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Wednesday, January 21, 2009

Nobel Laureates: Ulf von Euler and Julius Axelrod

 

The Nobel Prize in Physiology or Medicine 1970.

"for their discoveries concerning the humoral transmittors in the nerve terminals and the mechanism for their storage, release and inactivation"

Ulf von Euler (1905 - 1983) and Julius Axelrod (1912 - 2004) won the Noble Prize in 1970 for elucidating the role of noradrenaline (norepinephrine) in transmitting nerve impulses. Axelrad and von Euler shared the prize with Sir Bernard Katz who worked on the role of acetylcholine.

Here's the Press Release.

THEME:
Nobel Laureates
Professor Ulf von Euler has discovered that the substance noradrenaline serves as neurotransmitter at the nerve terminals of the sympathetic nervous system. He has also shown how this substance is stored in small nerve granules within the nerve fibres of this system.

Dr. Julius Axelrod's discoveries concern the mechanisms which regulate the formation of this important transmitter in the nerve cells and the mechanisms which are involved in the inactivation of noradrenaline, partly under the influence of an enzyme discovered by himself.

von Euler's and Axelrod's discoveries have not only increased our knowledge about the transmission in the sympathetic nervous system, they also form the basis for the understanding of the transmission in the central nervous system and its pharmacology. Thus in a very significant way, the laureates have presented basic data about the physical and chemical mechanisms of the synaptic transmission and thus given us basic information about how the messages are mediated between nerve cells. Their discoveries concerning these regulatory mechanisms in the nervous system are fundamental in neurophysiology and neuropharmacology and have greatly stimulated the search for remedies against nervous and mental disturbances.


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.

Tuesday, January 20, 2009

Gene Genie #42

 
The 42nd edition of Gene Genie has been posted at Genetic Future [Gene Genie #42 - focus on personalised genetics].
Welcome to the 42nd edition of Gene Genie, the blog carnival of clinical genetics and personalised medicine.

Most of the entries in this edition fall under the broad umbrella of personalised genetics, with posts emphasising both the pros and cons of the emerging consumer genetic testing industry.
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


Wealthy men give women more orgasms

 
A reader directed me to this article on The Sunday Times (UK) website: Wealthy men give women more orgasms.
Scientists have found that the pleasure women get from making love is directly linked to the size of their partner’s bank balance.

They found that the wealthier a man is, the more frequently his partner has orgasms.

“Women’s orgasm frequency increases with the income of their partner,” said Dr Thomas Pollet, the Newcastle University psychologist behind the research.

He believes the phenomenon is an “evolutionary adaptation” that is hard-wired into women, driving them to select men on the basis of their perceived quality.

The study is certain to prove controversial, suggesting that women are inherently programmed to be gold-diggers.

However, it fits into a wider body of research known as evolutionary psychology which suggests that both men and women are genetically predisposed to ruthlessly exploit each other to achieve the best chances of survival for their genes.
This explains why some women like being "trophy" wives.

I wonder if very rich women ever have orgasms?

The entire field of evolutionary psychology is becoming a farce. It's about as scientific as creationism. There must be some intelligent psychologists out there. Why aren't they speaking out?


Monday, January 19, 2009

Darwin and Gradualism

 
From DaveScot on Uncommon Descent comes this remarkable example of stupidity: Darwin’s Big Mistake - Gradualism.
The big mistake in Origin that Darwinists won’t admit is gradualism. Darwin explained that according to his theory we should expect to observe a continuum of living species each with only the slightest of variations between them. He postulated that we don’t observe this because the fittest species take over and the insensibly slight variants die off leaving species that are fully characteristic of their kind which then makes possible taxonomic classification by those characters. It’s in the full title in the latter half “The Preservation of Favored Races”.

That left Darwin with explaining the fossil record which is indisputably a record of saltation.
Bzzzzz!!!! Wrong!

Thanks for playing, DaveScot. Unfortunately, there are no consolation prizes for IDiots.


Princeton Professor denies global warming theory

 
This is embarrassing. I'm an alumnus of Princeton (GS '74) and it pains me to read this in The Daily Princetonian: Professor denies global warming theory.
Physics professor William Happer GS ’64 has some tough words for scientists who believe that carbon dioxide is causing global warming.

“This is George Orwell. This is the ‘Germans are the master race. The Jews are the scum of the earth.’ It’s that kind of propaganda,” Happer, the Cyrus Fogg Brackett Professor of Physics, said in an interview. “Carbon dioxide is not a pollutant. Every time you exhale, you exhale air that has 4 percent carbon dioxide. To say that that’s a pollutant just boggles my mind. What used to be science has turned into a cult.”

Happer served as director of the Office of Energy Research in the U.S. Department of Energy under President George H.W. Bush and was subsequently fired by Vice President Al Gore, reportedly for his refusal to support Gore’s views on climate change.
More proof, if it's needed, that Al Gore is smarter than George Bush (either one).
He asked last month to be added to a list of global warming dissenters in a Senate Environment and Public Works Committee report. The list includes more than 650 experts who challenge the belief that human activity is contributing to global warming

Though Happer has promulgated his skepticism in the past, he requested to be named a skeptic in light of the inauguration of President-elect Barack Obama, whose administration has, as Happer notes, “stated that carbon dioxide is a pollutant” and that humans are “poisoning the atmosphere.”
I've been watching the excitement build in Washington as the inauguration approaches. Who knew that one of the unintended consequences would be to flush out the kooks?1


1. For the record, I don't think it's helpful to call CO2 a "pollutant." That doesn't mean there isn't an optimal concentration; after all, there's also an optimal concentration of N2 (100% is too much) and O2 (more than 50% and fires become a really serious problem. I'd also like to go on record as one of those who think that human activity is an important part of global warming but it's probably not the only cause of the current trend.

Liberals won't back tax cuts

 
The Harper government will present its budget next week. The NDP and the Bloc have announced that Stephen Harper has lost the confidence of the House and they will vote against the budget. The Liberal Party under Michael Ignatieff hasn't made up its mind about whether Harper can continue to govern even if all the other parties don't trust him. But the Liberals seem to be clear on one thing; according to today's Toronto Star, Liberals won't back tax cuts.
The Liberals are opposed to making tax cuts the centrepiece of the budget, and new leader Michael Ignatieff signalled yesterday the party is prepared to dump the Conservative minority if the budget is inadequate.

...

As they position themselves in advance of the budget, the Liberals argue that, while they generally favour income-tax cuts, it's the wrong approach during the recession.

"We don't want to see the Prime Minister come up with the kind of broad-based tax cuts that put Canada in a permanent, structural deficit once we recover from this (recession)," Liberal finance critic Scott Brison (Kings-Hants) told CTV yesterday as his party gathered in Ottawa for the caucus meeting.

Liberal MP John McCallum said such cuts are fiscally irresponsible at a time when the Tories have already put Ottawa's books in a deficit position and there's no way to ensure tax cuts benefit those who have lost their jobs or otherwise need help during the recession.

"There's a very good argument to be made that this is not the right time for across-the-board tax reductions," said McCallum, MP for Markham-Unionville and chair of a party advisory committee on the economy.
This could get interesting. I would support the Liberals if they vote against the budget because it contains significant tax cuts. Cutting taxes is typical conservative dogma so we may be headed for an election.


Monday's Molecule #104

 
Name this molecule. We need a biochemically accurate name and the formal IUPAC name. The role of this molecule in biological systems was elucidated by one or more Nobel Laureate(s) in the second half of the 20th century.

Your task is to correctly identify the molecule and name the Nobel Laureate(s). The first one to do so 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 four ineligible candidates for this week's reward: John Bothwell of the Marine Biological Association of the UK in Plymouth, UK, Dima Klenchin of the University of Wisconsin, Bill Chaney of the University of Nebraska, and Maria Altshuler of the university of Toronto.

John, Dale, Bill, and a previous winner (Ms. Sandwalk) 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 so poorly in this contest, I'm going to make a special award this week. In addition to the normal winner, the first undergraduate student who can accept a free lunch will win a second prize. 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. Comments are now open.


UPDATE: The molecule is norepinephrine (noradrenaline) [4-[(1R)-2-amino-1-hydroxy-ethyl]benzene-1,2-diol]. The Nobel Laureates are Ulf von Euler and Julius Axelrod.

The first person to get it correct was Ramon, address unknown. The first undergraduate who can collect a free lunch is Jason Oakley of the University of Toronto. Jason can bring a friend.


Like this is going to happen

 
Normally A.C. Grayling makes a lot of sense and I enjoy reading his columns in New Scientist. Today's column is an exception: Universities should flag up which websites to trust.

Graying rightly points out that the internet is a mixed bag of mostly crap interspersed with the occasional website that makes sense at a level beyond kindergarten. His solution?
The lesson is that to make best use of the internet as an educational resource, its content has to be audited for reliability, and a system of classification introduced. Given that the internet is already the main resource for students, the need is urgent. I suggest that an international consortium of universities should set up panels to audit the worth of websites, endorsing those that are reliable. They should not censor, nor comment on matters of opinion - the price we pay for the internet's open democracy is the rubbish it contains. But they should authoritatively identify worthwhile sites, and warn of factual error when it occurs. Without such expert monitoring, the internet will increasingly be a problem rather than a boon, and limited in educational value.
Can you imagine a panel of Professors from different universities agreeing on which websites are reliable and accurate?

It might work for blogs. We all know which blogs to select, don't we?


John Hawks doesn't like random genetic drift

 
The human MYBPC3 gene encodes a muscle protein. A 25 bp deletion in that gene is associated with a large increase the risk of cardiomyopathy ("heart muscle disease"). The most severe problems appear when carriers reach the age of 40.

According to a recent paper by Dhandapany et al. (2009), the overall frequency of the deletion allele is about 4% in India but it ranges from 0% to 7% in different parts of the country. The allele is not present in most other populations outside of India.

The authors conclude that the allele has reached this frequency by random genetic drift beginning with an initial mutation about 30,000 years ago. This increase has occurred in spite of the fact that the allele is deleterious and should decrease overall fitness.

John Hawks disagrees: Could genetic drift really break your heart?.
The issue is not really whether a gene could go from 1 copy to 4 percent in 1200 generations by chance. That wouldn't be so terribly unlikely in Pleistocene humans -- in fact, the mean time for a mutation to go from 1 copy to 4 percent by drift in a population of effective size 10,000 individuals is not 30,000 years, but only around 20,000 years. On the other hand, mtDNA variation today suggests that South Asia experienced early and rapid population growth -- so we're not likely talking about a population of 10,000, but more like a minimum of 100,000 effective individuals through the past 30,000 years at least. It would take genetic drift at least 10 times longer to accomplish the requisite frequency change given that demographic history. Still, a single allele at a single gene locus might be exceptional.

But that scenario, however unlikely, is simply not the situation we have here. Here we have a deletion that must have some disadvantage, because it gives people a fatal disease. This disadvantage is apparently dominant in effect, based on the case-control study. Yet the deletion has managed to persist within the large South Asian populations of the last 10,000 years so that today it is still around 4 percent.
John is an expert on evolution within human populations but he seems to be basing all of his calculations on the idea that the mutation arose in a population of 100,000 individuals and that this population was the effective population (e.g. they all freely interbred). I don't think this is very likely.

The fact that the allele frequency varies within India suggests that there are many subpopulations. Some of them might have been as small as 1000 individuals at vary time over the course of the last 30,000 years. As I'm sure John knows, the populations dynamics of human groups is extremely complex. We only have to think about the allele frequency differences in the Pennsylvania Amish communities or French Canadians to recognize this fact.

And let's not forget that the frequency of Huntington's disease is high around Lake Maracaibo in Venezuela. Over a period of 200 years a single individual with the Huntington's disease allele has left 18,000 descendants.

When we look at modern allele frequencies we don't only think about average rates of change due to random genetic drift in panmitic populations. We also have to consider the unusual events that occur from time to time. These include founder effects, natural disasters, etc. etc. The MYBPC3 is a lottery winner. You can't dismiss evolution by accident just because the probability of any one event is low.

This is why John says that, "Still, a single allele at a single gene locus might be exceptional." But John seems to think that in this case the result is not just "exceptional" but extraordinarily exceptional. He suggests that the deleterious effects of the allele are a recent phenomenon and that explains why it survived in early populations.
I would hypothesize that the disadvantages of the deletion have actually increased over time. The average lifespan increased into the Upper Paleolithic and probably later as well. Meanwhile, as the population grew, larger completed family sizes became more important to fitness. As people became more sedentary, the accumulation and inheritance of possessions and land became an important means of investing in children. The increasing importance of later survival and investment in children should have raised the fitness cost of chronic disease. That would explain a pattern of evolution in which this deletion increased in frequency early in its history, but later remained static or declined.

So, I don't suppose I can say people are crazy for thinking genetic drift could explain this deletion's current high frequency. But considering the powerful effect of weak selection over the many generations involved here, and the very large size of the South Asian population during most of that time, genetic drift seems pretty unlikely.
This makes sense to me. It's consistent with John's idea that the rate of human evolution has changed substantially over the past 30,000 years but I don't see why he objects so much to a random genetic drift explanation. Why does he suggest the the authors of the paper are crazy to suggest drift as an explanation?

It seems to me that his explanation is consistent with an increase in allele frequency due to random genetic drift just as the authors claim.


Dhandapany, P.S., Sadayappan, S., Xue, Y., Powell, G.T., Rani, D.S., Nallari, P., Rai, T.S., Khullar, M., Soares, P., Bahl, A., Tharkan, J.M., Vaideeswar, P., Rathinavel, A., Narasimhan, C., Ayapati, D.R., Ayub, Q., Mehdi, S.Q., Oppenheimer1, S., Richards, M.B., Price, A.L., Patterson, N., Reich, D., Singh, L., Tyler-Smith, C., and Thangaraj, K. (2009) A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia. Nature Genetics, Published online: 18 January 2009 [doi:10.1038/ng.309]

When TAs Go on Strike

 
York University is the "other" large university in Toronto. The university has been closed since November 5th when members of the Canadian Union of Public Employees Local 3903 (CUPE Local 3903) went on strike.

The situation is a bit complicated because the union has three different groups and there are separate contracts for each group, even though the contracts are all part of the same negotiation package. The three groups are:
Unit 1 if they have a teaching contract (note - teaching includes demonstrating, tutoring, and marking) and they are a full-time graduate student.

Unit 2 if they have a teaching contract and are not a full-time graduate student.

Unit 3 if they have a graduate assistantship or research assistantship and are a full-time graduate student.
What I'm mostly interested in is the graduate students in Units 1 & 3.

After several months of fruitless negotiations, the university exerted its legal right to call for a ratification vote when the union negotiators turned down the latest offer. The vote will take place later this week and, as you might have guessed, the CUPE 3903 leaders are urging their members to "Kill the Rat."

What is the role of a faculty union in situations like this? It's really not complicated. Sister unions will invariably support the right to collective bargaining and demand that both sides negotiate in good faith. Faculty unions tend to tilt in favor of the TA union simply out of solidarity but also because both groups often have common grievances against the administration.

Here's where things get messy. As reported in several newspapers, a group of 300 faculty members recently signed a letter urging CUPE 3903 members to ratify the latest offer by the university administration. Here's how it was reported in the National Post.
Another group urging the union to vote yes is nearly 300 faculty members who signed their names to a letter urging CUPE to accept the current contract proposal.

The signees of the letter are also members of the York University Faculty Association (YUFA).

YUFA president Arthur Hilliker said while he does not endorse the letter, he does not condemn it or believe it to be illegal either, according to Eric Lawee, a York humanities professor and one of the letter’s signees. YUFA maintains it wants a fair and equitable offer for CUPE.

“We, the undersigned retirees and full-time faculty members of York University, urge our colleagues in CUPE 3903 who have been on strike since November 6, 2008, to end their labour action by accepting the current contract offer of the York University administration,” the letter begins.

The letter addresses specific concerns if the strike were to drag on, including the potential loss of the summer term, which not only would hurt the school’s undergraduate students, but would affect CUPE as well, with possible job losses due to the elimination of the summer term.

“In their own interest and that of the entire university community, we urge CUPE members to end their labour action and help the university resume expeditiously the provision of its full academic programs,” the letter concludes.

Mr. Lawee said that there were two main reasons behind the letter. The first was due to “a strong sense that the strike has dragged on too long and that the rights and needs of students must now take priority over all else,” he said. “And ... that this should be an easy settlement to endorse because the offer is very fair.”
Why is this a problem? Well, for one thing, it's a problem because these 300 faculty members are going against the advice of their own union.

The York University Faculty Association (YUFA) issued a press release today in which they reiterated their position.
Press Release

These are our principles with respect to the CUPE 3903 forced ratification vote. They are motions passed unanimously at the YUFA Executive meeting of 12 January 2009:
  1. YUFA Executive re-affirms its support of free collective bargaining and does not endorse a ratification vote of CUPE 3903 members as forced by the Employer.

  2. YUFA Executive strongly urges all YUFA members to respect individual CUPE 3903 members’ rights in the forced ratification vote to vote freely and according to their conscience. We urge all YUFA members to respect CUPE members’ rights to vote freely.

  3. YUFA Executive, recognizing the power relations implicit in the roles of YUFA members and CUPE 3903 members, does not endorse any YUFA member attempting to influence how a CUPE 3903 member might vote in the forced ratification vote.
We recognize the serious problems the strike is causing for the students and for York. We also recognize that the issues of this strike need to be resolved for the future of York University.
The second and third points are very important. Faculty members are often the bosses of teaching assistants and they need to be very careful to remain neutral in situations like this. Because they are in a position of authority over graduate students they should not be urging these students to vote one way or the other. You can see why this is a problem. If Professors tell their graduate student to vote for ratification when the student wants to vote the other way, then this sets up a dangerous conflict for the student. What can be gained by doing that?

This is not a new problem. It's been around for decades and faculty unions in dozens of countries have learned to deal with it by urging individual members to avoid taking sides. I'm surprised that there are nearly 300 retired and active Professors at York University who don't get it.

Some of these faculty members have been writing letters to the editors of various newspapers in defense of their position. Here's one from Bernard Lightman, a Professor of Humanities. It appeared in today's Toronto Star.
Professor Berland has claimed that the open letter by full-time faculty and retirees to striking members of CUPE 3903 is in direct defiance of motions passed by the faculty union's executive. The signees have never claimed to speak on behalf of, or to represent, the faculty union.

Professor Berland interprets the motions of the faculty union's executive as saying that faculty are not free to express their opinions on the strike. I do not believe that that is the correct interpretation. However, if Professor Berland's interpretation were correct, then I would have to defy the faculty union.

It is not the business of a faculty union to gag its own members. One of the most important priorities of a university is to encourage free discussion and expression. That priority is not suspended during a strike, especially when the fate of more than 50,000 students hangs in the balance.
Let's be clear about one thing. YUFA was offering advice to its members based on decades of experience. The advice was to keep your mouth shut because you are in a position of authority over your graduate student TAs.

Every Professor has the right to ignore that advice and try to influence the decision of their graduate students. That's what academic freedom is all about. Whether it's a smart thing to do is another question.1 I don't think it is.

Graduate students are smart enough, and mature enough, to make up their own minds. They don't need advice from their supervisors and bosses.


1. It may be illegal as well, but that's another thing entirely. I doubt that any Professor would be prosecuted for pressuring their graduate students unless that Professor holds a prominent administrative position where the potential for retaliation against a student is much more likely.

Saturday, January 17, 2009

Evolution News & Views

 
From time to time I mention the Disco site called Evolution News & Views. It has a lofty purpose that's prominently displayed on every posting.
The misreporting of the evolution issue is one key reason for this site. Unfortunately, much of the news coverage has been sloppy, inaccurate, and in some cases, overtly biased. Evolution News & Views presents analysis of that coverage, as well as original reporting that accurately delivers information about the current state of the debate over Darwinian evolution.
Here's a posting from Robert Crowther dated yesterday afternoon.
So, Darwinists are admitting that up until Friday, Jan. 16 2009 @ 4:10PM, evolution was “mostly theory.” Interesting. I am now certain that dogs adapt to their environment, too. Last night my dog kept barking and I shook my finger and spoke very firmly to her and made her sit on her bed. She stopped barking. So, at 7:10 pm I had a perfect example of evolution. Or was it adaptation? Or was it bad parenting? Whatever, we now see that dogs evolve, which previously had been believed to be “mostly theory.” My peers, who were there reviewing the moment, are skeptical because they think my dog is asexual. Regardless, this is all speculation — except for poor Kali. She still lacks an opposable thumb.
We may need a better word than IDiot to describe these people.

Is there an atheist bus campaign in Seattle? I'd like to donate.


Canadian Atheist Bus Campaign

 

Donate to The Canadian Atheist Bus Campaign and get those atheists signs on Toronto buses and subways.

The campaign is sponsored by the Freethought Association of Canada. They've raised over $10,000 in just a few days.


BioGPS

 
BioGPS is billed as a "Biology Gene Portal System." It's another database. You can read the review on genomeweb but you will have to register [GNF Team Rolls Out BioGPS Gene Portal for Users and Contributors].

The brains behind BioGPS is Andrew Su at the Genomics Institute of the Novartis Research Foundation (GNF) in San Diego (USA). According to the genomeweb article ...
As scientists move forward in analyzing experimental results, they generally consult up to a dozen "standard web sites" Su said, such as Entrez Gene, Ensembl, UniProt, or the Mouse Genome Informatics site. Each site delivers "partially overlapping gene annotation," so users must visit each, enter their search, learn the interface, and learn how to find each of the genes of interest on that site, he said. "Often that is a quite daunting process."

The idea behind BioGPS, Su said, is to avoid that process as well as reveal to researchers smaller and less-known gene portals that scientists might have missed.
Call me skeptical. The author of the article, Vivian Marx, contacted me and asked me to check out BioGPS. I have a long-standing interest in biological databases dating back to an early attempt to improve and update GenBank by adding annotation. That attempt was a failure—for very sound reasons [Errors in Sequence Databases].

I looked at my favorite genes on BioGPS. Here's the link to their homepage: BioGPS. The first thing you notice is that that database is restricted to rat, mouse, and human genes. The second thing you notice is that there's no value added. The data appears to be copied from other databases. This includes all of the errors, omissions, and misinterpretations found at each site. The emphasis is on expression data—that's what overwhelms the visible record of each gene.

Here's an example. This is the human HSPA1L gene. It happens to be a member of the HSP70 gene family. HSP70 proteins are the major chaperones of the cell. The HSP1AL version is specifically expressed in testes.


The expression data is correct but none of the databases mention that this gene is a developmentally regulated member of the HSP70 gene family even though that information has been in the literature for almost twenty years. You don't learn anything from visiting BioGPS that you wouldn't learn from visiting most other databases and, more importantly, you don't learn the information that might be most important to your research because it isn't in any of the databases. Anyone looking at this record would be puzzled by the lack of connection between the correct expression profile and all of the other information.

It gets worse. If you check out the rat HSPA1L gene you won't even learn that it is developmentally regulated because the expression profile doesn't include testes. The links to this genes suggest that it responds to stress, but it doesn't.

This is just one example of the problems with biological databases. Collecting together links from a variety of databases doesn't help. It just ensures that the errors from each database will be combined, creating maximum confusion.

I'm quoted correctly in the article ...
Larry Moran, a biochemist at the University of Toronto, told BioInform by e-mail that he had looked at a few of his "favorite genes" in the portal. "I don't think it's a very useful database," he said, since it is a summary of information gleaned from other databases with "no attempt at annotation."

In addition, he said, "much of the information is wrong or misleading," such as some of the expression profiles, which "seem to be incorrect; probably because the data is for another gene and not the one in the database record."

Users "who would rely on that sort of expression data would be making a very serious mistake," he said."

Reacting to these comments, Su said, "I think it is a good thing, in terms of making those errors more widely seen. The more eyes that see it, the more likely that that error will be fixed."

Being able to detect errors, however, has to be connected to the ability to fix it, he said. "This is the wiki principle, everybody can edit it, everybody can fix it, everybody has the responsibility and the power to make sure it's correct."
In an ideal world, researchers will fix errors in the databases and a Wiki-like system seems like a good idea. The experiment is already underway [A Gene Wiki]. But, as it turns out, this approach is incredibly naive as I discovered from attempts to fix GenBank a few decades ago. Nobody's going to do it. It's way too much work and there's no motivation to share information on public databases.

I received an email message from one of the authors of the expression data. As you might expect, the expression data profiles that are so prominently featured in the BioGPS database records are from the team at The Genomics Institute of the Novartis Research Foundation (e.g. Su et al., 2004). Much of it may be correct—it certainly succeeded with the HSP1Al gene—but I think it's wrong for HSPA1A.

My correspondent pointed out that his expression data has been widely used by hundreds of researchers and the papers have tons of citations.1 He described several studies that have made important discoveries based on the expression profiles that have been published. I don't doubt that this is true. That's not the point. The point is whether taking the expression data and adding links from other sources makes BioGPS a valuable resource.

Not as far as I can see.


1. The idea that just because a paper is widely quoted means that it must be correct is something that troubles me greatly. It seems to be part of the new way of doing science.

Su, A.I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K.A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., Cooke, M.P., Walker, J.R. and Hogenesch, J.B. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. (USA) 101:6062-6067. [PubMed]

Apple Software Update

 
Every few weeks I have to sit patiently and watch while Apple updates my iTunes and QuickTime software.1 Since I use three different computers (home, work, laptop), this becomes quite a pain and it gives me plenty of time to think about Apple software and it's update policy. They are not happy thoughts.

Maybe someone can answer the questions? Why are the update files so big and why does it take so long to install them? It seems as though I am reinstalling the entire suite of programs each time. Why are there so many updates? Is the software so bad that it needs constant fixing?

Is there any way to turn off the notices? I don't use iTunes but I don't want to uninstall it. Can't I just update it when I want to use it? Same for QuickTime; how important. really, are the updates? Does anyone know?


1. To be honest, I can do other things as long as I don't mind a very slow internet connection. The updates are huge and the installation takes up a lot of RAM.

Friday, January 16, 2009

What Homeschooling Can Do for your Children

 
Normally I don't make fun of spelling mistakes because I make lots of them myself and I don't think they're funny. However, from time to time the irony is just too delicious.

Leonard has a blog called Stand Your Ground. Who's Leonard, you might ask? Here's the answer ...
A Socially Conservative Don Quixote from Moncton. Strongly pro-life. Strongly pro-family. Strongly opposed to any attempts to turn my nation into something shapeless, cultureless, childless, gender-neutral and politically correct.
Here's the heading from Leonard's post on homeschooling [Homeschooling Is On The Raise].

More and more parents prefer to take control over their children's education, rather than trusting them to a public school system. ....

Sounds much better than a system which has become more about indoctrination (or at the very least - about merely keeping the kids busy from 9 to 3) than about education, doesn't it? Back in 1999, the CBC aired a short report on homeschooling in the National. I don't recall the exact number they mentioned, but there were between 20,000 and 25,000 homeschooled children in Canada back then. Since then we had the courts ruling that excluding books about homosexual cohabition from elementary school libraries is "discriminatory"; that a perverse graduate should be allowed to bring his partner in perversity to the high-school prom - even if it's a Catholic school.

Since then we had the BC government allowing militant homosexuals to monitor all the school curriculum to ensure it's "gay friendly". We had Quebec government introducing a mandatory "Chinese buffet" course in "world religions" which is nothing but a virtual indoctrination into social and moral relativism. How many parents have since resorted to homeschooling as the only way to save the children from becoming guinea-pigs in lefty's social experiments? I dare to assume it's in the 6 digits now.