Wednesday, January 28, 2009

Darwin Bicentenary Part 4: Monkeys, War Zones and Bullet Proof Jackets

Shoot Out At OK Stromatolite
This post on Uncommon Descent publishes a video of Kirk Durston (Seen left) introducing a mathematical definition of functional information. One of the remarks in the comments thread refers to the recent debate between the respective champions of the evolution and ID communities, PZ Meyers vs. Durston, claiming that Durston wiped the floor with PZ. Another commentator jokingly asks if Kirk is wearing a bullet proof jacket (Yes it does look like that). These remarks typify the jingoism required in the war zone that the ID/evolution question has become.

However, listening to Kirk’s message it was clear to me that he is still harping on about spontaneous probabilities rather than the much more difficult (perhaps even impossible) to calculate conditional ‘ratchet’ probabilities of evolution. In the commentary thread of the post it takes a mathematics professor to point this out. In ID theory all roads seem eventually to lead to the concept of irreducible complexity. For theorists emotionally committed to the concept of ID so much hangs on the validity of one concept: irreducible complexity.


Saturday, January 24, 2009

Darwin Bicentenary Part 3: Uncommon Opinions on Common Descent

Radical divergences amongst UD contributors
In this posting on Uncommon Descent Paul Nelson comments on an article in New Scientist. The article concerns “Horizontal Gene Transfer” between organisms, especially in the early days of unicellular life. The existence of HGT has the effect of modifying Darwin’s “tree of life” model to a “net of life”. Does this mean that Darwin’s original tree concept has been completely overthrown? New Scientist comments thus:

…the tree concept could become biology's equivalent of Newtonian mechanics: revolutionary and hugely successful in its time, but ultimately too simplistic to deal with the messy real world. "The tree of life was useful," says Bapteste. "It helped us to understand that evolution was real. But now we know more about evolution, it's time to move on."

Sensational eye catching headlines apart the tenor of the article is that the tree of life is, like Newton’s laws, a first approximation. It is a low resolution model of the descent structure of life, a structure that on closer look starts to break up revealing fibrils connecting the branches of the tree, thus making it less tree like and more net like. Horizontal gene transfer challenges the notion that common descent is an absolute rule. However, common descent as a low resolution phenomenon is still real; at least DaveScot, Paul Nelson’s fellow UD contributor thinks so. As I quoted in my last post Dave has said:

Common descent from one or a few ancestors beginning a few billion years ago has overwhelming evidence in support of it.

So, just as quantum theory succeeded in embracing systems successfully described by Newtonian mechanics the “net of life” concept must embrace the “tree of life” as a case observed under low resolution conditions. The “net of life” picture must approximate the tree of life picture seen at lower resolutions, just as quantum mechanics approximates Newtonian mechanics under the right conditions.

But on the subject of the ‘tree of life’ there seems to be little consensus amongst ID theorists. On the one hand we see DaveScot positing a history of common descent and on the other hand there is Paul Nelson who is a Young Earth Creationist who believes there is no history of life to explain: to him the clade structure of living things is not a product of a common descent but, presumably, an artifact of an act of Intelligent design creationism that took place little over 10,000 years ago. (re: “Evidence of common design” in my last post)

Once again we have here illustration of the difficulty that ID theorists have in reaching a consensus on the scientific heuristic to use in the research of the history of life. The premise that the generation of life requires special acts by an ID agent entails so many ways in which that agent could act that the possible interpretations of the data protocols proliferate. It’s no surprise then that the diversity of opinion amongst ID theorists ranges from evolutionary histories not dissimilar to the establishment picture (albeit with a very different concept of the mechanisms of evolution) through to YEC denials that there is in fact a history there at all. However, although the contributors on Uncommon Descent are a loose alliance of theorists who as group don’t exactly know what they believe they certainly know what they don’t believe. So all you hardened evolutionists out there, do yourselves a favour and run for cover.

STOP PRESS 28th January
Looking at this post it does indeed look as though some evolutionists are running for cover.

Wednesday, January 21, 2009

Darwin Bicentenary Part 2: DaveScot, ID Guru, Speaks Out

In my last post I said of evolutionary theory: “As an explanation of the taxonomy of natural history there looks to be no other game in town that is as good”, the implication being that ID theory was not as good on this score. However some recent comments by DaveScot on Uncommon Descent are relevant in this connection and throw some light on how a well established ID theorist views this matter. It’s only fair that I set these comments against my own. Dave says;

My position, which has remained unchanged for several years, is that phylogenesis was a planned sequence. Common descent from one or a few ancestors beginning a few billion years ago has overwhelming evidence in support of it. Gradualism however does not have overwhelming evidence.

He also says:

No Darwinists I know or read give saltation any credence. The reason why is because saltation implies front loading.

My interpretation of all that is as follows. Dave accepts that a wide variety of species evolved from a single ancestor thus implying the clade structure of organic taxonomy. But rather than seeing evolutionary change in terms of the gradualism of standard Darwinian Theory, Dave sees ‘evolution’ making the large discontinuous leaps of saltation. He pushes the boat out even further and proposes that the genetic resources needed for those saltational leaps is ‘front loaded’ into the DNA of organisms: that is, organism have ‘potential information’ in the form of front loaded DNA that is not initially realized phenotypically, but is in effect waiting in the wings ready to be called on, perhaps by environmental conditions. This 'potential DNA' might also be a means of explaining the clad structure of species: the genetic information would be sourced in a single ‘front loaded’ genome located in one organism, which then successively bifurcates into a variety of species each species taking some fraction of the potential DNA. According to Dave the information for major biological innovation, instead of being injected bit by bit from random mutations (something which ID theorists believe to be impossible), is already present in the genome, perhaps in the form of apparent 'Junk DNA'. Dave says that “saltation implies front loading” although I think he actually meant to say that front loading is just one mechanism of saltation.

I hope I have done justice to Dave’s position. Dave’s front loading model could be proposed as a working hypothesis and then used, regardless of one’s views about any background intelligence that might be responsible for the front loading, to see how well the model fits the data. Dave, I’m sure, believes his model is a good fit and presumably he sees it engaging the same facts about the fossil record that Gould attempted to engage with his punctuated equilibria.

However, in the comments section of Dave’s post someone points out that front loading isn’t the only way an Intelligent Designer can act in order to bring about saltation: for it is possible that a designer could tinker with the genome from time to time and release the products of these tinkerings into the environment in the form of new species. Herein lies rub for ID. The seemingly arbitrary ways in which such tinkering could take place has the potential to disrupt the rules by which a clade structure could be generated over time. I’m not the first to point out that the choices open to super sentience seem too vast for us to make ID the basis of a rule driven evolution. True, Dave suggests one way in which the Intelligent Designer might consistently work in order to produce the nested taxonomy of clades, but then along comes someone else with another suggestion showing that intelligence has no necessity to conform to this explanation of taxonomy. Yet another of Dave's commentators suggests that common descent, which is thought to be the cause of clades, may not be real but rather evidence of "common design". Hence the whys and wherefores of the clade taxonomy of biology remain a controversial mystery in ID theory.

At this stage I wouldn’t want to emphatically declare that ID is wrong; Let me just say that if ID is right then ID researchers have their work cut out finding any rules or principles that might restrict the options open to an ontology of creative intelligence and this has a series impact on ID's ability to explain the history of life. The open endedness of the ontology with which ID researchers are working makes moving toward a science of evolution difficult if not impossible and ID natural history is likely to remain narrative intense.

For a ‘hard cop’ response to DaveScot see here

Thursday, January 15, 2009

Darwin Bicentenary Part 1: A Brilliant Theory Says Ben Stein.

To commemorate the Darwin bicentenary I am bringing out a series of articles on the Evolution/Intelligent Design debate. This article is the first in the series

The theory of evolution raises intriguing and important questions about the nature of man and his place in the cosmic context and few would disagree. Although the status of evolution as a theory is more contentious it is nonetheless a very good theory. So good in fact that admission of its effectiveness comes from an unlikely source. Ben Stein, Intelligent Design aficionado and mischievous drawling roving reporter in the documentary film “Expelled”, praised evolution and Darwin in this YouTube Video. If Ben says that evolution is “a brilliant theory” and Darwin was “a brilliant guy” then it can’t be that bad. However, I don’t need to take Ben’s word for it. From my rather general layman’s perspective of the lie of the land, paleontologically and biologically, evolution appears to serve as an excellent background theoretical structure explaining the broad sweep of both prehistoric and extant life. Evolutionary theory joins the dots of the sample data very well in so far as it succeeds in uniting a diversity of organic forms into a single object called ‘Evolution’. The layman sees many fossils and many extant organic structures out there and although these are but a tiny fraction of the conjectured evolutionary tree of life that is supposed to sit behind them, evolution is one of those great organizing principles that succeeds in providing a compelling explanation of a gross aspect of both fossils and living forms, namely the clade structure of their categories. As an explanation of the taxonomy of natural history there looks to be no other game in town that is as good. In comparison ID theory as an organizing principle is no competitor: it is difficult to understand how positing a series of special acts by a super intelligence of unknown power and motive constitutes an effective organizing principle. From our lowly human perspective those acts appear, to all intents and purposes, arbitrary, and yet paradoxically, that mind seems to have created an organic taxonomy that looks suspiciously evolutionary. But then if the ID theorists are right one might expect the mind of a super sentience to confound us and have an agenda beyond our ability to comprehend.

In actual fact the case for evolution isn’t as clear cut as I make out. The overall layman’s impression that evolution provides an immediately to hand understanding of the gross cladistic aspects of the fossil record is one thing, but reading and trying to interpret the fine print of that record is quite another. For evolution the devil is in the detail. Enigmas and conundrums abound and these are not just about matters of fact, but also about matters of meaning. Take for example this upbeat assessment of evolutionary theory found in the British Open University magazine ‘Ozone’ (Winter 2008):

Among the scientific community evolution is a measurable, indisputable fact. The only debate that continues to engage them revolves around the precise mechanisms that drive evolution. But while academic niceties are politely batted to and fro at conferences and symposia, the rest of humankind (that sounds like me – ed) has been wrestling with the implications of Darwin’s monumental book ever since its publication in 1859.

That we are up against philosophical nuances and not just questions of science is suggested by the fact that many ID theorists would ALSO agree that evolution as a history of organic development is a fact. However where they would take issue with the evolutionary academic establishment is in that same question about the mechanisms driving evolution. But needless to say, in this case we are not talking about some minor academic quibble about the fine tuning of evolutionary mechanisms. Instead the ID/evolution contention is about a gross feature of the cosmos: namely, about whether or not the cosmos appears to make leaps of organization that can only be put down to the implementation of intelligent design with all the connation of non-human sentience that that notion suggests.

Philosophical, scientific and world view interests are well and truly entangled in this subject. So forget about academic niceties being politely batted to and fro: for the ID vs. evolution contention is far more sanguinary. Part of that may be down to the way the ID case proceeds in that it does so in way very reminiscent of the case for Young Earth Creationism. It is largely a negative science, a science that states that this, this and this could not have happened like that, that, and that. ID theory then attempts to satisfy the demand for predictions by recasting its negative predictions in positive mode, after the fashion one might recast the assertion “Black swans don’t exist” as “All swans are aren’t black”. This appears to make ID theory more falsifiable than standard evolutionary theory, a theory that makes existential statements about the historical existence of, say, illusive missing links. How annoying that must be to the atheist theorists who think of themselves as the bastions of empirical rationalism as they try to get the ID theorists to answer the evolutionary equivalent of the question “Just what colour are swans then?”. The ID theorists respond by rubbing salt into the wounds: they hint, more than hint in fact, that survive or die ‘Darwinism’ just may have something to do with the holocaust, one of the worst sins of mankind The evolutionary establishment retorts with the modern day equivalent of a charge of heresy: “ID theory is not science, it’s superstition”

But let me end on a positive note by acknowledging the help that good people on both sides of the debate have given me. I’m not keen on the abrasiveness of the contenders in this debate, but jointly both parties have given me a lot to think about. And that is much to be thankful for: for without these little problems to ponder, life would be so much more boring and this may have helped prevent me from being taken away by the men in white and diagnosed as pathologically bored. And finally I leave the last words to Ben Stein:

Bad Ben says "Evolution is a brilliant theory and Darwin was brilliant guy.”

Wednesday, January 14, 2009

Atheism is Bad News According to Atheists

The atheist bus poster in Genoa translates: (see picture right):

"The bad news is that God does not exist. The good news is that you do not need him."

Didn't we always know it - atheism is bad news. If my publicity agent came up with that one I think I'd ask for my money back. But then how does atheism come up with a positive sounding one-liner uttered with heart felt conviction and expunged of all cynicism? Anyone...?

Sunday, January 11, 2009

Poster Bus Improbability Drive Worry

The London Bus atheist poster campaign continues to attract a mixture of mirth, chagrin, and bother. Atheist Larry Moran, who, unsurprisingly, is not happy about the word ‘probably’, asks: “Are there bus and billboard signs that say, 'Jesus probably loves you?' ”. One of his commentators (Wandering Weeta) humourously renders John 3:16 thus:

"For God so probably loved the world, that He probably gave his probably only-begotten Son, that whosoever believeth on Him probably should not perish but probably have eternal life. Probably John 3:16."

….and remarks “Doesn't read quite as authoritatively.”!

William Dembski, big shot ID guru, also comments on the poster campaign on Uncommon Descent and asks: “What exactly is the probability that there is no God?”

According to this report in the New York Times Richard Dawkins didn’t want the word “probably” but “… the element of doubt was necessary to meet British advertising guidelines.” It is difficult to accept that this is the full story because with bit of imagination a more emphatic and unequivocal atheist message could surely have been devised; how about something along the lines “We know there is no God…”? Or how about this tautology: “Atheists know there is no God…”

In some ways I like the poster; it exposes to the ironies and paradoxes of both atheism and religion. On the one hand we have Christians who like the campaign to the point of wanting to help subsidize it and on the other hand there are atheists who don’t like its equivocation. The poster introduces an “element of doubt” that one might think would sit well with a contemporary atheism that all too easily drifts into nihilism and postmodern ambiguity but it is precisely the ambiguity that is the rub for the out and out atheists. Christians who like the campaign see an opportunity in that element of doubt for discussion and debate about God, yet doubt (and scepticism) is often regarded as an evil bogey amongst believers who equate it with a lack of spirituality, perhaps even a form of blasphemy.

The rendition of John 3:16 above underlines the asymmetry between atheism and religion: authoritarian religion simply doesn’t work with ‘probably’s’. And yet atheism, which one might expect to be comfortable with ‘probably’s’, loses it’s hard sell edge as soon as it incorporates scepticism into its texts - which only goes to show that atheism, as I have always maintained, has underlying intellectual instabilities and paradoxes in waiting. Perhaps people of a religious disposition, if they could just give up believing in God, would actually make the best and most convinced atheists!

Friday, January 09, 2009

On Epistemology

In blog entries here here and here biochemist Professor Larry Moran raises the important question of whether there are ways of knowing other than science. The professor is responding in part to Michael Egnor of the Discovery Institute who concludes that the qualia of consciousness are unknown to science. Egnor consequently defaults to a dualist mind vs. matter paradigm. In handling the question of qualia Egnor shows not the least sign of giving cognizance to the truism that all our experiential protocols and the theoretical frameworks with which we attempt to interpret them are not in a separate ‘materialist’ category but are themselves qualia, albeit highly differentiated and sharable qualia. But that is by the by.

Although I have some sympathy with the good Professor Moran’s opinion, I’m unable share his bullish and sanguine attitude toward the status of science. But then I know he has his own reasons for adopting a hard sell confident scientism which avoids a reflexive engagement with the philosophical small print. Hence my support for his position must be qualified. In this connection consider these questions:

Q1. Is science epistemologically replete? That is, are the methods of science sufficient to meet all the problems of acquiring knowledge of cosmic ontology and beyond?

Q2. Even if science isn’t epistemologically replete, we can still ask: Is science the only genuine epistemological method available to humans?

My answer to the first question is: Almost certainly no! To the second question I would give a very cautious and qualified ‘yes’. Science is a formalization of a very general but far more informal notion of rationality involving a kind of bartering dialogue between ideas, theory and experience (see my side bar). Our theoretical notions, if not tested by experience, at the very least engage that experience by acting as structures that attempt to make sense of that experience and this they achieve with varying degrees of effectiveness. Yes, as with so much else in our world rationality comes in degrees depending how close we can get to some optimum in the tradeoff between theory and experience. Science, as a formalization and institutionalization of a more general and informal rational process, classifies as a subset of rationality rather than the sum total of it: science is to knowledge as the law courts are to justice and truth.

Karl Popper was very clear that his relatively useful criterion of falsifiability (a criterion which, incidentally, doesn’t cover the whole of science) was a line to be drawn within rationality and not a circle drawn around the whole of it. The more general rational process of which science is a subset is, in my opinion, the only genuine epistemological method available to humans. However, in taking on board this view of rationalism we must be wary of the following:

The rational process is self referencing; it is itself a theoretical idea that can be submitted to the scrutiny of its own dialectic, namely the ideas verses experience contention. (Self reference is OK provided it proves to be self-affirming).

The distinction between experience and theory is not clear cut. As Popper said, our most basic language and thoughts are riddled with theoretical assumptions and therefore any act of observation is also an act of interpretation which in turn cannot be achieved without theoretical constructs being used as a resource of interpretation.

The man in the street does not base his knowledge directly on formal and institutionalized experimental science but rather on a complex interaction with the social texts of society. Of course, many of these texts are the products of formal science, but many have the status of legend, myth and rumor of varying degrees of quality.

Epistemology and ontology are coupled: the success of formal science and rationality depends on an a-priori science friendly and accessible ontology. However, there may be objects out there that science and human rationality in general cannot easily cope with or access and some questions will have indeterminate answers. We can thank God however, that much of the cosmos seems to be science friendly.

The explanatory activity of the physical sciences uses two types of mathematical object:
1. Highly ordered objects expressed as simple rules or ‘laws’ that act as pattern generators.
2. The given ‘brute fact’ patterns of maximum disorder referred to as ‘randomness’.
The exclusive use of these two objects begs the question of whether other mathematical objects intermediate between order and disorder like, say, a-prior intelligence, can be used as explanatory objects. Such exotic objects may be scientifically and intellectually intractable

The complex objects of historical (and prehistorical) ontology are a border line case of scientific intractability. Many historical questions will never be settled with anything like the precision and standard that can be applied to the test-at-will objects of the physical science. Theorising about human history is like interpreting the Bible: it is an open-ended activity with many impinging inter-disciplinary factors, with the result that some issues will be undecidable. This is one reason why I reply in the negative to the first question above.

All the above points are philosophical in nature and require one to stand back and look not at the objects with which science deals but at science itself. The science of science, (or meta-science, or the philosophy of science, call it what you like) shows that science itself is a very complex social object, far more complex than the relatively simple physical objects with which it deals. How it works and why it works is a matter of ongoing research. However, to the unreflexive follower of scientism the questions of meta-science do not register as issues simply because (s)he looks through science, and can no more see science as an object than one can see the eyes with which one habitually views the world beyond.

A Postscript for Religious Readers.
The above expressed views would very likely result in me being impugned by a variety of fideists, Gnostics and religious codifiers who would object on the basis that the rational process must be set over and against revelation. Revelation in their view makes itself known as sublime states of mind and/or uncritical assent to reams of religious articles and shibboleths. Hence they see themselves as transcending the rational process in favour of a superior epistemology of revelation.

But alleged sublime states of mind simply have the effect of introducing new kinds of experiential protocol into the rational process and religious articles based on scripture are inextricable from the inevitable knowledge resources one brings to scripture in order to interpret it and understand it. Hence in as much as revelation of any kind must ultimately impinge upon the stuff of our humanity for it to be known and interpreted and understood, then any claimed special revelations are organically joined to the rational process. In short it is not possible to opt out of the rational process except via denial. Thus I don’t accept the rational process is a category of epistemology distinct from revelation. To my mind all valid knowledge, however ever gained, is a form of revelation but I do recognize that there is a difference between Common Grace Revelation and Special Grace Revelation.