Thursday, October 27, 2005

Hydrogen bond angles and...cancer?

Occasionally alties throw out some really wierd things, but this just takes the cake I think:
Fifty years ago the hydrogen bond angle in water was 108° and you rarely heard of anyone with cancer. Today, it's only 104° and, as a result, cancer is an epidemic!! By using our machine you can increase the bond angle to 114° and, unlike any other water, doctors can see an immediate change in the red blood cells under a microscope! It's truly amazing!!
Hmmm, that certainly does sound convincing to me! Who would have thought that hydrogen bond angles would be the cause of all those pesky cancers. Who would have then guessed that someone had come up with a solution for it that you could easily pay for right now! Orac gives this little piece of nuttery the shake down over at his blog.

I wonder how people come up with this stuff though.

Monday, October 24, 2005

Rothschild pwnage

The prosecution lawyer Rothschild, came out with an excellent pwn (again) against Michael Behe at the Dover trial now that I've managed to find the time to slog through the transcripts. During a discussion on the origin of the flagellum, Behe was asked about the scientific dialogue concerning possible evolutionary pathways from the type III secretion system:
Q. Okay. But scientists, as they do with many
subjects on which there's disagreement, may continue to
be making arguments and writing papers and submitting
them to peer review journals and doing experiments to
see if they can come up with a consensus answer on the
subject?
A. Sure. And they may write books to try to come up
with an answer, too, as well.
Q. That's how you get the royalties, right?
A. (No response.)
ZING! I wonder what sort of look Behe gave...

Friday, October 21, 2005

More Behe fun

This trial is a never ending source of pure comedy from Michael Behe. First he tries to redefine the term "Peer review" and now he's trying to redefine the term "critical reviewer". This comes from the cross examination by the prosecution lawyer Rothschild when questioning Behe over his role as a 'reviewer' of the ID textbook of Pandas and People.
Q But you actually were a critical reviewer of
18 Pandas, correct; that s what it says in the acknowledgments
19 page of the book?
20 A That s what it lists there, but that does not mean
21 that I critically reviewed the whole book and commented on
22 it in detail, yes.
23 Q What did you review and comment on, Professor Behe?
24 A I reviewed the literature concerning blood
25 clotting, and worked with the editor on the section that
OFFICIAL COURT REPORTER
BEHE - CROSS
27
1 became the blood clotting system. So I was principally
2 responsible for that section.
3 Q So you were reviewing your own work?
4 A I was helping review or helping edit or helping
5 write the section on blood clotting.
6 Q Which was your own contribution?
7 A That s -- yes, that s correct.
8 Q That s not typically how the term "critical review"
9 is used; would you agree with that?
10 A Yeah, that s correct.
11 Q So when the publishers of Pandas indicate that you
12 were a critical reviewer of Pandas, that s somewhat
13 misleading, isn t it?
14 MR. MUISE: Objection. Assumes that he understands
15 what their purpose for listing him as a critical reviewer.
16 THE COURT: He just answered the question that
17 that s not a critical review, so the objection is overruled.
18 You can ask that question.
19 BY MR. ROTHSCHILD:
20 Q Advertising you as a critical reviewer of this book
21 is misleading to the students, isn t it?
22 MR. MUISE: Objection, that s argumentative.
23 THE COURT: It s cross examination. It s
24 appropriate cross. Overruled.
25 THE WITNESS: I m sorry, could you repeat the
OFFICIAL COURT REPORTER
BEHE - CROSS
28
1 question?
2 BY MR. ROTHSCHILD:
3 Q Telling the readers of Pandas that you were a
4 critical reviewer of that book is misleading, isn t it?
5 A I disagree. As I said, that s not the typical way
6 that the term "critical reviewer" is used, but nonetheless,
7 in my opinion I don t think it is misleading.
So Pandas has blatantly false information in it and yet it is not being 'misleading'? I guess Behes definition of 'misleading' must be similar to his definition of 'Peer review'. In other words, one that nobody else happens to share.

Behe castrates himself at ID trial

As with all creationist attempts to insert their babbling into classrooms, it always ends up being decided in court because they are unable to convince anyone in the normal 'peer review' systems all other scientists do. Michael Behe, author of the somewhat interesting work of fiction Behes Black Box (or was it Darwins Black Box?) has claimed on the stand his book went through:
peer review for Darwin's Black Box was analogous to peer review in the [scientific] literature
Oh really? One of the reviewers that Behe cited for this 'peer review' was a Dr. Michael Atchison, who is the head of biochemistry at the University of Pennsylvania vetinary school. Of course, I would immediately point out if you're going to criticise evolution in your book, wouldn't it be best to have reviewers who are evolutionists to begin with? Anyway, discrepancies aside let's look at an article published by Dr. Atchison around the same time that the prosecution then presented:

While I was identifying myself as a Christian in Philadelphia, a Biochemist named Michael Behe at Lehigh University was writing a book on evolution. As a Biochemist, Behe found the evidence for Darwinian evolution to be very thin. In fact, when he looked at the cell from a biochemical perspective, he believed there was evidence of intelligent design. Behe sent his completed manuscript to The Free Press publishers for consideration. The editor was not certain that this manuscript was a good risk for publication. There were clearly theological issues at hand, and he was under the impression that these issues would be poorly received by the scientific community. If the tenets of Darwinian evolution were completely accepted by science, who would be interested in buying the book?

The editor shared his concerns with his wife. His wife was a student in my class. She advised her husband to give me a call. So, unaware of all this, I received a phone call from the publisher in New York. We spent approximately 10 minutes on the phone. After hearing a description of the work, I suggested that the editor should seriously consider publishing the manuscript. I told him that the origin of life issue was still up in the air. It sounded like this Behe fellow might have some good ideas, although I could not be certain since I had never seen the manuscript. We hung up and I never thought about it again. At least until two years later.

So in other words, this 'peer review' that Behe claims comes down to 10 minutes on the phone with someone who has never read the actual book. Behes response to this?
Rothschild (Prosecution lawyer): "Is this your understanding of the kind of peer review that Dr. Atcheson did of your book?"

Behe: "No"

Rothschild: "he didn't review it carefully, he didn't review it at all."

Behe: "My understanding is different."

Oh your understanding is different is it Behe? I'm sure it is, just as your understanding of the evidence for evolution concerning things like the immune system and bacterial flagella is different too? Very well done Behe, you just ruined whatever remaining credibility the ID movement had left in one fell swoop. You should feel really proud because it's not often that someone just completely pwns themself in that manner in one fell swoop and in court.

For more trial shenannigans go to the ACLU blog on the case. It's hillarity the whole way through as the ID proponents get eviscerated, usually with their own words too.

Friday, October 14, 2005

A rare personal type post.

Finally completed the last of my main hurdles before the end of the year with my oral exams being finished today. Now I'll have plenty of time for blogging and other aspects of general internet fun. Of course it's time to start looking for a job, considering options for moving onto a PhD and importantly deciding if I want to go overseas for a bit. Although I would have liked to walk in the graduation ceremony in december I missed out due to being busy with other things (so forgot to submit the form, doh!). Oh well, the ceremony in may sounds more attractive anyway because all of my other friends who are still studying will be around to see me graduate.

Overall I've found my time at Otago University to be extremely enjoyable. I've learnt a lot in the four years I've spent there, and developed considerably as both a person and as a scientist. Additionally I've met a lot of great people along the way and made excellent friends. Sometimes things have become a little disconnected as I started originally trying to do multiple degrees (biochemistry and microbiology at first), which just unfortunately made for too much of a workload that certainly didn't help the old stress meter.

19th Skeptics Circle has been posted

Nurse Kelly has gone with a carnival themed skeptics circle this week over at time to lean. Once again there are some excellent examples of skeptical writing available for your edification.

Wednesday, October 12, 2005

Arachnids faking it during sex

I've always had a fascination with the way that spiders decide to mate with one another. Being heavily armed predators by having webs, a bad temper and a nasty bite, mating is a very dicey affair at the best of times. Male spiders pretty much face an up-hill battle as the female is usually bigger, meaner and hungrier than he is. Worse, many species of spiders are almost blind or their eyesight isn't the best meaning males have an even harder time. This has resulted in males often having odd mating behaviours or very elaborate dances so that they avoid being eaten.

A recent paper published online in Biology Letters discusses the mating behaviour of Pisaura mirabilis males. These spiders use a strategy where the male attempts to distract the female by giving her a 'nupital gift', which consists of an insect he's caught and wrapped up in silk. While she dines on his gift, he sneaks in to mate and then gets away as quick as he can. Unfortunately, this strategy doesn't always work and instead of going for the tasty gift, she decides the male would be a more tasty snack!

The clever male however has a devious way of getting around this problem, he falls into thanatosis (plays dead) putting her attention back on the gift and not him. When she moves on to dine on the snack, he slowly gets up and proceeds to sneak in a mating while she isn't paying attention. This strategy works remarkably well as most males succeed in mating by doing this. Of course, the male sacrifices any form of defence he may have previously had and is more open to being cannabalised than he was originally. Additionally, the male also doesn't get as long to mate with his rather bossy mate as one who succeeds in the original courting.

Interestingly, playing dead is a relatively uncommon strategy among spiders and many other invertebrates as well. This is probably due to the large amount of risk that is involved, particularly as it does leave the male utterly defenseless and with some predatory insects it might not be overly much of a defence (female would attack anyway). Overall, it's yet another file to add in the kinky sex files of spiders.

Image hosted by Photobucket.com
Quite cute! (Picture found here, which also has pictures of other spiders as well. The site is in German though).

Evidence for his noodly designer

Thomas D. Schneider, Ph.D., who I am sure is going to become a leading ID proponent, has published an amazing experiment verifying the intelligent designer as the noodly one. The paper, covering the spontaneous appearance of Noodleous doubleous has appeared in the peer reviewed internet site www.fred.net. As the author shows with a highly convincing set of experiments, the formation of these unusual double pasta lifeforms is so improbable it must be the work of an intelligent designer. Sadly, the lifeforms were consumed at the end of the experiment, but Schneider has promised future work to validate the exact mechanisms of how the flying spaghetti monster may be achieving the observed effect. The full paper is printed for free on the internet (no subscription required, like evilutionist journals) and may be read here: Origin of Noodleous doubleous.

PS: Irony meters may be required for viewing.

Friday, October 07, 2005

Boo!

I'm still around and have finished my course for the year (aside from a mere two exams). Now that everything is out of the way I can get back to doing, erm, whatever it is I normally do on here.

Tuesday, September 27, 2005

Gone AWOL

For those wondering about the lack of blogging, I'm currently writing the final report for my research this year so I haven't had a lot of time for blogging right now. Regular blogging will resume next week when I've finished and have more time.

Friday, September 23, 2005

Art imitates...life?

Reading around, I recently encountered an unusual new plague that has sprung up in the most unlikely of places, an online computer game called World of Warcraft. Apparently, the developers added in a new character that has an attack that is supposed to give the affected player a disease that kills them. Unfortunately, the disease actually doesn't always kill the player in question and they have been able to drag it back home with them. The remarkable result (and utterly unanticipated) is that the disease has actually begun to spread, laying waste to entire areas in the game and basically instantly killing any character under level 50.

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

Critic sticks its foot in it

The local student magazine around where I am is called Critic and today it looks to have thoughroughly managed to stick its foot in it. The article in question concerns the use of date rape drugs, namely what the particular drugs are and their various properties. While the article was probably either aimed at being some form of 'satire' or 'educational' it reads more like a 'how to' guide than anything else. In fact, the entire article, is really tasteless and I don't particularly feel adds anything in particular to the issue let alone being worth reading.

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.

Tuesday, September 20, 2005

A blog meme

Pharyngula has this odd little blog meme about what it feels like to be an academic scientist or for those who want to become academic scientists. As one of my inevitable goals is to become an academic scientist and to go and lecture students, while of course maintaining a rich research programme; I thought it would be worth doing.

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:
http://pixnaps.blogspot.com/2005/09/academic-blog-survey.html

Instructions:

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
Link List (or 'extended hat-tip'):
1. Philosophy, et cetera
2. Pharyngula
3. Immunoblogging
4. Add a link to your blog here.
Survey:

Demographics
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

Other Questions
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!

H5N1 and lethality

The pandas thumb has posted an article on the lethality rates of H5N1 (based on a new study) and how the virus may be evolving.
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

March of the Penguins and Family Values

Although it hasn't reached New Zealand yet, a movie that is out at the moment called March of the Penguins has been getting rave reviews in America and has surprised pretty much everyone. Of course, many of the general science blogs have been reporting that Conservatives in America are praising the movie for it's excellent lessons about morality, namely Christian morality. Apparently the penguins are brilliant examples of monogamy (actually, they re-choose a mate every year), sacrifice and child rearing. Well, aside from being a bit bizzaire, I have to wonder what the extent penguins are in terms of being good examples of morality.

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.

Medical Workforce crisis and Student Loans

Unsurprisingly to me, seeing as New Zealand likes to burden the people we train with oodles of debt after graduating from University, it seems that those in the Medical community are afraid of a potential lack of trained professionals in the medical fields.

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

A lesson in plant biology

This is the story of a cactus, once the strongest and happiest cactus in all the lands. Unfortunately, his owner continually kept overwatering him and despite his poor cries of "no more water, I'm a desert adapted plant and I don't actually need to be watered every single day!" they went ignored and he was watered even more.*

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.

Image hosted by Photobucket.com

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

Hurricane Katrina coverage

With the devastation that has hit New Orleans many have begun to ask if human induced climate change may have played a factor in increasing the destructive force of the hurricane. While it's an interesting question to ask, it would be premature to come to any conclusions on the matter. For those interested in learning more about this, I would suggest reading this post at Real Climate, Hurricanes and Global Warming - Is there a connection. It's very well written and gives a good balanced perspective on the issue.