The last "Monday's Molecule" was β-D-mannopyranose, shown in boat and chair configurations [Monday's Molecule #196]. The winners were Bill Chaney, Dima Klenchin, and Bill Gunn. Bill Gunn should contact me if he is within range of Toronto.
Students often find it very difficult to distinguish between various stereoisomers. For example, many of you thought that the last molecule was glucose. This week's molecule should present a real challenge for most of you. It's a common molecule, present in all cells and it has a common name by which it is identified in most textbooks. However, the common name isn't good enough because there are several different conformations. The conformation shown in the figure is the only one that's synthesized in the normal reaction. Name this molecule using whatever conventions you have to employ to identify it correctly. [Hydrogen atoms are omitted for clarity. You should be able to infer their positions.]
Post your answer 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.)
Here's a photo of my granddaughter, Zoë, flying her kite on Santa Monica beach on New Year's Eve. The kite was a present from Santa Claus.
Zoë turned three years old on January 5th.
The students in my Molecular Evolution class have to read the Spandrels paper by next Tuesday.
Ryan Gregory explains why this 35-year-old paper is just as relevant and important today as it was when it was first presented in 1978 (published in 1979). Read aall about it at: The great wrinkled finger debate.
Please leave comments on Genomicron and not here.
A group of skeptics have banded together to sue Shoppers Drug Mart for selling the homeopathic product Oscillococcinum. Watch the video on Think Again! TV produced by Centre for Inquiry, Canada. This is a class action lawsuit and anyone who has purchased Oscillococcinum from Shoppers Drug Mart may join the plaintiffs.
CFI is not a plaintiff but it has agreed to provide the court with "accurate scientific data on the efficacy and substance of the product."
My American friends need to watch this video. Be afraid, be very afraid.
I don't know how many people think like this but if it's more than a few thousand there's going to be trouble.
Isn't threatening to kill somebody a crime? Isn't he advocating the overthrow of the democratically elected American government by force? I don't think that's in the Constitution.
There are very few anonymous comments these days and those few that persist will not be missed. I've stopped accepting comments from people who won't identify themselves in some way.
I'd prefer if your identifier leads me to an actual name but for now I'll tolerate posting under a pseudonym as long as it's unique.
According to Careercast.com, I have the least stressful job of all jobs.1 Here's how it's reported in Forbes magazine by web staff writer Susan Adams: The Least Stressful Jobs Of 2013.
University professors have a lot less stress than most of us. Unless they teach summer school, they are off between May and September and they enjoy long breaks during the school year, including a month over Christmas and New Year’s and another chunk of time in the spring. Even when school is in session they don’t spend too many hours in the classroom. For tenure-track professors, there is some pressure to publish books and articles, but deadlines are few. Working conditions tend to be cozy and civilized and there are minimal travel demands, except perhaps a non-mandatory conference or two. As for compensation, according to the Bureau of Labor Statistics, the median salary for professors is $62,000, not a huge amount of money but enough to live on, especially in a university town.
Another boon for professors: Universities are expected to add 305,700 adjunct and tenure-track professors by 2020, according to the BLS. All of those attributes land university professor in the number one slot on Careercast.com’s list of the least stressful jobs of 2013. The ranking comes from an annual best and worst jobs list that began in 1995 under the auspices of the Wall Street Journal.
Ironically, this article comes out just as some of my colleagues are getting the bad news about their grant applications. Those who weren't funded face the end of their research career while they are still in their 40s. It also comes out at a time when two of my colleagues are starting to think about their applications for tenure. If they are unsuccessful, they will be out of a job in their late 30s with a family to support.
None of my colleagues took a month off at Christmas and I can assure you that all of my colleagues are here for almost the entire summer running a lab full of graduate students, post-docs, technicians, and summer students. The stress of running what amounts to a small business and getting papers published on things that nobody else has ever discovered is a lot more than most people could stand.
Read to the end of the Forbes article to see how the author responds to the many comments she received. The real problem here is that a prominent journalist could actually believe what she wrote in the first place!
I love the comment from Thomas Epps ...
Given your comment above indicating that you realize the source of your article was poor at best. I think you should consider retracting this article. I know that I would be severely sanctioned for writing this type of article with such questionable sourcing in my academic job. If the same is not the case in your job, then clearly your career is not a terribly stressful one. Maybe, "web staff writer" should be on the top of the "least-stressful jobs" list?
See ...
Do College Professors Have Less Stress?
Top 10 Reasons Being a University Professor is a Stressful Job
Before Professor comes Postdoc: Lower career rung, just as much job stress
1. I have no intention of supplying specific information about MY job but I'm happy to explain why every one of my younger colleagues is under a tremendous amount of stress every single day.
No comment is necessary except to say that this man, Louie Giglio, was all set to deliver the benediction at Obama's upcoming inauguration until it was discovered that he hates homosexuals. For me, this video would have been enough to disqualify him.
[Hat Tip: Hermant Mehta at Friendly Atheist: Louie Giglio, Who Thinks Laminin Molecules Prove Christianity is True, Will Deliver Obama’s Inauguration Benediction]
The Board of Directors of the Centre for Inquiry, Canada has mailed out the following press release. Unfortunately, nothing has been posted on the website [The Centre for Inquiry].
The Board of Directors would like to thank Justin for launching CFI Canada, growing it from one location in Toronto to across the country in short order. There are few individuals who possess the dedication, passion and tenacity to accomplish this. Justin was instrumental in making CFI the premier voice for reason, secularism and skepticism in Canada. We were fortunate to have him. Justin leaves CFI in good hands with our National Director, Michael Payton, and our incredible branch leaders and volunteers who are committed to continuing our growth and influence.
Justin, we look forward to watching you make further positive and lasting contributions to society, as no doubt you will.
Board of Directors, Centre for Inquiry Canada
I'm delighted that The Board and Justin were able to reach agreement on a new direction for CFI and usher in a new era under new leadership. I agree with the Board that Justin did an excellent job of creating CFI Canada and leading it through its formative years. I was happy to work with Justin and support him during those early years of building an organization (see photo).
In the past year I've been very critical of the CFI Board of Directors because I think they mishandled the firings and re-hirings that took place in 2011 and 2012. This time I think they've done the right thing during recent negotiations. Congratulations to Kevin Smith (President) and all the Board members for working hard to ensure the future success of CFI.
The email announcement also contained a letter from Justin Trottier to the Freehthinker members of CRI. It begins ....
Special Note from Justin Trottier, Founding National Executive Director, Centre for Inquiry Canada
To My Fellow Freethinkers,
It is with mixed emotions that I take this opportunity to announce the upcoming end of my leadership role with CFI Canada. March 15, 2013 will mark the end of my full-time position as National Communications Director; however, I will consider, if I am asked, continuing in part time or other status until no later than July 31. I am immensely proud of the contributions I've made to the organization over the last six years and plan to continue as a volunteer and active participant in CFI events and initiatives, but now it is time to start making the transition from CFI and pursue other interests and employment.
It has been a pleasure working with so many amazing people to form a unique Canadian educational charity and expand it into a national voice for atheists, humanists and skeptics from coast to coast. Leading CFI as it came to establish itself as the most visible, active and professional freethought organization in Canada, with employees, infrastructure and a growing budget will stand as one of the most important and certainly, matchless accomplishments of my life.
...
I'm looking forward to rejoining CFI Canada in just a few months.
Here's a video of my talk at Eschaton 2012 in Ottawa (Dec. 1, 2012).
Jerry Coyne has posted a video of a happy young antelope jumping up and down in a style called "pronking" or "stotting" [Antelope pronking].
If you're a certain type of evolutionary biologist you will immediately ask yourself what kind of selective advantage could have led to the fixation of stotting alleles in antelopes? Here's a list of possibilities that Jerry offers ...
- It allows an animal to jump out of high grass to look for predators
- The behavior startles the predator, giving the gazelle more time to escape
- It’s an alarm signal (like bird alarm calls), alerting herd members that a predator is nearby. This would probably evolve only if herd members were closely related, so the behavior could evolve via kin selection (assuming it’s individually maldaptive, which isn’t proven).
- It’s simply play behavior. But not only the young do it: adults pronk too when they’re chased by predators.
- It’s a way, in young gazelles, of letting the mother know the baby has been disturbed. This may be one function, but doesn’t explain stotting in adults.
- It confuses the predator. Presumably a herd of gazelle, all pronking, would puzzle a pursuing cheetah or wild dog, making it hard to pick out a given individual to chase. I don’t believe this for a second; predators aren’t that dumb, and in fact a predator would probably either learn to or evolve to concentrate on the stotting individuals because they might be easier to catch. (This “confusion” explanation was once used to explain zebra stripes: it might be hard to single out one zebra in a mass of fleeing stripey equids. But see my earlier post on another explanation for stripes.)
- It’s a way to attract mates, possibly by showing how fit you are. Sage grouse in the western U.S. form “leks” in which males group together and jump up and down for hours (making loud noises at the same time) while the females watch from nearby. Invariably it is the males who jump the longest that are chosen as mates. Females want a fit father for several reasons. This doesn’t wash for gazelles since both sexes do it, and not in a sexual context.
- This is a favored hypothesis: the “honest signal” theory. This posits that the behavior is saying to potential predators, “Don’t bother trying to catch me as I can bounce really high, so imagine how fast I could run if I wanted to!” In other words, the behavior deters the predator from attacking that individual.
- This is the hypothesis I find most credible: stotting warns the predator that it has been seen, thus discouraging it from pursuing the stotting animal. (Predators like to sneak up on a prey, getting as close as possible before they’re detected.) That is, stotting evolved via individual selection. Remember that predators often don’t go after a whole pack of quadrupeds at once, but single out certain individuals—often young or weak ones—to pursue.
Here's another example of animals jumping up and down in a stylized manner. Surely there are specific alleles that make them behave this way? And the alleles must have become fixed in the Maasi population by natural selection. In other words, it has to be an adaptation, right?
How many just-so stories can you think of?
The Atheist Census is a project of Atheist Alliance International. You have to answer a few questions but it won't take more than a minute or two.
Please fill out the form if you are Canadian because the reputation of our country is at stake. So far the top ten countries are ...
1. United States of America: 51,541
2. Brazil: 10,971
3. United Kingdom: 10,683
4 Turkey: 9,795
5. Australia: 7,593
6. Canada: 6,852
7. India: 3,100
8. Italy: 2,948
9. Iran: 2,797
10 Poland: 2,679
Do you see what's happening? Some upstart British colony from the bottom half of the world is beating Canada! We can't let that happen. If you are Canadian get yourself over to Atheist Census right away. If you're from Australia you can get your vote counted at Atheist Census for Australians. (Agnostics need not apply.)
[Hat Tip: Veronica at Canadian Atheist: Canada Versus Australia.]
It's pretty hard to ignore the ENCODE papers if you're selecting the top ten science stories of 2012. This doesn't mean it's a "breakthrough" as Science magazine claims [Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012]. And it doesn't mean that the results overthrow Darwinian evolutionary theory as implied by the Intelligent Design Creationists [Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2013].
The Scientific American article was written by Bora Zivkovic, a long-time blogger who knows the difference between hype and reality. He apparently knows which scientists to believe and which ones to ignore [The Top 10 Science Stories of 2012: Publication of the ENCODE Encyclopedia: A Milestone in Genome Research].
Unfortunately, much of the discussion surrounding the publication of ENCODE failed to focus on the usefulness of the catalogue and the techniques that built it. Instead, much of the debate centered on the failure to understand that transcription does not necessarily imply meaningful biological function. Cells are messy biological entities, with lots of gunk and goo floating around, so mistakes happen all the time. Many DNA sequences get translated into RNA, only to have the cell degrade that RNA. Much, perhaps most, of the DNA in our genomes—despite being occasionally transcribed, and thus recorded in ENCODE—is still functionless “junk DNA.” That is actually not surprising; it is in fact expected from evolutionary theory. Thanks to ENCODE, though, we should eventually learn which sequences are the junk and which are the gems of cell activity.
This is a very different take on the subject than that published by the editors of Science and the Intelligent Design Creationists.
I wonder why?
The folks over at Evolution News & Views (sic) have selected the ENCODE papers as the Number 1 evolution-related story of 2012. Naturally, they fell for the hype of the ENCODE/Nature publicity campaign as you can see from the blog title: Our Top 10 Evolution-Related Stories: #1, ENCODE Project Buries "Junk DNA".
Most of the article is just the reposting of an article by Casey Luskin but some anonymous editor has added ...
Editor's note: For the No. 1 slot among evolution-related news stories of 2012, this one was an easy pick. The publication of the ENCODE project results detonated what had been considered among the sturdiest defenses that Darwinian evolutionary theory could still fall back upon: "Junk DNA." Casey Luskin's initial reporting is featured below. See also our response to the ensuing controversy over ENCODE ("Why the Case for Junk DNA 2.0 Still Fails").
Normally I would make fun of the creationists for misunderstanding the real scientific results in the papers that were published last September but, in this case, there are lots of real scientists who fell into the same trap.
Even Science magazine selected the ENCODE results as a top-ten breakthrough and noted that 80% of the human genome now has a function [Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012]. Oh well, I guess I'll just have to be content to point out that many scientists are as stupid as many Intelligent Design Creationists! 
I can still mock the creationists for claiming that "Darwinian evolutionary theory" supports junk DNA.
Science magazine (published by AAAS) was one of the major news sources that fell hook, line and sinker for the ENCODE/Nature publicity campaign last September [Science Writes Eulogy for Junk DNA]. It even published a laudatory three page profile of Ewan Birney, the man responsible for misrepresenting the ENCODE results as evidence that most of our genome is functional [Ewan Birney: Genomics' Big Talker].
I was somewhat apprehensive when I saw that the editors of Science had picked the ENCODE results as one of the top ten breakthroughs [Genomics Beyond Genes]. Would the editors continue to promote the idea that most of the human genome is functional?
