Closed for the Winter

 
We've just had our first significant snowfall in Toronto and the campus maintenance people have sprung into action. The main ramp leading into my building from the subway station has been closed for the winter. You may recall that this is the entrance where the expensive stone walkway is useless [If you build it, will they follow?].

Toronto is in Canada. In Canada we have real winters, with snow and ice. You may be asking yourself why anyone would build an entrance that has to be shut down for five months of the year. That's a very good question.

This entrance was constructed a few years ago when the Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR) was built. The ramp consists of wood slats with about one centimeter spaces between them. I'm told that a special kind of wood was used and it's very expensive.

Here's the problem as it was explained to me. First, it is difficult to clean ice and snow from a wooden walkway without damaging it. Second, when this kind of wood gets wet it becomes very slippery. That means you can't use salt to get rid of the ice without creating dangerous conditions in the winter.

I'm told that the university and the architects have been unable to reach agreement on who should fix this problem.

CCBR was designed by the architectural firms of Alliance & Behnisch Architekten. The architects won the Royal Institute of British Architects Awards (RIBA) in 2006 for this building [RIBA 2006]. They also won the Governor General's Medal in Architecture for 2008 for this building.

Here's part of the press release from the University of Toronto.

The Governor General's Medals in Architecture recognize outstanding achievement in recently built projects by Canadian architects. These awards are administered jointly with the Canada Council for the Arts, which is responsible for the adjudication process and contributes to the publication highlighting the medal winners. The recipients of the 2008 Governor General's Medals in Architecture were selected by a jury of distinguished architects.

Elizabeth Sisam, assistant vice-president (campus and facilities planning), said buildings like the Donnelly CCBR are very complex and boast many notable features.

"The CCBR is a very clever design that knits the Medical Science Building to the CCBR while being respectful of the heritage buildings and at the same time maintains and enhances pedestrian routes and entrances through to the campus," Sisam said. "Below grade, there are research laboratories that extend all the way to the sidewalk. The inside of the building in the area of the laboratories is a flexible design allowing the research teams to expand and contract. The exterior has a very unique treatment, a 'double façade' which is an excellent example of sustainable design."

The original design did not "knit the Medical Science Building to the CCBR." That was only added after many of us complained about the original design and the Dean of Medicine (David Naylor) intervened to provide extra funding to build the proper connection. In the original plan the buildings would have been quite separate.

The end product does not "maintain and enhance pedestrian routes and entrances through to the campus." The entrance off College St. requires that you climb up an annoying two flights of steps inside the building before gaining access to the lobby where the cafeteria is located. The direct entrance to this lobby from the other side (see photo above) could only be considered an "enhancement" by someone with a wicked sense of humour.

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Science 2.0

 
You may have heard of Science 2.0. It's the latest "revolution" in science. You can read a nice summary from the Howard Hughes Medical Institute [Science 2.0 You Say You Want a Revolution?].


Personally, I think blogging is going the become part of the culture in the same way that newsgroups did in the past except that more people are going to read the blogs. I don't think it's going to be a revolution. I don't think the majority of scientists and students are going to become regular readers of blogs. The blogosphere culture is not for everyone. Many of my colleagues are completely turned off. Blogging is going to be just one more way of communicating science and sharing ideas.

I'm skeptical of OpenWetWare (OWW) and other software that allows you to put all your notes and protocols on the web. Right now, most labs don't make shared electronic versions of protocols and notes even though we've been able to do that for 25 years. I don't see why that's going to change. My notebooks have lots of comments that I've scribbled in the margins (F**k - forgot to add magnesium!). I don't know why I'd want to share that with everyone on the planet.

I've done lots of "secret" experiments in my lifetime just to check out some crazy idea. So have the graduate students and post-docs in my lab. Does this sort of thing never go on in the labs that have adopted open access lab books? That doesn't sound like any kind of lab that I'd like to be in. Too much control for my liking. (According to the article it's "where the cool people are." I don't think so.)

Open-Access Journals are here to stay and will only increase in popularity.

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[Hat Tip: A Blog Around the Clock]

Reprogenetics and Genetic Variants

 
Reprogenetics is a company that offers the following service.

Preimplantation Genetic Diagnosis consists of the biopsy of a single cell per embryo, followed by its genetic diagnosis through different techniques (FISH, PCR, or CGH), and the subsequent replacement to the patient of those embryos classified by genetic diagnosis as normal.

Reprogenetics provides PGD analysis to IVF centers, including diagnosis of aneuploidy for advanced maternal age (such as Down's syndrome), repeated IVF failure, recurrent spontaneous abortions, chromosome translocations and inversions, as well as for gene defects such as Cystic fibrosis, fragile X, Myotonic Dystrophy, Thalasaemia, Tay Sachs, and others. We can also provide an experienced embryologist to perform embryo biopsy and cell processing.

Other tests may be offered soon including predisposition for diabetes and other genetic diseases.

The research director of Reprogenetics was interviewed for an article that appeared today on the Nature website [Gene testing of embryos needs guiding]

Last week, at a meeting of the American Society for Reproductive Medicine in San Francisco, California, researchers cautioned that they do not yet advocate this use of genetic tests. But as the technology advances, consumer demand is likely to overwhelm societal ethical qualms. "If people think they can make their babies healthier at year one, year two, or in utero, they will do it," says Jacques Cohen, research director at Reprogenetics, a genetic-testing company in West Orange, New Jersey.

...

Cohen says that as the understanding of disease genetics progresses, use of tests that seem controversial now may become more acceptable in the future: "If you had the chance to decrease your child's risk of a disease like diabetes and you didn't, society would blame you."

I assume this is a profit-making company. I wonder why Nature chooses to rely on the opinion of someone who has a vested interest in the technology? Especially someone who has an opinion like that?

What can he be thinking? Does he think that the average American in the future will be forced to undergo in vitro fertilization to avoid being sued by their children?

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[Hat Tip: The Sciphu Weblog: This pisses me off a little]

Nobel Laureate: Sinclair Lewis

 


The Nobel Prize in Literature 1930.

"for his vigorous and graphic art of description and his ability to create, with wit and humour, new types of characters"

Sinclair Lewis (1885 - 1951) won the Noble Prize in Literature for his novels about average Americans doing non-average things. The prize committee specifically mentions Main Street, Babbitt, Arrowsmith, Elmer Gantry, and Dodsworth.

Sinclair Lewis was the first American to win a Nobel Prize in Literature.

Arrowsmith is a novel about a scientist. It is one of the first works of the 20th century to describe the realities of being a scientist and really should be required reading for all science students. Lewis relied heavily on his scientific adviser, the microbiologist Paul de Kruif, and the novel is based loosely on Félix d'Herelle. Here's how the novel is described in the presentation speech on the Nobel Prize website.

THEME:
Nobel Laureates

Arrowsmith (1925) is a work of a more serious nature. Lewis has there attempted to represent the medical profession and science in all its manifestations. As is well known, American research in the natural sciences, physics, chemistry, and medicine ranks with the best of our age, and it has several times been recognized as such from this very platform. Tremendous resources have been placed at its command. Richly endowed institutions work unceasingly on its development.

That even here some speculative persons want to take advantage of their opportunities may be regarded as inevitable. Private industries are on the alert for scientific discoveries and want to profit from them before they have been tested and finally established. The bacteriologist, for instance, searches with infinite care for vaccines to cure widespread diseases, and the manufacturing chemist wants to snatch them prematurely from his hand for mass production.

Under the guidance of a gifted and conscientious teacher, Martin Arrowsmith develops into one of the idealists of science. The tragedy of his life as research worker is that, after making an important discovery, he delays its announcement for constantly renewed tests until he is anticipated by a Frenchman in the Pasteur Institute.

The book contains a rich gallery of different medical types. We have the hum of the medical schools with their quarrelling and intriguing professors. Then there is the unpretentious country doctor, recalled from Main Street, who regards it as an honour to merge with his clientele and become their support and solace. Then we have the shrewd organizer of public health and general welfare, who works himself into popular favour and political power. Next we have the large institutes with their apparently royally independent investigators, under a management which to a certain extent must take into consideration the commercial interests of the donors and drive the staff to forced work for the honour of the institutes.

Above these types rises Arrowsmith's teacher, the exiled German Jew, Gottlieb, who is drawn with a warmth and admiration that seem to suggest a living model. He is an incorruptibly honest servant of science, but at the same time a resentful anarchist and a stand-offish misanthrope, who doubts whether the humanity whose benefactor he is amounts to as much as the animals he kills with his experiments. Further we meet the Swedish doctor, Gustaf Sondelius, a radiant Titan, who with singing and courage pursues pests in their lairs throughout the world, exterminates poisonous rats and burns infected villages, drinks and preaches his gospel that hygiene is destined to kill the medical art.

Alongside all of this runs the personal history of Martin Arrowsmith. Lewis is much too clever to make his characters without blemish, and Martin suffers from faults which at times seem obstructive to his development, both as a man and as a scientist. As a restless and irresolute young man he gets his best help from a little woman he encountered at a hospital where she was an insignificant nurse. When he begins to drift about the country as an unsuccessful medical student, he looks her up in a little village in the Far West, and there she becomes his wife. She is a devoted and simple soul, who demands nothing and who patiently waits in her solitude when, bewitched by the siren of science, her husband loses himself in the labyrinths of his work.

Later she accompanies him and Sondelius to the plague-infected island where Arrowsmith wants to test his serum. Her death in the abandoned hut, while her husband listens distractedly to another and more earthy siren than that of science, seems like a poetically crowning final act to a life of primitive self-sacrificing femininity.

The book is full of admirable learning, certified by experts as being accurate. Though a master of light-winged words, Lewis is never superficial when it comes to the foundations of his art. His study of details is always as careful and thorough as that of such a scientist as Arrowsmith or Gottlieb. In this work he has built a monument to the profession of his own father, that of the physician, which certainly is not represented by a charlatan or a faker.

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Gene Genie #40

 
The 40th edition of Gene Genie has been posted at Human Genetics Disorders [Gene Genie Edition 40].

NSGC Conference exibit and MBA thesis poster presentation videos from the October 24-28 2008 AEC Conference by Chavonne Jones

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

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My Desk

 
Eva re-starts another meme.

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I Hate Ironing

 
But these guys seem to like it. What am I missing?

I've been following this sport for several years and I still don't get how they do it. Maybe I need a new iron?

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[Hat Tip: Canadian Cynic, of course.

They're Coming to Your Town!

 
The American Family Association sells Christmas crosses that remind you of something evil [Hide it under a bushel? NO!]. But the website has lots more stuff as pointed out by one reader who commented on my earlier posting.

You really need to see They're Coming to Your Town DVD.

Residents of the small Arkansas town of Eureka Springs noticed the homosexual community was growing. But they felt no threat. They went about their business as usual. Then, one day, they woke up to discover that their beloved Eureka Springs, a community which was known far and wide as a center for Christian entertainment--had changed. The City Council had been taken over by a small group of homosexual activists.

The Eureka Springs they knew is gone. It is now a national hub for homosexuals. Eureka Springs is becoming the San Francisco of Arkansas. The story of how this happened is told in the new AFA DVD “They’re Coming To Your Town.”

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Arwen

 
This is Arwen. Ms. Sandwalk tells me there's a connection between her and Monday's Molecule #97. I didn't know that.¹ Did you?

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1. This is really just an excuse to post the photo.

Monday's Molecule #97

 
Today we're taking a bit of a break from boring old biochemical molecules and fruit flies to look at some specific individuals of the species Homo sapiens. Your task for today is to identify these men. I need all of their names and the name that collectively identifies them.

The answer is indirectly related to this week's Nobel Laureate. See if you can make the connection.

The first one to correctly identify the individuals and name the Nobel Laureate(s), 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 only three ineligible candidates for this week's reward: Bill Chaney of the University of Nebraska, Dima Klenchin of the University of Wisconsin and Dale Hoyt from Athens, Georgia. Dale has agreed to donate the free lunch to a deserving undergraduate so the first undergraduate to win and collect a free lunch can also invite 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. Comments are now open.

The band is Aerosmith and this should remind you of the book "Arrowsmith" by Sinclair Lewis who won the Nobel Prize for Literature in 1930. Arrowsmith is a book about scientists.

Three people knew who the band was—one of them was Ms. Sandwalk! Only one person saw the connection between Aerosmith and a Nobel Laureate but that person (Dima) is ineligible. I decided to award the free lunch to Ms. Sandwalk, making her ineligible for any more lunches for one month!!!

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Hide it under a bushel? NO!

 

This is the latest in Christmas decorations from the American Family Association.

Let Your "Light" Shine For Christ This Christmas Season!

Looking for an effective way to express your Christian faith this Christmas season to honor our Lord Jesus? Now you can.... with the "Original Christmas Cross" yard decoration.

Light up your front yard, porch, patio, driveway, business, organization or church this holiday season with a stunning Christmas cross.

Can't you just picture these five and-a-half foot crosses in the middle of front yards all across America?

What in the world are they thinking?

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[Hat Tip: LuLu at Canadian Cynic]

Be Afraid

 
There have been some changes on Uncommon Descent. Bill Dembski won't be posting as often (Boo!) and the chief web person will be Barry Arrington [What’s New At UD].

Here's a warning from the new chief IDiot.

We live in exciting times. The Darwinist/materialist hegemony over our culture has definitely peaked, and we are privileged to watch the initial tremors that are shaking the Darwinist house of cards. These are only the beginning of woes for St. Charles’ disciples, and I look forward to one day watching the entire rotten edifice come crashing down. I am persuaded that just as when the Soviet Union went seemingly overnight from “menacing colossus astride the globe” to “non-existent,” the final crash of the House of Darwin will happen with astonishing suddenness. You can be sure that we at UD will be there not only reporting on events, but also lending our intellectual pry bars to the effort.

Hmmm ... "intellectual pry bars" ... that's an image that's going to be hard to shake.

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Why do we blog and other important questions

 
OK, so I'm not a Nature Network blogger, but I thought I'd answer the questions anyway.

1. What is your blog about?
   It's about science, religion, universities, politics, and almost everything else I'm interested in. Mostly science and science education.


2. What will you never write about?
   Aha! A trick question! You almost got me!


3. Have you ever considered leaving science?
   No.


4. What would you do instead?
   I dunno, what do other people do? (Eva has a much funnier reply to this question)


5. What do you think will science blogging be like in 5 years?
   Pretty much the same as it is now. Which is pretty much the same as it's been for the past five years. Which isn't a lot different than the newsgroups were for the previous 20 years before that.


6. What is the most extraordinary thing that happened to you because of blogging?
   I've made dozens of new friends. (For me, that's extraordinary.)


7. Did you write a blog post or comment you later regretted?
   Yes.


8. When did you first learn about science blogging?
   I don't recall exactly. It was probably sometime around 2002 when I first learned that people were actually reading them.


9. What do your colleagues at work say about your blogging?
   Most of them don't understand the blogging culture. They think it's bizarre. They think I'm bizarre—but they thought that even before I started Sandwalk

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Be the First in Your School

 
Be the first in your school, or church, to have one of these T-shirts—or others like it. (It also comes in red and black.) Go to Evo-Ts.

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Making Sense in Biology

When I teach students how to read the scientific literature, I caution them not to believe everything they read. Science is, by it's very nature, tentative and exploratory. Much of what is published doesn't get confirmed and is quietly ignored. Many of the ideas and speculations that are published never amount to anything. Some experiments are flawed. Many skim over hidden assumptions so that the conclusions aren't valid.

How do you tell the difference between the wheat and the chaff? Well, for one thing, you ask yourself whether the results "make sense" in light of what you already know. Are there any basic principles of biology that conflict with the conclusions? You always have to be on the lookout for papers that just don't fit in with your current model of how things work.

There are two potential problems with this approach. First, your model may not be correct. Maybe you don't know enough to make a judgment. Second, it prevents you from recognizing truly novel results that may change your idea of what makes sense.

The first problem is curable. The second is more serious. Science is basically conservative in its acceptance of new ideas. This may seem like a bad thing but, in fact, it's the only way to do good science. You simply can't afford to believe in several paradigm shifts every day before breakfast because most of them will turn out to be wrong. Today, when scientists want to convince their colleagues of something new that may not "make sense", they are obliged to present solid evidence that will convince the skeptics. It's an uphill fight. And it should be.

One of my colleagues has been following the discussion about alternative splicing and he directed my attention to a paper he just published in Nature Genetics. He pointed out that far from being an overestimate of alternative splicing, the EST data actually underestimates the extent of alternative splicing.

The paper by Pan et al. (2008) makes two extraordinary claims.

1. Their data indicates that about 95% of all multiexon human genes undergo alternative splicing.
2. They estimate that there are, on average, seven (7) alternative splicing events per multiexon human gene.

Neither of these claims make sense. It's not reasonable to assume that most conserved housekeeping genes produce variants by alternative splicing yet that's exactly what would have to happen if 95% of all genes undergo alternative splicing. It means that most most genes for things like metabolic enzymes, RNA polymerase, ribosomal proteins and transport proteins will have variants due to alternative splicing. This doesn't make sense from an understanding of biochemistry and it doesn't make sense in light of evolution.

That's good reason to be skeptical.

But surely the data must be convincing? Surely the proponents of these extraordinary claims have extraordinary data to back their cease?

Frankly, I don't know. I can't evaluate the Pan et al. (2008) paper because I have no idea how they actually do their experiments and whether those experiments are reliable. Part of the problem is that the authors don't tell me enough and part of it is that this is unfamiliar technology (to me).

All I know is that it doesn't make sense. I've asked the author to give me some specific examples of alternative splicing predictions for common genes, like those in the citric acid cycle. By looking at specific, rather than global, data it might be possible to see whether the results make sense.

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Pan, Q., Shai, O., Lee, L.J., Frey, B.J. and Blencowe, B.J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genetics, published online Nov. 2, 2008. [DOI:10.1038/ng.259]