Wednesday, June 29, 2005

AIDS and Religious bias.

One of the most potentially devastating phases of the AIDS (Aquired Immune Deficiency Syndrome) epidemic is its spread through Muslim countries according to UNAIDS (TVNZ news). Although some countries may be resistant to efforts to combat the disease due to denial of the scope and rate of the epidemic. Surprisingly however, Iran has actually been leading the way among Muslim countries with needle exchange programmes and public education campaigns. Another Muslim country that is making great progress is also Bangladesh according to UNAIDS, but when it comes to AIDS more will also need to be done.

Interestingly, this reminds me very much of the inital situation that faced the United States government at the beginning of the AIDS epidemic in the late 1970s. It was marked by fierce denials from the conservative Reagan administration, which heavily stifled funding and hampered efforts to track the diseases epidemiology as a result. Add in some good old fashioned Christian bigotry with some fire and brimstone (see below for some examples) and you have a potential disaster.

Centers for disease control (CDC) scientists were often frustrated as a result and severely underfunded. Koop, C. Everett the surgeon general at the time, described the administration thusly:
"The Reagan revolution brought into positions of power and influence Americans whose politics and personal beliefs predisposed them to antipathy toward the homosexual community (1)."
This resulted in considerably reduced spending and action, which can be seen best in the response to a seperate outbreaks of other diseases:
"By that time the CDC had spent just under $1 million for some thirteen months of GRID [Gay-Related Immunodeficiency Disease] research. In roughly the same amount of time-or less- the CDC had spent $9 million in pursuit of the cause of death of twenty-nine Legionnaires in 1976-77; more than $1 million on Ebola hemorrhagic fever investigations in Central Africa; at least $135 million on Swine Flu investigation and vaccine development (2)."
"There is no doubt in my mind that if the disease had appeared among Americans of Norwegian descent or among tennis players, rather than gay men, the response of the government and medical community would be different," - Henry Waxman (Californian democratic party member) (3)"
"Finally, the [Democrats'] recommendations that an independant panel be created to develop a comprehensive strategy for responding to AIDs should be rejected as unnecessary." (4)"
and many on the religious right didn't make things any better (however shamful these sorts of quotes are)
"AIDS is a Judgement from God." - Reverened Billy Graham"
"AIDS is God's punishment," [Jerry Falwell] concluded. "The scripture is clear: We do reap it in our flesh when we violate the laws of God."(5) "
Even as developments progressed and it appeared that the disease had spread to those other than homosexuals, the intense bias from the religiously motivated right to the stigma of AIDS as a 'gay disease' resulted in denials and research was impeded. After the discovery of the virus that causes AIDS, HIV (Human Immunodeficiency Virus), there were still continued denials and emerging crack pot theories attempting to 'explain' the origin of the virus. For example, that vaccines caused the outbreak such as hepatitis B, smallpox, polio, or that the virus originated from influenza or more absurd still that the CIA created the virus to destroy Africa.

Most importantly, AIDS was a lesson that good science, epidemiology and more was ignored when the primary infected group was one that was generally disliked, very often for religious reasons. As the scenario in America in 1979-1985 demonstrates, religious bias at a governmental and even a social level allowed AIDS an easier time in spreading through the most susceptible populations. The governments of Muslim countries should take the American administrations previous mistake to note and not repeat them or run the risk of escalating an already progressing epidemic. In many respects, the positions of Iran and Bangladesh must be considered as a leading example to other Muslim countries.

AIDS is a terrible disease and not just one of the socially disliked or morally corrupt. It must be coordinately attacked on all levels, both through an individual level, at a societal level and at a governmental level.

1. The coming plague. Laurie Garrett. Pg. 302 (Brilliant book incidently and is a well researched read on many issues surrounding emerging diseases. Has a large and extremely depressing chapter on the initial outbreak of AIDS in America).
2. Pg. 303.
3. Pg. 303.
4. Pg. 318.
5. Pg 330.

Scientific Americans report on 2005 Evolution Conference

Scientific American has a fascinating article on a recent conference on evolution held on the Galapagos islands. The best quote I think in the article was this one and represents what science really is about, but most importantly also what it is doesn't do as anti-science opponents so often try to insinuate:
"Creationists and other outsiders contend that science is a cozy and insular club in which meetings are held to enforce agreement with the party line, to circle the wagons against any and all would-be challengers, and to achieve consensus on the most contentious issues. This conclusion is so wrong that it cannot have been made by anyone who has ever attended a scientific conference. The World Summit on Evolution, like most scientific conferences, revealed a science rich in history and tradition, data and theory, as well as controversy and debate. From this I conclude that the theory of evolution has never been stronger.
An incredibly true statement, because real science doesn't progress through popular votes, courtroom trials or any other such nonsense. Real science is carried out in a lab by researchers who have actual experimental data and results. Real science is determined in numerous peer reviewed journals all across the world. No amount of court cases or public affairs can change the fact IDists, creationists and other peddlers of anti-evolution/science nonsense will change that fact.

The entire article is well worth the read and raises numerous interesting points. It can be found right here.

Red State Rabble and the Grand Canyon

Over at Red State Rabble, Pat is having a trip around the Grand Canyon (which is a remarkable piece of scenery). Over the coming week he's going to be describing the canyon and some of the problems typically encountered when young earth creationists attempt to butcher geological science with their general nonsense. I suggest heading over and having a look at what he has to say.

Tuesday, June 28, 2005

Monday, June 27, 2005

Toll-like Receptors and You

One of the things that first got me interested in immunology was the concept that when our bodies are invaded by a pathogen, we go through a sort of 'molecular' war. Antigen presenting cells, such as Macrophages and Dendritic cells make up the scouts of our immune 'armies' detecting the initial enemy incursion. From here they report their findings to the T-cells and B-cells which employ the destructive molecular weaponry we possess to remove the pathogen. With such power however, I often wondered what mechanisms existed to prevent the immune system from recognising self tissues as an enemy. More importantly still, I wondered where these mechanisms evolved from and how they learnt to differentiate the enemy from us. At first I considered the innate immune system relatively unimportant in this process- just something to delay a pathogens replication until the big guns of the adaptive immune system could come into play. Essentially that the adaptive immune system was the one that did all the important decisions regarding the ensuing molecular battle.

Of course, now I realise that the innate immune system is more important than just a mere mecahnism for delaying replication of a pathogen, until the adaptive immune system can decide what to do about the invader. In fact, it turns out that the innate immune system is essentially responsible for restricting the pathogen and orchestrating the resulting adaptive immune response to follow. This is all coordinated by the immune systems recognition of pathogens through membrane bound receptors called Toll-like receptors, or TLRs for short. These receptors recognise different parts of microbial invaders, such as lipopolysaccharide, bacterial DNA (CpG motifs) and double stranded RNA (signature of viruses). Most importantly, depending on where the microbial product was detected in the body and what that molecule was, will dictate the entire immune response to follow.

This gives TLRs two key functions in the mammalian immune system. The first is that after recognition of a pathogen it activates the transcription of appropriate immune genes and regulators (such as cytokines). This promotes the initial response and gears up local lymphocytes such as macrophages, neutrophils and cells involved in the start of an immune response. Secondly, depending on the initial genes that were transcribed it biases the resulting adaptive immune response, producing antibodies to destroy extracellular pathogens such as bacteria or a cytotoxic (cell killing) response to destroy intracellular pathogens like viruses.

As a paper that was recently published in the Proceedings of the National Academy of Sciences (PNAS) shows, the TLRs of vertebrates are closely related in evolutionary terms, with most vertebrate receptors belonging to six specific families. They hypothesised that these general TLR families are continually present due to the inability of microbes to easily mutate or change the components they recognise. Additionally, they found that many of these TLR families have been specifically adapted to the patterns of pathogens that each animal has encountered. For example, although TLR 11 is functional in other animals, in humans it's nothing more than a useless pseudogene and is non-functional.

Additionally, some animals such as Rainbow Trout, express a soluble form of some of their membrane bound TLRs which consists of the LRR. These soluble mediators may be the precursors of mammalian LPS binding proteins. Additional hints of the origin of the immune system comes from analogous systems in Lampreys, which have been demonstrated to have variable lymphocyte receptors (VLRs). These have membrane bound receptors and soluble forms containing LRRs similar to the above TLRs. It's worth pointing out that VLRs are similar to TLRs in basic function, VLRs do not have the same function in coordination of an adaptive immune response which is not present in these animals.

In terms of evolution, TLRs have been highly conserved in function throughout many different animals, probably indicating the significance that microbial pathogens have imposed upon their hosts over evolution. Additionally, although the general function of TLRs has remained relatively conserved in their signalling function, they have taken on a new level of importance in mammals by coordinating a resulting adaptive immune response, which invertebrates like Drosophila lack. TLRs are a magnificent example of a system from 'simpler' animals that has been conserved throughout evolution and its functions altered later down the track to enable new uses.


Roach J.C., G. Glusman, L. Rowen, A. Kaur, M.K. Purcell, K.D. Smith, L.E. Hood and A. Aderem (2005). The evolution of vertebrate Toll-like receptors. Proceedings of the National Academy of Sciences, 102,27;9577-9582.

Sunday, June 26, 2005

Drug Resistance and Influenza

So it looks like that some farmers in China have been employing the antiviral drug amantadine to prevent the spread of H5N1. Unfortunately, this is a terrible idea as it has already been implicated in the spread of resistance to this drug. As amantadine is one of the main drugs that could be used to combat a pandemic, such resistance being introduced into the circulating avian flu strains could be devastating.

Amantadine was developed by Du Pont chemists more than 30 years ago and it was the first specific, effective antiviral drug developed. The drug itself works by targeting a specific structure on the surface of the influenza particle, the M2 porin. Once bound, it blocks this channel preventing the entry of protons into the viral particle. This stops the virus particle from uncoating once it has entered. Resistance to the drug is typically mediated by mutations that either prevent the drug from entering into the porin, or the drug cannot bind onto it at all in the first place.

Spreading resistance to the drugs that may potentially make up the first line of defence against influenza is not only irresponsible but potentially dangerous. China and other authorities should stamp down on these practices as quickly as possible before it is too late to go back.

Saturday, June 25, 2005

Do Evolutionary Textbooks Erode Faith?

On a CNN program "Lou Dobbs Tonight" one of the leading ID advocates Jonathan Wells made a claim that numerous evolutionary textbooks attack theism and Christianity.
"WELLS: I have a dozen biology textbooks at home that explicitly use evolution, misuse evolution, as an argument against theism, belief in god, Christianity, and so on
Aside from being a ridiculous assertion, it's also been shown to be blatantly false by Nightlight, who literally eviscerates the claims by Wells.
"I checked into close to fifteen biology textbooks, including the ones from the list sent to me by Dr. Wells. Not one of these texts uses evolution to argue against theism in any fashion. Not one of these texts tells students they were not created by design. All of them discuss the historical and cultural aspects of evolutionary thought in a manner that is measured and respectful.

This careless castigation of legitimate science texts by Jonathan Wells was an abuse of a national forum and will almost certainly have the effect of demagoguing the issue of origins. It seems likely that there were many theists in the national audience who heard Wells’ false charges who have accordingly adjusted their opinions on this issue - opinions that are, by most measures, already significantly misinformed about fundamental biological concepts (i.e. "it’s just a theory").

Jonathan Wells was wrong to make the claim that he did, and owes a retraction to biology textbook publishers and authors, to the CNN viewing audience, to the "intelligent design" community, and to the people on both sides of this debate who are trying to deal with the issues in a fashion that does not increase the amount of spurious "information" already in circulation.

Although I doubt any retraction is on the way, I can say myself that I never had my faith challenged due to anything written in a biology or evolution textbook. Other things did certainly, such as generally difficulties in school (non science-related) and other factors. I doubt that evolutionary textbooks do much damage to Christianity, in the same way that weather forcasting doesn't destroy it or anything else that posits natural explanations for phenomena we see around us.

Discovery Institute angry about "Design"

Over at the Pandas Thumb is a post looking at a statement by the Discovery Institute (the leading Intelligent Design body in America). Apparently, they are rather upset that people like to think they are for some reason religously motivated (imagine that!). Of course with such quotes like this from William Dembski

The mechanical philosophy was ever blind to this fact. Intelligent design, on the other hand, readily embraces the sacramental nature of physical reality. Indeed, intelligent design is just the Logos theology of John’s Gospel restated in the idiom of information theory

it's so terribly difficult to get Intelligent Design and religiously motivated pseudoscience confused isn't it.

Thursday, June 23, 2005

Victory on the Kitchen Front!

For the past few weeks we've had an infestation of mice in my flat, with several bread like resources being munched on and evidence that the mice have been going up into the oven. Although I find mice cute cuddly little animals, they are serious pests in the house and are a major health concern. I would have liked to get rid of them non-lethally, catching these ones has proved difficult due to the general design of the kitchen and the numbers of them. I resorted to using traps and it appears that the new trap has been massively successful. Within 7 hours it has caught 4 mice with this one I believe being the last (as I haven't heard any squeaking or noises)

Image hosted by

Incidently, that isn't blood on the carpet it's just a fruity floral design of some sort.

Wednesday, June 22, 2005

Influenza B outbreak in New Zealand

As some of you may have heard already, there is a current outbreak of influenza strain B, which was responsible for the epidemic in Hong Kong (1968) here in New Zealand in the North Island. Several children have already died and numerous students have been kept home from school. Thankfully, it doesn't appear that the epidemic has spread to the South Island and the upcoming school holidays will (with some luck) curb any further transmission of the virus.

Aside from being an unfortunate event, this epidemic is a reminder that viruses are not always completely absent just because the diseases they cause aren't around. It is likely that the resurgence of this virus is due to waning immunity from people born well after the original strain was circulating (hence the effects being seen among school children). Normally the virus is added to the current flu vaccine, but this year in an almost ironic twist the World Health Organisation decided to remove that particular strain from the vaccine. It is unlikely that this would have initially been any good at stopping the epidemic from starting, because the flu vaccine is generally only recommended to those at risk and the elderly (most school kids wouldn't be getting it) but it would have helped after it began.

This is yet another reminder that even viruses that we think are well under control can and will come back when immunity to them drops. This is why, even though diseases such as rubella, and measels aren't anywhere near as prevalent it is still important to keep vaccinations for them.

Influenza Wiki

With the emerging threat over a potential pandemic caused by avian influenza it's probably a good idea to make sure that clear information is available on it to the public. Particularly in what sort of symptoms may be expected and how authorities are planning on combating a potential outbreak. As a result a group of bloggers (Effect measure, Just a bump in the Beltway and The Next Hurrah) have decided to get together and produce a 'Flu wiki' discussing the subject of influenza, of which I'll probably contribute a few articles. The site will probably go up sometime over the weekend.

Tuesday, June 21, 2005

Michael Jackson appears on toast!

So the esteemed BBC is reporting that Michael Jacksons visage has appeared on some toast as of late. Typically I love it when things like this occur because I know two things will end up happening. The first is that this is going to sell for a large amount of money, because the internet loves to buy curiosities at immensely odd prices. The second is that this will start a phenomena of celebrity toast appearances with the Virgin Mary . I imagine that perhaps other celebrities may be coming to a toaster near you! Who knows, maybe we could get the Toast of Turin or famous icons in history could make appearances in toast form such as Thomas Jefferson. The possibilities are truly endless.

Perhaps though there is more significance to this than we might first realise. As ID advocates such as William Dembski have demonstrated, such complex patterns are extremely unlikely to arrive by random processes (especially on toast). Could it be that toast images are the product of intelligent design? It could definitely be proposed that toast images are more than they first appear. Maybe they are messages from a higher plane of existence. One that communicates almost exclusively in toast and are trying to communicate with us. I believe that perhaps we should get William Dembski and others in the ID movement to help explain, using the explanatory filter of course, if the toast is an example of intelligent toast designers communicating with us?

Perhaps there really is a scientific theory of ID? The scientific theory of toast images! I leave it up to you to mull over the incredible ramifications of this new and daring hypothesis made possible only by ID.


Nature as always provides an interesting article pertaining to bioterrorism and the responsibility of science to ensure that it is used responsibly. Among many of the issues raised in the article is censoring academic publications pertaining to methods that may be used for a terrorist attack. For example, Nature brings up:
"For instance, a researcher might choose to brief key government officials about a sensitive finding instead of publishing it in a widely distributed journal — a possibility raised in ongoing controversy over a paper that models a bioterrorist attack on the US milk supply. Publication of this study has been delayed after protest from the US government"

In many regards, I somewhat agree and disagree with the idea of restricting the publication of scientific papers regardless of if the restriction pertains to where or even if the paper could be published at all. In some respects, it will be about the security of the general public as it is certainly true that terrorists have used biological agents in the past such as anthrax. Caution pertaining to who can get access to scientific papers detailing methodology on making recombinant pathogens, or modelling potential bioterrorism attacks should probably be monitored.

At the same time, science itself relies on communication and interaction between scientists. Hampering the ability to post in journals may lower scientific understanding and ultimately make biological agents harder to fight. For example, the recent developments in making new influenza vaccines uses a modified eight (or six) plasmid system. This system allows for quick and efficient production of new influenza virus with different surface 'spikes'. The goal of this system originally was for the more rapid production of a vaccine against the emerging avian flu strain H5N1 (which can't be made by traditional methods). It's also unfortunately true that terrorists could potentially use a similar system to make a new virulent influenza strain as a weapon.

Ultimately, there needs to be a degree of responsibility from both scientists performing this work and from journals that allow it to be publicised. I just hope that Government legislation does not attempt to interfere too largely with the ability of scientists to publicise papers.

Sunday, June 19, 2005

The tactics of the anti-meningococcal B vaccine movement

Orac, who I linked to earlier has posted an excellent follow up to his vaccine-autism article over at his blog that again, I would highly recommend reading for anyone interested in this issue. One of the points that reminded me about typical tactics employed in this 'debate' is the misrepresenting of various facts and data. For example, Orac points out that;
"although I will concede that RFK Jr.'s article was so sloppy that he didn't mention if these patients had bacterial or viral meningitis, which would have made a difference"
which is similar to an argument employed over here. As mentioned in my previous post, the vaccine is against type B meningococcal disease (the one that is epidemic here). But meningitis is actually a more complicated and can be caused by several other strains of N. meningitidis such as type A and type C. Now aside from the fact this sounds like an alphabet, this represents different strains of this organism, in other words there are [i]multiple[/i] kinds of this bacterium that cause this disease. The A, B and C refer to different surface antigens, of which different countries have had various outbreaks and vaccines made against them. As mentioned previously, the B type is particularly nasty, because its surface antigens are like ours and so it wasn't as simple to make a vaccine against. Finally, it can also be possible for certain viruses to cause meningitis as well.

So it's no real surprise when I saw a TV special from 60 minutes present a woman whose child had died of 'meningitis' with the implication the vaccine had failed. Obviously this was used by anti-vaccinists to proclaim the 'ineffectiveness' of the MenB vaccine. Of course, this misses a few points about the actual epidemiology of meningitis as a disease in New Zealand. For one, while we are mostly at risk from group B, there are also infections with group C that occur from time to time as well. In this particular instance, it was made clear in a TV program just the next night that this womans child had died from a group C organism*, and not the group B meningitis the vaccine is designed to protect against. Such shoddy reporting only serves to turn people off and convince them that the anti-vaccine lobby actually has some form of credibility.

It's also worth noting that the information that comes with the vaccine for parents explicitly states that it doesn't protect against other forms of meningitis, namely group A or C. Unfortunately, when asked if she had read the information in question the response was that it wasn't regarded as important. Clearly there is some degree of parental responsibility and possibly that of the ministry of health to make 100% sure that people understand the facts about vaccinations. Clear information regarding what vaccines do and don't do is important in fighting the anti-vaccine movement.

*Incidently, it is pretty clear that from between the two shows, 60minutes and her appearance the next night someone had informed her that the meningitis in question was entirely different than the one vaccinated against. Sadly, the damage had probably already been done by that point.

Saturday, June 18, 2005

Anti-vaccine nonsense.

While perusing the fine New Zealand news outlet TVOne, I came across an article about opposition to the new Meningococcal B vaccine that is currently being administered in New Zealand. The usual kind of objections seem to turn up, such as vapid claims the vaccine is not protective and that it is unsafe among other things. It turns out that the ministry of health has decided to fight back with its own advertising campaign (see previous link). Of course, with such wonderfully intelligent people as the NZ Green party, labelling the vaccine as 'untested', the same party that made a claim GE potatos would turn someones DNA into a potato and tried to ban dihydrogen monoxide; it is no wonder so many are confused. Other than showing the scientific illiteracy these people tend to have, it's also plain dangerous for such people to spread their nonsense.

Since 1991 here in New Zealand we've been in an epidemic of meningitis, caused by the organism Neisseria meningitidis which has killed 231 people and has badly infected many others. Unlike other strains that cause meningitis, the N. meningitidis that causes the disease here has surface antigens (the stuff we typically use in vaccines) that is extremely similar to those on our own cells. This means that it's not really suitable for a vaccine as it will cause an autoimmune disorder.

The solution was to copy what other countries had done in the past to combat their strains of MenB, using outer membrane vesicles that in the past have proved to be effective. Additionally, even though the precedent that this vaccine is safe and effective is going on, it is still being evaluated constantly and of course appears to be passing with flying colours. In all, the vaccine is very definitely well proven to be effective, safe and with the epidemic figures available I would definitely say it is worth it. I even know many people who have had the disease in the past with two of them nearly dying of it, which was quite traumatic for me I can assure you.

Now with the option of a vaccine, we see all the cranks come out of the woodwork. Although the spectacle of watching them generally flaunt their ignorance about the origins of the vaccine, how vaccines work and more is mere amusement to someone trained in immunology or any other medical field, to the general lay person they sound fairly convincing. When it comes to playing with peoples lives with utter nonsense you really do have to be worried. Some parents have already withdrawn their children from the immunisation campaign. Although they are lucky that compliance rates are high, around 89% so herd immunity should still apply, if mass people left the campaign things would fall apart fairly quickly. Worse, I hope that these withdawls are not concentrated in any particular area, which could lead to a small local outbreak among the non-immunised individuals.

Of course, while I write this it should be important to bear in mind that anti-vaccine cranks are nothing particularly new. The controversy over thimerosal in vaccines and autism, which has been thouroughly debunked over at another blog, is just one example (or here for more). These people however are not just a threat because they are intellectually dishonest, they are also a risk to public health and safety by spreading their inane rubbish. Once again, as scientists and medical practitioners it should be important to make sure the public knows the facts and to thouroughly (and publically) debunk anti-vaccine movement claims.

Thursday, June 16, 2005

I hope Terri Schiavo rests in peace.

Well the autopsy reports are out about Terri Schiavo and it turns out that the medical consensus she was in a PVS was right. Of course this doesn't really come as a surprise to me, as I never suspected any conspiracy and felt that the media attention on the families involved was the worst part. What a way to die in the midst of a media circus. I hope that doesn't occur to me. In any event, while I saw little point for the autopsy at least it has answered many questions. One interesting revelation is that it turns out she was technically blind, even though she appeared to be able to see people in the room. Neurotopia comes to the rescue with a good explanation:

Your eyes are free to be controlled by your brainstem's SC, meaning that when somebody enters the room, you'll look at them. (I know, it's creepy.) In fact, the brain is wired with all sorts of redundant, partially overlapping control mechanisms for virtually every type of stimulus, explaining why Terri would respond to sounds or touch in a jumpy fashion, as if surprised; her inhibitions were removed when her higher processing centers died, and all that was left were brainstem and spinal reflexes.

In the end, I have no idea why people disputed the consensus agreement of multiple neurosurgens who all personally examined her. Their complete agreement should have been enough to avoid ever having to bother with cutting up her brain to begin with. The only neurosurgen to my knowledge that concluded otherwise never personally examined her, merely 45 minutes of video tape from her parents (hand picked from hours of footage of course).

At least this puts all the conspiracy crap and such forth to rest.

Wednesday, June 15, 2005

My future answer to any question.

PZ Meyers has been ripping into several creationist arguments as of late over at his blog, with one of the many arguments around Adam being 15 feet tall and how humans have gotton shorter. The "evidence" presented in favour of this idea was:

" If you doubt this is possible, how is it there are PYGMIES + DWARFS?? "

Aside from being utterly non-sensical, it gave me an idea that I should answer future questions in this manner. For example; it is possible that pathogens may have evolved from non-pathogens. If you doubt this is possible, how is it there are PYGMIES + DWARFS??

Truly brilliant.

I've decided to make my mid-semester break reading project a book about the anti-genetic engineering arguments that are frequently used (my pet topic). Unfortunately this happens to be one area that like with the above quote where some really ridiculous assertions are made. One that I remember was an anti-GE lobbiest directly claiming that GE-potatos would cause peoples DNA to mutate into that of the potato. I really have to wonder where people come up with this stuff.

Friday, June 10, 2005

Year of the Zodiac (and stuff)

Although I don't really take much of an interest in astrology, zodiac signs and other such quackery, I did notice the description of the 'boar' that is supposedly my zodiac sign:
People born in the Year of the Pig are chivalrous and gallant. Whatever they do, they do with all their strength. For Boar Year people, there is no left or right and there is no retreat. They have tremendous fortitude and great honesty. They don’t make many friends but they make them for life, and anyone having a Boar Year friend is fortunate for they are extremely loyal. They don’t talk much but have a great thirst for knowledge. They study a great deal and are generally well informed. Boar people are quick tempered; yet they hate arguments and quarreling. They are kind to their loved ones. No matter how bad problems seem to be, Boar people try to work them out, honestly if sometimes impulsively. They are most compatible with Rabbits and Sheep.
Well, it's accurate in some ways but I love arguing with nearly everyone and anyone. I'm always amazed though at how seriously some people take this sort of thing however, even if it sometimes rings somewhat true. Got to put your faith in something I suppose.

Wednesday, June 08, 2005

Scientific Integrity II.

One area in science that possibly has the worst confidence from the public, particularly in New Zealand and in Europe is Genetic Engineering (GE). Genetic engineering has for some time now been demonised as being controlled mostly by greedy, monopolistic corporations that seem to be out to get everyone (including you!). With such a massive amount of distrust and the continual erosion of public confidence by some of the outright distortions of fact given by anti-GE proponents; you would not be fooled for thinking these companies would be highly rigourous in their methodology to keep what (little) public confidence there is.

Sadly once again, we see that the publics perception and confidence in science as a whole is shaken.
European regulators should pursue their own investigation into how the 'wrong' genetically modified corn was allowed on the market for years. Unfortunately, their US equivalents show little sign of rising to the challenge.

What happened here is that a breed of Bt10 corn that contains a gene for an insecticide produced by a bacterium, Bacillus thuringiensis and a gene for antibiotic resistance (ampicillin) was able to get onto the market. Although there is a legally available version of this crop, Bt11 that lacks the resistance gene, it went undetected for four years before anyone realised what was going wrong.

The obvious ramifications in this whole controversy is to make the companies involved look really stupid. If they are unable to tell what they are putting into their seeds, how are they to know what other components may or may not come along with their seeds? To the general publics perception this is probably going to be a disaster for those campaigning GE is a safe technology. This once again highlights the importance of scientific honesty and to be as transparent as possible about the methodology used to make these seeds.

In any event, we need to consider why this has caused such alarm within many in Europe. Although the insecticide is of debatable importance, the antibiotic ampicillin is still used in vetinary medicine in the UK (K. L. Goodyear et al. Journal of Antimicrobial Chemotherapy. 2004:54,959). The spread of the gene containing this resistance might spread to soil bacteria and then onto pathogens is a potential worry, according to Gundula Azeez in the letters page of Nature:
In addition, it is worth noting that the ampicillin-resistance gene in Bt10 maize and other genetically modified crops is a remnant of the bacterial plasmid inserted into these varieties, and would therefore function very efficiently if taken up by bacteria as a result of horizontal gene transfer.
Of course, if this was such a worry for the UK, then they are probably already in trouble.

Matthew Gibbs et al. Characterization of -Lactamases Responsible for Resistance to Extended-Spectrum Cephalosporins in Escherichia coli and Salmonella enterica Strains from Food-Producing Animals in the United Kingdom. Microbial Drug Resistance, 2004:10(1),1-9. Here in this paper it is reported that:
Synergism experiments with benzo(b)thiophene-2-boronic acid (BZBTH2B) and isoelectric focusing (IEF) revealed the presence of an AmpC -lactamase with a pI 9. amp C multiplex PCR, sequence, and Southern analyses indicated that only the Salmonella isolate had a plasmid-encoded AmpC -lactamase CMY-2 on a nonconjugative 60-MDa plasmid.
This is the first report of a CMY-2 Salmonella isolate in the United Kingdom. These data imply that -lactam resistance in animal isolates can be generated de novo as evidenced by the E. coli strains, or in the case of the Salmonella strains be the result of intercontinental transmission due to an acquired resistance mechanism.
So it appears that ampicillin resistance genes are already present in the UK and are already present in the food chain. Not to mention that these antibiotic resistance genes are arising not from HGT from this GE crop but they are arising from HGT from other strains in other countries. In short, if Ampicillin resistance, and indeed other antibiotic resistance is a considerable problem for the UK why are they still feeding antibiotics to farm animals as growth promotants? Not to mention that the anibiotics they are using aren't always stated either.

While I do think that the GE company here made a serious mistake in this case, I think there is a more direct and worrying source of antibiotic genes that needs attention. Rather than focusing on the 'coulds', 'ifs' and 'what abouts' of HGT from antibiotic resistance markers, perhaps we should be focusing on the 'definitely' of resistance arising from feeding animals antibiotics.

Tuesday, June 07, 2005

Scientific Integrity.

In relation to the earlier post, I'd like to elaborate a bit more on why it's important for scientists to write into journals such as Nature, so their work can be critiqued by other scientists. Science ultimately isn't magic, it relies on other groups being able to faithfully and accurately replicate the results of an experiment. If I discover nuclear fusion in my basement for example, it's important that I am able to tell other people how to replicate and verify that my claims are true. If it turns out that I'm full of rubbish, peer review is one of the most efficient ways of discovering this. This is because the real importance of peer review isn't so much as announcing what you have done; it's more important that your work can be analysed and criticised by other scientists.

Unfortunately, sometimes this system is abused and companies deliberately attempt to not put all of their results in for such examination. An example of this occurred when GlaxoSmithKline (GSK), a large pharmaceutical company, was sued for fraud based on accusations that it had not released all the results of it's clinical trials to the public. The drug in question was called paroxetine, which was originally made to treat depression but was found to be ineffective and to make matters worse, increased the chances of treated individuals committing suicide. The trial in question was not released however until they sought approval for using the drug to treat another disorder. This unleased a proverbial storm of criticism and undermined public confidence in pharmaceutical research, and very possibly scientific research in general.

In many respects, this has resulted in a general review of the peer review process, particularly in how 'transparent' drug companies are about publishing all of the results of their trials. This highlights the issue as to what scientists should be presenting for critique in the literature. Negative results may not always be useful, indeed it might not even be relevant to demonstrate every failed trial or no result that comes along. At the same time, such openness would at least provide a method for analysing the experimental techniques and increase public confidence in these companies.

Unfortunately, it doesn't appear as if the lessons that were learnt with paroxetine have been fully realised. A recent report in Nature noted:

Drug giants fail to name compounds in trial database.

But the editors say that drug firms are inserting a "meaningless phrase" instead of the names of drugs, so patients aren't getting the full picture, including any negative data.

The New England journal's editor-in-chief, Jeffrey Drazen, says that Merck, GlaxoSmithKline (GSK) and Pfizer in particular "didn't meet the sniff test" in a review conducted early this month by Deborah Zarin, the database's director. Zarin found that specific drug names were missing in scores of trials, which used the phrase "investigational drug" to describe their products. Drugs weren't named in 36% of 75 Pfizer studies reviewed, in 53% of 55 GSK trials, and in 90% of 132 Merck trials.

Once again casting doubt upon the integrity of the scientific process and if these companies are being readily transparent. It is vitally important, particularly in keeping the publics confidence, that results are made available and people know exactly what they are getting into with such trials. In the end however, it is ultimately on the scientific community to regulate and ensure that proper ethics and scientific standards are applied in drug trials, especially when individuals lives are at stake.

Conclusions first and research second!

Over at pharyngula, PZ Meyers has posted an interesting comic featuring a common theme that most creationists/ID supporters seem to possess: Making their conclusions first and then deny any evidence to the contrary. This reminds me particularly of William Dembski when he was caught deliberately abusing a quote from Peter Ward to support his 'conclusion' that the Cambrian explosion is a problem for evolution (no matter what evidence comes up). I'm certain that years from now Dembski and the other ID proponents will still claim it's a problem, much like how they continually trot out things such as Haeckels embryos as being an example of modern evolutionary 'deceit' (even though it isn't).

Just another difference between proper science and what is ultimately theology dressed up to look like science.

Speaking of creationists and fun with quotes, here's an interesting post at the Pandas Thumb showing Behe clearly digging the quote mines.

Monday, June 06, 2005

Firearms and harry potter!

I thought this delightfully odd.

Two British men were charged on Saturday with firearms offences after allegedly trying to sell a stolen copy of the new Harry Potter book to a tabloid newspaper before its release.
Maybe certain pressure groups are right when they say that books like Harry Potter are destroying society D:

From: TVNZ news

The United States is only a theory!

Saw this over at Stranger Fruit and thought it rather amusing:

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Teach the controversy!

AIDs in the news

Being a microbiologist and a scientist in general, I've always been fascinated with HIV. One of the worst diseases that anyone can get; HIV is a death sentence to anyone who gets the virus unless they are able to get a hold of anti-retroviral drugs. Unfortunately, these drugs are only distributed in relatively limited amounts and are only affordable for those in developed countries (generally). The majority of the people who are needing these drugs sadly don't get them. This is partly why I read with no real surprise that the HIV epidemic is still increasing: Action needed to stem AIDS pandemic.

Of the rather depressing report, I think this is one of the things that stood out most to me.

But it is being pressured by conservative religious groups toward abstinence-only programs and away from vulnerable groups like prostitutes, homosexuals and drug addicts.

While I agree that abstinence only campaigns are a method that could be used to stop HIV, it has been demonstrated to be looking through rose coloured glasses at best. When we're talking about a virus that kills several million people every year and is infecting more we should be focusing on the best treatments available, according to the medical establishment and not what peer groups can exert the most pressure. It disappoints me to see America, which was the country to make some of the most key breakthroughs with HIV, give in to individuals who do not have any practical knowledge of the situation and are not recommending the best way to really approach the AIDs epidemic.

Edit: Speaking of sexuality and general retardedness, I also saw this over at tvnz news. Another failure of the NZ education system.

Paranoia Agent (anime)

Today I'd like to talk about an extremely wierd anime series that I have been getting into over the past week or so called Paranoia Agent. This series is highly twisted, essentially involving a boy on skates that attacks people putting them in hospital. The general catch is that nobody is sure if he's really real or not, plus the fact that most of the 'victims' are all under extreme duress at the time. So far I've only got the first two DVDs but it's been really good and I recommend anyone to have a watch of it, even if you don't typically like anime.

Sunday, June 05, 2005

Bible under threat from another evilutionist materialist atheist (as always!)

PZ Meyers is threatening to do horrible things to a bible he has held captive if he doesn't get a few links over to his blog at pharyngula. While I wouldn't normally give in to such shamless threats, I felt it was just in the interest of the community as a whole to teach the controversy surrounding Meyers sinister plot.

(Note: it has been discovered that Meyers may not in fact have as weak a bladder as claimed, or that the threat is real. Our intelligence was picked up from the post 9-11 American administration after all).

First post on this whole blogging thing

Well I suppose seeing as lots of others are starting to get into this whole 'blogging' thing I might as well have a shot at it myself. This blog will have all sorts of wierd goings on, namely my occasional thoughts and philosophies on life, but mostly I will be talking about my keen interest on various scientific matters. See my 'about' page for more on me if you're feeling bored.