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.

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.

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).

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.

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.

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.

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.

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.

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.



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.

MeNZB

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.

Hmmm

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.

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.

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.

Perry Bible Fellowship with another winner

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.

Influenza Viruses

For those still not concerned about the potential of an influenza virus, like H5N1 to become a lethal pandemic strain should read this news report about a paper in PLoS Biology about flu virus evolution. Essentially, the researchers found that influenza can exchange parts of its genome much more frequently than was originally anticipated. This is particularly worrying, especially as there are numerous benign strains that are going around each year, ones that we don't feel the need to vaccinate against which could all serve as a source for genes to make H5N1 more lethal than it currently is. Add to this problem that China may be hiding its total bird flu cases and we could be looking at something extremely dangerous.

How to argue with cranks

In my time on the internet I've learnt a considerable amount about debating and particularly how to debate with people on various scientific issues. In general, it becomes very evident in any sort of scientific debate if your opponent has much of a clue or not and here are are few handy hints to tell:

1) Quote mining: People who quote something, out of context from a secondary source are usually doing something fishy. Consider a review on a book on evolution; a typical tactic is to find a random review and then quote something from the reivew about the book and hold it as fact as the books 'opinion'. This tactic works on two levels, the first is it confuses the original citation making it much harder to tell if the individual is lying if they haven't actually read the book or not. Many people are not willing to bother looking up the entire book, so the quoting from a secondary source just makes it even less likely for someone to go to the work of verifying the claim. The second part is that if the book is rare or hard to get it makes it impossible to refute the point.

This is usually done by people who are merely parroting the opinion of someone else, usually from said reviewer particularly if the reviewer had a bias against the original book. The other form of quote mining is even more insidious. This time the citation from the original book is given, but a quote is cherry picked completely out of context and the indivdual knowingly misrepresents the opinion of the original author. Typically this is done as part of the logical fallacy of an 'appeal to false authority' to try and buy false credibility, or just to try and degrade the credibility of actual authority (such as an actual biologist working in that field of research).

2) Appeals to false authority: Now I've mentioned it, this is one that makes itself blindingly obvious extremely quickly. Typically, you end up with people citing their PhD they got from a diploma mill as is the case with Kent "Dr. Dino" Hovind. You can easily spot these by simply noting people quoting a chemist on a biology topic, an historian on geology, or a biochemist on detailed aspects on an obscure dead language. In general, if someone is quoting someone who has a degree completely irrelevant to the field they are in you can be sure it's an appeal to a false authority. This doesn't mean the authority being appealed to doesn't know anything about the topic however, but it does mean that if they are in blatant contradiction to those who are working in the field they have a good chance of being flat-out wrong.

It's worth noting that there are many times that appealing to an authority is not a logical fallacy. For example, I know my way around immunology, but I know virtually nothing on human neurophysiology. In this case, I wouldn't be incorrect to cite the work and opinions of scientists who are actually neurophysiologists. As with the above, this doesn't automatically make the source right, it just makes them far more credible than someone who has a degree in an irrelevant field for example commenting on the area.

3) Manipulation of statistics: This one is hard to spot unless you know what the answer is ahead of time. It's really common among anti-vaccinists, who love to present the dropping mortality graphs as evidence vaccines do not work. Unfortunately, they rarely present morbidity graphs where the actual number of cases or people being infected only drops after the vaccine has been introduced. The dropping mortality is usually explained by better water sanitation, medical practices and community awareness of that specific disease. Sometimes the statistics are just plain out distorted, as I detailed earlier with Ron Law trying to descredit the MeNZB campaign.

4) Strawmans: A strawman is the indication of the loser in a debate. A strawman is the last resort argument pulled out to try and avoid answering a superior positions arguments and instead distract from the issue at hand. For example, let's say that person A in the debate holds the opinion that when a disaster occurs and hundreds of people are made homeless because of poor water drainage planning, the residents will be extremely angry at the local council. In support of this statement, they note the numerous extremely ticked off people they've seen on the TV as evidence. Person B, who cannot answer the original argument, tries instead to distort it.

Instead of the argument person A gave as being "People I saw on the news were angry because poor planning from the council cost them their homes"

becomes

"The statement isn't valid because you don't know if someone wasn't angry and if everyone wasn't angry then it doesn't matter if it was poor planning on the councils part. Therefore people were not angry that their homes were lost."

Now, we can see that this is one mind bending leap of logic. First, they construct a strawman of the original argument, from noting that people person A had seen on the news were angry into everyone being angry in the town as the primary argument. If person A cannot establish everyone as being angry, it automatically refutes the remainder of the statement. This is a strawman, because it's distoring the original position, which never required everyone to be angry and was a simple observation based on the best available evidence person A had seen.

Strawmans are hence a very popular debating tool on the internet as a result as it avoids having to answer the actual argument and supporting evidence put forward.

5) The copy and paster: This is the internet debater I hate the most. Copying and pasting someone elses deficient arguments, aside from being plainly lazy, is just worthless when it's the same crap over and over again. This is very typical of 'minion' creationists, whom in any debate will bombard you with entirely copied and pasted sections of . This is annoying because they'll often make you refute the same thing several, if not multiple times constantly and then next debate they'll go back and RECITE the damn things again. One popular one is the appendix argument from AiG, no matter what happens it will always come up in any evolutionary based debate that mentions the word 'vestigial'. There are some AiG articles that I've seen copy and pasted spammed so many times now, that I could refute them in my sleep.

Copy and pasting large sections of a website is just lazy and demonstrates a lack of knowledge and evidence of the person who is doing it. Sadly, such copy and paste spam is usually very tiring and is one reason that many who try to combat crankery like creationism get very worn out doing it. You are refuting the same things over and over, and many of us have the intellectual honesty to make our own arguments and not just parrot other peoples.

But there you have it in any event, the five top ways to spot when you're arguing with cranks (or people who are just plain clueless).

1. Quote mining
2. Appealing to a false authority
3. Manipulating statistics
4. Strawman arguments
5. The copy and paster

Creationist actually stumped?

Jason Rosenhouse, one of the contributors to the Pandas Thumb went to the recent Creation Mega Conference in America. Aside from his sometimes amusing descriptions of the usual creationist rubbish he also managed to ask a few questions of the speakers after some of their talks. One was Werner Gitt, who proposes the concept that DNA and other aspects of biology are 'information' a lot like a dictionary or a computer program. It appears that Jason was, in a stunning move, actually able to stump Werner and get him to blindly contradict himself

I pressed on. But we're not talking about believing in God and evolution. We're talking about accepting your particular theories about information on the one hand and evolution on the other. You said explicitly that that was impossible. So you were being disingenuous when you told the other fellow that scientists accept your ideas.

And this is where Amazing Thing Number Two happened. He shrugged and looked down at the floor. He actually looked abashed! Since I didn't think creationists were capable of shame, I considered this a major victory.

Sounds like a good time all around really. Sometimes this is like shooting fish in a barrel however, because most ID-proponents and creationists are almost terrified to answer precise questions. This is particularly true of any pseudoscience in fact and is one of the primary means one can use to combat them.

Our Immune system isn't just our weapon anymore

One of the things that never ceases to amaze me is how 'clever' bacteria are. I don't mean to imply they are smart in the way we are of course, but in the tricks and methods they use to survive in a wide variety of different conditions and habitates. In particular, bacteria are already known to undergo germ warfare, spitting toxic peptides and other compounds at one another in the race for just a little more living room. An additional trick it turns out is to have the hosts immune system destroy the bacteriums competitors for them.

The particular paper appears in PLoS Pathogens and best of all it's free if you're wanting to have a look. The littlest organisms on the planet never cease to be the most ingenious.

Our domesticated animals and us

One of the things that has gotton me very interested in the examination of domesticated animals, is their ultimate effects down the line on other aspects of human health. As I discussed earlier, the reckless feeding of antibiotics to farm animals may have effects down the line on propagating antibiotic resistance to potential human pathogens. There are other effects on human health that are important as well, which of course primarily stem from our animal husbandry techniques.

Chickens for one, are commonly implicated in food poisoning by the organism Salmonella enterica. Salmonella is a relatively clever pathogen, being capable of escaping from the chickens gut and then invading the tissues of the bird. In addition to this, the organism is even smart enough to get into the developing eggs of the chicken meaning nothing about the animal is salmonella free. Unfortunately, it turns out that part of the reason why this is so common is because the chickens are kept so closely together. The young chicks have no inherent microbiota and the salmonella which gets into the chicks gut, from food mixed with feces or particles picked up from general pecking. This basically enables the salmonella a free opposition-less ride all over, increasing the amount of salmonella in all the chickens.

Another example is the diet of cows and a more recent human pathogen, Escherichia coli O7:H157. Cattle in some places in the world are fed on a carbohydrate rich diet, which when metabolised by the commensal bacteria in their rumen (cattle, unlike us, have a five chambered stomach) causes a considerable drop in pH. E. coli O7:H157 is more acid resistant than the normal bacteria that live in the rumen, meaning that as the pH of the rumen drops it also provides an advantage to the E. coli because it no longer faces the same competition. This means that you have the pathogen proliferating from its normal low numbers to much higher numbers in the gut.

The point that is important here is the addage "you are what you eat" is certainly very true. In our case, when we use practices that select and aid the proliferation of pathogens in the animals we eat; it's little wonder that we end up eating those pathogens more often as well.

Thirteenth Skeptics Circle Posted

Orac has posted the thirteenth skeptics circle over at his blog, I suggest you go over and have a read.

The last bottle of V

V is stuff that, since around the first year of university, I've been drinking incessantly. It's basically a sugar loaded highly caffeinated soup of stuff that is designed you keep you awake. Unfortunately, however much fun it has been for this wonderful drink and myself, it's time to give it up because I'm wanting to drop the caffeine from my diet. It's not as if I have anything in particular against caffeine, why we've had some great moments together in the past. Money just isn't that plentify and a V habit is actually fairly expensive.

So it's finally time to kick the habit.

In any event, caffeine is one of those wonderful substances that I'm sure I'm going to miss, even if just a little bit. Like many drugs, it works on aspects of the brain, in this case by targeting adenosine receptors that interact with dopamine receptors (the brains reward chemical). The antagonism by the caffeine on the adenosine receptor causes an upsurge in neurotransmission of the dopamine receptor, which is probably what contributes to the buzz that you get out of caffeine.

In any event, heres goodbye to a good green friend...right after one last bottle ;)

MeNZB feedback

A few posts ago I mentioned the debate on TV ones close up program on the MeNZB immunisation campaign. The feedback has been a mixed bag of both high points and some obvious low points. One of the respondants writes:

In order to do justice to the subject it requires a decent two-hour debate where probing questions can really be answered. Mud-slinging and misinformation on both sides on a very controversial and heated subject does little to help parents make informed decisions. We have decided against immunisation in this case, but boy - sifting through the misinformation to try and elicit any form of truth is harrowing. Good luck Susan, you can head this debate! Anna, Auckland

As I demonstrated just a few posts ago, the misinformation is certainly clear and it's coming from people who manipulate the truth and science for their misguided agenda. Apparently it seems a lot harder for the MOH and other pro-science groups to answer the distortion-a-minute rhetoric coming from the anti-vaccination groups. Another comments that;

This discussion was not long enough. I felt the ending was terribly rushed and the anti guy was cast in a bad light which may have aroused the anti group to be even more passionate about their cause. Margi.

Ron Law was not just cast in a bad light but he actually deserves it from his past history of distorting basic scientific facts. The fact at the end it was pointed out that Ron doesn't have any recent scientific expertise or training in the area he is criticising is a strong point, even if he didn't get the opportunity to respond, his poor answers on the program and the statements made with Barbara Sumner Burstyn, herself not having any scientific credentials either, in other public forums really says a lot about their credibility as I addressed earlier. That several viewers who responded to the program thought that Ron Law came off badly shouldn't be a surprise.

Unfortunately for Margi, these people are unlikely to be any more passionate about spreading their rhetoric because they already were extremely keen on doing so to begin with. Other feedback is more about being confused than anything else:

I am appalled at that woman on there tonight and how the doctors are too quick to blame any incidents of side effects on that 'the child must have been sick before the shot' or 'there are so many viruses around'. Define virus for us Mums and Dads! -Nikki, Waikanae

Firstly, the vaccine is clearly most effective early on and immunity has been demonstrated to wane over time. Although children should be protected for 2 years or so, it's unknown how effective the immunological memory to the vaccine will be after this time, although it is predicted to be good after the three shots (which is why the decision to use three shots was made to begin with). It's best to administer the treatment closest to the time that people will be at risk, because the immune response will be at its strongest during the immediate period after the shot. This also corresponds to the time that people are most likely to get the infection to begin with.

It is also unfortunate that this period does correspond to the time that the majority of viruses and other 'bugs' are doing the rounds. The colder winter months and chilly conditions naturally aid the movement of common flu viruses, such as rhinovirus or various influenza strains and many other nasties. It is going to be true that these will make the rounds and people will get sick at this time. However, as I've discussed earlier side effects with this vaccine are fairly common but the overwhelming evidence is that these are only minor and not significantly dangerous. As people who have seen the effects of meningitis first hand will testify, these are infinitely minor compared to the pain, suffering and potentially lethal effects of a full blown meningitis infection.

In some respects, those who have seen the disease are amazed that those who have no first hand experience would ever allow themselves to put their children at risk of meningitis. For example, Brendas feedback is a good example of this kind of sentiment:

In May 2004, my partner and I lost our 9 month old son to MENZB*. My opinion is that any parent risking their children to such a fatal disease must hope that they never get to see the devastating effects. At the time of losing my 9 month old I was again pregnant. Since the birth of my daughter, she has had all three of her injections. Any cover is so much better than no cover at all.

Sadly, there are many who may not heed this advice and I hope that it doesn't ever come back to bite them. For more feedback visit close ups feedback page for this week.

*Note, I would assume here that this is a typo and the disease she is referencing isn't MeNZB as in the vaccine, but the meningococcal group B organism that causes the disease. This is a bit of a gaff on TVones part however.

All hail the new lord of snacks

The invasion of the Pod people has been completed and humanity has finally been subjugated under the rule of our delicious masters. I for one, welcome our Pod biscuit overlords.

Mice Mass Attack

Nature recently reported a story about mice on Gough Island assaulting albatross chicks. The video of the attack is quite disturbing, but it's an interesting behaviour that has apparently been learnt by these mice. Yet another reason why rodents are some of the most effective predators and animals around, despite their size.

Speaking of anti-science idiocy

Ron Law who appeared on the close up program mentioned in the previous post, published this article along with journalist Barbara Sumner Burstyn. In their press release they claimed there was an increase in the risk of meningococcal infection in preschoolers as a result of the vaccine. This is an amazing example of their general ignorance and that they do not understand the science behind what they are claiming.

Firstly, the study did find that the vaccine they had given was ineffective in toddlers, for two doses. Studies that were conducted and used three doses found that the vaccine worked very well and was highly effective; from the paper in question

Infant participants in the Tappero et al. study were given three doses of either the NIPH, or the FI, or a control vaccine.12 After three doses, 98% and 90% of infants who received the NIPH or FI vaccine, respectively, were seroresponders against their vaccine strain (homologous strain); that is, they demonstrated a fourfold or greater rise in serum bactericidal antibody levels. Seroresponse in infants to strains other than the vaccine (heterologous strain) was poor. Tappero et al. noted that for the FI vaccine recipients, the percentage of seroresponders almost doubled from dose two to dose three, and that had the participants in the Sao Paulo study19 been given three doses, the efficacy of the vaccine may well have been found to be much higher. The New Zealand clinical trials are being conducted using three doses of vaccine, and the use in younger age groups of a fourth dose (if needed) has not been ruled out.

There is a very large body of applicable safety data on group B OMV vaccines that provides considerable reassurance that an OMV vaccine against the New Zealand strain,
although reactogenic, will be safe in all age groups.

Which is a very different tune than the claims Ron Law is trying to sell you. Of course, if Ron Law wasn't being disengenuous to begin with you'd realise there isn't any issue to make anything out of here, unless we take something horrifically out of context. The only significant finding that we can take from Ron Law and Barbaras distortion is that neither of them understand statistics! The first problem with their analysis is they try to posit that the confidence interval in the graph indicates that the children in those groups have increased sensitivity. This is not at all the case. If a confidence interval passes zero (IE goes negative) as it does in the presented graph, it does not mean that there is an increased risk, it means there is a strong indication of a lack of efficiency but not of increased disease.

Such elementary mistakes from people who are supposedly 'informed' about their crusade against the MeNZB campaign speaks volumes of their credibility.

Study cited:
Sexton K., D. Lennon, P. Oster, S. Crengle, D. Martin, K. Mulholland, T. Percival, S. Reid, J. Stewart and J. O’Hallahan (2004). The New Zealand Meningococcal Vaccine Strategy: A tailor-made vaccine to combat a devastating epidemic. New Zealand Medical Journal, 20-Aug-2004 - Vol 117 No 1200

MeNZB crankery

It is becoming more apparent that opposition from anti-MeNZB groups is growing here in New Zealand, particularly as it gains support from parents worried their children are being adversely affected by the vaccine. It is true that the side effects of the vaccine are fairly common, particularly pain, swelling, irritability and possibly a fever. Such side effects, however minor and ultimately trivial in the face of full blown meningitis are giving anti-vaccine campaigners ammunition. Needless to say, many of these effects are being completely over done and probably over dramaticised. I couldn't help but note the parents who appeared on TV1 on Close Up, who demanded that they have assurance of no side effects at all if they had their child get the other two booster shots.

Now, however distressing such side effects can be, especially when you watch these sort of things happen to your own children there are a few things to note. Firstly, the immune system is ultimately a biological weapon. It's an extremely potent and very well armed weapon that has been selected for over evolution for one task: To destroy invaders. To do so it uses numerous chemical, hormonal and cellular mediators to eradicate the invader and unfortunately like any human made weaponry sometimes there is a little collateral damage. Most of the 'side effects' that people think are horrible and the anti-MeNZB campaigners are so shrill about is the vaccine actually doing something. Such vigourous reactions, although thankfully not so vigourous as to be life threatening in any sense except for rare cases, is in fact demonstrating the vaccine is being recognised and the immune system is doing something about it.

Secondly, it's important to realise that this vaccine has been made with considerable difficulties that other vaccines (with less side effects, but often similar ones) do not end up with. The first problem is that the organism that commonly causes meningitis here in NZ, Neisseria meningitidis surface capsule is made of a substance similar to ones found on our cells. This induces considerable autoimmunity problems when it is used as a vaccine, plus it isn't very immunogenic anyway. Neisseria meningitidis group A and C have a different kind of surface and the vaccines produced from them have considerably less side effects.

As a result, we've based our vaccine on a similar one made in Norway to a similar group B strain of N. meningitidis. The way they (and ourselves) produced this vaccine was by spinning the bacteria to seperate out structures on the bacterias surface called outer membrane vesicles. These structures are known to be immunogenic (illicit protection) while they do not induce autoimmunity (they are novel to the bacteria). These vesicles also come with another bit of the bacteriums outer surface, lipopolysaccharide or LPS. LPS is something that the immune system really reacts vigourously towards and is probably why side effects such as irritability are so common with this vaccine.

In saying that however, LPS also helps what isn't the best antigen that we would like to do a lot better, although the studies in Norway confirmed that three booster shots are required to establish long term memory. Unfortunately, the very side effects which are lambasted by the anti-vaccinists are also the very proof that the vaccine is properly working and doing its job correctly. The difficulty, going back to my point about the family demanding assurance on close up, is in explaining that side effects are not always a bad thing. When you're essentially priming a weapon so that it is ready to meet an invader, it should be expected that in the build up of suitable arms and defences that you would get some indication of this process is going on.

Creationists at it again

I love the Intelligent Design Movement, no matter what happens they find a novel way to bury themselves further. One of the numerous ID lawsuits in America going on right now has gotton a copy of a previous manuscript of the ID book "Of pandas and people". Unfortunately for the ID is a science charade, it looks like ID wasn't used originally in the book.

We'll let the quote speak for itself though:

Rothschild also brought forth several other examples of the foundation’s possible religious ties, including an early draft of the book, which in its infant stages was titled “Biology of Origins.”

The draft mentioned “creationism” frequently. But in the final copy of the book, after the title was changed, the word creationism was replaced with the phrase “intelligent design.”

Buell said the word creationism was a “placeholder term.” The definition of creationism changed to include a religious context after the draft was written, so the writers changed the word, he said.

It's amazing to me that people still take the ID movement seriously as being anything other than redressed up creationism. You can read the rest here but make sure you bring a fresh irony meter.

Solution to the anti-vaccination cranks

This just struck me as a brilliant idea.



Thanks for the idea the parking lot is full! Even though you've been empty for several years, you still hold a warm place in my heart. In any event, I just watched the interview on close up (TV one earlier tonight) with the two women (one an immunologist from Christchurch hospital) and the other from the ministry of health ripping Ron Law (an anti-vaccination crank, who doesn't appear to have done any recent biomedical research) a new one. Although they did very well, it unfortunately just isn't enough for members of the public as the individuals near the end of the show demonstrated. Unfortunately, the anti-MeNZB rhetoric has really gotton through and cemented itself in some people here.

Sometimes you wonder why you fight the vast ignorance of these people and then I'm reminded that I've seen friends I know go down with this disease. Heck, I still remember about the student in my first year of University that died from Knox college of the disease. In many respects, anti-vaccine cranks as I mentioned earlier only exist as long as vaccines are working effectively enough to ensure these diseases aren't visible to the public at large at all.

Lord Vader holds a press conference

The great Lord Vader has held a press conference to discuss the Empires progress in crushing the Rebel Alliance and restoring peace to the galaxy.

Q: There are rumors that you might be stepping down due to ill health.

Lord Vader: There are no such rumors.

Q: There are no such rumors.

Lord Vader: You admire my bold leadership style.

Q: I admire your bold leadership style.

Lord Vader: Next.

I smell an analogy!

Antibiotics and farm animals

Over at the Pandas thumb, Professor Steve Steve is off on more crazy adventures telling scientists how it is, when I noticed the following quote that I thought pertinent to expand upon:

I don’t think Dr. Cassell was very amused when I suggested they should simply keep the population on antibiotics from birth to death, and we wouldn’t have to worry about this silly infection stuff.

First of all, I find it somewhat interesting that it is widely acknowledged by both the scientific and medical communities that wanton use of antibiotics is a bad thing. We've seen the emergence of virtually every kind of antibiotic resistant and disturbingly usual multi-antibiotic resistant bacteria since antibiotics were first used. It is ironic then, with these problems with human antibiotic resistance so widely reported, that the farming industry appears to completely ignore what we've learnt. Many places around the world feed animals antibiotics prophylactically as 'growth promotants'.

This does have some benefit that is not well understood and animals do seem to grow faster under such treatments. Unfortunately, it has been demonstrated the breed the resistance to the antibiotics used in certain hardy gut commensals like Enterococcus faecium. It has also been demonstrated that E. faecium can transfer the antiobiotic resistance it has picked up to other microorganisms it meets, including E. coli. While the antibiotics used in animal feed aren't always medically significant ones in humans, they sometimes still have potentially negative ramifications.

1) Some of these antibiotics are analogs, that is they have a similar structure and function to human antibiotics used in medicine. One such example is avoparcin, which is similar to vanctomycin (important in treating the superbug MRSA) and due to evidence of resistance to avoparcin conferring protection against vanctomycin, its use has been generally banned in many places.

2) One form of resistance often confers at least some protection against other forms of antibiotics, even if it doesn't directly affect the targeted structure or enzyme. This most commonly occurs with cell wall active antibiotics, where resistance mechanisms such as reduced surface charge can affect a wide range of antibiotics: not just one or two.

It just seems almost silly to me that its widely accepted to be bad practice to use antibiotics unnesessarily in humans, yet many places even now are just throwing them into farm animal feed. It's utterly irresponsible.

Scientologists after Anti-depressants again!

Oh dear, just when I didn't think it could not get any more nutty the scientologists have mobilised their celebrity forces to try and again disregard anti-depressants. This time the claims are that anti-depressants make children into walking, potential mass murdering time bombs and worse. It is true that in some respects, drugs like anti-depressants are overprescribed in some cases. What is being denied unfairly is that these drugs do help for a large number of people and that in many cases their use is essential. That these people are so ignorantly trying to peddle misinformation, see the Tom Cruise interview for some examples, but are in prominent positions in society as well is just making things worse.

Scientific threats.

Over at telic thoughts, Mikegene wonders why scientists don't seem to be giving vigorous opposition to animal rights activism and their generally disgusting tactics.

Thus, by factoring in the activity of the animal rights movement, we can help to perceive the ID movement in its larger sociological context. Where, on the scale of “threats to science,” does it truly rank? Each person must decide for himself, but to make a decent decision, plenty of information comes in handy.

Animal rights activists at least have a valid point. Science has done some horrific things to animals in the past in the name of research and these things, have painted it with the use of animals to this day. Of course, do you do research on animals Mike Gene? Are you aware of the ethical and similar requirements that are required? Additionally, the anmal rights movement, like the intelligent design movement, has its strongholds. The sort of opposition you have named is really prevalent in England, partly because it’s the birth place of the anti-vivisectionist movement and their very first defeat as well (a gaff in a trial ironically ended their ability to stop all animal testing).

Where I am, there is almost no such extremist opposition to animal research. Nutball groups in the US and England are the primary motivators but everyone knows that despite their threats, they will never be able to stop animal research because court decisions struck them down a long time ago. Ultimately, there are uses of animals that are borderline even know, do you agree with lobotomising a rat and then putting in electrodes into the brain to deliberately stimulate certain regions? Some that are perfectly necessary, such as common immunology/microbiology uses of rats and mice, where these animals are experimentally infected with pathogens then killed to extract lymphocytes to analyse immune responses to them?

Both of these are routine today and both can be argued on their merits to if they are ethical or not. What colours a lot of animal rights opposition is the use of animals that people associate best with, namely dogs, cats and rabbits. Additionally, as I pointed out, many of these groups have legitimate points against animal research especially due to the gross uses of primates in psychology- brutal experiments that I’m not going to bother describing as they were nothing short of inhumane. Anyone who wants to understand, even emphasise with these people should look up what was done.

And again, I come from someone who works with experimental animals and has direct experience in this area.

PETA are, ultimately just completely crazy and are not widely liked nor supported. Of course, it’s interesting that you’ve tried to make out that anti-IDists have a ‘pet’ obsession with ID as a big threat to science while ‘ignoring’ other aspects. Well actually, I’m particularly interested in the anti-GE lobby and have often engaged in debate with the anti-GE lobby here in New Zealand. I see the anti-GE lobby as a large threat to good science because they miseducate the public on basic facts about the technology. They move around and destroy research crops and threaten scientists. In many respects, they are the ‘real’ analogy for me between the animal rights movement so prevalent in England.

I spend much more time arguing with this lot than I do the IDists, but I do that in the forums where it counts (in New Zealand) because that is a ‘real’ threat that I can see. ID is largely American. At the same time, I regard these groups as a threat not just because they are crazy extremists, that is something the law will deal with, but because they attempt to miseducate the public. They miseducate the public in how research is carried out, they manipulate facts and shamelessly lie. Like any form of anti-science nonsense and particularly they directly target Children with gross distortions of truth (see Greenpeace books on GE aimed at kids, with golden gems that frog DNA if inserted into a banana will turn the banana into a frog/banana hybrid).

Another lobby I spend a lot of time arguing against is the abstinence only (no sexual education though) lobbies and those sort of groups. Another group is the anti-vaccination lobby which again, also has a presense here in New Zealand. I again, spend a great deal of effort arguing with these people. How about I look at these groups and compare them with ID (why don’t you?). Anti-vaccination lobbiests attempt to miseducate the public, they don’t directly threaten scientists or force the shutting down of labs however. Yet, I take a considerable interest in them and so do a large amount of other individuals. They present a threat to public education and if unopposed could potentially be a threat to public health- just not immediately.

Should I ignore them Mike and focus on ‘immediate’ threats as a priority? I don’t think that would be a good idea because it’s only after they’ve made ground that any problems become apparent.

So why do I regard ID as a threat then bearing in mind you’re rather correct that ID proponents do not try to cease research in evolution. You’re also correct that unlike the animal rights/anti-GE movement IDists do not try to shut down labs or similar. Now that I think of it, neither does the anti-vaccination lobby, the HIV denial lobby, or the lobby that doesn’t want to have sexual education taught in schools but abstinence only. Gee Mike, I should cease my opposition immediately to one form of anti-science simply because it doesn’t have instant ramifications on anything! Brilliant logic! You’ve successfully proved the anti-vaccination, HIV denial and sex-ed lobbies are perfectly fine because they are not whacky extremists on the far end of a scale like PETA.

I regard ID as a threat simply because they use similar tactics. Going through courts, misinforming the public and attempting to subvert education. These are tactics common to all pseudoscience movements Mike, they aren’t unique. The difference is that ID doesn’t go as far as the extremists who are usually extremely left wing and believe that vandalism, threats against scientists are legitimate forms of getting their way. Again, why don’t you make a distinction between the psychology of the majority left ‘animal rights’ and ‘anti-GE environmentalists’ that make up the ones that destroy labs and burn crops? The ID movement, anti-vaccine, anti-sexual education (or abstinence only) groups for but three examples are either more right wing (Christian religious groups) or more either or (you can find ‘naturalist’ nuts in the anti-vaccine group, who are very definitely left wing).

In your persecution complex (common of creationists too) you regard opposition to ID as being absurd because there are other threats to science from extremist nutters. I disagree, I think opposition to ID and the tactics they employ needs to be actively criticised and shown up for what it is. The threat that ID proposes to the public in terms of the misinformation and miseducation campaigns (slowly been dismantled and all major media outlets see through the facade, like CNN) is just as much as any other pseudoscientific group. There is no ‘threat’ level Mike, it’s all the same and all of it warrants the opposition from the scientific community.

I tend to put my efforts into the anti-genetic engineering and anti-vaccination groups. Others have different preferences but they represent what I see more often than other things. ID just turns up for me because it’s so prevalent among the internet forums that I visit and it nearly always turns up in the creationism threads (hence, where my interest came from).

But again, and I want to cover an underlying point that through all this you remain blissfully oblivious too: Many scientists can sympathsise with the basic ideals of animal rights activists. Maybe you don’t understand this point because you don’t work with experimental animals yourself, but it’s not something that I enjoy when I’m dissecting something I knew was a living animal that I’ve seen grow and associated with for several months. I also concede the gross and cruel use of animals in the past by science, which many of these people are afraid of.

I also understand that we (as scientists) have caused this opposition ourselves and given groups like PETA ammunition. We refuse to make public the uses of animals, leaving many in the public to swear we are hiding something behind our doors that is reminiscent of the hideous experiments done even a mere 50 years ago. As scientists we fail to properly educate the public in how we undergo research with animals and because of this the public falls to miseducation from the likes of PETA easily. This is exactly the phenomena seen in the anti-GE lobby and I will refer you to one of the most blatantly ridiculous anti-GE books:

Everything you need to know about GE… but the government won’t tell you. Charles Drace. Raven Press. Christchurch New Zealand.

Ultimately my point is you’ve set yourself up and argued against a wonderful strawman, but I don’t buy it. I regard anything that attempts to miseducate the public, which if you follow ID enough you can certainly see they do and promote an agenda (no matter what it is, religious or otherwise) as an equal threat. All of it deserves to be answered.

Your primary mistake and why this is a completely irrelevant strawman, is that really, most of us who argue against ID (and be aware, I’m talking about ‘teach the controversy’ ID here) also do argue against most other forms of pseudoscience/anti-science as well, often more vigourously. ‘Teach the controversy’ ID isn’t held on a pedestal as ‘the threat’ because there will be different opinions on that, but it is ‘a’ threat.

Flatworm penis fencing

Posted for the enjoyment of all, I bring you flatworm penis fencing. Just when you think nature cannot get more bizarre it just goes and stumps you once again.

Condolences to the British

I've been watching the aftermath of the attacks on London just now. It never ceases to amaze me why people do these sorts of horrible things to other people. I hope they get the bastards involved in this.

Turtles all the way down

Turtles all the way down.

Around the net I’ve seen this expression come up called ‘turtles all the way down’, usually referenced to intelligent design. The term comes from a story, of unknown source as it seems to come up often from different people, where essentially a famous lecturer was giving a talk on astronomy. After he was finished a little old lady came down and told him he had it all wrong.

“The world is really on the back of a giant tortoise” the woman said to which the scientist asked, in an attempt to stump her most likely, “Well then, what is the tortoise standing on?” To this the lady triumphantly replied “You’re very clever young man, but it’s of no use – it’s turtles all the way down”.

In many respects this is the problem that intelligent design faces when it proposes a ‘designer’ is natural. For example, when we take Dembski mathematics, fancy as they are and apply it to the designer we find, unsurprisingly, that the designer must himself be designed. If we do the same thing again, we find that each designer in turn requires another designer. Eventually, we have an infinite regress of designers, each one designing the previous one; turtles all the way down in other words.

The solution to this problem from ID, but the one they refuse to admit, is that inevitably they must admit somewhere down the line that there is a supernatural designer. Essentially a designer that according to their own ideas doesn’t require being designed first by something else and can do the ‘initial’ designer. Now this doesn’t invalidate immediately that we may have been designed as some assert. We could be the product of design from an alien race that was really created by a supernatural entity to begin with for whatever purpose- it is just that we have a perfectly good explanation in evolution already.

Unfortunately, when we meet that race and share tea we suddenly end up at square one anyway: What designed our designers? It’s not surprising to me that those who want to masquerade ID as some form of ‘valid’ science suddenly become completely allergic to this concept and try to explain it away as fast as possible. Essentially, they want to have their pet concept that things were ‘designed’ yet they don’t want to deal with explaining how it was designed.

For example, let us just say that there is some biological structure we want to know is designed. As scientists, natural questions arise such as how did the designer produce the structure in question, what method did the designer use and why did the designer make the particular structure in that matter. More importantly, they need to make a hypothesis that competes with the evolutionary hypothesis and provides a better explanation not just a explanation. The explanation of a designer must account for the methods, reasons and motivations for making that structure to be conclusive.

For example, let’s say there is a new terrible disease that has struck the world and is beginning to kill hundreds of people world wide. How could we tell if this is an organism that has evolved by chance or that it has been designed by terrorists wanting to use it as a biological weapon (say it escaped). We would have two competing hypotheses immediately for the origin of this disease, but not because of the ideas of the ‘intelligent design’ movement, but rather because of something we do know:

We know about human designers.

Firstly, I would try to isolate the organism that is responsible, most likely a virus of some sort and then isolate its DNA to sequence it. Once sequenced, in other words we have the ‘code’ of nucleotides (Adenine, thymine, cytosine and guanine) that make up this organisms DNA. We could infer it to be designed by humans or that it evolved by looking at this organisms genome.

In the case of a human designer, we could look at the series of genes and how they are linked together in the organisms DNA. Commonly used in the laboratory are enzymes called ‘restriction enzymes’ that cut DNA at specific locations. Importantly in genetic engineering, they leave little overhangs of the DNA strand they cut allowing you to ‘stitch’ the DNA fragments they produce together. This is important in making transgenic animals and producing novel gene clusters (for example to insert a gene into an expression system like a plasmid).

If we saw a series of genes along the organisms genome that look to have restriction enzymes placed exactly between each one, that would almost be ‘smoking’ gun evidence that this may have been an organism designed by human beings. If we look further and we find genes that would have been difficult, if not impossible to have been captured through horizontal gene transfer, such as entire genes of the human immune system like IL-4 (which when inserted into mousepox virus made it much more lethal) then that would be even better evidence for this organism being designed.

On the other hand, this hypothesis still has to compete with the current scientific understanding of evolution. We already know that viruses can exchange segments of DNA if they co-infect the same cell as another virus, and that bacteriophages can capture pieces of DNA from bacteria and transfer them to other species. Additionally, retroviruses can insert themselves into the genomes of their host, being a potential explanation for the origin of a human gene.

But again, I want to emphasise something we’re talking about an organism being detected by design yes, but because we know of the methods of the potential designer. As ID proponents often point out while they sneeze half to death, ID isn’t about trying to work out what the designer is or the methods that it used, just that somehow life is designed.

But let’s review that more carefully:

1) Life is designed

2) The mechanism of this design is not something we want to talk about

3) Ergo, if we don’t want to talk about a mechanism then by default we are admitting we can’t talk about the designer

4) With no mechanism or designer, how do you infer design at all to begin with?

Let’s go back over my potential bioweapon example

1) A new organism is discovered and it may have been a designed weapon

2) We know 1 could be possible, because human beings have the ability to manipulate the genetics of living organisms, using restriction enzymes, plasmids we’ve ‘domesticated’ and other techniques.

3) We know that humans would have the motivations to make such a deadly organism because biological weapons have been used in the past.

4) As we know 2 and we know 3, we can directly test 1 to establish if it was designed or not because we have suitable grounds to determine this by the methodology and knowledge of a potential designer (human beings).

Additionally, unlike claims of ‘design’ from most ID members, this is also inherently falsifiable logic because we can rule that another mechanism (evolution) may be a much better explanation. In fact, it may be it was simply an example of a newly evolved pathogen but it would at least in both cases be testable as to the origin of the newly derived organism.

Inherently ID has the problem where it is incapable and indeed unwilling to talk about their ‘designer’. They know, just as well as their opponent’s, that ultimately ID rests on no true empirical or testable ground without having an actual verified designer. There is no way for them to ever rule out evolution, which itself, has numerous testable and falsifiable claims about the organisms and structures we see. Without a way of providing the mechanism of design or the designer, they provide no logical reason to infer any sort of design in human beings or anything else for that matter.

ID is, without a designer and refusing to talk about anything to do with said designer isn’t “God-of-the-gaps”. ID is “No-designer-at-all-to-put-into-the-gaps” which is even worse, because at least with “God-of-the-gaps” you at least have named the designer. Even when you have you then end up at square one if that designer was natural, who designed them? Then it's back to turtles all the way down.

Media see through the ID spin

Despite the best efforts of the discovery institute and other ID proponents, they are slowly being exposed for what they are and the media no longer buys their facade now.

"It's not about education or science, it's about politics," Uselton told The Associated Press during a group interview of teachers at the National Education Association's annual meeting. "That's the problem, and that's what we have a hard time separating out. Part of it doesn't have anything to do with the science being right or wrong."

As it can be seen the 'teach the controversy' curtain has begun to be pulled back but unlike in the Wizard of Oz, ID doesn't even have a little man behind it. What is there is small, furry and has a really long pink tail...

Speaking of rats, the article also contains the usual "scientists have signed something we put forward to earn us false credibility" nonsense creationists like to resort to. It's as if they treat science as some form of popularity contest.

"We want the scientific evidence for and against Darwin's theory taught. That's it," Chapman said. He said intelligent design is not sufficiently developed to be required teaching, but he points to more than 400 researchers who have signed onto a scientific dissent of Darwinism.

If we want to play like that, how about going to the National Center for Science Education sites own list of scientists that support evolution. The catch? They are only allowed to sign if they are called 'Steve' and already outnumbers the list that the ID proponents constantly harp about. Scientific 'dissent' indeed.

Tom Cruise nuttery and psychiatry

A blogger at "you can't make it up" has posted a wonderful transcript of the interview where Tom Cruise made an ass of himself on public television. The best part of this transcript is the hillarious choice of pictures, so it is highly recommended read for anyone wanting a laugh.

More fun and political games

You know, it's just wierd when I hear that a politician agrees with a concept like stoning homosexuals to death. Apparently however he 'abhors' violence and wouldn't ever want to have someone stoned to death because they are homosexuality, but the concept is still right!

I'll leave that to the reader to decide for themselves how ridiculous it is.

Condoms and STDs part 2.

No sooner had I spoken the other day when I am sent a link to an article where groups are trying to trying to undermine the effectiveness of condoms against STDs. Of course, this is more politically rather than good common sense grounded muck from the abstinence campaigners, for example:

"The Medical Institute for Sexual Health’s board chairman, Dr. Tom Fitch, who has previously pushed FDA officials for label changes, said some STDs are much more easily spread than others. In addition, STDs such as herpes and human papilloma virus, or HPV, can be transmitted by contact with skin not covered by a condom."

As I discussed previously, some STDs do not require fluids to be passed from one person to another and genital warts (Herpes) is a classic example of that. Again, the solution to that is about education to try to reduce risky behaviours, not outright scare tactics and essentially manipulating the story to sound like all STDs are similarly effected. This doesn't change the fact the most common STDs (see the graph presented) are protected against by condoms if used properly, namely chlamydia and gonorrohea which are the two leading STDs in America. It's also worth noting that these are the same kind of 'abstinence only' groups that oppose the likes of making use of a vaccine against human papilloma virus, which can cause cervical cancer in extreme cases.

These people don't care about public health, or anyones health and merely wish to peddle their own beliefs onto everyone else. This is of course, all despite how much abstinence campaigns have been *demonstrated* to fail consistently at doing anything to reduce rates of sexual intercourse in teens.

STDs and failure rates.

One thing that irks me is how people apply statistics or similar rather erroneously to insinuate some sort of goal or aim. As I've shown in the past, many groups that are opposed to public health measures like vaccines, often manipulate or distort various statistics. So it seems that certain groups are again distorting facts away and trying to discredit the useage of condoms for preventing STDs.

Firstly, condoms when used correctly have been repeatedly demonstrated to protect against STDs such as gonnorhea and chlamydia. Unfortunately, this is not usually the ideal situation and condoms are not always used correctly each time. The fact is, many teens are confused about how to use condoms properly and this leads to condoms being considerably less effective than normal (Warner et al 2005). The same study also verified that many factors in reporting condom usage resulted in underestimating the effectiveness of condoms. Unfortunately, detractors of sexual education campaigns often use these as 'evidence' condoms are ineffective or similar.

A second problem occurs in that many teens do not recognise oral and anal sex as 'sexual intercourse' (Nicoletti 2005). Because someone cannot get pregnant through these routes, many do not regard it as significant to use protection. Unfortunately, diseases such as chlamydia and gonnorhea can be spread through oral sex (as an example). This means that even when condoms are not used in terms of vaginal sex, indivduals may still be infected by another route.

The best solution is to make sure that teens are well educated about how to use condoms properly, the risks associated with different kinds of organisms (Herpes transmission is unaffected by condoms generally) and what they should consider to protect themselves. Unfortunately, miseducating people about the effectiveness of condoms and what STDs can and can not do is not going to help.

Warner L., M. Macaluso, H.D. Austin, D.K. Kleinbaum, L. Artz, M.E. Fleenor, I. Brill, D.R. Newman, and E.W. Hook III (2005). Application of the Case-Crossover Design to Reduce Unmeasured Confounding. American Journal of Epidemiology, 161,8:765-773

Nicoletti A. (2005). The Definition of Abstinence. Journal of Pediatric and Adolescent Gynecolology, 18:57–58.

Meningococcal vaccine opposition debunked

Associate Professor Glen Buchan from the University of Otago has wrote a very readable and well argued letter to the ODT in support of the MeNZB vaccination campaign, debunking numerous claims from anti-vaccination groups in New Zealand. My favourite quote from the article and something I wonder about myself was this

"I am often astounded by some people’s opposition to something as positive as vaccination. I believe that the real issue that lies behind the frenzied attacks on the vaccination programme by a vocal few is a belief that vaccination is unnatural or unnecessary and that there is some great conspiracy under way to line the pockets of multinational companies. The purpose of a vaccine is to mimic infection in a safe way."

It is unfortunate that such beliefs are unreasonably propagated as 'facts' and are even required to be debunked to begin with. Indeed, as the conclusions sums up perfectly:

"My biggest fear is that, because of their efforts, the anti-vaccine lobby will be proved right. If more and more people withdraw from the programme it is only a matter of time before the numbers immunised drop too low to stop the spread of the disease. The disease will continue to kill and maim and the opponents will be able to say, “See, we told you so”.
My only question to them would be, “Will our children benefit from your pyrrhic victory?”"