Wednesday, 31 October 2012

Is evolution random?

In a recent perusal of The Blogosphere, my eye was caught by a post at A Tippling Philosopher entitled Far from random, evolution follows a predictable genetic pattern, Princeton researchers find. As I suspect most evolutionary biologists would, I got rather annoyed by this title. I should point out, however, that the Tippling Philosopher is not to blame - this is the title of the original Princeton press release.

Unfortunately, my VPN is playing up so I cannot access the original article (Zhen Y, Aardema ML, Medina EM, Schumer M & Andolfatto P (2012). Parallel molecular evolution in an herbivore community. Science 37(6102):1634-7) but I am a bit short of time anyway and don't want to do an in depth study. I suspect the press release actually does a fairly good job of summarising the main points as does the abstract:
Numerous insects have independently evolved the ability to feed on plants that produce toxic secondary compounds called cardenolides and can sequester these compounds for use in their defense. We surveyed the protein target for cardenolides, the alpha subunit of the sodium pump, Na+,K+-ATPase (ATPĪ±), in 14 species that feed on cardenolide-producing plants and 15 outgroups spanning three insect orders. Despite the large number of potential targets for modulating cardenolide sensitivity, amino acid substitutions associated with host-plant specialization are highly clustered, with many parallel substitutions. Additionally, we document four independent duplications of ATPĪ± with convergent tissue-specific expression patterns. We find that unique substitutions are disproportionately associated with recent duplications relative to parallel substitutions. Together, these findings support the hypothesis that adaptation tends to take evolutionary paths that minimize negative pleiotropy.
This is all very interesting and very cool - the power of evolution by Natural Selection demonstrated in replicate. The thing that irked me, though - and the focus of this (probably too hasty) post - is the title and the first paragraph of the Princeton press release:
Far from random, evolution follows a predictable genetic pattern, Princeton researchers find

Evolution, often perceived as a series of random changes, might in fact be driven by a simple and repeated genetic solution to an environmental pressure that a broad range of species happen to share, according to new research.
Evolution is not a series of random changes. At least, adaptive evolution, which is the subject of this paper, is not. Neutral evolution largely is random but that's only one part of evolution as a whole and to imply otherwise is rather misleading. The raw material for evolution is indeed random mutation but this is not the full picture. There was a clever chap who realised that heritable random variation in a trait, if it produced differential survival and/or reproduction, could result in the non-random change of that trait. Good ("fit") traits would increase in frequency and eventually dominate the population, while bad traits would be removed. He realised this over 150 years ago and called it Natural Selection. His name was Charles Darwin and his book is free on Kindle if you want to read it. (Yes, I know, this is a gross simplification of history!)

This is compounded by the title: "Far from being random, evolution follows a predictable genetic pattern, Princeton researchers find". Well, yes, sometimes it does (and in this case) but we've also known that for years. The argument about the predictability of evolution is one that has been going on for a long time. (Read Gould's "A Wonderful Life", for example.) If you were to rewind the clock and let evolution run again, how much would history repeat itself? We know the answer is not "always" and we know the answer is not "never" but we do not know where on the continuum between "always" and "never" reality lies. (Major catastrophic events notwithstanding. These are another role of chance but somewhat different to the one determining evolutionary trajectory.)

In evolution, the opposite of "predictable" is not completely "random". One has to be clear that even if we cannot predict a precise evolutionary trajectory due to the complexity (and, yes, randomness) in the system, trajectories that give rise to exquisite adaptations always have a large non-random component (selection). This may seem like a trivial thing but it's not, for this is the kind of language that feeds the misconceptions spread my advocates of Intelligent Design and other forms of Creationism. (Of course, this study also nicely blows such nonsense out of the water.) If it is "often perceived as a series of random changes", it is only because of misconceptions like this being repeated.

For me, it is the last line of the abstract that is most intriguing and possibly the big discovery:
"Together, these findings support the hypothesis that adaptation tends to take evolutionary paths that minimize negative pleiotropy."
The authors cite "the large number of potential targets for modulating cardenolide sensitivity". It seems that they think that the other possible target genes are more prone to affect other systems as well in a bad way. (I am not sure how they rule out the possibility that the selective advantage of changes in this particular pump are just much, much greater than the other genes and its just driven by the probability and rates of positive selection.) If this turns out to be a widespread phenomenon, it could indeed have implications for the predictability of future adaptation, which could be useful in our changing world!

This is just one example, of course. Another recent paper on parallel and convergent evolution in Proc. R. Soc. B (free this time), "The probability of genetic parallelism and convergence in natural populations" by Gina Conte, Matthew Arnegard, Catherine Peichel and Dolph Schluter, looked at a bunch of studies and concluded that "estimates [of the probability of gene reuse in parallel and convergent phenotypic evolution in nature] using data from published studies. The estimates are surprisingly high, with mean probabilities of 0.32 for genetic mapping studies and 0.55 for candidate gene studies".

I'm sure there's a bit of ascertainment bias towards traits under strong selection (as these are more obvious and thus more studied) but it confirms the Andolfatto study that in the right circumstances convergent evolution can make use of the same gene(s). (They also cite counter-examples, so be quite clear that this is not universal.) It's not a surprise that it happens but given the amount of diversity between genomes - and numbers of genes affecting many traits - the level is possibly surprising. To be honest, I can't decide if I am surprised or not as it is so hard to generate a reasonable a priori expectation.

I still don't think that all this means that evolution in general is predictable (we still need more studies) but it certainly does hammer yet another nail in the coffin of the old Creationist chestnut about evolution being random. Natural Selection is NOT random - that's the whole point!

Footnote: I must concede that in writing this post I realised that explaining the role (and meaning) of "random" in the context of evolution is not quite as simple as I thought. "Random" commonly does mean a lack of predictability but I maintain that it is not helpful to use this language for evolution without some serious explanation of what you mean by random. Random mutation plus Selection means that we are talking about a lack of determinism, not a lack of direction. (This was also supposed to be a quick/short post!)

h/t: A Tippling Philosopher and WEIT

Monday, 29 October 2012

It's pumpkin time!

Halloween is approaching and, thanks to an unexpected work trip for my wife, we have had to accelerate our preparations slightly. Last night, therefore, was pumpkin-carving time! We never really did anything for Halloween when I was a kind, so my first pumpkin carving experience had to wait until a few years ago.

In the past, we have made use of hand-drawn designs inspired by the internet. (For my first pumpkin, I was only involved in the design and my girlfriend (now wife) did the actual carving.) This year we got a pumpkin carving kit from Ocado that cam we a few designs, so we decided to use a couple of those. They were quite big but we got a couple of "monster" pumpkins from Sainsburys. Sitting on our dining room table, I think my "monster" lived up to its name!

I was a bit lazy and did not scoop the inside out as much as I should have done but I think the end result (below, left) was still pretty good. The carving tools in the pumpkin kit were pretty effective and a little less scary that hacking away with a knife or scalpel, although we still used one of the sharp pointy tools from Cait's Uni dissection kit to poke the outline of the designs. My wife remains the pumpkin champ of our house, though, as her haunted house (below, right) shows. (I'll try to get some better pictures on the night but these were just quick iPhone snaps should any evil befall our pumpkins in the meantime!)



Sunday, 28 October 2012

All aboard the Beagle with Darwin

If you've not already seen it, you can follow the adventures of Charles Darwin, who is posting updates of his voyage as @cdarwin on Twitter. (Delayed by 181 years, naturally):

  Geologist, naturalist and gentleman. On board The
  Beagle with Capt Fitzroy on a voyage around the world.


It's a five year voyage (near enough) and comes highly recommended. He's only just on board, so plenty of time to catch up.

h/t: WEIT

Saturday, 27 October 2012

Americans, please listen to the Rest of the World!

I've already had a bit of a rant that There is no "Leader of the Free World" but one thing seems clear: if Romney gets in, the Americans should finally give up all claims that there is. As blogged by A Tippling Philosopher:
"A BBC World Service opinion poll has found sharply higher overseas approval ratings for US President Barack Obama than Republican challenger Mitt Romney."
The graph says it all, really:

Friday, 26 October 2012

The badgers are safe (for now)!


Happily, following the House of Commons debate, the BBC today have reported that MPs reject government plans for pilot badger cull.
In a non-binding vote, MPs rejected the policy by 147 votes to 28, calling instead for vaccination, improved testing and bio security.
The vote is non-binding and the Environment Secretary remains committed to the mindless badger cull. Hopefully, now that MPs have been added to both scientists and the public as the people the government have to flagrantly ignore to go ahead with the plan, something will actually happen.

As revealed in another BBC piece (Analysis: The battle over brock):
Ministers say cattle vaccination is not currently an option due to EU regulations. The main problem is that a test developed by UK scientists to distinguish between vaccinated and infected cows has not been approved.
I guess this makes the EU is the next place to put the pressure - New Zealand has had a vaccination program since 2004:
Cattle can be vaccinated and their products consumed locally using a test that can tell between TB infection and vaccination, although the products cannot be exported to either the EU or the US, according to officials.
...
Field trials on cattle TB vaccines are banned in the UK, but scientists have been collaborating with countries where vaccination programmes are ongoing, including the US, Argentina, Ethiopia, Mexico and New Zealand.
It's not over yet but at least the badgers should be safe for the winter.

[Photo credit: Tim Matthews]

Thursday, 25 October 2012

Bella Lucca

I spent the past few days in Lucca, Italy, for a(n Irish) family wedding. I've never been to Lucca before but it was great and well worth a visit. It's a medieval walled city that is still completely surrounded by a city wall and, beyond, surrounded by the hills and mountains of Tuscany. Compared to the remains of Southampton's medieval walls, the walls of Lucca were surprisingly wide and flat - very easy for strolling, jogging or even cycling round.Of course, nothing quite sets off a stroll around some ancient city walls like some gelati and Lucca (as expected in Italy) has some great Gelaterias. I particularly recommend the pistachio gelati from the Gelateria L'Angolo Tondo in the Piazza Anfiteatro. (Another triumph was the chocolate gelati from the Caffetteria Colombano, located on the wall itself at Baluardo San Colombano.)

The other thing I love about Italy is the coffee. Italians really know how to make a good espresso! In fact, all the food and drink was pretty good. (They have some very pretty cats too!)

Wednesday, 24 October 2012

20% off The Cabbages of Doom!

Blogging has taken a back seat over the past few days because I have been in Lucca for a family wedding, where there was considerably better access to wine than wifi! More on Lucca later but for now just a quick plug: 20% off The Cabbages of Doom (and everything else at Lulu.com)!

Wednesday, 17 October 2012

Cull bad government policy, not badgers

As reported on the Badger Trust Facebook page:
"It is confirmed that there will be a full (6hr) House of Commons debate next Thursday 25th October."
It will be interesting to see if they pay attention to the science or just shout at each other, like most House of Commons debates I've seen clips of. The recent letter by top scientists has obviously made some impact but we need to keep badgering them. I suggest emailing your MP.

There's nothing scary about the Spice Kittens

It's Biology Week, so what better excuse to spend some quality time watching kittens! Thanks to felid-fancier Jerry Coyne at WEIT, I was alerted today to the presence of the Spice Kittens Live Webcam. Worry not, for though there is a ginger one, this has nothing to do with the Spice Girls:
Rosemary, a stray, gave birth to her kittens October 5th. She is estimated to be two years old. The two orange boys are Basil & Mace. The buff boy is Sage. The B&W girl is Nutmeg.
Cat coat genetics are actually quite complicated but we would know that Rosemary was (almost certainly) a dam (a lady cat) even if she had not given birth to kittens because she is calico. Calico cats are an interesting (and pretty) example of what is known as X-inactivation.

Cats, like all mammals (including us) have genetic sex determination. (Not all animals do. For some it is temperature dependent or they can even change sex during their lives - see "Finding Nemo's sex-changing father", for example.) Genetic sex determination does not necessarily need sex chromosomes (yeast manage with a single mating type locus (gene)) but in cats (and humans) it is determined by a pair of sex chromosomes. (A single pair of sex chromosomes is normal. The platypus has five pairs!) These are the famous "X" and "Y" chromosomes, pictured right. (Human ones but cats are probably quite similar.) As you can see, the Y (right) is a runty little thing compare to the elegant and well-formed X - and this is where X-inactivation comes in.

The problem is that, with the exception of some short regions at each end, the Y chromosome is missing most of the genes that sit on the X chromosome. This means that a female (XX) has two copies of these genes and males (XY) have only one. This in turn would mean that a female cell would produce approximately twice as much of the products of these genes. Gene dosage is often important: rather than the absolute level of something, it is often the ratio between two things that is important. To compensate for having two copies, therefore, the cells of female mammals switch off one of the copies. This is "X-inactivation".

Because it is random which X chromosome gets switched off, this can lead to some interesting chimeric patterns, including that of the calico cat coat. This in turn is because one of the main coat colour genes - the "ginger gene" - is on the X chromosome. The parts of the calico cat that have a functional ginger gene are like a ginger cat and the parts that inactivate this copy but instead have the recessive "black and white" variant are like a black and white cat. (An extra complication is the status of additional genes that determine how much white patterning there is.)

This also explains why two of the male kittens are ginger - they have inherited their Y chromosome from their father (no ginger genes) plus a random X chromosome from their mother - the ginger one in the case of Basil and Mace. I cannot quite work out whether Sage also has the ginger gene but it has been "diluted" by another coat gene, or whether he is a different colour variant. (The girl, Nutmeg, is a more simple black and white.) The other complicating factor with kitties is that different kittens in a litter can actually have different fathers, so the variety of coat colours within a little can exceed all the possible combinations of one tom and one dam. (It also means that I don't think we can use the colours of the Spice litter to work out what colour the fathers were, except that Nutmeg's father was not ginger.)

Anyway, I am pretty sure that watching kittens is good for your mental health (and you can't catch Toxoplasma gondii online) so do have a little look when you have a spare moment and ponder X-inactivation, study animal behaviour, or just admire their kittie cuteness! (I'm not sure how long the live stream will be up but I will try to remember to update this post if it disappears.) [Edit: The girl kitten now seems to be called Pepper.]

h/t WEIT.

Tuesday, 16 October 2012

25% off at Oxford University Press for Biology Week

Oxford University Press have some special Biology Week content on their website, including 25% off all Biology titles (with free P&P over £20) so now's the perfect time to get that popular science book you'd been coveting. (Or a textbook if you're feeling more hard-core.) The promotion is actually running until the end of December 2012 so might be good for Christmas presents too!

Badger Photo Credit: Tim Matthews

Yesterday, I posted about the mindless badger cull but did a bit of a naughty and didn't cite the awesome badger photo. (I intended too but it slipped my mind.) I am pretty sure that I originally got it from a BBC Autumnwatch photo competition but I cannot find that now. I think, however, I have tracked down the original to the flickr stream of Tim Matthews, so head over there and give his photo some love!

Monday, 15 October 2012

We need to keep badgering the government about their mindless disregard for science

As it's Biology Week, I was intending to only blog about biology matters this week. I did not, however, envisage starting things off with a post about such a flagrant disregard for biology in the form of the UK government's planned badger cull.

As reported in the BBC, this "mindless" cull currently set to go ahead despite both a massive e-petition (of which I proud to be a signatory) and, now, a letter to the observer signed by 31 top scientists:
"Bovine tuberculosis is a serious problem for UK farmers, deserving the highest standard of evidence-based management. The government's TB-control policy for England includes licensing farmers to cull badgers. As scientists with expertise in managing wildlife and wildlife diseases, we believe the complexities of TB transmission mean that licensed culling risks increasing cattle TB rather than reducing it.
...
We recognise the importance of eradicating bovine TB and agree that this will require tackling the disease in badgers. Unfortunately, culling badgers as planned is very unlikely to contribute to TB eradication. We therefore urge the government to reconsider its strategy."
These are not new revelations to the government and it is saddening to see them ignore both a large number of the population but, more importantly, such a large number of top scientists. This is not just about not killing badgers, although that is obviously important. This about a government going ahead with an inadvisable course of action that will quite probably make the situation worse just because of pressure from the National Farmer's Union.

Most tellingly, one of signatories was Lord Krebs, the designer of the original badger cull experiment, who was previously quoted by the BBC as saying:
"I have to say I've not found any scientists who are experts in population biology or the distribution of infectious disease in wildlife who think that culling is a good idea. People seem to have cherry picked certain results to try and get the argument they want."
Another was Professor John Bourne, who was in charge of analysing the data as Chairman of the Independent Scientific Group on Cattle TB, and was equally damning with his conclusions:
"As far as badger culling is concerned it has nothing to offer in terms of controlling TB in cattle, and could indeed make the situation worse."
Somewhat ironically, Defra Minister David Heath was quoted as saying:
"No-one wants to kill badgers but the science is clear that we will not get on top of this disease without tackling it in both wildlife and cattle."
The scientists are clear of "the importance of eradicating bovine TB and agree that this will require tackling the disease in badgers" but culling is not the way to do it. Even assuming that it is true that "no-one wants to kill badgers", you can't just pick and choose the things that "science is clear" about that you like (or are popular with your friends) and ignore the bits you don't. As the effects of climate change continue to be felt, we need a government that has the courage to listen to the science, whoever that might upset.

[Photo credit: Tim Matthews]

Saturday, 13 October 2012

Biology Week is almost upon us

The Society of Biology's inaugural Biology Week is almost upon us. Running from October 13-19, it will feature a bunch of biology-related activities going on around the country. So go forth and do/enjoy some biology!

Wednesday, 10 October 2012

We have a bit of situation


This genius cartoon is doing the rounds on Facebook thanks to I f**king love science. It's originally from XKCD. Despite the clear parallels with the recent Paul Broun nonsense, it's actually a pretty old one.

The problem is, the Universe not caring what we believe is not always a good thing. Take Mitt Romney's poor grasp of climate change, for example. We're in big trouble whether Romney thinks that we (or, more precisely, America) should do anything about it, or not.

The USA is one of the most technologically advanced nations on Earth and yet, despite this, some of its leading politicians are not only science illiterate but they seem to wear that illiteracy with pride, like some kind of badge of honour. That someone like Paul Broun can end up on the USA's House Science Committee (along with fellow Republican, Todd Akin) would be funny if it wasn't so downright disturbing.

I don't know what scares me more: the possibility of another Republican US President or the fact that it's even a real possibility that someone like Mitt Romney could end up wielding that much power. If US politicians do not wake up about Climate Change - and debate the issue at least - I fear that we are going to have a lot more than "a bit of situation".

Sunday, 7 October 2012

A fan fixes Star Wars (Machete Order)

Like many of my generation, I am big Star Wars fan. I watched the original films more times than I care to remember and many more times than I care to admit. I probably went through half my teenage years able to recite the entire script to Star Wars (or A New Hope if you must) - including sound effects. I played Star Wars: The Roleplaying Game (the original one) and kicked ass at X-Wing on the PC. I was a Star Wars nerd.

Also like many of my generation, I was less enamoured by the prequels when they came out (although I should have seen the warning signs in the Special Edition trilogy - Han Solo shoots first for crying out loud. Grrrr. (Let it go, Rich, let it go...)) The Phantom Menace in particular was pretty terrible, however much the fan in me tried to be convinced otherwise. I really wanted it to be good. But it sucked. Darth Maul was pretty cool (except his death, which was pretty lame,) but the young Anakin was terrible, Jar-Jar Binks was really terrible, Midi-chlorians were beyond terrible and, perhaps worst of all, the whole script was a shocker. The only good thing about Episode I was the number of fantastically therapeutic spoofs it has spawned, especially at the hands of Robot Chicken (e.g. here and here). Well, that and the poster with the young Anakin and the shadow of Darth Vader.

My own fix to The Menace was to watch the DVD and just fast-forward all the bits I really didn't like, which was basically every time Jar-Jar or Anakin were on screen (except the pod race, which had good sound effects). This, and excising the Midi-chlorian scenes, actually works surprisingly well at turning The Phantom Menace into something quite watchable (and shorter) even if the already weak plot of that particular movie is watered down further still.

Rod Hilton on his blog, Absolutely No Machete Juggling, goes one further and has a plan for fixing the series with The Star Wars Saga: Introducing Machete Order His recommendation:
"Next time you want to introduce someone to Star Wars for the first time, watch the films with them in this order: IV, V, II, III, VI"

As well as re-ordering the films to safeguard some of the plot twists that the prequels ruin mightily, he excises Episode I altogether.
"Episode I is a failure on every possible level. The acting, writing, directing, and special effects are all atrocious, and the movie is just plain boring. Luckily, George Lucas has done everyone a favor by making the content of Episode I completely irrelevant to the rest of the series. Seriously, think about it for a minute. Name as many things as you can that happen in Episode I and actually help flesh out the story in any subsequent episode. I can only think of one thing, which I’ll mention later."
I won't go into the rest of the reasoning here but will instead recommend that you scoot over to Rod's blog. It's an old post (November '11) and quite long but if you are a fan (or were) and you've not come across it before, it's well worth a read. I've not yet tried out Machete Order myself but will be remembering it should I ever need to introduce someone to Star Wars in the future.

Saturday, 6 October 2012

Olympic Highlights VII: Elbow

One of the highlights of the Olympic closing ceremony for me was definitely Elbow. They were also responsible for the theme tune of excellent BBC coverage. Off the back of these things, I have got myself a fair bit of Elbow, including (most recently) First Steps, the aforementioned BBC theme tune and just as good as I remember it. (Better, in fact, as I can now listen to the full 6min 21sec!) The reminder of the Olympics is a bonus!

The other Elbow album that I have been listening to a lot of late is Cast of Thousands which is simply a joyous stroll through mellow musical magnificence and gets better each time I listen to it, particularly the first half of the album. It's definitely headphones music: it deserves your full attention.

Like a fair few of my other music discoveries, this was in-part thanks to my emusic membership: Elbow are one of the decent bands that have albums on the site (including Cast of Thousands). If you want a trial, leave me a comment and I'll send an invite. (It used to get some extra freebies. You have to sign up but you can cancel before paying any money unless they have changed things.)

Friday, 5 October 2012

Religious tolerance and respect are not the same thing

Last week, coelsblog had a great post on religious tolerance: Religions are entitled to tolerance, but not to respect. In it, she lays out the important distinction between tolerance (allowing the existence) of and respect (having admiration) for something. She also calls out people who erroneously criticise Richard Dawkins for being intolerant, when he is only being disrespectful and religion has no right to respect.

It is an important distinction worth reminding people about and I wonder whether I sometimes fall into the trap myself. Tolerating a belief means that you do not try to forcibly stop people from holding it. It is not the same as letting that belief go unchallenged. (That is where the respect comes in.)

For me, I think the real issue is over the boundary between religious beliefs and religious practices. Whilst there is a definite need to tolerate the former, there is no need to tolerate the latter. (One only has to imagine a religion that features ritual murder and cannabilism to see this.) As coelsblog says:
"Yes, religious beliefs should be tolerated, and, yes, religious practice should be tolerated (provided only that it complies with the usual civil law)..."
One problem, I think, is that people often conflate refusal to tolerate certain religious practices that don't comply with civil law with refusal to tolerate religious belief, for they often see them as one and the same. So, the fact that Creationism is not tolerated in a science class (or the Giant's Causeway) is interpreted as a lack of tolerance for the religious belief behind it, whereas really it is the result of a lack of respect for that belief.

This is, in essence, the heart of secularism: people can believe what they want but it is up to society to determine what is acceptable behaviour and no belief system (religious or otherwise) gives one a "get out of jail free card" to ignore or supersede the laws, rights and responsiblities that follow.

Thursday, 4 October 2012

The National Trust does the right thing at the Giant's Causeway

Back in July, I stuck my oar in (as did many others) to the National Trust Giant's Causeway controversy when it was revealed that their visitor centre had an exhibit that appeared to (at best) appease or (at worse) endorse the Young Earth Creationist view of the age of the Earth (and the Causeway). (See here and here for more on how very wrong the Creationists have it.) Initially, I was sympathetic and supported them but was subsequently convinced by the arguments of others and withdrew my support.

The errors that I felt the Trust made (and emailed them about as a member, requesting a correction) were in some potentially misleading:
To suggest that the debate continues in this context does imply it is a scientific debate. It is not. The fact that the audio subsequently makes it clear that the debate only continues for "some people ... based on a specific interpretation of the Bible" does not entirely undo this initial error. Although I am willing to believe that this is an accident and the NT did not mean to imply that the scientific debate continues, the fact that some people interpret it this way is reason enough, in my book, to change it. This was the first big mistake.

The second big mistake was the use of the word "mainstream" in the sentence: "This debate continues today for some people, who have an understanding of the formation of the earth which is different from that of current mainstream science." Again, although this is immediately followed by a sentence that makes it clear that these people have a different understanding for religious (not scientific) reasons, I find myself agreeing with those commentors who see this sentence as implying that there is some other kind of science that disagrees with the current "understanding of the formation of the earth". There isn't. This is misleading and, even if not giving YEC legitimacy, it reduces the legitimacy of the NT exhibit.

I stand by my original view that the words themselves are true but it is clear that the context and exact choice of phrase - whether deliberate or accidental - is not giving an impression that is consistent with the Trust's stated position on this topic. For this reason alone, they must revise the wording of the exhibit, even if they do not drop the YEC reference altogether...
Happily, as reported today by BBC News (Trust amends Causeway centre 'Creationist' exhibit), the Trust has listened to all its members that complained and changed the wording:
The new audio now says there is a "clear understanding among scientists that the heat of the earth was the driving force behind the formation of the Giant's Causeway".

It adds that the earth is "far older than had previously been thought".

"All the scientific evidence points to a volcanic origin for the columns of the Giant's Causeway, around 60m years ago.

"However, not everyone agrees with the scientific view. There are some people who believe - often for religious reasons - that the earth was formed more recently: thousands of years ago rather than billions."
Although not far enough for some, I am happy that this solves the big problem and no longer implies that there is any scientific debate. YEC is a religious position, (im)pure and simple.

h/t WEIT

Wednesday, 3 October 2012

Are big pharma companies worse than homeopaths?

Ben Goldacre is well known for busting Bad Science and promoting evidence-based medicine. His latest book, Bad Pharma, goes beyond quackery and takes on Big Pharma, highlighting what are down-right dangerous practices in the industry. I haven't read the book but his recent article about it in the Business section of the Guardian, "The drugs don't work: a modern medical scandal", makes scary reading. You can also hear him talk about it in a recent Nature Podcast Extra.

It's common knowledge that Homeopathy is pure placebo and literally has no active ingredients. The danger of homeopathy is not that it will do you any harm - there is nothing in there to do any harm - but rather that people will be conned into using Homeopathy in place of treatments that could actually cure them. (Not all conditions can be treated effectively with a placebo and some drugs out there genuinely do work better than placebo.)

The same is not true of drugs. (Or herbal remedies for that matter.) They contain an active ingredient and therefore there is the very real potential for harm as well as the very real potential for an actual positive effect. It is therefore much worse to find out that Big Pharma companies are playing games with the clinical trials and evidence on which doctors base their treatments.

Big Pharma, Homeopaths and woo merchants are all in the business of making money and so it is perhaps not surprising that they use some of the same tricks to sell their wares but what is surprising (to me) is the extent to which the law lets them get away with it and regulating authorities are apparently powerless to do anything about it. Although it does nothing to undermine the need for evidence-based medicine, it massively undermines the access to evidence-based medicine - if the evidence the doctors get access to is hidden or distorted then what's the point?

It's a pretty stark picture. Indeed, Ben Goldacre starts the book thus:
"Medicine is broken. And I genuinely believe that if patients and the public ever fully understand what has been done to them - what doctors, academics and regulators have permitted - they will be angry... I'm going to tell you how medicine works, just over the page, in one paragraph that will seem so absurd, so ludicrously appalling, that when you read it, you'll probably assume I'm exaggerating."
Before I get to that paragraph, I would say that there is at least one other group that will be (and are!) angry - other academics. I am one! I am angry as both a sometimes patient and a scientist. (And, when it comes to medicine, a member of the public!)

The reason this angers me as a scientist are two-fold. First, the trivially obvious reason: such flagrant abuses of methods that are supposed to provide objective evidence not only undermine public faith in medicine but they undermine faith in science as a whole. (Not, sadly, that non-medical science is immune to these abuses but they generally seem to get identified by other scientists, who are all skeptics by nature, and rarely have the same capacity for harm.) The second reason is that it is not just doctors and patients that use these data. There is a lot of effort being put into mining existing drug actions and side effects to identify novel treatments (e.g. "network medicine") - often by people who do not stand to make money from the discovery. The weakness with all of these approaches is that "rubbish in, rubbish out" and if the pharma industry is systematically sabotaging the data that the scientific community are using for such endeavours then a lot of good scientists are wasting valuable time and money, not to mention missing important connections that could result in genuine treatments.

But now for that paragraph. You can read the full paragraph using Amazon's Look Inside feature but here's a taster:
"Drugs are tested by the people who manufacture them, in poorly designed trials, on hopelessly small numbers of weird, unrepresentative patients, and analysed using techniques which are flawed by design, in such a way that they exaggerate the benefits of treatments. Unsurprisingly, these trials tend to produce results that favour the manufacturer. When trials throw up results that companies don't like, they perfectly entitled [legally, not morally - RJE] to hide them from doctors and patients, so we only ever see a distorted picture of any drug's true effects. Regulators see most of the trial data, but only from early on is a drug's like, and even then they don't give this data to doctors or patients, or even to other parts of government. This distorted evidence is then communicated in a distorted fashion..."
The rest of the paragraph - and, judging by the intro, the book - is not much cheerier. It's no wonder he says that Medicine is broken. When I am feeling brave, I think I will order a copy for my kindle.

Nevertheless, I think there is something worth pointing out or reiterating: this is a problem of implementation, not theory. It is not that drugs cannot or do not work - some do and we have well-designed and well-executed studies that show this. (Generally, the older ones, when Pharma was not so desperate or, perhaps, cynical and there was more low-hanging fruit.) It is not that medicine should not be evidence-based or that we do not have methods for gaining that evidence. This does most emphatically not mean that homeopaths and woomeisters were right all along. The fact that some of their conspiracy theories have a semblance or truth about them does not mean that their pseudoscientific nonsense suddenly gains merit.

I'm not really sure what can be done about this but the first step on the road to recovery is admitting that you are sick, and it certainly cannot be swept under the carpet. Part of me still hopes that Ben Goldacre's new book is an exaggeration (or, at least, concentrates on all the negatives) but can we really take that chance? However widespread the problem in terms of current drugs that are affected, we must make some changes to things that are clearly broken. Making the clinical trials process entirely independent of drug companies would be a start and forcing drug companies to publish all of their data from trials for analysis by independent experts seems like such a no-brainer that my mind still boggles a little at the revelation that it isn't so.

Should it be needed, it's just another indicator of the dangers of privatising health care. When the bottom line is money not effectiveness, you know you are in trouble.

Monday, 1 October 2012

I just didn't expect it to be so big

This has been doing the rounds but, in case you've not seen it, there is a full screen version of XKCD's recent epic Click and Drag comic XKCD 1110 in a zoomable version - visualization created by dividuum. It saves a fair amount of clicking and dragging and let's you seek out all the hidden bits in the sky and tunnels (and works especially well on an iPad). I just didn't expect it to be so big
There is also a recent interview with XKCD creator, Randall Munroe, in The Atlantic, which is worth a read.

h/t WEIT.