Saturday, December 31, 2005
1) Save some money for a while. Important this one because I've experienced the fun of being a broke student and the one thing I know about that lifestyle is that it isn't a lot of fun. I'll need a kitty for some fall-back then.
2) Head to Canada and the US (Minnesota in particular). Always wanted to have a wander around the USA and also to go and visit my numerous friends in Canada.
3) Have a publication in a reputable journal by december, with some luck anyway although this will depend on what PhD project I end up doing probably.
4) Oh and see that special someone of course! :D
So there you are. Have a happy New Years to all!
Thursday, December 29, 2005
"The findings of three labs showed the number two and number three stem cell lines that needed confirmation with regard to the 2005 paper did not match with patient tissue cells and were found to be fertilised-egg stem cells of MizMedi Hospital," Roe said.The same panel that last week determined that Hwang had falsified photos has now determined that the two remaining stem cell lines are non-existant. It turns out that the two remaining lines weren't even produced in Hwangs lab and were from a lab in Seoul hospital. Neither of these two stem cell lines were clones from a patient.
If the entire thing could get worse, it would be with the discovery of falsification in the snuppy paper. The whole thing will become the greatest example of scientific fraud and this is even considering last century I think.
Update: I found the original Reuters article and it looks like Snuppy could be a ray of light in the whole thing.
Hwang did receive a bit of good news when a DNA lab in Seoul, which is not part of the panel's investigation, said testing they performed had indicated Snuppy was an actual clone. But that was a small ray of light on another somber day for the scientist.I'd certainly hope so.
Wednesday, December 28, 2005
BirdLife does not think that wild birds are vectors - carriers - of H5N1, and believes that the widespread speculation during the autumn that migratory birds would spread bird flu from Asia far and wide into Europe was entirely misplaced.What? Going to Nature and having a quick look, it turns out that Bird Flu has indeed been reported in Europe with several reported accounts.
"Millions of birds have now migrated, and it hasn't happened," said BirdLife's Director and Chief Executive, Dr Michael Rands.I think that is slightly erroneous considering the evidence.
He went on: "Wild birds are often being blamed for the spread of avian influenza, but as far as we can tell there is no clear evidence, in fact no evidence.Well, I think that the general scientific consensus on the matter would happen to disagree with him here. While I think there is merit to the idea that adding birds feces to fish stocks could be important, I do not think that it's the main form of transmission or the most important.
Monday, December 26, 2005
Saturday, December 24, 2005
“This galvanizes the Christian community,” said William Dembski, a leading proponent of the theory and a senior fellow at the Discovery Institute, a Seattle think tank that promotes intelligent design research. “People I’m talking to say we’re going to be raising a whole lot more funds now.”Wesley R. Elsberry has wrote an extremely good response that can be read here:
Where to start? Well, I do think that the Christian community should be galvanized, but certainly in a way different from what Dembski thinks. Judge Jones’ decision clearly lays out how both the specific actions of the Dover school district and the general tactics of “intelligent design” advocates have been based upon deception, subterfuge, and lies. We as Christians should reject utterly the sort of lies, mendacity, and innuendo that not just characterize antievolution, but comprise it. It is a blot upon the reputation of the body of Christ, an erroneous and injurious digression from the serious business of making our lives an example to the world.Exactly, I doubt anyone could have said this any better.
NZ authorities are acting dishonestly and reprehensibly by preying on unsuspecting foreign tourists, students and new immigrants, while failing to inform them about the dangers of exposure to the excessive UV radiation in New Zealand.If I didn't know better, I could swear this is some sort of parody of certain claims made by the Greens among other individuals here in New Zealand.
COLMES: What would be the other options if it's not God?
BEHE: Well, you know, other things that would strike us as, you know, as pretty exotic, you know. Space aliens or time travelers or something strange.
COLMES: What about any of this is scientific?
BEHE: I'm sorry?
COLMES: What about any of this is scientific?
That is a remarkable zing as it definitely gives the appearance the host saw straight through Behes charade. It seems that even conservative media outlets are catching on to the fact ID is a bunch of vacuous bunk.
In the case of the 9 cell lines for which evidence was lacking, DNA fingerprint tests purportedly matching the lines to specific patients were found to be worthless. DNA tests are now being carried out under the remit of the university investigation to see whether the two remaining cell lines are in fact cloned from specific patients, as claimed in the paper. The committee says these results should be back in a few days.So now there aren't even five surviving lines it turns out there are two and they aren't even sure if they are clones. The aftermath of all of this is going to be equivalent of a nuclear explosion, especially when the South Korean government begins asking "where did our 65 million dollars go".
Friday, December 23, 2005
1) Researchers at Seoul National University, led by Woo Suk Hwang successfully used a technique called somatic-cell nuclear transfer to produce a line of patient derived stem cells. This has basically been the holy grail of stem cell cloning, because developing such patient specific stem cells avoids problems like donor incompatibilities and allows for new sources of tissue to be derived easily. The importance of this should be fairly clear from the fact this was published in Science and if you're wondering, that is one of the most prestigious journals around so this was big news.
2) An anonymous writer on the 6th of December leaks word that some of the photographs of the original paper are suspicious. This culminates in a phone call between Hwang and the editors of Science, where it turns out that some of the photographs have been duplicated. Not only that, but closer inspection of the paper revealed that some of the genetic sequence traces also turn out to be suspicious.
3) Things rapidly get worse with Sung II Roh claiming that Hwang had directly falsified results and then the revelation that of 11 stem cell lines, 6 had been contaminated and destroyed (more on this below).
4) Escalation from this point is inevitable with one of the authors, Gerald Schatton who collaborated on the paper, asking for his name to be removed because he no longer trusts the result. For a scientist to declare this on a paper is a massive thing to do and also something you can't do. So instead, the editors of Science after consulting Hwang, actually retracted the paper.
5) Now the full weight of scientific scrutiny has been placed on all of the research from Hwangs lab. This starts with the observation that one of their earlier papers has also been found to be dubious:
And there are now concerns about earlier work. For example, in the paper in which Hwang claimed to have extracted the first stem-cell line from a cloned human embryo (W. S. Hwang et al. Science 303, 1669-1674; 2004), figures supposedly showing cloned cell lines are identical to those in an earlier paper showing normal embryonic stem cells (J. H. Park et al. Molecules and Cells 17, 309-315; 2004).Additionally, Nature has also decided that they should launch an investigation into another paper from the same group where they made the first cloned dog "Snuppy".
Lanza says that Snuppy, seen on the right with the dog from which he was supposedly cloned, might have been created by a technique called embryo splitting, in which cells from an early-stage embryo are divided and then implanted separately. The technique creates identical twins. One set of cells could have been used immediately to create a dog while another was frozen and stored. If the frozen cells were later used to create a dog with identical DNA, that could be presented as an SCNT clone.Such trickery could be caught by examining mitochondrial DNA, which is passed maternally with the egg cell. If Snuppy were really a SCNT clone, he should have the mitochondrial DNA of the dog from which the egg was taken. If he's a fake, he'd share it with the dog from which he was supposedly cloned. Mitochondrial DNA data have not been part of previous cloning papers, and were not presented in Nature. Lanza suggests that it would now be a good idea to do the test. "If the mitochondrial DNA is the same, that's the end of that paper," says Lanza.
Nature is starting an investigation, including a mitochondrial DNA test, that is unlikely to be complete before January 2006.Ouch.
6) Finally we come to the newest development (23rd of December), where a Seoul National University panel has determined that the research has been intentionally fabricated. This has resulted in Hwang deciding to step down. Now this is not confirmation of any particular fabrication as Hwang has defiantly said that the research will stack up, but at the moment it's sounding like the vultures are circling for him and his research team.
So with the background out of the way it's important to consider three seperate issues:
1) How likely is it that the results are falsified?
2) What does this mean in terms of stem-cell research.
3) How can this fiasco be prevented from happening again?
....the team had problems with their cell lines. He said that last January, contamination with yeast had destroyed at least six of the lines the team had created. Based on Hwang's statement, it's not clear whether any of these original six lines were alive at the time the Science paper was submitted in March. The group was "lax in our management and committed many mistakes," said Hwang. He said they would thaw the five remaining cell lines to try to demonstrate that they match their donors, a process that Hwang said could take about 10 days.Now let's be clear on one thing: developing these stem cell lines would have been expensive, highly time consuming and immensely frustrating. To have lost over 50% of the total stem cell lines they had created is highly suspicious. While I acknowledge how difficult it can be to keep a cell culture sterile and preserved, there is just something somewhat fishy about the entire claim. Considering that the security on these things was pretty tight and strictly controlled from what I can gather, for example from Nature we learn this tidbit:
When Nature visited in 2004, he declined to show his first cloned stem-cell line, kept under lock and key. "Many lab members aren't allowed to see it either," he said. Taken together, the concerns about Hwang's work leave biologists with no proof that stem cells can be extracted from cloned human embryos.So you can see that there was some fairly tight control over this because it was obviously recognised for the important development it was. Yet, months after the paper was published (with unsuccessful attempts at replication by other researchers) we suddenly learn when questions arise that six of the stem cell lines were destroyed? Oddly, only five of the original 11 stem cell lines are supposedly still around and we won't be able to verify anything about them until at least the 26th (they were thawed on the 13th as far as I know). This is all sounding very suspicious indeed as with the importance of these cells wouldn't someone have kept sterile backups? Remember that Hwang was keeping his first cloned cell line under lock and key, refusing to show it to anyone else (which is equally suspicious, but admittingly with the competition in this area of science is understandable). This clearly doesn't add up.
Aside from this issue about this destruction of the stem cell lines, we also see that there appears to be widespread falsification of figures. Now, I'll grant to the reader that this isn't an altogether clear cut thing in science, particularly as to what is making a figure, picture or similar 'clearer' and what is out-right falsification. However, once again I think a clear case can be made for simple 'out-right' falsification. Firstly, it had already been noted that some of the pictures used in the study happened to be duplications during the review process for the paper, and that some of these duplications apparetly survived into the final draft as well. The editors of Science happen to note:
When questions were first raised about duplicated images, editors at Science said that it appeared the duplications occurred after the paper was accepted and when new, higher-resolution images were substituted for publication. But Katrina Kelner, Science's deputy editor for life sciences, says it now appears there were problems in the original submission as well. Although the four duplications that Hwang pointed out to editors were not in the original submission, she says, the original figure had at least one apparent duplication that also appeared in the final version. Figure S1 shows 68 cell photographs, which purport to show evidence of 10 of the 11 cell lines expressing up to 6 different protein markers typical of ES cells. But one image labeled as cell line number 8, expressing a marker called SSEA-4, shows the same colony of cells, though slightly shifted, as an image labeled cell line 7, marker SSEA-3. Kelner says that editors have asked the researchers to explain the images, "but we haven't gotten answers."And also with a part high-lighted relevant to the above destruction of the stem cell lines.
It also seems that questions raised during the review process may have unwittingly helped undo the paper. In their original submission, Kelner says, the authors provided fingerprints from only some of the cell lines. Reviewers asked for fingerprinting data from the remaining lines. It is not clear if the questionable fingerprints were in the first submission or in the additional data the reviewers requested. Editors declined to specify which lines were missing in the original submission.It makes me wonder with that particular piece of information, which of the 11 cell lines have been destroyed and what are the 5 surviving ones? It seems awfully convenient that not all of the cell lines had fingerprinting data available, which would be able to verify the exact lineage these stem cells were derived from just happens coincidentally (it turns out) that 6 of the lines are destroyed? Oh now this is really not adding up.
Additionally, Nature reveals that Hwangs team may have falsified figures concerning the original extraction of a stem cell line from a cloned embryo may also contain falsified images.
And there are now concerns about earlier work. For example, in the paper in which Hwang claimed to have extracted the first stem-cell line from a cloned human embryo (W. S. Hwang et al. Science 303, 1669-1674; 2004), figures supposedly showing cloned cell lines are identical to those in an earlier paper showing normal embryonic stem cells (J. H. Park et al. Molecules and Cells 17, 309-315; 2004).Given an isolated incident that could be a very easily explainable mistake, just got a file name wrong and inserted it into the paper by mistake. In light of the deception given in the pre and post publication science paper that originally came under dispute, that this is deliberate falsification rather than a mistake becomes a much stronger argument. Worse for Hwang, if the investigation into the Nature paper on "Snuppy" the cloned puppy reveals the same mitochondrial DNA as the mother then the paper will have to be retracted, which will be a double blow for the Korean researcher.
So here we have documented and seemingly repeated incidents where results have been falsified by a particular group. Additionally, it appears that the original paper results are difficult to verify and have not been experimentally repeated by other researchers. The destruction of these 'break-through' stem cells is either some amazing incompetence or hiding the fact some of these lines may not have been what they were claimed to be. Although this would be in other cases just be paranoid rambling, the demonstrated falsification in two of their papers and lack of additional experimental verification lends considerable weight to this interpretation.
Frankly, I think things are fairly obvious that the results of the paper have been falsified.
In terms of the future for stem cell research this has probably done a lot of damage not just scientifically but politically as well. Opponents of stem cell research oppose the research based on moral, ethical, religious and political grounds. With a result like this, you can almost expect the knives to come out and opponents to get much more vocal. I think the editor of the American Journal of Bioethics on his weblog wrote a particularly telling point about what the whole affair will mean:
could firmly establish in the public mind the view that stem cell researchers as a group cannot be trusted, not only because they are in a hurry and miss things along the way, but because they may be willing to deceive their own peers and the public about their devotion to ethics.Bear in mind that to these people, embryonic stem cell research isn't able to "go anywhere" and is simply murder. This kind of mentality is well demonstrated by the likes of prolifeblogs where they write:
But while the reports of faked data and illegitimate results have cast a dark shadow on ESC research, the emphasis of criticism and debate needs to center on the intrinsic value of human life and not on the low probability of ESC success. The latter is a pragmatic argument that places the life of the embryo in a position that is subservient to the potential benefit his or her destruction will provide others. Conversely, the inherent dignity of human life impales any argument supporting pragmatism as a basis for bioethics.The worst part of all this is with the fine example that Hwang has now set, they will have genuine ammunition to add to empty rhetoric. To most scientists, the incident with Hwang will simply demonstrate irresponsible scientific fraud to 'publish first' in an incredibly competitive field. To the likes of prolifeblogs this will be confirmation of their beliefs that embryonic stem cell research is nothing more than a political tool to advance peoples careers and not legitimate science. However ill-founded this perception is in reality, this incident will not help by any means of the imagination.
This train-wreck (I don't think it can be called anything else at this point) will not prevent the funding or research into stem cells. In fact, in some ways it may even aid the call for increased funding of American stem cell research so that the practice may be more tightly regulated. This is probably an unlikely scenario however, but it will increase the amount of skepticism (ironic really) applied to the claims of researchers in this area. Additionally, the entire thing could potentially give fuel to the establishment or prolonging of laws that ban stem cell research as well. Although I would like to produce a positive note of increased awareness about scientific fraud and being more careful about results that seem 'to good to be true', the most likely result is a religous right led witch hunt that could have disasterous effects on future research.
Further, it's also worth considering that a large amount of data, seemingly critical to many of the papers claims appears to have been omitted such as sequence traces. Additionally, other independant researchers had considerable difficulties in replicating the results from Hwangs group. All of this leads to the unsettling prospect that none of the results are actually real at all and this incident is one of the worst examples of scientific falsification in history.
To avoid such an incident in future requires much more skepticism from even the top journals of the world it would seem, especially when it involves 'hot' science. Papers that appear to have omitted relevant or potentially important information on their results need to be double checked and such information added to the paper. Further, in my opinion there should be an analysis performed on the relevant figures and images that a paper uses, to check for potential duplications and otherwise misleading images. These measures are the sorts of things required to make sure that stem cell research is appropriately conducted so that the field can regain the publics trust.
And as for Woo Suk Hwang? It will indeed be a mighty fall from one of Times people who mattered in 2004 to the first biggest scientific fraud of this century.
"Now that the vaccine campaign is past its peak they don't want any bad news coming out."A child under the age of 1 was one of the victims and the second was a 60 year old woman of which, neither of the two people have been vaccinated (in fact, nobody over 20 has recieved the vaccine). So yes, this is certainly damming evidence that the vaccination campaign is all a sham isn't it Mr. Law? Maybe to someone living in a different reality it is, but in any event, going back to this reality let's look at the actual cases. Of the 32 meningococcal cases detected in the Waikato, 17 were confirmed to be of the epidemic B serotype and that none of these cases were in individuals who were fully vaccinated, though a few were partially vaccinated.
Carrying on through the stuff.co.nz article, we see anti-vaccination opponents have made noises regarding the noting of 'break-through' cases where several individuals who have been fully vaccinated have got the disease.
Meanwhile, opponents of the mass campaign are questioning its benefit after the release of figures from Counties-Manukau which showed several immunised people caught the disease. The Counties-Manukau campaign started first and by February there will have been a one-year observation period of fully vaccinated people.Firstly, we should investigate what the actual data from the region has been since the introduction of the vaccine (PDF document containing data and figures on the region from the ministry of health, a must have to follow the remainder of the post). The two figures demonstrate a quite significant drop compared to the previous years, with the rates of meningococcal B being immensely low at comparative periods. In other words, this is establishing that the vaccine has been fully effective in its intended original purpose, in other words to lower the number of cases of the disease. Now secondly, we'll observe that there have been several known examples where fully-vaccinated individuals have gotton the disease.
This is not an unreasonable or unexpected thing to have occured for two primary reasons. As the rates of vaccination go up, the only people that can potentially be infected with the organism coincidentally end up being those who are vaccinated. No vaccine can be 100% effective and instead the reliance of how a vaccine works is by herd immunity, where a virulent organism 'burns' itself out of susceptible hosts until it no longer encounters anyone it can infect. With such a large sample size (160,000 individuals have been followed in this case) for a mere 8 break-throughs among 6 weeks to 19 year olds, from a vaccine expected to be around 80-85% effective is very good. Additionally, the figures for those ages 4 weeks to 4 years (where the vaccine would be expected to be most effective, as the immune system is most active around this time) are even better with a mere 1 case.
Quite simply, the mewling about this coming from anti-vaccination groups is simple desperation to paint anything negative about a campaign that has worked brilliantly. By all means however, look at the simple reduction in cases since the introduction of the vaccine in the two graphs compared to the previous 4 years. Since the introduction of the vaccine it's self-evident to anyone without a clear anti-vaccine agenda this campaign has worked brilliantly. Speaking of those with an anti-vaccination agenda:
Mr Law said it was clear that the vaccine was not working in Counties-Manukau.Yes, well once again let's investigate the claims that Ron makes by again referencing the actual graphs from the region that the ministry of health have provided. Once again, if such a massive drop in the number of cases is 'not working' then you would have to wonder what Mr. Law would consider for the vaccine 'working' or not. Very clearly, Ron is making up any rubbish he wants to try and support his agenda, of which this statement is the true howler of the entire article.
"It hasn't made one iota of difference to the decline that was already occurring prior to vaccine rollout."This is a common anti-vaccination crank claim and is repeated endlessly no matter what the agent is, be it polio, measels, smallpox or any number of diseases. Unfortunately for Ron Law, his statement can quickly and easily be seen to be bunk by using the same two graphs provided by the ministry of health. The 'decline' that Ron Law is undoutably reffering to can be seen at the beginning of every single year in the two graphs. In fact, you'll notice that every year starts out with a small number of actual cases. Even the second highest year (2003 on the graph) started with 0 cases being reported in february and then, like every previous year spiked up sometime around may.
For those of you from overseas, around April-May is when New Zealand starts to get into its winter period and starts getting cold. This is obviously when all manner of diseases, including the flu which has similar symptoms to those of early meningococcal disease start to rise. The very fact that every year sees the same rise and then decline of the disease (with corresponding spike again the next year) should make it evidentally clear that Ron Law is full of rubbish. To see what might have been however, you should note that even with the vaccine the cases have still risen towards the end of the year just much less significantly.
As an analysis of the actual data shows (and I highly recommend downloading the ministry of healths report for yourselves and looking at the two graphs especially), all Ron Law has now is empty rhetoric to save face after every argument he gibbered about earlier in the year has been proven false. At least with such a brilliant art for spinning arguments he could also apply for a job at the Discovery Institute.
Thursday, December 22, 2005
Scott and Branch add, "... the sectarian orientation of ID renders it unsuitable for constitutional reasons."
As we all know what the result of exactly this kind of trial was, can we assume that Dembski will be able to live by his own words and indeed pass a bottle of single-malt scotch to his opponents? After all, he's just been proven categorically (and disasterously) wrong on nearly every single point.
Comment: They are herewith throwing down the gauntlet. I'll wager a bottle of single-malt scotch, should it ever go to trial whether ID may legitimately be taught in public school science curricula, that ID will pass all constitutional hurdles. To see why, check out the fine Utah Law Review article by David DeWolf et al. at http://www.arn.org/docs/dewolf/utah.pdf.
Incidentally, for the observant reader also note that most of the arguments presented in 2002 haven't altered even slightly from the arguments made these days. I guess even after 3 years of ID 'research' they still haven't gotten anywhere.
As many blogs have posted up their favourite quotes I think I'll just have to follow suit with this one:
Moreover, in turning to Defendants’ lead expert, Professor Behe, his testimony at trial indicated that ID is only a scientific, as opposed to a religious, project for him; however, considerable evidence was introduced to refute this claim. Consider, to illustrate, that Professor Behe remarkably and unmistakably claims that the plausibility of the argument for ID depends upon the extent to which one believes in the existence of God. (P-718 at 705) (emphasis added). As no evidence in the record indicates that any other scientific proposition’s validity rests on belief in God, nor is the Court aware of any such scientific propositions, Professor Behe’s assertion constitutes substantial evidence that in his view, as is commensurate with other prominent ID leaders, ID is a religious and not a scientific proposition.Considering that it was nonsense from Behe in "Darwins Black Box" that I originally encountered creationism for the first time, it's good to see that he's basically been shown up for being full of hot air and little else. Of course, since reading that book and admittingly, thinking it was somewhat accurate until I asked my professors about it, I've participated in a lot of written (online) and oral debates with creationists. In such mediums, things like spin, bait and switching and more play a bigger role in 'winning' the debate than the facts and evidence often. This is why I'm satisfied to see that in a court of law when facts and evidence rule the day, not only is ID defeated by their leading advocates like Behe end up impaled on their own dishonesty.
This victory hasn't just been one for science but one for common sense as a whole.
Oooh oooh! Update time, I have a new favourite quote
The immune system is the third system to which Professor Behe has applied the definition of irreducible complexity. Although in Darwin’s Black Box, Professor Behe wrote that not only were there no natural explanations for the immune system at the time, but that natural explanations were impossible regarding its origin. (P-647 at 139; 2:26-27 (Miller)). However, Dr. Miller presented peer-reviewed studies refuting Professor Behe’s claim that the immune system was irreducibly complex. Between 1996 and 2002, various studies confirmed each element of the evolutionary hypothesis explaining the origin of the immune system. (2:31 (Miller)). In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fiftyeight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not “good enough.” (23:19 (Behe).When I first read about Behe being 'unimpressed' by the amount of peer-reviewed studies and books on the immune systems evolution, I knew then that the Judge would pick up on that as one key sign of the vacuity of the Intelligent Design movement. It's very pleasing to read this statement in his decision, especially because it hits very close to home on my own interests.
Wednesday, December 21, 2005
It shouldn't come as a surprise then that numerous 'alties' and naturalists have decided to jump on this hypothesis to promote their agendas. For example, some anti-vaccination groups don't take vaccinations on the basis that the hygiene hypothesis supposedly 'supports' their idea that children should be exposed to potentially lethal pathogens. Of course, this ignores the fact that a vaccine works by stimulating immunity by the same kind of mechanisms as the original organism so isn't really that founded. Other alties have used the supposed support of the hygiene hypothesis to push things like probiotic treatments, natural health remedies and generally disparage conventional medicine.
This of course relies on somewhat of a distortion of what evidence the hygiene hypothesis actually has in support of it. The first thing to note is that the rise in allergies and other immune disorders has generally fit certain trends.
1) Allergies tend to fit a certain trend, where it's actually those in lower socio-economic brackets that tend to have the highest incidences compared to those who are better off [*].
2) It's not 'bacteria' and 'dirt' generally that people require but certain kinds of pathogens. For example, programs to remove intestinal worms like helminths and certain bacterial pathogens like Streptococcus pyogenes seem to be associated with increases of atopy (allergenic diseases).
3) Germ free animals that have been left without any exposure to microorganisms often demonstrate much higher levels of atopy than those unexposed. We will note however, that any establishment of a microflora, which is basically inevitable no matter how 'clean' you are tends to abrogate the increased incidence of atopy. In other words, every day microbes you are almost guaranteed to run into are likely to be protective so there is none of this 'needing to get plague' buisness [*].
So bear in mind that this increase in atopy is being explained not by a lack of 'germs' but rather by specific kinds of predictions. The lack of certain pathogens and the increase in pollution particularly in low socio-economic areas. When you see those alties blaming allergies on vaccines, no 'good' bacteria or other things, it would be best to cast a skeptical eye over the claims to see if they really understand the actual theory first.
*) J.F. Bach, The effect of infections on susceptibility to autoimmune and allergic diseases, N. Engl. J. Med. 347 (2002), pp. 911–920.
Welcome to the happy non-denominatonal sometimes religiously significant festivus holiday celebration for the 24th skeptics circle! While everyone else would normally have to wait until the 25th we in the skeptical community get some early presents: excellent skeptical blogging from across the skeptical community!
So let’s start opening up the early presents and get right into things, first we start with some light hearted fun with a bio-Christmas carol from the science creative quarterly. Following this up is asking the ever important question; can science determine if there really is a Santa?
Presents on the nature of skepticism are the next on the agenda. First, the good folks from Real Climate bring us an article discussing how to be a real skeptic. Daniel Morgan brings us a similar themed article where a man shows an unusual skeptical double standard in a museum in the master painter. Finally, the Uncredible Hallaq describes what good science looks like. This is definitely shaping up to be a great collection of presents!
For the next set of presents to unwrap, we’ll go to the syringe shaped package wrapped in tin foil. What could this be I wonder? Oh, it’s some anti-vaccination crankery from Bill Maher! I think we’ll hand this one to Orac and Skeptico to handle in their gifts, Bill Maher anti-vax wingnut and Drinking the anti-vax cool-aid respectively. I do so love the gift of a good logical smack down at designated holiday periods, don’t you?
What’s next I wonder, hmmm, what about this big box over here, must be something good in that for such a big box! Hmmm, but funnily enough it doesn’t make a sound when shook what could be inside and it’s pretty light too.
Oh let’s just open it! Aha, as I suspected, it’s just an empty box with nothing in it and must be the present the Creationists and Intelligent Designer proponents sent us God – oops I mean the unnamed unidentified intelligent designer bless them. Numerous gifts refuting this lot, beginning with Daniel Morgan trouncing the ID spin over the Sternberg Affair in the Sternberg saga continues. Following that, the Socratic Gadfly discusses the problems with biblical literalism in Ezra meet Snopes. Bora at Science and Politics brings us a gift imported all the way from
Continuing with the creationism and ID themed presents, which are always good presents to receive, we have the Pithing Contest explaining there is something fishy about fish eyes. Pooflingers demonstrates the gift of patience by suffering through more creationist nonsense to bring us crunch squared volume 4. Dump Bachmann finishes up the creationist themed presents this year with Micheles pal and donor Phyllis describing the crouching senator, hidden creationist (good movie that, I have it on DVD).
Time to look at some other presents I feel after all that creationism, so ahhh, what’s this I spy? Some more quack medical presents including A Himalayan salt crystal lamp? I seem to recall the Saga of Runolfr describing if a Himalayan salt crystal lamp actually worked or not. Speaking of Quack medical claims, Kevin Leitch sent us this present discussing a fertile breeding ground that alties find in making up causes for autism. Speaking of various alties, the second sight describes the placebo affect as a real alternative, however much it is maligned by those pushing alternative medicines. Finally, as a special present from myself I've written an article clearing up confusion about the hygiene hypothesis, which has occasionally been distorted by those who push alternative medicine to 'support' their cause.
Starting to run out of presents now, only a few more left and then all the presents will have been opened. This next present comes courtesy of the conspiracy theorists who claim man never landed on the moon, a hospital report for being punched in the face? What an odd present. Maybe the Bad Astronomer would know more about that, as he decided to go head to head on a radio program and describes his experience of taking the quacks on word to word (literally) in mooning St. Louis and the follow up, mooning St. Louis denouement. Congratulations to him as well, because I know from experience how difficult it can be to engage cranks in an oral debate where it’s harder to cover all the needed evidence.
This present is one that, with my specialty in microbiology and immunology I wished didn’t exist, but the HIV doesn’t cause AIDS wingnuts have sent something our way yet again. Personally, it’s the equivalent of the lump of coal in the stocking for me, but thankfully, Orac is on the case for the debunking sending some of his own gifts with one last thought about the Al-Bayati report and describing how ABC handled the Eliza scovill case on primetime. Hopefully I’ll be less naughty next year so I won’t attract the lump of coal again.
Finally, we’ll end the circle with the ultimate present, the theory of everything. Well, maybe not the theory of everything but something that claims to be the theory of everything, which Rock Star Ramblings has a look at with alert scientists we now have a theory of everything. I guess it really wasn’t quite the theory that it was claimed to be, oh well.
And with the last of the presents opened it’s time to say goodbye and happy holidays. I hope you have a stress free holiday period and that there are lots more interesting presents under the Christmas tree for you. The next Skeptics circle will be hosted by Ted of The Saga of Runolfr on the 4th of January to kick off the new year.
Thanks again for all of the submissions and keep the circle going by keeping up with the cranks by producing more skeptical blogging! Comments should ideally be left on their respective articles :)
Tuesday, December 20, 2005
Also, if I've seemed a little quiet it's because I am planning a few things for this special pre- happy non denominational occasionally religious festivius holiday season (with luck I've covered all bases so nobody can be offended), so blogging will be a little light until the circle is posted.
Monday, December 19, 2005
Friday, December 16, 2005
Thursday, December 15, 2005
Overall a brilliant action movie.
Wednesday, December 14, 2005
Tuesday, December 13, 2005
Looks like Steven Spielberg has managed to annoy aspects of the Jewish community, with his new movie about the reprisals Mossad took against those believed to be behind the Munich seige.
Steven Spielberg's new film, "Munich," about Israel's reprisals for the slaying of its athletes at the 1972 Munich Olympics, has not opened yet but already many Israelis are convinced that the world-famed creator of "Schindler's List" has missed the point.
Many veterans of Israeli spy agency Mossad are among those up in arms at the film Spielberg calls his "prayer for peace," even though it won't open in the United States until Dec. 23 and in Israel on January 26.
Personally, I happen to agree with Spielberg that taking an eye for an eye is not a suitable way of solving anything in many respects. You can call the systematic tracking down and then slaughtering of the individuals involed 'defence' to a degree, but in the end the reprisals probably created as many new terror threats as it did solve them. Nobody probably got anywhere as a result.
Monday, December 12, 2005
It is however good to see that many scientists have begun to respond to the militant animal rights movements, by for example becoming more transparent about the research they are performing. Additionally, public education about why scientists use animals in their research and the way the animals are treated are apparently having an effect. Finally, new laws to protect researchers and the facilities in question are all reducing the amount of influence the militant animal rights movement has.
But official figures show that in the past year or so the number of extremist attacks has fallen. New laws proposed shortly after the halt to building work in Oxford last year have helped. Introduced this summer, they make it illegal to protest outside people’s homes if this causes “harassment, alarm or distress”, and to use harassment to inflict economic damage on a company. At the same time researchers have changed tactics. Instead of avoiding the public eye, they are being more open about their work and educating the public about the benefits of animal research to medicine.This has been needed for some time, because there is nothing worse to make people think there is a conspiracy than hiding behind a wall of secrecy. The public does have a right to know how scientists use animals in their research and the reasons why an animal is being used instead of using a computer simulation for example. It's certainly not because scientists enjoy torturing animals in experiments as some animal rights groups would have the public imagine, but instead it's because in many areas of biomedical science especially animals are the best way to figure something out (particularly about disease interactions). Animals are, after all, extremely expensive to use in research and cheaper, more effective alternatives are nearly always used where available if they can get the same results.
Like many reactions of the public against certain aspects of science, the only way to improve the situation is through improved education, plus communication between the general public and the scientists actually doing the research.
Friday, December 09, 2005
The outbreak of the superbug MRSA (methicillin-resistant staphylococcus aureus) indicates a breakdown in the new hospital's infection-control procedures.Thankfully, none of the children appear to have had a severe infection or died from the disease. This could possibly be attributed to the children in question not being on any particular antibiotics when they contracted the organism. Without antibiotics to select for the growth of the MRSA it would have had a growth disadvantage against other normal microflora. For all intents and purposes, they probably got rather lucky with this outbreak and that it didn't occur in a ward where there were more vulnerable children (such as intensive care or similar).
However, none of the four babies developed a serious infection and none remained in the unit, Canterbury District Health Board chief medical officer Nigel Millar said last night.
Thursday, December 08, 2005
Also as an additional bonus, I'm also hosting the next skeptics circle as well so send your entries to odojo450 at gmail dot com. One thing to note is I am from New Zealand so I'm ahead of many of you in the states and such. I'll be posting the skeptics circle a little later than normal as a result so that I make sure I give everyone the right sort of time-frame that other hosts have done previously.
Japanese and drama are the latest NCEA exams to be re-marked after checks showed disparities in the way they had been assessed.
The latest re-marking brings the total of NCEA standards to nine, including a level-one Japanese, a level-three drama and a level-one economics standard, three English and three mathematics papers.
Oh of course, more like this time they are actually monitoring the results before they come out to avoid embarassment later.
Also yesterday, Education Ministry officials defended the process at a parliamentary select committee where National MP Bill English suggested they were using scaling by another name and "massaging" results to spare the Government the embarrassment of another exam debacle.Precisely Mr. English, precisely.
Of course the grey goo is basically a large set of replicating nanites that slowly eat their way through everything, as they madly replicate out of control until they swallow the planet and you with it. The concept is entirely bunk and is a gross misunderstanding of what the current 'nanotechnology' really means and not the one popularised in science fiction as I explained above. Just again so we're clear, nanotechnology in the current sense of the world doesn't involve little replicating robots, but is rather the fine scale manipulation of very small 'machines' like protein switches and structures like fibers at the nanoscale (very very tiny) level. What this sort of wierd comparison does demonstrate is we're well into the 'third' stage of new scientific developments, which is the 'irrational fear' part where people confuse science-fiction with science fact.
Some of the criticism against nanotechnology isn't all ridiculous notions of the worlds destruction at the hands of mad scientists, which is a fairly popular concept among fiction writers I have to admit, but is quite well grounded. Take this story from the New Zealand Herald I spotted this morning, discussing the use of nanotechnology although with a somewhat over emotional title, Tiny Technology Possibly Deadly. Some of the points that are raised are quite possible and definitely should be looked at during the future development of this technology:
Similar calls are being heard in America. At an Environmental Protection Agency nanotechnology workshop in October, Mihail Rocco, co-chair of the National Science and Technology Council, declared: "Federal agencies lack methods to monitor environmental releases of nanoparticles. Yet they can go to the brain and potentially cause damage."Which is quite true, although I would imagine this would be something that would have to be assessed on a case-by-case basis. In a similar manner to genetic engineering, you can't just use blanket laws on a technology just because it bears the same name. Each individual application is what must be assessed and obviously, different applications will have different kinds of risk associated with them. One of the things that I do wonder about with these kind of particles is how easily they would thwart barriers that otherwise block other 'nanoscale' dangers such as viruses. Again, concerns are raised in this area and highlighted in the article.
It states that, once in the blood, "nanoparticles can move practically unhindered through the entire body". During pregnancy, nanoparticles would be likely to enter the foetus.The effects of such nanoparticles, particularly their accumulation in food chains and in the human body must be assessed quite thoroughly. As an immunologist, I'm acutely aware of the growing numbers of people with immune disorders such as allergies and nanoparticles may provide an additionally risk to these inviduals. Of course, the nanoparticle itself may not be allergenic, but it could provide attachment sites for other kinds of allergens and together could make an 'adjuvant' kind of structure boosting the effect an allergen antigen would have. Of course, that's just theorycraft off the top of my head and should be taken as such, but it could well be plausible and these sorts of questions will need to be answered with regards to the safety of these applications.
Sadly though, the article isn't entirely quoting people who make sensible statements as one Bob Phelps from GeneEthics comments wildly:
Bob Phelps, director of the Australian lobby group GeneEthics, says: "Each type of nanoparticle may be as deadly as asbestos."While the statement may be true, it's somewhat wreckless and it doesn't really accomplish anything. If he were William Dembski, I'm certain he would describe this statement after the fact as a bit of 'street theatre', but it doesn't accomplish much except attempt to raise irrational fear over the technology. Compare the statement made above and the language used, to that from the more scientific sources listed in the article, which seem to have avoided making outlandish claims and are much more reasonable while still being cautious. What does the public tend to remember though? Usually the more outlandish claims (grey goo for example) are the ones that get remembered unfortunately (and nobody explains the actual technicalities to the public, one of the great failures of modern science I think actually).
This isn't to say that the article doesn't point out some of the, somewhat overblown claims of what nanotechnology will do for everyone.
Cancer cells could be destroyed by tiny silicon combs; "nanobots" could clear blocked blood vessels. Hydrogen-based fuel cells using "nanotubes" could allow cars to travel 8000km on a full tank. Minute solar cells in building facades and on road surfaces would produce cheap energy. Cancer cells could be destroyed by tiny silicon combs; "nanobots" could clear blocked blood vessels. Hydrogen-based fuel cells using "nanotubes" could allow cars to travel 8000km on a full tank. Minute solar cells in building facades and on road surfaces would produce cheap energy.That's some highly impressive stuff I'm certain! Those claims are even more impressive than those made by the probiotics fellows I talked about earlier. In reality of course, such claims are probably not incorrect, but they are more than likely exaggerated as a sales pitch. Funding is competitive at the best of times and everyone talks up their particular research areas. In infectious diseases for example, it's not uncommon for researchers to 'talk up' the effects of their pet disease of study over others (although this is easier in some cases than others). It's the same in other areas as well, such as the early research into genetically engineered foods claiming that they could 'solve world food shortages' (among other things). The reality is quite a bit different than that however, as while the above claims may be true there will be two conditions that will determine their overall success.
The first is that much of those applications are years off and even when they are developed, they'll still be years off while full safety trials and the like are conducted on them. So it's going to be a long time before any of those sorts of applications ever see the light of day. The second is that they may not be quite as effective as proclaimed and will possibly act not on their own, but in concert with other technologies coming out (particularly like other solutions for cancer, like possibly vaccinations targeting NK-T cells). If they did of course achieve what they are claiming that would be a wonderful thing, but the most likely probability is that the emerging science of nanotechnology is probably a long way off getting anywhere near those sorts of claims. The only thing it has to survive now in order to get there is the 'irrational fear' stage of scientific development. Responsible decisions are what is required to both foster the growth of nanotechnology and ensure it doesn't get out of hand.
Tuesday, December 06, 2005
So much for that 'ID' inspired research. More on this story can of course be found at the Pandas thumb (Who get a great amount of delight out of this sort of thing), here, here and here.
The Templeton Foundation, a major supporter of projects seeking to reconcile science and religion, says that after providing a few grants for conferences and courses to debate intelligent design, they asked proponents to submit proposals for actual research.
“They never came in,” said Charles L. Harper Jr., senior vice president at the Templeton Foundation, who said that while he was skeptical from the beginning, other foundation officials were initially intrigued and later grew disillusioned.
“From the point of view of rigor and intellectual seriousness, the intelligent design people don’t come out very well in our world of scientific review,” he said.
Monday, December 05, 2005
Probiotics are a concept that's been around for some time now since the late 1800s from Elie Metchnikoff; winner of a Nobel prize for his work on phagocytosis and who also happened to have an interest in the reasons why people age. One of the things that he noticed was people from Bulgaria who ate a lot of fermented dairy food products, such as yoghurt appeared to be longer lived. Metchnikoff thought that this was due to the addition of specific bacteria from these foods that outcompeted and prevented the 'toxin' producing bacteria from establishing. As a result for a while in Europe it was quite popular to have milk that had "Bulgarian bacillus" added to it. This addition of potentially beneficial bacteria to foods was the birth of 'probiotics' and has been developed upon ever since(1).
Possibly as a result of Metchnikoffs original observations, the bacteria typically used in probiotic treatments are of the genus Lactobacillus. Lactobacilli are fairly hardy organisms that are usually acid tolerant or acid loving. They are particularly common in fermented foods where the acid- notably Lactic acid - they produce as a metabolic by-product destroys other bacteria that would otherwise compete with them. Basically if you've ever eaten yoghurt, cheese and those sorts of foods you've basically eaten a large amount of Lactobacilli. Additionally if there was a candidate for Mrs. probiotic it would probably be Lactobacillus acidophilus. It's used in a wide range of products, such as milk, yoghurt (most commonly) and powder to stick in water. The claims made from the site in question are fairly common among probiotic advocates:
Sounds all well and good doesn't it, after all something that does even half of what is claimed would surely be a great benefit to a large number of peoples health. Of course, these products have to work by the bacteria in question establishing themselves and basically making a home in your stomach. If the bacteria don't get established in there then any benefit will be temporary or probably null and void. Additionally, a gut insult that disrupts the microflora* or makes things unstable may be equally as hostile to a newcomer and end up with no effect anyway. To assess the claims made above is actually surprisingly simple because the only question that needs to be answered is this: How easy is it to introduce and establish a new organism in a host?
Natren's Superdophilus benefits the small intestines of older children (over 7 years) and adults, and the vaginal tract of women. DDS-1 Super Strain is the most highly recommended of approximately 200 different known strains of L. acidophilus - many other strains cannot survive human gut fluid and bile salts. DDS-1 has been shown to be the most effective against the widest number of pathogens (disease forming microorganisms). Minimum 2 billion live active bacteria per gram (half teaspoon).
It is very important to replace your friendly bacteria after antibiotic use, steroidal drugs e.g. prednisone and birth-control pills with Superdophilus. Superdophilus generally aids your absorption of nutrients and may help deter invading bacteria and yeasts by producing natural antimicrobial substances and hydrogen peroxide - this strain effectively inhibits undesirable microorganisms that cause food poisoning, diarrhoea, yeast and thrush overgrowth (Candida). Assists lactose (found in dairy products) metabolism so enhances digestion of milk products - helps dairy food intolerance.
The answer? Bloody difficult. The one problem facing probiotics as a treatment or novel health supplement is that the established existing microflora doesn't take too kindly to the new comer (1, 2, 3, 4). In fact, the additional bacteria are only temporary and can only be detected for the period that the probiotic is being taken (3). This is because the gut microflora tends to end up in an homeostatic state where what bacteria got established first tend to stay there. Interestingly, this microflora tends to also rebound in the same sort of numbers even when it has been depleted, say after taking a broad spectrum antibiotic (the tiny scale equivalent of nuking all of Iraq to kill a handful of insurgents). It's also fairly unique and everyone will have slightly different compositions of bacteria in their gut, creating a unique 'poo-print' that identifies your insides as much as your finger print identifies your outsides. It's worth noting that detection of the probiotic bacteria says nothing about the number of bacteria that are actually there or doing anything in particular (1, 3, 4).
It is also questionable as to what these bacteria are doing even while they are present in the gut. Although there is research to suggest that gut bacteria are interacting with the hosts immune system (5) the actual extent of this interaction is relatively poorly understood (1). In fact, it isn't actually very clear what benefits probiotics may have at all (1, 3). While a lot of basic research has been conducted on the organisms responsible, there have been no rigourous medical or clinical studies performed on humans to assess the overall benefits these organisms may have. This is particularly true of meeting FDA (Food and Drug Administration) guidelines as the required phase I-IV trials have never been conducted on these probiotic organisms (1). Of course, it's worth noting that they can still be marketed with the above sorts of claims despite this, because Lactobacilli are "GRAS" organisms or "Generally Regarded as Safe" so haven't been put to the same vigourous review for a new treatment.
Although there are promising studies that have suggested probiotics can be effective, they are increasingly focusing on using specific bacteria for specific disorders and not the 'blanket' benefits as the advertising claims quoted above would have consumers believe. At the current moment probiotics are an interesting but very definitely unproven concept. With the expense of many of these new probiotic bearing foods over the normal ones, such as Acidophilus yoghurt which can cost twice as much as the regular product my advice is fairly simple. If you can afford it you are probably not going to be any worse off trying these probiotic products, but otherwise just buy the regular items until they have more definitive clinical studies to support their supposed health benefits.
*Microflora refers to the bacterial community in the gut, usually composed of a wide array of different species.
1) Tannock G.W. A Special Fondness for Lactobacilli (2004). Applied Environmental Microbiology, 70(6);3189-3194 (Free text available)
2) Tannock G.W. (2003). Probiotics: Time for a dose of realism. Current Issues in Intestinal Microbiology, 4(2);33-42.
3) Tannock G.W., K. Munro, H.J.M. Harmsen, G.W. Welling, J. Smart and P.K. Gopal (2000). Analysis of the Fecal Microflora of Human Subjects Consuming a Probiotic Product Containing Lactobacillus rhamnosus DR20. Applied Environmental Microbiology, 66(6);2578–2588. (Free text available)
4) Jenkins B., S. Holsten, S. Bengmark and R. Martindale (2005). Probiotics: a practical review of their role in specific clinical scenarios. Nutrition in Clinical Practice, 20(2);262-70.
5) Mohamadzadeh M., S. Olson, W.V. Kalina, G. Ruthel, G.L. Demmin, K.L. Warfield, S. Bavari and T.R. Klaenhammer (2005). Lactobacilli activate human dendritic cells that skew T cells toward T helper 1 polarisation. PNAS, 102(8);2880-2885. (Free text available).
The only way I can describe the reaction is just sheer blind...hatred and nothing more really. It has to be watched to be truly appreciated.
Friday, December 02, 2005
Yeah, the demonisation of men continues and now we're all pedophiles without trial. Imagine being that man, asked in front of other passengers minding their own buisness "could you please move so as not to sit next to that child". I cannot even begin to picture how humiliated, degraded and pathetic I would be as I clumsily moved to the new seat. The implication
Air New Zealand and Qantas have banned men from sitting next to unaccompanied children on flights, sparking accusations of discrimination.
The airlines have come under fire for the policy that critics say is political correctness gone mad after a man revealed he was ordered to change seats during a Qantas flight because he was sitting next to a young boy travelling alone.
alone and what other passengers would be thinking (consciously or unconsciously) would just be
terrible. Of course, not that the airline seems to be aware that they are sending a very clear message with this kind of policy:
Oh of course it wasn't Ms. Paul. Please do tell us then what exactly was your thinking for doing this? Were you afraid that the excessive body odor produced by males would upset children on the flight? Perhaps the sight of hairy arms or chins would terrify the poor dears? If you're moving male passengers (forbidding in fact) them to sit next to children what DO you think the implication is? Perhaps Ms. Paul could use a little help from the audience here, I'm afraid that she isn't quite sure if a policy that prevents men from sitting next to children is assuming men are inherently more of a 'risk' to the child. I couldn't get that sort of impression from this policy though, how ridiculous it's obviously "not what she said".
When the Herald asked her if the airline considered male passengers to be dangerous to children, Ms Paul replied: "That's not what I said."
When it was put to her that that was the implication of the policy, she repeated: "No, that's not what I said."
You know, this is just getting to the point of utter ridiculousness. There is a point where you can say there are measures that can be taken reasonably, like suggestions for women to watch their drinks in a bar or take precautions when walking alone at night, but this sort of thing is going way too far. Of course, it's just a continuing of the demonisation of fathers and men in general by various whacko groups and it's unfortunately just going to continue.