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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 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]

"Science is my job - faith is my rock"

 
"Science is my job - faith is my rock" is the title of an article in today's Globe and Mail. Zosia Bielski is a journalist who writes on a wide range of topics with an emphasis on social issues. She was prompted to write about the conflict between science and religion because of the controversy surrounding Canada's Science Minister, Gary Goodyear.

As usual, there's no mention of the fact that most active scientists are non-religious. The proportion of atheist scientists is much higher than the proportion of atheists in the general public. Apparently this fact has little to do with a conflict between science and religion.

Zosia Bielski takes the standard approach to this issue. She interviews three religious scientists and discovers that they can reconcile their faith and science. What a surprise!

She does not interview anyone who thinks there's a serious conflict between science and religion. If she had written an article about the lack of faith among scientists and had only interviewed atheist scientists, she would have been accused (rightly) of biased journalism. The lack of balance would have been recognized by any competent editor and she would have been told to go out and get statements from religious scientists. It seems like "balance" only works one way.

What's interesting about the article is that she interview Rev. Ambury Stuart, a climatologist who is also a United Church minister. What Stuart has to say about the conflict between science and religion is very interesting.
"I struggled with this all my life. I grew up in the United Church, I always attended. You say, 'Well, can you believe in God if you believe in Newton's laws?' And the short answer is yes, you can, but it takes a while," Mr. Stuart said.

"You have to think through a lot of stuff. It's not simplistic. You try and divide your brain into two bits: One bit you'll use on Sunday and the rest of it you'll use the rest of the week, and it doesn't work. It doesn't have to."

Evolutionary evangelist Michael Dowd's book "Thank God For Evolution" helped Mr. Stuart smooth out his own message at Glebe Road United Church in Toronto. He weaves his scientific passions into his sermons.

"You can look at scripture and say this means a whole lot more than we ever thought it meant before, because it applies to everything," Mr. Stuart said. "The idea that we are related, that we are kin with the rest of life, is essential for Christianity to do anything constructive in the ecological crisis."
This is about as honest as you get. Stuart is telling us that the conflict between religion and science is real and challenging. You have to work really hard at reconciling science and religion. Many religious beliefs don't survive the challenge.

That's an important lesson for people like Gary Goodyear. Any religion that denies evolution is incompatible with science. You have to choose one or the other. You can't be a Young Earth Creationist without being anti-science. If that kind of faith is your "rock" then science can't be your job.


Thursday, March 19, 2009

Nobel Laureate: Willard Libby

 

The Nobel Prize in Chemistry 1960.

"for his method to use carbon-14 for age determination in archaeology, geology, geophysics, and other branches of science"


Willard Frank Libby (1908 - 1980) won the Nobel Prize in Chemistry for using 14C decay to date organic material. Libby set out to study cosmic rays. He, and others, determined that one of the effects of cosmic ray is to produce carbon-14 atoms from nitrogen-14 atoms in the upper atmosphere.

He determined that the rate of production of carbon-14 and its rate of disintegration (half-life ~5600 years1) has reached an equilibrium. No matter where you find carbon, in the ocean, the atmosphere, or the biosphere, its radioactivity corresponds to about 14 disintegrations per minute per gram.

Living things incorporate this equilibrium mixture of 14C and 12C. Thus, we, like all other living things, are radioactive and this level of radioactivity can be measured using techniques that Willard Libby developed. When living things die, they stop incorporating carbon and the existing 14C continues to decay. As time goes on, the level of radioactivity declines with a half-life of ~5600 years. The age of organic material can be determined directly by measuring the remaining radioactivity of extracted carbon.

That's the basis of radiocarbon dating. Libby confirmed the feasibility of the technique by dating Egyptian artifacts, tree rings of known age, and the dead sea scrolls (labeled "Bible" in the figure). The results confirmed that radiocarbon dating works.


The results were published in the late 1940's. Since then, the technology has improved considerably. Today, scientists measure 14C directly using mass spectrometry so they don't have to wait for it to decay. Detailed calibration curves have been worked out to take account of the fact that cosmic ray intensity has varied somewhat over the past few thousand years.

With current technology, reliable dates back as far as 60,000 years can be obtained. This is about the limit of radiocarbon dating because the half-life of Carbon-14 is so short compared to more long-lived isotopes.

The presentation speech highlights the importance of radiocarbon dating in a number of disciplines.
THEME:
Nobel Laureates
Libby's dating method soon attracted attention from the scientific world, and it was not long before carbon-14 laboratories were set up in many countries. Today, some forty institutions carry on investigations in this field, nearly half of them in America. Also here, in Sweden, we have such institutions, and their investigations have given results of great value. All age determinations - nowadays several thousand every year - are published in a general review, and thus made rapidly available throughout the world. The literature in this field has grown from year to year, and at present covers an impressive area.

One of the scientists who suggested Libby as a candidate for the Nobel Prize has characterized his work in the following way: "Seldom has a single discovery in chemistry had such an impact on the thinking in so many fields of human endeavour. Seldom has a single discovery generated such wide public interest".

Professor Libby. The idea you had 13 years ago of trying to determine the age of biological materials by measuring their carbon-14 activity was a brilliant impulse. Thanks to your great experimental skill, acquired during many years devoted to the study of weakly radioactive substances, you have succeeded in developing a method that is indispensible for research work in many fields and in many institutes throughout the world. Archaeologists, geologists, geophysicists, and other scientists are greatly indebted to you for the valuable support you have given them in their work. The Swedish Academy of Sciences desires to join those who offer you grateful thanks for what you have done for the benefit of so many sciences, and has decided to award you this year's Nobel Prize for Chemistry. May I congratulate you on behalf of the Academy, and ask you to receive the prize from the hands of His Majesty the King.


1. The modern value is 5730±40 years.

[Photo Credit: University of California History Digital Archives, Copyright © 2006 The Regents of the University of California.]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Science Journalism in Decline

 
There's an editorial in Nature this week on science journalism [Filling the Void]. It's not very interesting.

There's an article by Geoff Brumfiel that's much more interesting [Science journalism: Supplanting the old media?]. Since I'm mentioned in that article, and since I can't comment on their site, I thought I'd make a few comments here.

First, I posted a comment on Chris Mooney's blog where I said, "Most of what passes for science journalism is so bad we will be better of without it." What I meant to say was, "Most of what passes for science journalism is so bad we will be better off without it". I just want there to be a correct version that everyone can quote.

The article correctly points to a trend ...
Traditional journalists are increasingly looking to such sites to find story ideas (see 'Rise of the blogs'). At the same time, they rely heavily on the public-relations departments of scientific organizations. As newspapers employ fewer people with science-writing backgrounds, these press offices are employing more. Whether directly or indirectly, scientists and the institutions at which they work are having more influence than ever over what the public reads about their work.
Over the past decade it has been the "professional" science journalists themselves who were the gullible victims of scientific hype and PR. The scientific accuracy of press releases leaves a great deal to be desired. They are, after all, intended to promote the researcher and the institution. They are heavily biased.

It is not a good thing that individual scientists and their institutions are managing the science news. It's a disaster.
The amount of material being made available to the public by scientists and their institutions means that "from the pure standpoint of communicating science to the general public, we're in a kind of golden age", says Robert Lee Hotz, a science journalist for The Wall Street Journal. But that pure standpoint is not, or should not be, all that there is to media coverage of science. Hotz doubts that blogs can fulfil the additional roles of watchdog and critic that the traditional media at their best aim to fulfil. That sort of work seems to be on its way out. "Independent science coverage is not just endangered, it's dying," he says.
I hear this a lot. Science journalists seem to think that they have served as watchdogs and science critics by tempering the hype and propaganda spewed out by institutional PR departments.

I wish it were true. If science journalists really did their job of separating the wheat from the chaff then I would be their biggest cheerleader. Instead, for the most part they have been completely seduced by the lure of scientific breakthroughs and revolutions promoted by self-serving scientists and their institutions. There are notable exceptions, but the majority of science journalists have failed at the one job they are supposed to do better than non-science journalists.

That's why we would be better off without them.

Coincidentally, Ryan Gregory has just posted an article about Scitable, "A Collaborative Learning Space for Science" hosted by Nature magazine. I'm pretty sure that Nature is proud of this site. They think the articles are good examples of science writing.

Ryan highlights an article by Leslie Pray, a free-lance science writer. The title is: Transposons, or Jumping Genes: Not Junk DNA?. Read what Ryan Gregory has to say at Scitable Again. He thinks the article is "total nonsense." I agree with him.

If this is an indication of the ability of science journalists to cut to the chase and give us the straight dope, then it's no wonder that scientists are skeptical.


Regulatin' Genes

 
Some of us old fuddy-duddies have been learning about the regulation of transcription for over forty years. When you've been teaching about regulatory proteins, like HOX proteins, for twenty-five years, the novelty sort of wears off.

It's fun to see the enthusiasm of students who have just recently been "turned on" by gene regulation, especially when one of them is also a Toronto Blue Jays fan! Strange that the university looks a lot more like Stanford than the University of Toronto [HumBio instructor, students rap about science on YouTube].





Time to Change the Channel

 
My local Liberal candidate is Omar Alghabra, who lost the last election to one of Harper's Conservatives. Omar sent me a link to this video. He though I might get a kick out of it.

I did.