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Monday, March 23, 2009

Old Tools

 
Eva has posted some photos of old lab equipment and tools [Old Tools]. Check them out to see if you recognize anything.

Here's another contribution. How many readers know what this is and what it was used for in prehistoric times? (Click to embiggen.)



Fox News host apologizes

 
From the CTV website: Fox News host apologizes in face of Canadian outrage. [See the video at: Here's What Fox News Thinks of Canada's Military.]
The host of a Fox News program has apologized for a segment on the Canadian military that Defence Minister Peter MacKay called "disgusting" and "crass."

A group of pundits on "Red Eye with Greg Gutfeld," which airs weekdays at 3 a.m. on Fox News, each took turns trashing Canada and its military during an episode that aired on March 17.

...

Gutfeld issued an apology Monday afternoon saying, "I realize that my words may have been misunderstood. It was not my intent to disrespect the brave men, women and families of the Canadian military, and for that I apologize."

But the host also seemed to defend his program, adding "Red Eye is a satirical take on the news, in which all topics are addressed in a lighthearted, humorous and ridiculous manner."
I wonder if they've ever treated 9/11 in a "lighthearted, humorous and ridiculous" manner? What about the USA? Have they ever mocked their own country on this show?


Monday's Molecule #113

 
Identify this molecule and briefly describe its function. You must supply the common name and one of the the formal IUPAC names.

I'm looking for the Nobel Laureate who discovered this molecule.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto, Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, and Alex Ling from the University of Toronto.

Dima has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

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 Prizes 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.


Dropping Courses

 
Chad Orzel of Uncertain Principles has started a discussion about when students should be allowed to drop courses [Academic Poll: Drop It Like It's Hot?].

Why not visit his blog and share your thoughts? I think this is an important issue. Universities may need to make changes.


Astrology in The Toronto Star

 
I read The Toronto Star every day but I missed this article published last Friday [The vernal equinox: Science and mysticism].

Staff reporter Nick Aveling thought it would be fun to contrast the words of a scientist (Astronomer Randy Attwood) and an astrologer (Michael Barwick). The title of the article implies that this might be an attempt at humor but I'm not sure.
What are the implications of today's equinox?

Attwood: As the earth goes around the sun it appears that the overhead sun seems to be creeping towards the north. For the next three months it will continue to creep north until the first day of summer, when it's at its farthest point north. As the sun gets higher that means it's able to concentrate more heat on the ground.

Barwick: Somebody who's born at 0 degrees Aries – that's a particularly strong Aries person ... William Shatner, Captain Kirk, has kind of the ultimate Aries energy in a way: going forth, boldly going where no one has gone before, pioneering, being in command, leading intuitively. This is Aries.
Phil Plait of Bad Astronomy didn't think it was funny: Canada slips further into goofiness. Neither did any of the people who posted comments on the newspaper's website.


Old Tools

 
Eva has posted some photos of old lab equipment and tools [Old Tools]. Check them out to see if you recognize anything.

Here's my contribution. How many readers know what this is and what it was used for in prehistoric times? (Click to embiggen.)




Sunday, March 22, 2009

Gene Genie #44

 
The 44th edition of Gene Genie has been posted at Mary Meets Dolly [Gene Genie #44].
My first Gene Genie! For my Catholic readers, Gene Genie is the "blog carnival of genes and genetic conditions." (No rubbing of ancient oil lamp necessary.) I hope I shall do it justice.
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
  44. Mary Meets Dolly




SEED Reviews The 10,000 Year Explosion

The latest issue of SEED praises US President Obama's emphasis on science and offers a list of ideas "for revising the role of science in America." The number one recommendation is "Make Scientific Literacy a National Priority."
What's needed is better ways of fostering critical thinking and imagination not only in the nation's schools but among its citizenry.

Scientific literacy is not just about being able to weigh in on scientific debates of the day by parsing climate change or understanding the difference between a theory and a guess. The ability to empirically test one's ideas about the world and discard beliefs in light of new evidence is fundamental to the ideals of a just and democratic society; it brings people to the table to debate issues reasonably and with minimum rhetoric.
Good advice, although I wish they'd mentioned the importance of skepticism along with critical thinking. Scientifically literate citizens should not blindly accept every new breakthrough that appears in the scientific literature.

We must rely on good science journalism to inform the general public. Good science journalists will analyze and distill the latest scientific information and help put it in context. They will explain things that are controversial, but exciting, and avoid being swept up by the inevitable rhetoric that accompanies every new discovery.

T.J. Kelleher is a senior editor at SEED. In this same issue, Kelleher reviews The 10,000 Year Explosion a book by Gregory Cochran and Henry Harpending. Let's see whether the review is an example of critical thinking.

This is a trade book, not a scientific publication. The main thesis of the book is that humans are evolving rapidly. This thesis is supported by several lines of evidence.
  1. A number of just-so stories from anthropology [see Examples of Accelerated Human Evolution]. Some of them are reasonable, many aren't.
  2. A paper published in Dec. 2007 claiming there are thousands of human genes being selected in various populations (Hawks et al. 2007). To the best of my knowledge this analysis has not been independently replicated in the scientific literature and the technology is not without critics.
  3. A paper by Hawks et al. (2008) claiming that human adaptive evolution has recently accelerated by acquiring genes from Neanderthals.
  4. A claim that within the past 1,000 years the IQ of Ashkanazi Jews has increased relative to the general European population because medieval Ashkanazi Jews engaged in occupations that required high intelligence (Cochran et al. 2006). [See Race and Intelligence, Evolution in the Ashkenazi Jewish Population.]
All this makes for a very interesting book and an idea that's worth serious consideration. It will be interesting to discover, over the next few years, whether there are thousands of genes under positive selection, whether there are only hundreds and the rest are being influenced by random genetic drift, or whether the genetic analysis is subject to artifacts.

Let's see what T.J. Kelleher thinks of all this. Here's the first two paragraphs of the review.
"The 10,000 Year Explosion" would be important even if it were only about population genetics and evolutionary biology, but Gregory Cochran and Henry Harpending, a physicist turned biologist and a biological anthropologist, respectively, at the University of Utah, have written something more. This book is a manifesto for and an example of a new kind of history, a biological history and not just of the prehistoric era. Covering broad ground over human history and prehistory, the authors argue for the singular importance of genes in human history, not just as markers but also as makers.

The first four of the book's seven chapters serve as something of a preamble to the final three. Cochran and Harpending first present the evidence for recent, accelerated human evolution after the invention of agriculture. In its own right that argument is a fairly revolutionary proposition, bit one with clear data, both skeletal and genetic, to back it up: investigations of the human genome undertaken as part of the International Hap Map Project and elsewhere have clearly demonstrated that selection has been ongoing and has accelerated over time. This has been a landmark finding in human biology, and Cochran and Harpending, building on their own work and that of others, including John Hawks of the University of Wisconsin-Madison, convincingly tie the advent of architecture—and the stresses resulting from the new diets. new modes of habitation, new animal neighbors, and new modes of living that agriculture made possible—to this accelerated evolution. It is work destined to launch a thousand careers.[My emphasis-LAM]
Is this an example of critical thinking? Is this the best way to enhance scientific literacy?


Cochran, G., Hardy, J., and Harpending, H. (2006) Natural history of Ashkenazi intelligence. J. Biosoc. Sci. 38:659-93.

Hawks, J., Cochran, G., Harpending, H.C., and Lahn, B.T. (2008) A genetic legacy from archaic Homo. Trends Genet. 24:19-23. Epub 2007 Dec 3. [PubMed] [DOI: 10.1016/j.tig.2007.10.003 ]

Hawks, J., Wang, E.T., Cochran, G.M., Harpending, H.C., and Moyzis, R.K. (2007) Recent acceleration of human adaptive evolution. Proc. Natl. Acad. Sci. (USA) 104:20753-20758. Epub 2007 [PubMed] [DOI:10.1073/pnas.0707650104]

New Scientist Sheds its Last Ounce of Credibility

Many of us were upset last month when New Scientists published some old news about the early tree of life and sensationalized it on their cover [Darwin Was Wrong?]. They claimed that "Darwin Was Wrong" when, in fact, Charles Darwin didn't even know about molecular evolution or the relationships of bacterial species.

The New Scientist editors admitted that the cover was designed to sell magazines and they seemed to be aware of the problem [Explaining the New Scientist Cover].

They even published a critical letter from Daniel Dennett, Richard Dawkins, Jerry Coyne, and PZ Myers [Blunt Talk from Four Evolutionists].

New Scientists has now begun an ad campaign to attract new subscribers and guess which cover they choose? Jerry Coyne and PZ Myers are advocating a scientific (Coyne) or personal (PZ) boycott of New Scientist. I'm conflicted about that. In spite of its recent errors, New Scientist is far superior to SEED and Discover as a science magazine. If we really want to punish the worst of the popular science magazines then SEED is a much better target.1




1. The monthly column by PZ Myers in SEED is the exception, not the rule.

Here's What Fox News Thinks of Canada's Military

 
The ignorance in this segment makes me very angry. Can anyone tell me what the US military is protecting Canada from? The Iraqis? Cubans? The people of Granada or Panama? Kosovo? Afghanistan? Lebanon? Maybe the Somalis, or the Vietnamese?

Canada has only been invaded once in its history (1812) and it wasn't by any of those countries.

Does this embarrass any of my American friends, especially those who like to defend the American media?




[Hat Tip: Canadian Cynic]

Saturday, March 21, 2009

What Is This?

 
This is cool (and refreshing). To find out what it is, visit Mentha ×piperita.



Canada Has Been Saved from George Galloway

 
George Galloway is a Scottish MP who speaks out on behalf of Palestinians and expresses support for Hamas. He was recently invited to Canada to give a speech in Toronto but Canada's Immigration Minister, Jason Kenney, immediately recognized that Canada can't tolerate that. Kenney determined that a member of the British parliament is a threat to our national security and Galloway was banned from entering Canada.

Jennifer Smith is embarrassed by her country's behavior [Jason Kenney's Personal War on Terror]. So am I.



"Science journalists? Don't make me laugh"

 
"Science journalists? Don't make me laugh" is the title of an article by Ben Goldacre appearing in The Guardian. Goldacre discusses how British health and science journalists covered the recent papers on testing for prostate cancer.

The bottom line is ...
Journalists insist that we need professionals to mediate and explain science. From today's story, their self-belief seems truly laughable.
Note to science journalists; people are beginning to catch on to your scam. Matt Nisbet helped a lot by making it obvious.

I want science journalists to start policing themselves. It's time to take off the blinders and recognize that many science journalists are not very good at accurately reporting about science. The good ones need to speak out instead of issuing motherhood statements about how good they all are.


Friday, March 20, 2009

Get a Job in Newfoundland

 
Memorial University of Newfoundland
Tenure-track Positions in Gene Expression and Metabolic Biochemistry

The Department of Biochemistry at Memorial University invites applications for two tenure-track positions at the level of Assistant Professor, one in each of the targeted areas listed below. Applicants should have a PhD or equivalent degree with a minimum of two years post-doctoral research experience and should possess a strong research record with significant future promise. The successful applicants will be expected to develop externally funded research programmes with relevance to one of the research foci of the department: 1) Development and health, and 2) Membranes and molecular interactions. They will also be expected to show a commitment to effective teaching at the undergraduate and graduate levels. The new faculty members will be encouraged to collaborate with the faculty in the department and elsewhere in the university.

1) Gene Expression (ref # VPA-BIOC-2008-001). The successful applicant for this position will be expected to develop a research programme focused on some area of gene regulation such as, but not limited to, transcriptional regulation by DNA-protein interactions, chromatin structure/remodeling, or gene expression profiling.

2) Metabolic Biochemistry (ref # VPA-BIOC-2008-002). The successful applicant will be expected to develop a research programme focused on some area of metabolic biochemistry such as, but not limited to, metabolomics, gene-nutrient interactions, or metabolic regulation including signaling pathways.

Applicants should submit a curriculum vitae, a summary of past research, a statement of proposed research and reprints of 3 publications. The application must be accompanied by the names, affiliations and contact information of three referees.

Memorial University is the largest university in Atlantic Canada offering diverse undergraduate, graduate and medical school programmes to almost 18,000 students. As the Province’s only university, Memorial plays an integral role in the educational and cultural life of the Province of Newfoundland and Labrador. The Biochemistry Department consists of 18 faculty with expertise in a wide range of biochemical areas. For information about the Department of Biochemistry please see the departmental webpage. St. John’s is a safe, friendly city with great historic charm, a vibrant cultural life, affordable housing and easy access to a wide range of outdoor activities. For more information about St. John’s please see the municipal website.

Memorial University is committed to employment equity and encourages applications from qualified women and men, visible minorities, aboriginal people and persons with disabilities. All qualified candidates are encouraged to apply; however, Canadian Citizens and Permanent Residents will be given priority. Partners of candidates for positions are invited to include their resumes for possible matching with other job opportunities.

Applications should be received by the Department of Biochemistry by May 15, 2009.

Applications should be addressed to: Dr. Martin Mulligan, Head, Department of Biochemistry, Memorial University, St. John’s, NL, Canada, A1B 3X9. Applications may also be submitted electronically to biochead@mun.ca or by fax: (709) 737-2422. Please quote the appropriate job reference number on all correspondence.


Happy Vernal Equinox!

 
Today at 11:44 UT (= 7:44 AM Eastern Time) the sun appeared to cross the celestial equator in its northward movement. (See Movement of Our Star for the real explanation.)

Most people in the Northern Hemisphere think of this as the first day of Spring. I prefer to think of it as the end of Winter. Springlike days are still a few weeks off in Toronto.

Here's a brief explanation from Wikipedia.
An equinox in astronomy is the moment in time (not a whole day) when the centre of the Sun can be observed to be directly above the Earth's equator, occurring around March 20 and September 23 each year.

More technically, at an equinox, the Sun is at one of two opposite points on the celestial sphere where the celestial equator (i.e., declination 0) and ecliptic intersect. These points of intersection are called equinoctial points—the vernal point and the autumnal point. By extension, the term equinox may be used to denote an equinoctial point.



[Photo Credit: The photograph shows the position of the sun at various times throughout the year at 12h (UT) over the Temple of Aphaia (490-480 BC), Athens (Anthony AYIOMAMITIS). The image is called the solar analemma. See here for an explanation. The celestial equator is perpendicular to the long axis of the image and half way between the top and bottom. The crossover point of the figure eight depends on your distance from the equator. I'd love to see one taken on the equator or in the southern hemisphere.]

[Image Credit: eSky]