You Talk Way Too Much

"What if everything you knew was a lie?" - well, that would clearly be on a par with the moon landing, the New Deal Jesus, Pearl Harbour, JFK assasination, Obamania, 9/11... and some other ones I can't work out, but don't seem too important. Our Air, Our Water, Our Life... Creation! 25/05/09!!! What on earth could this be?

Prepare to be underwhelmed. It's the unveiling of a fossil. Specifically, it's the unveiling of the first Darwinius masillae fossil, a very well preserved one, named Ida:

Ida is a VIP (very important primate) - and as Ed Yong reports, the media response has been nothing short of rapturous. This revolves around the notion of a "missing link" - even before we knew what the discovery was, John Wilkins on Evolving Thoughts had his doubts about this term - he also worries about announcing the "common ancestor of primates".

We are by now very much aware of the hype our media plasters over news stories. To translate them to large numbers of people in an interesting way, in our contemporary news-as-entertainment culture, they have to be blown up to significant proportions, and made 2-D and digestible in the process. It's difficult to imagine a more inappropriate or common example of this than in scientific discovery, where a public that often lacks the scientific knowledge to comprehend the raw importance of discovery needs it processed. This is the root cause of the foodstuff-causes-cancer news story.

In this week's Bad Science column, Ben Goldacre draws attention, as he does most weeks, to shoddy and hyped reporting of science news, including the current "men experience worse flu" story, which has nothing to do with flu (the pathogen tested causes food poisoning), may not be applicable to humans (tested in transgenic mice), and isn't as globally applicable as advertised. Scientific discovery gets mangled into headlines on a near-daily basis.

And in this case, there are even doubts as to the real meaning of this discovery - this article on Laelaps is fairly technical, but the consensus being reached is that the PR-heavy unveiling of Ida is ugly business. PZ Myers on Pharyngula describes it as Barnum-esque, and even to a total layman the comparison to the earth-shattering dates in the advert above seems totally absurd. For one thing, there is no single link between primates and the rest of the animal kingdom.

Ida is a significant fossil that should have been remembered for its incredible degree of preservation, and the energising effect it could have had on palaentology. Instead it could be remembered as a watershed event in our mangling of scientific coverage. Unfortunately, I fear it will be no more than a really great example - both as a primate fossil, and a hysterical headline.

A Placeholder; An Idea; A Dire Warning

I am very, very busy, being a very busy person.

However, I need to put up a thought while it's here in my head. Recently, friends have raised the idea of teleology in evolution. Traditionally, biologists are very much not fans of teleological notions in evolution, possibly much more wary of it than they should be - I think this is at heart a matter of starting points, of didactic necessity, of the tendency to over-stress differences between new and old schemas of thought in order to press their significance. Sometimes the short-term necessity is to rebuff too strongly, spilling over into the awkward reversal some way down the line, in our constantly-revised science.

I am specifically looking at Simon Conway Morris' speculation that convergence is meaningful, and too much emphasis has been placed on contingency. My major problem with Conway-Morris on this issue is that he is very happy to pick patterns of convergence in evolution, but it is unclear what they mean. For example - squid and humans develop eyes, independently (Praise the Lord! - unfortunately, this is ultimately where SCM's argument ends up). It is unclear to me why this is meaningful, and further, if it is meaningful, does the fact that our eye is wired backwards also become significant? What does it mean where species continue to diversify?

More specifically still; Conway-Morris seems to believe that the existence of human beings is a unique mould that life would inevitably pour into, a gentle restatement of the anthropic principle. I have always found this anthropocentrism to be scarcely above contempt - to postulate that because this universe exists in this way, and not another one, x must be true, seems to me to represent the most profound lack of imagination and wilful disregard for existence in general. To propose a convergent principle of my own: where sentient organisms exist, they will come to the conclusion they are unique and the universe exists in order for them to be just so.

With this in mind, it should be clear that certain tentative trends could be expected in evolution. In exploring the gene-space Dawkins postulates in The Blind Watchmaker (this is essential reading, a powerful visualisation of the step-wise nature by which incredible variation can be reached - and also a demonstration of how deploying simple computer programming can produce valuable models) we might realise we come across stronger forms and weaker forms. Flight, sight, predation on other species and increased decisison making power are good candidates here; major advantages that can be reached. And if they can, presumably they will, eventually. And if they will, one imagines they will establish a niche, all things being equal. But contingency must rule here also - the variety of individual steps that can be made are huge, and yet elephants will not develop wings soon, and bats have little use for eyes.

I find it amusing that the internal evolution of evolutionary theory into a non-directional and thoroughly atheistic area of study is in fact a work of contingency, as is the subsequent backlash. Let us re-wind the tape of scientific discovery, press "play," and see if Dawkins re-emerges. Another little aside to evolutionary history is the similarity of teleological rebranding with that of Stephen Jay Gould and the Punctuational Equilibrists - a re-placing of emphasis on a theory that can already handle the disputes being laid on it, possibly a useful re-balancing of certain skewed views.

Critically, however, Stephen Jay Gould and his cohort were not loading their rejection of gradualism with theology. Conway-Morris considers his convergence to give evidence for the theistic nature of evolution - a belief I've always felt one shouldn't think too hard about, and pressing onto others is fraught with difficulty. Assuming a deity is involved in a process in a manner basically indistinguishable from the naturalistic method itself kicks up endless questions, not least the harped-on-about-yet-very-real problem of suffering.

In this article, Conway-Morris reveals his hand. You'll have to imagine the sneer, and it is admittedly difficult to read:

"But there is more. How to explain mind? Darwin fumbled it. Could he trust his thoughts any more than those of a dog? Or worse, perhaps here was one point (along, as it happens, with the origin of life) that his apparently all-embracing theory ran into the buffers? In some ways the former possibility, the woof-woof hypothesis, is the more entertaining. After all, being a product of evolution gives no warrant at all that what we perceive as rationality, and indeed one that science and mathematics employ with almost dizzying success, has as its basis anything more than sheer whimsy."

There is a reason that scientific discovery heavily stresses experimentation, the referentiality of theory to the world outside it. We take apparent confirmation seriously - although unfortunately we don't have the luxury of a divinely-sustained universe with clearly delineated truths. Removing absolute knowledge of truth from the table is regrettable, but I'd be lying if I said I relied on it much in my day-to-day existence anyway. Relying on God to sustain a universe we increasingly describe in material terms is a folly - there are reasons to consider a deity, but these are not them.

To take issue with one more thing: SCM, having rather inelegantly and confusingly typed his way to conclusions, leaves a real horror for those who venture into the final paragraph:

"Of course our brains are a product of evolution, but does anybody seriously believe consciousness itself is material?"

As I have said in conversation: be very careful, theists. I don't want to watch anyone reaching their hand over the nearest boundary of human knowledge and plucking an argument for god out. It has happened before, again and again, and I don't expect it to ever produce empirical evidence for God - indeed, I think it would be a very cruel God indeed that would wait until we had developed so far, technologically speaking, before revealing himself. It would be some coincidence if the next frontier turned out to be the last one. This is a route religion does not want to go down.

Don't Lose The Faith

Did Darwin Kill God? aired a few weeks ago. Being produced by a member of the theology department here at Nottingham, it caused a buzz among many of my theologian friends! I had a few reactions and ideas at the time, typed a few out, but didn't click the publish button then. Belatedly, and after a re-watch, here are some thoughts, cleaned up and influenced in no small amount by several people I've discussed it with since. It's no longer on the iPlayer, but you can find it easily on Youtube. Apologies, this is gonna be long!

First, a confession: I am no longer watching for the science. Indeed, it’s becoming increasingly hard to remember a point in the BBC’s Darwinian double-anniversary coverage at which I was captivated by the obligatory re-hash of Darwin’s theory of evolution that must precede any discussion. I have a developing awareness that it is not normal behaviour to watch every one of these Darwin docs. It’s not a useful adaptation.

It’s OK this time, however, because we know what we’re really here for: a fight. In Did Darwin Kill God? University of Nottingham theologian Conor Cunningham promises to delve into the question of extremism on either side of the evolutionary ‘debate.’ Thus plugging directly into the reason we love this quarrel anyway – stupid rednecks vs snobby uber-atheists. There’s a voyeurism in observing this conflict. We want harsh words. We want blood.

Unfortunately, this is a BBC documentary through and through. Nothing terribly remarkable about the way it looks, the tone held the right side of respectability, but often flirting with cheesiness. Cunningham cuts a presentable and affable figure, and is lit dramatically while he whispers his way through Genesis. Establishing that Genesis was not taken as a literal account of creation, he travels to Israel and Oxford, tracing the roots of biblical literalism to the reformation, and explains that geology and Christianity were perfectly compatible in Darwin’s time – indeed, many of the top geologists were clergymen. This is all useful stuff. It’s good to put the current spasm of mouth-frothing evangelical protestantism in some sort of context. Heavyweights such as St Augustine are in his corner, after all.

We also have a brief look at the course Darwin’s own faith took following publishing the Origin. This thread of reasoning always bemuses me: the originator of the theory was a Christian, and became an atheist, so is atheism inevitable following understanding of his theory? The question is stupid; the undignified bickering over the beliefs of the late biologist by believers and atheists alike awfully ugly. Alongside whether or not “Hitler believed in evolution,” this is neither of scientific nor philosophical import. At least this segment was brief.

Enough of this moderation. Let’s go to America, where hillbilly music plays as we delve into the Scopes trial and an increasingly fundamentalist reading of the Bible in the 60s. We get to see inside a creationist museum and listen to some daft claims; it’s all rather predictable fare. More interesting is Cunningham’s contention that by treating the Bible as a science textbook, the creationist is effectively worshiping science. The transition to intelligent design raises the question for Cunningham of why an interventionist designer would allow evil to occur in the world. Unfortunately, this seems something of an own goal; it’s certainly not clear that his God allays suffering either. Indeed, one might say that natural selection is as suffering-intensive as creation is likely to get.

Similarly, Cunningham states he sees God operating through evolution, in a way that leaves one wondering: is this divine evolution still automated, unguided, without direction? If God is responsible for mutations that grant us intelligence, sight or even flight, is he also responsible for the mutations that cause Cystic Fibrosis or Tay-Sachs disease? If he was not the active evolutionary force, then what function does he serve in the Creation? Cunningham’s role for God in evolution seems no more robust.

Asserting that the ‘clash’ between Christian belief and evolutionary theory is an artificial one, Conor turns his attention to a different group of fundamentalists. Immediately the use of terms ‘Darwinian’ and ‘ultra-darwinists’ bother me. Generally speaking, these terms flag a less-than-amicable relationship between the speaker and evolutionary theory. They are also meaningless: modern ‘Darwinians’ have a very different view of evolution, one that involves genetics, for one thing. But I suppose, no-one does like labels. They are necessary evils. My main criticism here would be that having used ‘ultradarwinian’ as a slur for the final twenty minutes of his documentary, Cunningham ends imploring us to “let Darwin rest in peace.”

While discussing the atheistic side of evolutionary theory, the central argument is that scientific theory can tell us only about things material, and so cannot disprove God. It’s a pretty elementary point – indeed most atheists accept this but counter that “he who asserts must prove” – but a key one. Michael Ruse puts it best, saying “If one goes into the lab…to do science, one is, as a scientist, not looking for God.” Francis Collins agrees.

Possibly this is a problem with the documentary as a whole. The notion that Darwin could have “killed God” is garbage! Rather, evolutionary theory is key in this battle of beliefs because i) it is the clearest example we can point to where material evidence contradicts the literal word of the Bible and ii) belief in God is functional, regardless of fact, and understanding our origins and place in the universe better diminishes the functional utility of belief.

The descent into meme theory in the final ten minutes is confusing. We are truly through the looking-glass here, and Cunningham seems rather lost himself, telling us that at its heart meme theory tells us “there is no me or you,” and “everything is an illusion.” This is somewhat misleading. Unfortunately meme theory is at its heart no more than a philosophical analogy that shows how ideas could be spread like genes. It certainly lacks the power to bring down religion – it should be obvious that describing an idea, for instance that of a crucified and resurrected deity, as a ‘meme’ does not alter the actuality. If it took place, then it took place, meme or otherwise. For the same reasons, Cunningham’s supposedly damning attack on meme theory – that it is tautological – ultimately falls flat.

‘Memetics’ merely describes the way the idea or belief has spread, although its proponents have been guilty of doing so with some fairly emotive language, it’s true. Maybe this grants meme theory too much credibility anyway. It’s not a truly scientific concept. But it is amusing to imagine that Conor is actually so aghast at Rickrolling, or the notion that LOLcats have ended belief.

From the start cards were laid on the table. Conor Cunningham is a Christian and an evolutionist, and through to this last section we have little reason to doubt it. But as we get in to the realms of more modern theory, a flicker of doubt takes life in my mind. Little instances of innuendo creep in, such as when Francis Collins vaguely denies that evolution is “all about genes”. There is an underlying hostility towards the “selfish gene theory” that is not at its heart scientific. (Here, the rather clunky faux-dialogue interview style employed throughout does really grate. When a point is made that feeds into Cunningham’s argument, the camera cuts to him so he can smile and nod encouragingly. It comes across a trifle smug.)

It’s natural for a theist to be hostile to the idea that we are nothing but the sum of our selfish genes. The implications for our moral grounding seem dire – although we do exhibit many separations from our natural origins, after all. Our understanding of genes should broaden in years to come, but this ‘selfish model’ is still the closest approximation we currently have. What rankles is that Cunningham’s criticisms are not scientific in nature – they pounce on perceived “dissent in the scientific community” and take this as their evidence.

Oh well. It is perfectly natural to pick and choose which bits you want to believe, when there’s no practical reason to get it 100% right. And there really isn’t, in this case.

The worst horrors should always be saved for the final reel. So it was for an atheist and scientist who so far can agree, if grudgingly and with however much nitpicking, with some of our conclusions so far: Science and Religion are two different things. Christians are not normally quite so belligerent, only Americans. Darwin cannot disprove God. Meme theory certainly does not disprove God.

Enter Simon Conway Morris, who also sees evolutionary theory as incomplete, much to Conor’s glee. But more importantly, he considers evolution might be the method nature uses to reach underlying, (dare we say divine) conclusions. This mysticism seems a pretty unforgiveable attempt to shoehorn God into evolution, and it violates Cunningham’s own scheme of separate science and faith. Our truce is broken. It’s a shame.

It’s a shame because there was some good stuff in this documentary. A condemnation of extremism (which is ludicrous on both sides), and a reminder that Christianity isn’t all about what happens in Colorado Springs. A few examples of theists who can get behind evolution. And an attempt at reconciliation. I fear I have dwelt overlong on the contentious aspects. But the key is this: evolutionary science is incomplete, and we must test it and understand it. It will take us wherever it will. And one gets the feeling that just as Conor Cunningham has an idea of the kind of God he can believe in, so too can he deal with evolutionary theory – on his own terms.

There, maybe that will be it for Darwin for the time being. I only just bought a copy of The Origin of Species, actually, so probably not (You may be surprised to hear that it's far from essential reading for the modern science student. Maybe you shouldn't be). Apologies to anyone's ideas I have pinched, most of these thoughts were my own, as far as I can tell. Maybe they were no more than memes. If you missed it on TV and iPlayer, Youtube has your back.

Scientist Studies

Wow, this is really huge. John S. Wilkins at Evolving Thoughts reports on a paper that would rewrite the rulebook on evolutionary theory. It's not often, or ever, that you get to read about a change in a field so cataclysmic that it completely changes the outlook on a whole field, certainly not one so important or controversial as evolutionary theory.

If true, the theory of Empedoclean Evolution would totally discredit natural selection, in this Darwin anniversary year of all times. Professor Augustus P. Rillful's paper concerning the importance of horizontal transfer of genes (for example by viral and bacterial mechanisms) foreshadows a comprehensive understanding of all sides of speciation.

Looks like a Nobel-prizewinner, doesn't he?

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Meanwhile, a couple of other interesting links I found in my morning perusal:

A really fascinating post at Genetic Future about the marketing strategy personal genomics company 23andMe are using. I've always really liked that name, incidentally. Their plan is to form a community of users based around their "mommy bloggers" who'll chat about pregnancy and kids. Daniel McArthur suggests mothers-to-be might graduate from comparing weight gains to genotypes, splashing out on DNA testing kits for their loved ones to determine how their offspring might turn out. It really could be a fantastic marketing masterstroke, making this information seem relevant to a big-spending demographic.

It hasn't gone down well with Steve Murphy "The Gene Sherpa," who highlights the effect it could have on the clinical load. Imagine having to somehow convince a pregnant mother that their child will turn out perfectly normal despite that elevated heart disease risk factor.

It occured to me lately quite how fortunate I am. There are a few science columns I read by guys in their 50s that mention that they'll wait a couple more years for the price to drop on personal genome sequencing, and then they're doing it. That is, getting hold of the sequence for a fraction of their genome, the size and price of which is dependent on the package and company they go for. 23andMe's service tests for a number of significant (disease-indicating) variations at 600,000 positions, at the fairly affordable price of $399. A couple of other operators are in the $1,000-2,500 range, testing roughly a million polymorphisms. Each service is aimed at providing estimates of their customer's 'genetic risk.'

Meanwhile, Knome (another really great name, and tagline!) offer a complete personal genome sequence and analysis, for a somewhat-heftier price. This year-old article suggests a figure of $350,000 (wikipedia haggles down to $99,500) , which would include ongoing support by a team of geneticists and bioinformaticians, apparently (career bells start ringing...). And would you believe it, they output on a sparkly new USB key!

But it won't be in the hundreds of thousands forever. Certainly in 20 years we should anticipate it will be affordable for us regulars - indeed this wide availability is a crucial point of all the genetic dystopias we've been busily envisaging since Human Genome Project results started coming through in 2000. Of course, we all expect health insurance premiums to be calculated on the basis of our genetic disease risk. A short step indeed to Gattaca.

I fully anticipate that within my lifetime I'll be able to have a browse through the complete sequence of As, Cs, Ts and Gs that determine so much about me, without breaking the bank. I only hope I'll be savvy enough to understand what some of it means. It's magical really, and represents an comprehension of human biology standing on the brink of the unimaginable. Beyond it lies real sci-fi territory.

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Are viruses alive? Yes or No? This question is a controversial one at ERV, where there's frustration at a recent review in Nature Reviews: Microbiology (Bear in mind that with an impact factor of ~15, that's a pretty hefty journal to go spitting on virologists in). The notion of excluding viruses from the "Tree of Life" seems a peculiar one to me: they have played such a huge part in the development of life, and continue to have a huge role in living systems, it really doesn't make sense on a practical level. Ultimately the use of having such a tree is to understand the relationships within it between living things, and the history of their development, and given that viruses have such relationships, they should really be in. That would, at least, be my view from a practical standpoint.

There's an interesting question here anyway, about our definition, ever hazy, of life. It can't rest on autonomy, as last time I checked humans, among other species, wouldn't do terribly well left on our own. Nor can we disqualify viruses simply because it's hard to trace their lineages, as unsatisfying as it may be if we are unable to reach the root of the tree. As we scrabble around trying to find the boundary between living and non-living we naturally enter into questions of abiogenesis. It's a pretty fascinating area to think about, and ill-served by artificially imposing living/dead boundaries.

How to be Perfect Men

Yet another piece of the BBC's ongoing double celebration of Charles Darwin (200 years since his birth, 150 years since The Origin of the Species - do keep up), I found part 2 of Andrew Marr's "Darwin's Dangerous Idea" to be a decent hour's diversion. Telling the story of natural selection's place within political thought in the past 150 years, Marr rattles through the development of the depiction of natural selection as "Survival of the fittest," and the development from there of 'social darwinism.' Tracing this fibre leads us to some dark places: first to some 'harmless' eugenics, then the extremely harmful variety, from which we emerge to view a 'rehabilitation' of the theory in the service of equality and universal human rights. In polished, professional OU style Marr gives us a glimpse of the ever-shifting future before saying his adieus.
Marr is on good form, actually. He's a very likeable presenter, suitably wry for dealing with the charming Olde Worlde racism of the 19th Century gentlemen we encounter, but with the necessary solemnity for the more weighty and grave matters. And he does a pretty decent job with the science! There were a couple of mis-cues that niggled, but nothing terribly important. Towards the end he gets a bit eager over some recent research and starts talking about "joining his black brothers," but there's a scientist on hand to calm him down, thankfully. It's all rather endearing.

Well, maybe one thing. This Darwin season has been a bit of a mixed blessing. Fantastic that it gets people talking about important science, certainly. However, I have misgivings - increasingly one wonders if viewers grasp the separation between the Theory of Evolution by Natural Selection, and its originator, or its applications. These are separate things, and for the same reason I dislike terms such as "Darwinism," because we don't understand evolution as Darwin did. Indeed, we should to hone our understanding, not immortalise it.

After all, if Evolutionary theory best describes how the diversity of life on the planet came about, then its implications, applications or fanbase is irrelevant. Not that this will sink in with the sort of people who'll cheerfully tell you Hitler's acceptance of evolution is a dent to its credibility. Hardly a battle worth fighting.

Marr's story takes us from the entry of Darwin's theory into public understanding and explains its mutation by liberal thinkers into a eugenics movement. Improving the underclasses for work or war piqued many interests at the time, as did ridding the wealthy nations of the "feeble-minded" once and for all. This is an interesting segment. Bluff casual-racists take it in turns to say hopelessly un-PC things that a modern audience can chuckle at. We end up wondering about comparitive, situational morality, whether simply not-being-a-racist was truly saintly behaviour for the 19th century.

But of course these ideas are not as innocuous as they first seem. With a new age of understanding beckoning in genetics, the heinous acts when these ideas were last in vogue are an important reminder of why we do view eugenics as being as sinister as it is outdated. The Holocaust throws a large shadow over proceedings, as it must. As a culmination of 'bad Darwinism,' the most evil occurence in human history came about. Shortly afterwards, the UN considers common human descent a key part of the puzzle where human equality is concerned.

And like that, we're into the present, seeing how a gene database and genetic counselling service has allowed the near-elimination of Tay-Sachs disease in New York. This case is interesting, although it has much more to do with Mendelian genetics or Watson-Crick DNA modelling than it does Darwin! Still, as an illustration of the "personal genetic decisions of the future" it's a good point. The combination of modern technological advancement with a more traditional pro-life mindset is an interesting one, and the self-denial involved, in an age where we are meant to be able to have children as we like with whoever we like, is remarkable.

Finally, a consideration for the post-genomic age which will be upon us sooner than we think. Marr picks up on a "new intelligence gene variant" which has been proposed and may be more prevalent in Europeans than those of African descent. That's a maybe, controversial and recent. But with sequencing and bioinformatics getting cheaper and quicker, accurate and studies into the genetic basis of intelligence are virtually inevitable. The underlying fact is that we cannot naively wait for the new genetic technologies to creep into our lives. DNA analysis will have wide-ranging effects from job recruitment to health insurance. Coupled with IVF technology, gene manipulation can go further still, going beyond the boundaries of disease into realms that earlier eugenics proponents never dreamed of. Before too long we could find ourselves attempting to define 'feeble-mindedness' again, and our society needs to be robust enough to withstand that in advance.

Ultimately, we are still putting words in Darwin's mouth. Nice words, true, but just as the Nazis spun evolutionary theory into something terrible, we're taking the truth and reading it how it suits us. Which is a shame, really. If the history of science can teach us anything, it's that truths can be discovered, but that values must be hard-won.

The 3 episodes of Darwin's Dangerous Idea are available on BBC iPlayer here for a very short while, I'd recommend episode 2 mostly, but it's all good stuff.

When We Were Younger & Better

Having just finished and mostly enjoyed Blood Meridian by Cormac McCarthy, which I'd agree is a masterpiece but certainly a rather dense one, I embarked this morning upon The Blind Watchmaker by Richard Dawkins.

This is Dawkins c. 1986, a book as old as I am, and it's difficult to forget that he has yet to become a cause célèbre or go on the offensive. It predates The God Delusion by twenty years. That it was a different world is made evident by this sentence, on the first page of the preface:

"The computer on which I write these words has an information storage capacity of about 64 kilobytes"

I'm still only a couple of chapters in, but my first impression is that this version of Dawkins is much more constructive. I'm coming to think that he is foremost an evolutionist, and would not be at all interested in his present christian-baiting had they not 'started it.'

Here he is positive and wastes no time in celebrating the natural world. He goes so far as almost to praise William Paley, theologian and originator of the "watchmaker analogy," concluding that Paley has reached the wrong conclusion but understandably so, and in praising the diversity and apparent design of nature they are almost united!

It would be interesting to see how he felt about Paley now.

His extraordinary ability to introduce and explain scientific principles with the written word is astounding to me, and something nearly any science writer could learn a lot from. Even though I am well acquainted with the subject, I'm very much looking forward to my reading time in the coming week.