any pseudogenes in bacterial genomes. Why haven’t pseudogenes been eliminated from our genome?
- Explain the two-fold cost of sex. Why is this a problem in evolutionary theory?
- Richard Lenski’s group at Michigan State University has been following the evolution of 12 cultures of E. coli for over 50,000 generations. All 12 cultures are grown under exactly the same experimental conditions and the mutation rate is high enough that every culture has been exposed to multiple mutations at every base pair in the genome. Explain why only one of the cultures has evolved the ability to use citrate as a carbon source.
- Why is the Three Domain Hypothesis being challenged by some molecular evolutionary biologists? What are the alternatives?
- What do you think of Kirschner and Gerhart’s “Theory of Facilitated Variation.” Is this something that has to be incorporated into a new extended version of evolutionary theory? What, if any, are the limitations of the theory and what, if any, new insights into evolution does it provide?
Most of you think of Richard Dawkins as a "strident atheist" who doesn't suffer fools gladly.1 The first part of that reputation ("strident atheist") is unjust as Dawkins pointed out on several occasions when he was in Toronto earlier this week.
The second part ("doesn't suffer fools gladly") is quite true. Dawkins thinks that foolish things, like religion and other superstitions, deserve to be ridiculed.
Richard Dawkins and I agree on atheism but disagree on some aspects of evolution. I'm pleased to report that he didn't hold that against me when we met for brunch a few days ago. I guess that means I'm not a fool in his mind! 
For those of you who have never had the pleasure of meeting him, I want to assure you that in person he is a very pleasant fellow and lives up to the very British expression, "a scholar and a gentleman."
Some of the people I met were wondering about the reasons why I disagree with some aspects of Richard's views on evolution. They haven't heard of Stephen Jay Gould and I find that very sad. I still believe that everyone interested in evolution has to read and understand the "Spandrels" paper.
Here's a short reading list ....
Michael Lynch on Adaptationism
What Does San Marco Basilica Have to do with Evolution?
Michael Ruse Defends Adaptationism
Richard Dawkins' View of Random Genetic Drift
1. The phrase comes from the New Testament [Suffer fools gladly].
The last Monday's Molecule was medium chain acyl-CoA dehydrogenase (MCAD) (PDB 2AIT). Nobody got the right answer [Monday's Molecule #202].
Today's molecule is very important for humans. You need to supply the common name AND a more official IUPAC name that identifies the configuration of the bonds. You also need to briefly explain why this molecule is important in humans.
Email your answers to me at: Monday's Molecule #202. I'll hold off posting your answers 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 email message.)
Here's a CNN interview with Richard Dawkins and Lawrence Krauss. It was recorded this morning. It's very unfortunate that the reporter (Poppy Harlow) injects her own views on religion but at least they serve to illustrate the prejudice against unbelievers.
There are quite a few CNN reporters who broadcast their Christian views at every opportunity. They just don't get it.
Today is my daughter's birthday. She was born quite a few years ago in Geneva Switzerland while I was a postdoc.
Here's Jane with my grandchildren, Zoë and Luca (right). Below is Luca studying gamma ray bursts at the Griffiths Observatory in Los Angeles. Gamma ray bursts were the subject of Jane's Ph.D. thesis.
The Centre for Inquiry is sponsoring a brunch with Richard Dawkins and Lawrence Krauss on Wednesday morning. You can sign up at Brunch with Richard Dawkins and Lawrence Krauss. There are only 12 tickets left.
Here's the information you need.
Join us for an exclusive engagement with Richard Dawkins, named top world thinker by Prospect magazine, and Lawrence Krauss, renowned theoretical physicist and cosmologist.
It is rare for these two giants of science to visit Toronto so don’t miss this opportunity!
Please note that there are a limited number of tickets available for this event.
Standard Admission $250
Includes:
Admission to event
Light breakfast service
Brunch service
$200 tax receipt
Premium Admission: $300 (sold out)
Includes:
Admission to event
Light breakfast service
Brunch service
Preferred seating
Copy of Richard Dawkins’ new book The Magic of Reality
$230 tax receipt
Location: Park Hyatt Toronto, 4 Avenue Road, Toronto ON
Day and Time: Wednesday, May 1st
Please arrive by 8:30 am; the event begins promptly at 9:00 am.
Coturnix (aka Bora Zivkovic) is coming to Toronto. He is the author of A Blog Around The Clock, a blog that currently resides on the Scientific American website. Bora is the blog editor at Scientific American and the main organizer of ScienceOnline, an annual conference held in North Carolina in January.
This will be Bora's first time in Toronto—let's welcome him at the Duke of York pub on Monday night at 7pm.
Here's a Facebook page where you can sign up: Toronto Science Online Tweetup.
Some freelance science writer named Philip Ball has published an article in the April 25, 2013 issue of Nature: Celebrate the Unknowns.
The main premise of the article is revealed in the short blurb under the title: "On the 60th anniversary of the double helix, we should admit that we don't fully understand how evolution works at the molecular level, suggests Philip Ball."
What nonsense! We understand a great deal about how evolution works at the molecular level. Perhaps Philip Ball meant to say that we don't understand the historical details of how a particular genome evolved, but even that's misleading.
I've commented before on articles written by Philip Ball. In the past, he appeared to be in competition with Elizabeth Pennisi of Science for some kind of award for misunderstanding the human genome.
SEED and the Central Dogma of Molecular Biology - I Take Back My Praise
Shoddy But Not "Junk"?
Let's look at what the article says ...
Here (below) is my old friend, Keith Yamamoto, talking about taking risks in science. Keith and I were graduate students in Bruce Alberts' lab over 40 years ago. That's him on the left in the photo. I'm the one looking up and the third former graduate student is Glenn Herrick.
Keith and I learned a lot about science from our former mentor. I learned a lot from Keith; for example, he taught me that it is more important to print in your notebook than to use cursive writing. I've been printing ever since.
Keith also helped me learn that it's sometimes important to fight for a cause even if you know you're going to lose. (He was county coordinator for the George McGovern presidential campaign in 1972.1)
The take-home message in this video is that good scientists need to take risks. It's one of those "motherhood" kinds of statements that every scientist will support but few actually do it. It saddens me to say that today we live in a culture where mundane, data-collecting, science is often more successful than risky science (e.g. ENCODE). Risk entails the possibility of failure and even though you might learn from failure [Bruce Alberts on Learning from Failure], it won't do you much good if you don't get a job or you lose your grant.
So I disagree with Keith when he says that we should encourage risk-taking in young scientists. Some of the best scientists I know took risks and and the work didn't pan out. They couldn't get any papers published and they lost their grants. They were cut out of the system in favor of scientists who could guarantee successful results in their grant proposals. The fact that the results were boring and did nothing to advance our knowledge, wasn't important.
I advise young scientists, post-docs, and graduate students to always have a "safe" project. Don't put all your eggs in the risky science basket. It makes me sad to give that advice.
1. For those of you who weren't born in 1972, Nixon won that campaign and McGovern won only 17 electoral votes (Massachusetts and Washington, D.C).
Here's a short talk from my thesis supervisor on learning from failure. He tells the story of how he failed his Ph.D. oral and how he almost gave up writing his textbook.
I was a gradate student in his Princeton lab from 1969-1974. The most important lesson I learned from Bruce was the importance of knowledge and context. He taught a graduate course called "Macromolecules" where he explained both the basic chemistry and the basic biology. The lesson was clear. You can't do good science unless you see the big picture and understand the fundamentals of your discipline. He reminded us almost every day. As he says in the video ...
Theoretical biology is much more important than my generation had imagined. We were misled by the striking success of the 1953 Watson-Crick DNA model.
I also agree with another comment he makes in the video ...
Both book writing and teaching are really important for creative science, I believe.
Bruce also encouraged us to explore topics outside of our research project. This included Jacques Monod's book "Chance and Necessity: Essay on the Natural Philosophy of Modern Biology" and the writings of the best theoretical biologists of the time. We were encouraged to get involved in politics and society. It was a time of protest and revolution, and scientists had a role to play.
The last Monday's Molecule was α-linolenate [Monday's Molecule #203]. It is an omega-3 essential fatty acid. The winner was Anders Ehrnberg.
