The Biologista

Solidarity

2009-07-29T21:03:00.007+01:00

My apologies for the long delay in posting and the dearth of new material on this post. All I can do is assure you that I am still alive, but merely very busy with my PhD and a publication... Today sciencey and not so sciencey blogs across the web are re-publishing an article by Simon Singh about the many dubious claims of chiropractors and the British Chiropractic Association in particular. I have made reference to some of the poorly-supported claims of the BCA in a previous blog entry. I've also discussed how scientists go about refuting dubious claims. Science is an adversarial system in which our claims and the evidence upon which they are based are subjected to close scrutiny and, if they appear weak, are attacked. We debate, we refute with contradictory evidence, we put forward alternative explanations for the observable facts. We do not litigate, because litigation silences a scientific debate and transfers it into a courtroom so that some lawyers can have a financially ruinous legal debate.

But the BCA sees things differently. When last year Simon Singh pointed out how weak the evidence in support of chiropractic really is, the BCA reacted not with scientific evidence, nor logical argument. They sued him. That action is now ongoing and has been commented on by Bad Science. For science to progress, debate must be free and open and won on the basis of evidence, not legal funds. This is especially important when it comes to health, because when debate about medical science is stifled, bad practices persist and the outcome is suffering and death. Whether chiropractic is effective and safe will never be determined by a judge. If any of this bothers you sufficiently, the British organisation Sense About Science have a petition you can sign.

The original Singh article (modified to avoid the BCA's litigation bat) is reproduced below, as it has been reproduced by Sharon at The Voyage, Pharyngula and many other blogs. Feel free to refute it with scientific evidence!

Beware the spinal trap

Some practitioners claim it is a cure-all, but the research suggests chiropractic therapy has mixed results - and can even be lethal, says Simon Singh.

You might be surprised to know that the founder of chiropractic therapy, Daniel David Palmer, wrote that "99% of all diseases are caused by displaced vertebrae". In the 1860s, Palmer began to develop his theory that the spine was involved in almost every illness because the spinal cord connects the brain to the rest of the body. Therefore any misalignment could cause a problem in distant parts of the body.

In fact, Palmer's first chiropractic intervention supposedly cured a man who had been profoundly deaf for 17 years. His second treatment was equally strange, because he claimed that he treated a patient with heart trouble by correcting a displaced vertebra.

You might think that modern chiropractors restrict themselves to treating back problems, but in fact some still possess quite wacky ideas. The fundamentalists argue that they can cure anything, including helping treat children with colic, sleeping and feeding problems, frequent ear infections, asthma and prolonged crying - even though there is not a jot of evidence.

I can confidently label these assertions as utter nonsense because I have co-authored a book about alternative medicine with the world's first professor of complementary medicine, Edzard Ernst. He learned chiropractic techniques himself and used them as a doctor. This is when he began to see the need for some critical evaluation. Among other projects, he examined the evidence from 70 trials exploring the benefits of chiropractic therapy in conditions unrelated to the back. He found no evidence to suggest that chiropractors could treat any such conditions.

But what about chiropractic in the context of treating back problems? Manipulating the spine can cure some problems, but results are mixed. To be fair, conventional approaches, such as physiotherapy, also struggle to treat back problems with any consistency. Nevertheless, conventional therapy is still preferable because of the serious dangers associated with chiropractic.

In 2001, a systematic review of five studies revealed that roughly half of all chiropractic patients experience temporary adverse effects, such as pain, numbness, stiffness, dizziness and headaches. These are relatively minor effects, but the frequency is very high, and this has to be weighed against the limited benefit offered by chiropractors.

More worryingly, the hallmark technique of the chiropractor, known as high-velocity, low-amplitude thrust, carries much more significant risks. This involves pushing joints beyond their natural range of motion by applying a short, sharp force. Although this is a safe procedure for most patients, others can suffer dislocations and fractures.

Worse still, manipulation of the neck can damage the vertebral arteries, which supply blood to the brain. So-called vertebral dissection can ultimately cut off the blood supply, which in turn can lead to a stroke and even death. Because there is usually a delay between the vertebral dissection and the blockage of blood to the brain, the link between chiropractic and strokes went unnoticed for many years. Recently, however, it has been possible to identify cases where spinal manipulation has certainly been the cause of vertebral dissection.

Laurie Mathiason was a 20-year-old Canadian waitress who visited a chiropractor 21 times between 1997 and 1998 to relieve her low-back pain. On her penultimate visit she complained of stiffness in her neck. That evening she began dropping plates at the restaurant, so she returned to the chiropractor. As the chiropractor manipulated her neck, Mathiason began to cry, her eyes started to roll, she foamed at the mouth and her body began to convulse. She was rushed to hospital, slipped into a coma and died three days later. At the inquest, the coroner declared: "Laurie died of a ruptured vertebral artery, which occurred in association with a chiropractic manipulation of the neck."

This case is not unique. In Canada alone there have been several other women who have died after receiving chiropractic therapy, and Edzard Ernst has identified about 700 cases of serious complications among the medical literature. This should be a major concern for health officials, particularly as under-reporting will mean that the actual number of cases is much higher.

If spinal manipulation were a drug with such serious adverse effects and so little demonstrable benefit, then it would almost certainly have been taken off the market.

Casey Luskin is The Wedge

2009-05-12T00:24:00.006+01:00

There's a multimedia element to my post this time around. Well, an annotated YouTube video. Trust me, the stupid isn't nearly as compelling until you watch it.

Discovery Institute front-man Casey Luskin appeared on Fox News' rather conservative "Fox and Friends" show recently to warn us all that we're being hoodwinked by them mainstream science types. Biology textbooks, Luskin claims, neglect to incoproporate any scientific evidence which "contradicts Darwin". Apparently, the teaching of evolution in American schools (and perhaps elsewhere) is plagued with inaccuracies. This quite modest plague apparently consists of two items which, if you can believe it of a God-fearing institution, are total bullshit. Isn't it strange how the people raising this most important issue also happen to be peddling Intelligent Design, a crudely-disguised version of Creationism. The presenter correctly identifies that the teaching of evolution is a "white hot" issue. I guess the failure of the show to bring on someone from say, the other side of the debate, to speak on the show may have something to do with that "and Friends" bit of the show title.

First up in the non-torrent of non-issues is the apparent inclusion of the debunked "Haeckel's Embryos" illustrations in biology texts, which I have to admit I have never seen presented as factual. Of course, what Luskin does not mention is that the point that Haeckel's admittedly fabricated drawings of vertebrate embryos compared side-by-side has in fact been fully validated by genuine embryology work. This work has shown that we can find common combinations of morphological traits between the embryos of the vertebrate species. We gain an insight that we don't always get from comparing adult organisms. It is this modern and well researched take on Haeckel's work is what we typically find in biology texts. And it is that science which actually upsets Luskin and company who, it is repeated so many times as to be suspicious, do not want to teach your kids creationism. For definite. Okay?

Second, the ghost of a recent New Scientist article (which screamed Darwin Was Wrong from the front cover before going on to essentially admit that he... wasn't wrong) is summoned to frighten us. The article discussed the phenomenon of horizontal gene transfer (HGT), whereby genetic material can pass from one species to another without descent. HGT makes a mess out of the lineage of the bacteria because they make such transfers quite frequently. However, Casey Luskin would like us to believe that this has proven wrong the concept of the tree of life entirely. But HGT is quite remarkably rare amongst species bigger than the single-celled organisms that live in in the humid forests of Luskin's substantial eyebrows. The awkward truth that Luskin and other ID proponents need to explain is why when we arrange bigger, multicellular species by the combinations of common traits they posses, we get a tree shape. That's just how their traits are distributed, the tree is not a human fabrication and it is certainly not under threat. It's taught as a part of evolution because when it comes to the animals and plants we see around us, it's very much real and relevant.

Luskin's entirely unchallenged arguments are aired here, with some added annotations from yours truly.

The Jenny McCarthy Body Count

2009-04-10T13:40:00.007+01:00

Perhaps in response to Jenny McCarthy's afore-mentioned comments on allowing killer diseases to come back so that the non-effect of vaccines on autism can be avoided, a guy called Derek Bartholomaus has decided to keep a running count of vaccine-preventable deaths. He's called it the Jenny McCarthy Body Count. Since she seems quite comfortable to accept that her views on vaccination will inevitably result in deaths, it seems appropriate that she should be given moral responsibility for what that means. Although Ms. McCarthy can not of course be held directly responsible for a full share of all such deaths, you get the general gist. She's in a position where her word has enormous influence, and in the case of opinions on vaccination, that influence extends to people who have no regard for her views or who many never have heard of her. The anti-vaccination movement is resulting in preventable deaths, and they had better accept that reality.

Jenny McCarthy image by Flikr user gamerscoreblog and licensed under Creative Commons Attribution ShareAlike 2.0 License.

As A Parent, I Just Know Chemical X Isn't Safe

2009-04-03T19:01:00.009+01:00

I'm not sure why people should care what Jenny McCarthy thinks about autism or parenting, but they do care. I disagree with how she views autism. She talks of healing, of recovery, as though autism were in some manner analogous to a physical or mental disease rather than, as I view it, a kind of human mind that is not well accommodated for in a society in which it was once rare. If that were all she had to say, then I suppose we could consider this a strong difference of opinion. But of course there's more.

Jenny McCarthy on Autism and Vaccines

I do believe sadly it's going to take some diseases coming back to realize that we need to change and develop vaccines that are safe. If the vaccine companies are not listening to us, it's their f___ing fault that the diseases are coming back. They're making a product that's s___. If you give us a safe vaccine, we'll use it. It shouldn't be polio versus autism.

All I can do is sigh. Jenny McCarthy is a high-profile human being, so her views carry weight. The least she could do is honour the responsibility that carries and keep up with the scientific evidence, the expert views. But instead she continues to push the tired old vaccines = regressive autism canard, whilst suggesting that parents should be prepared to accept the resurgence of diseases which kill and maim people. McCarthy feels secure enough in her knowledge of vaccination and autism biology that she can make that undoubtedly harmful claim. She's basically making herself an expert opinion, without having to do the hard work that would really require.

I have a radical suggestion. Jenny McCarthy should present herself as an expert on things in which she is experienced. So parenting, sure. We may disagree with her, but she can certainly have that. Parenting with an autistic kid? Same deal. Virology? Vaccination? Autism biology? Cohort studies? Meta analyses? Risk factors? When she starts citing the studies, the analysing the data that back her up, rather recycling the anti-vaccination nonsense, I might start listening to her views on those.

Bacon Sandwich

2009-03-12T18:03:00.005Z

I'm pretty busy writing up my work at the moment, hence the long break in posting this month. I'll try to fire out a few short but useful entries over the coming weeks rather than saving it all up for the monolithic posts I usually make.

Every week, some newspaper or another makes us frightened or happy by covering the latest risk data regarding "causes" or "cures" for cancer, stroke, heart disease and the like. Apparently they won't be happy until they've fully catalogued all Things at least once over, and preferably twice with flatly contradictory information. They present us with statements such as "Bacon Sandwiches raise cancer risk by 20%". That would probably put quite a few people off eating bacon sandwiches, but it's not a statistic you'll ever find in a peer-reviewed scientific paper. And there's a good reason for that. This sort of figure is what is called a "relative risk increase". It's calculated by taking the dividing the new risk (with bacon sanswiches) by the normal risk (sans sandwich) and multiplying by 100. We can see the weakness of that way of representing the numbers with an illustration such as this:

The risk of killing yourself with a revolver loaded with only a single bullet in a random chamber is 1 in 6. Put two bullets into two random chambers and the risk is 2 in 6 (or 1 in 3). These are absolute risks as opposed to relative risks. In percentages, the absolute risk is just over 16% with one bullet, but twice that (32%) with two bullets. Now let's do a Daily Mail on it and express this as a relative risk increase. That's a 16% increase over 16%. So by putting in the extra bullet you've just increased your risk of killing yourself when you pull the trigger by 100%. That last number is certainly the scariest, although we must admit that none of these numbers is particularly fun.

But here's where it gets interesting (stop rolling your eyes please). Imagine the risk of catching a fatal dose of the flu is 1 in 10,000,000 for each time you go to work on the train, but is 2 in 10,000,000 if you take the bus. These odds are very much lower than the absolute risks relating to the gun. In percentage terms they sound comfortingly low too (0.00001% increasing to 0.00002%). You're probably not going to base your public transport decision making on these numbers. However when we convert these numbers into a relative risk increase, we get... 100%. A headline that says "Buses Raise Flu Death Risk by 100%" is certainly going to either make you think twice about using the bus, or is going to make you think that those silly boffins are just spoofing (didn't they say buses were better for some reason last week?). You get exactly the same punch in a Daily Mail headline as the gun risk, and yet in reality they're not even vaguely similar.

This week a nice site caught my eye which puts all of that statistical wonder into a fun little web program that allows you to see the various ways in which scientific data can be made more scary. There's all sorts of ways to make a scare story out of a non story, and you can rest assured that most of the newspapers are quite prepared to use them.

Image from Wikipedia released under the terms of the GNU Free Documentation License.

Holy F**king Sh*t: Daily Mail debunks MMR autism link

2009-02-19T16:02:00.013Z

This post may be unsuitable for minors or people upset by scenes of total doublethink.

Well, the day has finally come. The Daily Mail has finally joined the rest of the world in accepting that MMR is safe, and that the 1998 study by Andrew Wakefield has been "debunked" (even though the study never says that MMR causes autism, a press release did and it was debunked 10 years ago). Measles is on the rise again, and that's actually a big deal. Kids are getting sick, people have died and someone is going to hang. This isn't just Wakefield's fault of course. No, he should not be a scapegoat! There are others to blame. Us, apparently. In a remarkable display of doublethink, the Daily Mail points the finger at "middle-class MMR refuseniks". Parents who somehow bought the press-release pseudoscience presented by Wakefield (minus the et al). They must have picked it up off Reuters, the wiley middle-class (yet strangely uncritical and credulous) bastards.

Of course, the Mail don't mention the media frenzy that followed the "confirmation" of Wakefield's 1998 work (by, er.. Wakefield). The evidence-free total bullshitstorm that presented Wakefield's speculations directly to that middle-(and working-) class audience as if it were yet another scientific "breakthrough". The torrent of jargon filled trash that published everything that vaguely supported the hypothesis but ignored the dozens and dozens of studies debunking it, milking that story for every millilitre of newspaper sales it had. And how could they, since up until a month ago the Daily Mail were still doing it? Still implying that MMR was dangerous. But today they've hit the reset button. And I feel like I just fell through the looking glass. It's funny, in a totally horrifying kind of way. Well, let me just say, so that we can be clear. And you'll have to forgive me for my profanity because it just feels like that sort of moment.

THIS WAS YOUR FUCKING FAULT, YOU MORONS.

I mean, seriously. Read your own articles. People are going to hang for this, but the media are the ones judging who, so the list will doubtlessly be restricted to:

-A. J Wakefield
-The Middle Classes

I feel like I'm taking crazy pills.

Update 18:08: It's even crazier than I thought. A search for "MMR" on the Daily Mail reveals a similar article in 2008 blaming "mothers" for the oncoming measles epidemic. This article sits amongst yet more panic pieces calling MMR "controversial" and cagey coverage of the research that 'disproves MMR jab link to autism' (the quotes were in the headline as if incredulous). Clearly, the Mail spent 2008 being eased into a gentle but enormous u-turn.

Happy Darwin Day

2009-02-12T13:25:00.002Z

Happy Darwin Day! Today we celebrate the 200th birthday of a scientific revolutionary. Like Pasteur, Mendel, Newton and Einstein, Darwin ushered in a shift in our perception of the evidence. In Darwin's lifetime the nature of life and its place in the world was explained by a mixture of assumption and religion. The science that existed was disparate. Biologists were just starting to understand heredity and variation. That variation displayed such great diversity at times, and yet such curious similarities. The distribution seemed to make little sense. Geologists were pointing to the massively stratified nature of their favourite medium (rock) as evidence that the world was far older than they had expected and wondered at the curious sequence of petrified organic structures they found within. Layer upon layer, that same progression across every strata and every geological discontinuity, across the world. The evidence was all there, merely waiting for someone to bring it together into one clear picture.

In November, we'll celebrate the 150th anniversary of the publication of that clear picture. Darwin's most prominent work, On the Origin of Species. Just as Newton's world was superceded, but not destroyed, by Einstein's; so too has Darwin's work found itself but a small part of a grander theory. His Laws of Natural Selection remain intact, his notions on heredity and genetics superceded by his contemporary Mendel. Both now standing along side the molecular genetics of Watson, Crick and Franklin.

There are those who say that scientists hold Darwin sacred. That his theory has become dogma. But it is likely that if Darwin read a modern biology textbook today, he would certainly disagree. He might even be a little annoyed at the absence of some of his hypotheses. But he would be delighted that natural selection has endured so well. And delighted that humanity has cast aside the notions of racial species divides which he loathed so much.

He gave us a part of the picture. We have accepted those ideas of his which have been borne out in experimentation, and discarded those which did not. Concepts that brought the evidence together in a revolutionary way. He was the first to understand our true nature and our place in the world. For that, we celebrate a great man and a scientist who stands as an example of dedication and remarkable insight.

Happy Birthday Charlie.

The Streisand Effect

2009-02-10T15:14:00.004Z

The Jeni Barnett MMR story really has longer legs than many of us sciencey bloggers had hoped. A week after Barnett rehashed every cliché in the anti-vaccination handbook over roughly 40 minutes of hysterical melodrama, the subsequent attempts by both Barnett and her radio station LBC to silence Ben Goldacre's perfectly appropriate criticisms have exploded hilariously in what is called The Streisand Effect. Only the Bad Science followers were paying attention up until the point when LBC's lawyers forced Ben to remove a (rather long) clip of the entire MMR segment of the show in what was a rather dubious and aggressive copyright infringement claim. The Sciencey Blogsphere Collective as not amused. The clip was rapidly copied and redistributed across the interenet, effectively becoming entirely untouchable. Blogs everywhere began to report angrily on the incident and the feeling was almost universally in favour of Ben.

In an attempt to appear open to debate, Barnett's Blog (which rather scathingly dismissed one of her most polite pro-MMR callers as "viscious") called for comments. And the comments came. 121 comments, mostly annoyed but polite attempts to explain to Jeni why MMR is safe and important for public health. A follow-on post by Barnett sneered at the "Bad Scientists" and their "sarcasm". This post prompted a further 81 comments, again the vast majority being critical of Barnett's poorly-informed and irresponsbible stance on MMR.

More blogs reported, more segments of the radio programme were posted, this time in fragments too small and too many to be silenced by questionable copyright infringment claims. Transcripts appeared. PZ Myers rallied his atheist army behind the pro-MMR standard. The Times online noticed the story, and weighed in to defend Ben Goldacre. And, in a quite stunning moment, the great Stephen Fry called for Goldacre to be supported.

Perhaps understandably, Ben's website crashed several times under the weight of visits and messages of near-universal support. Perhaps panicked, Barnett deleted all 200 or so of the critical messages from her own blog and has attempted to move on. No meaningful apology. No recognition of the continuing damage this evidence-free nonsense has done to public health in the UK and Ireland. And of course, no glimmer of having realised that everything she and LBC have done so far, including this, is just making things worse for her and her employers.

For those interested, the deleted blog comments are available at the excellent Quackometer blog.

MMR is safe. Tell your friends.

2009-02-06T14:34:00.007Z

Bad Science writer Ben Goldacre recently reported on a stunningly ignorant radio broadcast by Jeni Barnett perpetuating the MMR vaccine scare. Ten years after a peer-reviewed paper didn't say there's a connection between MMR and autism but one of the authors told the media that it did, we're still going in circles. We can point fingers in all sorts of directions, including at ourselves, but the data has shown time and again that MMR is safe.

Ben posted the radio slot up to demonstrate that he was not cherrypicking the most stupid parts just to make Jeni look bad. But apparently this is legally not okay and so, because scientific debate has long ceased to matter in the MMR scare, the lawyers swooped in. Personally, I don't think any of us should allow fear to prevail when the cost is so great. The MMR scare is based on crap science and it's putting kids at risk. It has to stop.

Discuss it on Bad Science (there may even be some links to the radio programme): http://www.badscience.net/

On Jeni Barnett's blog: http://www.jenibarnett.com/2009/02/mmr_and_me.php

Update 16:52: Coincidentally, the BBC today announced that Measles cases rose yet again for the third year running. The cause is the reduction in MMR uptake and the result is going to be deaths. Not many deaths, but some.

Update 08 February 2009: And evidence has just emerged that the man behind the scare, Dr. Wakefield, falsified some of the original data showing a temporal association between MMR and autism. Far from there being even that correlation, it appears that some of the kids were showing documented autism characteristics prior to MMR vaccination and others displayed them much much later than was stated in Wakefield et al. (1998).

Accept Evolution, Eat People

2009-02-04T20:40:00.008Z

During the weekend Donna Garner, a former language arts teacher in Central Texas and a conservative activist, circulated an email in response to the recent move by the Texas State Board of Education to close a long-standing loophole in their policy on the teaching of science. Previously, it was a requirement to debate the "strengths and weaknesses" of the theory of Evolution (or any scientific theory). A requirement, even if the matter was not prompted by students. In practise, this has been used as a back door to introduce creationist and intelligent design arguments into the classroom. Not actual scientific weaknesses, but religious criticisms. Science is not debated in terms of strengths and weaknesses, but in terms of evidence. But I'll return to that point.

She begins:

Dear Friends of Students:

This year, 2009, is the 200th anniversary of the birth of Charles Darwin (born in 1809), author of Origin of the Species. Atheist groups across America are using this anniversary to move aggressively to force all 50 million public school students to be taught that macro-evolution (life spontaneously springing from a chemical reaction with all life stemming from that common chemical reaction and becoming different species through mutations) is a fact–without allowing the teaching or discussion of the scientific “weaknesses” increasingly being discovered concerning the theory of evolution. Texas, with its 4.7 million students, was selected as the first state to conquer. And, so far, the atheists are winning in Texas.

Let's just take a look at what has been said and left unsaid in her opening statements.

Garner immediately puts a suggestion into our minds without backing it up. "Atheist groups are using this...", "the atheists are winning". Immediately the subject is not education, but religion. In her mind (and she wants us to join her there), this is not about science, but faith. No names are named, no figures cited. We are to assume that science advocacy groups such as Texas Citizens for Science, The Texas Freedom Network and countless others are atheistic in nature. The atheists are doing this, and presumably it's part of a grand plan. A war to be won at terrible cost to you the reader, a cost to be outlined later.

Next she both introduces and defines "macro-evolution" and states that everyone will be forced to learn this thing that she has defined as fact. Macro-evolution is a term not used in the scientific literature or in text books, so it is good that Garner defines it for us. But her definition does not actually match up with anything taught in US schools. Her target, Evolution, does not attempt to explain the origins of life itself (which are not conclusively known) but merely the origin of the great variety of life that we now see. That origin is indeed a common ancestor, but for now at least, Garner's "spontaneous springing [of life] from a chemical reaction" remains within the realms of hypothesis. If it is taught at all, it is taught in that context. Macro evolution then, is something of a Straw Man.

Finally, she implies that Evolution has "scientific weaknesses" that are, she says "increasingly being discovered". Well I'm quite sure that evolution does have flaws, but with what relevance to high school students? With what support within the expert community? If a fringe group of historians contend that Abraham Lincoln's murder was motivated by Wilkes-Booth's phobia of beards (or something more plausible perhaps) we're not going to open up the floor for students to specifically "debate the weaknesses" in the theory that the assassination was politically motivated. This is not an end to questions about the motive or the politics which formed it, but the dishonest notion that a meaningful debate exists in the field is not entertained. And of course, the curriculum for a given subject should reflect the consensus of the relevant experts.

As for weaknesses "increasingly being discovered", well there's certainly nothing new in the pseudoscience that Ms. Garner will shortly inflict on us.

Let's move on.

For more than 20 years, the rule in Texas has been to teach both the “strengths and weaknesses” of evolution. Last week, by a margin of 1 vote, the Texas State Board of Education voted to remove the word “weaknesses” so that only the strengths of evolution could be “analyzed and evaluated” in all Texas public schools. The final vote is in March, so there is time to make a difference.

As I indicated previously, the "strengths-versus-weakness" model of debate or analysis is a curious idea, and it is not really one which applies to science, assuming we are seeking to invite serious debate in a classroom. If evolution is open to being "analysed and evaluated" (and of course it is), it stands to reason that this should be on the basis of evidence.

Some evidence will support evolution and some, if evolution is incorrect, will contradict it. The thing about scientific theories is that we do not weigh-up the "pros and cons" of a theory when deciding if it is legitimate. If one piece of evidence contradicts the predictions of a theory (and it can be shown that the evidence is real and reproducible), then the theory is dead. Totally dead. No balancing of strengths or weaknesses. The theory is in the bin and we have to build a new one. One piece of falsifying evidence automatically outweighs all the "strengths" we could care to present.

The strengths and weaknesses method of debating science is perhaps a reflection of a science curriculum that does not address how hypotheses, evidence and theories are constructed in science. Or perhaps it is a back door designed to allow spurious attack upon theories which are seen to contradict an agenda.

Garner then lists who voted on the new wording and how, providing contact details for each so that we can phone up and demand that somebody think of the children. I'll cut this on the basis of it also being really boring.

*Snip*

Garner continues with an attempt to make "the atheists" look like hypocrites. After all, everyone knows that if you're a hypocrite, you're wrong about everything, right? Ad hominem much?

Charles Darwin, in Origin of the Species said the following concerning the proper evaluation of his theory: “A fair result can be obtained only by fully stating and balancing the facts on both sides of each question.” Too bad Darwin wasn’t on the State Board of Education to vote to keep “weaknesses” in.

Darwin, of course, was stating the obvious. That we must consider all the evidence before making a decision about something. Ms. Garner won't like to admit it, but Evolution was accepted by scientific consensus by this very means a very long time ago. Debate over the course of some decades by the finest minds in science.

In a pedantic point, Darwin's book was not called "Origin of the Species" but "On the Origin of Species", being as it is a work explaining the emergence of species plural. You'll also note that it is not called "On the Origin of Life", and thus must not have anything to do with Garner's proposed "macro-evolution".

At least, he was intellectually honest about his theory.

Ah, "at least". Suggestion once again. He wasn't honest about everything. This casts doubt on evolution. Painful.

He recognized that science advances by constantly probing and questioning, not by censorship, intimidation, or indoctrination.

Are we talking about the advancement of science? I'm quite sure that Darwin would also have recognised that continuing to debate a scientific theory 100 years after it has come to be considered accurate by scientists is rather counter-productive. But that is not even the issue here. Whilst we should certainly teach our children about gravity, it wouldn't exactly be "scientific" to perpetuate a debate on the matter on the basis that we should never stop questioning. We never do stop questioning these theories, but what Ms. Garner has failed to grasp is the nature of that questioning. Scientific research. Experimentation. Not debate in a room full of teenagers. How would such a debate advance science or some other subject such as history?

We have debate in the public between creationists and evolutionists, although that debate is painted as a scientific one, the matter has already been resolved in the scientific community for some 100 years or more. Finally, we have debates like these. The reader can see Ms. Garner's side, and the side of people such as me. So it doesn't really look like anyone is pulling off the censorship routine. Or at least not doing it well. So I'm sure Darwin would be more than satisfied (well of course I'm not sure, I never knew the guy and neither did Ms. Garner). The question that remains is whether that debate has any place in the class room.

The 3 Republicans don’t seem to get it. They want to water down the current standard to eliminate any airing of “weaknesses” by eliminating the word “weaknesses.” The battle is over that one word. It needs to be there. As a lawyer, I know more than most that words are important. So don’t be fooled, the retention of the word is worth all of us fighting for.

Again, the "strengths versus weaknesses" model of assessment does not really work for science and really should be scrapped entirely in favour of teaching kids how to assess scientific evidence, form and test hypotheses and build theories.

Garner then decides to elaborate further on her definition of Evolution. In doing so, she describes a theory that only appears in one kind of text book or scholarly publication anywhere: creationist ones.

Short primer on evolution: In describing evolution, there are 2 catagories: (1) Micro-evolution, and (2) Macro-evolution. Micro-evolution (small changes over time within the same species) is something we can observe today (bugs become resistant to drugs; birds beaks grow longer, moths change colors).

Biologists make no such distinction, and for a very good reason. There are no differences in the underlying mechanisms that drive the micro or the macro. Evolution is driven by replication, mutation, genetic drift, natural selection, gene transfer. Ask creationists what micro-evolution is driven by and they'll give the same answer. So it's rather like making a distinction between taking a walk in your garden (by using the easily provable micro-walking) versus going down to the shops (which would require the obviously impossible macro-walking).

If we're agreed that some evolution can generate some variation, then why can we not agree that more evolution can generate more variation?

But Garner has evidence that there's a difference between the macro and the mirco.

I personally think it makes perfect sense that a good Designer would design each creature with built-in abilities to adapt to survive. But the debate before the Board is not over micro-evolution, but over the teaching of macro-evolution. We have never observed one species becoming a different species (macro-evolution).

In fact, we have observed species become a different species quite a number of times both in the lab and in the wild. Some nice (but not at all exhaustive) examples of these are detailed at the following links:

http://www.talkorigins.org/faqs/faq-speciation.html
http://www.talkorigins.org/faqs/speciation.html

But on to more "evidence". Am I using sarcastic quotes too much?

And we have never observed how life began.

Indeed we have not, but then we don't teach highschool kids how life began. We don't teach abiogenesis as fact to anyone at all. It's not a part of the theory of evolution at this time and won't be until that evidence is in. At this time, the origin of life is rather irrelevant to the debate.

This is where we need to examine the scientific strengths and weaknesses. And with respect to macro-evolution there are numerous scientific weaknesses, to name a few: (1) the Cambrian explosion of life; (2) gaps in the fossil record; (3) the intractable origin of life chemistry problems; (4) the origin of information in the DNA molecule; and (5) irreducibly complex features. Honest scientists acknowledge these and other weaknesses—but atheists don’t want these weaknesses highlighted—particularly not to our children. This is the Scopes Monkey Trial in reverse.

It would take another blog post in itself to fully refute the five points outlined here. They are classic cliches, and nothing new at all. But briefly, number 1 is something of a mystery. That is to say, I have little idea what Garner is getting at and it's unlikely that she does either (I have seen one argument regarding the Cambrian Explosion used by creationists, but that argument was dropped some years ago when it was mysteriously removed from the creationist website that had hosted it). Number 2 represents limitations to our knowledge. I think we can safely say that were there no gaps in our observations, we would have little need for theory (or religion) and science itself would become a job dedicated to teaching rather than research. If the reader has been following closely, we can of course immediately dismiss number 3 as having exactly nothing to do with how evolution is taught. Number 4 is in a similar vein since it deals with events prior to the origins of life and with concepts of "information" that are perhaps rather beyond a high school class. Number 5 is a topic I've already made a nonsense of here.

She concludes her list of "weaknesses" by claiming that "honest scientists" acknowledge these issues. Certainly, mainstream biologists don't assume that abiogenesis is an answered question, but they also don't consider it a part of theory. The vast majority of biologists, and the scientific community at large, consider evolution accurate. Just as consensus determined by historians informs the history syllabus, so too does the scientific consensus inform the scientific syllabus. What Garner of course means by "honest scientists" is creationists and intelligent design proponents. What "atheists" refers to here is not clear, but is presumably "everyone else" including the scientific community and all of the science advocacy groups. And the Catholic Church. Hmm...

Because their fields are a pseudoscience (as distinct from a fringe science), these people are considered to be scientists only by themselves. But what if we decided to include creationists and intelligent design proponents in our definition of the scientific community? Would evolution remain accepted by consensus? Are scientists redrawing the lines of the definition of "scientist" so that they can maintain an artificial consensus?

In terms of raw numbers of people, it's hard to assess just how many creationists are active in research. Newsweek puts the figure at approximately 700 in the United States. There are 480,000 life scientists in the United States, and evolution also is accepted by the overwhelming majority of scientists in the physical sciences, an even larger group. Not to mention almost universal support in scientific communities across the world. Let us generously suppose then that we are talking about 2000 creation scientists in a worldwide community of just 1 million biologists and geologists. 0.2% of a community does not break a consensus. So even if we include creationists in the scientific community the consensus, unsurprisingly, remains that evolution is valid and thus it should be taught as valid.

The "scientific debate" is a fabrication. To the scientific community, it is a (scientifically) small and illogical tantrum. It is only in the public eye that the debate has any validity or support at all. And the bulk of creationist efforts are bent towards increasing that validity. We need only look at the publication patterns of the creationists to see evidence of this. They produce little original research, preferring instead to publish essays and glossy text books. In 2008 alone, biologists published over 3000 research papers with the word "evolution" in the title (plus over 400 reviews, an unknown number of essays and textbooks). We can assume that there were many more on the topic of course, since most papers would not mention such a broad topic as evolution in their titles. It would greatly surprise me if the various creationist communities combined have managed to publish 3000 research papers in the last 20 years. Or even an output of research comparable to their small size. This is not reflection of general poor output or funding,creation advocacy groups generate plenty of essays and command tens of millions of dollars annually. Propaganda is the priority, not science.

Ms. Garner has one more shot to fire. The cost. The terrible danger that exists if we do not allow the Creation Tantrum to be given the validity of discussion in the classroom. The cost of accepting that evolution is both a valid theory and a reflection of fact.

Thus she concludes:

Jeffrey Dahmer, one of America’s most infamous serial killers who cannibalized more than 17 boys before being captured, gave an last interview with Dateline NBC nine months before his death, and he said the following about why he acted as he did: “If a person doesn’t think that there is a God to be accountable to, then what’s the point of trying to modify your behavior to keep it within acceptable ranges? That’s how I thought anyway. I always believed the theory of evolution as truth, that we all just came from the slime. When we died, you know, that was it, there was nothing….” (Dateline NBC, The Final Interview, Nov. 29, 1994).

The implication is clear. Evolution is part of a nihilistic and atheistic attack on religion. It leads to more atheism. And atheism leads to cannibalism (oh okay, at least to immorality). And the moral expert she cites to both imply and support this? A serial killer and cannibal. It makes my mind sore.

Will evolution kill faith? The Catholic Church seems to think not. The 1 billion Christians who follow that church seem to have no issue accepting evolution and their faith side by side. Evolution only poses a threat to Christian faiths which consider the book of Genesis to be a literal account of Creation. And that by no means assures that those who lose their faith in that literal truth are destined to become atheists. And what if they do become atheists? It is, of course, utterly unsurprising that someone like Dahmer could only build morality on the basis of personal consequence meted out by authority. He was a psychopath. He did not value human life in itself.

If the punishment of God is all that keeps Ms. Garner from killing and eating people, then I do hope she retains her faith. But I suspect that this is not the case. There is, in truth, no evidence at all that atheists are less moral on average than Christians. But we're rather getting away from the point, which is that the path from evolution to people-eating is a fantasy. One dreamed up by people who seem to think that morality is a very thin veil, a tenuous construction drawn over the amoral animal that is man. And held in place only by the ten commandments. I do wonder how strong the faith of the Creationists must be if they really see science, the simple observation of nature, as this manner of threat. But certainly, a little more faith in people is sorely needed.

Things Happen After Event Shock

2009-01-21T17:35:00.006Z

The Daily Mail have decided to have a go at MMR again as pointed out by Ben Goldacre at Bad Science. A child has fallen terribly ill "six months after MMR jab". Ten years after Andrew Wakefield speculated himself into the headlines by suggesting a link between MMR and autism (in a press-release mind, not in a research paper), this misguided rubbish is still being presented as "science news". Actually, most of the papers now seem to reject the link and are thus in the business of demonizing Wakefield himself, as if they had nothing to do with the scare. But the Daily Mail is apparently not quite ready to take even that ass-covering step. They cite the 1998 Wakefield paper (it was a press release that actually made the claims) and I have responded, though I wonder if it will be published.

Daily Mail, please read the 1998 paper by Wakefield et al. It does not suggest anything more than a temporal connection between the MMR vaccination and the onset of a symptom associated with autism (colitis) that's a long way from even suggesting a possible connection between MMR and autism. Wakefield decided to make that particular suggestion directly to the press, perhaps because the evidence did not support him and he knew it would not be published. More tellingly, ten of his his co-authors on the 1998 paper retracted their support for that claim.
So here we have another temporal association. Thing Y has happened after thing X. And so we must assume that X caused Y, right? Rubbish. I'd imagine a whole load of things happened before this poor kid fell ill.

At this point I ran out of words in the little submission box, so I'll conclude as I would have liked.

The child doubtlessly slept, ate breakfast and breathed constantly just prior to falling ill. So far as we can actually gather from the evidence here, almost anything could have "caused" this tragedy. The likeliest explanation though, is that it was nothing we could have predicted. You write that the child had previously suffered brain damage due to a Herpes Simplex infection at the age of two weeks. Anyone who has had coldsores will know that re-activation of that virus (it never leaves us) is not a predictable event and it has never been causally linked to events such as vaccination, as far as I'm aware.

To imply that MMR was responsible for this sad event is deeply irresponsible journalism and it will doubtlessly further the anti-vaccination movement and lead to more sick kids, and probably more deaths from measles- a disease that was nearly extinct in Europe before this totally unfounded scare.

Update 23 Jan 2009: Predictably enough, my comment has not appeared on the Daily Mail article. Nor have any at all, for that matter. Given that the Goldacre Evidence Army was alerted, that seems just a little suspect to me...

Why You’re Awesome: Part 1

2008-12-30T22:08:00.005Z

I thought I'd finish 2008 with the first in what I intend to be a semi-regular series on some of the random cool stuff that's going on with your biology and how evolution got you there.

The first time single-celled organisms decided to switch to communism (i.e. stick together to become multi-cellular organisms like cabbages, hamsters and us), they immediately faced a compromise. Sure, sticking together meant more food and more safety, but reproduction was now a more complicated matter. And as life became more complex, reproduction just got slower and slower. And because the rate that we can evolve is strongly influenced by our reproduction rate, this means that the bacteria and other little blighters that like to infect us have a massive evolutionary edge. We measure the time it takes for organisms to reproduce in terms of generation times, the average time it takes between a new organism being born and it getting around to reproducing for itself. After millions of years of evolution, the differences between the generation times of single-celled organisms such as bacteria and us humans is massive. The average human takes some 25-30 years to reproduce. Bacteria can divide and then divide again in 20 minutes. And so, bacteria and viruses evolve at a simply astounding rate by comparison to us big old lumbering animal types. Although we’ve had immune systems since those earliest days of multi-cellular life, the mutation rate problem was still there. Our immune cells work by recognising patterns- bits of bacteria, the surfaces of viruses, maybe some of the proteins from a parasite. But what good is it having cells that see what’s on the outside of a bacterium when a bacterium can change its outfit a million times before your cells can get their pants on in the morning? Our immune cells had to work in terms of broad patterns, and if one of those patterns changed due to mutation, things invariably got ugly.

Of course, if that had been the end of the story, we wouldn’t be here to talk about it. There’d just be a load of bacteria hanging around wondering where all the easy food went. Evolution, in its elegant non-wisdom, provided a solution. The key was to fight fire with fire. We vertebrates evolved a special group of cells that, when first made by our bodies (and we make loads of them every day), undergo their own randomised mutations. These special mutations occur only within a set part of our genetic code- right in the part which recognises those nasty bugs and parasites. Just by allowing chaotic re-arrangements of that little part of our DNA in a select set of cells, we we’re suddenly back in the game. With enough of these cells, we can now recognise some 10e12 patterns (that’s one thousand billion). In effect, we harnessed the driving force of evolution itself. Tightly controlled chaos. And it worked. Every animal with a spine has those precious cells. The lymphocytes, also called T cells and B cells. They’re awesome really.

Flu virus image from the Centers for Disease Control and Prevention's Public Health Image Library (Public Domain). Lymphocyte image from the National Cancer Institute (Public Domain).

Hypothesis, theory and fact: First Assumptions Part 2

2008-12-02T22:04:00.006Z

I said I'd write something about conferences and fashionable science, but it didn't come. Until it does, here's something else I'm toying with.

"All perception of truth is the detection of an analogy." -Thoreau

In my first post to this blog I discussed the meaning of the scientific concepts of hypothesis and theory. I highlighted how the public tend to think of “theory” in the same way that scientists think of hypothesis, in other words as an idea or educated guess. In fact theory is a word we use to describe the scientific models that we have the utmost confidence in. I’d like to elaborate a little on the concepts of hypothesis and theory and how they relate to what we call reality or fact.

All of science begins with observation. We sample the world and derive data from it. We can make data from all sorts of measurements, indeed from literally anything we can observe and measure. We might be measuring the height of people, the amount of heat produced by chemical reactions or counting the number of bacteria on people’s coffee mugs.

Analogy time

Let’s consider a simplified and slightly unrealistic analogy. First, we’ll pretend that we know very little about the subject of the study we’re about to do; people. Perhaps we’re aliens (or just really antisocial) but we don’t know much about people and we want to find out more. We’re most interested in the relationship between the size of people and how old they are. So we plan to measure the height of people and their age and plot this data on a graph called a scatter plot. Every person we measure appears as a blue dot. The higher up the graph they are, the taller we’ve measured them to be. The older they are, the further to the right they’ll be.

When we first begin to measure a thing, it can be difficult for us to determine if there are any patterns in the data, any meaning to be found. Look at graph 1. We antisocial scientists have made our first few measurements. Although it is far too soon to be confident that there’s a pattern here, it looks a bit like there’s a relationship between height and age in humans.

So we can create our first hypothesis. In graph number 2, we create a line which joins the data points together and also projects beyond them. We’re assuming that the relationship will hold for all people we measure, just for the moment. Just to make it sound important, we call our new hypothesis the Linear Growth Model or LGM (scientists love acronyms). The line is the hypothesis, a provisional model that we’ll cautiously use as a starting point. Put into words, the hypothesis would state: there is a linear relationship between the height of people and their ages. A statement of fact that we can now test.

The LGM is a good scientific hypothesis for that one important reason; it makes predictions that we can test. If the Linear Growth hypothesis is correct, then we expect that when we make more observations, they’ll appear on or near to our line. The scientific philosopher Karl Popper considered one other feature to be essential for a hypothesis to be valid; falsifiability, the possibility that our hypothesis can be shown to be incorrect by testing. At this early stage, our hypothesis could be falsified by finding just a few data points that fall far from out trend line. So of course we further test our model, measuring more heights and more ages. And when we look at graph 3, it seems we’re on to something! At this point it’s worth mentioning error. Measurements may often be subject to error. When measuring height, we might make a mistake. Or the height for people of the same age may vary (we know that it does of course, but for the purposes of our analogy let’s play dumb). So we often make the same measurement numerous times, or test many people of the same age. What we’ve done is measure our uncertainty and we can represent that uncertainty by drawing error bars that come out of each data point. We won’t worry about this further, but the point is that even though our data points may not exactly land on the red line, we are satisfied as long as the line passes through the area of error that lies around the data point.

With more and more data collected, our imaginary scientific colleagues now accept the Linear Growth Model as a satisfactory and useful model. It has become the Theory of Linear Growth. However, as often happens in science, it turns out that our theory is not entirely accurate. We realise that we’ve been building our model, the line, based on a very narrow data set. Because if you recall, we’re not all that familiar with how people work. And what we’ve gone and done is only measure the humans hanging around a playground. Some bright spark twigs that humans have loads of other habitats we didn’t observe. But maybe it’ll be okay, let’s find out. If the theory of Linear Growth is universally correct, then any new data points we get should continue to fit on our line. Of course we can see where this is going now, but let’s play dumb and continue.

When we extend our observations to older and older people, we start to see some data points that don’t fit our model at all. Had we seen these first few contradictory data points back at the start, it might have immediately caused us to discard our hypothesis before it even became theory. But with so much data in support of the theory, a few pieces of data are not sufficient for us to throw out the Linear Growth theory at the drop of a hat. As the saying goes, extraordinary claims require extraordinary evidence. But as we make more observations, the evidence becomes more compelling. In graph 4 it finally becomes clear to us that our theory has been falsified by the new data points shown in green. Too much of that data does not fit our model and thus we can no longer say that it represents fact.

Revolution!

So it turns out our old model doesn’t really work. But all is not lost. With our new data we can create firstly a new hypothesis and, in time, a new theory. In graph number 5 we see a curved red line that is the new Growth Plateau Model, a more comprehensive development of the now discarded Linear Growth Model. And so the old theory must be put aside- it serves as a model for the growth of children but is not useful outside of that context.

Our brand new Growth Plateau Model is testable and it has predictive power. We’re not concerned about gaps between the data points, because gaps do not falsify a model- contradictory data does. Were we to find many data points far from our line, we’d know our model was not accurate, assuming this was not explainable by some other means. But as the data keeps coming in, we find that the model holds for every observation.

Of course, hypothesis and theory aren’t strictly about scatter plots and trend lines. But this serves well as an analogy for how the process really works in science. Real hypotheses may be just as simple as that single statement about the linear relationship between aging and height. Theories however, are typically built from the combination of many hypotheses and unlike our analogy; they must not only have predictive power but also have explanatory power. We must be able to test the mechanisms that underlie the relationships we’ve modelled. But that concept of modelling reality, of joining the dots between our observations and testing that model, is fundamental to science. Just as fundamental is the moment we falsify our model and thus discard it. It is this moment, in which we build a new model upon the data, which sets science apart from dogma, in which no change is permissible, and diagnosis, in which we attempt to fit the data to various pre-determined models. Sometimes, as we saw with the Linear Growth Model, we don’t need to discard the old model, as in essence it becomes a small part of a bigger model and can still be useful in a limited way. In real science we can see many examples of this sort of “re-framing” of a theory rather than outright scientific revolution. For instance, although we’ve since come to understand modern genetics, the processes of variation and natural selection explained by Darwin are still a part of the modern theory of evolution. Similarly, the rise of Einstein highlighted the shortcomings of the Newtonian explanation of gravity, but we still use Newton’s laws for many simple applications. These theories, and indeed all good theories, share the predictive power of our made-up theory. Evolutionary theory allows us to predict what we’ll find in the fossil record and the genetic codes of organisms, and provides an explanation for those findings. To date, it has not failed us in either regard. Relativity explained peculiarities in the orbit of the planet Mercury and predicted strange effects of high speed upon the flow of time that would later be observed in experiments. So we can have great confidence that the untested predictions of these theories are accurate, that our models represent fact.

What's the Storey?

2008-11-09T01:20:00.004Z

This week, due to finding myself very busy, I haven't had a chance to write my usual (vaguely) weekly blog. I did manage to write a letter to the Irish Times newspaper after being rather incensed by the comments of Northern Irish politician Cllr. Mervyn Storey. Since it has been a week and I'm very impatient, I decided to post it here. Cllr. Storey, it seems, would like to bring creationism to European shores. He would also prefer to see the theory of evolution removed from sylabbuses in Northern Ireland, but seems to have a fairly hazey notion of what it is he wants rid of. His poorly-researched thoughts on the matter may be read here. My general thoughts on evolution and creationism can be read elsewhere on this blog.

Madam,

Mervyn Storey (Opinion and Analysis, November 3rd) describes a scientific theory called "naturalistic evolution" in his argument for the teaching of creationism in Northern Irish schools. "The central, core belief of naturalistic evolution", Storey claims, "is that somewhere in the universe at some time in the far distant past, non-living matter of itself, with no outside influence or mind to guide it, gave rise to living creatures." As a biology research student, I must confess to having never heard of the theory of naturalistic evolution. However, on examination of Storey's description, I find that it summarises the hypotheses on a process called abiogenesis, the emergence of life from non-living matter. A hypothesis is a candidate theory, not yet accepted by the scientific community as a model or representation of reality. With regard to abiogenesis, there are several of these hypotheses, but no accepted theory. Biochemists know of many plausible means by which simple life might emerge by materialistic means, but whether any of these actually occurred is very much an open question. Mr. Storey might well delight at such an admission from a biologist, however I should point out that abiogenesis is not in fact an element of the theory of evolution. Rather, evolution is a theory which explains the emergence of the many varied species from a single common ancestor species, and does not address the first emergence of the first life from lifelessness. This is why Darwin's 1859 work describing evolution was entitled "The Origin of Species" and not "The Origin of Life". Whether that single-celled Adam or Eve emerged by abiogenesis, fell from the sky or was sculpted from clay by the hands of the Creator is largely irrelevant to the veracity of the theory of evolution.

It is troubling that Mr. Storey is either ignorant of the theory he is attacking, or has knowingly constructed a straw man in this "naturalistic evolution" concept that no scientist accepts as fact or teaches as fact. Such ignorance and misrepresentation are common tools of the American creationist movement, and it is most saddening to see such stock anti-scientific rhetoric finding receptive minds on our shores. It is also very worrying that such a flimsy argument is being used to promote what Mr. Storey must consider to be the automatic alternative to evolution. He is presenting us with the same old false dichotomy; that if evolution is false, creationism is true. The veracity of evolution relies on evidence; creationism, to judge from Mr. Storey's argument, on the falseness of evolution.

Requiem for a Culture

2008-10-29T22:01:00.012Z

When the world’s first clone, Dolly the sheep, took her first tentative steps, some more lateral thinking conservationists might be forgiven for having imagined that this new technological triumph could well herald the end of extinction. For what better way could there be to immortalise a species under threat than to sequence its gene in their entirety and simply clone new individuals on demand. So long as tissue or blood samples could be taken from an ailing species, they could even be frozen and preserved long after the extinction of a species, simply waiting for the technology to catch up. Of course some manner of artificial womb or surrogacy system would be needed in order to create a viable and reproducing population of adequate size, but to imagine that such technical hurdles could be overcome would not at all be unreasonable. The problem of premature ageing that faced poor Dolly is also unlikely to be an insurmountable obstacle. Despite all of this, I suspect there is in fact something that will stand in our way, something much more difficult to replicate than mere DNA.

Our understanding of evolution has perhaps led us to think in too narrow terms about what it is that makes a species. It is certainly conceivable that the technology that created Dolly could well become streamlined and commonplace enough to be applied to almost any species, but is that in fact enough to return a species from extinction? Consider the case of the curiously named Poʻouli, a bird native only to Hawai’i. Tragically, for those who consider biodiversity to be of benefit to the world, the last known individual of the species died whilst biologists attempted to locate a possible female still in the wild. Tissue samples were taken from the male before its death in the hopes that developments in cloning technology might one day revive the species. Of course, without samples from a female, it is debatable as to what good cloning males will do. But this is not the greatest impediment to resurrecting the Poʻouli. After all, we know biochemically and genetically what sets male and female apart. At a push, we might be able to engineer a female based on the male genome. But when we finally manage to create the new generation of Poʻouli hatchlings, who will they look to for guidance?

That might sounds like a pretty odd question to ask about birds. But of course, imprinting upon a parent animal is extremely important for hatchlings to develop normal behavior; in many repects they learn how to be birds from their parents, who learned from their parents. Whilst we’ve managed to emulate imprinting for some endangered species of wild geese by doing clever things such as having them fly alongside people in hang-gliders, it is questionable just how well we can emulate the imprinting behavior and training of a species we can no longer study. Imprinting in birds is just one example of the countless forms of learning that are seen throughout animal species. Although it would probably not be a popular application of the term I view this non-genetic inheritance as the simplest form of culture. And in my view, even simple culture is no trivial component of any species. Of course we tend to think of culture as a strictly human phenomenon and certainly our species demonstrates just how complex culture can become. From the simple act of imparting knowledge between countless generations, we have gained everything from agriculture to religion and of course science. I am quite sure that many of the primatologists studying our closest animal relatives would not hesitate to extend the concept of culture beyond humans.

So although we have genetics in the bag, it is culture that potentially becomes irrecoverable whenever a species becomes extinct. The day an extinct species is reborn, how do we know they’re behaving as they used to? Will the Poʻouli species actually be restored if we clone a thousand chicks, raise them by hand and release them? To this day we are discovering new facets of the cultural inheritances of many species, even in those species that ought by now to be well-known to us, such as chimpanzees. Of course, for “simple” species such as birds and the smaller mammal species, it may be that we could restore a viable culture by simply cloning large numbers of individuals and allowing random behavior, time and pure natural selection to do their work. After all, cultural elements, like genes, are subject to a form of evolution. Those that confer advantage will be inherited at a higher rate than those that do not. This is something like Dawkins’ meme hypothesis, albeit extended to all life forms capable of learning. But how will we know if the emergent culture really resembles the original? The problem really is our lack of knowledge of the “memetics” of the species. While we may sequence a genome, even store it as pure computer data for later replication, how do we so accurately measure the culture of a species?

Behavioral biology is of course the field that provides our answers, but there’s no escaping the realization that what we are struggling with is something far less tangible than genes, and far more open to human ignorance or misinterpretation. In the 35 years that biologists had to observe the Poʻouli, can we be sure that every aspect of their simple culture was studied? Can we be sure that every nuance of their social interactions was even noticed? This is the intimidating challenge that really faces conservationists. With so many species now endangered, the task at hand is staggering. We may have to accept that no matter how much DNA we sample and sequence, species such as the Poʻouli, the Dodo, the Golden Toad and the Tarpan are lost to us in a manner we probably couldn’t have measured when they still lived.

Po'ouli image courtesy of the United States Federal Government under the terms of Title 17, Chapter 1, Section 105 of the US Code. Obtained from Wikipedia.

Moronic Design

2008-10-21T21:58:00.004+01:00

November of next year brings to us biology-types, and to all of the scientifically-minded, a very special anniversary. It will mark the 150th year since the publication of what is certainly the most significant scientific work in the field of biology and one which would easily make the top three across the entirety of science. The publication in question is of course Charles Darwin’s “On the Origin of Species”. In it, Darwin laid out his case for his hypothesis on, as the title suggests, the origins of the variety (and similarity) we see between the many species of our planet.

The theory states the following. A common ancestor species once existed which produced offspring. As new generations of offspring were produced, inheritable differences (variations) began to appear in them. Some variations produced a benefit, others did not. Those variations that were beneficial enhanced the survival of the altered offspring and so those new traits were more likely to be passed on. The detrimental variations, whilst not always fatal, were less likely to be passed on simply because they reduced the carriers’ chances of survival and reproduction. Thus we have three simple mechanisms; reproduction, variation and selection. Add enough time, changing environments, migrations, separations and countless other influences and you get groups of organisms that have changed so much that they can no longer interbreed. These are broadly called species. So when you have these mechanisms working across an entire planet for over 3 billion years, you get a whole lot of species. I covered this whole process in a whimsical little story, posted a couple of months ago.

The scientific crisis and revolution that followed lasted decades, and was mostly heralded by Darwin’s supporters, rather than the man himself. His book and the works which confirmed his observations made a compelling case, and 150 years later his theory of evolution is accepted as the standing model of how life on Earth derived from a common ancestor. It is a theory that is so simple to explain that it is often described by scientists of all fields as “elegant” or even “beautiful”.

You may recall my explanation of how scientists develop a hypothesis, a testable idea, and then make observations and measurements that have the potential to disprove the hypothesis. If the hypothesis survives many observations, can be shown to predict bits we haven’t looked at yet, and can be confirmed independently, it becomes theory. A theory is the currently accepted model. That’s an important definition, because in common language “theory” generally has a meaning more like what scientists call a “hypothesis”. So when say, a creationist calls evolution “just a theory”, they are being rather misleading. Evolution (the process) is a fact and the model of that fact (the theory of evolution) is accepted by the vast majority of scientists as being entirely valid. So, more accurately, the theory of evolution is “just a (robust) theory (that has been re-tested and confirmed countless times over the course of 150 years and is now accepted as entirely valid by greater than 95% of scientists and greater than 99% of biologists”. Phew. I can see why they shorten it.

The metaphor-free zone

What I’m trying to get across is that evolution is a theory, in other words a model of reality, which is as well-accepted by scientists as Einstein’s theories of relativity. It’s important to remember that when considering the arguments of those who would tell you that evolution did not happen. I will generically refer to these movements as creationism, though that will certainly annoy them. Their common element is that they ascribe the creation of the Earth and of all life to a supernatural intelligence. In most variants this is the Christian God, and the basis of their “theory” is a fully literal interpretation of the book of Genesis. No, symbolism, no metaphor. A literal six day creation of the universe and all life in it.

There’s insufficient space here (and I have insufficient time) to fully explore the evolution versus creationism debate, but I would invite readers to visit TalkOrigins or explore various internet debates on the matter to get a feel for how in-depth the row has become over the past few decades. Leave your sanity at the door, it will only hinder you. Rather than delve into that whole mess, I will instead focus on the core issue that is used by one branch of creationists; the “intelligent design” (ID) proponents. ID proponents believe that life was designed by a great intelligence. They are unspecific as to the age of the Earth (traditional creationists put the limit at around 10,000 years) but believe that life was created in a single creation event and has varied only within tight boundaries since then. They also contend, as do most creationists, that mutation (the process that causes the variation in evolution) cannot create new function, but rather can only break the function of a gene or restore its previous function. Officially, they do not identify the intelligent designer as “God”, but internal documents leaked from the ID inner circle reveal that they are in fact Christian creationists with a secular gloss over them. This is apparently to make their ideas appear more palatable to institutions such as the secular US education system into which they would like to insert their “science”. So we can quite confidently label intelligent design as creationism.

If ID constitutes science then it must have a testable hypothesis at its core. Evolution states as its core hypothesis that all life derived from a common ancestor by variation and selection. That statement has many implications which we may test. We should, for example, be able to find evidence of organisms, perhaps extinct, which show a transition between known species. Evolution thus makes a prediction that we ought to be able to find such species in the fossil record. And we do. What does ID predict? Not much. If life is entirely designed by a creator with only one specified trait (intelligence), it could look like almost anything at any level. It could even be made to look entirely as though it evolved. It’s thus rather unsurprising that creationists in generally spend most of their time trying to discredit evolution rather than testing things such as ID. They propose a false dichotomy (a made-up two way choice); if evolution is false, creationism must be true. All other imaginable or unimaginable options are somehow off the table.

Scientism

In their flailing attempt to make ID into a science, its proponents latched onto the work of ID defender Michael Behe who suggested in his 1996 book Darwin’s Black Box that intelligent design was proven plausible by the existence of what he termed “irreducible complexity” in biological systems. Irreducible complexity, according to Behe, is a property of any system which performs a function but which is disabled entirely if we remove any critical part of that system. Thus, a clockwork pocket watch would be considered irreducibly complex, as removing a cog will cause the watch to stop functioning as intended. Behe firstly contends that this is a property we expect to see in any intelligently designed system and secondly that the property is observable in life forms. He also claims that such systems cannot arise by evolution, since the various parts would have to evolve at the very same time and this is improbable. I will now attack all three assertions.

In the first instance, Behe is essentially claiming that irreducible complexity is a testable implication of the ID hypothesis, much as we can say that transitional fossils and genetic similarity (we share common DNA with all known life forms discovered to date) are testable implications of the evolution hypothesis. This is logically flawed in many respects. Firstly, in the design of various mechanisms, a human designer must consider a number of factors that will determine the amount of redundancy (or back-up systems, if you like) that a mechanism will have. The intended life time of the mechanism, the replacement cost of it and the practicality of repairing the object will all feed into that decision. A pocket watch can be repaired, as can a car. We’ll certainly build in some backup systems here and there, but where that isn’t practical, or essential, we’ll leave a number of critical systems in our design. Thus the pocket watch and the car become, “irreducibly complex”. By assuming that this feature is something we expect to see in designed life, we are making a rather significant assumption about the intention of the designer. We are assuming that the design considerations for an organism are in some manner similar to those for a mechanism such as a car or pocket watch. However, in a system that is difficult to repair (without modern medicine; a recent development), intended to last decades without maintenance and prone to replication errors (DNA mutation), do we really want to have critical systems with no backup? More to the point, if we assume that we do want such dangerous breaking points built into an organism, wouldn’t it make sense to build redundancy into the most important systems? Let’s consider some of the systems that Behe claims display this lack of redundancy in humans; the blood clotting cascade and the sight cascade. A biochemical cascade is a system in which a protein is affected by something (for example, light from our eye) and reacts by signalling another protein, which signals another and so forth until that signal is propagated to our brains. So we can see in the clotting cascade and the sight cascade that non-redundant points exist. Mutate specific proteins and the cascade breaks like the pocket watch. The sight and clotting cascades are extremely important systems for our survival and yet for some reason, redundancy exists in other, less (or equally) important biochemical systems. The chemokine system that controls the communication between our immune cells has multiple backup levels built into it, for example. We are thus forced to conclude that whether irreducible complexity is an expected feature of designed life depends heavily on the capabilities, level of intelligence, desires and intentions of the designer. If we assume that humans were directly designed, we are also forced to conclude that the designer is either technically limited, rather dim, malevolent or disinterested in individual human survival. Or a combinations of these traits. If we assume that our designer is actually fully “omnipotent”, we actually cannot make any assertion at all about what features we’d expect to see in designed life, since that designer could make life appear any way it chose without consequence.

The remaining two of Behe’s assertions can be refuted together. Whether we actually observe irreducible complexity in organisms and whether such systems could have arisen by a process of evolution go hand in hand. By definition, if we can imagine a means by which an irreducibly complex system could have arisen by evolution, then it is not in fact irreducibly complex. This is actually quite easy to show, and gives me a chance to crack the flow charts again! Let us imagine a simple “reducibly complex” protein cascade, in other words one which has redundancy. A “signal”, such as light, enters the system and can be picked up by protein A or B. These proteins can then interact with either of another two proteins C and D, which all may interact with more proteins further along the signal chain. Here then, is a fully redundant system which could easily have evolved by totally conventional means. We need to make only one change in order to create one of Behe’s “irreducibly complex” cascades. We delete A, B, C or D. So let’s take D out of the cascade. In nature, this could easily occur as a result of a mutation resulting in either a loss of function or a change of function. If we get the second case, a change in function (and one that is beneficial in its own respect) then successive mutations will make it difficult for us to connect the new protein to its historical role in the old cascade. Behe will see that cascade as being irreducibly complex, but that is an illusion created by evolution. The cascade is merely “complex”.

Such plausible evolutionary histories have now been demonstrated for most of Behe’s major examples of irreducible complexity, including both the sight cascade and the clotting cascade. Indeed, in the latter case, proteins that Behe claimed to be critical to certain cascades have been demonstrated to be absent in other species, with no ill effect. We can even see backup systems in these species which are related to systems in humans that have now been diverted towards alternate functions. Whilst the evolution of many cascades has not been fully explored, this does not for a moment suggest that irreducible complexity exists in organisms, since at the very least the simple method I’ve outlined allows the illusion of these to emerge by evolution. So, do we see irreducibly complex systems in organism? Nope, just the illusion of them.

Triplethink

So where does this leave ID creationism? In an awkward position really. Irreducible complexity, if we assume it to be real (and deliberate), represents a significant set of design flaws. These flaws are compounded by the Designer’s perplexing choice of a DNA-based inheritance system that is so very prone to replication errors. This then, gives us not an intelligent designer, but a being who is, frankly, a bit of a moron. I’m not saying I could do better, but nor am I claiming to be an intelligent designer. In some debates with creationists, I have seen this argument countered with the suggestion that the lack of redundancy in some systems is the result of the “degeneration” of the creator’s perfect design, due to the Fall of Man. By that logic, all life must have been created fully redundant, or at least with key systems featuring back-ups. These were then lost due to mutation, resulting in the very same systems that creationists now claim represent evidence of design. So this thinking would force creationists to abandon irreducible complexity as evidence of design. In reaction to that annoying point, others still contend that life was created “perfect”, in an entirely different way, in that it was entirely irreducibly complex throughout and that the redundancies which exist are some manner of reaction to the expulsion of life from that “perfect” first environment. By this of course they are referring once again to the expulsion of life from Eden. This though, demands that the creator must either have intervened to modify his creation (which is not supported by their literal interpretations of Genesis) or, and this is the part which really upsets creationists, we must have gained some functional back-ups by mutation; a process they need to claim is impossible in order to discredit evolution.

By bringing irreducible complexity to the table in the great creation versus evolution debate, the ID proponents actually force themselves into trap. If they will not accept evolution (or at least some other alternative to creationism) then they must accept one of three things; that the Designer is fallible, that irreducible complexity is not evidence of design, or that mutation can generate new functionality. Oops.

Image credits: DNA double helix by Michael Ströck. Released under the GFDL. Flow chart by the author. Creation of Adam by Michaelangelo. Public domain.

Connected Spaces

2008-10-05T22:23:00.009+01:00

It has been an exciting few days for those of us geeky types who follow developments in space exploration. For those of you who would question just why we should have such an interest, I'd urge you to read on. On Sunday, we witnessed the world's first ever privately researched and funded orbital launch. The following day, China became the third nation (after the United States and Russia) to successfully conduct a spacewalk under their own power. These events stand as examples of two of the major trends in modern space exploration; commercialisation and the emerging new space race in Asia. This week also saw the 2008 International Astronautical Congress. The opening day brought talks from the heads of several space agencies, including our own European Space Agency (ESA) as well as the Russians, NASA and of course, the now rather smug Chinese. One significant point of discussion, as reported by Short Sharp Science, perhaps reflects the recent global economic chaos. That topic of course was the cost of space exploration. There's no two ways about it, space exploration is expensive. Getting objects into a low orbit costs in the region of €6000 per kilogram and that's about as cheap as it gets. That cost reflects the sheer energy required to break free of the Earth. Research and development for new vehicles, probes and experiments is very pricey too. It’s unsurprising then that NASA's annual budget is somewhere in the region of €20 billion; a figure that will likely come under scrutiny now that the USA is in recession. The justifications presented by these representatives perhaps play to what the public are interested in. Every-day personal benefit. NASA's Mike Griffin pointed out the considerable number of technological advancements that arose out of the research needed to go to space. The miniaturisation of electronics being an obvious development that has lead to the various gadgets we have in our homes. He also pointed to weather satellite technology and the satnav network that many of us now use in our cars. The director general of ESA echoed this sentiment, pointing to Columbus in 1492. We couldn't have imagined the gains we would make from exploration until we set off down that path.

Isolation fallacy

I can see why such points are made, but I see them as being just as short sighted as the criticism levelled at space exploration, and manned space travel in particular. It's often claimed by some that we should fix the problems we have here on Earth before we venture into space. Quite how much time it would take for us to eliminate war, famine and poverty I have no idea. But I consider such thinking to be very silly indeed. The reason I say this is because I suspect that part of the drive to "prioritise" our budgets stems from a severe misconception. I call it the isolation fallacy; the mistaken belief that we are meaningfully separate from "space". In other words, many people tend to think of space as a location that is in some manner distinct from Earth. I think they're wrong. We can imagine the universe as a wild landscape. Vast and wide, with mountains and valleys. The Earth sits in a bit of a depression in that landscape. Being in a shallow hole, it can be tricky for us explore the landscape. The only thing that separates us from the rest of the universe are the practical difficulties we face in getting out of that hole. The aforementioned launch costs, the research and development costs and of course safety concerns. However, none of these things affects anything that might want to come in the other direction. Solar flares, gamma ray bursts and bloody big rocks, to name a few. Although these things are extremely rare, they are all things which can wipe out our civilisation irrespective of how we think about the Earth and space. They see no boundary and we're only beginning to understand what risks we face. We need to learn, but what is perhaps equally important is our need to spread.

Go forth

Civilisations can be fragile things. The ancient Greeks floundered. The Roman Empire was sacked. However, despite these individual failings, human civilisation as a whole has proven rather resilient. We have certainly been set back culturally many times. But for every collapsed civilisation there have been others who inherited their knowledge, technologies and philosophy. Who learned from their mistakes, and moved forward once again. Our culture, taken on a worldwide scale, has become extremely robust. Even were modern western civilisation to collapse, it would not set back human culture by much. This robustness is a product of two factors; how far our species has spread and how well we communicate. To destroy our culture would now require the death of pretty much all humans. Even a small remnant could now rapidly regain our lost culture. The previously mentioned threats from outside of Earth certainly hold the potential to land that killing blow. We also now have an unprecedented capacity to destroy ourselves via nuclear war or ecological disaster. There is an imbalance there. Our capacity to destroy ourselves has never been greater, yet we lack the ability to spread ourselves further and thus enhance the stability of our culture and ensure the future of our species. We cannot readily escape Earth, nor can we settle elsewhere in a self-sufficient manner. We have much to learn, and given that we could well annihilate ourselves without help of anything from space, time is of the essence. The manned space programmes of NASA and the Russian and Chinese space agencies represent the only means by which we can learn the lessons needed to achieve those goals. To view their work as some sort of luxury is to entirely underestimate the risks we face and misunderstand what space represents; our only realistic shot at long-term survival.

Fear and Vaccination in London

2008-09-25T19:45:00.010+01:00

Author's note: After my successful foray into soapboxing with the LHC story, I decided to get back up on the box again to trumpet my current hypothesis. Science, the scientific method and scepticism are misunderstood by almost everyone and something has to be done. For more evidence of just how bad things are, check out the ongoing research into the dangers of dihydrogen monoxide. The research itself is satire (sorry to spoil the fun, but I certainly don't want people to think I don't get it). The reactions of the public are the really frighetning part. Anyway, on to the self-righteous ranting.

In 1998 a British-based surgeon, Dr. Andrew Wakefield published a research paper in which he and his team tentatively identified a bowel disorder associated with autism which he coined “autistic enterocolitis” and speculated (a very important word there) that this might be caused by vaccination with the MMR vaccine. Most people are roughly aware of what MMR is. The measles, mumps and rubella triple vaccine. It is a mixture of the three viruses, alive but weakened to the point that they’re not even able to infect infants. They do however cause the recipient’s immune system to generate lots of cells and antibodies that will basically squash the three viruses should they ever be seen again. The need for vaccination against these three diseases is an easy case to make. Measles in adults can cause brain damage. Mumps may cause infertility in males, especially kids. Rubella, if it infects the unborn through the mother, can cause a wide range of birth defects. These complications don’t occur often- but the viruses are so infectious that those rare cases would be a big deal in any highly populated country.

Cause and Effect

So MMR was suggested to have an influence on autistic intestinal inflammation, but there was more. According to Wakefield’s paper, there also appeared to be a connection between the time of administration of MMR to a child and emergence of autism, though that element of the study was retrospective. The paper itself did not rock the boat in the mainstream media, though the scientific community began criticising it immediately. The connection between MMR and autism was not clear, and the study group was small. Just twelve children, all selected because they had autism. At best, that sort of study would represent a starting point for some more solid research. To be meaningful and to make that connection really clear we’d need thousands of examples, and we’d to be able to compare our results with loads of non-autistic kids.

It wasn’t until Wakefield decided to jump outside of the peer-review system that things began to go bad. I discussed in a previous posting how science makes its way into the mainstream media. I even included a flow chart, which I’ll reproduce now. What Dr. Wakefield did was follow the path on the far right. Skipping all external controls and critique he instead decided to talk directly to the press. And what he had to say would cause a sensation. He called for a halt to administration of the MMR vaccine in favour of vaccinating for each of the three diseases separately over an extended time of several years. His stated reasoning was that he believed that MMR might be causing Autism. The initial response in the media was muted. The press release and an accompanying video released by Wakefield’s hospital drew some attention. Wakefield found himself defending his work in letters to the journal that had published his paper, Lancet. In 2000, Wakefield published more papers pushing his MMR hypothesis. Then in 2001, something snapped. Perhaps it was the publicity, the momentum built in the last couple of years. Perhaps Wakefield’s recent high-profile exit from his hospital position (a “mutual decision”) was noticed. Perhaps some of his new research papers pushed the right buttons. Whatever it was, the MMR and autism story hit the mainstream.

What Grows in Darkness

The newspapers went wild, particularly in the UK. By 2002, the stories in the press questioning the safety of MMR numbered in the thousands. Few dealt with the inconvenient peer-reviewed research papers that refuted Wakefield’s findings and the controversy dominated health reporting for several years. Here was a piece of news based on the (very carefully worded) concerns of a single surgeon. But somehow the line (in the Daily Mail at least) became “Scientists Fear MMR Link to Autism”. “One Scientist Cautiously and Inappropriately Suggests MMR Link to Autism” is not very catchy perhaps, but the fear mongering sentiment went further than headlines and permeated the reporting. As a direct result, MMR vaccination rates in the UK fell to 80% by 2003. In some urban areas of London, the rate was as low as 65%. When we learn a little about how vaccination works these, figures become even more alarming.

Vaccination is not 100% effective on a person-to-person basis, though it is usually above 99% effective. This is generally not an issue however, as vaccination also serves to protect the unvaccinated by eliminating the pool possible hosts for a given virus. Because your neighbours are all immune, your chances of even encountering the virus, let alone contracting it, are dramatically reduced. The virus is much less likely to be passed around by accident. This effect is called “herd immunity”. For the three viruses that MMR protects against, the threshold for good herd immunity is around 95% of the population. With the rate of uptake so low in 2005, the risk was rapidly increasing that herd immunity would collapse, resulting in large scale epidemics amongst the roughly 20% of unvaccinated children and the 1% for whom the vaccine had failed to take.

Predictably, the epidemics began around 2000, when the earliest signs of concern had begun to filter through to the public. Measles epidemics were reported in Ireland, Austria and Italy. Most significantly, measles incidences in the UK have increased steadily over the last eight years. Although the increase may appear minimal (from 56 cases per year in 1998 to an estimated 900 cases per year by 2006) the disease was declared “endemic” in the British population earlier this year. This means that the virus is now circulating freely in the population without need for re-infection from outside sources. So anyone without immunity is immediately at much greater risk. Herd immunity is degenerating. There is also evidence that travellers to and from Europe triggered minor outbreaks in the United States. Mumps is on the rise again also, primarily hitting age-groups who passed through infancy prior to the introduction of MMR. Some 70,000 cases were reported between 2004 and 2006. There were a handful of deaths as a result of the measles and mumps resurgences. Three deaths were reported in Ireland, one death in the UK and two cases of brain damage. Not many, but a reminder to us of times when these diseases were a true threat.

The degeneration of herd immunity is just the first step, there is another risk associated with allowing these viruses to become endemic. For every infected person there are literally billions of mumps, measles or rubella viruses in their system. The more viruses there are, the faster they reproduce. The faster they reproduce, the more often they mutate. With part of the population vaccinated and part not vaccinated, what we are doing is presenting the mutating viruses with an obstacle to overcome. The risk is growing that one of these three viruses may undergo the mutation required to evade MMR entirely.

In 2004, ten of Wakefield’s co-authors on the 1998 paper withdrew their support for the work. Since the first publication, at least twenty peer-reviewed research or review papers have discredited the MMR link to autism. Wakefield’s suggested new “autistic enterocolitis” has been dismissed by autism researchers as a common symptom of the condition. Ten years after the controversy began, MMR is not the only vaccine to fall victim to the resurgent paranoia and disillusionment with modern medicine, though this is a trend which predates the MMR scare. Some papers continue to lead a crusade against any proposals for new “multivalent” vaccines that, like MMR, would combine protection from several diseases.

Apportioning Blame

It was a need for a simple cause which ultimately brought the MMR crisis into being. But the fact is, there’s no known single cause for autism. And nor are the causes of the vaccination crisis as clear as they seem. It would be easy to point the finger at Dr. Wakefield. He’s certainly not free of blame. Wakefield’s 1998 study was prompted when he was approached by solicitors representing a group planning to sue MMR manufacturers for causing the autism. According to a Sunday Times report in 2006, Wakefield received money from that group to perform his 1998 study and it appears that some of the study participants were sourced by them too. It is also alleged that Wakefield’s hospital, who were quick to back his findings and arrange press contact, also received money in the form of legal aid. It seems clear from interviews at the time that Wakefield was aware of the fine balance of risks associated with his bold statement. He was aware that switching from the use of MMR to using three vaccines over a number of years very significantly increases a child’s risk of contracting one of the diseases in that time. Wakefield’s point was that the risk of autism outweighed both the fact that his results were unclear and the fact that his suggested course of action brought great risks. He should absolutely not have been going public with his poorly-conceived idea, yet his language in the press release and interviews was actually quite suitably cautious. The subtlety was lost on many news outlets. Rather than exhibit caution themselves, they perpetuated a fear-laden story that has done incalculable damage to public health in Europe. Many of these are the same papers that, years later, are now assassinating Wakefield’s character in light of professional misconduct charges. Ultimately we have to blame pretty much everybody; parents looking for simple answers, lawyers looking for litigation, a surgeon with a bias, a hospital looking for publicity, a media willing to spin anything to sell papers. Not to mention the confused reactions of most GPs and politicians (a blog in itself). And then there’s us. The scientists fought the good fight on the day, sure. But it could be argued that our aloofness from the public has created a culture in which science is only noticed when it is sensational; a culture in which the people have neither the education nor the inclination to view science with proper scepticism. It’s conceivable that just one of those groups had it in them to prevent this whole huge mess. Instead we are now facing continued vaccine paranoia and a dangerous resurgence of diseases we once had on the run.

Horsey

2008-09-16T01:26:00.003+01:00

Author's Note: This week The Biologista is doing science and also going to a sciencey conference. Hence, the re-run of one of his favourite posts from way back when. That being July. He will return later this week with a brand new post about Vaccination and Fear.

Current speculative thinking is that the immune systems of many individuals co-evolved in the presence of persistent parasitic infestation. The immune system therefore evolved to over-compensate along the anti-parasite axis. It needed to be able to deal with new parasitic infection on top of the un-clearable persistent infection. We call this parasite killing axis the Th2 response. We can imagine our immune system as a sort of see-saw, but with many sides. As one side, or axis of our immune response raises, it pushes the others down. Some infections require a broad, balanced response. Others need a strong, single axis attack. Our persistent parasites evolved, adapting to evade our Th2 response. Some would push our immune response along other axes, perhaps towards our anti-bacterial response. The upshot of this was that we required further Th2 over-compensation. This co-evolution has probably been ongoing since our pre-mammalian ancestors. This is evolution over a time on the order of hundreds of millions of years.

Suddenly, in the space of a mere 200 years, the western world eliminated normal everyday parasitic infection. From an evolutionary point of view, an advantageous trait had become redundant in the blink of an eye. Individuals who previously had an evolutionary edge suddenly had a disadvantage. The asthamtic, the hayfever sufferer and the general sneezy snot bag has an immune system that resembles a race horse suddenly lacking its burden. The jockey, that nasty little parasite, has fallen off. The horse is gleefully running for the finish line, thinking he is about to win.

This stands as a wonderful example of the importance of context in evolutionary traits and in the emergence of new mutations. Allergy is today seen as some sort of genetic "defect". In African countries where the parasitic trypanosome and schistosome problems are finally starting to be reduced, allergy is starting to emerge. Perhaps this is mere coincidence, but if our thinking is correct, allergy and asthma will increase considerably there over the coming years. That is of course assuming that the western world gets off its arse to help do something about health in Africa.

Science Goes Boom: The Large Hadron Collider

2008-09-04T01:30:00.015+01:00

Update 10 September 2008: Well, the world is still with us. The LHC has powered up and run a successful one-way test collision. We live to collide another day. The real experiments are due to begin on October 21st so I expect we shall hear more from the panic mongers. But for now, every-day scientists, a funky-looking picture (the first data produced by the LHC).

Author's note 04 September 2008: Beaten to the punch! A geologist friend of mine suggested an article debunking the LHC panic a few weeks ago, but I thought it more appropriate this week. The Short Sharp Science blog (1st September) however, has pretty much pre-empted my own commentary, practically down to the last point. Here's my take anyway.

On the 10th of September, if Dr. Walter L. Wagner is correct, there’s a pretty good chance that the world is going to end. Or at least begin ending. On that day, the scientists at the Large Hadron Collider (LHC for short) will power it up and perform their first experiments. The LHC is a particle collider, a giant ring tube, 27 kilometres in circumference and buried beneath the Swiss countryside at a depth of about 50 to 100 meters. The point of this ring, as the name suggests, is to collide particles. Particles can be atoms, the building blocks of all matter, or even pieces or these. The particles are launched into the ring tube in opposite directions. Large electro magnets keep the particles traveling along the same line inside the ring and ensure that they follow the curve of the ring around to the far side. At the far side, the particles collide. When this happens, the particles effectively explode on a tiny scale, producing new and even smaller particles. This effectively replicates the sorts of collisions that occur between cosmic rays and the upper atmosphere of the Earth.

The collision is timed so that it happens just as the particles enter an enormous eight-storey-tall detector (pictured to the right). There are already many devices like the LHC in the world, and they’ve taught physicists a whole lot about the universe, but the LHC is different. It’s the biggest particle collider to date, and it can throw the particles out with greater energy than any device previously built. In fact, the LHC will propel tiny particles about 1x1025th (that’s 1 with 25 zeros after it) the size of a grain of sugar, with the same energy as a high speed train. The goal of this €5 billion project is to test the current major hypothesis in physics, the Standard Model. This includes the search for a particle that has been predicted to exist by our current understanding of physics, but which has never been observed; the Higgs boson, the particle that is thought to give all matter its “weight” or more correctly, its mass.

If these collisions are so very common in the atmosphere of Earth, why bother with the LHC at all, you might ask? The answer is in that eight-storey tall detector. Not an easy thing to lug around, let alone fly into the atmosphere. And since we can never predict where a particle collision may naturally be about to occur, we would have no chance to move the detector to the correct spot, let alone line it up so that the collision happened exactly at the centre of the detector. The far more sensible option is to bring the particles to us, which is what the LHC is for. If the experiment fails or succeeds, it might well usher in a paradigm shift in physics.

Doomsday

The problem is that some hypotheses about the universe predict that we’ll find something much less pleasant than the Higgs boson in our detector. Amongst the suggested doomsday outcomes of the LHC experiments are the creation of stranglets, magnetic monopoles and, Dr. Wagner’s favourite, mini black holes. It’s unlikely that most people (including me) will know what those first two things are, but pretty much everyone has heard of black holes. And pretty much everyone knows that they are, to put it mildly, A Bad Thing. And it’s black holes that are what Dr. Wagner is warning the world about. If formed, Wagner predicts, such tiny black holes would not be detected at first. They would zoom right through the LHC (they’d be too small to interact with matter) and off into space, at least for a while. Caught in the gravity of Earth, a micro black hole would fall back and right through the planet before flying into space again. This might happen a number of times before the black hole starts to collect matter, and starts to slow down as it does so. Eventually, it would settle down in the core of the Earth. And there, it would literally swallow the planet in just over two years. We would probably figure out that something had gone wrong when the earthquake would start. Things would get very nasty very quickly after that, and it is unlikely that anyone would survive to see the actual imploding death of Earth itself.

Scary stuff, and with that kind of story making the rounds, it’s little wonder that some people are calling for the LHC to be stalled, shut down or destroyed. The tinfoil hat brigade on the internet (conspiracy theorists), are out in force and claiming that the LHC is in fact a weapon to destroy life on Earth. A story that has something to do with aliens seems the most popular motive for such an expensive way to do a job that could be more cheaply and easily performed with a few nuclear warheads.

But let’s take a step back from Crazyland for a moment and take a look at what the scientists who started the controversy are actually saying. They’re not actually claiming that the LHC will cause catastrophe, but rather that it might. Nor are they calling for the dismantling of the LHC, but rather for an injunction to stall experimentation while safety assessments are carried out. Further safety assessments, that is. A major independent safety review already concluded that the LHC was safe in 2003. Another review confirmed this in 2008, and that review was double checked by yet another independent scientific council. Two groups of physicists have also published peer-reviewed papers backing up these claims of safety. So the majority of the science brigade stand on the side that says everything is going to be okay. And the critics are not even sure that they’re right. The problem for those of us outside of physics (and The Biologista is very much unsure what a Higgs boson actually is), is that the portents of doom, and the defences against these, are delivered in very difficult physics-speak.

Look up

So how do we satisfy our scepticism and sooth our, let’s face it, fear? There is on easily palatable piece of scientific knowledge that can put our minds at ease. The collisions that will take place in the LHC in these coming years have already happened countless trillions of times all around us, or more specifically, above us. As I already stated, the upper atmosphere is constantly bombarded with particles from space. These particles are of all shapes and sizes and impact at energies that are higher than anything the LHC can produce. Indeed, even stronger impacts than these occur around neutron stars and white dwarf stars. And these bodies have such a huge gravity that any possible micro black holes formed would surely not escape to space but would come to rest within the stars, gobbling them up from within in a spectacular and frightening manner. Given how often such collisions take place that ought to mean we’d see loads of white dwarfs and neutron stars popping their celestial clogs left right and centre. But we don’t. In fact, we never have.

It could also be said that at a certain point we have to have, I hesitate to use the word, faith in the physicists. I can feel fairly certain that the very clever employees at CERN, which hosts the LHC, would rather not die. And despite media portrayals to the contrary, scientific experimentation has a great safety record. The Mad Scientist bringing doom due to his meddling with nature is a myth based more upon the failings of the products of science in the hands of others than on the actual practice of research itself. Three Mile Island and Chernobyl were built upon scientific knowledge, but they exploded in ignorance of science.

Whilst we might doubt the motives of military research and commercial research such as the big pharmaceuticals companies and the nuclear industry, the LHC is something quite unique. You see, there’s no direct commercial or military benefit to it at all. On the contrary, the LHC represents the rarest of things in modern science; billions of euros spent in the pursuit of... knowledge. Nothing more. In June, Wagner’s case in the US was dismissed, and a similar case brought in the EU was dismissed just last week.

Trillions of natural test runs in our atmosphere, numerous independent safety reviews, two peer reviewed defence papers, the survival instinct of scientists and above all, a noble goal. Perhaps I’m naieve, but that’s good enough for me.

You Are What You Code

2008-08-26T17:44:00.005+01:00

If you take a cotton swab and scrape it along the inside of your cheek, you can dab the soggy end onto a glass slide, put a drop of blue stain on it and, under a microscope, see the very building blocks of what you are. The average person is pretty unlikely to get hold of a microscope. So in some ways, you’ll have to take what I write here on the basis of some kind of authority, safe in the knowledge that you can test it yourself, at least in principle. Let’s imagine you’ve done it so. What you’ll see down that eyepiece will look something like the picture I’ve provided, a strange blob with a distinctive dark dot somewhere inside it.

This is one of your cheek cells. Cells are the units that make up our bodies. Each of us is composed of about 100 trillion of these units. That’s means that there are about 10,000 times more cells in your body than there are people in the world. Break down those cells into their component parts and you get the same stuff that everything around us is made of. Loads of water firstly. Then carbon, which we see in diamonds and in the black stuff in pencils. There’s also loads of oxygen, hydrogen, nitrogen and even metals such as iron. These are quite literally the very same substances which make up the atmosphere, landscape and the everyday objects we see around us. The iron in your frying pan is no different to the iron in your blood. One is a solid lump; the other is in tiny microscopic pieces.

The DNA Blueprint

Cells are themselves very complicated structures, though we can’t see much detail through our microscope. They come together to form the structures of our body. Our muscles formed from muscle cells, our skin from skin cells, even our bones are formed from cells which eventually become solidified. It’s hard for many people to imagine how all of this non-living stuff can come together to form a person. The secret to all of this lies in that dark dot inside the cell. We’re going to need a bigger microscope.

That blob is called the nucleus. We can imagine it as being the brain of the cell, though of course it is not aware of itself in any way. If we tease the nucleus open and look inside, we get lots of protein and water. And we get 46 strange little bundles of carbon, nitrogen, hydrogen and oxygen. These are our chromosomes, within which the carbon and its friends are combined to make that most fabled of compounds; DNA. That stands for deoxyribonucleic acid. I’m not even 100% sure what that means incidentally, but trust me we’ll get by.

If we could somehow take a hold of one of those chromosomes and tug it apart, we’d find that this DNA isn’t a blob at all, but a single long string wound around itself and bundled up countless times. And if we look closer still, we find that the strand is composed of repeating patterns. Each unit of that pattern is called a nucleotide. There are four different nucleotides and each is given a letter to represent it. a, c, t and g. When we read off a given bit of our DNA, we can write it down something like this:

acactcgcttctggaacgtctgaggttatcaataagctcctagtccagacgccatgggt

Imagine that going on for roughly another three billion letters, that’s how long human DNA is, if you count all 46 chromosomes. Looking at that all day will really make your eyes sore. I have great admiration for those patient, or perhaps mildly crazy geneticists.

What does this pattern of letters actually mean? It’s a blueprint for you. The pattern is identical inside the nucleus of every cell in your body. After all, your cells were all copied from that one first cell created when you were conceived. Whether it’s in a muscle cell or a cheek cell, all that changes is which bits of the blueprint the cell reads. The way it reads them is really quite ingenious too.

The Code

Our DNA directs the way we are built. If we take cells from just one part of our body, we’ll find that they have exactly the same DNA code as every other cell, down to the last letter. But unlike the others, the cells usually use or “express” a part of that code which the others ignore. Some parts of the code are used by every cell we have, but many are unique to some part of us. When a piece of DNA is expressed, the cell makes a copy of that piece out of a similar substance called RNA. RNA too is a strand composed of four letters, but is only a copy of the specific part of the DNA that this cell is interested in. Once it is made, the RNA “message” travels right out of the nucleus of the cell and is captured by tiny structures floating around outside. The RNA message is spooled through these structures which read the message and spool out a protein. Proteins, just like DNA, are long strands. However, proteins are made up of an entirely different set of letters to our DNA. There are 20 protein letters, and although they look a lot like DNA letters, they’re quite distinct. A protein sequence looks a bit like this when we write it out:

MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN

It looks meaningless, but it is a translation of the message sent by our DNA. The message is read in groups of three letters. Every three RNA letters corresponds to one of the 20 protein letters. So for example, the message “aag” gives us a K. “agc” gives us an S. It’s a code.

As the new protein created, it starts to wind up, tangle, knot and generally form a blob, but with a shape that is the same every time that same protein is made. This is because, as well as sticking together end-to-end in a line, some of the protein letters also like to stick together sideways. What happens next depends on what protein has just been built. Keratin, for example is one of the proteins unique to our hair follicle cells and our nails. To make hair, the keratin protein is moved to the outside of the cell where it begins to harden. DNA is transcribed to RNA messages. RNA messages are translated into proteins. And proteins can do almost anything. Some, like keratin, are exported from the cell where they may serve to build structures or alternatively to send signals to other cells. Others, called enzymes, make new substances themselves such as fats and sugars. Still others stick around inside the cell to help the cell function, perhaps building new parts for the cell or deciding which pieces of the DNA code the cell will express and when. Some proteins will even add metals to themselves. Iron, for example, makes up a part of the haemoglobin protein in blood, capturing oxygen to bring it all around our body.

Any part of our DNA which codes for a protein is called a gene. Some are expressed constantly, others in response to information and, as I said before, many will only express when the cell is in the correct part of our body. So muscle cells make strong muscle fibres, our eye cells make amazing proteins that can detect light and our immune cells make lethal poisons to kill invaders. We each have over 40,000 genes, but because of the ways that the genes can interact with each other through the actions of proteins, the actual number of proteins those 40,000 genes can make is much, much greater. Since many of those proteins can combine together or make new substances, it’s easy to see where our complexity comes from. And all of this comes from that one identical blueprint, at the core of every cell, expressed in different ways. Of course what you are is also modified by your environment. Diet, exercise and countless other influences change your body. Memories reshape your brain. That’s really a whole other story. But it all starts with the code. It’s pretty astounding what each of us can do with just four letters.

Alternative Expectations

2008-08-18T19:17:00.009+01:00

Scepticism is a balancing act. It’s not about a dismissive nature, any more than a credulous one. I like to think of myself as being a balanced, quite open-minded sceptic. Doubt, but don’t reject without evidence. Mind you, I get it wrong sometimes. Watching a fairly mindless piece of entertainment TV last week, I was introduced to the concept of light therapy, in particular for the treatment of depression as well as skin conditions. I could barely contain a snort of mockery as the wide-eyed presenter explained the serotonin-inducing and antibiotic wonders of various shades of intense light. Actually, I’m pretty sure I didn’t contain it at all. My automatic mistrust of the concept was hasty. After all, it is quite well established that sunlight may have all manner of influences on us, both emotional and physical. However, my scepticism led me to investigate further, which is never a bad thing. I visited Google Scholar to browse some of the peer-reviewed journals on light therapy. My aim; to find out if any evidence of the effectiveness of this therapy actually exists. Sure enough, there is some manner of science in there. Broadly, the studies performed to date have tended to be pretty inadequate in terms of sample size (rarely more than 20 patients) and time scale (weeks when we’d like years). So let’s say that the jury is still out, but that I look more favourably on the concept now than I did previously. I’m still a little dubious as to whether such treatments should already be available in clinics, when it appears as if a full-scale trial has yet to be conducted. It wouldn’t happen with a drug, after all. The wide-eyed presenter, perhaps familiar with the concept of “scepticism”, ensured us that the treatment was “scientifically proven”. Whatever that means.

So I figure that light therapy should not be dismissed. But it should certainly not be accepted on the basis of a TV personality’s assessment of what constitutes “scientific proof”. While light therapy may not be something that would conventionally be classed as “alternative medicine”, it did get me thinking about the topic. The very concept of alternative medicine is often offensive to many medics and scientists. It is a notion that thrives on the modern public’s disillusionment with science in general and the misguided concept that “another way” exists. The disillusionment is not entirely unjustified. And the philosophical rejection of reason shouldn’t prejudice our scientific judgement of the individual therapies classed under the blanket term of “alternative”. Just where did this sense of disillusionment with conventional medicine come from? I have some notions on that. Following the sudden revolution that began with the sanitation practices of the late 19th century, the western world witnessed an unprecedented improvement in public health. The work of scientists such as Koch and Pasteur did away with vague notions of the nature of disease. Ever hear of miasma theory? Nope, because it’s rubbish. Koch and Pasteur, giants of medicine, saw to it that the war upon germs could begin in earnest. Within a century the world’s greatest killers, smallpox, tuberculosis and polio, were either utterly destroyed or reduced to a shadow of their former threat. It was a true revolution. It was the end result of a paradigm shift in biology; the formulation of germ theory. But things have settled down now, we’re back to normal science. Cancer, once largely unheard of, is now the big killer. Many blame modern life, and the science that brought it, for putting things into their food and environment. The newspapers are obsessed with reporting on “things that cause cancer”, which apparently is almost everything. It’s easy to forget of course that 100 years ago very few people lived long enough to get cancer. Modern medicine’s perceived inability to “cure” cancer, heart disease and AIDS, has lead people to lose faith, even to become cynical about the means and even motives of doctors and the health industry. Of course, we scientists and doctors have not helped. Our curious culture of maintaining aloof superiority has fuelled the common man’s sense that science has become disconnected from humanity. In the absence of understandable contact from us, what has anybody to go on other than the caricatures of the media?

So, the “other way” becomes attractive. Dismissive scepticism, the worst kind of scepticism, now rules when dealing with doctors. Many have come to the assumption that alternative medicine forms part of what They Don’t Want You to Know, for reasons that are never entirely clear. A grand conspiracy. This attitude is no better than the average scientist’s blanket views on alternative therapy. It’s really just a matter of getting more information, and if we actually look for it, the beginnings of what we need to know are often already there in the journals. What should the average prospective patient look out for? The journals don’t make for an easy read, but I’ll try to summarise what makes for good testing.

In evidence-based medicine, efficacy and safety are tested using clinical studies. Because humans are so very unique and variable, the only way to be sure that a technique or drug is effective and safe is to go large. To use the biggest study groups possible. We also have to ensure that we study the effects over extended time periods. Both features are vital for the statistical analysis needed to make sense of all that human unpredictability. Most importantly of all we must use what scientists call “controls”. A control in a clinical study is essentially a group, as large and as similar as possible to the group receiving the test treatment, which is treated differently for the sake of comparison. To properly test acupuncture, for example, the bare minimum would be a study of several thousand patients with one group receiving conventional treatment, one receiving acupuncture and one receiving “sham” acupuncture in which the needles are applied but applied incorrectly. The last two groups must be “blinded”, which is to say that neither group should be aware of which is receiving real acupuncture.

A recent-ish study of acupuncture for back-pain followed this very template. They found that acupuncture beat conventional therapy for pain relief. But that isn’t the full story. Firstly, the volunteers consisted of patients for whom conventional therapy had failed. Secondly, they found that the sham acupuncture was just as effective as real acupuncture. This may be an indication of what is called the placebo effect. This is an apparent beneficial effect caused by a fake control treatment, be it the administration of a sugar pill or random pinpricks. Or perhaps there’s some peculiar value to being poked with needles in general. Put simply, it’s not clear what’s going on there. Acupuncture must remain in the realms of the untested for now and we should treat it as such. With doubt, but not with contempt.

On the flip side, we can ditch reiki and reflexology as they have been tested quite thoroughly and found to have no greater benefit than a massage. “Allergy tests” based upon applied kinesiology (the one where bottles of varies substances are held near your muscles) are pure and utter witchcraft in my view. There’s no connection between the results of these and the standard medical allergy test. Hell, some of those tests use sealed bottles, so quite how your body could ever react to the contents is a mystery. As for chiropractic... don’t get me started. Few studies have been able to demonstrate anything more than a placebo effect. Most damningly of all, as pointed out by Ben Goldacre, some chiropractors would rather block the process of scientific criticism of their field. The New Zealand Chiropractors Association has taken the highly suspicious step of attempting to sue a peer-reviewed journal. With your health on the line, is this the sort of carry-on you should accept from your doctor? (Author's Note 21 Aug 2008: The British Chiropractic Association are also sueing journalist Simon Singh for an allegedly libellous article on their faith. I mean, science.)You can be quite sure that no reputable scientist has ever sued in response to academic criticism. Proper studies such as I outlined above are hard to conduct on chiropractic spinal manipulation. This is primarily because the medics who usually run studies are not trained in the methods and chiropractors are reluctant to get involved. What information there is tends to be both limited and self-contradictory. This isn’t a nail in the coffin by any means, but it’s clear that the professionals could be doing more to make us trust them. The general folk and herbal medicine scene is a whole can of worms in its own right. It’s quite clear that some of it works, after all many modern drugs are derived from plant and fungal components. But it’s clear that we don’t know enough about the complex mixture of active ingredients in many such preparations to draw generalisations. Much like light therapy and acupuncture, it remains for me at the fringes of reason for the time being. Ultimately, the advice for navigating the maze that is alternative medicine is much the same as my advice regarding the reading of science in the mainstream media. Scepticism, but open scepticism. Demand evidence, statistics and hard facts. Mechanisms must be rooted in what we can observe. As for doctors, expect more from them too. Ask for explanations, don’t just accept prescriptions. Doctors are often impatient with patient questioning and take a dim view of patients coming to them with their own research from books or the internet. This needs to change. Try to open a dialogue, one that is respectful and yet still sceptical. Never forget that your doctor has some ten years of training and perhaps decades of practical experience. The relationship should ideally be a two-way communication.

As for “alternative medicine”, the term encompasses too wide a range of ideas and carries too much prejudice. To my mind there should be only two kinds of medicine. Tested and not. Only the successfully tested has a place in our lives. Much of what is now untested may one day be worthy of our trust, but right now our health and our lives are at stake. Nothing is more valuable, and nothing is more worthy of healthy scepticism.

It's Revolution, Baby

2008-08-12T00:15:00.005+01:00

Science is usually portrayed and imagined as one of two clichés. The scientific establishment is a vast panel of crusty old sceptics, dismissive of innovative thinking and ever willing to attack upstarts. On the flip side of this, “revolutionary” science is so frequently fanfared to the front pages of newspapers that we could almost believe that scientists are as excitable and credulous as the tabloids appear to be. Everyone loves a David and Goliath story, so it is hardly surprising that every controversial finding is pounced upon. Miracle cures and perpetual motion machines are all the more exciting when it appears that they show up those stuffy old boffins. Strange how the rebels and their miracles most often vanish without further updates. With so many contradictory findings being touted each week, it’s easy to see why so many people become disillusioned with science. Going by the newspapers, I’m still not sure if my coffee addiction is going to give me a stroke or save me from a heart attack. In my previous blog (Science Says) I talked about why I think this happens, and why it’s not actually a reflection on proper science at all. True scientific revolution is another story and an exciting one. Maybe not “tabloid exciting” though.

The best explanation as to How Breakthroughs Happen goes like this. A couple of years ago I was fortunate enough to work with a rare kind of scientist. The man, who we shall simply call Oz, is to my mind one of an elite subset of scientists who dedicate their careers to answering a single, if profound question. Oz is also something of a philosophy buff and introduced me to the scientific philosophies of Thomas Kuhn, a man who had a lot to say on the matter of scientific revolutions. On the small scale, science is a cyclical process, as I outlined in First Assumptions. Hypothesise, test, refine, repeat. In time, hypothesis becomes theory or a new part of an existing theory. We can call the prevailing set of theories the “standing model” as they represent a human modelling of reality as we see it. Conferences and the peer review process serves as a rigorous test of the output of the scientific cycle. Scientists are a competitive, aggressive bunch. Attack, until only the truth remains. This constitutes what Kuhn called “normal science”. An overall model, the standing theory is in place, and scientists are filling in the blanks. It is tough work and worthy work. But, as the normal science phase drags on, discrepancies begin to arise.

When Isaac Newton published his theory of universal gravitation in 1687, it represented a fundamental change in the scientific understanding of the universe. It was a true piece of revolutionary science that dismissed theories as old as Aristotle. Once it was put forward and accepted by the community, normal science proceeded. Newton’s theory remained the standing model for over 200 years as the universe was measured and scrutinized using newer and better technologies. The cracks began to show. The movements of some of the planets didn’t fit the theory. The effects of gravity on light didn’t seem to either. And there was more. As always happens, a few contradictory measurements will tend to be dismissed as errors. But as they mount up, efforts will be made to explain them away within the context of the current model. This may well resolve the situation, but for Newton’s legacy this did not suffice. The physics community had entered what Kuhn called a “crisis phase”. The standing theory was clearly inaccurate, yet no theory existed to replace it. New hypotheses were put forward, amongst them the notion that the universe was filled with some manner of “aether”.

In 1905, almost unnoticed, a patent office clerk called Albert Einstein suggested a few things that might help explain how light worked. He demonstrated his ideas via some nice publications which were pretty much entirely dismissed as being a bit strange. A few years later, with a PhD under his belt, Einstein went the whole hog and published General Relativity, a new model that explained pretty much everything that was inconsistent in the Newtonian model and blew the aether out the window. The new thinking was so fundamentally different to Newton’s view of the universe that there was considerable resistance to his new model. As with all new science, revolutionary or otherwise, it had to face the purifying fire of skepticism, particularly from the aether heads. It wasn’t until 1919 that the experimental confirmations finally started to emerge. Einstein’s hypothesis prevailed and within a few years the scientific crisis was resolved. Kuhn called this sort of changeover a “paradigm shift”. The information, the observations, they’re still the same. The understanding has changed. Although the more recent notions of the aether-filled universe was now dismissed, Newton’s theories were not abolished. Instead they became merely a small part of a much bigger picture. Used for simple calculations where Einstein’s equations would be overkill. And so, the task of filling in the blanks in the new model began. Normal science was resumed.

Whilst scientists are often painted as inflexible types sticking to their established knowledge and rejecting change, the reality is that this resistance to change is as valuable as the change itself. It ensures that only the most robust hypotheses become theory. We stuffy boffins are always aware that one day the theories that we hold to may be superseded just as Newton was or may be overturned completely. Almost 100 years later, General Relativity, with additions, is still the accepted model. Yet at the extreme ends of physics the cracks are showing once again. It is perhaps ironic that it was Einstein’s ideas regarding the nature of light that would lead to the birth of Quantum Theory, a model which may one day lead to the next great paradigm shift in physics. For those interested, read up on the Large Hadron Collider. This year it may just prove or disprove a huge chunk of Quantum Theory. I have only a vague idea how, mind you. Physics is witchcraft in my books.

Normal science, crisis, paradigm shift, repeat. It’s a pattern that gave birth to giants of science such as Theory of Evolution and the Galilean model, or such field-specific shifts as the discovery of adaptive immunity. Don’t worry, I’ll probably write about those ones some day. My point is that paradigm shifts may change an entire arm of science, such as Biology, or just a small corner of that arm. Dr. Oz is, to my mind, on his way to heralding a paradigm shift in Biology. He’s in one of those small corners of the field, but the implications of his work speak for themselves. He’s convinced me, at least. The information hasn’t changed, but the way I understand it will never be the same. Let the crisis begin.

Science Says: Popular Science “Will Give You Cancer”

2008-07-31T20:14:00.014+01:00

"Digressions, objections, delight in mockery, carefree mistrust are signs of health; everything unconditional belongs in pathology." -Nietzsche

How often do we pick up a newspaper to find that science has yet again warned us of the dangers of something we all like doing? Power lines cause cancer. Coffee causes strokes. Wait no, it protects against heart attacks. So does wine. But it causes liver disease. Several weeks later, it’ll be something else. Fear it. What passes for science news in the mainstream media, be it highbrow or tabloid is often understandably simplified. Maybe it is too simplified, but what is perhaps of more concern is just where this science is coming from, and whether the editors of our beloved media outlets have sufficient knowledge of the workings of science to make good calls on what is likely to represent real findings.

Take the recent (ish) example cited by Ben Goldacre in his column, Bad Science. It all started when the British newspaper the Sunday Express ran with a headline that said:

Suicides “Linked to Mobile Phone Masts”

This front page article revisited the recent epidemic of suicides in Britain, citing the opinion of a certain doctor “who sits on a government advisory committee on mobile radiation” and who has apparently discovered a link between mobile phone deflector masts and depression. The opinion was presented as a revolutionary scientific finding and doubtlessly caused many people great concern. Ever sceptical, Bad Science found out that said scientist is not part of a government advisory committee but of an independent group which interacts with the British department of health via a mediation group. They’re quite far removed from the government and have no official standing. They further found that said scientist had not published his findings via the conventional route and that the data was not readily available. To a scientist, this sort of evasiveness sets off major alarm bells. And they were justified in this case. It emerged that the same scientist has previously made the claim that AIDS is not caused by the HIV virus but by electromagnetic radiation. In scientific circles, this is roughly equivalent to holocaust denial. Not very coincidentally, this claim looks very much like the claims he is now making regarding depression in the Sunday Express. This smacks of an agenda, and an agenda was indeed found. The “scientist” has numerous books available to buy online regarding the dangers of electromagnetic radiation and the healing power of magnets. Magnet healing kits may also be purchased from him, albeit with no explicit (or legally-binding) claims of having any sort of healing power at all. To put it bluntly, The Sunday Express have given their front page to the science world’s version of Delboy.

There’s far more to the story but Ben Goldacre explains in much greater depth and with greater eloquence than I could. His website comes highly recommended.

What should the non-scientist reader believe these days? To my mind, the best way for the average Joe to approach mainstream science reporting (and all popular science in print or on TV) is with scepticism and basic knowledge of how scientific findings are published and validated. So let’s look at that process. Please? I’ve even provided a flow chart as a visual aid! See, the mainstream press is represented by a small explosion which I hope makes the flow chart exciting.

So, scientific research is conducted all over the place. It is done to varying standards and with varying bias or agenda. For a recap on how proper research is conducted check out my previous posting, First Assumptions. This research is submitted to science journals. These are like ultra specialist magazines, and they mostly will only publish raw science, fresh from the lab. Scientists don’t get paid for this. It’s a privilege to be accepted. In order for that to happen, the work has to pass through “peer review”. This means that the work is assessed by an independent group of scientists in the appropriate field. Every figure, graph and photo is scrutinised. Every turn of phrase dismantled. It’s rather like sending your work to a whole group of Simon Cowells. A lot of research gets rejected out of hand or must be brought up to scratch. Mean things are said, feelings are hurt. The best stuff, the most solid stuff, gets into the journals. Unless you are a scientist or an extreme enthusiast, don’t even think of trying to read these journals. The boredom alone may actually make you die.

If your material is particularly hot, it may well feature as a part of a review paper. These are articles that the journals publish in an attempt to summarise the current cutting-edge of a given field for easier reading. “Easier” being very much a relative word. These reviews are only likely to maim the average reader via boredom and an unforgiving learning curve.

If the research has broad appeal to the scientific community as a whole, it may get picked up by the specialist press. Publications such as Focus, Scientific American or New Scientist cater for scientists who like to read news from other fields. The Biologista, for example is a life scientist who also happens to enjoy reading about robots, dinosaurs and jetpacks. New Scientist provides, and it has pictures.

Finally, the very most relevant and exciting research with the broadest appeal possible reaches the mainstream press. Many newspapers have science supplements, many websites carry science news and some papers will go so far as to carry science-oriented stories on their front pages at times. Radio programmes will often do a round-up of the most amusing science of the week.

This system, from peer reviews through the journals and finally to the mainstream is how things would ideally work. What actually happened in the case of our Prof. Delboy is that information was passed from research of unknown quality directly to a credulous newspaper. No peer review or quality control. No vetting for relevance or, most importantly, bias or agenda. This happens a lot in the mainstream press when it comes to science. The source material appears tricky, so information is accepted on the basis of authority, rather than evidence. Newspapers rarely cite anything more than a name as a source, but that’s the starting point for critical reading, as Dr. Goldacre has ably demonstrated for us.

You don’t have to go read those tricky journals. You don’t even need to read the specialist magazines, though it helps. Just do a little digging. Google a name and look for connections to industry or lobby groups. If you want to see if a named source publishes their research much, follow the link on this blog to Google Scholar and put their name in the search box. Ask yourself, did this pass through peer review? Most importantly of all, demand more of your news source. Look for multiple opinions in science articles. Look for evidence and look for data. Demand critical coverage. Above all, be a sceptic, but reasonable. Be a scientist in your own right.

Horsey

2008-07-28T01:17:00.011+01:00

Author's note: Analogy is wonderful thing. Let's do some analogy about allergy. Oh man I'm sorry. Really the main point is to do with how context is important in evolution.

Current speculative thinking is that the immune systems of many individuals co-evolved in the presence of persistent parasitic infestation. The immune system therefore evolved to over-compensate along the anti-parasite axis. It needed to be able to deal with new parasitic infection on top of the un-clearable persistent infection. We call this parasite killing axis the Th2 response. We can imagine our immune system as a sort of see-saw, but with many sides. As one side, or axis of our immune response raises, it pushes the others down. Some infections require a broad, balanced response. Others need a strong, single axis attack. Our persistent parasites evolved, adapting to evade our Th2 response. Some would push our immune response along other axes, perhaps towards our anti-bacterial response. The upshot of this was that we required further Th2 over-compensation. This co-evolution has probably been ongoing since our pre-mammalian ancestors. This is evolution over a time on the order of hundreds of millions of years.

Suddenly, in the space of a mere 200 years, the western world eliminated normal everyday parasitic infection. From an evolutionary point of view, an advantageous trait had become redundant in the blink of an eye. Individuals who previously had an evolutionary edge suddenly had a disadvantage. The asthamtic, the hayfever sufferer and the general sneezy snot bag has an immune system that resembles a race horse suddenly lacking its burden. The jockey, that nasty little parasite, has fallen off. The horse is gleefully running for the finish line, thinking he is about to win.

This stands as a wonderful example of the importance of context in evolutionary traits and in the emergence of new mutations. Allergy is today seen as some sort of genetic "defect". In African countries where the parasitic trypanosome and schistosome problems are finally starting to be reduced, allergy is starting to emerge. Perhaps this is mere coincidence, but if our thinking is correct, allergy and asthma will increase considerably there over the coming years. That is of course assuming that the western world gets off its arse to help do something about health in Africa.

The Great Wormtown Spade Disaster (Part 2)

2008-07-28T00:14:00.000+01:00

Wormtown is about to face a natural disaster of sorts, although of course the reader will know better than the worms do! A huge shovel crashes through Wormtown, scoops a huge chunk out of it, and throws the chunk into a neighbouring field. Quite a sight, if one had eyes. The surprised Worms within this temporarily-airborne piece of home are fairly resilient creatures and survive the unceremonious landing with only a few fatalities. They quickly abandon the collapsed ruins of their part of Wormtown (it has now become aerated and quite uncomfortably cold) and burrow into the new field to found the community of Farland. Back in the old field, the survivors of the Great Wormtown Spade Disaster proceed to put their lives, such as they are, back together.
The day that Farland is founded, the populations of Farland and Wormtown are quite similar in size and composition. Although the Sharpies have a harder time escaping underground during the foundation of Farland, none-the-less roughly one in ten worms is still a Sharpie. This state of affairs won’t last for long though, because things in Farland are different. The Worms aren’t in Kansas anymore (or Wormtown for that matter).
Farland is a hostile land. Foods are in short supply, and a strange local kind of Foods called Fast Foods are more common but are often too quick to catch. Fast foods make life a lot tougher for the Farland Sharpies. Also, Eaters are more numerous here, and more aggressive, something which makes life very very difficult for the Farland Smoothies, who quickly find themselves being gobbled up by the hundreds. Within a few years it becomes clear that one of these two great pressures of life outweighs the other. The Smoothies of Farland are extinct because of the Eaters. The Sharpies struggle on, though their numbers are limited from generation to generation. It’s not the Eaters that are making life difficult for the Sharpies though, as the Eaters find the Farland Sharpies rather unpleasant to consume due to their pointy texture. No, what troubles the Sharpies is the shortage of Foods. Just as it seems the new community will never reach the heights of the long-forgotten and now mythical Wormtown, a child is born to an unassuming Sharpie.
The child is called Flash, because the muscles around his sharp graspers are larger and stronger than most Sharpies, allowing him to get over the Sharpie movement impediment and move quickly. Flash does very well in Farland. He finds that his speed allows him to eat the elusive Fast Foods. He still has his Sharpie features too and so Eaters avoid him. Flash easily finds several mates and has plenty of kids. Just like his distant ancestor Sharpie, Flash’s kids are a mixture of normal Sharpies and a smaller number of little Flashes. As the years pass, the Sharpies and Flashes mate with each other, but with each generation, the numbers of purebred Sharpies becomes less and less as the Flashes as Foods tend to get snapped up by the quicker Worms. The purebred Sharpies, who once struggled but survived in Farland, become extinct just as the Farland Smoothies before them.
The Flashes of Farland thrive. Their kingdom spreads widely. Just like Sharpie and Flash before them, special kids are sometimes born. Not all of them do so well. Some die before they can have kids. Others have kids who find themselves beaten in the race for food or gobbled by Eaters. But some survive to bring great changes to the Farlanders.
The Farlander civilisation spreads so far that they one day encounter a strange new kind of animal in a distant land. Not small like Foods or big like Eaters, they have found the Fast Smoothies. The Fast Smoothies are descendants of the Smoothies who stayed behind in Wormtown. In the great many years since the Shovel came they spread out into the lands between Wormtown and Farland. Just like the Flashes, they became faster to catch the local Fast Foods they encountered and now they have found their long lost brethren. The Fast Smoothies have long since out bred the old Wormtown Sharpies and Smoothies because they could eat even more of the Foods of Wormtown. So much has changed that the Farlanders and Wormtowners wouldn’t recognise each other any longer. The bulky, spiky Flashes of Farland only vaguely resemble the lithe Fast Smoothies of Wormtown. And the more adventurous of them find that interbreeding produces no young.
And so the lands between Farland and Wormtown (which the locals would call Fencepost, if they were able) come to support a mixture of both communities, a balance which prevails for many years. But the Flashes and the Fast Smoothies never successfully interbreed. They have become different species, all thanks to strange Worms like Sharpie and Flash, and an even stranger phenomenon called The Shovel.

To learn more: Google these terms: Introduction to Evolution, Speciation, Mutation, Genetic Drift, Natural Selection, Habitat Fragmentation, Peripatric Speciation.

The Great Wormtown Spade Disaster (Part 1)

2008-07-28T00:12:00.004+01:00

Author's note: The story below is my attempt to put some of the core concepts of Evolution into terms that are accessible to a wide audience. I'd hope it could be read and understood by anyone from the age of 10 without patronising anyone over the age of 12... a tall order maybe. For anyone interested in what it all means, I've listed some of the concepts touched on in their scientific terms at the end.

Wormtown isn’t much to look at. Given that its inhabitants lack eyes, perhaps that does not matter. It consists of little more than some earth in a field Somewhere. It is inhabited of course by some Worms, who would have given Wormtown its name, if they had a language or indeed any means to speak it. The soil is warm, rarely disturbed and the general conditions are mild. The worms themselves are a simple bunch. They are microscopic and quite smooth. They have just three small grasping stubs on each side of their long bodies to aid their movement through the soil. And of course they also have the bits needed for eating and reproducing. Although the reader might have difficulty telling the difference, there are both male and female worms. The females lay eggs in large communal nurseries and their chosen male partners fertilise them. The process is a little messy though, and sometimes the wrong eggs get fertilized by accident (or on purpose if a male worm in question is a bit of a creep). Other inhabitants of the area include smaller animals called Foods and bigger ones called Eaters. The Worms, called Smoothies because of their appearance, eat the Foods when they can catch them and sometimes fall prey themselves to the Eaters. Aside from eating and mating, the Smoothies do little more than move around through the soil. Sometimes the Smoothies burrow to the surface and feel the Sun, which is rather painful and makes them burrow back down again. This state of affairs persists for a Very Long Time.
Every now and again a Special Child is born. Sometimes they have brightly a short body or coloured skin (the Smoothies can’t see this but the Foods and Eaters sure can). Sometimes they have no graspers or a stomach that won’t work. Special Children almost always die early. The ones that do survive pass on their dangerous characteristics to some of their children who themselves, sadly, die early.
One day, a worm is born with strange graspers. Instead of short and blunt graspers made toughened skin, this strange child has longer, sharper graspers. Of course, Worms have previously been born with bigger or smaller graspers than usual, but these differences never seem to help much. This sharpness is new and strange and the child is named Sharpie. Being simple souls (and also blind), the worms don’t hold this peculiar look against Sharpie, not that they could do much about her if they did. Still though, Sharpie finds her life a bit more awkward than the other worms. Her pointy horns make movement more difficult, which makes Foods harder to catch. Luckily, Foods are quite plentiful in Wormtown and so Sharpie survives, albeit struggling somewhat, and even lives to find a free-thinking mate and have children of her own.
Most of Sharpie’s kids are quite normal-looking Smoothies. But a few, males and females alike, have the same strange horns as their mother. Sharpie herself dies rather young as a result of her impaired movement, but having had a number of children, the reader can feel satisfied that Sharpie has made her mark on the world. So it is that a generation of Sharpies goes out into Wormtown. And they fair reasonably well. Sharpies still struggle to catch Foods when compared to Smoothies, just has their mother did, but their sharp horns give them a new edge that only now becomes clear; Eaters are less afraid to eat them! Sharpies and Smoothies mate frequently, producing litters that are a mixture of Sharpies and Smoothies. As the generations pass, this means that Sharpies are born that are distantly related enough to mate with each other without making the reader feel vaguely uncomfortable.
The years pass and the population of Wormtown settles into an equilibrium, a balance of sorts. So long as there are plenty of Foods, both the Smoothies and Sharpies can survive, though at different success rates. As long as there are predators attacking both, the Sharpies can partially overcome their disadvantage when it comes to getting Foods. And so at any one time, about one in ten citizens of Wormtown is a Sharpie. They form a sort of racial minority who thankfully don’t suffer from much by way of discrimination, if only because the Worms are rather lacking in the brains required for one to be properly ignorant.
The idyllic, peaceful and now quite diverse community of Wormtown is about to face disaster.

Part 2: In Which Disaster Happens

To learn more: Google these terms: Introduction to Evolution, Speciation, Mutation, Genetic Drift, Natural Selection, Habitat Fragmentation, Peripatric Speciation.

First assumptions

2008-07-27T14:17:00.000+01:00

Beginnings are tricky. I feel like I should make a good impression. I've had a haircut and a shave. I'm wearing a trendy shirt and some sort of designer smell. I'm going to start at the beginning...

As infants, each of us begins to form what a scientist would call “hypotheses”. Most, less pedantic, people would call them “theories”. That word has another meaning for the scientist, but I’ll come back to that. A hypothesis is an idea, a position we assume based on some limited information. Amongst the first hypotheses that infants will form goes something along the lines of “stuff falls down”. The gleeful child will test this new idea by experimentation. Hence the wondrous phase during which the child will pick up any and all objects within reach simply to give them forcefully to the floor. The reproducibility of this experiment convinces the child that the hypothesis is good and the idea finally graduates to a loftier status, probably giving birth to a new hypothesis in the process; “parent-things get angry when I make stuff fall down”.

Scientists adopt a similar method. Starting with some previously-solidified information, they adopt a hypothesis. Just as a child will do, until the complexity of life leads them to question the world less, they adopt an initial position, for the sake of argument if you like. The scientist has faith in one notion alone, that the universe may be tested by observation. So, the one essential requirement for a hypothesis to be valid is that it must be testable. The philosopher Karl Popper advocated going one step further, stating that the only valid hypotheses are those that could be falsified, that could possibly be proven wrong. A good scientist conducts his experiments, his means to observe the universe, in order to do just that. He seeks to falsify his hypothesis.

It is only when repeated attempts to prove himself wrong have failed that the scientist comes to believe his hypothesis at last. And it is only when those observations have been attacked and reproduced by many others, by colleagues and competitors, that the scientific community accepts the hypothesis. It is then that hypothesis becomes “theory”. There is in truth no such thing as scientific fact, at least not in the sense that most people imagine. Instead, theory is the highest status to which our knowledge may ascend. That difference between what scientists call theory and what the common man calls theory is the reason why a scientist will never say “it’s just a theory”.