Tuesday, August 30, 2005

A cartoon that gets to the point

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Saw this originally at Stranger Fruit.

Famous dictators are rising from the dead!

First Orac makes an unsettling discovery when a rock turns out to be none other than the brain eating intelligent designer, the Hitler Zombie. To add to the trauma, Phil Plait discovers that his shower curtain has been hiding communists while he wasn't looking.

The only question is, who is next? Pol Pot? Ghengis Khan? Who knows, who knows.

Monday, August 29, 2005

Tuberculosis in Africa

Tuberculosis is one of those problems that many people just aren't aware of anymore. Certainly in modern developed countries, TB is almost non-existant these days as we're more than capable of detecting and then treating anyone who we see with the disease. This means there is a considerably low rate of disease in developed countries and it's well out of the minds of most people. Unfortunately, this isn't the case in the poorest places of the world such as Africa, which have been hard hit by famine and HIV.

Typically, you can live with the bacteria that cause tuberculosis, Mycobacterium tuberculosis rather well and it doesn't cause disease except in very rare cases. The general scientific consensus is that over 1/3 of the worlds population is actually infected with TB, yet not many people will actually die of the disease. This particular curiosity is what my research is about, in that it's hypothesised that certain mutations in immune receptors or cells causes certain individuals to be more likely to get full blown disease than others. While that hasn't been fully established yet, where you do get an increased source of mortality as the link to the BBC story above illustrates, is in the areas that are worst hit by malaria and also AIDS.

HIV, malaria and tuberculosis have an almost synergistic relationship despite being very different kinds of pathogens. HIV is a virus that infects the immune system, malaria is caused a protozoan parasite (Plasmodium falciparum), which infects red blood cells and tb is caused by the previously mentioned Mycobacterium tuberculosis that is commonly found in the lungs. By themselves, someone infected with one of these organisms is going to have a pretty hard time but together they exacerbate the chances of dying. For example, someone infected with AIDS has a considerably lower life expectancy, but someone infected with both AIDS and tuberculosis will die even earlier.

This is because all three pathogens, as part of their survivial strategy interfere with the normal function of the human immune system. Get them together in the same person and the resulting chaos on the immune system essentially ensures an extremely rapid death. This is a confounding problem that makes the current HIV/Malaria/TB epidemics in Africa even harder to treat and manage, because managing one disease only isn't likely to actually help the local population that much: one of the others will step in.

There are also other unfortunate realities which the BBC article also highlights:
There have been no new tests or treatments for TB developed in decades and the ones that are available are difficult to administer.
As I mentioned at the beginning, for the most part diseases like TB just aren't particularly prevelant in western societies. This means there really isn't much of a push from general medical establishments to come up with new treatments for diseases like tuberculosis: it's just not cost effective researching new treatments for an already 'cured' disease. This has made things difficult, because the current TB treatment is similar to the sort of thing you do for HIV: effectively bombard the organisms with a large amount of systemic antimycobacterial agents (like Isoniazad). This requires said individual to be carefully monitored however and generally dosed with fairly high concentrations of the drug on a regular basis.

You can probably picture that can be a problem in certain areas of Africa, where it can sometimes be difficult just reaching people let alone attempting to treat them. This doesn't mean that nobody is trying however, as there are moves to make an improved vaccine against the organism (using BCG, an attenuated form of Mycobacterium bovis, which is closely related to M. tuberculosis). It is just unfortunate that such improved vaccines are still a considerable period of time away and that the epidemic is still going to continue and probably increase.

Credentials this!

In the comments over at the Pandas Thumb about the recent developments surrounding Iowa University faculty asking the University Board to reject ID as science, after certain pro-ID comments by one of the astronomy professors Guillermo Gonzalez shows William A. Dembski (A leading ID proponent) having a bit of a bad day:
PvM: Do you have an anti-ID text generator? Plug in the names, places, and a few other specifics, and just let it run? Such a generator is easy enough to program since it depends on only two rules: First, if you criticize Darwinism or defend ID, it doesn’t matter how many credentials you have, or in what fields — you are by definition ignorant, stupid, insane or wicked (witness RS and GG). Second, if you defend Darwinism or criticize ID, it doesn’t matter whether you have minimal credentials in unrelated fields — or no credentials at all — you are licensed to spit on anyone in the first category. And get quoted as an authority in the mainstream media (witness NM).
The first thing is that he seems to make this an issue about credentials, which is typical of creationists who constantly appeal to their lists of scientists who reject evolution or similar (see here for one such scientist leaving one of their 'lists'). Ultimately, it's an irrelevant side issue and I don't regard that as being the most important issue. Sure, we can note that many ID proponents don't have degrees in a relevant field of biology, but this by itself doesn't make their arguments irrelevant or automatically without merit. All that matters is if their arguments can stack up under scrutiny and hold up scientifically.

ID arguments, like those in the Privileged Planet that Guillermo Gonzalez authored have had numerous arguments presented against it and cosomological ID (That the universe looks designed for life and discovery, note this isn't a biological ID argument). This is similar to the numerous critiques of both ID books and papers that have come out from the likes of William Dembski and Michael Behe. Unfortunately, rather than trying to work through the problems presented the ID movement seems to ignore the critical failings of its hypotheses and that they have a serious lack of hard verifiable data. Dembski in particular, seems to prefer comparing his critics to Russian leaders rather than bothering to address the actual science in the critiques of his work.

When scientists complain that ID is without merit and scientifically vacuous, they say so for precisely these reasons. ID proponents would sooner whine about credentials than actually address the scientific deficiencies and problems with their own arguments. They would sooner spend money on a political campaign, namely the 'teach the controversy' campaign and not on doing real research on making testable predictions using ID. ID is, in a word, scientifically vacuous and without merit because they simply refuse to do the same scientific process that everyone else has to do.

I'll leave this quote from Lenny Flank from the previously linked Pandas Thumb comments to sum up things appropriately:

Posted by 'Rev Dr' Lenny Flank

Posted by William Dembski

PvM: Do you have an anti-ID text generator?


Do you have a scientific theory of ID?


Game over.

Sunday, August 28, 2005

Rhetoric switch: The Game!

One of the old propaganda pieces published by the anti-MeNZB cranks had a paragraph, that now I think about it, sounds strangely familiar.
Science and medicine are by no means unanimous about vaccines. In fact, there is a long-running controversy about both the safety as well as the effectiveness of many vaccines. Many doctors and scientists believe that vaccines are generally safe and effective. However, many other doctors and scientists disagree. The safety and effectiveness of the NZ Meningococcal B vaccine are also now a matter of contention among doctors and health professionals.
This wouldn't look out of place in many other kinds of quackery press releases such as from the discovery institute (The Intelligent Design movement think tank). For example, I could see the DI using that statement with a few modifications, particularly as it already has the 'teach the controversy' slogan;
Scientists are by no means unanimous about evolution. In fact, there is a long-running controversy about both the theory as well as the importance of natural selection. Many scientists believe that evolution has generally occured. However, many other scientists disagree. The theory of evolution is now a matter of contention among scientists.
Hmmmm, not bad for just chopping out and inserting the odd word here and there. I wonder how it would do for those that deny HIV causes AIDS, let's have a look!
Science and medicine are by no means unanimous about AIDS. In fact, there is a long-running controversy about both the ability of HIV to cause AIDS as well as the effectiveness of HIV prevention methods. Many doctors and scientists believe that HIV is the cause of AIDS. However, many other doctors and scientists disagree. The ability for HIV to cause AIDS is now a matter of contention among doctors and health professionals.
Hey, this is pretty easy! It's no wonder you get so many similar sounding kinds of statements from various groups pushing crank theories, they probably all steal eachothers statements and change a few words around. Sure beats having to come up with something new each time.

How to respond to critics

I think certain individuals, like William A. Dembski from the ID movement could learn a lot about how to respond to criticism from Elizabeth Lloyd. E. Lloyd wrote a book called The Case for the Female Orgasm, which explores the possible evolutionary mechanisms that might account for what it is. Unfortunately, this generated a wide degree and array of criticism from many feminists who sought to label her all sorts of unflattering things. Her response to many of these criticisms is very rational and she handles things extremely well, especially as many of Lloyds critics demonstrate they haven't read the book to begin with.
As I point out in the book, feminists who claim that the byproduct account “belittles” or “diminishes” female orgasm - simply in virtue of its evolutionary origin - are succumbing to the archest of arch-adaptationism. They appear to be saying that orgasm *needs* to be an adaptation in order to be culturally important. But we’ve already noted that we don’t accept that reasoning in everyday life - so why should we make an exception for female orgasm? Besides, the evolutionary research program of adaptationism has absolutely nothing to recommend it to feminists. But if there are no legitimate grounds for the feminist inferences, above - that my account makes female orgasm “unimportant” - what are these bloggers and journalists doing?
The whole thing, including links, is well worth reading. I think this should be held up as a model reply to criticism, due to how polite and well reasoned it was, even if the critics in this case did not have a reasonable foundation for their arguments.

Saturday, August 27, 2005

American Thinker Article Dismantled

Over at Evolutionblog, Jason takes the time to dismantle this piece from the American thinker.
As it happens, however, anyone familiar with the literature of “Scientific Creationism” will recognize that the arguments of ID's are different only in style, not in substance, from those of the YEC's. Furthermore, ID hit the scene shortly after YEC suffered several court defeats during the eighties. And considering the copious writings from the Discovery Institute and leading ID proponents about wanting to destroy naturalism and restore their version of a Christian worldview to intellectual respectability, it is not at all unfair to describe ID as a form of creationism.
Also, let's not forget that the original version of the Intelligent Design 'textbook' Of Pandas and People originally used the word creationism. This was later replaced with 'intelligent design' after creationism was smacked around in the US courts in order to get around this little problem. Really, despite what the Discovery Institute and the likes of the author of the American Thinkers article would have you believe, the current ID movement is nothing more than redressed up creationism. Simply because there were previous notions of 'design' in nature doesn't change the origin or general character of the current ID movement.

Friday, August 26, 2005

A tale of two gases

As our understanding of the natural world around us grows, we often find things that are distinctly surprising to say the least. Firstly, Nature has a news item discussing a paper from a Swedish group that looked to see if trees actually take up excess CO2 (one of those gases that is important in the greenhouse effect), which as plants use CO2 to 'breathe' they figured would grow better with excess CO2. It turns out that really isn't the case,
The team artificially created sustained carbon-dioxide-rich conditions in the patch measuring 500 square metres by spraying pure carbon dioxide into the canopy of about a dozen mature deciduous trees. Each day during the six-month annual growth season, the scientists sprayed two tons of extra carbon dioxide, from industrial waste, into the canopy. This simulated an atmosphere loaded with about 530 ppm of carbon dioxide, roughly 1.5 times what exists today.

But after four years the researchers found no signs of enhanced biomass growth in stems or leaves, they report in Science1. The trees had merely pumped the extra carbon through their bodies, quickly re-releasing it through root and soil microbe respiration; there was no lasting effect on growth and photosynthesis.
Which is a bit of a bummer, although it will be good if it turns out that the excess CO2 is stored by soil microbes (possibly used up, some bacteria can use CO2 in their metabolism, much like plants). On the other hand however, a group working on methane, a gas even worse than CO2 in terms of the greenhouse effect, found that despite the large amounts of methane produced by swamps, the majority of it is actually retained rather than being a massive production house of the gas. The reason why?
A clue comes from the fact that most of the carbon in peat bogs ends up in the form of peat, an accumulation of dead sphagnum moss. The methane discrepancy could be explained if the living moss plants gobble up the gas as it's produced. But one snag in this explanation is that plants don't have the biochemical tricks needed to oxidize methane into a form they could use for energy.

Suspecting that the moss may be getting help from a microbe, a team led by Jaap Damsté and Marc Strous, microbiologists at Radboud University in Nijmegen, the Netherlands, and the Royal Netherlands Institute for Sea Research in Den Burg, respectively, gave moss plants a vigorous washing and then probed them for the presence of bacterial RNA. Sure enough, they found telltale sequences of methane-munching bacteria and also found dense clusters of the bacteria within the plant's tissue.
Once again, life manages to make use of things in equilibrium despite what may seem intuitive to us. The trees and plants from the nature news item didn't appear to get any particular benefit out of using excess carbon. This is probably because things are similar to the scenario in the peat bog. The amount of total excess carbon has been produced in an equilibrium with the amount being lost for a considerable amount of time and the natural environment has become 'used' to that scenario. Excess carbon is merely kicked out, rather than being used because the plants and trees in the ecosystem aren't really metabolically 'geared up' so to speak to be able to use that carbon. Given time and assuming that using the excess CO2 would provide an appropriate selection pressure, plants and microbes may develop means to use the excess CO2 more effectively.

This is similar to what has happened in the peat bog, over evolutionary time bacteria in that environment have had the selective pressure and time to be able to use the methane that is produced, ensuring that excess methane isn't spat out into the environment and things are pretty much in balance. The question that should be important to us, especially as we're the ones who are increasing the amounts of greenhouse gases in the environment, is how quickly can bacteria/plants adapt to make use of the excess gases (bring things back to a sort of balance) we are providing and can they do it before any damage is done?

Thursday, August 25, 2005

One scientist sees through the ruse

Anti-evolution groups like the Discovery Institute in America, like to compile lists of scientists that apparently 'disagree' with evolution. Apparently, this gives them some sort of credibility because rather than bother to do any actual science and publish in journals, the way anyone else proposes their new ideas to the scientific community, the DI thinks it can get away with propaganda and politics. We'll note here, that most of the scientists on the list don't have degrees in biology, making it about as useful as a list of biologists who think astronomy should give credence to the 'theories' in astronomy. Unfortunately, one of the members of their 'list' has realised the entire thing is a sham and has decided to have his name removed.
But I bring you Davidson's views because I suspect he is a bellwether for the Discovery Institute and intelligent design, as more scientists learn about them. He was attracted to an institute that embraced both science and religion, yet he found its critique of existing science wrong and its new theory empty.
The best thing about this article is the conclusion, which is just fantastic:

Science is about measuring things, and God is immeasurable, the pastor said.

"It just clicked with me that this whole movement is wrongheaded on all counts," Davidson said. "It's a misuse of science, and a misuse of religion.

"Why can't we just keep the two separate?"

That's a good question, especially coming from someone who believes strongly in both.

I wish this sort of common sense was used more often.

German Green Party

It's always interesting to see how other countries political climates sometimes match our own at times. In Germany for example, it appears that the German green party isn't going to get back into parliament. Nature has posted an article on the German Greens and how they stood with numerous issues in science. Some of it was good, such as increased funding for biodiversity, new energy sources and other projects but sometimes blind ideology got in the way of good science.

For example:

The same applies to plant biotechnology. Although Germany iswell positioned in plant genetics, the restrictive regulatory framework set up by Künast makes it difficult to reap the benefits of basic research. Recently proposed liability rules are far stricter than anywhere else in the European Union and will deter investors. If the law passes, Germany could suffer the same fate in its crop trade as it did in the past with genetically engineered drugs. For example, despite its strong pharmaceutical industry, Germany has to import insulin.

Which is quite familiar in many ways to me. For example, here in New Zealand we lead the world in aspects of farming technology, animal genetics and environmental science. I believe we were the first to discover and improve the ability of certain bacteria to digest DDE (the dangerous form of the infamous insecticide DDT once it has sat in soil for a bit). Despite our 'clean' image that we portray overseas, there are vast dumps of this chemical buried all over certain places in New Zealand. These bacteria, engineered as they are, would be immensely useful in being able to break down and detoxify the DDE in the contaminated areas. Unfortunately, we are unable to reap the benefits of our own technology because of overly restrictive and completely idiosyncratic rules about releasing GE organisms (even if this organism has had no new genes added to it at all, merely a change in the genes regulation). These regulations are largely driven by the New Zealand Green Party, who have often demonstrated they don't really know much about the science of genetic engineering.

Interestingly enough, the Green party over here has a good chance of failing to get back into Parliament as well.

Wednesday, August 24, 2005

Updating Germ Theory

Everything I've learned in microbiology is evidently a great atheistic materialistic lie and that I've been duped by the king of dupers Louis Pasteur! I'll let this site, that really should be used to teach the controversy as it emerges, that opened my eyes to the truth open yours!
Pasteur continued to adhere to the idea of Monomorphism, the belief that all microbes and bacteria have only one form. Beauchamp was able to prove, however, the existence of Pleomorphism, that microbes can alter their form to appear as different germs. This discovery was confirmed by many scientists that came after Beauchamp, including Gunther Enderlein.

In his experiments, Enderlein found that every living cell contains two distinct kinds of microorganisms called endobionts (which means "inside life"). These microorganisms live inside the cell and cannot be removed from it. They play an important role in cellular health. The state of a person's health is determined by the stage of development of these organisms. Enderlein found that all microbes that live permanently in our bodies go through three stages:

The Primitive Stage (microbe)
The Middle Stage (bacteria)
The End Stage (fungus)

Other scientists were later able to confirm that there was a fourth stage which occurs only after extreme toxicity in which the fungus goes through a transformation, mutating into the Virus.

It's so obvious!

[Note, the author of this post cannot be held accountable for any irony meters lost]

Sunday, August 21, 2005

Ancient Pathogens

Science has an interesting article about a paper from PLoS Pathogens that has reanalysed the tuberculosis complex.
Tuberculosis (TB), an infectious disease that damages the lungs and kills approximately 2 million people each year, is caused by thousands of extremely closely related strains of bacteria collectively known as the Mycobacterium tuberculosis complex (MTBC). Their remarkable lack of genetic variation led researchers to propose that MTBC members are all the progeny of a single bug that flourished worldwide between 20,000 and 35,000 years ago. But a unique TB strain found in Africa in 1997 made some researchers wonder whether the bugs were really as homogenous, and thus as young, as scientists had believed.
Interestingly, they found that the organisms that cause tuberculosis might be even older than 35,000 years, possibly having spread to humans as early as three million years ago. That's been a long time to have gotton aquainted with us. It's interesting to note that Mycobacterium bovis, which infects farmed animals dates back roughly to the time we domesticated animals proving that for a change, we gave one of our pathogens to an animal and not the other way around.

Thursday, August 18, 2005

Selling Tamiflu over the counter

With the looming potential of an outbreak of influenza H5N1, it should be important for health officials to remain calm and not do anything particularly silly. Unfortunately, it looks like someone may be thinking of doing just that and may in fact end up throwing one of our main anti-viral drugs out for public sale (not by prescription)
A medical committee has delayed a decision on whether an anti-flu drug can be sold over the counter, while it investigates the safety of such a move.
While this may seem like a reasonable decision, it's overall far too dangerous if we just allow people to buy an important anti-viral drug simply willy nilly. Viruses, especially viruses like influenza are just like bacteria in terms of being able to develop new forms of resistance to the drugs we use to treat them with. For example, there are already strains of influenza resistant to the drug amantadine due to feeding it without proper regulations and restrictions to chickens in China. In the event of an outbreak, where developing a vaccine in time may not be possible we are going to be relying on drugs like amantadine and tamiflu to stem the tide and protect those most vulnerable. If we're just going to throw these into an unrestricted environment where people may irresponsibly breed resistance, just like what was experienced with the over prescription of antibiotics, we are just going to be ensuring that more coffins will be required if it does get to the point of a pandemic.

Crocodile serum to cure HIV?

Reuters have come out with a fascinating article that crocodile serum may yield powerful new 'antibiotics'. Aside from the obvious nitpick, that crocodiles are clearly not microbes, which makes the concept of them providing new antibiotics somewhat odd, there are some extremely unusual claims made by one of the researchers involved.

The first thing that should be noted from the article, is that the majority of the work has been done on the North American Alligator Alligator mississippiensis by Mark Merchant (see below references) and they have found its serum is rather good at killing HIV. Unfortunately, it also happens to be toxic to the cells you are trying to treat too:
Higher serum concentrations (50% serum) reduced cell viability by
60%, while the anti-WNV effect was reduced to 32%. The full potential of the anti-WNV properties of alligator serum are difficult to evaluate due to the toxicity of the serum toward the Vero cells(1). [emphasis mine]
It's a treatment that would not only take out the virus but indiscriminately kill the patients cells in a non-specific manner. In a test tube they've had some wonderful results, but the actual useage of putting this into a treatment you can give to patients, immunocompromised patients at that, is highly suspect. That is probably why they have concluded the piece as follows
However, the crocodile's immune system may be too powerful for humans and may need to be synthesized for human consumption.
May, as we will see, is quite an understatement.

Sometimes you have to wonder why the media ask the wrong people about things, for example I don't see why they didn't continue to query Mark Merchant about this research (who has done the majority of it) and instead where they dug up this Britton fellow.
Initial studies of the crocodile immune system in 1998 found that several proteins (antibodies) in the reptile's blood killed bacteria that were resistant to penicillin, such as Staphylococcus aureus or golden staph, Australian scientist Adam Britton told Reuters on Tuesday
No duh. Antibodies do not function in the same way that antibiotics like penicillin do. Penicillin compromises the bacterial cell wall by inhibiting enzymes called transpeptidases, gradually causing the wall to become structurally unstable and the bacterium to explode from building internal pressure. Antibodies however work differently, they are produced and bind to certain structures on the surface of the organism. Once bound, antibodies function to lyse the cell through complement or to function as an 'eat me' signal for other cells.

The comparison is simply nonsensical. He might as well have compared deaths from heart attacks to deaths by being hit by a large asteroid as being equivalent.
"If you take a test tube of HIV and add crocodile serum it will have a greater effect than human serum. It can kill a much greater number of HIV viral organisms," Britton said from Darwin's Crocodylus Park, a tourism park and research center.
And most other things too, including cells you aren't particularly wanting to destroy. The positive thing of course, is that this can be up to 10x more effective than the human immune system, it's just not as specific. The advantage with using antibiotics made by microbes, is these are pretty specific for targets on other microbes and are generally not going to recognise and react with human 'bits' (some exceptions do exist).
Britton said the crocodile immune system worked differently from the human system by directly attacking bacteria immediately an infection occurred in the body.
Except the human immune system is perfectly capable of doing this and does. Complement, neutrophils and many other aspects of the immune system are immediately around to attack and attempt to destroy invaders right from the outset. It takes specific virulence factors to get around these mechanisms to even begin establishing any meaningful infection to begin with. This is because the innate vertebrate immune system is prepared to fight immediately. If it didn't we'd be in a lot of trouble.

What the difference actually occurs in is that crocodilian serum factors like complement, have a much higher binding affinity than human complement and have a wider range (not as specific). Additionally, I would probably hypothesise that their convertases, the enzymes that make complement proteins turn into lethal killers, are 'simpler' to make and hence destroy the bacterial cells. As Mark Merchant summarises from another paper (2) :
The antibacterial activities occurred relatively quickly in vitro, with significant activity occurring within 5 min of inoculation with E. coli and maximal activity at 20 min. Also, the antimicrobial activity exhibited temperature dependence, with a substantial decrease in activity below 15 degrees C. These data suggest that the antimicrobial properties of alligator serum may be due to an active serum complement system (2)

Both systems have mechanisms for 'immediately' attacking bacteria, it seems clear at the moment that crocodiles are extremely good at doing this (which, given what they encounter in the environment makes perfect sense).
"We may be able to have antibiotics that you take orally, potentially also antibiotics that you could run topically on wounds, say diabetic ulcer wounds; burn patients often have their skin infected and things like that," said Merchant.
Antibiotics are molecules produced by microorganisms like bacteria and fungi, to either kill or restrict the growth of other microorganisms. It's rather bizzaire that Dr. Merchant would describe using crocodile serum as an 'antibiotic', even if I can appreciate what message he was trying to convey, but it's not technically accurate to call it an antibiotic. I wouldn't want to be injecting this stuff into people, because aside from its potential general toxicity, it may also be reacted to by the human immune system and be only very limited in use (one use then it's stuffed effectively). This is because the antibodies in the serum are themselves recognised by the human immune system and will be eliminated the next time they are encountered: reducing their effectiveness.

It has potential, but there are numerous drawbacks to using this as a potential treatment for anything to be overly optimistic right now.

(1) Merchant ME, Pallansch M, Paulman RL, Wells JB, Nalca A and Ptak R (2005). Antiviral activity of serum from the American alligator (Alligator mississippiensis). Antiviral Research, 66(1):35-8.

(2) Merchant ME, Roche C, Elsey RM, Prudhomme J (2003). Antibacterial properties of serum from the American alligator (Alligator mississippiensis). Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 136(3):505-13.

Wednesday, August 17, 2005

Prepare your irony meters...

From scoop, the same website that often posts the various diatribes of Ron Law comes this little gem:
Paediatric pneumonia is more common here than in other industralised countries and a poor record of immunisation translates into high incidence rates of pertussis - a disease which has now reached epidemic proportions.
With people spreading pure nonsense about how vaccines work and are produced like Ron Law, is there really any wonder as to why rates are so poor?

Tuesday, August 16, 2005

The problems with antibiotics

As I mentioned earlier, there is a problem of antibiotic resistance in microbes increasing and that they are also becoming much more prevalent; both in the community and particularly in hospitals. Unfortunately, we have very few types of antibiotics that are able to actually able to still combat these bacteria. There are two reasons for this problem overall:

The first is that antibiotics were originally derived from microorganisms like soil bacteria and fungi, that have co-evolved with their enemies for billions of years. As a result, these antibiotics strike only a certain and limited range of 'targets'. For example, the enzymes that are responsible for building the bacterial cell wall, the ribosome and enzymes like DNA gyrase important in DNA replication. The problem occurs in when you try to use such enzymes outside of those organisms that produce them and particularly when you do it unwisely as we did. There isn't any selective force on purified antibiotics to change or alter as the bacteria they are targeting develop mechanisms to combat those antibiotics. Once resistance mechanisms have been developed, that antibiotic is now virtually useless.

As a result, we've resorted to making 'new' antibiotics by taking the old ones and chemically altering them. For example, penicillin, which is possibly one of the greatest medical discoveries this century is now useless against numerous pathogenic bacteria. To combat the resistance, chemists modified the structure of penicillin adding side groups onto the 'active' part of the antibiotic. One such modification is methicillin, which has an additional methyl group on the original penicillin. Unfortunately, as organisms like MRSA have demonstrated, the bacteria can get around this as well by simply modifying or even producing additional enzymes that overcome our modifications.

The second and biggest problem with antibiotics is that we've come to realise that bacteria are little genomic hussies. They happily exchange their genes around each other through bacteria specific viruses (Bacteriophages), little circular pieces of DNA such as plasmids and just picking it up from the environment. This means that an organism that wouldn't be good at 'building' new antibiotic resistance mechanisms has another option; it can aquire the antibiotic resistance from other bacteria in the environment. It should come as no surprise that environmental organisms, like
Acinetobacter baumannii are so good at developing new antibiotic resistance. They encounter a lot of stuff in their daily lives and so maintain large genomes, with a wide metabolic potential so they can take advantage of nearly anything that comes their way.

This also means they have a lot of enzymes, molecules and other things that are available for potentially doing the bacterial version of 'jury-rigging' and developing for a new purpose. Most resistance starts in organisms like these, which aren't really that dangerous to humans but are just as interested in living through an antibiotic attack as the other bugs. Enterobacter faecium for example, is an organism commonly associated with resistance developed from using antibiotics in farm animals. Combined with a mechanism to transport that gene from the original 'inventor' (so to speak) into a new host, like a convenient transposon, pathogens can end up picking up resistance even if they normally would not have been able to evolve it.

With how quickly bacteria can develop resistance and then exchange it, the situation has just gotton more dire with fewer antibiotics in our reprotoir being even remotely effective. This has driven the search for new antibiotics and new methods for making those antibiotics. The technique being used now is to randomly 'stick' different parts of the protein together like lego, and is being used in bacteria to produce novel antibiotics:

To achieve this, Santi's team added special sequences to the ends of their genetic fragments that in turn made the protein fragments 'sticky'. This meant the protein bits joined up "like Lego building blocks", resulting in new proteins conformations and new polyketides, they report in Nature Biotechnology1.
Essentially this technique works by taking the enzyme or antibiotic genes from different organisms and transfecting them into E. coli. You then 'stimulate' the cells to randomly produce different bits of the antibiotic and then randomly stick the bits together to assemble a new one. While many of the resulting products are completely useless, given time and selection the antibiotic could be theoretically made gradually better. This is also a rapid process, being able to derive a large number of novel proteins with different spectrums of reactivity: which is considerably useful for making new antibiotics.

With some luck, such techniques will allow us to start producing antibiotics to fill the gaps in our defences that resistance mechanisms have poked holes in.

Monday, August 15, 2005

Twisting the truth about MeNZB

Scoop provides a moment of hillarity with this disclaimer about a talk Ron Law will be giving tommorow in Christchurch
Please note: Ron Law is not pursuing an anti-vaccination agenda, but rather is drawing the public’s attention to important information required to make a truly informed decision regarding the MeNZB™ vaccine. Ron’s presentation is solely about the MeNZB™ vaccine and meningococcal disease in New Zealand.
This is why he deliberately misrepresents scientific data? This is why he makes absurd claims that because the vaccine hasn't gone through a phase III trial it's untested and children are being used as medical experiments? Why he claims the vaccine has not been effective, yet the latest epidemiological data supports that notion?

His 'agenda' is certainly not easily described as an anti-vaccination agenda I guess. His agenda is clearly to lie about basic facts and manipulate the truth to try and hawk his [incorrect] point of view. I wouldn't call that an anti-vaccination agenda, I'd just call it lying.

Sunday, August 14, 2005

Environmental Wierdness II

First we have the nuclear disaster at Chernobyl helping to increase the local biodiversity around the area, it turns out that Nature follows it up by reporting a study that found military training grounds have higher biodiversity than the nature reserves around it;
"[Tanks] replace to some degree the processes that have been stopped," Warren says. The same goes for fires caused by bombing. "We've trained generations of people that fire is bad," he says, "but in fact it's crucial for ecosystems."
I think this is an interesting point that has been made. In an attempt to 'save' the environment we've prevented what are natural events from occuring. Fires, floods and other means of destruction are processes that shape and remodel the environment. As opinion has changed in ecology over the years, it's been found more and more that areas that go without high amounts of disruption are actually worse off than those without. It may seem completely silly that areas that have nuclear disruption, military blasts and vehicles being moved through it would be doing better for endangered species than ones without but this does seem to be the case. It's probable that many of those species are endangered because we are denying them habitats they would get after natural disasters cleansed the area.

In many respects, by attempting to save the environment we are possibly reducing the total biodiversity and as the authors conclude, human activities that disrupt portions of it like a military testing range actually help. This doesn't mean we should go around blowing holes in every forest however or getting the military to declare war on Jellystone park. Though then again, I have heard that Yogi Bear does have stocks of PBMDs (Picnic Baskets of Mass Destruction).

Friday, August 12, 2005

Science blogging

Living the scientific life has an interesting article on the increasing interest in science blogs, particularly in the number of science blogs written by actual scientists. It's a good read and they made a lot of good points.

Thursday, August 11, 2005

Another emerging superbug

Acinetobacter baumannii is probably not a name many would associate with the current lot of 'superbugs' such as methicilling resistant Staphylococcus aureus (MRSA). As it turns out, this bacterium, normally content to live in soil and water is becoming a considerable threat to those in hospitals. In particular the bacterium is good at infecting people in the intensive care ward and unfortunately has a fairly high rate of infection, up to 40%. Additionally, the bug appears to be fairly wide spread having been noticed infecting US army soldiers to being found in numerous hospitals in London.

Once again it's a familiar story. Overuse of antibiotics encourages the development and maintenance of resistance in A. baumannii, which appears to be both extremely good at aquiring new resistance and appears to also bring existing resistance mechanisms (enzymes) with it. Additionally, unlike other superbugs like MRSA, A. baumannii doesn't tend to be easily controlled by hygeine practices as it's quite capable of living on plastics or other surfaces that are normally hostile to other bacteria.

There is one thing to be thankful for however, A. baumannii unlike MRSA isn't well adapted to living in the community and out of the hospital. Additionally, it doesn't have the virulence characteristics needed to cause infections in healthy non-immunocompromised people, which is largely the reason this has become known from hospitals where the highest numbers of immunocompromised people would be found.

Anti-GE proponents suffer another blow

One of the most common talking points you get from those opposed to GE is the supposed 'destruction' of wild Mexican maize by transgenes that were introduced into the country. This comes from a paper published in Nature (D. Quist and I. H. Chapela Nature 2001, 414:541–543) originally, where the authors claimed they could detect transgenes in wild maize and not only that, but claimed that the transgenes in question were entrenched in the genomes and were essentially permanent. This predictably caused a considerable row and the paper was crucified in Nature with criticism of the inverse PCR technique used to detect the transgenes being heavy.

Now Nature reports that the original work has been replicated by other researchers, attempting to find two of the transgenes that were reportedly found in the original research. The new paper by S. Ortiz-García et al in PNAS found that there were no transgenes at all in the seeds that they tested (150,000 seeds). This result essentially buries Quist and Chapelas claim that the transgenes were 'entrenched' in the Mexican maize population and will be yet another drawback for the anti-GE lobbies crusade. I would of course expect, that if Greenpeace were being honest about GE they would immediately retract claims made in this piece on the risks of importing GE maize into Mexico:
Further proof of contamination came on 29 November 2001 when the journal, Nature, published research by David Quist and Dr. Ignacio Chapela providing detailed scientific information on the contamination of native maizes by transgenic maize genes (transgenes) in Oaxaca. Dr. Chapela, a professor at the University of California at Berkeley confirmed:
Noting particularly the lack of discussion given in the greenpeace document to the problems other researchers had with the Quist and Chapelas papers methodology, not to mention that Nature released a statement that they would have not published the paper had their reviewers been aware of such problems. With the collapse of this paper and the lack of detectable 'entrenched' transgene contamination of wild maize the remainder of the arguments in that news release also collapse. As it always seems to end, doing repeatable science and properly testing hypotheses before making ill-supported alarmist claims wins once again.

Wednesday, August 10, 2005

Nuclear Fallout for...improving the environment?!

This is just amazing
Chernobyl's ecosystems seem to be bouncing back, 19 years after the region was blasted with radiation from the ill-fated reactor. Researchers who have surveyed the land around the old nuclear power plant in present-day Ukraine say that biodiversity is actually higher than before the disaster.
Life once again manages to trump humanity.

Tuesday, August 09, 2005

Epidemic among possums- go pathogen go!

Although new emergent diseases are often horrible things and something to worry about, every so often the little microbial invaders do manage to get it right. In this case, a mysterious epidemic of an unknown pathogen has been killing possums.

"While the suspected disease appears to affect only possums at this stage, we strongly recommend that people wear gloves if handling them," DOC Otago Conservancy animal pest ranger Bruce Kyle said today.

"It does not appear to have affected livestock or other wildlife, so it looks like a possum-specific disease at this stage."

Possums are probably one of the worst things to ever come to New Zealand. They destroy thousands of hectares worth of forest and like many introduced animals are also opportunistic predators of the indigenous wildlife, particularly our native birds. It's encouraging to see a new pathogen develop among these animals as a result, because it provides the promise of being able to drop possum numbers considerably and bring previously out of control populations to a manageable number.

Of course, this really isn't something that should be surprising. When a population gets to a large enough number, there is a considerable selection pressure applied on numerous microbes to take advantage of the new 'ecology' that has opened up as a result. With possum densities as they are, such a new pathogen wouldn't find things to difficult to spread to new individuals and further selection for higher virulence would be the result. Both of these phenomena are already well established in human pathogens, for example emerging new viral diseases such as HIV and the dramatic increase in virulence of Vibrio cholerae after a water treatment plant broke down.

Overall with a bit of luck, this new organism will be able to ravage the possum population and bring numbers down to at least somewhat manageable levels.

Monday, August 08, 2005

MeNZB and Phase III trials

One of the more common things you hear and read in the news from certain 'individuals' is the problem that MeNZB has that it hasn't been subjected to a phase III clinical trial. This is harped on repeatedly like it's some sort of damning point against the use of the vaccine - the implication being of course that it is insufficiently tested and potentially harmful as a result. Unfortunately, as always this point is rather moot and in fact doesn't actually apply to the situation in New Zealand to begin with.

Firstly, the obvious question to answer is to actually define what a phase III clinical trial is to begin with. When we are talking about a phase III trial, we're asking a basic question of how well does this thing work? In other words, the goal of a phase III trial is to establish the efficacy of the treatment in question by comparing a group of people that you vaccinate with a group that you deliberately didn't vaccinate. If much less people in the vaccinated group get the disease compared to the unvaccinated group you can say that the treatment did its job. On the other hand, if the disease rate is the same then you can establish that the vaccine probably isn't going to work.

Seems like good common sense doesn't it? So why wasn't a phase III clinical trial done for MeNZB in New Zealand?

Firstly, there are in fact several vaccines that are similar to MeNZB being used at the moment, including the 'parent' vaccine that MeNZB was based on that was developed in Norway. The Norway outer membrane vesicle (OMV) vaccine had a large phase III trial performed on it with a high efficacy of the vaccine, around 87% after 10 months. This was performed on teenagers and was only done with two shots of the vaccine (we are using three, due to the 'memory' of the response waning after 3 years from only two doses so a third was added). Ultimately however, the Norweigan vaccine was never actually used in the general populace although for different reasons that Ron Law et al would have you believe.

The epidemic that Norway had been experiencing of the time from their Meningococcal B strain had clearly begun to come to its end point. It's worth noting that this was after a considerable period of time, 19 years, which is one of the reasons we are bringing out the MeNZB vaccine quickly because epidemics of Meningococcal B do tend to last a considerable amount of time. The second reason was the lab that made the Norweigan vaccine shut down, not because the vaccine was shown to be ineffective but simply because there wasn't any market for the vaccine (as the epidemic had begun to die down).

Despite this, the fact a phase III trial has already been done on the parent vaccine establishes very clearly that the current MeNZB vaccine doesn't require this to be done on it specifically. The only considerable difference between the Norweigan vaccine and MeNZB is the antigen (the bit the immune system responds to in the vaccine) is different: the two vaccines were produced in the same way. Another vaccine we use every year, that also only undergoes a change in the antigen inserted but doesn't have a phase III trial with each release is the influenza vaccine. Conceptually, there is little difference between the concept behind the MeNZB vaccine and changing the antigens in the influenza vaccine every year except that certain groups complain about one and not the other. At the very least, they could be consistent and demand that the flu shot go through a phase III clinical trial every year as well.

The final point is one ultimately about ethics. We are at the moment in an epidemic from a disease that either has an extremely high chance of causing permanent disabilities or even death in those that get it. Preventing the vaccine from being given to one group of people and not another, considering that we have data that indicates the vaccine works, would technically make the researchers directly responsible for anyone killed/disabled in the group that didn't get the vaccine. Ultimately, if we use the vaccine now with good scientific data indicating this will be an effective treatment we should use it. At worst, we've lost a few million dollars but at best we've saved peoples lives. I know which option I prefer.

So ultimately, when you hear the anti-vaccine lobbies general rhetoric on the lack of a phase III clinical trial it's probably because they haven't a clue what one is.

Sunday, August 07, 2005

Hummingbird vs. Mantis

This is insanely wierd, a Preying Mantis managed to catch and actually kill a hummingbird then devoured it until it had its fill. Just goes to show you that you should never ever underestimate the little guy.

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Go to Bird Watchers Digest for more to the story and more pictures. Hat tip to PZ Meyers at Pharyngula, who also understands our insect overlords will soon dominate us, where I originally saw the link.

Father Greely gets it right

In an article from the chicago times, Father Andrew Greely demonstrates his take on Cardinal Schoenborns recent comments about evolution where it was implied we must accept 'design' in nature and anything else is unscientific. I think this is a very good article and he certainly puts the issue into good perspective.

IT appears now that that Cardinal Christoph Schoenborn of Vienna, a student of the current pope, a man with considerable clout at the Vatican, and a likely heir apparent, has intervened in a New York Times article in which he seems to say that Catholics must believe that God's design directs the evolutionary process and thus apparently putting them on the side of the Evangelicals. The cardinal also dismissed Pope John Paul II's comments on the issue as being "vague and unimportant" -- something he would never dare to say while the pope was still alive.

Unless I misunderstand the cardinal completely, he is saying that Catholics must believe that God works within the evolutionary process directing it and guiding it. With all due respect to the cardinal, I don't think that's true. Catholics have to believe that God created everything and set the various natural processes in motion (and sustains the cosmos in existance), but we do not have to believe that God is intervening constantly in the processes, fiddling with them, as it were, to make sure of the outcomes. God did not have to interfere with the results of the Big Bang to make sure that life would be possible on Earth. Rather the biopolymers were inherent in the Bang itself.

Friday, August 05, 2005


It appears that the MeNZB vaccine is having an effect with the number of Meningococcal cases having dropped significantly this year compared with last year;
The current total number of notified cases for 2005 so far is 151 with nine deaths. Not all of the cases reported in 2005 so far are due to the same strain that the vaccine is designed to protect against. The average number of cases per year for the last five years over the same time period is 266.
It's worth noting that not all of the country has been vaccinated yet, for example the vaccine was only recently released down in the South Island and so the organisms have had time to wreak a bit of havoc. It will be interesting to see what the numbers are like next year, when the majority of those eligible for the vaccine have aquired it.

Thursday, August 04, 2005


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There is something wrong about that image and I'm pretty sure it's because I find the idea of being touched by a large anthropomorphic pile of sphaghetti vaguely erotic.

Teach the controversy about our (flying) spaghetti masters.

Wednesday, August 03, 2005

Legionaires disease in Christchurch

Christchurch had a rare outbreak of Legionaries disease, caused by an organism that typically lives in water condensation that forms in the likes of air vents. One man is dead and another eight are in hospital recovering from the disease. As the TVNZ article notes, the disease was first seen in an outbreak among a meeting of the American Legion in Philadelphia. The response from the American government at the time was very swift, with over a million dollars committed to tracking down the disease and where it came from.

A good contrast to the relative unimportance that the administration of the time placed on AIDS, now one of the most important diseases in the entire world.

Tuesday, August 02, 2005

Student Loan Fun

The New Zealand Labour party, while desperately trying to drag themselves out of the quicksand they have made for themselves have come out with an absolute shocker: Remove all interest on student loans. Firstly, I don't believe they will go through with it for the simple reason that they've been getting hammered in the polls and they know that New Zealands right has finally found some teeth. It seems like blatant electioneering and they are deliberately trying to grab votes from students, who are under a considerable burden from their student debt. The desperate go and try to appeal to the equally (in some cases) desperate. I myself have a loan and I'm going to have to think about paying it off when I enter the 'real world', but I'm not likely to be bought by such cheap promises when they can so easily recant on their promise.

The second, and strongest point I feel against believing this absurd promise is that labour can very easily 'run the maths' so to speak and recant on what they are offering or simply compromise. 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. I wouldn't be surprised with a scheme more along the new one that National is proposing making the interest on the loan tax deductible, which would decrease the total loan repayment by around 25%.

Quite frankly, you'd have to be amazingly gullible to think that Labour will firstly do as they are promised or even if they do actually find a way to pay for it.

Invaders and Biological control.

At the thumb, everyones favourite panda philosopher Steve Steve had a trip to over to Haiwai'i and the following comment caught my eye:
New Zealand, which has - or had before feral cats arrived and possums from Australia were let loose - some of the most extraordinary fauna anywhere
Feral cats aren’t really much of a problem, it was the rat and the original humans that came to New Zealand that did everything in. The original rodent invader was the Kiore, or the pacific rat (which is also found on Haiwai'i coincidentally) killed a lot of our bird life, although this will never be properly quantified and what the rats didn't get the Maori wiped further bird species out. For example, the Moa and the great eagles that hunted them both went extinct due to the actions of the Maori. When Europeans arrived it just went from bad to worse, because not only did we bring further invaders (Gorse, possums and the european ship rat, which is bigger and meaner ) we also bought guns. Birds that had been difficult to kill previously, like the Kereru (wood pidgeon) became a snap to kill with a gun and they were very nearly driven to extinction. Strong conservation laws were about the only thing that ended up saving the species from extinction.

There are numerous other biological invaders as well that we’ve bought in too. For example the beloved fishermans catch, the trout, is like a nuclear weapon in fish form for streams that it is put in. It’s an amazingly aggressive predator and in the streams it is present in has eliminated small invertebrates entirely like the freshwater crayfish Koura. Additionally, for those wanting another example of evolution in action, fish called galaxids in streams with trouts have been under intense selection in two regards: the first is to be active at night when trout aren’t around and the second is to have a much darker colouring so they aren’t seen as easily. Trout free streams have considerably more variation in galaxid behaviour and colour than streams with trout. For obvious reasons.

Thankfully, New Zealand conservation scientists are very good at figuring out ways of killing these various pests and we lead the world in biological control and trapping programs. For example, work has been ongoing in New Zealand for several years in using parasitic nematodes to sterilse possums. We've also introduced a form of spider mite that attacks gorse and chokes the ability of the plant to grow by webbing up the growing stem. The only unfortunate thing is that such measures can never bring back the numerous species, some we probably never even knew of, back from the dead.

Monday, August 01, 2005

Perry Bible Fellowship with another winner

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For more fun and general insanity, visit the perry bible fellowship, probably one of the more interesting and original web comics around.

Evolution and atheism

While perusing the carnival of the Godless, I spied that one of the posts referred to the old 'evolution is atheistic' kind of argument you usually get from creationists trying to imply that evolution is an evil godless theory. In this case the author isn't a creationist, but still finds merit in the argument that maybe evolution does actually degrade the importance and even requirement for God.
If this is a reasonable way of thinking, then evolution is not actually irrelevant to the issue of theism vs. atheism; obviously, the pattern of life on this planet is one of the things which appears considerably more comprehensible if one assumes there's no God pulling the strings. Certainly it's hard to see why the God of any of the major religions wouldn't have done lots of meddling, and yet to all appearances life has developed over time in ways completely explicable by evolution, with no signs of meddling whatsoever. So, it seems to me that the anti-evolutionists are, kind of, right; evolution provides a reason not to believe in God (though, sadly for their cause, it provides a good reason).
This is actually a fairly common line of thinking, because nature is on the whole rather overtly violent. It doesn't seem like the sort of thing that would have been build by a benevolant God of any description and the almost "cobbled together" fashion of life as we see it. Of course, even though I have a theistic belief, I still do not see how evolution producing organisms as they are is a challenge to God. God, for all intents and puporses probably made the laws and principles that guide the universe. This doesn't mean he had a direct hand in every little detail, in other words he didn't bother 'poofing' a flagellum into existence through a miracle. Rather natural laws that were set in place originally may have allowed life to 'self' assemble itself. It seems to me that a 'designer' that doesn't have to do the work himself, rather lets a series of basic laws design everything without his direct influence is much more intelligent than one that micromanages every aspect of life. This is why we don't see any 'meddling' at all, because it was never required to begin with because the natural laws put in place to begin with were more than sufficient (which we know are still operating today)

Of course, this is heavily putting God around 'evolution', clearly knowledge that humans have accumulated but it's so well and truly supported that for the creation story to be true, it makes God a distinct liar. As a result, the only 'God' that evolution seems to contradict is those that read a literal 6 day creation model, which time and time again has been found to be deficient in terms of scientific evidence. Of course, I fully understand that many also see that evolution and natural laws providing evidence that you don't need God is perfectly reasonable as well. I often wonder why it is that the religious require to concile their belief in God with evolutionary science, but not germ theory, weather forcasting or any number of other sciences that do not claim God was an essential part in the way they work.