Tuesday, September 27, 2005
Friday, September 23, 2005
The interesting thing about the whole situation is how well it fits the natural way that diseases emerge and spread. You have a population of individuals who you could describe as immune naive (those under level 50 in this case) who are being wiped out and a considerable selection pressure for those players over level 50 (who are able to survive). Although these characters are unable to reproduce, in the analogous natural situation it would be those individuals over level 50 that survived would carry on to reproduce. Over time, the viral agent would either be forced into extinction as it wiped out its potential hosts too quickly, or alternatively it becomes 'domesticated' becoming less virulant so it has a better chance of spreading itself between more limited hosts.
Overall, it's a really remarkable and somewhat surprising result that shows that perhaps art can imitate life every so often.
Update: There is also a video of the plague in action.
Thursday, September 22, 2005
Of course, sure date rape drugs are generally pretty nasty things and everyone should be educated about them, focusing on these really misses the key culprit: Alcohol consumption. Alcohol is probably one of the most important factors in many rapes, because alcohol does a lot of funny things to the brain including dulling your ability to recognise objects (this is why people someone wouldn't consider attractive originally become more attractive). Over consumption of copious amounts of alcohol and then not watching your drink, enabling someone to slip things in, is a key factor in many rapes. Often, it's just the whole over consumption of alcohol thing that ends up being the most important part, especially as women may be more susceptible to the effects of alcohol than men.
Overall, the article is a tasteless pile of general idiocy and it makes me ashamed to say that it came from my Universities Student Magazine.
Wednesday, September 21, 2005
Tuesday, September 20, 2005
Anyway, here are the original instructions from Philosophy, et cetera (who originally posted it):
The following survey is for bloggers who are actual or aspiring academics (thus including students). It takes the form of a go-meme to provide bloggers a strong incentive to join in: the 'Link List' means that you will receive links from all those who pick up the survey 'downstream' from you. The aim is to create open-source data about academic blogs that is publicly available for further analysis. Analysts can find the data by searching for the tracking identifier-code: "acb109m3m3". Further details, and eventual updates with results, can be found on the original posting:
Simply copy and paste this post to your own blog, replacing my survey answers with your own, as appropriate, and adding your blog to the Link List.
Important (1) Your post must include the four sections: Overview, Instructions, Link List, and Survey. (2) Remember to link to every blog in the Link List. (3) For tracking purposes, your post must include the following code: acb109m3m3
Survey:Link List (or 'extended hat-tip'):
1. Philosophy, et cetera
4. Add a link to your blog here.
Age - 22
Gender - Male
Location - New Zealand
Religion - Christian
Began blogging - June 2005
Academic field - Immunology
Academic position [tenured?] - Aspiring to become an academic scientist in future, but one day at a time ;)
Approximate blog stats
Rate of posting - About once a day, sometimes patchy depending on work
Average no. hits - No idea actually.
Average no. comments - A few every so often
Blog content - Majority on science, particularly environmental issues
1) Do you blog under your real name? Why / why not?
- Yes. It doesn't really seem appropriate to blog under a pseudonym anyway.
2) Do colleagues or others in your department know that you blog? If so, has anyone reacted positively or negatively?
- Yeah a few people in the department know of my blog. The general reaction is fairly good although one of my professors remarked I should spend less time blogging and more time studying ;)
3) Are you on the job market?
- I will be just as soon as I finish my honours report and exams in october. Then I'll be looking to start my PhD.
4) Do you mention your blog on your CV or other job application material?
- No, not at the moment.
5) Has your blog been mentioned at all in interviews, tenure reviews, etc.? If so, provide details.
- No, I wouldn't think so as it's not a particularly widespread blog (yet).
6) Why do you blog?
-Generally for the reasons that many science bloggers are doing this now, so I can try to demystify aspects of science and generally make the public more aware about certain issues (like feeding antibiotics to farm animals).
There we are. Pass the meme along!
The problem with the figure Garrett cites is that it kills ~55% of the cases we know about. This is a classic case of sample bias. Those who are most sick (and thus, most likely to die) are also most likely to go to a hospital or clinic to be examined—and therefore, are also the most likely to have a clinically-confirmed case of influenza due to the H5N1 strain. Hence, the mortality data we have for H5N1 only comes from this sickest segment of the population—artificially raising the mortality rate. Puzelli et al.’s study, then, is timely due to the fact that it shows that sub-clinical infection with avian-type influenza viruses does occur (in almost 4% of their cohort of poultry workers).Now while this is true and it could well be that the virus is less lethal than has previously been described, there are several worrying aspects of this kind of revelation. The most important, as discussed at the article at PT, is that this is where pandemics can come from. It isn't the people who are infected with the virus at a 'lethal' dose and die from the infection. For the virus that kills its host it will end up at an evolutionary dead end and won't have the chance to get anywhere. Subclinical infections, where the host isn't adversely affected and the virus gets to persist and spread for a while are the dangerous kinds of infections.
Here the avian influenza virus has time on its side, because here it can build up mutations and run the standard evolutionary experiments that influenza is capable of, namely by swapping segments of its genome with existing human influenza viruses. As the main impediment so far to H5N1 being able to spread between humans is simply the lack of key genes to be able to functionally replicate in humans, this is an incredibly worrying study. More so than if the viruses lethality rate was found to be as high as originally thought, because at least a high lethality rate reduces the chance of the virus having time to start aquiring new genes.
This virus is becoming more and more of a threat every day as a result. It really should not be ignored or trivalised.
Thursday, September 15, 2005
Well a new blog I noticed recently, Positive Liberty has an interesting post discussing homosexuality in penguins. Firstly, it turns out that homosexuality in penguins isn't actually very uncommon at all and several zoos have noticed it. One zoo in particular, in Germany, flew in some Swedish penguins to try and 'taunt' the homosexual penguins into mating with them. These males had none of it however and protests by gay rights groups had the plan to use the penguin seductresses ended.
Most interesting however was that studies on the chick raising ability of gay penguins has found them to be fairly good parents
Studies on these gay penguin marriages, by the way, show that they haven’t affected any of the straight penguin marriages in the same aquariums and zoos. The straight penguins have continued to mate and raise their kids despite the presence of the avian sodomites.So I wonder if we continue to use penguins as moral bastions for humanity, we should be accepting of homosexuality, realise they aren't going to destroy human society (assuming penguin society is truly comparable to human society), treat them as equals and not assume that children raised by homosexuals will be horribly abused and grow up distorted? All of this is contrary to the rhetoric you often hear from conservatives in America of course, but then again, who cares about facts? Apparently the fact these penguins treck thousands of miles, have immense risks at losing their chicks to freezing, a parent dying causes the other to leave the chick to die, which is quite a moral lesson I'm sure, is even evidence of 'intelligent design'.
Once again, just a brilliant example of cherry picking the facts to say what you want them too rather than what reality is really like. That reality is unfortunately, one where these animals make a long harrowing journey over thousands of miles in the worst conditions imaginable. They then spend all of their effort raising usually a single chick whose life hangs on a thread on numerous factors. It's a system that ultimately only appears wasteful when we humans view it with our anthropoentric lenses on, but is one that ultimately works because this is the sort of idiosyncratic system that nature ultimately builds.
The association says the major parties acknowledge that the medical workforce faces chronic shortages, but their recently released health policies barely touch on it.
Medical Association chairman Ross Boswell says the parties' plans to reduce student debt are ad hoc measures and insufficient to secure a stable health workforce.
This is a really key issue for me. As someone who is about to graduate and move into the greater workforce, the debt I have accumulated is going to make me seriously consider a period of time overseas. For example, I could earn more working in a lab overseas than I could here in New Zealand, which will greatly speed up the rate at which I would pay off my student loan. Now my loan isn't anywhere near as bad as those of Medical students, who often have loans well in excess of $20,000 or more. With the large amount of interest that gets piled onto that figure and the fact pay rates here aren't as high eslewhere, prospects for paying off that loan aren't good without sacrificing home ownership, starting a family and other significant purchasing decisions.
The attraction of moving overseas, where pay is a lot higher can naturally be understood and unfortunately, many of the Kiwi medical and scientific professionals who do go overseas don't bother coming back. This is leading to the problem we are now facing at the moment, where we cannot recruit our own medical professionals (who are among the best trained in the world) and aren't able to attract equivalently trained staff from elsewhere.
One of the prime effects of this has to make student loans one of the most important election issues this time around. Unfortunately, neither party has really come up with a very good solution to the problem. Labour has promised to abolish the interest from student loans altogether, while National proposed something that is a lot more modest but at the very least is affordable. Labour however, appear to have been highly deceptive in their initial costings, for example you can see the "original" estimated cost here:
Minister of Finance Michael Cullen provided a backgrounder on the two sets of costings, but no Treasury papers.
Cullen says Treasury's initial $390 million costing was based on a 95% uptake by eligible students and the second $300 million figure was based on different take up assumptions.
However, he says he is withholding all other information to protect confidentiality in the ongoing review of tertiary education spending.
In reality, the cost of their student loan scheme is much higher than expected as papers released by the Ombudsman demonstrate that Labour grossly underestimated the costs. Protect confidentiality of the process? More like attempt to directly lie about it and put a good spin on an inherently flawed concept. In my opinion, Labour have been entirely deceptive and manipulative in their presentation of the 'costs' of this policy and it has indicated to me that they are certainly not to be trusted about this issue. As I blogged earlier, I didn't believe Labour were being honest about the cost of the scheme and as far as I can see this is the nail in the coffin for them.
For example, we can see from the TVNZ source linked above,
Treasury says the policy would cost more than $900 million a year by 2020 - that's about three times what Labour said it would need to spend.
Treasury also estimates that within 15 years student debt will be $5 billion higher than it would have been under the current scheme.
Oh dear, you mean what I predicted back in August that when Labour did the 'real' numbers they could use it as a backout plan to try and avoid following through with the policy.
National estimate that this policy is going to cost the government up to $300 million more, but Westpac trust (a bank) have done their own numbers and they think the number could be as high as $700 million. If this is the case, Labour could very well realise (assuming they win the election) that the interest write off is utterly untenable and compromise.
Of course, now the cat has ended up coming out of the bag, despite Labours best effort to attempt to hide the actual estimates which indicate their policy is going to cost more than they said. The real numbers are out there now and so it won't be an amazing revelation to bring them out later down the line. There will be no running away now with the excuse that a recost had showed the policy was too 'expensive' to maintain, so they are either going to be forced to put up or completely embarass themselves on the issue.
However, considering this is the teflon government and none of their idiotic mistakes have come back to bite them, in the past, I don't think the public will realise how badly Labour have attempted to decieve them over this issue. None the less, I'm a registered voter and I can make them pay for this piece of insanity in the only way I can. By making up my mind to vote for the opposition.
Tuesday, September 13, 2005
Today, his fight against the inundating tides of water has claimed him, probably due to bacteria and other microorganisms getting in and rotting it from the inside out.
RIP our spikey friend, RIP.
Incidently, the sign behind the cactus advises only watering during specific months when the cactus is growing. We had warned the person who owns said cactus not to water it continuously to no avail. Now a poor innocent cactus is dead. It's always the ones with no voice who become the victims and I see there is a clear need for an advertising campaign:
NEVER OVER-WATER A CACTUS.
*Note, it is debatable if the cactus could at any point actually speak. I would say a definitive "maybe". The slight drooping of a spine could have been the silent cry for help that nobody noticed.
Sunday, September 11, 2005
Saturday, September 10, 2005
As I mentioned in a previous posting on antibiotic resistance development in farmed animals, resistance to one kind of antibiotic often increases the resistance to the other drugs even though the bacterium never encountered them initially. The FDA had Cipro banned for precisely this reason as it was correctly noted, that resistance to Cipro could increase the chances of Campylobacter jejuni infections becoming much harder to treat with other fluoroquinolone type antibiotics.
Although it's a far cry from having these things outright banned as I would like to see, it's a small but important victory against this practice.
The other and final problem is the hinderance to basic research on these genes that would ensue. This is because these ESTs are commonly used in many labs to be able to detect and then enable scientists to actually work with the genes in question. If someone happens to own these ESTs that would mean scientists would have to pay the owner of those patents before they can do any work on those genes. Laboratory work is expensive enough, without extra costs like this to get in the way as it is.
This doesn't mean I'm against patenting genes however, but only where they have been used for a novel function and in a specific application. For example, the Bacillus thurnigenesis toxin genes that have been added to certain breeds of corn by monsanto is certainly right to patent. This is because the application is novel and has a defined function, but it is worth noting that even in this case monsanto do not own the original toxin gene just the way the gene has been used. As the court decided with these ESTs, they did not have a direct specific application* and neither was this application novel.
*Note that monsanto did argue that the ESTs had a use in finding new promotor regions, but the court rejected this as it was not the specific purpose of the EST.
Thursday, September 08, 2005
An editorial in the recent issue of Nature gives a good overall summary of the whole mess:
Knowledge of the risk of a storm-induced flood in New Orleans has been widespread in the scientific community for years, and researchers have sought to improve our understanding of it. Much of this work has taken into account stubborn facts such as the propensity of the poor, the elderly and the sick to ignore evacuation orders.If in the aftermath of this disaster heads in certain administrative positions do not roll I will be sorely disappointed. Many people died that shouldn't have, if only a fraction of the total monetary cost of the damages had been spent a few years earlier to upgrade levees and other systems that were sorely understregth.
There seems to be a disconnect, however, between the process that identifies such risks and the people who make the decisions that might manage them. There are indications that many senior politicians — not just President Bush — were simply unaware that the New Orleans flood risk even existed.
Wednesday, September 07, 2005
(Note: movie is in quicktime format).
Once again, I can only express disappointment that even after all this time, it appears American leaders still continue to ignore their scientific community and instead pander to fringe lunatics when it suites their agenda.
More on the report at science.
Monday, September 05, 2005
Human remains in cattle feed could have caused the first case of mad cow disease, two UK researchers propose. The hypothesis seeks to answer lingering questions about the fatal infection, which has affected 180,000 cows in Britain alone since the mid-1980s, and has gone on to cause more than 100 deaths in humans.I don't know if I find the idea of cows passing such horrible diseases onto humans so easily more disturbing than the fact the cows may have ate human remains to begin with. So much for being vegetarians I guess.
Friday, September 02, 2005
Once again, the warnings were ignored and innocent people were the ones who had to pay with their lives. This is from the same administration that ignores the general scientific consensus on climate change and other environmental issues. It's just a shame that it's not the ones who make these disasterous decisions that end up having to pay for it.
If Congress and President George W. Bush hear a unified call for action, authorizing it would seem prudent. Restoring coastal Louisiana would protect the country's seafood and shipping industries and its oil and natural-gas supply. It would also save America's largest wetlands, a bold environmental stroke. And without action, the million people outside New Orleans would have to relocate. The other million inside the bowl would live at the bottom of a sinking crater, surrounded by ever higher walls, trapped in a terminally ill city dependent on nonstop pumping to keep it alive.
Hat tip to Pharyngula, where I saw the link to the Scientific American article originally.
IDT claims that there is no evidence for large-scale evolution. This is nonsense. Genomic science has provided conclusive evidence for human evolution. We share common ancestors with chimps, all other primates and other mammals. IDT denies evidence-based science.And that it is also poor theology:
Darwin (as a conservative English gentleman) believed in precisely this god. This god is a distant abstraction that is not personal, communicating, holy, loving, redeeming.I agree with everything he says in the article really and it's a good example of the fact that you can be both Christian and have no problem with modern science. Finally, if you want even more ID trouncing, which has been occuring quite frequently in the media as of late, you should have a look at this piece in the Guardian Unlimited by Richard Dawkins and Jerry Coyne. An excellent quote that cuts to the heart of the issue is this one:
The deist god of 19th-century Europe is a stark alternative to the passionate God of the Bible who is revealed in Jesus. It is ironic that IDT rejects Darwin's science even as it settles for Darwin's god.
If ID really were a scientific theory, positive evidence for it, gathered through research, would fill peer-reviewed scientific journals. This doesn't happen. It isn't that editors refuse to publish ID research. There simply isn't any ID research to publish. Its advocates bypass normal scientific due process by appealing directly to the non-scientific public and - with great shrewdness - to the government officials they elect.It's not enough in science to wave your hands and make 'claims' that you've got some idea that challenges a known theory. You have to back it up with actual experimental data published in actual journals. This is what ID advocates and proponents fail to understand, those that have challenged aspects of evolution in the past have presented testable predictions about their theory. For example, Lynn Margulis who first proposed that organelles such as mitochrondria and the choloroplast were better explained by the original host cells taking up the original bacterial ancestors of these organelles and forming a symbiotic relationship with them.
The theory, called endosymbiotic theory was not well accepted among microbiologists and these organelles were still seen to have developed in a gradualistic 'darwinian' mechanism. However, oevr time and particularly after publishing Symbiosis in Cell Evolution, opinion gradually changed on the status of her theory. All the while, what seperates this form of controversy from the ID movement is that L. Margulis and other proponents of endosymbiotic theory supported their ideas in the scientific literature with actual experiments and observations. It was, for example, noted that mitochondria are very similar to bacteria in many respects, such as having bacterial (but not eukaryotic) ribosomes.
I cannot really stress enough that ID knows it has nothing like the above in terms of predictive power and actual scientific evidence. They know this, so instead of trying to do real science they try to whine about a 'Darwinian' orthodoxy that doesn't let them publish. Yet above, we had L. Margulis completely challenge what was at the time a well accepted darwinian process for the development of those organelles and through sound hypotheses and experiments, completely disprove it. Quite frankly, the Darwinian orthodoxy that the IDers complain about is just a load of rubbish to avoid answering to scientists in actual peer reviewed journals. Instead, ID proponents attempt to dishonestly avoid this and instead go through political means to force ID to be accepted.
As you can probably imagine, having your theory accepted due to political and not scientific means was the sort of thing that Lysenko did. ID is not science, it makes no testable predictions about their designer and it is thrown out by scientists because of that reason.
Thursday, September 01, 2005
"To simply say that this is about healthcare companies wanting to make profits is a cheap shot, and ignores the concerns of nearly seven out of ten New Zealanders who are worried about lack of access to medicines and want PHARMAC to be reviewed."Of course. Personally, I think we do at times make some ridiculous decisions with the drugs we choose to stock. For example, anti-TNF-alpha inhibitors which have been proven to be very effective at relieving the pain and suffering caused by rheumatoid arthritis are not subsidised here*. That puts these drugs well out of reach of those who need them, who have to rely on less effective alternatives that don't work nearly as well.
*Correction: Actually it turns out that they are subsidised for individuals who have the childhood form of the disease but not adults.
TNF inhibitors have recently been found to be the most effective therapy available for rheumatoid arthritis. In New Zealand they have been made available over the last year, to those with the childhood form of this disease, however, they must stop treatment at 18. The Rheumatology Association estimates that 300-400 people aged over 18 would fit the stringent criteria of the drug, however, standard intensive drug therapy can cost up to $7,000 a year in costs for hospitalisation to these people often totals more than $600 a day, on top of that and surgery.From what I understand, the childhood form of the disease is pretty rare while this is much more common in those who are elderly. Basically, the best available treatment isn't able to reach the majority of people that actually have the disease. Of course, the fact this treatment is so expensive is probably one of the main reasons Pharmac is refusing to subsidise it. For a list of some other Pharmac quibbles that have turned up over the past few years, scoop has an article detailing many of the drugs that Pharmac has come under criticism over.