You are right that we should not beg questions by imposing methodological naturalism with the underlying philosophical materialism that lurks therein — denials notwithstanding. However, all that requires is that we be open to the three major causal possibilities [which can interact] i.e. chance, necessity, agency. In the end, that is what ID asks for,t hen puts on board a reliable tool for identifying certain important cases of the last of these three mechanisms. Reliable? [In every case where the explanatory filter votes, design, in which we have independent knowledge, it is accurate.)

On the second point, it is worse for the chemistry reductionist thesis than that, for dead organisms may have living tissues and cells in them – the whole living organism is plainly more and different from the simple sum of the physical parts.

Then, when it comes to minds that we need to think credibly about such matters . . . it seems evolutionary materialist thinkers have inescapably undercut their own ability to think. We are looking at self-referential inconsistency here.

GEM of TKI

I know I haven’t said it recently but I have always maintained that if living organisms didn’t arise from non-living matter via stochastic/ blind watchmaker-type processes then there would be no reason to infer those processes have sole dominion over any subsequent evolution.

Also I should note that dead organisms have the SAME chemicals as their living counterparts. Yet they are still dead.

That alone refutes Art2′s premise about chemistry and living organisms.

It seems Art is incommunicado for a week or so, and that the above was in effect his last post, absent the thread keeping going for the week intervening. So, in effect we are looking at wrap-up, methinks – unless someone else steps up to the plate.

BTW, BA, thanks for the kind words. [I do quietly note my last formal qualification in Math is the third major in my u/grad degree, supplementing my “home” double physics major. Beyond that, I am an applied physicist, who also broadened to take in an MBA with a focus on strategic change.]

A few quick thoughts:

1] Elephant Hurling, Literature Bluffing and Selective Hyper-Skepticism:

These are of course colourful names apparently originating in the apologetics and ID movements for persuasive but misleading arguments often directed at them/us. Some have objected that adverting to the issues by those names is improper, I suppose by extending the “taint” of those movements. But if targets/victims of a certain tactic give it a convenient name, the substance stands/falls on the merits, not the name. So, to definition:

ELEPHANT HURLING: giving a one-sided summary or declaration of “expert” or “credible” claimed “consensus” opinions on a matter in dispute as if that settles the matter without having to refer to the discussion and resolve the question on the merits of fact and logic. It persuades by the “credibility” of the authorities on the favoured side, thus is an example of improper – because biased — appeal to authority. This is of course to be distinguished from citing authorities on “your” side of a dispute in a context that is either engaging in the discussion or is balancing remarks made on the other side, so that onlookers may see for themselves well enough both sides of the issue.

LIT BLUFFING: On being challenged on hurling, some artful debaters will proceed to do a literature reference “dump” that may sometimes be hard to track down or address in a live debate; i.e they are claiming through merely piling up numbers of cites, that the “weight”/ “consensus” of “credible” scholarship is on their side. However, on tracking down the references, it soon turns out that he cites are irrelevant to the matter at stake, i.e the cites may use terms that happen to show up in a search engine’s results, or may brush at the issue tentatively, or may be speculative, or the like. In any case, the pile of cites is insufficient to settle the matter, and the matter should be addressed on the merits clearly and fairly to come to a well-warranted conclusion.

SELECTIVE HYPER-SKEPTICISM: My own modest contribution is here to give a descriptive title to a common skeptical debate tactic long since addressed by the likes of a Simon Greenleaf and frequently used in theological, historical, statistical, philosophical and scientific contexts, e.g. Sagan’s “extraordinary claims require extraordinary evidence.” No, they only require ADEQUATE and reasonable evidence! The fallacy works by the asserting of the idea that, in effect, if I can doubt your claim [as opposed to my own claim] relative to arbitrarily high standards of proof, I can dismiss. The core issue is, of course, that by consistent application of that standard, the whole field of knowledge vanishes (including those knowledge claims that lurk under the assertions of such skepticism), poof; radical and universal skepticism is self-referentially absurd. But, if one can SELECTIVELY apply skepticism to ideas one is inclined to disbelieve, that one in fact does not apply to similarly supported ideas one accepts — e.g. both are based on similarly warranted claimed matters of fact or use similar scientific or statistical approaches — one can pretend to be “rigorous” while begging the question and being inconsistent in his handling of issues. This of course frequently backs up the other two fallacies just above. If we insist on adequate and consistent standards of warrant, especially by giving clearly parallel cases where the same approach and substantially the same conclusion are generally accepted, then that suffices to expose the selectiveness of the radical skepticism being used.

2] Joseph, 89: the same holds for Art2- IOW he is also going to have to bring chemistry and biology into the picture if he is going to assert that all of life’s diversity owes its collective common ancestry to some unknown population of single-celled organisms.

Actually, this misses the core challenge; on evolutionary materialist views, one properly has to account for the ORIGIN of life relative to the plausible physical, geological and chemical factors present in the observed cosmos and especially earth at the relevant time – this is to get TO the claimed population of last universal common ancestral unicellular organisms. THEN, on examining the information systems, storage media and scale, and molecular nanomachines in the cell, one also has to credibly and empirically account for body-plan level biodiversity. In short, there are challenges on abiogenesis and on macroevolution.

Cf my always linked for a balancing discussion – IMHCO, neither of these challenges has been adequately acknowledged much less faced squarely and addressed properly on the merits by the many evolutionary materialism advocates – especially on the origin of biologically relevant information.

3] Art2 what is the biological data which can account for the physiological and anatomical differences observed between chimps and humans?

In Art’s absence, are there any takers? [Remember, this is not even really a serious step to answer to the challenges just identified – we share a fundamentally similar body plan with the chimps. But there are certain issues to be addressed: haldane's dilemma, Genetic Entropy, behe's observed “edge” of evolution, the infamous “98% similarity” in genes – and I hear (kindly address) the 2% difference is mostly in inconsequential stuff too, also that we have very similar genes to worms, fish and the like – was the banana our chimp has in mouth in the picture on that surprising degree of overlap, too? If NDT is the biological equivalent of atomic theory, surely it can give us a good account here.]

GEM of TKI

My assertion that all of what we do know about cells reduces to chemistry is a spot-on, completely accurate, if very abbreviated statement.

If that is what we “know” about cells then I would have to say that we don’t “know” very much at all.

To close (at least for now – we’ll see where things stand at the end of the month), I think discussants here need to face the fact that, somewhere in any discussion of information, evolution, the OOL, and whatever, one is going to have to bring actual chemistry and biology into the picture.

And the same holds for Art2- IOW he is also going to have to bring chemistry and biology into the picture if he is going to assert that all of life’s diversity owes its collective common ancestry to some unknown population of single-celled organisms.

Because as of this moment there isn’t anything in chemistry or biology which demonstrates such transformations are even possible.

I’m seeing more than a reluctance, but even a disdain here for chemistry and biology.

Nice projection.

So tell us Art2 what is the biological data which can account for the physiological and anatomical differences observed between chimps and humans?

Thank you for so solidly refuting my claims, NOT! Or as KF pointed out hurling an elephant!
This has to be the most lame rebuttal I have ever seen in my life. You address no specific evidence I site and worse yet you site absolutely no references to back your claims of fraud.
I truly respect kf’s solid refutation of your “non-complexity issue” and respect his integrity as a scientists/mathematician, but you sir have lost any respect you may have had from me because of your shoddy technique of discerning the truth.
Remember Art, science follows the evidence wherever it leads no matter if it is distasteful to our biases. You Sir are guilty of favoring your biases over evidence~!

I was about to go.

By focussing on the information carrying capacity of the digital strings involved, I am in effect saying: how many yes-no Q’s are required to specify what is to be done?

1] If there are no y/n elements – all is necessity, then we have not any capacity to convey information, we are in effect forced to use all AAAAAAAAA’s and cannot encode information at all. But, once we have at least two alternatives at any one step or element, and capacity to chain, we can store a lot of information, including where to go in our encyclopaedia of the forces, effects, properties and materials of nature to — purpose! — get what we want done. DNA uses 4-state elements and proteins use 20-state ones with very interesting chemical and physical properties that act like a super-meccano set or super swiss-army knife.

2] Now of course in the latter case, some of these properties of the links in the chain may in part constrain which elements can be where relative to other elements, and may leave certain chain sections relatively free – i.e., e.g one hydrophobic amino acid may substitute for another and permit the same type of folding to happen, i.e we see here don’t care elements and degeneracy, common enough in discrete state control systems. These may partly constrain the utilisation of the ideally available config space and so the in praxis equivalent yes-no chain information content per symbol, but it does not materially alter the overall picture. Indeed the idea that we are looking at and measuring “encyclopaedia”-ndexing information – which BTW is by def’n information — tells us that life systems are MORE complex than even these measures indicate, i.e we have a lower bound estimate – which is quite okay for our purposes!

3] So now we come to the issue of where did such code-bearing, algorithm-implementing chains come from?

4] As my always linked discusses, in principle it is logically and physically possible that any and every digital string we have seen is the product of lucky noise. But when the resulting config spaces exhaust reasonably available probabilistic resources, then we see that functionally specified complex information is best explained as the result of agent action. Just as we do not revert to chance to explain the strings in this blog thread.

5] Additionally, once we observe WD’s UPB as a reasonable limit, 1 in 10^150, and give room for the sort of freeness and constraints above, we see that a string equivalent to 1,000 to 2,000 bits or more [yes/no steps] is beyond the credible reach of chance on the gamut of this observed cosmos. That is easy to pass in this blog’s threads, and – sand kicked up to blind onlookers and cloud the issue notwithstanding — it has long since been passed in the nanotech of life.

6] Then finally observe that in every case of FSCI that we directly know the causal story for, we see that such originates in agency. Thus, it is very reasonable indeed to infer that in the cases where we happen not to have seen the process, such is the most likely cause to a degree of reliability that exceeds many things we routinely bet our life and limb on.

GEM of TKI

On measuring information it seems there’s a twist in figuring out the information content of a gene. The problem is that the gene specifies a protein but the protein is a reference to further information entailed by the physical properties of the protein. So the gene is analogous to references into an encyclopia of physics. Wouldn’t that mean that one has to include the information in the references instead of just the raw bit capacity of the media containing the references?

On another topic you were of course exactly right to tell Art that everything is physics not chemistry. Unfortunately it appears it will fall on deaf ears. Art’s convictions are both false and immutably held.

This is of course a dismissal attempt, without actually addressing the issue on the merits.

Relative to measuring “information,” onlookers will note that I have stressed the term: information-carrying capacity, which is directly measurable in bits once we see empirically the length of a digital chain and the number of states elements in that chain may take. This is not a bare “assert[ion],” it is an empirically anchored measurement and/or calculation that is commonly used in work with information and communication systems. (For instance one can measure a volume by taking certain linear measurements and calculating through well-founded formulae, not just by pouring in a liquid and observing in a measuring cylinder how much it took to fill up. Indeed, the cylinder was designed using the same sort of formulae.)

If you want to make an example of direct empirical “measurement” of information carrying capacity and scale of config space, set up a 16-bit ripple-carry counter based on JK flip flops and step it through all accessible states, counting the number of clock-ticks and negative edges [for say a good old 7476 dual JK TTL chip] till it recycles to the initial reset state; you will immediately see the exact number calculated for a 16-bit system below. You can then reconfigure the counter as a 4-decade binary coded decimal counter and see how you have reduced the effective carrying capacity by specifying the zone of the config space that it can access. [I doubt that we would bother with such an exercise even at High School level these days!]

Similarly, the related deduction of the number of states in the resulting configuration space is a common, real-world measure – it is the reason why an old fashioned 16-bit address space in the old 8-bit microprocessors was of maximum length 65,536, and why moving to 32 bits address space (and internal bus widths) on the 68000 opened this up to 4,294,967,296, but using only 20 lines on the 8088 (16 internal data bus, 8 external!) left this address space at 1,048,576. From that hangs much of the story of the kludgish evolution of the PC over the 1980′s, to find workarounds – including on address segmentation. [Then in the 1990's when Motorola failed to come through with the 68050 in good time, Apple went Power PC; I wish the common hardware reference platform had won the day then. Now that Intel has fully dominated the market Apple has gone to the Pentium. A real pity.]

Had Art looked at my always linked, Appendix 1, point 9, he would have seen also excerpts from Bradley’s recent discussion on the case of Cytochrome C, showing the measurement or calculation of information in it relative to the observed frequency of occurrence of specific monomers, leading to the average information per residue, via i = – ∑ pi log2 pi, yielding 4.139 bits per residue, or 455 bits of Shannon Information, and a config space of 1.85 x 10^137.

He then further adjusts as per Yockey on observing: “. . . . Some amino acid residues (sites along chain) allow several different amino acids to be used interchangeably in cyctochrome-c without loss of function, reducing i from 4.19 to 2.82 and I (i x 110) from 475 to 310 (Yockey). This yields, “Wo / W1 = 1.85 x 10^137 / 2.1 x 10^93 = 8.8 x 10^44,” which is a non-log information metric. He concluded by citing two experimental studies that produced similar low probabilities for getting to a functional protein from a racemic prebiotic soup. This cumulates from the multitude of required proteins etc into the DNA. And, we have not yet addressed the issue that all of this is in a functionally integrated system architecture irreducible to mere chemistry . . .

3] Art, 82: “electricity” and mechanical operations in living cells are all matters of chemistry. My assertion that all of what we do know about cells reduces to chemistry is a spot-on, completely accurate, if very abbreviated statement.

First, as a physicist: Chemistry is a function of Physics [it is in effect an effect of that property of particles we call charge], and electricity is physics not chemistry; indeed, with quantum effects and related magnetism [which traces to relativity BTW], physics grounds the chemistry in fact. So, should we next argue by your logic that Chemistry is not “real,” it is physics only . . . and so on, philosophy and psychology lurking behind physics as the empirical sciences rely on those factors to function, and so on to infinity in an absurd regress . . .?

More on the point you are missing the key issue, just as materialist reductionism tends to miss the mind in the midst of its fascination with the meat and the conditioning. Namely, a cell is no more reducible to a cluster of chemical reactions than is a PC reducible to the electrical currents, emfs and resistances etc in its components.

It is the specific, functional organisation of carefully designed and assembled components that makes all the difference, and it is the production of that configuration that is characteristically a known artifact of mind. This, I pointed out above, and this the ancients knew, in how they distinguished material cause and cause tracing to active intent of agents, who USE the materials and forces of nature to achieve their ends. And, that is also what DS pointed out.

4] Dismissive aside to BA:

Again, sadly, Art resorts to dismissal by elephant hurling, rather than addressing the merits.

GEM of TKI

OOPS: WD’s June 07 paper is here.

Thank God, it was “only” a side-swipe for Jamaica.

DV, later this morning I’ll call my folks later and see how they fared. Now, my family over in Cayman are under the gun, but it is even more distant of a side-swipe that they most likely face. [BTW, the just linked has in it my set of rules of thumb on where hurricanes are likely to go in 1 – 3 days . . . of course, monitor weather and disaster officials and heed their counsel, noting that any probabilistic estimate or likelihood estimate -- apart from 1 or 0 -- is by definition an index of ignorance to one extent or another, as modified by our leaning on whatever grounds towards occurrence or non-occurrence. This of course bridges into our discussion below too.]

Now, on points of note:

1] BA, 83: Is it ok if I quote what you wrote [on: “foundational math for the protein specificity that gives a protein its inherent and obvious complexity”] in the future . . .

Of course you can quote what I wrote, but it is a simple matter to do the math yourself and IMHCO, far more effective.

For instance, DNA uses 4-state elements in a chain that runs from about 500k – 1 mn up to 3 – 4 bn. For the first item, X, that is 4 states. For each of those, the second item, Y can take up 4 values as well, so X-Y has 4 * 4 = 16 possible states.

Chaining, for N elements, we have 4^N possible configurations. Using base 10 logs, log [4^N] = N log 4, say ABCD. EFGH = ABCD + 0.EFGH. The easy way for big numbers is to subtract off the power of ten, ABCD, and report it as 10^ABCD, then multiply by antilog 0.EFGH, ie say LMNO. So 4^N ~ LMNO*10^ABCD. This defines the scale of the configuration space, and illustrates the power of scientific notation for compactly expressing large and small numbers.

Once we have a space equivalent to more than about 500 – 1,000 bits of information-carrying capacity [think of a 500-bit or 1,000 or 2,000 -bit memory, say a one-bit wide slice off a typical eight-bit or byte-wide RAM chip], we are dealing with 10^150 to 300 to 600 possible states. With 10^600 states, it would be hard to argue that any reasonable island or archipelago of functional configurations is accessible to a random-walk or exhaustive search that begins at any arbitrary initial point. Also, one DNA 4-state element encodes up to 2 bits of information, so chains of 250 to 500 to 1,000 DNA elements correspond more or less to 500 to 1,000 to 2,000 bits of information storage capacity. [WD discusses the effect of among other things fractional occurrence of given states of the elements in the chain in his latest paper here, i.e a confining to a specified zone in the config space.)

Now, cells use a nanotechnology that implements step by step algorithms to create and use the macromolecules of life, embedding the blueprint as a part of the system, i.e DNA. So, in aggregate we are looking at vastly more possible configurations than even 10^600 or so. This propagates into proteins, esp enzymes, esp if we look a the required large cluster of such required for life. So if even 90% of the chains in these molecules are is relatively unconfined as to specific residue, we are looking at a large number of 20-state elements in aggregate, and again that puts us rapidly beyond the reach of reasonable random walk or exhaustive searches. Then, thirdly, we have to address the issue of chirality, which leads to a very similar result for the chains, which are L- or R- for proteins and nucleic acid polymers respectively. Just 2 to 3 or so typical 300-residue proteins gets us close to the upper limit for any reasonable random walk search or search by exhaustion.

You will note the attempted dismissal without addressing on the merits, the issues. This I turn to in a moment:

. . .