Saturday, December 29, 2012

Rom 1 reply, 30: The ghost of William Paley speaks -- Stephen Meyer's minimalist case for intelligent design in the face of claims that Hume and Darwin had refuted it

In July 2012 Stephen Meyer of the Discovery Institute's Center for Science and Culture presented a lecture at Tyndale House in Cambridge on the minimalist case for design in the face of the legacy of Hume and Darwin. 

Food for thought:

I find it particularly interesting how in his opening points, he highlighted how Hume (died, 1776) is often presented today as presenting the philosophical refutation of the case for design made in William Paley's 1802 work on Natural Theology (which work was quite influential until Darwin's proposal of adaptation through chance variation and natural selection were seen as overturning it). 

Hume of course emphasised a claimed dis-analogy between living systems and machines, attempting to cast doubt on the cogency of the analogy.

Meyer only vaguely spoke to the issue of additional complex, specific functionality Paley raised when in Chapter 2 of his Natural Theology he extended the famous Watch Analogy from Ch 1. However, as the picture of the Watch taken from the Wikipedia attack piece on ID shows, objectors to the inference to design in the world of life appeal down to today to the first part of Paley's argument but conspicuously and consistently fail to address the point in Ch 2, only a few pages further on. This seems to me to be a longstanding case of a strawman fallacy.

{Added, Dec 31st: I return the compliment paid by Dr Torley of UD, by inviting interested onlookers to see his excellent  take-apart of twelve myths concerning William Paley's case. Dr Torley, as usual, does a first class job of research and analysis rooted in well-documented facts. The core thesis is that Paley puts forward the point that from contrivance, we immediately and deductively infer design, as a conclusion in light of our experience and insight about the nature of reality, so the mere presence of contrivance, which entails purpose and composition of parts to work together to achieve such, immediately entails design. That is an historical fact that Dr Torley documents wonderfully well, regardless of whether we are apt to accept Paley's logic. 

As for me, my own view is that I would argue an inference to best [current] explanation in light of the known alternative causal factors and their characteristic signs that are supported by our general pattern of experience and insights as intelligent, reflective, insightful agents.  

Where, I explain such abductive inference on sign thusly:

I observe one or more signs [si in a pattern], and infer the signified object O, on a warrant W:

I: [si] –> O, on W

a –> Here, the connexion is a more or less causal or natural one, e.g. a pattern of deer tracks on the ground is an index, pointing to a deer.

b –> If the sign is not a sufficient condition of the signified, the inference is not certain and is defeatable; though it may be inductively strong. (E.g. someone may imitate deer tracks.)

c –> The warrant for an inference may in key cases require considerable background knowledge or cues from the context.

d –> The act of inference may also be implicit or even intuitive, and I may not be able to articulate but may still be quite well-warranted to trust the inference. Especially, if it traces to senses I have good reason to accept are working well, and are acting in situations that I have no reason to believe will materially distort the inference.

Such a frame of thought may not give deductive certainty but it is fully capable of compelling moral certainty in many cases, as as high a degree of warrant as we finite, fallible, morally struggling and all too often ill-willed creatures may attain or reasonably require on matters of fact. That is, my way of reasoning on such matters is in the end in light of well-tested forensic principles of establishing conclusions on evidence, along the lines of Simon Greenleaf's counsel in his seminal C19 Treatise on Evidence, Vol I Part I, Ch 1:
 None but mathematical truth is susceptible of that high' degree of evidence, called demonstration, which.excludes all possibility of error [--> SG was nearly 100 years too early to know of Godel's work on the limitations of Mathematical thought], and which, therefore, may reasonably be required in support of every mathematical deduction.
Matters of fact are proved by moral evidence alone ; by which is meant, not only that kind of evidence which is employed on subjects connected with moral conduct, but all the evidence which is not obtained either from intuition, or from demonstration. In the ordinary affairs of life, we do not require demonstrative evidence, because it is not consistent with the nature of the subject, and to insist upon it would be unreasonable and absurd. The most that can be affirmed of such things, is, that there is no reasonable doubt concerning them. The true question, therefore, in trials of fact, is not whether it is possible that the testimony may be false, but, whether there is sufficient probability of its truth; that is, whether the facts are shown by competent and satisfactory evidence. Things established by competent and satisfactory evidence are said to he proved.

By competent evidence, is meant that which the very-nature of the thing to be proved requires, as the fit and appropriate proof in the particular case, such as the production of a writing, where its contents are the subject of inquiry. By satisfactory evidence, which is sometimes called sufficient evidence, is intended that amount of proof, which ordinarily satisfies an unprejudiced mind, beyond reasonable doubt. The circumstances which will amount to this degree of proof can never be previously defined; the only legal test of which they are susceptible, is their sufficiency to satisfy the mind and conscience of a common man ; and so to convince him, that he would venture to act upon that conviction, in matters of the highest concern and importance to his own interest . . . 
I would further argue that in scientific matters,we are dealing with inference to best current explanation, provisionally, and should be humbly aware of the abstract possibility (and historical frequency) of error or significant limitations in even the most successful theories such as Newtonian Dynamics. So, we reason across live options and come to conclusions that are empirically well grounded as the general pattern of observed nature, but strictly subject to further development or correction.}

Let us now observe from Paley:
Nat Theol Ch 1 (The watch parable):
The new Paley watch photo from
the Wikiperia article on ID (intended
by the Wikipedians to dismiss ID
as a mere appeal to analogy)

In crossing a heath, suppose I pitched my foot against a stone and were asked how the stone came to be there, I might possibly answer that for anything I knew to the contrary it had lain there forever; nor would it, perhaps, be very easy to show the absurdity of this answer. But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place, I should hardly think of the answer which I had before given, that for anything I knew the watch might have always been there. Yet why should not this answer serve for the watch as well as for the stone? Why is it not as admissible in the second case as in the first? For this reason, and for no other, namely, that when we come to inspect the watch, we perceive -- what we could not discover in the stone -- that its several parts are framed and put together for a purpose, e.g., that they are so formed and adjusted as to produce motion, and that motion so regulated as to point out the hour of the day; that if the different parts had been differently shaped from what they are, of a different size from what they are, or placed after any other manner or in any other order than that in which they are placed, either no motion at all would have been carried on in the machine, or none which would have answered the use that is now served by it . . . . Nor would it, I apprehend, weaken the conclusion, that we had never seen a watch made -- that we had never known an artist capable of making one -- that we were altogether incapable of executing such a piece of workmanship ourselves, or of understanding in what manner it was performed; all this being no more than what is true of some exquisite remains of ancient art, of some lost arts, and, to the generality of mankind, of the more curious productions of modern manufacture . . . .
Ch 2 (The Additionality issue):
Suppose, in the next place, that the person who found the watch should after some time discover that, in addition to all the properties which he had hitherto observed in it, it possessed the unexpected property of producing in the course of its movement another watch like itself -- the thing is conceivable; that it contained within it a mechanism, a system of parts -- a mold, for instance, or a complex adjustment of lathes, baffles, and other tools -- evidently and separately calculated for this purpose . . . .

The first effect would be to increase his admiration of the contrivance, and his conviction of the consummate skill of the contriver. Whether he regarded the object of the contrivance, the distinct apparatus, the intricate, yet in many parts intelligible mechanism by which it was carried on, he would perceive in this new observation nothing but an additional reason for doing what he had already done -- for referring the construction of the watch to design and to supreme art . . . . He would reflect, that though the watch before him were, in some sense, the maker of the watch, which, was fabricated in the course of its movements, yet it was in a very different sense from that in which a carpenter, for instance, is the maker of a chair -- the author of its contrivance, the cause of the relation of its parts to their use.

[[Emphases added. (Note: It is easy to rhetorically dismiss this argument because of the context: a work of natural theology. But, since (i) valid science can be -- and has been -- done by theologians; since (ii) the greatest of all modern scientific books (Newton's Principia) contains the General Scholium which is an essay in just such natural theology; and since (iii) an argument 's weight depends on its merits, we should not yield to such “label and dismiss” tactics. It is also worth noting Newton's remarks that thus much concerning God; to discourse of whom from the appearances of things, does certainly belong to Natural Philosophy [[i.e. what we now call “science”]. )]

What is interesting to me is that this is actually a discussion that, over 150 years before the facts of molecular biology were elucidated, brought out the question that is now on our table, as we today know sufficient details concerning life to know that the origin of life and the molecular machinery of the cell connected to the roots of cellular self replication far exceed the requirements of comparability that makes an inference to best explanation on credible similarity of cause per reliable signs of design highly persuasive, save to those committed not to see such.

As I noted in the IOSE unit on origin of life (OOL):
Observed cell-based life precisely fits the pattern Paley highlighted. 
Also, going beyond what Paley could have known, it uses coded symbolic information, has digital storage of this information, and also reading and guiding mechanisms that direct the replicating machinery and process. So, it is reasonable to consider whether “. . . its several parts are framed and put together for a [[functionally specific] purpose.”
 In fact, the observed cell -- which is what we need to explain the origin of -- joins together (i) a metabolising entity that draws in energy and materials from its surroundings and processes them, ejecting wastes, to (ii) a symbol-based coded system that allows it to replicate itself.
That is, we are looking at a molecular scale von Neumann self-replicating, metabolising automaton, functionally similar to that in Fig G.2 as was presented with a more elaborate description than the following, above:
Fig. G.2, copied: A schematic, 3-D/“kinematic” von Neumann-style self-replicating machine. [[NB: von Neumann viewed self-replication as a special case of universal construction; “mak[[ing] anything” under programmed control.] (Adapted, Tempesti.) 

Fig. G.2 (b), copied: Mignea's schematic of the requisites of kinematic self-replication, showing duplication and arrangement then separation into daughter automata. This requires stored algorithmic procedures, descriptions sufficient to construct components, means to execute instructions, materials handling, controlled energy flows, wastes disposal and more. (Source: Mignea, 2012, slide show; fair use. Presentation speech is here.) 

Now, following von Neumann generally (and as previously noted), such a machine uses . . .

(i) an underlying storable code to record the required information to create not only (a) the primary functional machine [[here, for a "clanking replicator" as illustrated, a Turing-type “universal computer”; in a cell this would be the metabolic entity that transforms environmental materials into required components etc.] but also (b) the self-replicating facility; and, that (c) can express step by step finite procedures for using the facility;
(ii) a coded blueprint/tape record of such specifications and (explicit or implicit) instructions, together with 
(iii) a tape reader [[called “the constructor” by von Neumann] that reads and interprets the coded specifications and associated instructions; thus controlling: 
(iv) position-arm implementing machines with “tool tips” controlled by the tape reader and used to carry out the action-steps for the specified replication (including replication of the constructor itself); backed up by 
(v) either: 
(1) a pre-existing reservoir of required parts and energy sources, or
(2) associated “metabolic” machines carrying out activities that as a part of their function, can provide required specific materials/parts and forms of energy for the replication facility, by using the generic resources in the surrounding environment. 
Also, parts (ii), (iii) and (iv) are each necessary for and together are jointly sufficient to implement a self-replicating machine with an integral von Neumann universal constructor.

That is, we see here an irreducibly complex set of core components that must all be present in a properly organised fashion for a successful self-replicating machine to exist. [[Take just one core part out, and self-replicating functionality ceases: the self-replicating machine is irreducibly complex (IC).] 

This irreducible complexity is compounded by the requirement (i) for codes, requiring organised symbols and rules to specify both steps to take and formats for storing information, and (v) for appropriate material resources and energy sources.

Immediately, we are looking at islands of organised function for both the machinery and the information in the wider sea of possible (but mostly non-functional) configurations 
In short, outside such functionally specific -- thus, isolated -- information-rich hot (or, "target") zones, want of correct components and/or of proper organisation and/or co-ordination will block function from emerging or being sustained across time from generation to generation. So, once the set of possible configurations is large enough and the islands of function are credibly sufficiently specific/isolated, it is unreasonable to expect such function to arise from chance, or from chance circumstances driving blind natural forces under the known laws of nature . . . . 

A typical “consensus definition” of biological life is that living organisms exhibits “all or most” of:
  • organisation based on functional cells
  • homeostatic regulation of the resulting internal environment
  • metabolic processing of energy and materials (with elimination of waste)
  • growth and development across the life cycle
  • individual and collective adaptive responses to environmental circumstances
  • responsiveness to stimuli
  • reproduction
[[NB: the “most” here signifies that the “definition” is based on typical examples and cases that sufficiently resemble them. For example mules, worker bees and the comatose are alive. That is, it is based on appeal to sufficiently close analogy. (This also means that -- contrary to much popular rhetoric -- inductive argument by analogy is alive and well in biological science.)]

The above definition underscores just how central the cell is to biological life, and just how difficult the challenge to propose an empirically credible spontaneous origin model for the cell is.  
Key to that challenge is how central programmed, digital information processing is to the cell's functional organisation and ability to replicate itself. This can best be seen from the process of protein synthesis, which creates the workhorse molecules of the cell through a regulated process:

Fig. G.8 (a): Overview of Protein Synthesis: [[Courtesy Wikimedia, under GNU. (Also, cf a medically oriented survey here.)]  . . . . 

Protein codes are stored in the DNA molecules of cells, and when a particular protein is to be made, it is (a) transcribed to messenger RNA, and – if the cell has a nucleus – (b) it is passed through a port to the ribosomes in the endoplasmic reticulum. There, through (c) step by step translation, the protein chain is assembled, starting with the START three-letter codon, extended codon by codon, and then completed with the STOP codon. [[Codons use a genetic code based on three DNA or RNA letters, each of which can hold the states: G/ C/ A/ T (or for RNA, U).]  
Then (d) post-translation, the protein folds itself (perhaps with the help of a barrel- shaped chaperone molecule; cf M. pneumoniae below) and may have effector elements added. (NB: It may also be transported to the site where it is needed along an internal transportation network.)

Already, terms such as “transcription,” “step by step translation,” “start,” “stop” and “codon” tell us that we are dealing with symbolically coded digital (i.e. discrete as opposed to continuous state) information that is being algorithmically -- i.e. step by step -- processed. A closer look at the ribosome in action confirms this impression, and highlights how the mRNA chain acts as a digital information storing tape:

Fig. G.9: Protein translation using mRNA and tRNA -- an expansion of the Ribosome at (c) in Fig G.8(a).  [[Courtesy Wikimedia under GNU.]

From this figure, we see that a crucial role is also played by transfer RNA, where the tRNA molecules have an attached amino acid at one end (20 AA's are used for most proteins), and the corresponding anti-codon at the other. Once the correct tRNA locks to the codon in the A site, the amino acid then attaches to the growing protein chain as it passes to the P site. As a result proteins are informational macro-molecules, which is what causes them to have precisely controlled functional properties in the cell . . . . 
Cells use hundreds or more proteins to carry out their work, embedding many thousands of bits of functionally specific digitally coded information. 
The required protein synthesis system also exhibits irreducible complexity, and uses algorithmic processing. Thus, the “analogy” between the cell and electronic information processing systems is sufficiently close to again raise questions of purposeful design of codes, storage systems, readers, and effecting machinery.  
(Indeed, since the actual essential nature of digital, flexible, code-based algorithmic processing systems is a mathematical one, it is also reasonable to say that the protein synthesis system instantiates such a digital information system. And if that is at all a reasonable inference, then all objections that pivot on dismissing "analogies" collapse  -- even, if we for the moment ignore the key role analogy plays in inductive reasoning.)
Further to this, Tokuriki and Tawfik note how islands of function for proteins are strongly constrained, thermodynamically and kinetically:
The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability--the ability of proteins to acquire changes in sequence and function.  [["Stability effects of mutations and protein evolvability," Curr Opin Struct Biol. 2009 Oct; 19(5):596-604. Epub 2009 Sep 16. Emphasis added.]
Moreover, the expression of such stability constrained functional proteins and the development of  body plans are based on a complex regulated process . . . . complex regulatory networks (with duly complex "wiring plans") are intimately involved in the development of a body plan from embryonic stages onwards, and in the responsiveness of life forms to their environment. 

We may thus easily see how such functionally specific, integrated complexity can present a challenge for the various origin of life models . . . 

In fact, such OOL models are in a state of mutual ruin, as advocates of one spontaneous origin model decisively undercut the grounds for the other, whether Genes First/RNA World or the less popular Metabolism First.  As Shapiro and Orgel summarised:

[[Shapiro:] RNA's building blocks, nucleotides contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern . . . .  [[S]ome writers have presumed that all of life's building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case.

A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . .

To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . .

Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . . 

[[Orgel:] If complex cycles analogous to metabolic cycles could have operated on the primitive Earth, before the appearance of enzymes or other informational polymers, many of the obstacles to the construction of a plausible scenario for the origin of life would disappear . . . .

It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . few would believe that any assembly of minerals on the primitive Earth is likely to have promoted these syntheses in significant yield . . . .  Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of [[for instance] the reverse citric acid cycle was present anywhere on the primitive Earth [[8], or that the cycle mysteriously organized itself topographically on a metal sulfide surface [[6]? . . .  Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . . 

The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help.  [[Emphases added.]

Mutual ruin, in short.

Paley's self replicating watch is back at the table as a cogent and compelling comparison on the origin of life, especially when one is willing to see how functionally specific, complex information and associated organisation are inductively strong signs pointing to design as cause.

But of course OOL is the root of the tree of life, the analogy used by Darwin to promote the concept that life forms can be seen as diverging through chance variation and culling out of less successful forms that lose out in the competition to survive to grow and branch out across the world of life:

Darwin's branching tree of life analogy -- the ONLY illustration in Origin of Species

So, we have design at the table of explaining biological diversity from the very root of the tree of life proposed by Darwin, as of right, not sufferance. This puts a very different colour on the closing remarks from the well known 6th edn of his Origin of Species:
It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved. [[Origin, Ch 15. Emphasis added.]
All we have to add here, is the understanding that the increment of biological information to form a novel body plan easily exceeds 10 - 100 million new bases, from observed genome sizes. This by far exceeds the 500 - 1,000 bit threshold at which FSCO/I is best explained on design, once it is present. Where also it is well known that complex function requiring the specific arrangement and interfacing of well-matched parts normally comes in isolated islands of function in the space of possibilities for scattering or clumping the same or similar parts. (Those who would argue the opposite need to actually SHOW their case, where for instance the problem with so-called genetic algorithms and the like, consistently, is that they are working WITHIN islands of function.)

So, it seems that William Paley is the ghost that roared. END