Saturday, December 09, 2006
Wednesday, November 01, 2006
The defense also said the embezzlement charges, involving funds provided by corporate sponsors, should be dropped, as most of the funds in question are accounted for or still in the bank. Hwang stood by his previous claims that suspicious personal items--such as a car for himself and his wife--were bought with money earned from lectures and publications. Hwang said that some of the allegedly misappropriated money was used for expenses in pursuing unsuccessful projects, which included an effort to clone a mammoth that involved the Russian mafia, and another project to clone a Siberian tiger native to North Korea. In official documents, he claimed to have used the money to buy cows for research.
Thursday, October 26, 2006
Friday, October 13, 2006
Wednesday, October 11, 2006
Here’s how the GAO targeted four nutrigenetics company websites. They took DNA from a 9-month-old girl and from a 48-year-old man. Then they concocted diet/lifestyle profiles for 14 “fictitious consumers,” 12 from the baby’s DNA, and 2 from the man’s. For example, the baby girl was transmogrified into a 6-foot-tall, 210-pound 45-year-old man who smokes and doesn’t exercise, drinks a lot of coffee, and eats a lot of fat. The baby also became a 72-year-old woman who weighs 100 pounds and stands 4’9”, regularly exercises, never smoked, doesn’t drink coffee, and eats fried foods. To make it interesting, the researchers also submitted cat and dog DNA but did not disclose whether the cat preferred Friskies to Fancy Feast or the dog Alpo to Purina so as not to tip their hand.You'll have to read the whole thing, because spoiling the result would really ruin all the fun.
Tuesday, October 03, 2006
ID has a prosperous and highly successful research program. Yeah right.As it still appears that the ID movement doesn't even have a theory to begin with you can imagine my skepticism at anyone claiming there is ID 'research' being done using a DOA "theory". This really isn't the point I want to talk about though from Jasons post, but rather this from a little later in:
You know, I have to agree entirely with this but with a slightly different tangent. Once upon a time I used to learn a lot out of arguing with creationists and the ID crowd on the various issues about biological evolution. Having to look through the scientific literature on a wide range of subjects from geology, mathematics, biology and more to whack the various pseudo-babble put forth used to be an entertaining and perhaps dare I say, even educational, enterprise. I would always come away having found something new in my searches for counter arguments.
Which brings me to the title of this entry. When I got started in this biz, I felt like I learned something by taking the ID folks seriously. The No Free Lunch theorems are beautiful and fascinating, but I would know nothing about them if the sordid little mind of William Dembski hadn't figured how to use them to bamboozle people into thinking their were mathematical flaws with evolution. The research I did while investigating the claims of Jonathan Wells and Icons of Evolution taught me a great deal about the real state of biological research. Fighting these ignorant charlatans was an act of grim necessity, but at least they provided some food for thought.
But look where they are now. They had their day in court and came off looking like fools. The only books they talk about now are the hysterical political screeds by Ann Coulter and Jonathan Wells, neither of which presents anything remotely new. And when you ask them to tell you about the state of ID research, not even actual results mind you but just a description of the work itself, they get belligerent and nasty.
Now, tying in things about why I've been so absent from blogging as well, is the fact I've been reflecting somewhat on the whole issue and my attitude has changed heavily. You see, while once I was like Jason always learning something from these debates, I now fail to get anything out of them at all anymore. After a while, it's always the same arguments, it's always the same counter-arguments that can effectively deal with that nonsense and just as soon as you do it, the same crap comes up again. It ends up after a while getting to a never-ending game of whack-a-mole and to be perfectly honest I find that extremely boring and just not worth my time anymore.
Sure, the political arguments of creationists (like the ID movement) have advanced continually in trying to strawman some thing or another, but these usually have little or no relevance to anything scientific at all. In fact, there is a complete lack of any new science in terms of the latest creationist nonsense. It's always the same flagella, darwinist conspiracy, second law of thermodynamics (dressed up with new rubbish to make it seem more intelligent than it really is) and such forth arguments that have been put up for years. The terms change, but ultimately it's just the same nonsense, it's been refuted by many others (usually more specialised than me) and usually really well at that.
So linking things back to my disappearance from blogging, I've had a good think about what I really want to say online and how I want to present myself. To put it simply, the same idiotic creationist arguments just make me highly antagonistic these days. I'm not sure how to describe the feeling I get from arguing with creationists, other than saying it's equivalent to the feeling you would get from telling someone not to put a fork in the electrical socket and watching them do it anyway. It's just got to the point where playing whack-a-mole just gets highly derisive or sarcastic replies from me. I can't even be bothered really arguing much with creationists now like I used to.
For example, I would once have spend most of an afternoon or evening researching the topics in question, interpreting things (or asking someone who did know) and then posting my counter arguments. This of course is very time expensive as you can imagine, unless of course the argument moved into my areas of interest in microbiology or immunology (where I already knew the required information). But over time, I've found that I can literally, search back posts I've written elsewhere and just copy and paste it. The arguments put forth in a post from 3 years ago (if it still exists) can often suffice completely for answering a creationist argument today. Again, this is because creationist arguments have merely adapted depending on political circumstances and putting new lingo on old redundant arguments. It's still the same broken arguments despite the changes in how it's presented.
This has just led to me getting more sarcastic in my posting style with creationists and I no longer bother putting in the time or effort. To neutral observers, I'm sure at times this has seemed that I've either not had an answer to the argument or that I've given up in frustration. In reality, it's just getting bored of whack-a-mole and wondering why I'm wasting my time. Even after taking a huge break from blogging and even generally arguing about the subject on internet forums, I just haven't been able to lose that feeling of "Yay, whack-a-mole again, what could I be doing with my time?".
Inevitably, there comes a point where you just have to say to yourself "Why bother anymore?". I don't get anything out of arguing with creationists anymore, I don't learn anything, I've heard all the defunct arguments they can put forward before and so I really wonder "What's the point?". It's not like I've got some complacency about creationists, just because they continually make themselves to be idiots in the most public of ways possible like at the disasterous Kitzmiller vs. Dover trial doesn't mean they aren't a very powerful political (but note, not scientific) movement. There are places on the internet however that cater to smacking creationists around very efficiently, like the Pandasthumb, Pharyngula and of course Talk Origins.
With my time however, I feel I can get a lot more about talking about issues in science that actually interest me. How biological systems like the immune system evolved, issues in science like the ethics surrounding gene therapy, public and animal health issues like the Escherchia coli H7:O157 outbreak in spinach (or Tb in badgers ;)) for example. Playing whack-a-mole with creationists is just not worth the time or effort anymore, especially considering how many other fascinating things in science there are to discuss (plus I still have a looooong list of stuff to write about ;)).
Finally, to end this rather large rant I'd like to comment that I don't care what ID researchers think of their own research. Until they publish some of this much vaunted 'research' that is always just around the corner (Always...) I couldn't care less. Talking about doing research is entirely irrelevant to the point of actually doing it. When the ID/creationist movement produces actual science I think it will be worth discussing. Somehow I doubt the ID/creationist lot are bothering with the "science" part and will stick to the "baffling people with bullshit" part.
Oh and I am in an especially good mood because I just began my PhD <3 Yes, that does mean new website soon, because I've been meaning to move to a new site once I got all of this sorted out.
Saturday, September 16, 2006
Now that everything appears to be in order and that I'm starting to get re-interested in blogging again, means that with some luck I should be moving to my new website at some point soon. This of course is all conditional on other things, such as my initial workload in the lab and other things that could potentially interfere.
I do apologise for the long stretch of absence and general lack of blogging on my part.
Thursday, August 31, 2006
See what I mean? Absolutely crawling with the undead [they are there I assure you, they are just camera shy]. Can't cross the street without having to dodge numerous zombies all after your brains. What's worse is they are all into various forms of pseudoscience, woo and quackery. Perhaps it might all be the result of dumping too much nuclear waste into the rivers and I assure you, we'll be returning to the subject of nuclear waste later in the circle. Everything ultimately is blamed on nuclear waste eventually anyway. First it's poisoning the water, then ruining the air quality, then making people sick and eventually raising the living dead. You know how it goes.
So it's a good thing you've all turned up so we can try and set them straight with some good old fashioned skepticism to the head. I've personally always liked the sledgehammer of science myself, but the lawn mower of anti-woo has its own appeal [even if it's very messy] and there is always the shotgun of reason. Whatever your weapon of choice, there are many ways of dispatching crazy pseudoscientific zombies, but the problem with the living dead and I'm sure you can appreciate the many problems we are facing, is that they keep coming back regardless. Reminds me of arguing with creationists, no matter how many times you dispatch their arguments there are always more of them and the old ones come back anyway [tis quite the problem with the unliving dead, you can't kill them you see, because they are already dead. Haha, see the dilemma?].
Currently the creationists have been shacking up with a really good friend of theirs: the dreaded Hitler zombie. While not hanging out in my pool (making it all mucky) and shouting incomprehensible things at people he doesn't like, the Hitler zombie often enjoys eating the brains of people making ridiculous comparisons between evolution, himself, NAZIdom and various other aspects of the third Reich. Thankfully, Scientia natura tackles some of the ridiculous arguments creationists make on this topic in evolution, Darwin and Hitler. When they aren't trying to compare evolution with Hitler, creationists resort to other ridiculous arguments instead as Tara Smith from Aetiology covers in Influenza viruses = evidence for design. Those whacky ID creationists, what won't they claim? Finally, the Pandas Thumb has a lovely series covering the latest collection of ridiculous claims in Johnathan Wells' new book. I don't recommend buying the book and instead just reading the rebuttal. Your sanity will thank me for it later. If you ask me, I'd rather face the zombies than deal with creationists nonsense.
Staying on the science front in this circle, Jonswift has another piece of wonderful satire covering how science is undead-errr how science is dead. Haha. *Ahem*. Sorry about that, couldn't resist a little zombie themed humour there. Carrying on, Divided we Stand, United we Fall takes on some of the bizarre claims that Anne Coulter has made about global warming researchers (among other thing). Personally, I keep a copy of her book around with me at all times as zombies won't attack you when they see it. Seems to fool them into thinking you're one of them, which is very handy for popping down to the dairy for a few moments without harassment.
Speaking of taking creationists to task, the Pooflinger writes about the stupidity inherent in having to consider 'both sides' in back of the book. Rockstars' ramblings also comments on the fallacy of using 'both sides' to justify anti-evolution nonsense. Finally, speaking of math, the Bad Astronomer also has a public service announcement, reminding us in the skeptical community that it's always healthy to correct your own mistakes. Especially when they are mathematical.
Moving along from the creationists, remember earlier on how I mentioned that Nuclear Waste? Well, it turns out there is a great solution for that and it's even sponsored by a celebrity! Yes, I'm talking about using Kabbalah Water to clean up nuclear waste and Madonna apparently really likes the idea. Thankfully, some of our contributors have decided to wham some sense into this undead beast, with Skeptico commenting that Madonna solves nuclear waste problem. If that wasn't enough, Humbugonline also tackles the issue in Mad Madonna the Comedian. I wonder if that water works on zombies- or was it holy water that was supposed to be effective against the undead?
The subject of this circle now turns onto the ever fun topic area of medical woo, pseudoscience and just plain crazy. Firstly, we'll begin with the Beaver examiner noting that South Africa donates $100-million towards garlic research. This should show those normal 'HIV priests' that clovology should be taken seriously as garlic research is seriously important for numerous reasons. Take it from me, when you're knee deep in zombies then come the vampires. What's good on vampires? That's right, Vampires. South Africa will be making a good investment in anti-vampire technology for the future. Speaking of Garlic, scientia natura also recognise how powerful it can be in a quack healers deception.
Orac from Respectful Insolence brings us some more skeptical blogging to do with medical woo in two cases, firstly the pause that refreshes and heals. I always wondered why people told me yellow snow was bad for you. He also brings us a look at Abraham Cherrix, a child whose parents are attempting to avoid conventional treatments so they can use nutty altie ones in starchild Abraham Cherrix: It's over. Unfortunately, when it comes to mistakes that occur with normal conventional treatments and alties, things never work out as Bronze Dog explains.
Carrying onto our final skeptical topics for tonight, a guest post by Mum to Laura on Autism Street wonders what people would think of a "blindness spectrum". EoR, over at the second sight wonders at the tactics some crazies will go to try and sell their books to the gullible in Jesus is real - Oh, and buy my book! PS: You should buy my upcoming book as well: How to defend yourself from a zombie attack with nothing but a spoon, a wire and some table salt. Speaking of somewhat strange things people propose, Socratic Gadfly covers the use of regaining your 'inner child' to treat abuse cases in some thoughts on child abuse recovery counseling, AA, PTSD and related matters. Finally, the Saga of Runolf wonders just what happened to animal planet in the great animal planet disappointment.
Also, before we all leave satisfied in a skeptical driven zombie genocide well done, let us all bear tribute to Douglas Adams who has long since ceased to be with us. Nothing with the number '42' in it can go without at least mentioning him. He was a really great writer and he will always be missed. So that's all for the circle this week and most importantly, thanks to all those who submitted articles. I do hope you've enjoyed this entertaining romp around skeptical thinking and be prepared for the next circle, which will be hosted by Janet D. Stemwedel at Adventures in Ethics and Science. Anyway, it's time for me to go and- wait, what's that sound at the door? Moaning? Hungry moaning? Scratching? Cracking... Oh no...they've breached the defences! There are hundreds of them, they're in the room and oh dear Go[.sd.assd.zhjai
[Disclaimer: Yes, somewhere along the line I have gone completely and utterly mad. MUAHAHHAHAHAHAHA]
Friday, May 26, 2006
As for me, things will be starting to change shortly although it will be after the weekend or so. I'm going away for a weekend to help move stuff around in a relatives house so I probably won't be available. After that, it's about time to move things along with my new blog I think :D
Friday, May 19, 2006
Thursday, May 18, 2006
Until then, I've been a little active on another blog I'm a co-contributor on, namely Limed for the Truth, which is a blog set up by members of the Penny Arcade community and has a wide array of different posts and topics. I recently re-wrote and updated an earlier piece I did on this blog discussing antibiotics over there if you're into that sort of thing. As for the exact future of this blog, it's probably going to be inactive shortly and this will probably be one of the last updates here. Once I've got my new blog up and functional I'll obviously be posting a link. Until then there won't be a lot of activity here except for the odd random post. I'll be posting more frequently (on similar topics) over on Limed for the Truth though. Including the importance of keeping your dental microbes in check, especially when you crack a tooth and don't go to your dentist until it's too late....
For reading in the mean-time, I would suggest having a look at the stony skeptics circle over at The Second Sight, which was posted a wee while ago (I've been on the net a bit sporadically as of late ;)). Additionally, tommorow there will be the carnival of the wee animacules at Aetiology if you're wanting some microbial goodness.
So the short and skinny of it all is that I'm making a new site and organising stuff in "real life" (whatever that is ;)). As I'm rather keen and interested in my new site, I've kind of relegated this one a wee bit while I work on there. If you want to know what I'm doing in the mean-time, I will be posting every so often over at Limed for the Truth. Oh and yes indeed Mr. Swift, I did take a bit of time to play some videogames ;) Gotta get them before I start my PhD and subsequently won't have the time to play them :D
Wednesday, May 03, 2006
Normal blogging will resume eventually, but I've given up trying to make predictions on when exactly that is going to happen. :)
Sunday, April 30, 2006
|Your Theme Song is Born to Be Wild by Steppenwolf|
"I like smoke and lightning
Heavy metal thunder
Racin' with the wind
And the feelin' that I'm under"
A total independent spirit, you can't be held down or fenced in.
You crave the feeling of wind on your face... and totally freedom.
At least it isn't Hit Me Baby One More time or something. That would be just sneaky.
Friday, April 28, 2006
At least he has a sense of humour.
Thursday, April 27, 2006
Now I'm not saying there is anything wrong with the good old blogger.com template. It's perfectly functional and my numerous experiments with it have allowed me to figure out quite a bit of HTML. The guy who made the thing originally certainly did a very good job, but it's just not mine if you can appreciate what I'm getting at. So I intend to 'personalise' the site over the next couple of weeks. What this means is all sorts of random errors and general chaos. I don't expect most of the things I try and do to work the first time (if at all), so if the blog explodes or something then just assume I've done something horrible to it.
The other thing I'm trying to figure out is my RSS feed. Apparently it's not working, or working some of the time or it just doesn't behave in any sensible manner. To be honest I'm still rather clueless as to what I've done to it and am working to correct the problem. With luck the site redesign will allow me to figure out what exactly I did to it.
Finally, if you're looking for some reading to do and haven't seen the latest carnival of the wee animacules, then that was posted recently at the Biotech Weblog. It was fairly small last week though so we need a few more people making submissions. Or alternatively, a couple of regular submitters not playing computer games :p
Sunday, April 23, 2006
In future I think I shall remind myself to never buy a new RPG when I intend to do a large amount of blogging. It's usually not a very good idea for my overall productivity :p In any event, while I was effectively taken out by the charming nature of Dragon Quest VIII, I did get time to read an excellent paper in Nature Immunology by several Pandas Thumb posters. Essentially Andrea Bottaro, Matt Inlay and Nicholas Matzke clearly describe the devastating role that immunology played in the defeat of 'Intelligent design' in the Kitzmiller vs. Dover trial in december last year. Effectively the Nature Immunology paper gives a clear message of thanks to the many hundreds of scientists who actually do research into the evolutionary origins of the immune system (one of my key interests these days). Additionally, to give ID adovcates even more of a headache is this annotated bibliography of the 68 articles presented to Behe at the trial.
Finally, apologies to anyone looking forward to the posts outlined previously, but rest assured I haven't forgotten to do them and I'm certainly not forgetting about the blog. Just a tad distracted tis all ;)
Saturday, April 15, 2006
Hopefully it won't affect blogging too much ;)
Friday, April 14, 2006
So the result really is now to establish a more solid direction to what I want to do with the blog. I've become less and less interested in nuts as time has gone on. For example, there are many blogs that are dedicated to the debunking of claims from creationists like the Discovery Institute, general nutters and all sorts of others. While I will definitely continue to add my 2cents on discussions on claims from said groups in my relevant subject areas (Microbiology and immunology), it's unlikely that I'll have a lot to add in other subjects as many other blogs cover the area (quakery debunking) quite well. For example, see this post by Ian Musgrave from the Pandas thumb on the hillariously ineffective response of the DI to the recent hormone evolution paper in Science, as a good example of what I'm meaning. Many more examples abound on many other blogs I visit regularly like Pharyngula, Respectful Insolence and Dispatches from the Culture Wars.
Where to go on this blog? Well, I'll probably continue to write on subject areas that interest me (or manage to rile me up) more so than plain 'debunking' of various claims, which are usually the same ones as made last month/week/year that never seem to die. As a result, I'll probably blog a lot more about microorganisms, their relationships with us and how we can benefit from microbes. For examples of what I mean, my series on bovine tuberculosis in britain (Part I, Part II, Part III and Part IV), farm animal cannibalism, probiotics (here and here), microbes I find interesting like the plague (Here and here*) and mare reproductive loss syndrome. Additionally, I also hope to write a lot more about the vertebrate immune system and why immunity to microbes has been such a critical factor in our evolution. This will be along the lines of my current posts on MHC (Part I, Part II and Part III, with some updates to come as I've read a lot more since) and I intend to elaborate more on the evolution of Toll-like receptors in future (a very soon future) as well.
Most importantly, I intend to keep more to things that I say I will do. For example, I have not forgot that I was supposed to write more about TLRs, the alternative theories about the black death* and such, it's just I unfortunately haven't managed to get around to doing the reading. In future, I hope to keep more to what I say I will write, so that if you see "post tommorow" that post will turn up 9/10 tommorow. Not uhhh, next week or maybe even a couple of months as the current blogging schedule seems to work with me :p
So what is to come? Well there will be the continuation of the Bovine tb series next week and future posts on the ethics of talking openly about bioterrorism, which is why this series hasn't been continued yet if you've wondered. In fact, I was going to delete the post until it was included in a carnival of the wee animacules, so I decided to keep it up but not continue it. There will be many toll-like receptor posts next week and how zany those scientists who work with Drosophila melanogaster are. For a change, I also intend to write a post about how bacteria help us in our daily lives as opposed to their typical PR of being evil pathogens (among other things). Finally, I hope to go over how plausible a 'doomsday' virus could be and how we could combat it.
So the new direction is really more about writing about and explaining interesting science on evolution and microbiology, which would otherwise go unnoticed to most non-scientists. I'll leave the debunking of creationists (for example) in areas out of my field of expertise to the professionals.
*There is quite a lot of debate on the issue, so I'm taking my time to read everyones opinion andvarious back and forth exchanges in certain journals.
Abstract: When proponents of Intelligent Design (ID) theory deny that their theory is religious, the minimalistic theory they have in mind (the mini-ID theory) is the claim that the irreducibly complex adaptations found in nature were made by one or more intelligent designers. The denial that this theory is religious rests on the fact that it does not specify the identity of the designer — a supernatural God or a team of extra-terrestrials could have done the work. The present paper attempts to show that this reply underestimates the commitments of the mini-ID Theory. The mini-ID theory, when supplemented with four independently plausible further assumptions, entails the existence of a supernatural intelligent designer. It is further argued that scientific theories, such as the Darwinian theory of evolution, are neutral on the question of whether supernatural designers exist.I certainly think that Sobers essay is interesting and he makes some new points that I hadn't considered much before. Personally however, I've never thought that the way "ID" is set up now would ever include aliens period. Natural aliens would have methods that we could potentially establish and look for in making life as we knew it. The fact ID research don't try to establish anything about the potential methodology the designer(s) 'used', indicates heavily that their 'designer' is supernatural and as a result doesn't have a detectable methodology.
*You see what I did there? I took the guys name and made a witty pun with it in the title of the post. I'm so awesome!
Wednesday, April 12, 2006
It's hard to imagine that so many of these underage boys, some as young as a mere 14 years old, would want to sign up and join a brutal pointless war of attrition where nobody really actually won. Out of what, you would have to imagine, would possess someone of that age to want to join into the military? Some sense of patriotism that they would serve their country in a glorious war (that turned into nothing more than a meat grinder)? Worst of all, was that with the high attrition rate on British forces in France, many of them were simply 'coerced' into joining the army and often without their parents knowledge. Possibly the most inhuman aspect of it (to me) was that the British army knew that many of their supposed 'soldiers' were underage and just pretended to ignore the problem.
I knew before that in both World Wars underage boys had served in the military by lying about their age, but I had no idea that so many underage boys served in World War 1 and just how young some of them could get. Well worth viewing this documentary if you can catch it on the history channel or similar in future.
Tuesday, April 11, 2006
Update: Actually it appears the articles may not have been altered but instead have just been replaced. The April 2nd article from the Seguin Gazette-Daily does not appear to have survived and these are just other articles. I'm not sure if these have been updated as it appears that the reason for their disappearance has been explained thanks to the investigation undertaken by the Questionable Authority.
He was actually quite surprised to hear that the articles were not available online. Apparently, the company had directed that the transcript and the audio recording from the speech be removed because both were at least partially incomplete. That was apparently misunderstood, with the result being that all of the materials were removed. He has since gotten back in touch with the Gazette-Enterprise, and the articles are now back online.Now everything makes sense. They were removed originally as the transcripts posted were incomplete at the companies request and now two of the articles (From april 4 and april 5) are back. The april 2nd article is still missing.
Further Update: Now the April 2nd article is back as well. Looks like it was just a mistake.
Anyway, Steve notices that Jonathan Witt quotes a paleontologist called Henry Gee in responding to the fossil finding. Somewhat unsurprisingly, like most creationist quotations of actual scientists, it seems that Jonathan Witt has hopelessly mangled the meaning of the quote. Additionally, it seems that Henry Gee is a fairly popular target of quote mining, so much so he even has made a public statement on the matter.
More analysis of the DIs farcical posts on Tiktaalik can be found on the Pandas Thumb (here and another post here) and on Ed Braytons blog, Dispatches from the Culture Wars. Also, just so nobody can claim that I've forgot that Answers in Genesis still writes stupid things as well, Lancelet has given a suitable paddling to AiG nonsense on the fossil here and a second post here.
It's link love to takedowns of creationist nonsense tuesday!
Since that, there have been two very good responses to the nonsense thrown out by the DI response. Firstly, I would point you to this excellent post by Carl Zimmer at the Loom. His commentary is particularly cutting but he makes one particularly brilliant point (emphasis mine):
Is it me, or is it strange that intelligent design advocates are telling biologists that they aren't working hard enough, that they are not getting enough results from their lab work? Remember, this is the same Michael Behe whose sole peer-reviewed paper in the past eight years was a computer model (and a pretty poor one, it turned out). Compare that to the work of Joe Thornton, the principal investigator on the new paper. In the past eight years he's published twenty papers on hormones and their evolution: he's been sequencing hormone receptor genes, working out how they respond to different hormones, determining how they're related to one another, and even resurrecting them after 450 million years of oblivion.Ouch. I felt that one from all the way over here in New Zealand! Further, another response that is worth noting is from the Pandas Thumb (of course), where Ian Musgrave notes how slippery the definition of IC is. Additionally he also shows how the definition of IC isn't really that well defined to avoid any form of significant falsification.
Yet this “system” is precisely the thing that Behe uses in his exemplar for the Behe and Snoke paper, the binding of DPG to haemoglobin. And Behe has said in testimony to the Dover trial (3) that the Behe and Snoke paper on evolution of binding sites is about irreducible complexity. So if the evolution of the DPG binding site (where you only need two mutations to make a functioning DPG binding site) is an example of IC, then the evolution of the aldosterone binding site is also (note 2). As the BCT paper specifically cites the Behe and Snoke paper, you would expect they would look at the ideas contained in the paper, not “Darwins Black Box”. Behe has had a long history of citing examples of molecular IC. He has even called disulfide bond “irreducibly complex” (2). So his disavowal of an example that directly addresses the Behe and Snoke paper (3) is particularly disingenuous.Not that Behe has ever thought much of actual scientific research anyway.
Monday, April 10, 2006
Personally, I like both styles but I do admit that the organic style of animation does seem to be going out of fashion a bit.
Saturday, April 08, 2006
Although bovine tuberculosis (BTB) is known to spread through wild-animal populations and is readily transmissible between cattle, the role of large scale cattle movements could be an important indicator for the spread of BTB. The current epidemic is concentrated in a large central area in the south west of
Gilbert et al., 2005. Cattle movements and bovine tuberculosis in
In their study Gilbert et al., (2005) made a computer model designed to predict the spread of BTB to new areas from the ‘core’ region by using movement data obtained from the British Cattle Movement Service (BCMS). The BCMS was set up in 1996 after the BSE outbreak in
Importantly they avoid a problem with the way that the CTS records the cattle movement data, which may have compromised the papers results considerably (See supplemental material). You see, every cattle ‘movement’ recorded by the CTS is in reality recorded twice. Once for the “on” movement and another for the “off” movement meaning that all cattle movements have to be paired to make sense of it. When this procedure is actually done, a large amount of the data from before 2000 is shown to be rather inaccurate (there aren’t two movements recorded correctly for example), but is very accurate data for the period from 2000-2003.
Another limitation of the study that the authors put forward (again, supplemental material) is the reliability and time disparity between tuberculin testing. Depending on when an animal is tuberculin tested, it may show to be positive for BTB before or after it has moved, giving an inaccurate impression of where the animal actually was infected and if it was pre or post movement. This would particularly affect the results from regions with less BTB than other areas of the
Bearing these two factors in mind the question really is: Does their predictive model correlate with the observed BTB spread? The answer in short terms is that it does and it does so with quite a high degree of accuracy. For example, take one of the figures showing the models BTB prediction against the actual observed rates of BTB:
Figure adapted from Gilbert et al., 2005. Cattle movements and bovine tuberculosis in
Here you can see that their modeled BTB distributions and the projections from their model on the larger map of the
What the model doesn’t show and how to experimentally confirm the study
One place where the model shows abnormalities is that there are regions that have numerous cattle imports, yet the disease fails to persist for any meaningful period of time. It’s important to bear in mind that this could have several explanations, the first of which being that the cattle are only temporarily held in the region. For example, they could arrive and be immediately slaughtered on arrival, such as to an abattoir, which wouldn’t give any time to spread the disease. Another possibility is the lack of wildlife reservoirs, namely badgers in any meaningful capacity in the region, which is also the explanation I would favor, in particular given the association between badgers and BTB (see part III). A final explanation may be that these regions are not prone to many movements from ‘core’ areas, which reduces their risk considerably.
This study could also be interesting to contrast with the known spread of BTB in general regions. As it predicts BTB spread based on cattle movements, it does immediately present a means to experimentally verify it on the ground (so to speak). Given their model, it should be expected that movements from areas with BTB should be associated with the detection of certain Mycobacterium bovis spooligotypes (basically strains). This is because the imported infected cattle should bring with them their M. bovis types and therefore spread that to the uninfected herd. Over time, based on what cattle movements went into a region and what spooligotypes infected cattle bought with them, you would expect to see those spooligotypes in subsequent herd breakdowns.
Here is where I become somewhat skeptical. It’s known from previous experiments which have analysed the spooligotypes of M. bovis from badgers and cattle that these tend to be shared between the two species (see part III). This also tends to be isolated by geographical regions, with a mixture of spooligotypes but only a few ‘oddball’ ones that aren’t shared between badgers and cattle. In the model predicted by Gilbert et al., 2004, where cattle movement is the primary motivator for BTB spread it also implies cattle to cattle spread. The lack of spooligotype mixing between regions from studies conducted in Ireland (for example) have shown spooligotypes of M. bovis tend to be similar in a region but not between them, raises concerns over cattle movement as a predictor of M. bovis. It may be likely that cattle movement helps to spread the infection to a new region, but is not sufficient to determine if the disease will be able to establish in the new region.
It’s clear from the Gilbert paper that cattle movements are playing some role in the spread and establishment of BTB in the
In any event, this does not resolve the problem with badgers as a large reservoir for M. bovis. Ultimately, this debate has become rather invective and polarized over one key issue: If the control of M. bovis requires the culling of badgers in order to be accomplished. In the next part of this series, this immensely important aspect of the control program will be discussed in Part V: Will culling badgers have any effect on the control of bovine tuberculosis?
Gilbert M., A. Mitchell, D. Bourn, J. Mawdsley, R. Clifton-Hadley and W. Wint (2005). Cattle movements and bovine tuberculosis in
Friday, April 07, 2006
The other organism involved is the Eastern tent caterpillar (Malacosoma americanum):
You might be thinking at the moment as to how that tiny caterpillar interferes with a horse. After all, the caterpillars in question are a communal bunch that spin little “tents” and horses shouldn’t really have any particular interest in caterpillars. Most remarkably however, these caterpillars are known to be associated with a disorder in pregnant horses called Mare Reproductive Loss Syndrome (MRLS). Most interestingly in this story is the proposed mechanism by which, this tiny (6cm long) caterpillar is responsible for causing a bacteriological infection of the developing fetus and ultimately killing it. But first, it’s time for a bit of background.
What is MRLS?
(Information is from Webb et al. 2004, unless otherwise referenced)
In central Kentucky USA from late-April to May of 2001 an unusually high number of spontaneous equine abortions suddenly started to occur. The rapid rise in abortions among early mare fetuses (a gestation time of around 40-150 days) was particularly prominent, with some farms having up to 60% higher early fetal losses compared with the ‘normal’ rate of 3-5%. As
Investigation of pregnant mares by ultrasound revealed that the fluids around the fetus were often extremely cloudy. Examination of the dead fetus revealed the presence of numerous bacterial species, but most interestingly no specific pathogens known to be associated with fetal abortions in horses. Instead, the isolated bacteria tended to be associated with commensals such as non-β haemolytic streptococci, actinobacilli, Serratia marcescens and many other bacteria. The majority of these identified with either oral commensals (like the streptococci) or bacteria commonly associated with the gut microbiota such as Enterobacter and Serratia spp.
More curious was the lack of pathology observed in the mother horse itself. Although some horses had some symptoms, such as pericarditis, the majority did not present with a fever or other indication of a systemic bacterial infection (despite this being present in the fetus). This unusual pathology raised the question that the bacteria were a secondary infection and something else, such as an ingested toxin was causing the spontaneous abortions. During the investigation of the outbreak of MRLS, it was found that a caterpillar, the Eastern tent caterpillar (ETS) had a large population explosion at around the same time that the outbreak of MRLS occurred. Could the caterpillar population explosion explain the sudden appearance of MRLS?
Demonstrating a link between caterpillars and MRLS.
The most conclusive paper on the link between MRLS and the ETC was performed by Webb et al., 2004 (See the full reference below). This study performed three experiments that demonstrate ingestion of ETC is associated with MRLS after the results of a pilot study (also performed by these authors) showed promising evidence of a link between MRLS and caterpillars. The three experiments were:
Experiment 1: This compared three groups of pregnant mares in the pasture to replicate what would be ‘natural’ transmission of caterpillars into the horse. One group was on a caterpillar diet, which involved adding a certain density of caterpillars onto a sealed off section of pasture and allowing the horses to basically eat them with their usual feed. Another group was exposed in the same manner to caterpillar frass (see the picture of the caterpillars above, frass is, as far as I understand, what the stuff they spin is called). Lastly, there was the control group that lacked any caterpillars or frass.
Experiment 2: This is very similar to experiment 1 except that this time they fed pregnant mares directly either frozen or autoclaved M. americanum caterpillars or alternatively, another species of caterpillar called Lymantria dispar.
Experiment 3: Finally, they wanted to investigate which part of the caterpillar was specifically involved in causing MRLS. They used saline, whole M. americanum larvae and several different dissections (Such as cuticle, hind-gut and haemolymph*) of the caterpillars and fed these again to pregnant mares.
To put a long story short, their results demonstrated a clear link between the caterpillars and MRLS. Experiment one demonstrated that horses in pasture would ingest the caterpillars and would go on to develop MRLS, while horses fed on caterpillar frass and not fed on anything caterpillar associated did not.
The second experiment demonstrated something very interesting the autoclaved caterpillars did not produce MRLS in any of the 5 horses, while the frozen caterpillars did induce MRLS (in 3 of 5 mares). We’ll come back to this later so bear this in mind for now. The control L. dispar caterpillars did have one abortion in the group but it was not associated with MRLS.
Finally, the last experiment demonstrated that whole caterpillars were able to induce MRLS (as expected) and that MRLS abortions were associated with the outer cuticle (exoskeleton) of the caterpillars most strongly.
Now, the results of this research are incredibly interesting as it hasn’t really been seen before that an insect like a caterpillar could cause such an unusual disease. It’s especially surprising that this disease has only been discovered recently, especially because it’s caused by a common insect that covers a wide area of the
However, perhaps the most intriguing answer to this puzzle isn’t a toxin, poison or similar, but instead a quirk from the caterpillars physical defenses.
Caterpillars with built in bacterial syringes
(The reference for this section comes entirely from Tobin et al., 2004, which is a fascinating paper).
An interesting hypothesis for the potential pathogenesis of MRLS is the “Septic penetrating setae”. Now setae are fairly common structures on a lot of different insects and are basically pointy tubes on the surface of the animals’ exoskeleton. These pointy tubes have numerous functions, but the most obvious is for defense by basically making the insect unpleasant to eat. This is because setae are basically pointy sticks*** and they penetrate into tissues causing considerable irritation. The hairs of the red rump tarantula are basically hollow spikes that are flung into the skin and eyes of an attacker. This causes severe irritation and allows the spider time to flee the scene of the crime.
Image of setae showing their general structure, with the size of these being around 20μm in diameter and demonstrating the pointy ‘barbs’ that cover the structure. The image was acquired from Tobin et al., 2004, and the photos were originally from Henry H. Southgate,
So what is the relation between Eastern tent caterpillar setae, mare reproductive loss syndrome and the bacterial infection that induces the abortion? It turns out that the setae are structures that happen to be hollow and they are also liable to fragmenting once they are ingested. Their small size, which is small enough to fit inside a large enough blood capillary (especially when fragmented) and is sharp enough to penetrate tissue, may be able to cause MRLS. The mechanism that is proposed works something like this:
1) The pregnant horse starts to snack down on a nice lunch of caterpillar.
2) A) Setae are broken off the caterpillar, penetrating gum tissue and other areas of the mouth to enter into the bloodstream. This is aided by the ‘spikes’ on the setae that allow the structure to progress more efficiently in moving tissue.
B) Alternatively, the setae make it through to the gut where they penetrate the thin epithelial lining. Again, movement of the intestine and the sharp spikes on the setae enable the fragments to enter into the bloodstream and move around the body.
3) Along with the penetrated setae, bacteria are carried along as passengers inside or alternatively on the surface of the setae until they hit a suitable ‘target’. In this case, certain ‘immunoprivileged’ organs such as the eye, reproductive organs and yes, even the amniotic fluid/uterus where the fetus is developing.
4) Once the setae ‘hits’ one of these organs with its bacterial passengers, or alternatively a critical number of setae have hit, it establishes an infection. This infection then progresses rapidly (less than 38 hours) and leads to the development of MRLS.
This hypothesis for the mode of action that ETCs cause MRLS is actually quite compelling as an explanation. Firstly, it demonstrates the link between the typical commensal bacteria often found in aborted fetuses, recalling they are primarily from the mouth and also some from the gut. It’s unlikely that the setae are punching a hole in the mouth or gut, followed by general septicemia as recall that the mare itself rarely has any associated symptoms. This provides weight to the explanation that the setae (or fragments) carry the bacteria to their target without exposing its passengers to the immune system. Basically a ‘direct delivery’ style system and finds the uterus often (compared to other regions, which is much less frequent) due to its general size, significant movement and shape.
Further, remember how I earlier said to keep in mind the autoclaving experiment from the Webb et al., 2004, study? Autoclaving basically works by heating up stuff to a large temperature, usually about 121-124 degrees. As well as intense heat, there is also a considerable amount of pressure in the chamber during a cycle as well. If you recall, the autoclaved caterpillars were not able to cause MRLS and this could have been the result of the disruption of the internal structure of the setae. Although this concept hasn’t been proven and doesn’t rule out a toxin (which could be deformed as well), it provides a compelling piece of evidence that could corroborate this hypothesis.
What to take from this
This entire line of enquiry shows that diseases and other disorders are not always the simple interaction of X pathogen causing Y disease in a specific host. Sometimes there are some very complicated external factors that may cause a disease but not be directly responsible for it. The association of these caterpillars and an abortive disorder in horses is one such example. Additionally, the implication that setae cause the entire disorder by a simple quirk of their structure is a fascinating finding. It is worth noting, before I get too enthusiastic, that the “Septic penetrating setae” hypothesis has yet to be experimentally confirmed. For my money though, I hope it’s the correct answer because it would provide a fascinating and highly novel mechanism. Microbes gaining entry into vulnerable tissues by using a ‘built-in’ syringe from another organism is just too interesting a concept to be wrong.
*Haemolymph=Insect blood. It’s a combination of interstitial fluid and their oxygen transporting blood vessels. In us, as an example, our interstitial fluid is separated from our blood and not mixed together.
***Yeah, this is a simplification.
Potter D.A., L. Foss, R.E. Baumler and D.W. Held (2005). Managing Eastern tent caterpillars Malacosoma americanum (F) on horse farms to reduce risk of mare reproductive loss syndrome.
Tobin T., J.D. Harkins, J.F. Roberts, P.W. Vanmeter and T.A. Fuller (2004). The mare reproductive loss syndrome and the Eastern tent caterpillar II: A toxicokinetic/clinical evaluation and a proposed pathogenesis: Septic Penetrating Setae. The International Journal of Applied Research in Veterinary Medicine, 2:142-158.
Webb B.A., W.E. Barney, D.L. Dahlman, S.N. DeBorde, C. Weer, N.M. Williams, J.M. Donahue and K.J. McDowell (2004). Eastern tent caterpillars (Malacosoma americanum) cause mare reproductive loss syndrome. Journal of Insect Physiology, 50:185-193.
Update V 10/4/06: The Telic Thoughts bloggers have decided to retract their articles on the subject. Kudos to them.
With the whole hoop-la over the Dr. Pianka speech it turns out that a full transcript of a speech he gave at St. Edwards has been released and is available here. I'm going to quote two parts of this speech that disregard and annihilate the account of the disgruntled creationist Forrest Mims, who evidentally lives in a very different reality than we do.
No advocacy for the annihilation of the human race and the full transcript even demolishes my previous essay on the topic. Going by what I originally understood, which was admittingly very limited, it turns out that I responded to things that Dr. Pianka doesn't actually think himself either. I do intend to readdress the "Killer virus" scenario in a future post, but Dr. Pianka answers a lot of the 'criticisms' I bought up in my post anyway in the full speech. I find it hard to disagree with what he says, although I still think the death toll is absurdly high and there are numerous problems with the 'viral doomsday' scenario I'll cover in a new post. In any event, I don't see him advocating the genocide of the entire human race at all there. However, let's contrast what Dr. Pianka has actually said with what Forrest Mims, disgruntled creationist, had to say:
This is an AIDS infected piece of a human. Each of those little round things is an HIV virulent that can infect a new human. Basically, they use their T-cells to they make copies of themselves.
HIV is a pandemic spread worldwide. It's increasing in frequency in a lot of places and it's a big concern to everybody. But, it's not gonna be the one that gets us cause HIV is too slow, it lets us live several years so it can pass itself on to new hosts.
Uh, it's no good, it's too slow.
Now when you get to these viruses — Ebola Zaire has potential. It kills nine out of ten humans. It's never gotten out of Africa cause its so virulent it kills everybody before they can move. I mean it kills you within a day or two.
Uh, you can only catch Ebola Zaire by contact with a human that's infected. It causes you to bleed. It breaks capillaries and you bleed out your orifices and if you go out and touch somebody who's sick with it you get it and you die, too — or nine times out of ten.
Ebola-Reston did get out of Africa and to the U.S. in the form of green monkeys that were imported for medical research and it's named after Reston, West Virginia where they have quarantine facility for these monkeys. And, uh, they had this epidemic and all the monkeys died but they didn't have contact with each other. But they were sharing a common, uh, ventilation system. So, this is in this room, air was circulating being pumped back, and so on. Uh, monkeys in a room that breathe the same air caught it.
Now it is only a matter of time until Ebola got here evolves and mutates a little and it will be airborne, and then I think we might finally get a take. And when it sweeps across the world — we're gonna have a lot of dead people. Every one of you that is lucky enough to survive gets to bury nine. Think about that. I doubt Ebola is gonna be the one that gets us. I think it will be, uh, something else.
But did you ever wonder why things like SARS and now what the Avian Flu are continually cropping up? They're cropping up because we were dumb enough to make a perfect epidemiological substrate for an epidemic. We bred our brains out, and now we're being pegged. The microbes are gonna take over. They're gonna control us as they have in the past. Think about that.
Here's a breath of fresh air: Aldo Leopold. This is the start of the tiny little up. You've got to the lowest of the low where the microbes are gonna get you. Now, were gonna try to come up a little bit. Aldo Leopold was a conservation biologist before anybody else was. He was in wildlife management at the University of Wisconsin back in the ‘50s. And Leopold died young, but his children have put together a collection of his essays and made this book, "A Sand County Almanac." I encourage all of you to read it. It brings tears to my eyes at some of the things in it. I mean I literally break down and weep.
But one of the things Leopold said was each generation doesn't know what it lost — the last generation remembers.
"This guy is a loose cannon to believe that worldwide genocide is the only answer," said Mims, who filed two formal petitions with the academy following the meeting.
“He recommended airborne Ebola as an ideal killing virus,” Mims said. “He showed slides of the Four Horsemen of the apocalypse and human skulls. He joked about requiring universal sterilization. It reminded me of a futuristic science fiction movie with a crazed scientist planning the death of humanity.”And
But there was a gravely disturbing side to that otherwise scientifically significant meeting, for I watched in amazement as a few hundred members of the Texas Academy of Science rose to their feet and gave a standing ovation to a speech that enthusiastically advocated the elimination of 90 percent of Earth’s population by airborne Ebola.And finally, let's contrast what Mims claims above with the final part of the St. Edwards speech:
So he says in a stationary world as opposed to one that's grow, grow, grow where everybody has to elbow the other guy and compete to get to the front and be concerned about who's going to win and who's going to lose everyday in the stock market. And in a stationary world we can focus in on things that really matter. And he used a phrase that I really love — the art of living. We can work on the art of living. Think about that.The art of living? From Dr. Doom? Dr. Death? Dr. Wipe out all humanity with a virus? But this man hates humanity, hates life and thinks that genocide is the only option to humanities over-population. With the clear honesty and integrity of Mims, how could this possibly be true! Clearly the transcript at the Gazette-Enterprise is a fake!
/Sarcasm off for now, I believe that anyone who reads the transcript kindly provided by the Gazette-Enterprise, reads the accounts from Mims and puts 2+2 together can clearly see Mims has really got it horrifically wrong. It's also clear that someone, namely Forrest Mims owes an apology to Dr. Pianka and I feel should even resign from his position. He's made Dr. Pianka out to be a terrorist, he's humiliated the University of Texas and he's made a mockery of himself. Even with the fact this is a different speech, the content is so similar to what we understand of the Texas Academy speech that I've no real reason to think they are significantly dissimilar.
Update: Now I think of it, also make sure you check out the Pandas thumb account and the numerous quotes from media and others who took Mims seriously. There are going to be a lot of people feeling silly tommorow.
Update II: An interesting analysis of the Edwards transcript compared with quotes from the newspaper that started it all, the Sequin Gazette Daily, has been posted at the Questionable Authority. It's a very interesting post and raises some real doubts about some of the media frenzy over Dr. Pianka.
Update III: I also noticed this post on Ocellated, where Jay has actually been speaking with several students who attended the talk and gives a good impression of what Dr. Pianka is like. I recommend reading his entire post, but if you want what I think is the part that really cuts through many of the core issues it's this part:
Immensely well said.
While I may be disappointed and certainly find things to disagree with Pianka about, his accusers sink to new depths. Wanting to follow my own advice and not show angst myself, I simply cannot articulate my frustration that people are so convinced of their position, that lying then becomes a justified means to defeat their “enemy.” Indeed, viewed in this light, we can understand that hate has become their prime motivation.
And they do all this in the name of Jesus. What a crazy world we live in.
When I became a convert from Judaism to born-again Christianity after watching The Chronicles of Narnia, I thought things were going to get a lot easier for me. After all, Jews have historically been the most hated people on Earth. And while Jews are a minority in this country, 85% of Americans call themselves Christian. I thought I would be sort of like a black person who suddenly turns white or a gay person who suddenly turns straight (which apparently happens all the time according to my new Christian brothers).Oh dear and that's just the introduction! What I like most about his blog is how he is plain enough about the satire he writes to be obvious, without sounding completely unlike what he is trying to make fun of.
Thursday, April 06, 2006
So much interesting research to write about, so little time.
Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex. Belov K. et al 2006. PLoS, 4:317-328.