Monday, March 30, 2009

Darwin Bicentenary 17: Information and Evolution - Some Preliminary Thoughts

Shannon’s concept of information leads, in some cases, to trivially obvious conclusions. Consider for example the illustration of DNA (example 5 in part 15): As we get to sequence DNA it gives up its information, and thus it becomes less information bearing simply because we have less to learn from it. The information has moved from DNA to our heads and books. The reason for this is that Shannon was concerned with the transmission of information, its movement from place to place. Once the information has been successfully received, whatever it means to the recipient, the signal is now redundant (literally) and Shannon’s job is finished. (Shannon was not concerned with the “meaning” of information; the latter is bound up with the epistemological effect of information once it has been received) Trivially, then, DNA loses its information as we learn from it. However, in spite of that, what DNA doesn’t lose is its potential to inform an ignorant recipient, like for example a ribosome. DNA’s potential load of information is never lost and so in this sense DNA, even after its information has passed on to us, remains information rich.

But now consider the examples I related in part 15 of this series; the crystal lattice, the Mandelbrot set and a pattern of 1s and 0s generated by a “random” sequence generator. In each case a simple algorithm is used to generate a pattern, although the resultant patterns have a diversity of form that spans a very large window of the order-disorder spectrum. In spite of their complexity the Mandelbrot set and the output of a random sequence generator are potentially informationless. This is because a pattern that can be described using a relatively simple algorithm has the potential of losing its ability to inform to any recipient coming into possession of the algorithm and who knows how to operate it. But to an observer who doesn’t know the Mandelbrot algorithm or the algorithm of a random sequence generator, the patterns generated by these methods are information rich because this observer is unable to store their information succinctly. And yet relative to another observer who knows the algorithms and can therefore effectively store the patterns in a few bits of information, the Mandelbrot set and the output of a random sequence generator are information sparse. For the ignorant observer the in principle compressibility of the Mandelbrot set, becomes practical incompressibility. These information sparse patterns are only information rich relative to uninitiated observers. This relativity becomes even more apparent from a Divine perspective. God, presumably, knows everything with certainty and thus no pattern holds any surprises for Him. Moreover, His own being, in spite of being the seat of infinite complexity, is presumably based on some kind of logical truism and is thus absent of all information. Information in Shannon terms is a measure for the ignorant, for the fallible, and for the human.

As I pointed out in part 15 of this series, information is an observer relative term and therefore conflating observers really can give the impression of lots of information being created out of next to nothing. I have heard ID theorists say that one can’t create information. To that I would say “yes and no”. “No” because it is conceivable that an information rich pattern in actual fact has its origin in the few bits of information implicit in a simple algorithmic recipe; under these circumstances conflating observers leads us to the conclusion that information laden patterns may have their origins in something containing very little information. “Yes” because an improbable information rich pattern may be derived from the information inherent in prior conditions. That is, if a pattern is strongly conditioned on antecedent patterns, then it must derive its improbability from those antecedent patterns. Human probabilities are always conditional, and as such based on assumed circumstances. Consequently a pattern with a high information content may condition on a succession of preconditions that are themselves the source of improbability and thus of information.

Given the precedents of the foregoing paragraph it is natural to ask: Is it possible that the complex patterns of DNA potentially contain a lot less information than is apparent to the know-nothing reader? This is indeed what evolutionists are effectively claiming about life; that is, that life has a high probability given the relatively simple laws of the cosmic physical regime*. If evolutionists are right in assuming that the cosmic regime elevates the probability of the structures of life, thus depressing their information content (or at least to someone who knows that physical regime and understands its implications), then life’s information content is actually embodied in the relatively elementary algorithmic forms of physical law. Needless to say ID theorists believe that physical law has not achieved this feat of elevating the probabilities of living structures or implicitly containing life’s apparently rich information content.


The number of simple algorithms is in limited supply because simple algorithms, by definition, are constructed from a relatively small set of parts. A small set of parts can only be combined in a relatively small number of ways, thus severely limiting the number of possible simple algorithms that can be constructed. Hence, the class of simple algorithms capable of generating complex forms in realistic time runs out before it covers even the tiniest fraction of the class of complex configurations. The same mapping argument applies even if (in line with a more real world scenario) these algorithms are simply required to raise the probability of complex forms rather than generating them with a probability of unity. It therefore seems very unlikely that simple algorithms could be used to generate something as complex as life, or even flag it with an elevated probability.

But I only said “unlikely” because given that simplicity can create complexity (if only a limited class of complexity such as fractals), it remains conceivable that there is some relatively simple algorithmic regime out there capable of raising probabilities on living structures away from the uniform light grey spread implied by absolute randomness. If this is actually the case then the structures of life are potentially a relatively high probability, low information phenomena. If such a regime has a platonic existence, and moreover has been reified in our cosmos, this would mean that trying to get an estimate of the information content of life from the enormous combinatorial space of possibilities using unweighted probabilities, as ID theorists so often do, doesn’t tell the whole story; for it is conceivable that the use of unweighted probabilities is only valid relative to observers who either do not understand and/or do not know the full implications of the physical regime. Under such conditions the probability of evolution is, in fact, a conditional probability conditioned on the probability of the “chosen” physical regime of the cosmos. And yet I would concede that ID theorists are right in delivering an important challenge to evolutionists: OK, so we can find simple algorithms that generate complex fractals and nearly random sequences; but chaotic patterns are one thing; the cybernetic complexity of living structures is something different again.

At this stage in my investigation, however, I feel I cannot absolutely rule out that a relatively simple algorithmic physical regime can weigh probabilities in favour of the evolution of complex living structures. But in the same breadth I would want to acknowledge ID theorists’ robust challenge to this possibility (not to mention the challenges over the interpretation of paleontological evidence). But ironically herein is the rub for ID theorists: once the concept of a quasi-divine designer is invoked as the source reifying the apparently remote probabilities of living configurations by means of a special creative dispensation, there is no telling where such a Designer might employ his creative skills in reifying low probability configurations - for example, perhaps in the selection of a rare elegant algorithmic regime (if such has a mathematical existence) that elevates the probability of life. If a Divine Designer is capable of providing a special creative dispensation directly to living structures He may of take one step back and select a life enhancing algorithmic regime expressed by elementary laws, and this act would be a design feat in its own right.

It is surely an irony that the biggest challenge to haunt ID theory maybe the notion of design itself; once one allows in a designer who offers special Providences the floodgates of possibility are open. Contemporary Design theory with its antievolution ethos may prove to be its own worst enemy. The question I am left with is this: Did intelligence fill in for the very low probability of life by direct action, or does it work through a very elegant but very rare (and therefore low probability) algorithmic regime? Expressed theologically the question is this: Has God provided two special creative dispensations; one for the physical regime and yet another for living matter, or is creation a single dispensation? I am hoping the answers to such deep questions will come to light as I proceed in this investigation.

* I disagree with ID theorists that given what ID theorists call “chance and necessity” (What I call “law and disorder”) it is chance that is called to do the “heavy lifting” in aid of evolution. If evolution is to work, the extreme improbabilities of pure chance have no chance of generating life and thus it is down to physical law to elevate negligible chances to realistic probabilities, perhaps via the structure of morphospace.

Friday, March 27, 2009

Darwin Bicentenary 16: Waving Flagella and Waving Hands

I’m rather getting ahead of myself here but I’ve just got to tag this post on Uncommon Descent. Here William Dembski tells us about an email he received from someone who was “thoroughly convinced” of ID theory but then went on to read “The Language of God” by Francis Collins. In the said email Dembski’s correspondent mentions Collins’ challenge to the claimed irreducible complexity of the iconic bacterial flagellum (see picture on left). Dembski’s inquirer also contacted Collins himself who forwarded a review article by Mark Pallen and Nicholas Matzke on the flagellum. Dembski quotes Pallen and Matzke who state “designing an evolutionary model to account for the origin of the ancestral flagellum requires no great conceptual leap.” Dembski responds thus:

“Of course it doesn’t — one can always imagine some way that natural selection might have brought about the system in question. ….Requiring no great conceptual leaps or being unable to find a case where Darwin’s theory could not possibly apply is not the same thing as providing evidence. Sure, the proteins in the flagellum may have homologues that serve functions in other systems. And we can imagine that the parts were co-opted over time by selection to produce the flagellum. But so what? We can imagine lots of things. Where’s the evidence that it happened that way? And why isn’t the exquisite engineering that we observe in the flagellum evidence for ID?”

This little dispute is something I have commented on before. At the time I asked on whom does the burden “proof” lie? Evolutionists demand that ID theorists show that there are no incremental paths through morphospace along which evolutionary shuffling can diffuse. Therefore, say the evolutionists, the case for ID is not proved. Ahh!, gasp the ID theorists, on contrary it is for evolutionists to show that those evolutionary paths through morphospace exist:

Evolutionist: “You ID theorists haven’t provided evidence that the bacterial flagellum is irreducibly complex”
ID theorist: “But you evolutionists haven’t provided evidence that is reducibly complex!”
Evolutionist: “No, it is you who should be providing evidence that the flagellum is irreducibly complexity”
ID theorist: “On the contrary it is you who should first provide evidence that the bacterial flagellum is reducibly complex!”

I suppose a methodological judgment could be made in favour of one party or the other; perhaps in favour of the evolutionist on the basis that the burden of proof is on the ID theorists because they are making an extraordinary claim….. or perhaps in favour of ID theorists on the basis that evolutionists are making an unfalsifiable existential statement. I think I’ll leave them to discuss this matter; last time I attempted to arbitrate in this dispute I got myself into hot water, so I won’t comment this time. In any case methodological decisions are likely to evaluated from the perspective of those with vested interests and preferred decisions are therefore likely to embody the value judgments of partisans.

What I want to draw attention to, however, is that William Dembski is conceding a possibility; namely that it is possible to imagine a flagellum that is not irreducibly complex. Dembski is alluding to the very conjectural structure of morphospace, so let’s forget all about evidence and ask ourselves if evolution is at least conceivable as a possibility if not as a reality? A condition of the latter, if not sufficient condition, is that the set of stable structures in morphospace form at least a partially connected set not unlike the connectedness of the Mandelbrot set. But, needless to say, unlike the Mandelbrot set there is no easy analytical way to handle morphospace or prove that it is connected. If evolution is a possibility then presumably the structure of morphospace is implicit in the laws and statistics of the cosmic physical regime. However, proving the connectedness of the set of stable structures is nigh on impossible. In morphospace we have an object of such complexity that it clearly confounds both evolutionist and ID theorist and leads to their polite hand waving exchange of “After you”… “No after you”.

Morphospace is a highly complex object that is unlikely to reveal its secrets easily; our theories about it are likely to be an intricate amalgam of succinct theoretical insights embedded in a very narrative intense body of knowledge - that and, no doubt, a lot of hand waving. One obvious complexity is that morphologies are only rated as stable with respect to the environment they are in and therefore environment is one of the dimensions of morphospace. Moreover, survivable morphologies are themselves part of the very environment in which they are placed thus leading to an analytically inconvenient feedback effect and non-linearities. Morphospace is undoubtedly one of those theoretically intractable objects that must take its place alongside God himself as an object beyond the human mind to handle succinctly and fully. However, as with theology one can but try.

In the absence of analytical answers to the questions of morphospace we depend on real life history having done the simulation for us. Hence paleontological evidence must have a strong showing in the evolution/ID debate. If sufficient missing link evidence comes to light it could weigh the argument in favour of evolution. But in the absence of evidence that is compelling to all parties methodological policy decisions will have to be made. But that takes us back to square one and the conflicts of the wild web.

Characters of the Wild Web 5: Would be Pat Garretts are gunning for Billy the DembskID.

William Dembski says he is revisiting evolutionary computation.(See here)

Wednesday, March 25, 2009

A Reminder: ReMine’s Message Theory

Here is yet another line of inquiry in the evolution/ID debate: “Message Theory”. It is a post on Uncommon Descent by Walter ReMine, who claims that “Message Theory” is a testable alternative to “Darwinism”. But he rightly tells us that repeatability must be distinguished from testability. This, of course, is acknowledgment that different ontologies have differing levels of accessibility and complexity and this impacts epistemology perhaps even to the extent that an ontology is not even testable.

Complexity of ontology is an ascending scale and so in consequence is epistemic tractability. Complex objects under study may have so many adjustable variables that strong refutability/testability is impossible. It is then that strong testability, like repeatability, is left behind and we have to resort to fuzzier concepts like “explanatory potential”, “sense making power” and “elegance”. It is very difficult to index such vaguely sensed attributes and assessing the comparative merits of competing theories may be difficult.

However taking ReMine at his word; if “message theory” is as testable as he claims I had better keep tabs on it. I am also interested in the sense making power of Message Theory re common descent, cladistics, paleontology, embryology, etc

In the linked post ReMine, as per the robust debating style of the evolution vs. ID scene, comes in with all guns blazing accusing evolutionists of willfulness:

“.. their posturing is a tongue-in-cheek mockery – and they know it.”… “They know full well ….” “They are attempting to belittle Message Theory” … “They are attempting to fabricate an excuse for avoiding the challenge posed by Message Theory.”

Characters of the Wild Web Number 4: Message Theory in Action: Walter ReMine sends evolutionists a six-bit hand shake

Monday, March 23, 2009

Darwin Bicentenary 15: A critique of the mystique caused by the information conflation

This post was going to be a discussion of William Dembski on “Active Information and Intelligent Design” (which I’ll now have to postpone). It has turned into a digression on the intellectual hazards of the concept of information. Before I get back to active information and ID I am going to look at this concept and try to flag some of the pitfalls.

Shannon’s technical definition of information certainly helps to clarify the situation. However, whether we are talking about Shannon information or a more informal concept, in general information is an extrinsic property of a system; that is, a system possesses information by virtue of its relation to another system capable of reading and responding to that information. For example, a digitized computer program on a CD is information only in as much as it contains patterns that can be used by a computer as instructions. Likewise a book only contains information by virtue of its relation to human beings who have the power to correctly interpret the black and white patterns in the book. In both cases, without the potential to invoke the appropriate reactions from computer and human beings respectively, the black and white patterns of CD and book are devoid of any informative content and they remain as just patterns. The general lesson here is that the informational property of a pattern is not intrinsic to the pattern itself, but exists extrinsically by virtue of its relation to other complex systems capable of interpreting the patterning, thus bestowing upon it the property of being information. Without this potential relation to computers and humans respectively the CD and book contain nothing at all apart from patterning. In a word information is not a standalone property

It is this extrinsic property of information that causes a real headache for the analyst who is trying to get to the bottom of the evolution/ID debate. ID theorists, in particular, are very fond of the idea of information and this I think sometimes clouds the issue. Why? Because if an ID theorist is talking about the information in a structure, there is the implicit suggestion of relatedness either within the structure itself or, and this is where it gets tricky, to some system beyond the structure that reads and reacts to the patterns of the structure in some way. This latter case is an open ended system, and for the analyst who likes to isolate systems under study open-systems leaves him with inconvenient wildcards. This situation can be resolved, however, if the analyst is then allowed to include the system that bestows the property of information: for example, if the analyst is handed a digitised program along with the computer that uses it, he then has a self contained system and can get to work. But the real problems come when the analyst is just told “This structure contains information” but is given no indication what kind of external system it is information for. In particular, if there is a hint that the destination of the information is something as complex as a human level reader, then the analyst has got his work cut out trying to crack the code. In fact he may not be able to proceed at all as there may be too many cultural unknowns.

Shannon’s formal definition of information does help alleviate the problems somewhat, but his definition has been contrived, needless to say, with communication in mind and is therefore implicit about extrinsic properties derived from relatedness. But even Shannon’s definition, if we forget that it has been contrived with a third party in mind, can come up with some surprising results. Firstly Shannon’s definition makes use of the probability of an outcome. This use of probability should itself be treated with caution because of the philosophical contentions surrounding the nature of probability; namely the question of whether probability is an objective propensity or a subjective property bound up with knowledge (see my paper here). Thus, for example if probability is an objective propensity it really does look from Shannon’s definition that “information” is a property intrinsic to a system regardless of its relatedness. However I hope the following illustrations of the use of Shannon information will settle the question in favour of information being an extrinsic property bound up with an observer’s knowledge.

Example 1: Tossing a coin. Informally speaking a sequence of coin tosses carries no information because we don’t think that it encodes any secret messages. But in Shannon’s technical sense the tosses of a coin do carry a lot of information because at each throw an attentive observer passes from complete ignorance about the outcome to a full knowledge of the outcome. Once the outcome is a happened event, however, it loses its information “content” because the attentive observer is no longer ignorant about the outcome and therefore the outcome loses its power to inform him. Thus in prospect, a sequence of heads and tails is packed with information but in retrospect, for the attentive observer, has no information. Now, let’s imagine that our first observer subsequently transmits his record of the sequence of throws to a second observer over a transmission line. The second observer is effectively observing the sequence of heads and tails via the first observer’s signal. Before the second observer receives the signal he is in the same position of ignorance about the sequence of heads and tails that the first observer was in before he observed the sequence. Thus prior to receiving the communication from the first observer, the second observer is faced with a sequence that is still information rich; but only up until he receives and registers the signal from the first observer. This illustration shows how the same pattern of throws can pass from a sequence full of information to one of zero information, back to one full of information, depending on the state of knowledge of the observer. “Information” is an observer relative quantity.

Example 2: Crystal lattice. I have heard an ID theorist claim that crystal lattices contain no information. The response to that is “yes and no”. “Yes” because in the Shannon sense, which is probably the sense intended by the ID theorist, the crystal contains very little information if the observer knows the simple periodic algorithm that can be used to generate the lattice points. Under these circumstances the observer can’t learn anymore from observation of the crystal itself; ergo a crystal lattice, under these circumstances contains no information. But there are other circumstances where the lattice can “contain” information. If the observer knew that he was dealing with some kind of crystal lattice, that in itself would be very informative: he would at least know that the structure was highly organised and that would eliminate an overwhelmingly large number of disordered configurations. However, that still leaves a large number of possible regular lattices, and the only way our observer is going find out which one he has on his hands is by interrogating the actual lattice in order to discover which particular periodic algorithm can be used to generate the lattice points; while he is trying to do this the lattice contains the information he is after, but once he has worked out the algorithm then, and only then, would the lattice contain no information. We conclude that a crystal lattice can contain some information, depending on the state of knowledge, or lack of knowledge, of the observer. (However I stress the word “some” here because it wouldn’t take long for observer to work out the pattern and thus for it to cease being a learning experience) Note what’s happened here: the information “in” the lattice is not actually in the lattice itself; the information is, as I have said, an extrinsic property bestowed upon it by the observer’s state of knowledge. The extrinsic nature of information means that the information “content” of a lattice is a relative and variable property.

Example 3: The Mandelbrot Set. This set is a very rich pattern of variation that at first sight one might think clearly contains an enormous amount of information. But the answer to that is both “yes and no”. An observer armed with the Mandelbrot algorithm effectively knows the position of all the pixels; hence he can predict the state of each pixel just as he could for a simple lattice. Thus, on these terms the Mandelbrot set contains no information! But think again; what about if the analyst threw the algorithm away and forgot about it, or what if he was culturally medieval? The Mandelbrot set would then be a source of endless surprise to him and would in Shannon’s terms be information rich. However, even though the pattern has a degree of regularity, and thus from inspection the analyst may be able to better his guesses as to what each pixel contains, without the Mandelbrot algorithm it would be a source of information.

Example 4: Random sequence generator. Random number generators can generate very disordered patterns of 1s and 0s and are random to a reasonable approximation. Such a pattern of 1s and 0s, statistically speaking, will be all but indistinguishable from a sequence generated by the tosses of a coin. So does such a sequence contain information? Once gain it depends on the observer. If the observer knows the algorithm then the pattern contains as little information as a crystal lattice. But someone coming to the sequence without knowledge of the algorithm would find it difficult to distinguish from the tosses of a coin and it would then contain a lot of information.

Example 5: DNA. It seems indisputable that DNA clearly contains a lot of information. But as we get to know more about, say, the human genome, the less informative it becomes and therefore the less information it contains. Of course that doesn’t apply to the ribosomes that construct proteins: they know nothing at all about the DNA until they get a messages from the nucleus where DNA resides. Thus as far as the ribosomes are concerned DNA always contains a full quota of information.

Unless we are aware that information is an extrinsic property of a pattern, a property defined by the pattern’s relation to an information user, then we are liable to fall for the mystique of information; it will appear to us as some mysterious almost vitalistic property of a system that we can’t quite put our finger on; a ghostly lurking presence of unknown power that makes the analyst recoil in fear of the unknown.

In truth information arises out of the epistemic relation an observer has with the system under study and thus effectively the observer, via his measure of knowledge becomes a variable in the system that we are trying to express quantitatively using the concept of information. Unless we are aware of the extrinsic nature of information the state of the observer can become inconveniently entangled with the system under study. When we discuss a system in information terms it is easy to conflate observer and observed and thus strange counter intuitive statements can be made about a system if we don’t realize that we are actually talking about a joint system (e.g. “DNA contains no information”). This, I suspect, will have a bearing when we go on to consider the work of William Dembski who to quote one of his detractors is “some big shot intellectual”.

Characters of the Wild Web Number 3: Billy the DembskID – Intellectual sharp shooter or a peddler of disinformation?

Friday, March 20, 2009

Split Loyalties and Split Brains

In this post on Sandwalk atheist Larry Moran quotes Rev. Ambury Stuart, who is a climatologist and a Church minister. On the subject of religion and science Stuart says:

You have to think through a lot of stuff. It's not simplistic. You try and divide your brain into two bits: One bit you'll use on Sunday and the rest of it you'll use the rest of the week, and it doesn't work. It doesn't have to."

For Larry this is surefire evidence of the conflict between religion and science:

This is about as honest as you get. Stuart is telling us that the conflict between religion and science is real and challenging. You have to work really hard at reconciling science and religion. Many religious beliefs don't survive the challenge.

Funnily enough I agree with Larry Moran: there is, repeat, is, a deep conflict between religion and science - it’s just that I think the conflict is part of a more general cultural and temperamental clash. As I have intimated before the intuitive poetic/artistic mentality may be tempted to set its teeth against science:

Thoreau: You tell me [the colouring of the clouds] is a mass of vapour which absorbs all other rays and reflects the red, but that is nothing to the purpose, for this red vision excites me, stirs my blood, makes my thoughts flow… what sort of science is that which enriches the understanding, but robs the imagination?

Keats: Do not all charms fly at the mere touch of cold philosophy? Philosophy will clip an Angel’s wings, conquer all mysteries by rule and line, empty the haunted air, and gnomed mine – unweave a rainbow, as it erewhile made the tender-person’d lamia melt into the shade.

…and as I commented when I first quoted the above:

And so the apparently competing polarities of science versus art, analysis versus intuition, cold description versus beauty, demystification versus mystery, knowledge versus feeling, head versus heart are sustained. But why? Why is this polarization such a common theme? Why does the elementalisation that science appear to introduce grate so with the poetic mentality, a mentality that revels in unreduced experience? Why do people hark back to an imagined rustic idyll when life was more instinctual and intuitive? Why are the objects and activity of science regarded as soulless? Why is science’s analytically reduced reality considered so profane in comparison with the unreduced reality of the mystic? Is the analytical left-brain to be forever at odds with the intuitive right brain?

I have already made moves toward addressing these questions* but I have a feeling that I’ll be saying a lot, lot more about them in the future. I'm probably only scratching the surface of the mystery here.

However, let me just quote Gavin Pretor-Pinney who, with some jocularity, also comments on Thoreau and Keats:

I can see what Thoreau and Keats mean. But they do sound a bit like the arty kids in class taunting the science nerds. Having opted for all sciences at secondary school, I have painful memories of bullying classmates goading me for emptying the haunted air, and gnomed mine. OK, they might not have quite put it in those words, but the sentiment was the same.

“Bullying” is perhaps too strong a word for the pressures found in today’s hyperfeminised church favouring the intuitive over and against the analytic. (on second thoughts....!) Unlike Ambury Stuart, however, I am not going to act out of character and try to split my brain into two bits (left and right brain?) on Sundays. I am who I am, and I refuse to play the hypocrite in order to look “religious” by “swooning for Jesus” or selling out to inscrutable gut reactions. For me the quest to connect with the primary ontology of our world will always be temperamentally skewed toward the analytic. But that quest must be prepared look beyond the simple descriptive algorithms of natural law and statistics.

Characters of the Wild Web number 2: Sheriff Larry Moran - no one breaks the (scientific) law on his patch.

* See:

Uncommon Descent has a post on dualism here

Thursday, March 19, 2009

Characters of the Wild Web

In view of the recent comments I made concerning my perplexities over the politics and policies at Uncommon Descent and how the DaveScot-Paul Nelson axis actually worked here is an interesting blog entry that might throw some light on the matter. This entry was written, it seems, well over a year before I had even heard about the existence of Uncommon Descent. In the linked blog post DaveScot comes up smelling of roses, but I won't pass judgment on that matter here.

The man with no shame: Did DaveScot succeed in teaching Uncommon Descent supporters how to shoot straight?

Monday, March 16, 2009

Interactive Computation: Computing without Boundaries

As a bit of light relief from the entrenched world views and ill-tempered politics of the evolution/ID debate I read this paper after being tipped off by my son. It’s called “The Interactive Nature of Computing: Refuting the Strong Church-Turing Thesis” by Dina Goldin and Peter Wegner. Its thesis is that in the contemporary environment of ubiquitous interactive computing Turing's mathematical function model of computation, namely “Input=>Process=>Output”, makes heavy weather of today’s realities and needs upgrading. They propose a three tape machine model that supplements the input/output tape(s) of standard Turing computation with another tape that represents that the results of the machines output interacting with the surrounding world.

My first thoughts here were that it all depends on where one is drawing the boundaries. The closed systems of deterministic physics conform to the non-interactive Turing model in that the triplet “Input=>process=>Output” maps to “initial-conditions=>process=>outcome”. Even within a deterministic system one can draw boundaries in that system in such a way that subsystems become, in effect, computing machines that interact with their surroundings after the manner of Goldin and Wegner’s modified model. Hence, in one sense the old functional model of computing seems, at first sight, to include the new model.

However, Goldin and Wegner’s model really comes into its own when one realizes that it is not humanly possible to draw boundaries round total systems: the real systems we study are in the final analysis open systems and thus Goldin and Wegner’s model of computation is the more natural one and a better approximation to reality; that’s my current opinion anyway. All in all I think this is an area research to keep an eye on.

Sunday, March 15, 2009

Politics at Uncommon Descent

DaveScot, Intelligent Design guru, is no longer posting at Uncommon Descent. (see here) There seems to have been some kind of infighting at UD. Larry Moran picks up the story and suggests it may be because DaveScot challenged the UD policy of linking Darwin to racism. (A policy I believe to be a faux pas) The comments in this link record DavesScot’s insulting attacks on another UD contributor: perhaps that has something to do with it as well. I mention this matter because it puts into perspective my own recent comments and queries about DaveScot in relation to his openly espoused views favouring the notion of common descent on a blog that calls itself “Uncommon Descent”. Did these views also contribute to his demise? This gossipy affair only serves to bring the same questions back to the surface: what is UD asking me to believe or rather disbelieve: evolution as a history, evolution as a mechanism or both?

Interesting in this connection are GilDodgen views defending UD’s science of negation in this post on UD where he tells us that evidence against “Darwinism” (="chance&necessity") is evidence for Design; this, presumably, is an example of Dembski’s explanatory filter at work. Ahh! Perhaps I get it now: By a process of elimination I am supposed to believe that life was Designed!* But alas, it still leaves open questions about the more detailed means by which the design was implemented, whether by a history or by a mechanism, or neither, ….which only takes me back to square one.

PS: On the whole I regret that UD have lost DaveScot - I think they needed his particular emphasis in order to show the breadth of interpretation that can come under the heading of ID.

* Footnote 18/3/2009
As I have asked before why should "chance&necessity" (as the ID community puts it) be so sharply distinguished from design? Are "chance&necessity" any more logically self sufficient and in less need of design than the structures that occupy configuration space between the ends of the order-disorder spectrum? Dembski's explanatory filter works in a fuzzy heuristic sort of way within this world, but can that heuristic be lifted from this world and extrapolated to a super-cosmic perspective?
From the christian theist's perspective everything cosmic is designed (or rather selected for reification from the platonic world of the possible). Therefore, is it really natural to contrive such a sharp category distinction between "chance&necessity" and design?

Thursday, March 12, 2009

Darwin Bicentenary 14: Active Information and Evolution

In part 11 of this series I provided a digest of William Dembksi’s paper on active information, a paper that introduced us to the Avida program. Avida is an experiment in evolutionary computation and was used to evolve the complex XNOR function from basic “atomic” components consisting of NAND gates. In this post I make the assumption that Avida has abstract isomorphisms with evolution proper and consider the experiment from an evolutionist’s perspective.

The authors of the Avida program analysed the XNOR function and broke it down into a hierarchical structure of components, sub-components and sub-sub-components. The XNOR function was then subsequently evolved by building into the software a “ratchet” using a scoring system that assigned a fitness value to the components and sub-components of XNOR. Hence, the software can, in stages, arrive at the top of XNOR’s structural hierarchy because the “ratchet” suppresses the tendency to slip back down the component hierarchy if during the random shuffling of components a “higher” component happens to come together. The Avida program works, in effect, by incorporating a stratified stability into its “search”

If the dynamic in morphospace is simply that of an isotropic and homogenous diffusion, then ultimately no particular configuration is statistically weighted; for any given boundary condition the end result is that in time probability spreads itself evenly over all configurations in a light uniform grey. Thus, isotropic homogeneous diffusion is extremely unlikely to evolve any complex organized structures because these structures constitute such a small class of possibility. In any case if in the remote chance they did make an appearance they would not persist and would soon melt back into the background sea of randomness.

To get the Avida category of evolution to work the required members of the class of complex organized structures must have probabilities weighted in their favour. There is more than one way of doing this but the Avida program builds in this weighting using a “configurational ratchet”; that is, the algorithmic regime of Avida is such that should perchance a required complex ordered configuration come into existence it has a high chance of persisting and will not quickly dissolve back into its surroundings. Moreover, although the system is suppressed from going “backwards”, it is, nevertheless allowed to go “forwards” in the sense that “higher” components are allowed to be formed from assemblages of sub-components. The higher components which once formed are themselves “fixed” by the ratchet.

In terms of random walk the introduction of a configurational ratchet into the system is the equivalent of giving the random walk a directional bias; there is then a greater chance of stepping in one direction than the other because a particular configuration is more likely to be assembled than disassembled. This has the effect of introducing a directional drift in the diffusion created by the random walk.

Did I just say “directional drift”? Isn’t it the height of scientific incorrectness to say that evolutionary change has direction? Have the Avida builders committed a “scientific heresy”? It is, in fact, possible to drop an anisotropic random walk and instead introduce heterogeneity in the walk by allowing the step size of the walk to vary from place to place in morphospace. The random walk is then isotropic, but the step size is contrived to be very small around the area of certain complex organized configurations (like XNOR and its components), thus endowing them with a degree of persistence. However, my own mathematical work shows that the effect on the morphological diffusion equation of a varying step size of this sort is that it still introduces a directional drift toward the persisting configurations. Another way of favouring the required complex organized configurations is to introduce a term into the morphological diffusion equation that is analogous to the potential term in the Schrödinger equation of quantum mechanics. Yet another method is by weighting the probabilities in morphospace in favour of organized complexity by applying some kind of constraint that eliminates the enormous numbers pathways in morphospace leading to disordered configurations. However this effectively reintroduces anisotropy into morphospace.

However one cuts it, somehow those required complex organized configurations must be awarded a probability weighting that compensates for the highly atypical nature of their class. If the above considerations port to the evolution of biological configurations then it really does give the lie to the idea that complex organized configurations do not have a favoured status; clearly they must have a favoured status otherwise evolution simply cannot happen. Thus, within the visible cosmos, generalized Copernicanism, in the sense that no point is has a preferred status, does not apply to morphology; this is apparent because in morphospace, where the overwhelming numbers of configurations are disordered, complex organized configurations must be favoured with extraordinarily high probability weightings in order to compensate for their very sparse representation in the class of all possible configurations.

But Avida leaves us with another point to ponder. In Avida it is clear that the XNOR function cannot be assembled without passing through the “lower levels” of the component hierarchy; that is certain sub-components must precede “higher” components. If the initial boundary condition is that we start with a soup of basic atomic NAND gates, then Avida evolution has to proceed by first traversing the “lower” levels of the structural hierarchy and then work its way “up” the hierarchy. Once again Avida challenges “generalized Copernicanism” in the sense that the structures of morphospace don’t stand in symmetrical relationship to one another; in order to arrive at the “higher structures” certain antecedents must necessarily be realized first, but the converse is untrue: the “lower” structures need not be necessarily be preceded by the “higher” structures. In a word, the formation of the “lower” structures are necessary to the formation of the “higher” structures, but not vice versa.

The hierarchical structure of Avida’s logical components crudely echoes the hierarchal structure of biological components: Viz: atoms, organic molecules, cells, and multicell organisms. Hence biological evolution also has imposed on it a necessary sequence of events, although the real picture is complicated by the likely hood that in actual evolution the different levels of the hierarchy probably evolve in parallel.

All this, however, doesn’t tell us anything we don’t already know in a more general form: namely that some problems are intrinsically more difficult to “solve” than others because they require more steps, more time, and more resources in general. It is therefore no surprise if some structures are more complex than others in the sense that they demand more computational resources, or stand in a hierarchal relation to other less complicated structures that serve as necessary precursors. Therefore when discussing evolved structures it is difficult not to use such terms like “higher”, “lower”, “complex”, “simple”, “progress”, “developed”. These terms arise out of a natural way of describing the mathematical necessities of computation, necessities telling us that certain outcomes put a greater demand on computational resources than others. Even the word “solve” is a problem, in that it carries a goal seeking intentionality, but the fact is that evolution is a consequence of a world in morphological disequilibrium, just as it is in thermodynamic disequilibrium, and thus there is an asymmetry between beginnings and endings.

But terms like “higher”, “lower”, “progress” and “more complex” sit uneasily with an instinctive hyper Copernicanism which is inclined feel that preferred frames smack of theism and creationism; generalized cosmic mediocrity, the feeling goes, is ever the evidence of the absence of deity. But the fact is that if evolution is to work certain structures have a “preferred” status in that their probability must be elevated by the algorithmic regime to be considerably above that implied by a bland random walk. Nevertheless it has to be admitted that such terms as “preferred”, “higher”, “lower”, and “progress” have associations linked to our system of values, and religiously sensitive people, whether believers or atheists, pick up the signals immediately along with any implicit attack or corroboration of their views. This makes a detached discussion of the subject all but impossible. See for example this post on Sandwalk where I was involved in a discussion on the subject of the dynamics of evolution with an atheist who was reluctant to admit the presence of asymmetries in morphospace, perhaps because he felt this somehow threatened his world view.

If the Avida experiment has anything to tell us about real evolution, it does, as Dembksi suggests, show that a workable evolution must make use of active information. In this case
intrinsic active information built into the mechanics of the system. This means that the actual outcomes of evolution have an elevated probability which in turn depresses their information value on occurrence because the information is intrinsic to the organization of the system from the outset. Thus an observer who understands the physical regime is less surprised by evolutionary outcomes because information has shifted from these outcomes to his knowledge of the organization of the underlying mechanics.

There is one final question here that really takes me onto the next stages of this investigation. What is it that raises the weighting of certain configurational forms well above an even handed “Copernican” treatment? In Avida the weighting was effectively put in by hand. However in natural evolution this weighting it is undoubtedly bound up with the possibility of cybernetic structures that, given the context of the natural physical regime, have a self perpetuating/self maintaining structure. This subject will in due time take me onto the knotty issue of irreducible complexity and Dembski’s infamous concept of “Complex Specified Information”.

Coming soon… Active information and Intelligent Design

Sunday, March 08, 2009

Atheist Theology

Some atheists need to brush up on their theology and philosophy.

Here’s evidence that the atheist mind is capable of some level of theological thinking if only as a set of counterfactuals: This post by atheist Larry Moran touches on two themes that he repeatedly comes back to:

1) The belief that only deism is compatible with science.

2) The belief that evolution is incompatible with the concept of God.

Obviously such beliefs can only be worked out if one has in one’s head notions about the nature and purposes of Deity and its relation to the cosmos.

Deism: Science is about pattern description. Unless one projects very anthropomorphic qualities onto the Godhead, it is very difficult to see why the patterns of evolution are any more self sustaining than even the pattern of discontinuous leaps demanded by YEC creation theory. Thus under any circumstances deism is difficult to maintain, but, the thought goes, only departures from patterned normalcy are sure fire evidence of God's reality. In order to secure their respective positions both YEC and atheists may view God as a kind of powerful cosmic Godfather whose evident existence is largely manifested when He steps in here and there with acts of divine fiat defying the work-a-day pattern of a cosmos that otherwise proceeds with a quasi-autonomous normalcy. Hence the YEC position is sustained by a vehement belief in special creation 6000 years ago and the atheist position is sustained by a vehement belief in patterned normalcy. It is an irony that to secure their respective positions, YECs and atheists invoke similar concepts of Divinity and project this onto the Godhead.

Incompatibility of Evolution and Theism: Once again we have here an argument that, if it is to be worked out, must tap into theological assumptions about the nature of the Godhead and His relation to the cosmos. In particular God is often assumed to be a benevolent cosmic intervener who, in the absence of the culpability of Satan and man, would have a free run and would intervene rather than allow evolution and suffering in general. On this point many atheists and YECS would see eye-to-eye; as I have often maintained atheists and YECS have a lot of common ground in their concept of Deity

These two areas are very dangerous ground for atheists who, unless they have given some thought to the subjects of suffering, evil and theodicy, may not be theologically savvy. Atheists are on the horns of a dilemma. On the one hand they can spend time with theology, become conversant with it, and attack the concept of God by exposing inconsistencies. On the other hand, if they are unwilling to dignify theology with their time they can simply declare religion to be worthless and unintelligible. But then they will remain theological dunces, and philosophically minded believers will run rings round them. So which is it to be?

Wednesday, March 04, 2009

Darwin Bicentenary Part 13: Is Evolution a History, a Mechanism, or a Conspiracy?

The paradoxes, ironies, and questions deepen at Uncommon Descent. Here on UD is a very interesting article revealing that social realities seldom fit a simple pattern. It tells us how Hegel, years before Darwin’s "Origin of Species", appeared to deny the existence of evolution. My understanding of Darwin’s contribution, however, was that he tendered a proposal which sketched out the mechanism of evolution in more detail, supplemented with a wealth of observational data. Hegel, presumably, was thinking of evolution in the sense of being a history of Common Descent. But hang on isn’t Common Descent what UD's DaveScot believes? So just what is UD's point here and what is their concept of evolution?; is it as a history or is it as a (“mindless”) mechanism?

The post I have linked to provides an insight into a complex blended world where the “goodies and baddies” model of reality breaks down. And a good thing too: if life was straight forward and simple it would be incredibly boring. In any case the goodies vs. baddies model of social reality is about as effective as conspiracy theory.

STOP PRESS 6/3/2009.
On the subject of evolution and conspiracies have a look at these two links: here and here. PZ Meyer’s enjoys his favourite pass-time of shooting fish in a barrel; in this case a creationist who thinks the sales of his book are being impeded by the evolutionist’s conspiracy against it. (Don’t such authors ever get attacks of self doubt, or are their egos really that big?) Larry Moran quotes the author of the book and is left uncharacteristically speechless; well, if the material he quoted is a fair sample, I am too.

Monday, March 02, 2009

Darwin Bicentenary Part 12: Is Evolution a History or a Mechanism?

In this post on Uncommon Descent DaveScot makes it clear that he is inclined to accept the likelihood of common descent. Hence Dave doesn’t have problems with evolution in the sense of being a history of an apparently branching pattern of descent. Dave’s problem is with the view that a blend of physical law and randomness (what ID theorists habitually call “chance and necessity”) is sufficient to explain this history. Using Dembski’s explanatory filter Dave would then conclude that intelligent design needs to be invoked. A regular contributor to UD’s commentary threads, called Jerry, seems to agree:

Evolution is the change in the frequency of genetic elements in the population gene pool from one generation to the next. How it happens is the issue and if it has an intelligent assist by some process then it is still evolution whether you call it genetic engineering or something else.

According to Dave and Jerry the real question is not so much over evolution as a history, but evolution as a mechanism. In some ways this distinction really expresses my own terms of reference as to what I am investigating: the mechanism of evolution.

However, having said that my guess is that many YECs are forming a tense alliance with people like Dembski, Behe and DaveScot. YECs would certainly not agree with evolution even as a history. I also notice that on the post I have linked to comment number 14 has been left by an author of a book called “The Evolution Conspiracy”. This suggests to me that ID is attracting people responsible for some rather off the wall socio-political stuff. This may be down to the attraction of the kudos the ID movement has acquired, otherwise denied YECs, through the stature of figures like Dembski and Behe. What unites this disparate community is an anti-evolution ethos shared by all parties that identify with it. But many within its broad church may not be aware that DaveScot’s position is a relatively nuanced one involving quite technical and philosophical questions over whether the two classes of conceptual objects of physical law and randomness can describe our universe in its entirety. I’m left wondering just what are the anti-evolutionists calling a cruel and evil process; the mechanism or the history?

In any case what is it motivating DaveScot’s belief that a third class of conceptual object must be invoked to describe evolution’s mechanism? If it were possible to show that physical law and randomness are sufficient explanation for life’s history would Dave conclude that intelligence is obviated, throw in the towel and join Richard Dawkins? As I once commented on Uncommon Decent here:

Let’s say for the sake of argument that evolution has actually happened. Are you then telling me that if that is the case then Divine creative and sustaining providence is logically obviated? Does evolution really equate to a logically self sufficient cosmos? Creation ex-nihilo, in my opinion, is about reifying the platonic and not about configuration changes that occur within one reified contingent story taken from the platonic. Just because our contingent cosmos has been chosen for a particular history of configuration changes there is then no logical warrant to dispense with God’s Aseity and Creativity. If evolution should prove true, do you then stop believing in God? Is your faith based on a counter factual (That is, evolution => no God) and a conditional? (That is, no evolution => God). ‘Materialism’ is less about a commitment to a particular cosmic story, than it is about what constitutes the primary ontology of our cosmos.