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Wednesday 25 June 2008

Conservapedia vs The Scientific Method [DrDave]

In the last month or so, evolutionary biologist Richard Lenski published one of the most ground breaking scientific papers of recent years, though it may not appear that way at first glance. The paper describes the latest findings of a 20 year study into the evolution of E. coli bacteria.

The details of the experiment are simple, but extremely elegant. Lenski's team started with 12 populations of E. coli, and transferred them daily into environments of fresh nutrients. Samples were tested regularly for changes in mean fitness and interesting variations were noted. Cleverly, every 500 generations samples of each population were removed and preserved - creating a snapshot of the evolutionary history.

At around generation 33,000, Lenski's team began to notice an interesting change. Members of one of the populations had suddenly gained the ability to ingest citrate. Now, one of the defining characteristics of the E. coli family is its inability to use citrate, so the development of such a novel trait was extremely interesting.

Lenski's team then looked back through the 500-generation snapshots of this population and replicated the experiment with progressively older samples. The results showed that the citrate ingesting ability was re-evolved by samples preserved after about generation 20,000 with a high frequency, but that samples preserved before this generation didn't evolve the trait. The conclusion being that the citrate ability is contingent on an earlier, possibly neutral mutation.

The significance of this result may not be immediately obvious. It is really a confirmation of Steven Jay Gould's famous prediction concerning the reproducibility of evolution:

If the tape of life were rewound and played again a quite different set of organisms would probably succeed.

In other words evolution has no goals, no defined end-point. Since mutations are dependent on contingency, the probability of reproducing any particular trait is low.

However, though this is an interesting affirmation of a famous prediction, it may be seen as somewhat obvious. Of far more interest is the fact that Lenski's team observed not one, but two (and possibly more) subsequent ultimately beneficial mutations and the evolution of a complex, novel function. This is, naturally, quite a blow for intelligent design creationism, since this is precisely what they claim cannot happen (or happens with such low probability as to be ignorable). In fact, Michael Behe, the closest thing ID has to a real scientist responded to Lenski's findings with a quite perplexing turnaround. Behe's writes:

I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. "If two mutations have to occur before there is a net beneficial effect -- if an intermediate state is harmful, or less fit than the starting state -- then there is already a big evolutionary problem." (4) And what if more than two are needed? The task quickly gets out of reach of random mutation.

What Behe is saying here amounts to "I predicted that getting two mutations is impossible, and now this paper has shown it happening, it has proved I was right all along". Erm, what?

But this blog isn't really about Behe, it's about conservapedia (the self styled "trustworthy encyclopedia"). Conservadepia, being the religious right's response to wikipedia, naturally has a vested interest in creation "science", so took it upon itself to challenge the filthy liberal Lenski, who had obviously falsified or misinterpreted data in order to shore up the collapsing edifice of materialism.

Andrew Schlafly, a lawyer and conservapedia founder took up the fight, sending a rather terse and unfriendly letter to Lenski. Schlafly's letter is rude, and contains a number of factual inaccuracies, and in it he demands that Lenski send him the experiment's data so that an independent party can verify the findings. Here's a sample, see if you think this is a reasonable tone to take:

Skepticism has been expressed on Conservapedia about your claims, and the significance of your claims, that E. Coli bacteria had an evolutionary beneficial mutation in your study. Specifically, we wonder about the data supporting your claim that one of your colonies of E. Coli developed the ability to absorb citrate, something not found in wild E. Coli, at around 31,500 generations. In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000. ... Please post the data supporting your remarkable claims so that we can review it, and note where in the data you find justification for your conclusions.

Nice eh? Lenski responds, pointing out politely the error in Schlafly's claim of three new proteins, and urging Schlafly to actually read the paper - which already contains all of the data Schlafly requests.

Of course, Schlafly ignores this and once again reiterates his demands for the data (that he already has access to):

Given that this is my second request for the data, a clear answer is requested as to whether you will make the key underlying data available for independent review. Your response, or lack thereof, will be posted due to the public interest in this issue. Thank you.

At this point, even Schlafly's toadies and sycophants are cautioning him that he's acting like a complete tool. Have a read of the discussion page. Schlafly, naturally, responds by banning dissenting users.

Lenski's second reply is a thing of internet smackdown beauty. Have a read. Here's a good bit:

It is my impression that you seem to think we have only paper and electronic records of having seen some unusual E. coli. If we made serious errors or misrepresentations, you would surely like to find them in those records. If we did not, then – as some of your acolytes have suggested – you might assert that our records are themselves untrustworthy because, well, because you said so, I guess. But perhaps because you did not bother even to read our paper, or perhaps because you aren’t very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants.

Brilliant. Lenski goes on to offer to send Schlafly samples of the living bacteria, provided all necessary protocols for exchanging biological material are followed. One suspects that Schlafly will not call his bluff.

You may think that this exchange is trivial, that it is representative of what can be found on most forums on most of the internet these days. That no reasonable minded person would place any credence in the ramblings of an obvious nutcase. But you'd be wrong. A recent Gallup poll of Americans showed that a staggering 60% of republicans and (alarmingly) 38% of democrats subscribe to a young earth creationist viewpoint. If there is any truth to this poll, it suggests that getting on for half of all Americans would side with a lawyer over a biologist in matters of good science, no matter how elegant or enlightening the experiment is, just as long as the lawyer took his cues from a 4000 year old manuscript.

Does this not strike anyone as extremely disturbing?

Sunday 15 June 2008

The triviality of British Politics [Lurks]

I'm struck by a sense of deja-vu concerning the latest wranglings over the 42-day terrorism suspect detention bill. It feels to me like fox hunting all over again. That is to say, it feels to me like a trivial issue picked out of a massive cauldron of simmering issues of the day, purely for it's merits on being able to actualy win on the issue and thereby divert attention from an otherwise beleaguered government.

Hang on a moment, I hear you say, surely Brown can't have picked the 42-day dentention issue as a popularist issue? Actually that's exactly why he did it. See there's not a whole hell of a lot of Brown policies today that the public do feel a great affinity towards, as evidence by his remarkably low poll scores. In fact when polled, the public come up north of 66% approval concerning the 42-day issue.

Browns miscalculation here, and it's a hell of a miscalculation, is that he's picked precisely the sort of issue where actual politicians examining proposals are going to make a heck of a better informed judgement than the public will (who will just hear the question 'are you in favor of locking up terrorists longer?'). Politicians might and have noted that virtually no one is actually asking for 42-days. There's no cases where it was necessary. There isn't a shred of evidence to say it's worth doing at all.

The heart of the bill also rudely points out the odd streak of British politics. Socialist government but with a heavy authoritarian theme up against a conservative oposition with a libertarian theme. The issue is more of a socialist traditional fighting ground so it's hardly surprising that when it comes to the fight suddenly there's a heck of a lot of genuine dissent on the labour back benches. Right at the time when Brown really can't afford more hard questions be asked of his judgement and, yes, his leadership of the party.

Convservatives were all set to benefit from rising popularity, yet another major strategic Brown blunder which was going to undermine the only Brown policy that had popular support. Then David Davis resigned as an MP (and hence his shadow home secretary role - a very senior role indeed it should be noted) and chucked a proverbial sack load of spanners into the works.

Cameron's problem is that he opposes the bill, but wont say up front that they'll reverse it if (let's face it, when) the Conservatives get in power. David Davis is abit of a maverick who really isn't enjoying time under Cameron, not agreeing with the leader on several key points. He's decided to make his personal play here but who knows how he's actually justified it in his head because his friends around him are really none the wiser. What does seem clear is he's not exactly slashing his wrists about the headache this is all proving for Cameron.

The rest of the Conservative party are rightly, very displeased. As one of them, unnamed, in a recent Guardian story sdescribed Davis as being 'out of his fucking mind' for drawing attention to one of Brown's few popular policies.

Course things have taken an unexpected turn with rebel Labour MPs feeling so strongly they've announced they'll campaign for Davis' in he by-election which kind of forces Brown to sack him and potentially escalate the issue further.

With all this cut-and-thrust of political activism and, you might say, genuinely heart-felt cross-party support on issues people obviously feel very strongly about, how can I say it reminds me of something as trivial as fox hunting. The trivality is why although it is more significant in one major way:

If you look at the bill itself, it's been watered down so much with so many safe guards - Eg. prosecution has to present cause to a judge to apply for an extension, it only applies to terrorism cases, the order lapses after a fixed period whether applied or not and hefty compensation for victims etc - that really, it doesn't represent this great evil it's been made out to be. It's just representative of an idea, the authoritarian versus libertarian debate. It looks like it's really not the actual bill but the idea of it, the straw that broke the camel's back. There's an upwelling of feeling that the years of labour have eroded too much.

Which is all very nice and a debate worth having but let's just stand back a bit for a moment shall we? Take a look at what's going on in the world. Rampant oil price rises, Zimbabwe, Iran and of course the horrifying prospect of a genuine recession. Yet what our MPs are arguing about is the theoretical ability to detain suspected terrorists for a couple more weeks without charge.

It's a fucking insult to be honest. If we had an effective political system the cut and thrust of political debate would be on these issues. Not grand standing and party politiking on absolute diversionary nonsense such as this! Yet this is the crap on the front pages of papers. Not fuel running out in petrol stations across the country. Not Zimbabwe (former British colony right) decending into a military junta. Not climate change, the very real prospect of a frighteningly militant Islamist state aquiring nuclear weapons. Fucking 42 days.

Not for the first timeI feel like we need a new political party altogether.

Thursday 12 June 2008

Neglect or Independance [Slim]

A parent has been labelled the worst mother in america by the press for allowing her nine year old to return home alone, via the public transport system from a shopping trip in New York.

A modern day parental dilemma. Give your kids independance and let them get around themselves, and you're a slack parent raising uncontrollable ferral kids. Ferry them about everywhere and keep them in the house all other times and you're a cotten wool wrapping nanny who's stifling their kids independance. How do you win? I'm trying to let me kids have some independance, my 9 and 11 year old walk to and from school themselves, and the older one will go to town on her own or with mates, but it's definately not the easiest thing to do here on the Isle of Man, let alone in a huge place like New York. I think I'm doing the right thing, and I could be doing more. I am accutely aware however that if something happened to my kids on that trip, the finger of community judgement would be pointing directly at me for carelessly letting them out of my sight. Where's the guidebook anyway? What age can you leave a kid home alone? What age can they use the bus system alone? What time should they go to bed? Nobody will tell you, but ever bugger will judge you on it.

Thursday 5 June 2008

The Right To Offend [DrDave]

I've recently been following the case of Mark Steyn, a Canadian conservative journalist and polemicist. Steyn is a well known critic of the "Islamiphication" of the west, having published articles and books on the subject, including the gloriously rabble rousing America Alone. He also appears regularly on Rush Limbaugh's radio show, as well as other conservative outlets in the US. In short, he sounds like the kind of person I'd vehemently disagree with on a number of issue, but, to use the usual paraphrasing of Voltaire, "I may not agree with what he says, but I will defend to the death his right to say it."

Not everyone is as enlightened as Voltaire and me though. In 2007, a group of law students associated with the Canadian Islamic Congress issued a complaint to the Ontario Human Rights Commission accusing Steyn of promoting hatred of Muslims. What in particular has promoted this particular complaint? It seems that the following passage is one of the offending bits of writing:

Signora Fallaci then moves on to the livelier examples of contemporary Islam -- for example, Ayatollah Khomeini's "Blue Book" and its helpful advice on romantic matters: "If a man marries a minor who has reached the age of nine and if during the defloration he immediately breaks the hymen, he cannot enjoy her any longer." I'll say. I know it always ruins my evening.

The offending part being the accurate quote of Khomeini, rather than the tasteless gag at the end. The complaint lists a number of other pieces of writing, including a piece where Steyn quotes a Norwegian Muslim Iman as saying that "Muslims were breeding like Mosquitoes", and a review by Steyn in which he unfavourably reviews a Candadian sitcom "Little Mosque On The Prairie". I'm really not making this up, the meat of the complaint centres around Steyn's quotation of what leading muslims actually said.

Now, you may be sketical. In cases like this, there is normally the hidden detail that the sensationalist news media or blogosphere fail to mention. There must be more substance to the complaint than this, right? Well, apparently not. If you have a spare 20 minutes watch this Canadian broadcast. Initially supposed to be two seperate segments in which Steyn puts his case forward, then his accusers do the same, Steyn instead hijacks it and turns it into a full on debate. It's clear from watching this that the three over-achieving law students plainly have no case, or no case in any sensible system at least. A point highlighted beautifully when one of the complainants makes the ludicrous claim that if she wrote a book quoting Hitler, then white Christians in Canada would be equally offended. Right.

So there you go. In an otherwise progressive and civilised society like Canada, what passes for hate speech is the accurate quotation of one of the most influential figures in one of the world's largest religions. Or failing to enjoy that religion's comedy. Does this not strike anyone as a little bit absurd?

Free speech is a very important right to defend. It ensures that the publication of unusual viewpoints is not met with state-sanction, and allows for criticism of governments and institutions that might otherwise run amok. Similarly, the right for members of groups to not be the victim of organised hatred and oppression is also a value that should be defended. But there needs to be a line drawn between the two rights, and a clear differentiation made between them.

What Steyn has done clearly falls under the protection of free speech, and the correct way to oppose it is to counter it with your own free speech. Attempting to label it as a "hate crime" and to oppress it through the courts is no more acceptable than attempting to suppress the publication of the Danish cartoons by burning down embassies.

Wednesday 4 June 2008

Be Ray Kurzweil: EED-Predict-o-Tron [DrDave]

I frequently see frothy news articles like this one that wax lyrical about how ace life is going to be in the future (presumably when we invent proper VR porn). The one thing these articles all have in common is the wisdom of reknowned futurologist Ray Kurzweil. Now, I'd always assumed that Kurzweil had the best job in the world. Write a couple of books, crop up every now and again and make wildly speculative predictions about times in the future that are so far away that no-one will remember what you said. Sit back, rake in the cash.

But reading through his wikipedia biography reveals that he's actually quite acurate. For instance, his predictions about 2009 (published in 1999) include:
  • Solid state memory taking over from hard drives;
  • Distributed computing becoming prevelant;
  • Cheap laptops for kids.

Of course, he was wrong on some things, but he gets a pretty good hit rate normally.

Now, it seems reasonable to assume that barring a catastrophic BeejTech incident or epic huffquit, this blog will exist in ten years time. So wouldn't it be interesting to see if we can out-Kurzweil Kurzweil and come up with some predictions of our own for the year 2018? Just imagine, we can dig up this blog and gaze at our younger selves' naivity (before returning to our VR environments to have Gail Porter (1997 edition) lick our cyber-balls). To kick us off, here's what Ray himself reckons will come to pass by 2019:
  • A $1,000 personal computer has as much raw power as the human brain.
  • The summed computational powers of all computers is comparable to the total brainpower of the human race.
  • Computers are embedded everywhere in the environment (inside of furniture, jewelry, walls, clothing, etc.).
  • Three-dimensional nanotube lattices are the dominant computing substrate.

Have a think about it, and post three (or more, if you're feeling particularly Nostradamian) predictions for what luxuries we'll enjoy in 2018.