Mendel's Garden #28

 
The 28th edition of Mendel's Garden has just been posted on Quintessence of Dust [Mendel’s Garden 28th Edition].

Hello and welcome to the 28th edition of the genetics blog carnival known as Mendel's Garden, where we celebrate blogging on topics related to anything touching on what Mendel discovered (or thought he discovered). While reading these interesting and informative pieces, please think about work that should be featured in a future edition and/or blogs (like yours) that would serve well as future hosts.

So do tomato seeds get you excited? No? Oh. Well, they should, if you're at all interested in evolutionary genetics.

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This is what we're up against.

 
PZ posted the first video on Pharyngula. I think it's important to watch both of them to see what goes on in church basements. How can we deal with this level of ignorance about science? It's especially frustrating because these young women are obviously intelligent enough that they should know better.

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Monday's Molecule #106

 
This is the second week in a row that Monday's molecule has been on a Tuesday. Sorry for the delay. I promise to get back on schedule next week.

The observant among you might have noticed that this "Monday's" molecule is not a molecule. It's my version of a machine. You have to identify what kind of a machine this is and what it does.

There are two Nobel Laureates who get credit for developing the technique shown here. One of them is responsible for the specific technique and the other for a similar variant. Name the two Nobel Lauretes.

The first person to identify the machine/technique and the Nobel Laureates 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 six ineligible candidates for this week's reward: Bill Chaney of the University of Nebraska, Maria Altshuler of the university of Toronto, Ramon, address unknown, Jason Oakley of the University of Toronto, John Bothwell from the Marine Biological Association of the UK, in Plymouth (UK), and Wesley Butt of the University of Toronto

Bill and John 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. Since undergraduates from the Toronto region are doing better in this contest, I'm going to continue to award an additional free lunch to the first undergraduate student who can accept a free lunch. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

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.

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What Timothy Sandefur says ....

 
I very much admire Jerry Coyne's article on science vs religion in The New Republic [see: Jerry Coyne on Science vs. Religion]. There's been some discussion on The Edge where participants are asked to address the question Does the empirical nature of science contradict the revelatory nature of faith?.

Timothy Sandefur discusses Coyne's article and the various commnents on his blog Freespace [The future of science teetering on the Edge]. He does such a good job that you should all hop over there as soon as possible and read what he has to say.

Timothy points out that the debate is really about ways of knowing. Can we obtain valid information using the scientific way of knowing? Yes we can. This is rationalism, in my terminology.

Can we obtain valid information using faith as a way of knowing? No we can't. This is superstition and it is the opposite of rationalism.

Is it possible to simultaneously practice both ways of knowing? Here's part of the response by Timothy Sandefur.

Keep the issue in mind: the question is not whether it is possible for someone simultaneously to hold unproven, baseless beliefs about a supernatural dimension and scientific, reasoned conclusions with regard to observed phenomena. It is possible for all sorts of people to believe all sorts of things—just as Humpty Dumpty practiced every day believing six impossible things before breakfast. But it is not possible to do these things and still have intellectual integrity. It requires instead intellectual dis-integration: the skill (if it can be called a skill) of not thinking about the possible connections between the phenomena of the universe. That is, it requires precisely the opposite effort that science requires. It requires one not to think. Alas, as Coyne observes, this effort is officially endorsed by many organizations motivated by political expediency:

It is in [scientists’] personal and professional interest to proclaim that science and religion are perfectly harmonious. After all, we want our grants funded by the government, and our schoolchildren exposed to real science instead of creationism. Liberal religious people have been important allies in our struggle against creationism, and it is not pleasant to alienate them by declaring how we feel. This is why, as a tactical matter, groups such as the National Academy of Sciences claim that religion and science do not conflict. But their main evidence—the existence of religious scientists—is wearing thin as scientists grow ever more vociferous about their lack of faith.

But it’s not just that there aren’t as many religious scientists as some claim. It’s the fact that these two ways of knowing are and always have been, incompatible by their nature, and that those who pledge allegiance to both are either dishonest or simply wrong.

It's nice to see a lawyer making sense.

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Gene Genie #43

 
The 43rd edition of Gene Genie has been posted at Pharmamotion: pharmacology animations and resources [Gene Genie #43: Personal genomics, health and evolution].

Once again, PharmaMotion is hosting a blog carnival. This time is the turn of Gene Genie, a carnival dedicated to cover the buzz around the web about genetics (with some orientation to personalized genetics). I hope that PharmaMotion readers find it interesting.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....

1. Scienceroll
2. Sciencesque
3. Genetics and Health
4. Sandwalk
5. Neurophilosophy
6. Scienceroll
7. Gene Sherpa
8. Eye on DNA
9. DNA Direct Talk
10. Genomicron
11. Med Journal Watch
12. My Biotech Life
13. The Genetic Genealogist
14. MicrobiologyBytes
15. Cancer Genetics
16. Neurophilosophy
17. The Gene Sherpa
18. Eye on DNA
19. Scienceroll
20. Bitesize Bio
21. BabyLab
22. Sandwalk
23. Scienceroll
24. biomarker-driven mental health 2.0
25. The Gene Sherpa
26. Sciencebase
27. DNA Direct Talk
28. Greg Laden’s Blog
29. My Biotech Life
30. Gene Expression
31. Adaptive Complexity
32. Highlight Health
33. Neurophilosophy
34. ScienceRoll
35. Microbiology Bytes
36. Human Genetic Disordrs
37. The Genetic Genealogist
38. ScienceRoll
39. Genetics & Health
40. Human Genetics Disorders
41. ScienceRoll
42. Genetic Future
43. Pharmamotion

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Should senior scientists be bloggers?

 
Eva asks the questions on her Nature Network blog [Bloggers]. I was going to leave a comment there but I can never remember my login name and password.

I hate sites like that.

The answer seems pretty obvious to me. Some small percentage of senior scientists will enjoy blogging but most won't. It's not a big deal. There's no reason to encourage more senior scientists to blog. They'll do it naturally if they feel the need.

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The University of Vermont Does the Right Thing

 
My impression of the University of Vermont has just gone way up. According to WCAX News in Vermont, the University has decided that Ben Stein is not an appropriate commencement speaker [Stein Withdraws as UVM Speaker].

Burlington, Vermont - February 2, 2009

Ben Stein won't be bidding UVM graduates goodbye after all.

Just last week, the university announced that Stein, who is highly acclaimed as an actor, author, and economist, would be delivering this year's commencement address. But Monday, the school announced that he has now withdrawn as speaker.

Stein has made headlines recently for his views regarding Darwin's theory of evolution, intelligent design and the role of science in the Holocaust. Several people from the academic community-- both locally and beyond the UVM campus-- quickly expressed concern over his selection and once notified of that, Stein withdrew from the ceremony.

"This is not, to my mind, an issue about academic freedom or the openness of the campus to all points of view. Ben Stein spoke here last spring to great acclaim," UVM President Dan Fogel said. "It's an issue about the appropriateness of awarding an honorary degree to someone whose views in many ways ignore or affront the fundamental values of scientific inquiry and I greatly regret that I was not attuned to those issues."

Fogel said the school's honorary degree committee has a list of potential candidates and he will consult others before extending an invitation to another potential commencement speaker.

Good for President Fogel. He's right. It is not appropriate to award an honorary degree to "someone whose views in many ways ignore or affront the fundamental values of scientific inquiry."

I wonder if Dan Fogel realizes that he has just earned himself a prominent place in "Expelled II"?

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A Message from Genome Canada

 
Genome Canada did not get the funding it requested in the latest budget. In fact, it got nothing at all. Here's a message from the Board of Directors of Genome Canada [Federal Budget 2009].

• Genome Canada is pleased with the federal government’s 2009 budget in which millions will be invested in research infrastructure over the next two years. This is good news for the scientific community across the country that needs to be at the cutting-edge of research infrastructure and new technologies in order to maintain Canada’s competitiveness at the national and international level.
• Although Genome Canada did not receive funding in the 2009 federal budget to fund new genomics research projects, this will not impact Genome Canada’s current projects that received a full commitment of funding from previous federal government investments in 2007 and 2008.
• Genome Canada has in place two five-year funding agreements with the Government of Canada for a total of $240M: $100 M (2008-2012) $140 M (2009- 2013)
• These investments flow to Genome Canada on a cash requirement basis. Thus, a total of $107M has been invested in 2008-09; and a total of $106.5M will be invested in 2009-10, creating and maintaining over 2,350 HQP positions per year.
• Over the same period of time, Genome Canada has raised over $225M from other strategic partners in the private, public and philanthropic sectors to support genomics research in Canada.
• Since its inception in 2000, Genome Canada has provided operating funds to Canadian genomics researchers, while complementing other sources of funds for infrastructure coming from such agencies as Canada Foundation for Innovation, to allow them to be among world leaders in their respective fields such as human health, agriculture, environment, forestry, fisheries, new technology, and GE3LS (ethical, environmental, economic, legal and social issues).
• Genome Canada is confident that the Government of Canada and its other financial strategic partners will do everything possible over the coming years to secure additional funding to support new initiatives in genomics research in Canada while increasing Canada’s productivity, wealth and well-being of all Canadians.

What a bunch of wimps. Here's the list of the Board of Directors.

It's one thing to praise the government for not giving you the money you requested but it's quite another to heap praise on a government that is cutting funding to the major granting councils. Yes, it's true that the budget contains money for infrastructure support but that money will be useless without operating grants. Operating grants are the bread and butter of scientific research. They are what pays for the day-to-day expenses of operating a research lab. It doesn't matter how nice your building is if you can't buy enzymes and chemicals. Modern science is expensive.

Operating grants also pay the salaries of research assistants, graduate students, summer students, and post-docs.

Myopic governments don't like to fund operating grants because that's a long-term commitment. One-time-only (OTO) money is much better 'cause you can get a big bang for your buck (publicity and votes) and you don't have to make any promises.

Genome Canada's directors should know this. They should not be sending out a press release that looks like they are backing the government decision to destroy basic research. Unless, of course, they agree with that strategy.

This brings up another point about Genome Canada. Many scientists, including me, don't think that the Genome Canada model is the way to fund research. In that sense, I'm not all that upset that it wasn't funded. If you want to learn more about the problems of co-funding and market-drive science then read the latest posting from Chris Hogue [Market Driven Science in Crisis?]. He knows what he's talking about.

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Hat Tip: iBiome: Genome Canada cut good for science?, And now, the walkback

My New York Ancestors

 
The January 24th issue of The New York Times has a article on what New york City must have looked like 400 years ago. The image is based on work by Eric W. Sanderson [Henry Hudson’s View of New York: When Trees Tipped the Sky].

The first Dutch North American Ancestors in my family were Hendrick Harmensen who was born about 1590 in Lent (Netherlands) near present day Nijmegen and his wife Catherine. They came to North America around 1638 with their daughter Grietje and her husband Abraham Rycken or (de Rycke) who was born about 1618, also in Lent (van Lent).

It is said that Harmenson was the first European to plant crops on Long Island. His farm was near the place where La Guardia airport is today. Harmenson was a blacksmith and he used to make tomahawks for the Indians. He was murdered in a local uprising in 1643. The cause of death was a blow to the head from one of his own tomahawks.

Arbraham Rycken and his wife owned a lot of property on Long Island, including a small island off the coast near their farms. Their children adopted several names including "van Lent" and "Riker." The small island remained in the family for several hundred years and it is still known as Rikers Island—now the site of a large prison.

Their daughter, Aeltje, married Captain Jan Harmse, a descendant of German/Dutch immigrants. Captain Harmse was born in New Amsterdam (New York) in 1657. Their son, Harmen Harmse (1684-1720), married Margaret Montras (1691-1739) thus uniting my French and Dutch ancestors. Harmen took his wife's last name. They moved to Tarrytown New York and joined the congregation of the Dutch Reformed Church of Sleepy Hollow.

The son of Harman and Margaret Montras is Peter Montras (1715-1790). He was my great⁶ grandfather.

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Intelligent Design Creationism

 
During the Kitzmiller v. Dover Area School District trial the question of whether Intelligent Design Creationism was really creationism was a hot issue. Professor Barbara Forrest's testimony put to rest any doubts on that score.

You can read the trial transcript on the TalkOrigins website. In this excerpt she is addressing the various editions of the creationist book that is now called Of Pandas and People.

You'll notice that the word "creation" has an ending, it has an "-is" ending. That is so that the counter will pick up any cognate of that word, creationist or creationism, that both will be counted, and here we're looking for the term "intelligent design" rather than just "design." What this indicates is that you see the same thing in these drafts. In the early drafts you see the use of the term "creationism" and its various cognates. Not very much use at all of the term "intelligent design." In fact, in Creation Biology it's zero times. And then subsequent to the version 1 of Pandas 1987 you see a steep decline in the use of the term "creation" and its various cognates, and you see a very sharp rise in the use of the term "intelligent design" in that second version of Pandas of 1987.

You can see that creationism morphed into Intelligent Design. The biggest shift occurred in 1987 when the US Supreme Court ruled, in Edwards v. Aguillard, that creationism was religious and couldn't be taught in public schools. The replacement of "creationism" with "intelligent design" was a political move designed to make belief in a creator sound less religious.

It's not a surprise that old-school creationism became Intelligent Design Creationism. After all, the same players were involved and 99.99% of those who advocate intelligent design also believe in a creator God. All this is old news to most of you but it bears repeating from time to time.

What's surprising is that there are Intelligent Design Creationists who deny that they are creationists. Usually they try and restrict the term "Creationist" to the Young Earth Creationism of the biblical literalists but the evidence in "Pandas" is conclusive. The Intelligent Design Creationism in Of Pandas and People is clearly derived from creationism.

Here's an example of our most famous Doctor IDiot (Michael Engor) bending over backwards to make a fool of himself in Reviewing Jerry Coyne. He's pushing the claim that there's no connection between "creationism" and "intelligent design."

Dr. Coyne misunderstands the history of this issue. Regardless of whether or not creationism has undergone an “evolutionary” process, ID isn’t on the historical continuum with creationism. Creationism is the opinion that Genesis is more or less literally true as science. Many Christians hold to that view, and they have my respect, but I (and the vast majority of I.D. advocates) disagree.

Intelligent design is the opinion that design is empirically detectable in biology, and that it is the best scientific inference to explain many aspects of biology, especially the genetic code and the complex molecular machinery inside cells. I wasn’t a creationist, ever. I was a Darwinist, for most of my life, until I looked closely at the evidence. Most ID advocates have had similar experiences. Most ID advocates were never creationists, and ID is not creationism nor is it derived from it. In fact, ID has been criticized by the creationist community. ID is an appeal to evidence in the natural world, not an appeal to Biblical revelation.

Hmmm ... "ID is not creationism nor is it derived from it." I guess Michael Engor has never read anything about that little episode in Dover only four years ago.

I believe that Michael Egnor is a creationist. I think he believes in a God who created the universe. I will continue to call him an Intelligent Design Creationist—as opposed to a Young Earth Creationist—unless he's willing to deny the existence of a Creator.¹

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1. Who, coincidentally, just happens to be the intelligent designer as well.

Shame on The University of Vermont

 
The University of Vermont will be awarding an honorary degree to Ben Stein, the man behind the movie Expelled. Here's the press release from the University of Vermont [Ben Stein to Deliver Commencement Address]. Notice that they don't mention the movie. That's no excuse.

The multi-talented Ben Stein, actor/comedian/lawyer/economist/presidential speechwriter/filmmaker, will address the graduates and receive an honorary degree at the University of Vermont's 205th commencement ceremony on Sunday, May 17.

Popularly known as the host of Comedy Central's seven-time Emmy award winning game show, "Win Ben Stein's Money," and for an iconic classroom scene in the film Ferris Bueller's Day Off, Stein is also an accomplished writer who has published 30 books and written for publications ranging from the Wall Street Journal and The New York Times to E! Online and New York Magazine. Stein earned his undergraduate degree with honors in economics from Columbia University and went on to graduate as valedictorian of his class from Yale Law School. He has taught at American University, the University of California at Santa Cruz and Pepperdine University in subjects ranging from political and social content of mass culture to securities law. Along with his academic and entertainment achievements, Stein has as served as a trial lawyer for the Federal Trade Commission and as White House speechwriter for presidents Nixon and Ford.

The University of Vermont offers a Major in Biochemistry. Before enrolling, students need to check out the courses to see if they encourage critical thinking and to see how evolution is presented.

The University of Vermont has every right to award honorary degrees to anyone they want. That's what academic freedom is all about. The downside is that the University of Vermont will be judged by who they choose to get an honorary degree. That judgment is not going to be favorable.

UPDATE: Ben Stein has decided that he has another commitment that will prevent him from receiving the honorary degree from the University of Vermont [Stein backs out].

Having been involved in selecting honorary degree recipients, I can assure everyone that you don't make public announcements until the candidate has agreed. Thus, it looks very much like Ben Stein and the university have made a joint decision that inviting Stein to accept an honorary degree was a mistake.

I'm glad the University of Vermont came to its senses.

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Professor Alex Palazzo Is Coming to Toronto!!!

 
Alex Palazzo has been hired by my department as an Assistant Professor (tenure-stream). He'll be arriving in a few months to set up his lab.

Most of you know Alex from his blog The Daily Transcript. Pop on over there to congratulate him [The Deed is Done].

The Department of Biochemistry should also be congratulated for landing such an outstanding candidate. You can leave comments here and I'll make sure everyone sees them.

Alex's work on the targeting of messenger RNA is extremely impressive. Everyone in the Department wanted to offer him the job as soon as he finished his visit last summer. We all look forward to having him as our colleague. The fact that we will now have two blogging Professors is a nice bonus.

Palazzo, A.F., Springer, M., Shibata, Y., Lee, C.S., Dias, A.P., and Rapoport, T.A. (2007) The signal sequence coding region promotes nuclear export of mRNA. PLoS Biol. 5(12):e322 [doi:10.1371/journal.pbio.0050322]

In eukaryotic cells, most mRNAs are exported from the nucleus by the transcription export (TREX) complex, which is loaded onto mRNAs after their splicing and capping. We have studied in mammalian cells the nuclear export of mRNAs that code for secretory proteins, which are targeted to the endoplasmic reticulum membrane by hydrophobic signal sequences. The mRNAs were injected into the nucleus or synthesized from injected or transfected DNA, and their export was followed by fluorescent in situ hybridization. We made the surprising observation that the signal sequence coding region (SSCR) can serve as a nuclear export signal of an mRNA that lacks an intron or functional cap. Even the export of an intron-containing natural mRNA was enhanced by its SSCR. Like conventional export, the SSCR-dependent pathway required the factor TAP, but depletion of the TREX components had only moderate effects. The SSCR export signal appears to be characterized in vertebrates by a low content of adenines, as demonstrated by genome-wide sequence analysis and by the inhibitory effect of silent adenine mutations in SSCRs. The discovery of an SSCR-mediated pathway explains the previously noted amino acid bias in signal sequences and suggests a link between nuclear export and membrane targeting of mRNAs.

More papers are in the works.

I hope to see Alex very soon. I owe him a beer.

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Randolph Nesse on Darwinism

 
Randolph Nesse is the co-author of "Why We Get Sick: The New Science of Darwinian Medicine" (along with George C. Williams). This is the uncut version of an interview with Richard Dawkins. Thanks to RichardDawkins.net for posting the video.

The subject is evolutionary medicine.

It's interesting how one's perspective can be distorted by only thinking about animals. Nesse wonders how large multicellular species can survive when bacterial pathogens can evolve so rapidly. Part of his answer is the immune system but he also talks about pain and vomiting as adaptive responses to disease.

If you think about trees and tulips, you might come up with very different answers to the same questions. Plants survive very well without an immune system or pain. It makes you realize that there are different ways of solving a problem.

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Are You as Smart as a Second Year University Student? Q5

 
Are You as Smart as a Second Year University Student?

Question 1
Question 2
Question 3
Question 4
When you ask my students to remember some important facts about evolution and biochemistry, 98% of them get it right. This question was way too easy. How do Sandwalk readers do?

The evolutionary approach to biochemistry is often called “comparative biochemistry” because it involves comparing enzymes and pathways in different species. The objective is to recognize the fundamental principles that apply to all living organisms. Which of the following insights gained from such an approach is WRONG?

a) the enzymes of the gluconeogensis pathway evolved before
      those that are specific for the glycolytic pathway
b) not all species have a citric acid cycle
c) you can have membrane-associated electron transport
      without oxygen
d) the plant photosynthesis pathway arose from combining two
      different photosystems
e) the P/O ratio is the same in all species

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Are You as Smart as a Second Year University Student? Q4

 
Are You as Smart as a Second Year University Student?

Question 1
Question 2
Question 3
My students love doing problems. 91% of them got this one right.

In a typical bacterial cell the membrane potential across the inner membrane is –0.15 V. The protonmotive force is –21.2 kJ mol^-1 at 25°C . If the pH in the periplasmic space is 6.35 what is the pH in the cytoplasm?

a) between 6.40 and 6.69
b) between 6.70 and 6.99
c) between 7.00 and 7.29
d) between 7.30 and 7.59
e) between 7.60 and 7.89

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