On reading "Signature in the Cell"

I was recently prompted to read outside of my methodological naturalist’s bubble and delve into Stephen C Meyer’s argument for intelligent design “Signature in the Cell: DNA and the evidence for Intelligent Design” . As a general principle if you want to argue against the misconceptions people hold it is not always enough to have mere facts at your disposal, it helps also to mine the source of their misunderstanding and the plausible quasi-scientific arguments of the likes of Meyer and Michael Behe are fundamental to those who would argue against naturalist theories of the origin of life.

The first thing to say about Meyer is that he is an extremely well qualified philosopher of science and there is very little in Signature in the Cell insofar as it relates to the actual molecular biology of DNA and its role in protein synthesis that I would argue with. In fact the opening chapters would make quite a good undergraduate primer on the subject. He correctly points out that a modern living cell is an incredibly complex machine of interrelated systems capable of transcribing information from the genetic code held in DNA and translating it into large functionally specific molecules such as proteins. He also, and equally correctly, observes that many of these proteins are necessary for the very processes of translation and transcription that the cell relies on to create them, in particular Ribosomes , the RNA / Protein complex that “stitches” amino acids together to make other proteins.
This interrelatedness and complexity forms one plank of his assertion that naturalistic processes cannot be responsible for the origin of life since even a minimally functional cell could not arise without a DNA code and the code could not be translated without specific decoding machinery. Then for further support he argues that there is no known mechanism by which a specific and information rich system can arise by chance alone. All such other know systems; computer code, written language etcetera have an intelligent source: us.

From these he builds a long and rather repetitive argument using abductive reasoning to draw an inference to the best explanation for the origin of life and specifically the information carried by DNA. He cites a number of statistical reasons why chemical theories of the origin of life are impossible, why chance cannot produce specified information and debunks the RNA world hypothesis as a precursor to a full blown DNA code. By systematically eliminating all possible natural explanations for life he seeks to establish that intelligent design is the only possible alternative. However, many of the assumptions he makes to suggest that a naturalistic origin of life is impossible are in my view flawed.

For example there is no necessity for a “minimally functional cell” to arise in one fell swoop and there is no necessity either for replication and metabolism to arise simultaneously or in the same place. There are credible metabolism first scenarios in which thermodynamically favourable conditions can allow spontaneous simple metabolic cycles to emerge. It has been postulated that alkaline hydrothermal vents would have been one such favourable environment. Meyer also insists there are no fundamental forces of nature driving systems to self-organise and increase in complexity but in the last couple of years Jeremy England at MIT has developed a thermodynamic theory that suggests entropy actually favours organised and replicating structures as they are more efficient at energy dispersal. Combinations of replicators and metabolisers allows for the possibility of some kind of biological bootstrapping.

Meyer makes something of a schoolboy error when he argues that the active sites that confer the catalytic specificity to enzymes are so specific that a single amino acid out of place would render them useless. This is something like the classic anti evolution argument of “what use is half an eye?” The answer of course is more use than none as long as it performs the function to some extent. This is true of enzymes as long as they are more efficient at facilitating a particular chemical reaction than would be the case if they were absent, then natural selection will do the rest. In fact it is not even correct to say that enzymes are so constrained. In his book “The arrival of the Fittest” evolutionary biologist Andreas Wagner concludes that no enzyme is really that special, in fact there are usually an astronomical number of alternatives that work and, interestingly, functional intermediates that allow for enzymes to mutate. He also demonstrates similar functional redundancies in the genetic code itself which added together make the probability of specific information bearing molecules arising randomly much greater than Meyer would have us believe.

It gets worse for Meyer when you consider that as things stand we only have one working model for how life is organised, life on earth. For all we know there could be many ways, with alternative molecules and alternative codes for complex evolving systems to arise. Like a Texas sharpshooter he has drawn a bulls eye around one object out of many and made a miracle out of the fact he’s hit it. Should we ever discover extra-terrestrial life with the same familiar genetic code that would be a real argument against random processes and would bolster the case for intelligent intervention but personally I would bet against it.

A parable that Meyer returns to several times goes like this…

"Imagine a team of researchers who set out to explore a string of remote islands near Antarctica. After many days at sea, they arrive on an icy, windswept shore. Shouldering their packs, the team hikes inland and eventually takes shelter from the bitter cold in a cave. There, by the light of a small campfire built to cook their freeze-dried rations, they notice a curious series of wedgelike markings vaguely reminiscent of Sumerian cuneiform. It occurs to them that perhaps these scratches in the rock constitute some sort of written language, but dating techniques reveal that the markings are more than five hundred thousand years old…"

He concludes that in this situation once all of the other possible natural causes for the information rich markings are exhausted the researchers would reasonably conclude that an intelligent agent was responsible even though the marks predate writing by many millennia. He then equates this with the information rich genetic code and having (he believes) eliminated natural explanations arrives at the same conclusion. But, these two situations are not equivalent. For one thing markings in a cave would show evidence of tool use. The form and disposition of the rock would indicate whether it had been chiselled with bone, stone or metal implements for example and the marks would have had a predetermined meaning. DNA however is both the medium and the message; there are no fingerprints on it to suggest what mechanism was employed by an intelligent designer to forge a molecule that is self-replicating, prone to mutations and contains multiple redundancies in translation. It’s as if the researchers came across rock markings with no evidence of how they were made, which highlights one of the philosophical problems with the whole book. Meyers argument to a best explanation is really no explanation at all. There is no attempt to explain how the designer achieved this feat of molecular engineering, nor why it bothered. Meyer is of course a Christian so for him the answers would be theological, although he is at pains to tell us that intelligent design says nothing about the nature of the designer only that there must be one.

If, as many religiously motivated people are, you were predisposed to distrust naturalistic explanations for the origins of life this book would be convincing. It’s plausible, so if you were not scientifically literate or up to speed with the latest research into biological origins it could easily confirm your preconceptions. But approached sceptically there are many holes and logical non-sequiturs hiding in the narrative particularly in the latter sections where Meyer attempts to defend intelligent design as proper science. But it’s not enough to posit a cause that itself has no explanation. It’s a philosophical dead end unless you can define who or what the intelligent designer was or at least identify a line of enquiry that may expose it. Meyer denies it at length but it’s hard to distinguish “signature in the cell from any other god of the gaps argument.

John Gray strawmans new atheism...again.

Philosopher and polemicist John Gray has a lengthy piece in the Guardian titled “What Scares The New Atheists” which in his usual straw manning style attempts to argue against his own cartoonish concept of secular humanism.

"The belief that the human species is a moral agent struggling to realise its inherent possibilities – the narrative of redemption that sustains secular humanists everywhere – is a hollowed-out version of a theistic myth. The idea that the human species is striving to achieve any purpose or goal – a universal state of freedom or justice, say – presupposes a pre-Darwinian, teleological way of thinking that has no place in science."

I am certain that Dawkins, arch new atheist and author of the selfish gene, is under no such illusion and neither am I. Humans are moral agents in the sense that we make judgments about good and evil, right and wrong, but we are not striving towards a pre-conceived or pre-ordained evolutionary goal. What humanists do say, in contrast with the monotheisms, is that humanity is not fallen and in need of salvation but rather as an evolved pro-social species we have the resources and disposition to collectively improve our own wellbeing.

Gray, like many New Atheist bashers, also misses the point about our beef with religion.

"Though not all human beings may attach great importance to them, every society contains practices that are recognisably religious. Why should religion be universal in this way? For atheist missionaries this is a decidedly awkward question. Invariably they claim to be followers of Darwin. Yet they never ask what evolutionary function this species-wide phenomenon serves. There is an irresolvable contradiction between viewing religion naturalistically – as a human adaptation to living in the world – and condemning it as a tissue of error and illusion. What if the upshot of scientific inquiry is that a need for illusion is built into in the human mind? If religions are natural for humans and give value to their lives, why spend your life trying to persuade others to give them up?"

Apart from the fact that both Daniel Dennett and Richard Dawkins have speculated endlessly about the evolutionary utility of religion and both concede it may have or have had survival value the target for criticism is rarely private faith. New Atheism was spawned for Sam Harris by 9/11 and for Dawkins by the rise of creationism in the U.S and it is the indulgence of religious thinking in the public and political sphere that is the objection. It is true that arguing for secularism and a scientifically informed public policy comes with collateral damage to the privately religious if they cannot live with the resulting cognitive dissonance but this is surely not a new experience for them and the determinedly faithful will continue to be faithful whatever.

A slightly more interesting observation that Gray makes is about the assumption of an inevitable triumph of liberalism

"The conviction that tyranny and persecution are aberrations in human affairs is at the heart of the liberal philosophy that prevails today. But this conviction is supported by faith more than evidence. Throughout history there have been large numbers who have been happy to relinquish their freedom as long as those they hate – gay people, Jews, immigrants and other minorities, for example – are deprived of freedom as well. Many have been ready to support tyranny and oppression. Billions of human beings have been hostile to liberal values, and there is no reason for thinking matters will be any different in future."

Here at least he is not wrong in his characterisation of humanist thought as most of us do believe that liberal values should prevail which is why we agitate for evidence based thinking and maintain that religious intolerance is irrational. Humanist’s belief that liberal values are worth promoting and arguing for is as integral to our philosophy as homophobia is to a Westboro Baptist and far from thinking success is inevitable we are more than aware of the conflict we face. Stephen Pinker gives some cause for optimism in his well-researched and quantified book The Better Angels of Our Nature in which he charts quite convincingly a general declining trend in conflict and intolerance over millennia of history but even he doesn’t make a teleological case for this continuing without concerted effort.
In fact Gray unintentionally makes the point himself.

"This is, in fact, the quintessential illusion of the ruling liberalism: the belief that all human beings are born freedom-loving and peaceful and become anything else only as a result of oppressive conditioning. But there is no hidden liberal struggling to escape from within the killers of the Islamic State and Boko Haram, any more than there was in the torturers who served the Pol Pot regime. To be sure, these are extreme cases. But in the larger sweep of history, faith-based violence and persecution, secular and religious, are hardly uncommon – and they have been widely supported. It is peaceful coexistence and the practice of toleration that are exceptional."

Ignoring the first sentence where once again he is attacking a construct of his own imagination the fact that totalitarian ideologies emerge both politically and religiously to supress liberalism is what the culture wars are all about. Of course some people will always think they know better how others should live their lives and nobody thinks they know this better than the religious.
The claim is also made that despite the efforts of secularists religiosity is, in many places, on the rise but I suspect this is cause and effect. As secularism, particularly in the west, has become accepted by liberal religion the faithful at the extremes have become marginalised and much of what we are seeing is a backlash. The fundamentalists are more vocal, more visible and sometimes more violent than previously because their worldview is no longer passively accepted even by the moderates of their own faith. Whether this is a tide that can be turned is debateable but for those of us who do not want to live in theocracies it is worth the attempt.
Yes, humanism has its origins in theism, or at any rate in post enlightenment deism, but that is not where it lives today. Humanism, which incidentally is not as synonymous with the new atheists as Gray would have it, is a secular scientifically literate philosophy with ethical principles founded in a deeply pragmatic utilitarianism. It is no longer concerned with human exceptionalism - we know our evolutionary place better than most – and in fact humanism actively fights attempts by the church to reclaim the term “Christian humanism” since it is contrary to the modern movement entirely. It is entirely possible I suppose that some future scientific discovery could make racism, anti-Semitism, homophobia and misogyny intellectually justifiable, but frankly I doubt it. Science has no moral arc but facts, at least when viewed through the lens of utilitarianism, do have a liberal bias.

So to Gray’s parting shot

"More than anything else, our unbelievers seek relief from the panic that grips them when they realise their values are rejected by much of humankind. What today’s freethinkers want is freedom from doubt, and the prevailing version of atheism is well suited to give it to them."

One can only assume that he is unaware of the dangers that humanists, secularists and liberals are subjecting themselves to in theocracies around the world. They are being assassinated or arrested, flogged and executed merely for promoting the idea that all people should be treated equally against the prevailing religious dogmas. Even if we would like to think that a liberal view of moral progress is inevitable we know it isn’t. But it’s a rational goal for those who, like Gray himself, understand that “Considering the alternatives that are on offer, liberal societies are well worth defending” and surely, if they’re worth defending they are worth expanding.

"Three Parent" IVF is not a moral issue

A recent vote in the house of commons means that Britain is one of the first countries in the world to legalise an IVF procedure that involves taking the nucleus of one egg and inserting it into the cytoplasm of another egg which has had its own nucleus removed while , crucially, retaining its mitochondria.

a mitochondrion

Mitochondria are organelles whose primary function is to supply energy to the cell and during reproduction they are passed down in the cytoplasm of the egg which means they always travel down the maternal line. Defects in the mitochondria can cause debilitating diseases and infant mortality and it is these conditions that the technique is designed to prevent by substituting healthy mitochondria prior to fertilisation. This will of course be a boon to couples at risk of passing on mitochondrial diseases to their offspring as it enables them to have a healthy child with nuclear DNA from both natural parents; up until now it has only been possible for such couples to conceive with a complete donor egg or a surrogate.
Offspring born of this technique are referred to as “three parent babies” which I think is unfortunate because for one thing it’s not strictly true from a genetic standpoint and for another I suspect it has contributed to some of the unnecessary moral panic that surrounds it.
Much of the objection to legalising this form of IVF has come (predictably) from the Church with both Catholics and Anglicans claiming scientific uncertainty as their rational but in fact the technique has been well tested and the people who actually understand the science are satisfied of its safety, with the usual caveats. Given the Vatican’s antipathy to any artificial fertilisation techniques I suspect their objections are entirely ideological and can therefore be ignored. For example Bishop John Keenan, the Bishop of Paisley, was among the Catholic leaders who condemned the technique claiming it “seeks to remove anyone affected by certain conditions from the human gene pool”. Of course what it actually does is remove the condition from the gene pool, the “anyone” in the above nonsense never existed except in the abstract.
Other objections seem more reasonable, for example the concern that the mitochondria continue into subsequent generations, but are grounded in a misunderstanding of mitochondria and their origins as the “powerhouse of the cell”. The “three parent” moniker is inappropriate because although the mitochondria contain DNA it is their DNA and does not contribute to human characteristics outside of the somatic effect of its function. The entire nuclear DNA in this technique, the stuff that can be considered to count, is derived from the natural parents and not from the donor of the egg. Ethically this is more akin to a transplant than genetic engineering.
Another point that has been missing from the public debate is that mitochondrial DNA is not really ‘human’ at all because these organelles are endosymbionts, remnants of previously free-living proteobacteria that either infected or were absorbed by other primitive cells over 1.5 Billion years ago. Over evolutionary time the mitochondria lost the genes necessary for autonomy and retained just enough for their own reproduction and metabolic function within their hosts. The gestalt of these two primitive cells formed the first truly eukaryotic cells that are the basis of all complex life.
I’m not convinced that any ethical Rubicon has been crossed by approving this technique. In fact, even if at some future date it is discovered that by some genetic tinkering in the nuclei of eggs destined for IVF we could eliminate cystic fibrosis or some other debilitating genetic condition we should do it. I do not subscribe to the sort of genetic essentialism that some, including rather bizarrely the church, seem to indulge in and although I’m prepared to accept that somewhere amongst all possible applications of human genetic engineering there will be some ethical red lines we’re nowhere close when it is used solely for the elimination of heritable diseases.

On "The Experience of God" by David Bentley Hart: Part 3 of 3

David Bentley Hart

Prompted by Jerry Coyne’s critiques of David Bentley Hart’s latest book The Experience of God: Being, Consciousness, Bliss I have bought my own copy as it is apparently the latest sophisticated argument for God that atheists now have to refute in order to qualify for the right to an opinion on the subject and so I have decided to post my own thoughts on this latest ‘best argument for God’.
As Hart’s sub-title implies the book is split into three divisions; Being (the existential question, essentially the cosmological argument), consciousness (or why the “hard problem” of consciousness points to God) and Bliss (The experiential evidence). I intend this to be a series of three posts addressing each in turn so today’s is Bliss.

BLISS
Given his teleological and platonic presumptions the first two sections Being and Consciousness make interesting if unremarkable arguments for the existence of an ultimate causational ground of something or other that Hart likes to call God. However in Bliss he provides little argument (beyond reiteration) and less evidence for a series of assertions concerning our human experiences of desire for love, morality, status and altruism et al which must, he insists, really be nothing but stops on the way to bliss; a union with the divine.
How, he wonders, can we strive to be moral if there is not some extant perfect morality or feel the urge to pursue happiness if that abstract concept is not in some sense all pervasive? He speaks as though he has already established the case but whereas the universe and, arguably, consciousness are things seeking explanation internal emotions really aren’t. They are already contingent upon physical reality, somatic organic states and consciousness (magical or otherwise) and it makes no sense to insist that they must be representative of “pure” emotions.
Hart pre-empts the obvious evolutionary rebuttal in the most bizarre way by embarking on a tirade against Richard Dawkins’ seminal concept of The Selfish Gene which having ridiculed as a terrible metaphor he then goes on to dispute by treating it as though biologists really believe genes are intentional “imps” with Machiavellian designs on our bodies and minds. In fact Hart’s entire world view seems to make him incapable of understanding the fundamental point about evolution which is that it is an entirely contingent process, unintended and undirected. He claims to get that the idea of “genes for” a particular trait is a naïve simplification of how things work yet attacks gene centric explanations for the evolutionary utility of emotion entirely on that basis and he certainly does not realise that epigenetic phenomena where the organism apparently effects the genes are themselves evolved mechanisms to cope with short term environmental changes.
Biology is a messy business and natural selection may act reflexively and on different levels from DNA through individuals and maybe even populations although as I have said before my intuition is that at bottom the gene (broadly defined) is the ultimate agent of evolutionary change. But Hart wants to turn the narrative on its head and insist that, for example, a mother’s love preserves the genes through her child, rather than genes survive which promote the emotions conducive to nurturing a child. While the observable effect would be indistinguishable either way Hart’s version is un-falsifiable and has none of the explanatory power of Darwinian selection (Ironically in consciousness Hart scorned the concept of memes as units of ideas that preferentially spread through cultures but in bliss partly exculpates Dawkins for the success of the selfish gene metaphor because it has spread organically through media to become a cultural trope. So how does he think that happened exactly? Well, he doesn’t say but I think he’d be hard pushed to supply a non-Darwinian explanation).
This section of the book contains the most word salad by far, in fact in places it’s so unintelligible the circularity of his thinking is sometimes difficult to pick out. Or perhaps that’s the point. For example he insists in various tortured ways that our quest for beauty, love and conscience is in reality our yearning for God because God is good and the good is God (so even if you’re an atheist desiring to do good you are also tacitly accepting Gods existence; handy that…) and waves away the Euthyphro dilemma as irrelevant because God’s goodness is sufficient unto itself. Hart is defining God in his own self-referential terms just like every other theist who needs their god to conform to their own concept.
It is interesting to note that although Hart constantly reminds us that God is everything, is the cause of everything, sustains everything, contains and is contained by everything as the ground of all being, consciousness and bliss his God is always referred to as “he”. For some reason this all-consuming deity (which should definitely not be anthropomorphised in any way, dearie me no!) is resolutely male even before we ascribe other characteristics such as goodness etcetera. Why, for example, shouldn’t such a deity be perfectly evil, hateful or vain or perfectly any other thing that human beings are capable of pursuing when not seeking love or the good?
All told, it’s not that this book is a poor argument for God, more that it’s an argument for a rather poor God and definitely not for the God of most believers. If Hart really accepted only this amorphous definition of God he would be almost as much an atheist as I am. As it is I started his book agnostic about such a ground of being and finished it with the same attitude. Yes, it is logically possible for Hart’s God to exist, but except from a purely metaphysical point of view it is hard to care one way or the other. I am an atheist because I don’t believe in (amongst others) Hart’s other God; the one he is not attempting to defend but the one of his professed Eastern Orthodox faith that made man “in his own image” ,incarnated in the person of Christ, and was crucified. The Eastern Orthodox God that has attitudes and preferences and speaks ambiguously through the bible of dietary laws and sexual taboos. Hart may want to avoid drawing a face on the apophatic God of Being, Consciousness and Bliss but by doing so he is arguing for no kind of God at all.

Footnote: You may have found these three posts a little tedious to read so by way of an antidote I offer this video via the much wittier and entertaining NonStampCollector.

The birds are singing to Yahweh according to Rabbi Sacks.

Oh Dear! Rabbi Lord Jonathan Sacks has fallen into the “Darwin was wrong about some things” trap to deliver a puerile homily about taking ...

...Darwinian selection to be more than a law about biology, and turn it into a metaphor for life itself, as if all that matters is conflict and the struggle to survive, so that love and beauty and even birdsong are robbed of their innocence and reduced to genetic instincts and drives.

Yes, once again Radio 4’s Thought for the Day has come up trumps as an inspiration for a blog post and for me this one touched all the bases; Darwin, evolution, covert creationism and intellectual dishonesty all in one three minute segment. So where to begin?
Well, Lord Sacks has decided that the account of a revised understanding of the sexual mores of birds in a new book The Wisdom of Birds by ornithologist Tim Birkhead is sufficient to impugn the scientific understanding of evolution because it now transpires that Darwin’s assertion that female birds are faithful and monogamous and the promiscuous males sing to attract mates has proved to be less than universally true. It is now recognised that female birds are also opportunistic in their mating strategies and that some species have females that are as vocal as the males as evidenced by genetic studies of wild populations and observation by ornithologists.
The first thing to say about this is that Darwin was wrong about the specifics of many things, most importantly from an evolutionary point of view he completely misunderstood the true nature of inheritance, ignorant as he was of even the Mendelian laws of inheritance being developed around the same time. This is both understandable and widely recognised by biologists who do not see this as a reason to reject what is arguably the most powerful explanatory scientific theory of the millennium. Given that context, minor observational errors on sexual selection in birds should not be a big issue. Although in fact Tim Birkhead says this of Darwin who, as a pigeon fancier, would most likely have been aware of the truth of the matter.

He was probably playing it safe. In Victorian England it simply wasn’t appropriate for a well-respected gentleman scientist to draw attention to the existence of female promiscuity, let alone to justify it in biological terms.

Be that as it may avian female promiscuity and vocalisation does not lead to the conclusions that Lord Sacks would like to infer with this:

A century and a half ago Darwin argued that birdsong was all about sexual selection. It was males who did the singing, hoping to make female birds swoon at hearing the ornithological equivalent of Justin Bieber, giving the most tuneful males a better chance of handing on their genes to the next generation. Well, it turns out to be not quite like that after all, because scientists have now discovered that female birds do almost as much singing as the males, and it has less to do with sexual selection, than with simply saying: I’m here.

and this:

Not all is wrong in a world where birds sing for the joy of being alive.

Birdsong fulfills several functions not, or only partly, related to mating strategies. For some species it is territorial, a signal to deter members of the same species from invading its feeding and breeding grounds. In flocking birds it can be a means of maintaining colony cohesion and for warning against predators. Singing has to be explainable under natural selection as making a noise can be a risky strategy for a prey species and would only persist in a population if it had other survival advantages: saying "I'm here" just for the sake of it could result in "the joy of being alive" a very short experience. Skylarks for example, while on the wing, will use song as a form of defense against predator birds. By singing, the skylark signals that it is in good condition and will be difficult to catch as only a fit skylark can afford to sing whilst being chased by a predator.
Moreover even if both males and females are singing to attract mates it does not negate sexual selection as both sexes would be advertising their fitness to potential partners which is still true even if strict monogamy were not the expected outcome. Lord Sacks seems to be suffering from the delusion that it can only be sexual selection if the male is behaving like a peacock and the female is a coy recipient of his advances which may say more about his cultural biases than about his grasp of biology. After all, both partners will usually be involved in feeding the brood so fitness, for which singing is a proxy, is advantageous to both birds.
Lord Sacks cannot make any of this mean what he would like it to mean which is birds sing because of God.

[…] like all those psalms that speak of creation singing a song to the creator, and the wonderful closing line of the last psalm of all: Let everything that breathes praise the Lord.

Birds sing for survival and not to praise a deity that only human minds can afford the luxury of inventing and no faux pas of Darwin’s changes that. However that does not render the dawn chorus any less uplifting or appealing, in fact the complex twists and turns of natural selection that have granted the birds their vocal abilities are mirrored in our own to appreciate them. Which is a much deeper and richer truth that it may benefit the good Rabbi to contemplate.