Friday, May 30, 2008
Thursday, May 29, 2008
Check out a series of photos of a chicken developing. The very early ones are especially interesting. Now I know what to look for if I think that my breakfast has been fertilized.
In the wake of AC's State of Science Blogging post, Stephanie Z has done some data mining. She examined the content of 5 blogs over a month of posting - Pharyngula, Greg Laden's Blog, Tetrapod Zoology, Cognitive Daily and ourselves. The results can be found in a guest post at Greg Laden's place.
Monday, May 26, 2008
Such measures are totally uncalled for and if enacted, would represent a serious impediment to the daily activities of the thousands of scientists who rely on communicating and exchanging ideas around the globe in order to do their work.
Read about this nonsense here. Michael Geist provides more in depth coverage.
UPDATE: Orac expands on ERV's post
Thursday, May 22, 2008
Recently, I caught a TV program called "Braniac: Science Abuse". It's a British program (or is that programme?) The episode I saw involved various segments including what happens to toothpaste when you put it in liquid nitrogen (it freezes), what happens if you put the ingredients for a parfait in the microwave with a fluorescent lightbulb and a bowl of flammable liquid (it explodes), can an aerobics teacher do her job while being randomly given an electric shock (she can't) and what happens if you blow-up a shed full of fireworks (they go off). It also included more scientific segments: an attempt to replicate Galileo's Leaning Tower of Pisa experiment, and an experiment intending to determine whether a person performs better when starving or when over-stuffed. (There were many other segments of both types) In all cases, the background science wasn't well explained and the experiments were poorly designed. The show has even been accused of forging results. 'Science Abuse' is an accurate subtitle.
This is a particularly bad example, but there are other science shows that aren't exactly rigorous with the scientific method (Mythbusters, for example, is a great show but the experimental design is sometimes lacking). I understand that these are television programs and the goal is to entertain, but it seems to me that those kind of changes needn't get in the way of the watchability. In the feast or famine performance example above, adding a person who had neither over-eaten nor been starved for a day wouldn't be difficult (forgetting that it's still an n=1 experiment). Or breaking up the tasks and assessing them individually rather than one mega-challenge of both physical and mental events.
So my questions are these:
Is it more important to have an accurate portrayal of the scientific method, or an entertaining program that attracts kids to science even if it mostly portrays it as blowing things up?
Is it impossible to make a more rigourous science program fun?
[Comic credit: xkcd]
For those of you who can't remember the difference between standard deviation and standard error of the mean, or who never bothered to learn this paper is a good primer on when to use which, what independent replicates really means, and how to interpret the error bars on the graph presented at yesterday's seminar. It's the kind of thing we should all know but many of us don't bother with.
Tuesday, May 20, 2008
Lord of the Rings: an allegory of the PhD?
The story starts with Frodo: a young hobbit, quite bright, a bit dissatisfied with what he's learnt so far and with his mates back home who just seem to want to get jobs and settle down and drink beer. He's also very much in awe of his tutor and mentor, the very senior professor Gandalf, so when Gandalf suggests he take on a short project for him (carrying the Ring to Rivendell), he agrees.
Frodo very quickly encounters the shadowy forces of fear and despair which will haunt the rest of his journey and leave permanent scars on his psyche, but he also makes some useful friends. In particular, he spends an evening down the pub with Aragorn, who has been wandering the world for many years as Gandalf's postdoc and becomes his adviser when Gandalf isn't around.
After Frodo has completed his first project, Gandalf (along with head of department Elrond) proposes that the work should be extended. He assembles a large research group, including visiting students Gimli and Legolas, the foreign postdoc Boromir, and several of Frodo's own friends from his undergraduate days. Frodo agrees to tackle this larger project, though he has mixed feelings about it. ("'I will take the Ring', he said, 'although I do not know the way.'")
Very rapidly, things go wrong. First, Gandalf disappears and has no more interaction with Frodo until everything is over. (Frodo assumes his supervisor is dead: in fact, he's simply found a more interesting topic and is working on that instead.) At his first international conference in Lorien, Frodo is cross-questioned terrifyingly by Galadriel, and betrayed by Boromir, who is anxious to get the credit for the work himself. Frodo cuts himself off from the rest of his team: from now on, he will only discuss his work with Sam, an old friend who doesn't really understand what it's all about, but in any case is prepared to give Frodo credit for being rather cleverer than he is. Then he sets out towards Mordor.
The last and darkest period of Frodo's journey clearly represents the writing-up stage, as he struggles towards Mount Doom (submission), finding his burden growing heavier and heavier yet more and more a part of himself; more and more terrified of failure; plagued by the figure of Gollum, the student who carried the Ring before him but never wrote up and still hangs around as a burnt-out, jealous shadow; talking less and less even to Sam. When he submits the Ring to the fire, it is in desperate confusion rather than with confidence, and for a while the world seems empty.
Eventually it is over: the Ring is gone, everyone congratulates him, and for a few days he can convince himself that his troubles are over. But there is one more obstacle to overcome: months later, back in the Shire, he must confront the external examiner Saruman, an old enemy of Gandalf, who seeks to humiliate and destroy his rival's protege. With the help of his friends and colleagues, Frodo passes through this ordeal, but discovers at the end that victory has no value left for him. While his friends return to settling down and finding jobs and starting families, Frodo remains in limbo; finally, along with Gandalf, Elrond and many others, he joins the brain drain across the Western ocean to the new land beyond.
Monday, May 19, 2008
Friday, May 16, 2008
What C-51 is, quoting from the bill, is an attempt
to modernize the regulatory system for foods and therapeutic products, to strengthen the oversight of the benefits and risks of therapeutic products throughout their life cycle, to support effective compliance and enforcement actions and to enable a greater transparency and openness of the regulatory system.In other words, it's an attempt to regulate therapeutic health products to ensure their safety and efficacy. Obviously, this has raised the ire of the natural products industry who has responded with 'news' pieces like this with alarming 'facts' such as "C-51 is outlawing herbs, supplements and vitamins", or "a mother giving an herb to her child, under the proposed new language, could be arrested for engaging in the sale of unregulated, unapproved 'therapeutic substances.'" (more on that one in a moment). This alarmism is stirred in with a nice painting of draconian enforcement and a dollop of Big Pharma conspiracy theory to make it an amusing, if typical, propaganda piece.
I'm obligated to point out that I am not a lawyer, but I've read the bill. It is NOT outlawing products, but rather bringing the natural health product industry up to a certain standard of testing. It's an attack on deceptive labeling, improper health claims and pseudoscience. No thug is going to kick down your door for serving dandelion greens at dinner. What is being outlawed is selling dandelion greens in a misleading way (eg. with untested health claims).
This brings us to the definition of 'sell', which is a major point for the alarmists. The amended act, if passed, will define sell as
offer for sale, expose for sale or have in possession for sale — or distribute to one or more persons, whether or not the distribution is made for consideration — and, in relation to a device, includes lease, offer for lease, expose for lease or have in possession for lease.The phrase that the bill-opposers have latched onto is 'distribute to one or more persons'. They take that to mean that, to use the above example, serving dandelion greens for supper counts as 'selling'. While this interpretation of the new wording is technically true, one has to look at the contexts in which the word "sell" is used in the bill. Reading through it, it becomes clear that it's very specific things that run contrary to the proposed law. For example, 'selling' dandelion greens is only prohibited if they have a poisonous or harmful substance in or on it; if they are unfit for human consumption; are adulterated; are injurious to human health; or are processed, manufactured, stored, etc. in unsanitary conditions. That does NOT sound like draconian restrictions on what you can put on your table or give your family. It sounds like common sense. The bill goes further than that, prohibiting 'selling' "a food in a manner that is false, misleading or deceptive or is likely to create an erroneous impression regarding its character, value, quantity, composition, merit, safety or origin." For a therapeutic product, this is expanded to include "creat[ing] an erroneous impression regarding its benefits, risks, conditions of use." In other words, no false claims. So, to the people who oppose this language change, is it because you want to be free to distribute harmful goods, or because you're interested in making false or untested claims about your product?
Shawn Buckley, natural product lawyer, has weighed in with a 20 page review of C-51. (You may remember his name being thrown around by the pro-algae folks on the StemEnhance thread) He goes on to list a number of concerns. First on his list is that roughly 60% of of natural health product licenses are failing, meaning that with this amendment over 60% of the products on the market will become illegal and can be removed from the market by Health Canada. What is implied in this statement, is that 60% of the natural health products already on the market are not licensed. Nor does he state why these licenses are being denied. Is he seriously pushing for unlicensed health products - products that have failed to get government approval - to remain on shelves?
Buckley tries to portray the government as being bullies towards the natural health product industry. He points to language changes proposed by the act, such as replacing 'drug' with 'therapeutic product' and then asks "is the change of terminology directed at the Natural Health Product industry or are there other reasons?" My guess is that the answer is 'yes' and I would respond with the question 'So?' The changes in the act seem to have in mind the goal of bringing the natural product industry to a particular standard. The pharmaceutical industry is already regulated in terms of safety requirements, evidence-based results, etc. Obviously bringing drugs and natural products under the same 'therapeutic product' umbrella is designed to ensure that ALL of these products are safe, effective and work as advertised. As Buckley himself points out, the pharmaceutical industry already has a high compliance rate with Health Canada rulings, while 60% of natural products go to market having their licenses denied.
What is more concerning is the National Health Products Protection Association (NHPPA, of which Buckley is president) position. In the legal review of C-51, their goals are listed as a regulatory environment where, among other things, "NHPs [natural health products] are presumed to be safe. A NHP cannot be taken off of the market unless the Government can prove that it is unsafe." This is just a ridiculous attitude. If the default position for a natural product is 'safe', that means people have to start getting ill or dying before somebody steps in. The reality is that health products should be deemed safe before they go to market. Just because it's labeled natural doesn't make it safe. As I've pointed out before, several potent cancer drugs are natural products. Would the NHPPA have these, or any future similar discoveries given a blanket 'safe' label and start selling to people?
Therein is the lunacy of the natural product position: The want their products to be at once efficacious and totally harmless. For any product to be useful in some therapeutic way, it has to have a biological effect. If it has a biological effect, then you have to start thinking about how it works, safe doses, potential side-effects, etc. Now don't get me wrong, I don't think the bottle of vitamin C in the medicine cabinet is particularly dangerous (of course, anything is at a high enough dose), but natural health products include more than standard vitamin supplements with known tolerances. They include products that claim to mobilize stem cells, alter gut flora composition, and stimulate the immune system as well as non-standard megadoses of of common vitamins. All of these effects have the potential to cause adverse events. The default position is not 'totally harmless'.
Mr. Buckley does raise some interesting points about the use of the word 'government' in the bill, and how it may affect adoption of future regulations. In C-51, the definition of government includes international bodies and foreign governments and states that "A regulation may incorporate by reference documents produced by a person or body other than the Minister of the Canadian Food Inspection Agency including ... (c) a government." This sounds like the amended bill makes it easier to incorporate foreign policies into Canadian law. However, given Buckely's position with the NHPPA, I doubt the sovereignty of Canadian law is his primary concern.
Of course there will be people arguing that the government has no right to tell us what to put in our bodies. That's not what these changes are doing. It doesn't say you can't eat your dandelion greens, take your garlic supplement or multivitamin. It says that the products must be safe and that their sales and marketing can't be false, misleading or deceptive. You can eat your greens, but they can't be sold as age-reversing. You can take your garlic pills, but they can't be sold as cancer-curing. Unless, of course, there's evidence.
Wednesday, May 14, 2008
Posted by Kamel at 9:12 PM
The octane rating is based on results using a test engine. It is the resistance to autoignition that is being measured. Autoingition is undesirable in a gasoline engine as this produces knocking. It is called an octane rating as iso-octane is defined as 100 and n-heptane is defined as 0. So a mixture of 87% iso-octane and 13% n-heptane would have an octane rating of 87%. However that doesn't mean that a fuel with a 97 octane rating has 97% octane, it just has characteristics as if it was 97% octane and 3% n-heptane.
Tuesday, May 13, 2008
"Another $123,703.20 in expenditures appeared to be "inconsistent" with his research grant proposals, the documents say. But university investigators gave him the benefit of the doubt saying the nine computer monitors and other items "might have been related" to his research from a "general scientific perspective."
The university then made an arrangement with the researcher that in the "event of timely repayment" of $24,767.33, it would not ask for the rest of the money back.
The university returned $21,485.67 to NSERC. The documents indicate the other $3,000 refunded by the scientist was sent back to other agencies that had also financed his research."
Posted by Bayman at 12:32 PM
Monday, May 12, 2008
Anyway it's interesting to note that over in Europe they seem to be having a lot more success getting cool new gene therapies into the clinic. Hence, as this Molecular Therapy editorial points out, the "vector drain" phenomenon, where vectors being developed in North America find the clinic in Europe. Will this also lead to a brain drain? It would be pretty attractive for vector researchers to just move the whole operation to an environment where their creations are likely to see implementation. Not to mention, you get to live in Europe. If some of these countries get their acts together and set up more research facilities, they'd be in position to score a real research coup.
Maybe the imminent end of oil doesn't spell Armageddon for civilization after all. Although it's not clear how efficient fertilizer production would be without fossil fuels as a hydrogen source, and we'd still need to come up with a replacement material for the plastic in those Falcon tubes. But, unlike biofuels, solar power may provide a feasible option for a sustainable, but still modern economy.
ERRATUM: I believe I erroneously cited that a 100 mile squared piece of land would collect enough solar power for the US. I think what they actually say is 100 miles by 100 miles, or 10,000 square miles. Thus proving that you're better of just listening to the podcast yourself...
Friday, May 09, 2008
Try it out or read more about the game here.
Thursday, May 08, 2008
So that's the challenge: Pick a classic, write a post and submit the link in the comments over there so they can all be compiled in one list. Get it all done by the end of May. Have fun!
Wednesday, May 07, 2008
There is experimental evidence for a universal genetic code:
mRNAs can be correctly translated by the protein synthesizing machinery of very different species. For example, human hemoglobin mRNA is correctly translated by a wheat-germ extract [...] bacteria efficiently express recombinant DNA molecules encoding human proteins such as insulin.A universal code is the basis of many techniques (and headaches) in the lab. For example, in vitro protein synthesis can involve rabbit reticulocyte lysates (or wheat germ, as above) translating non-rabbit proteins. Non-mouse sequences can be used to introduce genes into mice. E. coli is often used for recombinant protein production. In this latter case, the difference in codon preference between E. coli and other species is a common problem for high level recombinant expression (eg. if a codon is preferred in humans - CCC for proline - but not in E. coli, this limiting tRNA could hinder protein production).
(Stryer, L. Biochemistry 3rd Ed. p 108)
That the genetic code is universal is not entirely true; some inter-species differences are being discovered. There are some species, such as ciliated protozoa have slight variations (in ciliates, TAA and TAG are glutamine rather than stop codons). Mitochondria are another important exception.
Mitochondria carry their own circular DNA which encodes for, among other things, a set of 22 tRNAs. Because it doesn't use the set of nuclear-encoded tRNAs, it isn't restricted to the standard code. In fact, human mitochondrial codon use differs from nuclear codon use in 4 places. For example, in the isoleucine example above, the codon AUA codes for methionine in mitochondria (see table, reproduced from Stryer). This isn't news, but something I failed to appreciate before. A difference in codon usage between species might not be surprising (in fact the consistancy in usage among species is surprising - until you consider the far reaching effects a change in codon use would have: Every protein would be affected). A difference in usage within a single cell is more striking, unless you're familiar with endosymbiotic theory.
Endosymbiotic theory, popularized by Lynn Margulis, describes the origins of eukaryotic organelles: mitochondria and chloroplasts. These organelles were once autonomous organisms that were taken up by other cells in a symbiotic relationship. Both organelles have strong resemblences to the proposed parent prokaryotes, as detailed in the above link. Codon use separate from nuclear DNA can be added to that list.
Read more about the different codon usage sets here.
Codon preference numbers from here.
I have had to euthanize mice for experiments before. The animal care people here are very adamant that the animals experience the least amount of discomfort as possible, as they should, it's their job. One acceptable way to euthanize a mouse is an intraperitoneal injection of euthasol, which is a barbituate, a class of CNS inhibitors commonly used as anesthetic.
If this is the most humane way to euthanize that should mean that lethal injections, as practiced by countries that euthanize convicted criminals as part of capital punishment, should be the same. I guess, that is, assuming that the point of lethal injection is to be more humane than previous methods of euthanization. I was surprised to learn that lethal injection is not very simple.
Lethal injection in the United States consists of three sequentially administered drugs. These drugs are sodium thiopental, pancuronium bromide, and potassium chloride given intravenously in that order. This is a similar procedure to what is on wikipedia for physician assisted suicide.
Sodium thiopental, also used as 'truth serum', induces relaxation and release from social inhibitions. It is a short-acting barbituate that at the doses for lethal injection rapidly induces a coma. It inhibits CNS activity by activating GABAa receptors. Alcohol acts on these same receptors, however, barbituates are not used much recreationally anymore, I think, as they have been largely replaced by benzodiazepines. 'benzos' (apparently safer and more fun). Relevant to lethal injection is that sodium thiopental has no analgesic effects ie. not a painkiller.
Then comes the pancuronium bromide. This blocks acetylcholine at neuromuscular junctions, rendering the convicted paralyzed, including breathing muscles. Hopefully that thiopental coma is going well or it would be like drowning.
Then just to ensure death, potassium chloride. Such a simple salt of two ions that are very common in your body is deadly? Really it is because the large bolus IV injection at a high dose messes with the electrochemical gradient needed for proper cardiac muscle function. The heart is stopped.
I wonder how much this combo has to do with ensuring death, and making it less traumatic for the witnesses than it does with being humane. A good way to go might be an overdose of an opiate or something but seeing a convict get all high and say weird things might be too much.
Tuesday, May 06, 2008
Monday, May 05, 2008
I watched the newest vidcast of diggnation over the weekend, as I usually do. It is a reasonably good show about the most popular stories covered on digg.com. Alex Albrecht is too cool, mostly because he drinks beer, plays pencil and paper D&D, is on the totallyradshow, and kicks Kevin Roses arse at Call of Duty 4. That is some serious geek street cred.
This past eppisode though, they revealed some ignorance about the mechanism of Viagra. Kevin Rose (seriously check out how badly he is pwned by Albrecht on CoD4) thought that you could take Viagra and have a voluntary errection where you would have to 'be in the mood'. Someone from the audience who identified themselves as a 'life scientist' said that it was not voluntary. Well, Kevin Rose was right and the 'life scientist' was wrong. Strange since I find Kevin Rose usually talks out his ass.
As I understand it viagra mearly inhibits the degradation of cGMP, which directly initiates and maintains an errection. However it is produced in response to nitric oxide. The nitric oxide is produced upon sexual stimulation, therefore even with viagra it should still be a voluntary thing. That's got to be a relief for those who take the drug since you are supposed to take it 4 hours before you think you will need it. That would be a long 4 hours if it was involuntary.
Friday, May 02, 2008
This photo of the Governator in 'research mode' is just begging for a witty caption, so have at it! After an inderminate amount of time, the funniest one will be chosen arbitrarily and the author showered with praise (sorry, our prize budget doesn't allow for much more than that).(Photo source: Nature News)
Just to get things going, here's my entry: "It's not a too-mah."
Penguins are famous for engaging in animal homosexual behaviour. They even sometimes steal eggs from heterosexual couples and rear the youngs. A famous case at the NY zoo, and reports in zoos from all over the world have confirmed that not only are homosexual couples frequent, but the bonding between the gay partnersis strong . Case in point: a zoo in Germany tried importing Swedish chicks and even they couldn't lure the males away!
Penguins are also known to prostitute themselves for a rock. They will let other penguins exchange sexual favors for nest building material.
Penguins sometimes engage in inter-species sex. Perhaps unwillingly. sometimes sexually frustrated seals molest penguins on the beach. I am not even making that stuff up!
Thanks to Alexey for a great job and, as always, hats off to Ben for designing the logo.