I haven't been extremely generous in my estimation of how science has fared under our current government - I'm not a big fan of Gary Goodyear's take on evolution, his lack of research experience, or Harper's prioritization of science funding in the budget.
It was nice to feel supported in these opinions by an editorial in Nature last week, blasting the Conservative treatment of science from a policy perspective. Science sits in the portfolio of the Minister of State - Science and Technology, a junior cabinet position that reports to the Minister of Industry. The only contact the Prime Minister had with science was a National Science Advisor, a position he abolished two years ago.
The editorial calls for the establishment of a clear and progressive science policy, and I couldn't agree more. There are a number of reasons this hasn't happened yet. One of them is that Harper doesn't seem to care much about science, whether it's the application of basic health research findings into clinical practice or the models of environmental impact of the oil sands projects.
But I think that we, and by that I mean scientists, fail to give him reason to care. One of the things that the article mentions is the lack of a national organization for science. The American Association for the Advancement of Science predates Canada itself by almost 20 years; their publication, "Science," is one of the most respected journals in the world. Because of our Commonwealth status, British organizations like the Royal Society served this role early in our history. As a result, 142 (and a half) years after Confederation, we still have no equivalent unifying body in Canada.
Without any semblance of organization, the scientific community cannot even begin to think about influencing policy. We do not provide a national organization independent of government and funding agencies that takes official stances or even makes commentary on policy decisions. We don't have a publication in which we provide news about science and science policy or publish important research.
Science in Canada lacks organization, leadership, and vision. In this day and age, things like geography and multilingualism are no excuses. Until we establish a body representing the Canadian scientific community, we are naive to think that science will impact the way our government to behaves without a venue to provide recommendations on how to solve important scientific problems like we have at the Chalk River reactor.
It's long past time we caught up to the Americans - and virtually every other country in the world - in this respect. We are a country with a very strong research program, thousands of bright scientists at hundreds of institutes from coast to coast; we have internationally renowned universities and respected figures in every field of study under the sun. Our scientists publish in top-quality journals, win Nobel Prizes, and are world leaders in their spheres. They save lives, improve our environments, and change the way we will live in the future.
Without an organization to serve as a mouthpiece for Canadian scientists, we can expect our science policy to be rudderless and ineffective. While we have important things to say, it's impossible for a government to listen to scientists when we're not even speaking.
Sunday, January 24, 2010
Monday, January 11, 2010
Pharma shrinking, Proroguing the inevitable
For some reason, the Montreal Gazette has a piece from the Windsor Star on the website this morning, and it freaks me out. The headline runs: "Workforce expert predicts future jobs." Which is a little like a meteorologist predicting that the future will have weather.
Apparently she's been waiting for a long time for appointments in offices that contain 5-year-old copies of The Economist; arguing that economic growth will depend on local people training and upgrading their skills. "You can't deny the importance of the knowledge economy," she is quoted as saying. The article also says she offers the pharmaceutical industry as a growth area for job seekers.
Now we'll leave alone the fact that we have more people with university degrees than our economy knows what to do with, and just point out that last year alone, Pfizer cut 19 500 jobs. This is the 2nd time in three years they've topped the pharma charts; in 2007 they cut another 10 000 jobs. This past year, Merck cut another 16 000 jobs; Johnson & Johnson slashed almost 9 000; and AstraZeneca lost about 7 500. Between the top 6 job cuts in the industry, over 63 000 jobs went to the big market in the sky.
The reason for this is that the pharmaceutical industry is scrambling to make money right now. There are no blockbuster drugs waiting for approval from the FDA, no huge breakthroughs that promise huge profits. Without the ability to provide any goods, big pharma is reduced to making money in the way that corporations usually do it: mergers, acquisitions and cuts. This is bad news for the workers, none of whom have the advantageous situation of, say, a GM employee.
All that to say that big pharma is not a growth industry in real terms, and anything decent in "little" pharma is going to get its intellectual property snapped up by one of the big boys, leaving little but empty infrastructure and unemployment in its wake. Not what I would describe as a strong market.
* * *
A couple of words on prorogation.
Proroguing Parliament is nothing new. Everyone has done it, from Sir John A to Jean Chretien. Normally, however, Parliament is prorogued to start a holiday break or to end a session. Harper's prorogations have been special, certainly in the modern Parliament (last 30-40 years).
Last time, Harper prorogued Parliament because he was facing a vote of confidence that he thought he might lose, and that a coalition of opposition parties might form a government. So he asked the Governor-General if he could buy some time while he talked with various parties long enough to let the coalition run its natural course: failure. This was annoying, but it was smart politics.
This time, however, the reasons for prorogation are less clear. There is a scandal before the government regarding Afghan detainees, the Olympic Games in February, and another vote of confidence coming in March (the budget). However, these issues don't seem overwhelming - not while important bills are waiting before the House (the anti-crime legislation that is an integral part of the Conservative platform, for example).
This prorogation comes during a scheduled break from Parliament. This is pretty much unheard of, and extends the break from 39 days to 76 days. It is disingenuous for Harper to say that this is a routine procedure: the only other prorogation that lasted this long since 1968 (as early as I checked) was Chretien's 82-day prorogation in 2003-2004; executed mostly to avoid Sheila Fraser's report on the Sponsorship Scandal and inquiries into military conduct in Somalia. For the Conservatives to criticize Chretien's move while defending Harper is outright hypocrisy.
Which shouldn't surprise me, I suppose. What does surprise me is that something was worth wasting political capital on prorogation. What's waiting in the wings when Parliament resumes in March?
Apparently she's been waiting for a long time for appointments in offices that contain 5-year-old copies of The Economist; arguing that economic growth will depend on local people training and upgrading their skills. "You can't deny the importance of the knowledge economy," she is quoted as saying. The article also says she offers the pharmaceutical industry as a growth area for job seekers.
Now we'll leave alone the fact that we have more people with university degrees than our economy knows what to do with, and just point out that last year alone, Pfizer cut 19 500 jobs. This is the 2nd time in three years they've topped the pharma charts; in 2007 they cut another 10 000 jobs. This past year, Merck cut another 16 000 jobs; Johnson & Johnson slashed almost 9 000; and AstraZeneca lost about 7 500. Between the top 6 job cuts in the industry, over 63 000 jobs went to the big market in the sky.
The reason for this is that the pharmaceutical industry is scrambling to make money right now. There are no blockbuster drugs waiting for approval from the FDA, no huge breakthroughs that promise huge profits. Without the ability to provide any goods, big pharma is reduced to making money in the way that corporations usually do it: mergers, acquisitions and cuts. This is bad news for the workers, none of whom have the advantageous situation of, say, a GM employee.
All that to say that big pharma is not a growth industry in real terms, and anything decent in "little" pharma is going to get its intellectual property snapped up by one of the big boys, leaving little but empty infrastructure and unemployment in its wake. Not what I would describe as a strong market.
* * *
A couple of words on prorogation.
Proroguing Parliament is nothing new. Everyone has done it, from Sir John A to Jean Chretien. Normally, however, Parliament is prorogued to start a holiday break or to end a session. Harper's prorogations have been special, certainly in the modern Parliament (last 30-40 years).
Last time, Harper prorogued Parliament because he was facing a vote of confidence that he thought he might lose, and that a coalition of opposition parties might form a government. So he asked the Governor-General if he could buy some time while he talked with various parties long enough to let the coalition run its natural course: failure. This was annoying, but it was smart politics.
This time, however, the reasons for prorogation are less clear. There is a scandal before the government regarding Afghan detainees, the Olympic Games in February, and another vote of confidence coming in March (the budget). However, these issues don't seem overwhelming - not while important bills are waiting before the House (the anti-crime legislation that is an integral part of the Conservative platform, for example).
This prorogation comes during a scheduled break from Parliament. This is pretty much unheard of, and extends the break from 39 days to 76 days. It is disingenuous for Harper to say that this is a routine procedure: the only other prorogation that lasted this long since 1968 (as early as I checked) was Chretien's 82-day prorogation in 2003-2004; executed mostly to avoid Sheila Fraser's report on the Sponsorship Scandal and inquiries into military conduct in Somalia. For the Conservatives to criticize Chretien's move while defending Harper is outright hypocrisy.
Which shouldn't surprise me, I suppose. What does surprise me is that something was worth wasting political capital on prorogation. What's waiting in the wings when Parliament resumes in March?
Friday, December 4, 2009
Pfizer on CIHR board no conflict of interest
Poor Leona Aglukkaq is getting ripped apart in the news these days for appointing Bernard Prigent, vice-president and medical director of Pfizer Canada, to the governing council of the Canadian Institutes of Health Research (CIHR). The CIHR is the major funding organization for life science research in Canada, distributing some $800 million of taxpayers' money to various facilities in the form of tax-free research grants.
It's easy to see why people are upset about this, the kneejerk reaction is to see this as a classic conflict of interest, a fairy tale where the benevolent non-partisan funding organization is corrupted by that most evil of nemeses, Big Pharma - all because of a plot by the Big Bad Government.
The error here is that Pfizer isn't eligible for most of that research money, which makes them ineligible for a conflict of interest. However, over half the CIHR governing council are university professors from research centres that do actually compete for CIHR funding. Part of success on a CIHR grant application is based on how many other grants have been given to your institute. This strikes me as being more of the classic conflict of interest as most people define it.
I don't think the problem is with Big Pharma making its way into CIHR. Business has a place in science no matter how many people - researchers and laypeople alike - wish it weren't so. The perspective on science is different between academia and industry. Both have their pros and cons, and I think that CIHR and academia in general might profit from exploring some of the alternative ways of looking at science.
My problem is that when I look though the CIHR website, I can see that Pfizer has been spending millions on funding CIHR grants over the last couple of years - and now an exec is on the board. This looks like patronage of the basest sort, but it isn't conflict of interest. Even if it does leave the same sour taste in your mouth.
What I don't find immediately apparent is what kind of return Pfizer is getting on their millions of dollars of investment, apart from tax breaks. A single position on a board of roughly 20 members isn't exactly overwhelming power or voice in the policy or direction of CIHR. What's so great about that?
It's easy to see why people are upset about this, the kneejerk reaction is to see this as a classic conflict of interest, a fairy tale where the benevolent non-partisan funding organization is corrupted by that most evil of nemeses, Big Pharma - all because of a plot by the Big Bad Government.
The error here is that Pfizer isn't eligible for most of that research money, which makes them ineligible for a conflict of interest. However, over half the CIHR governing council are university professors from research centres that do actually compete for CIHR funding. Part of success on a CIHR grant application is based on how many other grants have been given to your institute. This strikes me as being more of the classic conflict of interest as most people define it.
I don't think the problem is with Big Pharma making its way into CIHR. Business has a place in science no matter how many people - researchers and laypeople alike - wish it weren't so. The perspective on science is different between academia and industry. Both have their pros and cons, and I think that CIHR and academia in general might profit from exploring some of the alternative ways of looking at science.
My problem is that when I look though the CIHR website, I can see that Pfizer has been spending millions on funding CIHR grants over the last couple of years - and now an exec is on the board. This looks like patronage of the basest sort, but it isn't conflict of interest. Even if it does leave the same sour taste in your mouth.
What I don't find immediately apparent is what kind of return Pfizer is getting on their millions of dollars of investment, apart from tax breaks. A single position on a board of roughly 20 members isn't exactly overwhelming power or voice in the policy or direction of CIHR. What's so great about that?
Tuesday, March 17, 2009
Church and State Don't Mix Like Chocolate and Peanut Butter
Around the web:
Well, no. By definition, evolution happens over multiple generations rather than within lifetimes. Evolution also posits that we are the descendants of multicellular organisms that split from the algae a little over 500 million years ago, rather than having been more or less popped into existence in 4004 BC.
Dr. Marc Garneau - ex-astronaut, D.Eng. and Opposition Science Critic - says that believing in evolution is a personal choice, and Dr. Jacques Galipeau says he wouldn't have cared if the budget last month hadn't slashed research funding (if not in so many words). And they're right - I don't care what my boss believes in, just so long as I get paid. But you have to wonder just how passionate a guy can be about funding for biology and basic medical research when he doesn't believe in evolution...
- Canadian Transport Minister hopes that one day, in the future, the trains between Montreal and Toronto will run as fast as they did 35 years ago...
- The Pope drops the ball on potentially thousands more Africans and South Americans by denying condom use can help stop the spread of AIDS...
- Stimulants are addictive? Wha?
* * *
Our Minister of State - Science and Technology, the Hon. Gary Goodyear is on CBC today being grilled for potentially being a creationist. He refused to answer a question about believing in evolution on the grounds that he's "a Christian, and I don't think anybody asking a question about my religion is appropriate." Which is kind of disturbing from a Science and Technology perspective.
So then he does a follow-up with the Globe and Mail, who got the original story, clearing the air saying he believes in evolution, and clearly goes on to demonstrate he does not understand evolution at all:
"We are evolving every year, every decade. That's a fact, whether it is to the intensity of the sun, whether it is to, as a chiropractor, walking on cement versus anything else..."
Our Minister of State - Science and Technology, the Hon. Gary Goodyear is on CBC today being grilled for potentially being a creationist. He refused to answer a question about believing in evolution on the grounds that he's "a Christian, and I don't think anybody asking a question about my religion is appropriate." Which is kind of disturbing from a Science and Technology perspective.
So then he does a follow-up with the Globe and Mail, who got the original story, clearing the air saying he believes in evolution, and clearly goes on to demonstrate he does not understand evolution at all:
"We are evolving every year, every decade. That's a fact, whether it is to the intensity of the sun, whether it is to, as a chiropractor, walking on cement versus anything else..."
Well, no. By definition, evolution happens over multiple generations rather than within lifetimes. Evolution also posits that we are the descendants of multicellular organisms that split from the algae a little over 500 million years ago, rather than having been more or less popped into existence in 4004 BC.
Dr. Marc Garneau - ex-astronaut, D.Eng. and Opposition Science Critic - says that believing in evolution is a personal choice, and Dr. Jacques Galipeau says he wouldn't have cared if the budget last month hadn't slashed research funding (if not in so many words). And they're right - I don't care what my boss believes in, just so long as I get paid. But you have to wonder just how passionate a guy can be about funding for biology and basic medical research when he doesn't believe in evolution...
Tuesday, March 3, 2009
Child abuse rips genes
Again on the pet peeve of flu shots for healthy people and antibacterial soaps - a recent report shows that 98% of influenza A strains in the US, and 100% in Canada, are resistant to the flu drug Tamiflu. Hardly surprising given that we've treated about 50 million people with it, and chances are that most of them were improperly medicated.
So once again, my boss is making waves in the news, this time with actual science, which is a bit of relief. A study mostly carried out by one of our post-doctoral fellows has been getting a great amount of media attention, as it's a very interesting finding. He shows that suicide victims with a history of abuse carry a higher amount of an alteration to DNA structure (but not sequence) that controls the expression of a gene involved in the stress response (glucocorticoid receptor Nr3c1 promoter methylation in hippocampus, for those keeping track). This alteration may "silence" the gene and have rendered these people more subject to anxiety and other negative effects of stress.
My favorite thing about this study has been the press, particularly the BBC's headline of "Child abuse 'impacts stress gene'." One thing I can't figure out about the BBC is why they put those little single quotation marks around a couple words in about 50% of their headlines: "Staff 'too timid' on child abuse," "'Ethical' stem cell hope," or "Veterans at 'higher suicide risk.'"
What do these little quotes mean? They certainly aren't a direct quotes, as my boss would beat you about the head and shoulders for saying the glucocorticoid receptor is a stress gene. They seem to serve no purpose other than to confuse people who want to use real quotation marks on their headlines for citation purposes.
In any case, people tend to take findings like this WAY too far to support whatever point of view that they have. Take the CBC's angle on the story, for example. We've got a journalist claiming that "in a way... the men were programmed to be more vulnerable to overwhelming feelings of despair," which didn't come from any of the researchers on this study (trust me, I know them all personally). Then we have a pharmacologist saying we should aim to "identify these people and then probably offer them some sort of intervention," which is interesting because 1) we have no indication whatsoever that the methylation changes actually cause the suicides, and 2) it's a real bastard trying to get those samples out of living human brains.
From the blogosphere, I think my favorite quote so far has been something along the lines of how obvious it is that abuse is bad and should we really spend millions on research to prove it? I can hardly claim impartiality here, seeing as how my salary gets paid directly from those grants, but the answer is "yes we should, because it's not obvious at all."
OK, so it's obvious that beating your kids is bad (unless you're Russell Peters), but what isn't obvious is why, on a biological level, child abuse is harmful for development. Is it obvious that DNA methylation patterns along the Nr3c1 promoter would be different in the hippocampus of abused suicide victims? Is it obvious that beating your children is like picking up their DNA and twisting it around? Is it obvious why legislators feel like there has to be some kind of biological correlate in order to make a disease somehow legitimate?
We're on your side, people. Don't accuse us of wasting government funds by proving the "obvious." If it's so obvious, then I'm in the comments section waiting patiently for a scientific explanation of the precise gene-environment interactions leading up to suicide.
* * *
So once again, my boss is making waves in the news, this time with actual science, which is a bit of relief. A study mostly carried out by one of our post-doctoral fellows has been getting a great amount of media attention, as it's a very interesting finding. He shows that suicide victims with a history of abuse carry a higher amount of an alteration to DNA structure (but not sequence) that controls the expression of a gene involved in the stress response (glucocorticoid receptor Nr3c1 promoter methylation in hippocampus, for those keeping track). This alteration may "silence" the gene and have rendered these people more subject to anxiety and other negative effects of stress.
My favorite thing about this study has been the press, particularly the BBC's headline of "Child abuse 'impacts stress gene'." One thing I can't figure out about the BBC is why they put those little single quotation marks around a couple words in about 50% of their headlines: "Staff 'too timid' on child abuse," "'Ethical' stem cell hope," or "Veterans at 'higher suicide risk.'"
What do these little quotes mean? They certainly aren't a direct quotes, as my boss would beat you about the head and shoulders for saying the glucocorticoid receptor is a stress gene. They seem to serve no purpose other than to confuse people who want to use real quotation marks on their headlines for citation purposes.
In any case, people tend to take findings like this WAY too far to support whatever point of view that they have. Take the CBC's angle on the story, for example. We've got a journalist claiming that "in a way... the men were programmed to be more vulnerable to overwhelming feelings of despair," which didn't come from any of the researchers on this study (trust me, I know them all personally). Then we have a pharmacologist saying we should aim to "identify these people and then probably offer them some sort of intervention," which is interesting because 1) we have no indication whatsoever that the methylation changes actually cause the suicides, and 2) it's a real bastard trying to get those samples out of living human brains.
From the blogosphere, I think my favorite quote so far has been something along the lines of how obvious it is that abuse is bad and should we really spend millions on research to prove it? I can hardly claim impartiality here, seeing as how my salary gets paid directly from those grants, but the answer is "yes we should, because it's not obvious at all."
OK, so it's obvious that beating your kids is bad (unless you're Russell Peters), but what isn't obvious is why, on a biological level, child abuse is harmful for development. Is it obvious that DNA methylation patterns along the Nr3c1 promoter would be different in the hippocampus of abused suicide victims? Is it obvious that beating your children is like picking up their DNA and twisting it around? Is it obvious why legislators feel like there has to be some kind of biological correlate in order to make a disease somehow legitimate?
We're on your side, people. Don't accuse us of wasting government funds by proving the "obvious." If it's so obvious, then I'm in the comments section waiting patiently for a scientific explanation of the precise gene-environment interactions leading up to suicide.
Wednesday, February 18, 2009
Remixing memories
I'm thinking that The Globe and Mail has been checking out my blog, seeing this article from earlier in the week talking about the things from my last post. Particularly how other countries are pumping money into research while Canada is cutting. Interestingly, they interviewed my PhD supervisor, who is apparently "one of Canada's top scientists".
I'm pleased how closely his opinions follow mine, and that they're publishing them in the Globe and Mail. I'm a bit disturbed about being so similar to my boss, though. I'm also disturbed that he apparently has fantasies of moving to Signapore...
I'm pleased how closely his opinions follow mine, and that they're publishing them in the Globe and Mail. I'm a bit disturbed about being so similar to my boss, though. I'm also disturbed that he apparently has fantasies of moving to Signapore...
* * *
A genetic therapy approach to treating AIDS that I blogged about last summer is currently recruiting for its first clinical trial. This is pretty incredibly quick, but it seems very safe - take some of a patient's blood, take out the T-cells, culture them, insert the gene, grow a whole pile of the modified cells, and then return them to the patient. This follows on the footsteps of another successful trial of gene therapy for AIDS treatments.
The risks of these treatments seem minimal. The gene transfer isn't contagious to other cells, and the T-cells come from the patient's own body so there should be no risk of rejection. Assuming the cells aren't grown in an animal serum, which could induce a rejection response in patients. But I imagine these guys know what they're doing.
Of course, the guys injecting a Russian boy with stem cells also knew what they were doing, and they knew the risks. Turns out they lost this bet - the kid developed extensive tumours throughout his nervous system. While this was a predicted potential side effect, I don't think anyone was expecting this to go so spectacularly wrong.
The risks of these treatments seem minimal. The gene transfer isn't contagious to other cells, and the T-cells come from the patient's own body so there should be no risk of rejection. Assuming the cells aren't grown in an animal serum, which could induce a rejection response in patients. But I imagine these guys know what they're doing.
Of course, the guys injecting a Russian boy with stem cells also knew what they were doing, and they knew the risks. Turns out they lost this bet - the kid developed extensive tumours throughout his nervous system. While this was a predicted potential side effect, I don't think anyone was expecting this to go so spectacularly wrong.
* * *
If there's one thing I've been wanting to blog about this week, it's this story about using a heart medication (propranalol, a beta-blocker) to "block bad memories." People are going buck-wild about this - I even saw it on Facebook (I have some geeky friends). But the study is not all it's cracked up to be.
The researchers conditioned people to be "afraid" of spiders by showing them pictures of spiders and then shocking them, a Pavlovian paradigm that couples a neutral stimulus (spider) to an averse stimulus (shock), and transfers the unpleasant feeling associated with the shock to the spider. The drug was able to reverse this conditioning, so people no longer had an adverse response to the spiders. And now it's being touted as a treatment for PTSD and anxiety disorders.
First of all, I would like someone to explain to me and a couple of war veterans exactly how shocking someone while looking at pictures of spiders is anything remotely like traumatic experiences like losing a limb in a firefight or having your friend's brains blown out all over you. Or even like being in a car crash.
Secondly, even something like a phobia against an object (say, spiders) isn't like a conditioned association. In fact, it's the opposite. The reason it's a phobia is precisely because it's an unconditioned and irrational fear of an object. Show me a trial with arachnophobics on propanalol viewing pictures of tarantulas and I don't think we'll see such stunning claims being made.
The idea is that when we remember things, we take the representation out of long-term storage in our brains and move it into "working memory," a sort of RAM buffer memory for your brain. When we're done with it, it gets re-programmed back into the long-term storage. If we can remove the bad associations from the memory before we code it back into long-term storage, then we can remove some of the anxiety and pathology that comes from remembering it.
I, for one, am not sure that this will work. I think that removing a simple conditioned association is a lot different from removing the particularly vivid memories that many PTSD patients have, and that the emotional component of these memories is much more intense than a simple shock to the finger. I think the biochemical underpinnings are significantly more complicated than simple noradrenaline release as well. That being said, we can condition men to respond sexually to an old boot, but again I would argue that this neither a complex behaviour nor particularly difficult to accomplish. Now if we could do it in women, then we'd be on to something.
I'm not sure what it will take to "erase" these memories, but I refer you back to an earlier post I made on memory manipulation and Joe Tsien's quote: "All memories, including the painful emotional memories, have their purposes. We learn great lessons from those memories or experiences so we can avoid making the same kinds of mistakes again, and help us to adapt down the road."
If there's one thing I've been wanting to blog about this week, it's this story about using a heart medication (propranalol, a beta-blocker) to "block bad memories." People are going buck-wild about this - I even saw it on Facebook (I have some geeky friends). But the study is not all it's cracked up to be.
The researchers conditioned people to be "afraid" of spiders by showing them pictures of spiders and then shocking them, a Pavlovian paradigm that couples a neutral stimulus (spider) to an averse stimulus (shock), and transfers the unpleasant feeling associated with the shock to the spider. The drug was able to reverse this conditioning, so people no longer had an adverse response to the spiders. And now it's being touted as a treatment for PTSD and anxiety disorders.
First of all, I would like someone to explain to me and a couple of war veterans exactly how shocking someone while looking at pictures of spiders is anything remotely like traumatic experiences like losing a limb in a firefight or having your friend's brains blown out all over you. Or even like being in a car crash.
Secondly, even something like a phobia against an object (say, spiders) isn't like a conditioned association. In fact, it's the opposite. The reason it's a phobia is precisely because it's an unconditioned and irrational fear of an object. Show me a trial with arachnophobics on propanalol viewing pictures of tarantulas and I don't think we'll see such stunning claims being made.
The idea is that when we remember things, we take the representation out of long-term storage in our brains and move it into "working memory," a sort of RAM buffer memory for your brain. When we're done with it, it gets re-programmed back into the long-term storage. If we can remove the bad associations from the memory before we code it back into long-term storage, then we can remove some of the anxiety and pathology that comes from remembering it.
I, for one, am not sure that this will work. I think that removing a simple conditioned association is a lot different from removing the particularly vivid memories that many PTSD patients have, and that the emotional component of these memories is much more intense than a simple shock to the finger. I think the biochemical underpinnings are significantly more complicated than simple noradrenaline release as well. That being said, we can condition men to respond sexually to an old boot, but again I would argue that this neither a complex behaviour nor particularly difficult to accomplish. Now if we could do it in women, then we'd be on to something.
I'm not sure what it will take to "erase" these memories, but I refer you back to an earlier post I made on memory manipulation and Joe Tsien's quote: "All memories, including the painful emotional memories, have their purposes. We learn great lessons from those memories or experiences so we can avoid making the same kinds of mistakes again, and help us to adapt down the road."
* * *
My other blog, for those who are interested, is up. The first post is enititled "Douglas Zombies Need Brains." And if that doesn't pique your interest, then I don't want you reading it anyways.
Wednesday, February 11, 2009
Blowing Ourselves (another bubble)
I was amused a couple months ago by this comic from Jorge Cham at phdcomics.com, which depicts a graph of changes in enrollment to grad studies over time superimposed over the unemployment figures. The correlation is incredible.
Being all in fun, you'd be excused for thinking the artist was just exploiting a quirk of statistics to get a laugh. But then you see Nature reporting exactly the same thing last week and realize that it's not funny, thousands of people think that getting a Ph.D. is worth money. Many people accept this as true, but I think you'd have a hard time convincing Bill Gates or Warren Buffet of that. Or me, for that matter.
For their sakes, I hope that a good portion of these thousands are working on M.B.A.s rather than Ph.D.s, particularly in science. Nature also had a feature last week about two very successful US scientists closing their labs because their funding has simply dried up. An editorial in the same issue points out that "The career crisis is especially stark in the biomedical fields, where the number of tenure-track and tenured positions has not increased in the past two decades even as universities have nearly doubled their production of biomedical doctorates. Those who do land jobs in academic research are struggling to keep them..."
All that to say professors doing academic research in their ivory towers are being as hard hit by the budget cuts, loss of endowment funds and general financial crisis as anyone else. And they don't get severance packages in the millions of dollars. Even still, I guess starting a doctorate is a bit like signing a 4-6 year contract at a meagre (but fairly secure) salary, and maybe some kind of health coverage, which is better than a lot of American citizens can say.
Maybe it is the smart move. Presumably, you set yourself up for a better job by working on an advanced degree during the recession, which will be a couple years long anyways. Good jobs should become available as we begin blowing ourselves another economic bubble to drive unsustainable expenditure - I predict some kind of -tech bubble, be it bio-, nano- or green-. Plus, it won't be long before some genius figures out a new way to create money out of nothing now that subprime mortgages are bust.
But bubbles always burst. That's why they're bubbles. When the economy crashes, it does so like a plane. It doesn't care if you're Richie Valens, the Big Bopper and Buddy Holly; or how many fancy-pants letters there are after your name. There will be blood.
Being all in fun, you'd be excused for thinking the artist was just exploiting a quirk of statistics to get a laugh. But then you see Nature reporting exactly the same thing last week and realize that it's not funny, thousands of people think that getting a Ph.D. is worth money. Many people accept this as true, but I think you'd have a hard time convincing Bill Gates or Warren Buffet of that. Or me, for that matter.
For their sakes, I hope that a good portion of these thousands are working on M.B.A.s rather than Ph.D.s, particularly in science. Nature also had a feature last week about two very successful US scientists closing their labs because their funding has simply dried up. An editorial in the same issue points out that "The career crisis is especially stark in the biomedical fields, where the number of tenure-track and tenured positions has not increased in the past two decades even as universities have nearly doubled their production of biomedical doctorates. Those who do land jobs in academic research are struggling to keep them..."
All that to say professors doing academic research in their ivory towers are being as hard hit by the budget cuts, loss of endowment funds and general financial crisis as anyone else. And they don't get severance packages in the millions of dollars. Even still, I guess starting a doctorate is a bit like signing a 4-6 year contract at a meagre (but fairly secure) salary, and maybe some kind of health coverage, which is better than a lot of American citizens can say.
Maybe it is the smart move. Presumably, you set yourself up for a better job by working on an advanced degree during the recession, which will be a couple years long anyways. Good jobs should become available as we begin blowing ourselves another economic bubble to drive unsustainable expenditure - I predict some kind of -tech bubble, be it bio-, nano- or green-. Plus, it won't be long before some genius figures out a new way to create money out of nothing now that subprime mortgages are bust.
But bubbles always burst. That's why they're bubbles. When the economy crashes, it does so like a plane. It doesn't care if you're Richie Valens, the Big Bopper and Buddy Holly; or how many fancy-pants letters there are after your name. There will be blood.
Wednesday, February 4, 2009
In these troubled times...
I've been committing adultery on this blog, by which I mean I will soon be writing a blog for the research institute where I work. However, being a public institution, they made me promise I wouldn't talk about politics on that blog and stick to science. So as long as there are still politics, I will still feel the need to rip on policy in this space.
Take the new federal budget, for example. Now, I'm not going to talk about Harper's bold-faced lie last fall that there would be no deficit for Canada this fiscal year. Nor will I rail on the other parties for not pushing the Government hard enough to create a great budget. No, here I'm going to stick with the science part of the budget, particularly the health research part. Because I hate it.
Shocking, I know.
The CBC generously refers to the budget as a "mixed bag" for science. The best news is the $2 billion to repair and expand existing facilities. Working in labs that don't have a) water dripping on experiments from pipes above, b) ceilings falling on machines worth a quarter-million dollars, and c) luxuries like proper ventilation and working temperature controls will be highly beneficial for Canadian science. This infrastructure spending will also help create jobs through construction projects, many of which will also be funded through the $1 billion the government is giving for green energy and the $750 million for the Canadian Foundation for Innovation, which offer key grant competitions for institutions needing to upgrade equipment and research infrastructure.
Other perks in the budget include some $87.5 million for new scholarships for students - although Science magazine reports that "an unspecified chunk" will go to business-related degrees. There's $351 million for Atomic Energy of Canada, which is probably overdue seeing as how Harper fired the head of the Nuclear Safety commission last year when she deemed the Chalk River reactor was unsafe, and another $110 million or so for the Canadian Space Agency - Marc Garneau's presence in Parliament makes it hard to keep cutting that program.
What most of the budget wonks don't say is that the feds are only providing about half of the promised $2 billion in infrastructure spending here - universities will be expected to raise the other half through municipal and provincial governments and potentially even private or corporate investors. Which means that some of that cash may never show up, particularly for small universities in "have-not" provinces that are struggling as it is.
The bad news doesn't end there. The budget also shaves about $150 million from the main Canadian funding agencies - CIHR, NSERC, and SSHRC. This is close to a 10% hammering, and will only serve to shave down the already outrageous odds of winning a grant. They are also gutting the funding for Genome Canada, which is a brilliant project that brings the cutting edge of genetics research techniques to universities across Canada. They are a major supporter of the provincial genome projects, some of which - such as Génome Québec - are extremely successful in their own right. While they had already been promised about $240 million over 4 years, the current budget allots them absolutely nothing. Not a sausage.
Now, in these troubled economic times, yadda yadda yadda. In these troubled times, the US is injecting some US$3.5 billion to their National Institutes of Health alone; and tens of billions more for other science organizations. Note this not a reduction in spending or in grant money, which is what Canada seems to think was the right thing to do. A mere 5% of the $3.75 billion set aside for infrastructure and such would provide for all of the money being cut from the granting agencies.
It's nice to have renovated labs, but if there's no grant money with which to fill those labs, these billions in infrastructure expenditures are little better than federal make-work projects. Frankly - particularly here in Quebec - the money might be better spent on the roads.
Take the new federal budget, for example. Now, I'm not going to talk about Harper's bold-faced lie last fall that there would be no deficit for Canada this fiscal year. Nor will I rail on the other parties for not pushing the Government hard enough to create a great budget. No, here I'm going to stick with the science part of the budget, particularly the health research part. Because I hate it.
Shocking, I know.
The CBC generously refers to the budget as a "mixed bag" for science. The best news is the $2 billion to repair and expand existing facilities. Working in labs that don't have a) water dripping on experiments from pipes above, b) ceilings falling on machines worth a quarter-million dollars, and c) luxuries like proper ventilation and working temperature controls will be highly beneficial for Canadian science. This infrastructure spending will also help create jobs through construction projects, many of which will also be funded through the $1 billion the government is giving for green energy and the $750 million for the Canadian Foundation for Innovation, which offer key grant competitions for institutions needing to upgrade equipment and research infrastructure.
Other perks in the budget include some $87.5 million for new scholarships for students - although Science magazine reports that "an unspecified chunk" will go to business-related degrees. There's $351 million for Atomic Energy of Canada, which is probably overdue seeing as how Harper fired the head of the Nuclear Safety commission last year when she deemed the Chalk River reactor was unsafe, and another $110 million or so for the Canadian Space Agency - Marc Garneau's presence in Parliament makes it hard to keep cutting that program.
What most of the budget wonks don't say is that the feds are only providing about half of the promised $2 billion in infrastructure spending here - universities will be expected to raise the other half through municipal and provincial governments and potentially even private or corporate investors. Which means that some of that cash may never show up, particularly for small universities in "have-not" provinces that are struggling as it is.
The bad news doesn't end there. The budget also shaves about $150 million from the main Canadian funding agencies - CIHR, NSERC, and SSHRC. This is close to a 10% hammering, and will only serve to shave down the already outrageous odds of winning a grant. They are also gutting the funding for Genome Canada, which is a brilliant project that brings the cutting edge of genetics research techniques to universities across Canada. They are a major supporter of the provincial genome projects, some of which - such as Génome Québec - are extremely successful in their own right. While they had already been promised about $240 million over 4 years, the current budget allots them absolutely nothing. Not a sausage.
Now, in these troubled economic times, yadda yadda yadda. In these troubled times, the US is injecting some US$3.5 billion to their National Institutes of Health alone; and tens of billions more for other science organizations. Note this not a reduction in spending or in grant money, which is what Canada seems to think was the right thing to do. A mere 5% of the $3.75 billion set aside for infrastructure and such would provide for all of the money being cut from the granting agencies.
It's nice to have renovated labs, but if there's no grant money with which to fill those labs, these billions in infrastructure expenditures are little better than federal make-work projects. Frankly - particularly here in Quebec - the money might be better spent on the roads.
Wednesday, December 10, 2008
Smarter, faster, stronger
A stunning opinion piece in Nature on Monday encouraging the use of cognitive-enhancing drugs, which has been all over the news and brought me to remember a problem I have with Ritalin. I'll have you know this is completely different from having a Ritalin problem. I'm not saying I don't believe in ADHD, although I do believe it is over-diagnosed, but I'm not getting into that. What I want to get into is Ritalin. And most of what we have in the way of ADHD drugs.
The simple fact of the matter is that these drugs are cognitive enhancers. They're a couple of chemical steps removed from amphetamines (speed), which are well-known for improvement of certain parts of thinking - short-term memory and attention particularly. Now, the ADHD drugs seem to work in a select number of specific areas of the brain whereas the speedball drives an entire neurotransmission system into overdrive (to make a gross oversimplification), but people without ADHD still see an enhancement of performance on tests of cognitive performance when they take Ritalin. That's why people buy it illegally during exam periods.
I'm about to make a brutal analogy here, so cover your ears - this is like letting Special Olympics athletes go to the other Olympics, but doped up on whatever performance-enhancer is big right now. No, really. My problem with Ritalin is that gives improvement on performance of tests that we use to diagnose ADHD in in both controls and ADHD patients. We're not treating ADHD necessarily - just improving performance on diagnostic tests, performance on which corresponds closely to that on academic exams.
Most of us are already users of cognitive enhancers. During my undergrad I smoked 15-20 cigarettes and swilled maybe 2-4 litres of coffee daily (thankfully, I've since cut down on both significantly). Both nicotine and caffeine are clinically proven enhancers of performance on pretty much any cognitive task you could name. We drink Red Bulls and coffee to make us sharper, we take sleeping pills to help us calm down, we take alcohol to enhance our social performances.
Which brings us back to the topic of the editorial that brought me to this piece in the first place. Why shouldn't we use drugs to become more intelligent? In what way is this possibly a bad thing? There are side effects; many not as bad as are present in a large number of other commercially available drugs (especially alcohol and tobacco). Why shouldn't my doctor, my lawyer, my accountant, my Member of Parliament and my future kid's teacher be on these drugs all the time?
Personally, I think that the means here don't require justification by the ends. There's no ethical dilemma about taking vitamins, or antioxidants, or coffee. We already use pharmacology to improve our quality of life in so many ways, and I see this as no different than taking drugs for anxiety, diabetes, or metabolic syndrome. Better living through pharmacology is still better living, and I don't think anybody should have a problem with a better life.
The simple fact of the matter is that these drugs are cognitive enhancers. They're a couple of chemical steps removed from amphetamines (speed), which are well-known for improvement of certain parts of thinking - short-term memory and attention particularly. Now, the ADHD drugs seem to work in a select number of specific areas of the brain whereas the speedball drives an entire neurotransmission system into overdrive (to make a gross oversimplification), but people without ADHD still see an enhancement of performance on tests of cognitive performance when they take Ritalin. That's why people buy it illegally during exam periods.
I'm about to make a brutal analogy here, so cover your ears - this is like letting Special Olympics athletes go to the other Olympics, but doped up on whatever performance-enhancer is big right now. No, really. My problem with Ritalin is that gives improvement on performance of tests that we use to diagnose ADHD in in both controls and ADHD patients. We're not treating ADHD necessarily - just improving performance on diagnostic tests, performance on which corresponds closely to that on academic exams.
Most of us are already users of cognitive enhancers. During my undergrad I smoked 15-20 cigarettes and swilled maybe 2-4 litres of coffee daily (thankfully, I've since cut down on both significantly). Both nicotine and caffeine are clinically proven enhancers of performance on pretty much any cognitive task you could name. We drink Red Bulls and coffee to make us sharper, we take sleeping pills to help us calm down, we take alcohol to enhance our social performances.
Which brings us back to the topic of the editorial that brought me to this piece in the first place. Why shouldn't we use drugs to become more intelligent? In what way is this possibly a bad thing? There are side effects; many not as bad as are present in a large number of other commercially available drugs (especially alcohol and tobacco). Why shouldn't my doctor, my lawyer, my accountant, my Member of Parliament and my future kid's teacher be on these drugs all the time?
Personally, I think that the means here don't require justification by the ends. There's no ethical dilemma about taking vitamins, or antioxidants, or coffee. We already use pharmacology to improve our quality of life in so many ways, and I see this as no different than taking drugs for anxiety, diabetes, or metabolic syndrome. Better living through pharmacology is still better living, and I don't think anybody should have a problem with a better life.
Tuesday, November 25, 2008
Science cuts and general news
From the news:
- Interesting article on anti-aging drugs from Wired, where scientists think that this new class of drugs might be the key to fighting cancer, diabetes, Alzheimer's, and just about everything else under the sun.
- A great piece in CBC suggesting that forward-facing strollers are bad for a child's social and verbal development. This makes a lot of sense: kids of stroller age have brains that are designed for learning about faces and language.
- Wired's 10 favourite biology videos. Just awesome (except the PCR song - man, I hate the PCR song). I'll be commenting on at least one or two over the next while.
* * *
According to this CBC article, Statistics Canada reported Thursday that federal spending in science and technology is about to drop for the first time in 5 years, which is about the same time we elected Paul Martin to a minority government. Now admittedly these cuts seem small - about 3% - but this represents hundreds of millions of dollars lost for funding science and innovation in this country.
I don't think this is a good idea, but I'll declare a conflict of interest being a scientist who would like to be employed in Canada. Even still, it seems natural that investment in alternative energy production will create domestic skilled jobs desperately needed by Canadians. Of course, it would cost money now, and it will be years before we see any real return from this investment. But unlike investing in shady debt trading - asset-backed commercial papers, or subprime mortgages - this economic activity would create real wealth, and by that I mean jobs, clean energy, and Canadian businesses with a head start in a globally important industry.
According to this CBC article, Statistics Canada reported Thursday that federal spending in science and technology is about to drop for the first time in 5 years, which is about the same time we elected Paul Martin to a minority government. Now admittedly these cuts seem small - about 3% - but this represents hundreds of millions of dollars lost for funding science and innovation in this country.
I don't think this is a good idea, but I'll declare a conflict of interest being a scientist who would like to be employed in Canada. Even still, it seems natural that investment in alternative energy production will create domestic skilled jobs desperately needed by Canadians. Of course, it would cost money now, and it will be years before we see any real return from this investment. But unlike investing in shady debt trading - asset-backed commercial papers, or subprime mortgages - this economic activity would create real wealth, and by that I mean jobs, clean energy, and Canadian businesses with a head start in a globally important industry.
Monday, November 17, 2008
Garneau vs. Goodyear
The Opposition Liberals have named their new Science critic, and it is former astronaut and generally awesome guy Marc Garneau. This is a good move by the Libs, as Garneau actually has a Doctorate in engineering and therefore knows something about science. Oh yeah, and he was the first Canadian in space, with almost 678 hours over three trips total. That's mad geek cred right there.
Gary Goodyear may not be as well-known as Marc Garneau, but is our newly-appointed Minister of State - Science and Technology (I know, what kind of title is that?). Wikipedia lists him as a physiotherapist and doctor of chiropractic, having graduated from an established college that engages in multidisciplinary research and involves about 4500 hours of coursework. However, I couldn't find him in PubMed so I don't think that he's ever actually performed research.
I'd like to see some more Ph.D.s in our legislature's ranks. People that actually understand the cutting edge of their science and can talk about research in a meaningful way. Harper's treatment of science hasn't been cruel, but it hasn't been kind, either. But I'd like to see someone that can actually sell the importance of research through their experiences to the Prime Minister and the Canadian people. It will be interesting to hear Garneau defend the Canadian Space Agency from further budget cuts.
Economics rant. Feel free to skip.
Bush was at the G20 summit last week talking about how free markets need to remain free, and that this is how global economic progress will be made.
Let me point out three perfectly obvious things. First of all, the U.S. is not interested in free markets. That's why we have things like NAFTA, to make sure that American economic interests get certain advantages. This is not necessarily a bad thing (for the US, at least), but it is definitely not a free market. Secondly, the government is spending up to $700 billion to bail banks out of bad business practices. The very definition of capitalism and free markets demands that governments not engage in massive market manipulation. Thirdly, the only way to have prevented the current economic meltdown would have been to actually regulate the banks and what they were doing, which is also not a free market approach.
Alan Greenspan, former head of the Federal Reserve (and by extension the US economy) said he made a key error during his tenure - "I made a mistake in presuming that the self-interests of organizations, specifically banks and others... were best capable of protecting their own shareholders and their equity in the firms." In other words, he assumed that the banks would follow base capitalist economic assumptions: turn profits, perform due diligence, cover their asses. But they only got one out of three on that quiz, and a suddenly socialist US government is now paying them truckloads of money - skyscrapers full, actually - for this colossal failure to do their jobs.
This is not a free market approach, which just goes to show that capitalism and free markets don't work, and never have. Not that socialism does, but I'm sick of hearing about the power of free markets when 1) there aren't any, and 2) the closer we go towards a free market, i.e. the less closely government regulates, the worse things get.
Gary Goodyear may not be as well-known as Marc Garneau, but is our newly-appointed Minister of State - Science and Technology (I know, what kind of title is that?). Wikipedia lists him as a physiotherapist and doctor of chiropractic, having graduated from an established college that engages in multidisciplinary research and involves about 4500 hours of coursework. However, I couldn't find him in PubMed so I don't think that he's ever actually performed research.
I'd like to see some more Ph.D.s in our legislature's ranks. People that actually understand the cutting edge of their science and can talk about research in a meaningful way. Harper's treatment of science hasn't been cruel, but it hasn't been kind, either. But I'd like to see someone that can actually sell the importance of research through their experiences to the Prime Minister and the Canadian people. It will be interesting to hear Garneau defend the Canadian Space Agency from further budget cuts.
* * *
Economics rant. Feel free to skip.
Bush was at the G20 summit last week talking about how free markets need to remain free, and that this is how global economic progress will be made.
Let me point out three perfectly obvious things. First of all, the U.S. is not interested in free markets. That's why we have things like NAFTA, to make sure that American economic interests get certain advantages. This is not necessarily a bad thing (for the US, at least), but it is definitely not a free market. Secondly, the government is spending up to $700 billion to bail banks out of bad business practices. The very definition of capitalism and free markets demands that governments not engage in massive market manipulation. Thirdly, the only way to have prevented the current economic meltdown would have been to actually regulate the banks and what they were doing, which is also not a free market approach.
Alan Greenspan, former head of the Federal Reserve (and by extension the US economy) said he made a key error during his tenure - "I made a mistake in presuming that the self-interests of organizations, specifically banks and others... were best capable of protecting their own shareholders and their equity in the firms." In other words, he assumed that the banks would follow base capitalist economic assumptions: turn profits, perform due diligence, cover their asses. But they only got one out of three on that quiz, and a suddenly socialist US government is now paying them truckloads of money - skyscrapers full, actually - for this colossal failure to do their jobs.
This is not a free market approach, which just goes to show that capitalism and free markets don't work, and never have. Not that socialism does, but I'm sick of hearing about the power of free markets when 1) there aren't any, and 2) the closer we go towards a free market, i.e. the less closely government regulates, the worse things get.
Monday, October 27, 2008
Transsexuals, farts, stem cells and memory manipulation. Just another day...
From the news:
- Australian study finds correlation between transsexuality and the gene coding a male hormone (androgen) receptor. Apparently, the long version of the gene has a less efficient product, and was found significantly more often in 112 male-female transsexuals compared to 258 control subjects. Which makes me wonder what this finding means to transsexuals, if anything at all...
- Solomon Snyder, an interesting character in the history of neuroscience, stands behind a study linking the stink-inducing chemical in flatulence and blood pressure. Apparently the foul smell, hydrogen sulfide, can lower blood pressure significantly. Reported with a sort of childish glee by both the BBC and the CBC (and others)...
- While Britain relaxes certain stem-cell laws, it is pointed out that Canada is the about the only country in the world that does not currently allow the use of animal eggs in the production of human embryonic stem cells. I would bet a hefty sum of cash that stem cell technology will cure at least some neurodegenerative disorders within my lifetime. However, it is up to legislators to determine whether it will be 10 years from now or 25...
* * *
A very interesting piece from CBC reports on scientists who seem to succeed at wiping a specific memory from a rat. They do this by using mice who have a very fancy piece of genetic engineering on board. The scientists built a gene construct where they could make a certain protein become more abundant in certain areas of the brain through pharmacological manipulation. Then they tested if a mouse could remember a certain place by shocking him there, and seeing if he shows behavioural signs of fear the next time he gets put there.
By overexpressing the protein in question when the mouse was put back in the chamber, the researchers could effectively make the memory disappear. Now, as we all know, memory is a strange thing. It consists of four processes that we call "acquisition," "consolidation," "storage," and "retrieval," which we could equally call "getting," "coding," um, "storing," and "remembering." But it's more complicated than that - when a memory is brought back from storage to become part of conscious thought, it has to be re-encoded, and stored. Even worse, it becomes flexible while we remember it - numerous studies show memories are influenced by current emotions and knowledge, become mixed up with the present.
Instead of altering the memory, the overexpression of this protein (αCaMKII for those keeping track) seems to destroy the memory when it's being remembered, perhaps with a sort of excessive brain "noise" level that obliterates the memory signal during the process of recalling it. This paper is a tome, so I haven't been through it very thoroughly, but it's in an amazing journal (Neuron) and looks pretty watertight. Really an amazing study.
That being said, this is a bit of what a former colleague of mine calls a "sledgehammer" approach, because it lacks precision as a tool. Gene expression is affected through an enormous population of cells, so it could be the case that more than the memory being recalled is affected . Other limitations make it extremely tough to try pulling this off using similar methods in humans. Firstly, the behaviour is not very sophisticated, even for a mouse. More importantly, human memories - particularly the bad ones - are probably richer and more complex than those of mice, and will be consequently harder to "knock out."
The best part, however, is this very wise comment by senior author Joe Tsien: "All memories, including the painful emotional memories, have their purposes. We learn great lessons from those memories or experiences so we can avoid making the same kinds of mistakes again, and help us to adapt down the road."
Good advice, and wise words for the future of memory manipulation.
A very interesting piece from CBC reports on scientists who seem to succeed at wiping a specific memory from a rat. They do this by using mice who have a very fancy piece of genetic engineering on board. The scientists built a gene construct where they could make a certain protein become more abundant in certain areas of the brain through pharmacological manipulation. Then they tested if a mouse could remember a certain place by shocking him there, and seeing if he shows behavioural signs of fear the next time he gets put there.
By overexpressing the protein in question when the mouse was put back in the chamber, the researchers could effectively make the memory disappear. Now, as we all know, memory is a strange thing. It consists of four processes that we call "acquisition," "consolidation," "storage," and "retrieval," which we could equally call "getting," "coding," um, "storing," and "remembering." But it's more complicated than that - when a memory is brought back from storage to become part of conscious thought, it has to be re-encoded, and stored. Even worse, it becomes flexible while we remember it - numerous studies show memories are influenced by current emotions and knowledge, become mixed up with the present.
Instead of altering the memory, the overexpression of this protein (αCaMKII for those keeping track) seems to destroy the memory when it's being remembered, perhaps with a sort of excessive brain "noise" level that obliterates the memory signal during the process of recalling it. This paper is a tome, so I haven't been through it very thoroughly, but it's in an amazing journal (Neuron) and looks pretty watertight. Really an amazing study.
That being said, this is a bit of what a former colleague of mine calls a "sledgehammer" approach, because it lacks precision as a tool. Gene expression is affected through an enormous population of cells, so it could be the case that more than the memory being recalled is affected . Other limitations make it extremely tough to try pulling this off using similar methods in humans. Firstly, the behaviour is not very sophisticated, even for a mouse. More importantly, human memories - particularly the bad ones - are probably richer and more complex than those of mice, and will be consequently harder to "knock out."
The best part, however, is this very wise comment by senior author Joe Tsien: "All memories, including the painful emotional memories, have their purposes. We learn great lessons from those memories or experiences so we can avoid making the same kinds of mistakes again, and help us to adapt down the road."
Good advice, and wise words for the future of memory manipulation.
Saturday, October 18, 2008
Glowing rats & adventure!
The other Nobel Prize I felt qualified to comment on was that awarded for chemistry, where researchers were honoured for the discovery of green fluorescent protein (GFP), which is a protein native to jellyfish and, as implied by the name, can glow green. Now green glowing proteins may not seem like a big deal, but this discovery also brought about fundamental changes in the way we do biology (although the use of luciferase, a light-generating protein from fireflies, was also a big step along the same direction).
In my last post I talked about using the HIV virus a "shuttle" for genetic material, able to insert genes into a host's DNA after infection. Now, if you wanted to look at whether your cells were infected or not, a great way to do that would be to make the virus carry GFP. If you want to know whether a gene is being expressed, you can make a construct that has the same regulatory regions as your gene of interest, but make it code GFP. Instead of performing time-consuming experiments to measure expression, you can literally just look. And then there's the "Brainbow" mice, which have genes for several fluorescent proteins in their neurons. Their stunning pictures (amazing gallery here) will drastically change neuroanatomical methods forever.
Discoveries of this magnitude, like the discovery of the HIV virus, are huge not because of any single aspect of the discovery, but also for the development of tools that literally change the way science is done. The same thing was true of Mello and Flame's Nobel last year for the discovery of RNA interference. This was such a paradigm-shifting discovery that the committee gave out the Nobel to what must be two of the youngest researchers to ever be considered for it, and a discovery that was barely a decade old; normally the Nobel is reserved for the final coup-de-gras of a senior scientist's long and storied career (like Kandel, Greengard and Carlsson in 2000). It heartening to see the Nobel going to researchers who are changing the ways we do science, rather than given out as an honorarium, like a degree to PhD students who've been chugging along as best they can for the last decade.
In my last post I talked about using the HIV virus a "shuttle" for genetic material, able to insert genes into a host's DNA after infection. Now, if you wanted to look at whether your cells were infected or not, a great way to do that would be to make the virus carry GFP. If you want to know whether a gene is being expressed, you can make a construct that has the same regulatory regions as your gene of interest, but make it code GFP. Instead of performing time-consuming experiments to measure expression, you can literally just look. And then there's the "Brainbow" mice, which have genes for several fluorescent proteins in their neurons. Their stunning pictures (amazing gallery here) will drastically change neuroanatomical methods forever.
Discoveries of this magnitude, like the discovery of the HIV virus, are huge not because of any single aspect of the discovery, but also for the development of tools that literally change the way science is done. The same thing was true of Mello and Flame's Nobel last year for the discovery of RNA interference. This was such a paradigm-shifting discovery that the committee gave out the Nobel to what must be two of the youngest researchers to ever be considered for it, and a discovery that was barely a decade old; normally the Nobel is reserved for the final coup-de-gras of a senior scientist's long and storied career (like Kandel, Greengard and Carlsson in 2000). It heartening to see the Nobel going to researchers who are changing the ways we do science, rather than given out as an honorarium, like a degree to PhD students who've been chugging along as best they can for the last decade.
* * *
Most interesting thing I've read this week: in high school, I was taught about a 1953 experiment by a guy named Miller, which remains one of the most fascinating I've ever heard of. He designed a closed system with an atmosphere similar to what was, at the time, believed to comprise the early Earth's atmosphere - methane, ammonia, carbon dioxide and such. He introduced some sparks and water vapour, and voila - found a couple of amino acids were produced, perhaps giving some insight into abiogenesis (how life came from inorganic precursors).
Miller died last year, and the researcher who inherited his labs and equipment found a series of tubes marked "experiments 1952-1953." He took some vials from the very same experiment and subjected it to much more advanced analysis than was available at the time. These researchers found dozens of organic compounds Miller was unable to detect, lending great support to the original experiments.
While today we acknowledge that the early atmosphere of the planet was not exactly what was envisioned in 1953, this experiment is a fascinating example of a sort of adventurous scientific spirit that I don't think is as prominent today as it was 50 years ago, and I think science is probably the worse for it.
Most interesting thing I've read this week: in high school, I was taught about a 1953 experiment by a guy named Miller, which remains one of the most fascinating I've ever heard of. He designed a closed system with an atmosphere similar to what was, at the time, believed to comprise the early Earth's atmosphere - methane, ammonia, carbon dioxide and such. He introduced some sparks and water vapour, and voila - found a couple of amino acids were produced, perhaps giving some insight into abiogenesis (how life came from inorganic precursors).
Miller died last year, and the researcher who inherited his labs and equipment found a series of tubes marked "experiments 1952-1953." He took some vials from the very same experiment and subjected it to much more advanced analysis than was available at the time. These researchers found dozens of organic compounds Miller was unable to detect, lending great support to the original experiments.
While today we acknowledge that the early atmosphere of the planet was not exactly what was envisioned in 1953, this experiment is a fascinating example of a sort of adventurous scientific spirit that I don't think is as prominent today as it was 50 years ago, and I think science is probably the worse for it.
Wednesday, October 15, 2008
Viral Marketing
Well, no surprises for me in the election, which frankly makes me sad, actually. I am predicting that the Libs will have a new leader by November 2009 (if not sooner) and will force another election 18 months or so thereafter. Not really Dion's fault, but he didn't help himself much. It was very telling that the separatist leader Gilles Duceppe is significantly more comfortable in English than the Liberal PM hopeful.
* * *
I wanted to speak briefly about the Nobel Prizes this year, or at least those in medicine and chemistry - I don't know enough about physics to even begin to comment on that work. And of course, the Nobel Prize in economics is really the Swedish Central Bank Prize in memory of Alfred Nobel, because economics isn't so much a science as it is a crapshoot.
The Nobel Prize in Medicine went to a number of people (details here) for work on viruses, two of them for the discovery of the HIV virus. It was a little shameful that a certain other party didn't get some credit, but the Nobel can only be given to 3 people, and he doesn't seem as broken up about it as it might be.
What you probably don't know about the HIV virus is how it blew away the biology community when they discovered how it worked. It is literally capable of taking its own genetic information and downloading it into the hard drive of your genome. Then your own cells start manufacturing the virus and it spreads. It uses a special enzyme for this, known as reverse transcriptase, which itself allowed the development of a process called RT-PCR, one of the most important tools in the field molecular biology.
Now, AIDS and other retrovirally-transmitted diseases are important enough on their own to merit consideration for a Nobel, but an important development in recent years has made the discovery even more important. Since this virus can insert genetic material, scientists wondered if they could use the virus as a tool to put genes into mammalian cells.
I wouldn't be talking about this if it was unsuccessful. The virus has been extensively genetically engineered to be able to carry genetic payloads into cells that it can infect, without replicating new virus and harming the host. Today, I myself use a heavily modified version of the AIDS virus to insert genes into rat brain cells and perform experiments looking at how certain genes affect the expression of other genes.
The importance in this case wasn't just the discovery of the viral agents, or showing that these agents caused much more serious diseases. These things were vital contributions to medicine. This discovery went on to reverberate through the field of biology and changed the way we do experiments and perform the science. There are few nobler things that could have been honoured.
Soon - the chemistry Nobel, another (related) paradigm-shifter.
I wanted to speak briefly about the Nobel Prizes this year, or at least those in medicine and chemistry - I don't know enough about physics to even begin to comment on that work. And of course, the Nobel Prize in economics is really the Swedish Central Bank Prize in memory of Alfred Nobel, because economics isn't so much a science as it is a crapshoot.
The Nobel Prize in Medicine went to a number of people (details here) for work on viruses, two of them for the discovery of the HIV virus. It was a little shameful that a certain other party didn't get some credit, but the Nobel can only be given to 3 people, and he doesn't seem as broken up about it as it might be.
What you probably don't know about the HIV virus is how it blew away the biology community when they discovered how it worked. It is literally capable of taking its own genetic information and downloading it into the hard drive of your genome. Then your own cells start manufacturing the virus and it spreads. It uses a special enzyme for this, known as reverse transcriptase, which itself allowed the development of a process called RT-PCR, one of the most important tools in the field molecular biology.
Now, AIDS and other retrovirally-transmitted diseases are important enough on their own to merit consideration for a Nobel, but an important development in recent years has made the discovery even more important. Since this virus can insert genetic material, scientists wondered if they could use the virus as a tool to put genes into mammalian cells.
I wouldn't be talking about this if it was unsuccessful. The virus has been extensively genetically engineered to be able to carry genetic payloads into cells that it can infect, without replicating new virus and harming the host. Today, I myself use a heavily modified version of the AIDS virus to insert genes into rat brain cells and perform experiments looking at how certain genes affect the expression of other genes.
The importance in this case wasn't just the discovery of the viral agents, or showing that these agents caused much more serious diseases. These things were vital contributions to medicine. This discovery went on to reverberate through the field of biology and changed the way we do experiments and perform the science. There are few nobler things that could have been honoured.
Soon - the chemistry Nobel, another (related) paradigm-shifter.
Thursday, October 9, 2008
Fair is fair - Science Under Harper
So it's been awhile. I've been restraining myself because what I really want to write about is the election next week and the US subprime crisis. But I write about science, mostly (go Habs go), and so have tried to avoid these topics, which then keep me from writing. Which brings me to a summary of Canadian science news during Harper's term as Prime Minister. Election- and science-related, which is a big coup for me.
I could bring up that Harper backed us out of the Kyoto protocol, news about which seems to come up in "Science" sections of the news frequently. Seriously, our response to this relatively slow-moving but incredibly serious threat resembles that of FEMA's to Katrina, i.e. to lay back and hope the problem will blow itself out before anybody has to do anything. Harper's environmental plans are simply awful. I don't know if carbon tax is the right way to go, but Harper's plan will lead to increased emissions. Simple as that. Not that Dion's record on emissions was spectacular as Minister of the Environment, but you have to limit the amount of blame you can put at his feet, as he was only there two years.
I have to mention a positive thing - long deserved tax exemptions for graduate students. Graduate students make very little money - averaging under $20 000 annually - so getting that kickback really makes a difference. Plus, it never made sense to me that our government charged taxes on money they gave my boss in order for me to study. Harper actually increased the number of fellowships available to students - in science, anyways, I don't know about anywhere else - which is pretty good. Harper has given modest increases to funding agencies, but any government will have trouble keeping pace with the Chretien Liberals, who did things like increase the budget of the Canadian Institute for Health Research from $289 million to $666 million over 6 years, which is a stunning feat.
Another big thing that Harper got press for was dropping the position of National Science Advisor. This got him condemned by Nature, one of the most important journals in the world. They readily admit that the post was woefully underpowered and underfunded upon its creation by the Liberals, but relegating it from direct Prime Ministerial interaction to a subdivision of some Ministry, and then phasing it out for the Science, Technology and Innovation Council wasn't a step forward. This represents a typically Canadian approach to politics - create 18 jobs where one would do, and give at least 9 to your friends.
But then there some other things I wasn't a fan of. Him opposing safe injection sites when there's a pile of evidence they work. Health Canada started calling for them as early as 2002, and Harper wants to eliminate those few that exist. This is an example where the Prime Minister is refusing to let science shape policy. Him firing the head of the nuclear commission when she shut down a potentially unsafe Chalk River nuclear plant. His then-Environment Minister Rona Ambrose engaging in a little old-fashioned Big Brother-type censorship.
All in all, I think science and technology would fare better under someone that wasn't Harper, and allows science to have a role informing policy, and doesn't engage in downright lying and bullying to advance their agenda. Science should change your policies - it apports new information. That's what it's for, and why the government funds billions in research and development projects. The least we can ask our politicians to do is to take some return from that investment.
Next week - the Nobel Prizes.
I could bring up that Harper backed us out of the Kyoto protocol, news about which seems to come up in "Science" sections of the news frequently. Seriously, our response to this relatively slow-moving but incredibly serious threat resembles that of FEMA's to Katrina, i.e. to lay back and hope the problem will blow itself out before anybody has to do anything. Harper's environmental plans are simply awful. I don't know if carbon tax is the right way to go, but Harper's plan will lead to increased emissions. Simple as that. Not that Dion's record on emissions was spectacular as Minister of the Environment, but you have to limit the amount of blame you can put at his feet, as he was only there two years.
I have to mention a positive thing - long deserved tax exemptions for graduate students. Graduate students make very little money - averaging under $20 000 annually - so getting that kickback really makes a difference. Plus, it never made sense to me that our government charged taxes on money they gave my boss in order for me to study. Harper actually increased the number of fellowships available to students - in science, anyways, I don't know about anywhere else - which is pretty good. Harper has given modest increases to funding agencies, but any government will have trouble keeping pace with the Chretien Liberals, who did things like increase the budget of the Canadian Institute for Health Research from $289 million to $666 million over 6 years, which is a stunning feat.
Another big thing that Harper got press for was dropping the position of National Science Advisor. This got him condemned by Nature, one of the most important journals in the world. They readily admit that the post was woefully underpowered and underfunded upon its creation by the Liberals, but relegating it from direct Prime Ministerial interaction to a subdivision of some Ministry, and then phasing it out for the Science, Technology and Innovation Council wasn't a step forward. This represents a typically Canadian approach to politics - create 18 jobs where one would do, and give at least 9 to your friends.
But then there some other things I wasn't a fan of. Him opposing safe injection sites when there's a pile of evidence they work. Health Canada started calling for them as early as 2002, and Harper wants to eliminate those few that exist. This is an example where the Prime Minister is refusing to let science shape policy. Him firing the head of the nuclear commission when she shut down a potentially unsafe Chalk River nuclear plant. His then-Environment Minister Rona Ambrose engaging in a little old-fashioned Big Brother-type censorship.
All in all, I think science and technology would fare better under someone that wasn't Harper, and allows science to have a role informing policy, and doesn't engage in downright lying and bullying to advance their agenda. Science should change your policies - it apports new information. That's what it's for, and why the government funds billions in research and development projects. The least we can ask our politicians to do is to take some return from that investment.
Next week - the Nobel Prizes.
Tuesday, September 9, 2008
Genome or Playstation? Hmmm...
Well, we're still here, so the LHC hasn't destroyed the universe... yet. Good news.
Recently there was some not so good news for people who deposited their genetic information (not that way!) into public databases - there is some concern that this information can be tracked back to individuals. This doesn't seem like such a big deal, and it won't be until one day we apply for life insurance and they tell us, "Well, we found your genome online and it looks like you have a 10-fold elevation in your risk for contracting the hoobajabbies within the next 11.6 years, so we're going to need to increase your premiums." Seems a little science-fiction and Big Brother, until you find out that 23andMe (who I've talked about before) can now "sequence your genome" for the same price as a Playstation 3.
Now, I say sequence in quotation marks because they don't really sequence the whole thing, which so far only Craig Venter can really do, at the cost of tens of millions of US dollars. Before the currency started plummeting. Only two people have a data file containing their whole genomes at this point, and they are Dr. Venter and James Watson, and even what they have is a "best guess" from a computer-guided reassembly of their whole genomes from sequenced fragments.
The As, Cs, Ts, and Gs that make up your DNA are known as nucleotides, and there known places where there are differences in the population. These are known as single nucleotide polymorphisms (SNPs), and we have discovered thousands of them. Some of them are even associated with certain (real) diseases, although these studies represent correlations rather than causes. Still, insurance companies calculate premiums based on actuarial tables - statistical correlations - and I don't want them exploiting a $400 sequencing service to make a couple bucks by nailing people who happen to be born with a couple bad nucleotides.
I am seriously impressed that our legislators have already been thinking about this, but clicking on the government link for information about genetic discrimination legislation gets 404'd, which leads me to be believe that it's not exactly a hot issue these days. Like puffin poop.
Recently there was some not so good news for people who deposited their genetic information (not that way!) into public databases - there is some concern that this information can be tracked back to individuals. This doesn't seem like such a big deal, and it won't be until one day we apply for life insurance and they tell us, "Well, we found your genome online and it looks like you have a 10-fold elevation in your risk for contracting the hoobajabbies within the next 11.6 years, so we're going to need to increase your premiums." Seems a little science-fiction and Big Brother, until you find out that 23andMe (who I've talked about before) can now "sequence your genome" for the same price as a Playstation 3.
Now, I say sequence in quotation marks because they don't really sequence the whole thing, which so far only Craig Venter can really do, at the cost of tens of millions of US dollars. Before the currency started plummeting. Only two people have a data file containing their whole genomes at this point, and they are Dr. Venter and James Watson, and even what they have is a "best guess" from a computer-guided reassembly of their whole genomes from sequenced fragments.
The As, Cs, Ts, and Gs that make up your DNA are known as nucleotides, and there known places where there are differences in the population. These are known as single nucleotide polymorphisms (SNPs), and we have discovered thousands of them. Some of them are even associated with certain (real) diseases, although these studies represent correlations rather than causes. Still, insurance companies calculate premiums based on actuarial tables - statistical correlations - and I don't want them exploiting a $400 sequencing service to make a couple bucks by nailing people who happen to be born with a couple bad nucleotides.
I am seriously impressed that our legislators have already been thinking about this, but clicking on the government link for information about genetic discrimination legislation gets 404'd, which leads me to be believe that it's not exactly a hot issue these days. Like puffin poop.
Sunday, September 7, 2008
The End of the World?
The Large Hadron Collider comes online Monday and starts doing weird things that the universe hasn't seen happen to its particles since around the Big Bang, apparently. For an easy-to-follow lay explanation, see this link, which beats the hell out of the biology songs cropping up on YouTube. Some are arguing that this thing could end our world by creating black holes on the planetary surface, but I feel that if black holes were that easy to make, we'd have them in our backyards. Or maybe that's where lost dryer socks really go.
In a similar vein, it's also the end of the longest minority government ever in Canadian history, as Stephen Harper asked Michaelle Jean to dissolve the Parliament this morning. We'll head to the polls for another election on the 14th of October - the 3rd time in 11 years - and we'll end up with another Conservative minority. Harper's strategy must have something to do with massive turkey consumption influencing voter choices, as last time we had elections just after Christmas.
This blog will get hijacked by incredibly amusing (and potentially vindictive and offensive) political tales every once in a while, because election time is my favourite. We'll start by ripping into David Emerson, the shifty representative from Vancouver who crossed the floor 2 weeks after being re-elected as a Liberal in his traditionally left-wing riding. His quotes in the CBC's article are gold - "I was never a Liberal," he says, seemingly forgetting the years 2004-2006 and missing the signs festooned around his riding during both those elections proclaiming him as a Liberal candidate. "I think I had a good shot at winning [this election]," he speculated, although a Conservative hasn't been elected in that riding since 1958, and his own Conservative opponent in 2006 finished 7, 000 votes behind the 2nd-place NPD candidate.
A particularly astute commenter on the CBC site theorizes that, although Emerson says he's leaving politics because of the commute from Vancouver to Ottawa, Harper will appoint Emerson to the Senate and his Cabinet, much like he did with Michael Fortier in 2006. Although I'm not sure that he'll end up as a Minster again, I think Harper will push Senate reform to the back-burner of this election campaign, and there will be another Senate appointment when he wins another minority. After all, it's not like Emerson would even have to show up for that job...
In a similar vein, it's also the end of the longest minority government ever in Canadian history, as Stephen Harper asked Michaelle Jean to dissolve the Parliament this morning. We'll head to the polls for another election on the 14th of October - the 3rd time in 11 years - and we'll end up with another Conservative minority. Harper's strategy must have something to do with massive turkey consumption influencing voter choices, as last time we had elections just after Christmas.
This blog will get hijacked by incredibly amusing (and potentially vindictive and offensive) political tales every once in a while, because election time is my favourite. We'll start by ripping into David Emerson, the shifty representative from Vancouver who crossed the floor 2 weeks after being re-elected as a Liberal in his traditionally left-wing riding. His quotes in the CBC's article are gold - "I was never a Liberal," he says, seemingly forgetting the years 2004-2006 and missing the signs festooned around his riding during both those elections proclaiming him as a Liberal candidate. "I think I had a good shot at winning [this election]," he speculated, although a Conservative hasn't been elected in that riding since 1958, and his own Conservative opponent in 2006 finished 7, 000 votes behind the 2nd-place NPD candidate.
A particularly astute commenter on the CBC site theorizes that, although Emerson says he's leaving politics because of the commute from Vancouver to Ottawa, Harper will appoint Emerson to the Senate and his Cabinet, much like he did with Michael Fortier in 2006. Although I'm not sure that he'll end up as a Minster again, I think Harper will push Senate reform to the back-burner of this election campaign, and there will be another Senate appointment when he wins another minority. After all, it's not like Emerson would even have to show up for that job...
***
I don't have a lot to say on science today, although it was kind of gratifying to see an entire issue of Nature devoted to "Big Data" and its impact on science, which I touched on months ago. More on this to come later in the week, with incisive political commentary on the mousiness of Stephane Dion.
Another interesting tidbit - a huge ice shelf has broken free of our very own Ellesmere Island (the big one in the Arctic beside Greenland). This is not only just a sign of global warming and the problems we can expect, but also a none-too-subtle reminder that the fabled Northwest Passage will soon be open for business. We don't tend to think that much about borders in this country, but we definitely have them, and there is definitely territory under dispute in the Arctic between ourselves and the USA, Russia, and Denmark. Most of these disputed borders are in areas close to the Northwest Passage, and will become the subject of heated diplomacy between our countries as the prospect of profiting from goods shipped through this nautical shortcut to the Panama Canal becomes a reality.
Another interesting tidbit - a huge ice shelf has broken free of our very own Ellesmere Island (the big one in the Arctic beside Greenland). This is not only just a sign of global warming and the problems we can expect, but also a none-too-subtle reminder that the fabled Northwest Passage will soon be open for business. We don't tend to think that much about borders in this country, but we definitely have them, and there is definitely territory under dispute in the Arctic between ourselves and the USA, Russia, and Denmark. Most of these disputed borders are in areas close to the Northwest Passage, and will become the subject of heated diplomacy between our countries as the prospect of profiting from goods shipped through this nautical shortcut to the Panama Canal becomes a reality.
Tuesday, September 2, 2008
We are nihilists, Lebowski! We care for nothing!
I commented a while ago on something that Dean Ornish calls genetic nihilism, a great turn of phrase that I will deftly procure for myself. This is a sort of view in which we say "well, my DNA has already programmed my health and/or behaviour, whether I will get diabetes or cancer or an aneurysm while doing backstroke in the community pool." Which, in addition to being untrue, is a pretty irresponsible way to live.
I thought of it because of a Swedish study showing that the presence of a certain variant of a gene in males is associated with increased prevalence of "marital crisis" in the last 12 months, reduced proportions in number of men married, and lower scores on a sort of "pair-bonding index." And the headlines were awesome - "Why men cheat" (Science Magazine), or "Commitment phobes can blame genes" (BBC). These are great examples of genetic nihilism. We are expected to take it at face value that men fear commitment and cheat on their wives and girlfriends, and furthermore that these are parts of being male programmed into DNA as much as a penis is, so we should be able to find a gene that makes it so.
No one is ever going to find that gene, because it doesn't exist (along with the "penis gene"). The authors of this study do some fancy calculations and say that about 28% of the variation they saw in the study were inheritable from their parents. Now, I'm going to say that heritability is not just a question of genes being passed down, and if you want to argue about that let me know. The rest is from "environmental factors," which is to say everything other than your parents.
We have roughly 25 000 protein-coding genes in our cells. Let's say 1% are involved in mating behaviour, which is probably a ridiculous underestimate given the importance of mating to continuing the species. That's 250 genes involved in mating behaviours, which are only the genetic part of their heritability measure, which in turn only accounted for about 28% of the variation in the study. While some of these genes might be more important than others, the assertion that a different version of a single gene will double your chances of being unmarried or in a turbulent relationship seems unlikely at best.
This study does have an interesting design, however, involving some 500 same-sex twins both married and unmarried. I hope they run some fishing trips (technical term: gene microarray) looking at polymorphisms on other genes that might be related.
I thought of it because of a Swedish study showing that the presence of a certain variant of a gene in males is associated with increased prevalence of "marital crisis" in the last 12 months, reduced proportions in number of men married, and lower scores on a sort of "pair-bonding index." And the headlines were awesome - "Why men cheat" (Science Magazine), or "Commitment phobes can blame genes" (BBC). These are great examples of genetic nihilism. We are expected to take it at face value that men fear commitment and cheat on their wives and girlfriends, and furthermore that these are parts of being male programmed into DNA as much as a penis is, so we should be able to find a gene that makes it so.
No one is ever going to find that gene, because it doesn't exist (along with the "penis gene"). The authors of this study do some fancy calculations and say that about 28% of the variation they saw in the study were inheritable from their parents. Now, I'm going to say that heritability is not just a question of genes being passed down, and if you want to argue about that let me know. The rest is from "environmental factors," which is to say everything other than your parents.
We have roughly 25 000 protein-coding genes in our cells. Let's say 1% are involved in mating behaviour, which is probably a ridiculous underestimate given the importance of mating to continuing the species. That's 250 genes involved in mating behaviours, which are only the genetic part of their heritability measure, which in turn only accounted for about 28% of the variation in the study. While some of these genes might be more important than others, the assertion that a different version of a single gene will double your chances of being unmarried or in a turbulent relationship seems unlikely at best.
This study does have an interesting design, however, involving some 500 same-sex twins both married and unmarried. I hope they run some fishing trips (technical term: gene microarray) looking at polymorphisms on other genes that might be related.
Sunday, August 24, 2008
Best addresses and more
So, apart from having the best corporate domain name (gene.com), street address (1 DNA Way) and stock symbol (DNA), Genentech is also doing some excellent science. Antibodies are used ubiquitously in pretty much any biology involving proteins - commercially available antibodies are supposedly highly specific for their target proteins, although inconsistencies in the quality of reagents is a huge problem. I use them regularly for identification and/or manipulation of proteins, and a paper this month is using antibody-conjugated toxins to kill cancer cells.
Now, this is pretty awesome, and the antibodies approved for clinical use are far better than almost all of the of the commercially available "research-only" types. By "better," what I mean is that they are more specific for their targets - ideally, they would bind to that target and nothing else, i.e. an infinite signal:noise ratio. In practice, this is almost impossible, as there is always some random "non-specific binding," but the clinical antibodies are as close as it gets.
As with all biological molecules, their structure dictates their function. For an antibody, the structure of a certain part will determine what protein it will bind. What this team has done is to engineer changes into another part, without changing the protein-recognizing structure. These changes will allow biochemists to tack various useful things onto the antibody, like cytotoxins or fluorescent tags. This is good news for biology, as the antibodies used in research are not as good as they could be. More developments in antibodies as tools will, in the long run, mean improvements to their protein recognition abilities as interest revitalizes investment, and would overall be a good thing for biological science as a whole.
Now, this is pretty awesome, and the antibodies approved for clinical use are far better than almost all of the of the commercially available "research-only" types. By "better," what I mean is that they are more specific for their targets - ideally, they would bind to that target and nothing else, i.e. an infinite signal:noise ratio. In practice, this is almost impossible, as there is always some random "non-specific binding," but the clinical antibodies are as close as it gets.
As with all biological molecules, their structure dictates their function. For an antibody, the structure of a certain part will determine what protein it will bind. What this team has done is to engineer changes into another part, without changing the protein-recognizing structure. These changes will allow biochemists to tack various useful things onto the antibody, like cytotoxins or fluorescent tags. This is good news for biology, as the antibodies used in research are not as good as they could be. More developments in antibodies as tools will, in the long run, mean improvements to their protein recognition abilities as interest revitalizes investment, and would overall be a good thing for biological science as a whole.
***
Some Canadian news:
Some Canadian news:
- Health Canada flexed its regulatory muscle to clean two natural health products off the shelves. Life Choice Ephedrine HCL is getting yanked for having way too much ephedrine in it, which is not very good for you and is also contaminated by a nasty strain of bacteria(!). Life Choice Kava is getting pulled for liver toxicity, which is also a pretty good reason. Compounds marketed as homeopathic drugs are not always subject to the same quality-control tests as pharmaceuticals, which in this case ended up being a bit scary. Interestingly, the "Standards and Ethics" section of the website for the Canadian Association for Naturopathic Doctors is "currently being updated."
- Canada comes up short on OECD standards for medical imaging machines per capita. While we have have increased our tally significantly over the last 4 years, we have roughly 12 CT scanners and 6 MRI machines per million people, well-short of the average 15 and 7. The Brazilian working in my lab was told that he could get on a waiting list to have an MRI on his knee here in Montreal, but if he was going back to Brazil in the next 6 months, he would get it done there quicker. To me, this raises serious questions about accessibility to health care in urban centres, let alone the beleaguered rural areas...
Tuesday, August 19, 2008
Working out in my chair, reading minds.
So there's been a fair amount of talk lately in the news about how the US defense department special forces researchers are trying to read minds. It shouldn't be a surprise that DARPA is funding research like this, people have been trying it for years (to take a Canadian example, read up on the MKULTRA experiments performed for the CIA at McGill). This is pretty science-fiction so far, but there has been some limited success recently in the literature, where a computer can choose which of a small set of nouns the subject is thinking of.
Now, if you look into it closely, mind-reading is still fundamentally impractical and therfore nothing to worry about. In addition to large, unwieldy and highly sensitive machines, you also need a coherent and compliant subject, and a ton of scan data from that subject - just to achieve the aforementioned limited success. So far, anyways. Expect this research to continue, because it doesn't seem to be a question of "if," but of "when." Legislators should be thinking on seemingly SF topics like mind reading and control already, but probably won't until it's in the courts. "What do you mean, you read her mind?!"
Now, if you look into it closely, mind-reading is still fundamentally impractical and therfore nothing to worry about. In addition to large, unwieldy and highly sensitive machines, you also need a coherent and compliant subject, and a ton of scan data from that subject - just to achieve the aforementioned limited success. So far, anyways. Expect this research to continue, because it doesn't seem to be a question of "if," but of "when." Legislators should be thinking on seemingly SF topics like mind reading and control already, but probably won't until it's in the courts. "What do you mean, you read her mind?!"
***
- Interesting news showing that smoking is probably responsible for less "smoking-related illness" than I thought. My favourite part: "Dellinger noted, however, that one would have to smoke about 300 cigarettes a day to be exposed to the same level of environmental free radicals found in moderately polluted air."
- Canadian researchers figure out how to program stem cells to develop one step (and only one step) into a certain route towards specialization. This is interesting because it will help lead to the transformation of stem cells into useful, transplantable tools and maybe even allow the production of things like skin grafts or whole livers in culture dishes.
- Finally, a real use for chemistry and materials science - what may become a seminal work on hair care is released by German researchers. If they get public money for that, I'll consider doing some research there on something appropriately scientific involving beer after my doctorate.
***
We are now seeing the first drugs in what will no doubt one day be a multibillion dollar industry: exercise mimetics. These compounds, which got huge exposure in a Cell paper released last month, work in muscles to improve endurance. The data are really interesting, and some is pretty stunning. First, they use a drug that activated gene expression in a way similar to exercise. However, they didn't see any difference in endurance with just drug treatment. However, by training the mice to run for increasing time at increasing speed over several weeks, they found that the combination of exercise and the drug allowed dramatically increased running times (3.5 hours vs. 2) and distance covered (about 3 km vs. 1.8) compared to mice that only got exercise. Interestingly, the combination of the treatments activated some gene expression that neither exercise or drug alone did, suggesting at the very least some new performance-enhancing drug targets.
They go downstream on the biochemical cascade one step and manage to induce increases in endurance - without exercise this time. However, the running tests were much different - they took completely untrained mice, who could run only about 30 minutes (40 after drug treatment) and cover only about 400 m (around 550 m after the drug). While this is a much more modest effect (and probably wasn't additive with exercise, or they'd have shown data on it), it is very interesting to see the induction of some effects of exercise through only pharmacological means. However, it remains highly unlikely that we will be able to reproduce all the benefits of real exercise with chemistry. I mean, we're still working on bad hair days...
We are now seeing the first drugs in what will no doubt one day be a multibillion dollar industry: exercise mimetics. These compounds, which got huge exposure in a Cell paper released last month, work in muscles to improve endurance. The data are really interesting, and some is pretty stunning. First, they use a drug that activated gene expression in a way similar to exercise. However, they didn't see any difference in endurance with just drug treatment. However, by training the mice to run for increasing time at increasing speed over several weeks, they found that the combination of exercise and the drug allowed dramatically increased running times (3.5 hours vs. 2) and distance covered (about 3 km vs. 1.8) compared to mice that only got exercise. Interestingly, the combination of the treatments activated some gene expression that neither exercise or drug alone did, suggesting at the very least some new performance-enhancing drug targets.
They go downstream on the biochemical cascade one step and manage to induce increases in endurance - without exercise this time. However, the running tests were much different - they took completely untrained mice, who could run only about 30 minutes (40 after drug treatment) and cover only about 400 m (around 550 m after the drug). While this is a much more modest effect (and probably wasn't additive with exercise, or they'd have shown data on it), it is very interesting to see the induction of some effects of exercise through only pharmacological means. However, it remains highly unlikely that we will be able to reproduce all the benefits of real exercise with chemistry. I mean, we're still working on bad hair days...
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