High profile studies in conflict/ Antonis Rokas, Vanderbilt University

A friend thinks confessions don’t get much better than this screed at ScienceDaily for this paper in Nature:

These days, phylogeneticists — experts who painstakingly map the complex branches of the tree of life — suffer from an embarrassment of riches. The genomics revolution has given them mountains of DNA data that they can sift through to reconstruct the evolutionary history that connects all living beings. But the unprecedented quantity has also caused a serious problem: The trees produced by a number of well-supported studies have come to contradictory conclusions.

“It has become common for top-notch studies to report genealogies that strongly contradict each other in where certain organisms sprang from, such as the place of sponges on the animal tree or of snails on the tree of mollusks,” said Antonis Rokas, Cornelius Vanderbilt Chair in Biological Sciences at Vanderbilt University.

And the further back they go, the less reliable the genetic data becomes.

Keep this story in mind when a coworker splinters the table insisting that Darwinian evolution is supported by “mountains of evidence,” or, better yet, “mountains and mountains of evidence,”or even just plain “fact! fact! FACT!”*

What is the mountain of evidence evidence for, specifically? Nothing the next paper won’t overturn, it seems.

*Michael Ruse, Darwinism Defended: A Guide to the Evolution Controversies, (Addison-Wesley, 1982) 1983, Third Printing, p.58. Emphasis Ruse’s.

Here’s the paper’s Abstract:

To tackle incongruence, the topological conflict between different gene trees, phylogenomic studies couple concatenation with practices such as rogue taxon removal or the use of slowly evolving genes. Phylogenomic analysis of 1,070 orthologues from 23 yeast genomes identified 1,070 distinct gene trees, which were all incongruent with the phylogeny inferred from concatenation. Incongruence severity increased for shorter internodes located deeper in the phylogeny. Notably, whereas most practices had little or negative impact on the yeast phylogeny, the use of genes or internodes with high average internode support significantly improved the robustness of inference. We obtained similar results in analyses of vertebrate and metazoan phylogenomic data sets. These results question the exclusive reliance on concatenation and associated practices, and argue that selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences. – Leonidas Salichos, Antonis Rokas. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature, 2013; 497 (7449): 327 DOI: 10.1038/nature12130

Seeing morality as the product of contingent evolutionary processes was in line with the dominant trend toward historicism that permeated nineteenth-century Western thought. However it was a radical departure from pre-nineteenth century views about ethics as timeless and universal. Darwin clearly contributed to the historicization of ethics in the nineteenth century by portraying morality as changing and by denying its universality. (p. 93) More.

The intriguing part is that so many people who think this an entirely laudable trend in ethics are nonetheless angry and disbelieving when a scholar like Weikart explains the role Darwin played in it. Apparently, it is bad form to embarrass Christian Darwinists by spelling it out?

Weikart explains how he first became interested in Darwin’s role here:

Weikart is sometimes attacked in print for having had a sordid motive for even raising the issue. So why did he do it? And how did he get interested in the first place?

Actually, at first, he wasn’t interested. While living in Germany some years ago to improve his German, he was mainly interested in the nineteenth century. He doubted that he would uncover anything new about the Third Reich. For one thing, in his view, it was an overworked field. But then he discovered one neglected point … More.

Neglected? Shucks.

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Paper can be read here.

Also cf. The Music of Life sourcebook, here.

A key step in the reasoning:

The rise of a more interactive understanding of how DNA, environment and the intracellular network interact with the cell and even organism as a whole in its environment: the DNA and genome as an organ of the cell, not its “dictator”

Noble’s pivotal point in light of his detailed argument:

Dennis Noble’s pivotal point in light of marshalled facts, as we move to a new synthesis for inheritance and mechanisms of “evolution.” The intracellular network changes everything

This is meant to support a thread of discussion, so kindly comment here. END

Evolutionary theory itself is already in a state of flux…

all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproven

Denis Noble
Physiology is rocking the foundations of evolutionary biology

Nice to hear the truth for a change. The paper drew on the work of James Shapiro (who by the way had co-authored a paper with Discovery Institute Fellow, Richard Sternberg here).

Jerry Coyne has a dislike of Shapiro’s writings:

I hate to give attention to my Chicago colleague James Shapiro’s bizarre ideas about evolution, which he publishes weekly on HuffPo rather than in peer-reviewed journals. His Big Idea is that natural selection has not only been overemphasized in evolution, but appears to play very little role at all. Even though he’s spreading nonsense in a widely-read place, I don’t go after him very often, for he just uses my criticisms as the basis of yet another abstruse and incoherent post. Like the creationists whose ideas he appropriates, he resembles those toy rubber clowns that are impossible to knock down…..

His never-ending attacks on natural selection and neo-Darwinian evolution should be an embarrassment to HuffPo, which will apparently publish anything since they don’t have to pay for it; but they’re also an embarrassment to me, for Shapiro works at my university and, in my view, his writings impugn our reputation for excellence in evolutionary biology.

So again, I tender my challenge: tell us, Dr. Shapiro: you’re always banging on about new sources of genetic variation, but you never seem quite able to tell us how that variation is translated into adaptive evolution. If it’s not natural selection, what is it?

Jerry Coyne James Shapiro goes after natural selection again (twice) on HuffPo

Coyne thinks Shapiro has appropriated creationist ideas. Shapiro’s ideas are referenced in the above peer-reviewed article. I’d say that’s progress.

Coyne laments elsewhere of the battle between molecular biologists and evolutionary biologists:

Virtually all of the non-creationist opposition to the modern theory of evolution, and all of the minimal approbation of Shapiro’s views, come from molecular biologists. I’m not sure whether there’s something about that discipline (the complexity of molecular mechanisms?) that makes people doubt the efficacy of natural selection, or whether it’s simply that many molecular biologists don’t get a good grounding in evolutionary biology.

Coyne laments molecular biologists haven’t been sufficiently indoctrinated with evolutionary biology. Paul Nelson once observed:

molecular biology graduate students (for instance) don’t know much, or any, evolutionary theory… Students don’t see the point of storytelling. They could take a Fiction Writing course for that.

Paul Nelson

It was nice to see Coyne’s name not mentioned in this article, and the only mention of Richard Dawkins was in reference to Dawkins mistakes.

Reviewer Terry Scambray thinks Nagel is on to something, but that no accommodation with materialism really works:

Nagel’s probes or “speculations,” the word he consistently uses, are characteristic of the style of much of the book which is sketchy when it isn’t down right contradictory.

For example, while he trashes Darwinian natural selection as a phony explanation for how minds were made, nonetheless, he continues to believe that natural selection has explanatory power. And though he correctly understands that a materialist explanation of mind destroys any notion of “values” while skewing even the baked-in imperatives of logic, nonetheless, he sees Darwinian evolution as the only credible support for materialistic solutions to all the big issues, including the mind problem.

And while he is grateful to individuals like Michael Behe and Stephen Meyer for showing the weaknesses in evolutionary explanations, Nagel notes that they both “are motivated at least in part by their religious beliefs.” And whereas David Berlinski is also given a pat on the head for dissecting Darwin’s theory without having ulterior “religious” motives, he is also commended for refraining from advocating design.

Apparently Dr. Nagel, wants to have his cake and eat it too. Read, for example, this sentence: “Those who have seriously criticized these arguments have certainly shown that there are ways to resist the design conclusion; but the general force of the negative part of the intelligent design position—skepticism about the likelihood of the orthodox reductive view, given the available evidence—does not appear to me to have been destroyed in these exchanges.”

Hard to track ? More.

Hard to track? Hard to say. Nagel’s biggest problem is probably to hold off Darwin’s thugs, which even the great Karl Popper was unable to do.
These days, only a person who just does not care what some government’s tagged herd is currently fed can afford to really genuinely doubt Darwin or any key materialist hero.

See also:

Movies: The History of the World in Two Hours and, oh, on two legs …

Where human uniqueness apparently does NOT lie …

Linguist: What we can and can’t learn about vanished languages, and how

Can we really identify words that have come down to us from 10,000 years ago?

* Thomas Nagel, The Last Word (Oxford University Press: 1997), pp. 130-131: http://tinyurl.com/4yh27e5

First, whether or not the ‘Darwinian paradigm’ is crumbling depends on what the next generation thinks and does. As long as the paradigm retains its current levels of control over who and what passes as ‘scientific’, I see little prospect for change. I doubt that any particular piece of evidence will change minds by itself. One should not underestimate the amount of bigotry against Christianity at work here, albeit in the relatively unself-conscious way that in the past had been associated with anti-Semitism. (I am especially struck by how self-regarding ‘liberals’ are quick to bring up how the supposed financial might of ID people distorts scientific discourse.) What is required for the sort of change that Meyer would like to see is a more systemic disillusionment with the scientific establishment in terms of its failure to live up to its own ideals. My guess is that this is more likely to help ID’s fortunes than any new research, which can always be spun in multiple ways.

More.

Note: A UD news writer (Denyse O’Leary)* remembers encountering an atheist professor in Toronto at the TVO station at Eglinton & Yonge some years ago. The prof swore that the ID-promoting Discovery Institute had scads of money. News writer, as it happened, had visited their office in 2007. The DI crowd were a great bunch, but their office was the usual not-for-profit dump in what was (or should be) a low rent neighbourhood. (They’ve since moved, but from what I hear, the new digs aren’t that much better.)

So their luxury yachts must be anchored off their private islands somewhere …

PS: UD News* operates at least one division from somewhere near a cell tower somewhere in Canada, which narrows things down a lot.  ;)

Original Big Bang theorist, priest

We’re not doing this just because it makes atheists mad. Honest. It’s instructive:

Atheists are just as likely as anyone to resist research findings that challenge their views. Here’s the romp in four short posts:

The “I hate the Big Bang” Cosmology Club

Cosmologist Christopher Isham:

Perhaps the best argument in favor of the thesis that the Big Bang supports theism is the obvious unease with which it is greeted by some atheist physicists.

Still under construction: A No Big Bang Universe

Stephen Hawking has been arguing against the Big Bang at recent public appearances, and has himself proposed various alternatives. (He has also made his atheist leanings quite clear in recent years.)

The Big Bang: Are the fireworks still on despite the downpour?

The Big Bang is not direct proof of God’s existence, but if God exists and did create the universe, we might expect something like that. And something like the ensuing reaction of world-famous atheists in science as well. They have put a great deal of effort into developing alternative models that would point away from God. The problem is that for sixty years and more, the evidence has favored the Big Bang.

Manufacturing doubts about the Big Bang

Here’s a sample from the news desk of Nature, which gives some idea of the available no-Big Bang fare in the light of recent results from particle physics: In “Higgs data could spell trouble for leading Big Bang theory,” we learn first that the most recent research, as of March of this year in fact, “was seen as in line, for the most part, with the standard theory of cosmology” (the Big Bang). That’s probably why we didn’t hear much about it.

But, we are also told, “a controversial analysis,” putting together different data streams, “paints the prevailing theory in a dim light.” That striking news deflates, a paragraph later, to the fact that a paper was posted the previous week by an astronomer who “is no novice when it comes to making controversial cosmic claims.”

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Food for thought.

As a stimulus to such, let us next note how the bloggist Wintery Knight has given an interesting summary of the challenges involved if a chance-dominated process is invoked for a hypothetical 100-AA polypeptide:

Let’s calculate the odds of building a protein composed of a functional chain of 100 amino acids, by chance. (Think of a meaningful English sentence built with 100 scrabble letters, held together with glue)

Sub-problems:

• BONDING: You need 99 peptide bonds between the 100 amino acids. The odds of getting a peptide bond is 50%. The probability of building a chain of one hundred amino acids in which all linkages involve peptide bonds is roughly (1/2)^99 or 1 chance in 10^30.
• CHIRALITY: You need 100 left-handed amino acids. The odds of getting a left-handed amino acid is 50%. The probability of attaining at random only L–amino acids in a hypothetical peptide chain one hundred amino acids long is (1/2)^100 or again roughly 1 chance in 10^30.
• SEQUENCE: You need to choose the correct amino acid for each of the 100 links. The odds of getting the right one are 1 in 20. Even if you allow for some variation, the odds of getting a functional sequence is (1/20)^100 or 1 in 10^65.

The final probability of getting a functional protein composed of 100 amino acids is 1 in 10^125. Even if you fill the universe with pre-biotic soup, and react amino acids at Planck time (very fast!) for 14 billion years, you are probably not going to get even 1 such protein. And you need at least 100 of them for minimal life functions, plus DNA and RNA.

But, some will object, it’s not just chance involved!

That is, they are appealing to self-organisation and/or mechanical necessity, or incremental complexification — a sort of pre-life evolution.

Especially, with RNA acting as a catalyst and potential information store.

Mechanical necessity, a forced sequence of bonds, is both counter to what we know of the chemistry of both AA and D/RNA chaining, and would undermine the flexibility of sequence required. Templating, in which a clay bed or the like would force the sequence only displaces the informational specificity one step back.

And while pebbles on Chesil Beach are sorted by size along the beach and while similar self-ordering phenomena for instance explain hurricanes and the hexagonal polar cloud ring on one of our gas giant planets, that is not even comparable to the functional and aperiodic, non sorted sequence chaining we need for the information-rich polymers of life.

Functional sequence specificity simply is not explained by forces of order or of randomness, once we have to deal with relevantly complex sequences and organised clusters of hundreds or thousands of molecules required to achieve cellular function.

They don’t even plot to the same zones on a graph of random, ordered and functional sequence complexity, as Trevors and Abel remind us from 2005:

No wonder, the making of proteins in the cell is such a meticulous, organised step by step process:

The step-by-step process of protein synthesis, controlled by the digital (= discrete state) information stored in DNA

Zooming in on the ribosome:

Step by step protein synthesis in action, in the ribosome, based on the sequence of codes in the mRNA control tape (Courtesy, Wikipedia and LadyofHats)

Let us remind ourselves: cells are gated, encapsulated, metabolic automata with self maintenance, responsiveness to environment and a code based self replication. As Mignea summed up in the context of requisites for a minimally functional, self-replicating cell:

Fig. A: 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.

That means, there is a stiff irreducible complexity threshold involved, which locks out incrementalist solutions, as we confront Menuge’s criteria C1 – 5 to get incrementally additive cobbling together (NB: Menuge set these in the context of the flagellum, but the challenge is much broader in relevance as anyone struggling to get a rare car part can tell us):

For a working [bacterial] flagellum to be built by exaptation, the five following conditions would all have to be met:

C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.

C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly.

( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

No wonder, then, that a few years back, Berlinski commented:

At the conclusion of a long essay, it is customary to summarize what has been learned. In the present case, I suspect it would be more prudent to recall how much has been assumed:

First, that the pre-biotic atmosphere was chemically reductive; second, that nature found a way to synthesize cytosine; third, that nature also found a way to synthesize ribose; fourth, that nature found the means to assemble nucleotides into polynucleotides; fifth, that nature discovered a self-replicating molecule; and sixth, that having done all that, nature promoted a self-replicating molecule into a full system of coded chemistry.

These assumptions are not only vexing but progressively so, ending in a serious impediment to thought. That, indeed, may be why a number of biologists have lately reported a weakening of their commitment to the RNA world altogether, and a desire to look elsewhere for an explanation of the emergence of life on earth. “It’s part of a quiet paradigm revolution going on in biology,” the biophysicist Harold Morowitz put it in an interview in New Scientist, “in which the radical randomness of Darwinism is being replaced by a much more scientific law-regulated emergence of life.”

Morowitz is not a man inclined to wait for the details to accumulate before reorganizing the vista of modern biology. In a series of articles, he has argued for a global vision based on the biochemistry of living systems rather than on their molecular biology or on Darwinian adaptations. His vision treats the living system as more fundamental than its particular species, claiming to represent the “universal and deterministic features of any system of chemical interactions based on a water-covered but rocky planet such as ours.”

This view of things – metabolism first, as it is often called – is not only intriguing in itself but is enhanced by a firm commitment to chemistry and to “the model for what science should be.” It has been argued with great vigor by Morowitz and others. It represents an alternative to the RNA world. It is a work in progress, and it may well be right. Nonetheless, it suffers from one outstanding defect. There is as yet no evidence that it is true . . .

Origin of life is the root of the tree of life, and so that is the decisive issue:

The Smithsonian’s tree of life model, note the root in OOL

No roots, no tree.

And, on blind watchmaker mechanisms, there is no good reason to expect a root to form.

Where also, there is one reliably known adequate causal source for functionally specific complex organisation and/or associated information (FSCO/I).

Design.

Which is in the main being disregarded on a priori ideological grounds such as Lewontin so tellingly documented:

. . . It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated . . . [["Billions and billions of demons," NYRB, Jan 1997. (If you imagine this is quote-mining, as a common how dare you cite that talking point alleges, cf. the fuller cite and notes here.)]

No wonder ID thinker Philip Johnson replied:

For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

. . . .   The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

There is no good reason why design is not sitting at the table as a serious explanatory candidate for the FSCO/I in first cell based life, and therefore also, in explaining the origin of major body plans. Motive mongering games and dismissive remarks notwithstanding.

In short, it is time for a serious re-think on the science of origins. END

Then in 2005 Bill published Specification the Pattern that Signifies Intelligence where he includes the identifier “v1.22″, but perhaps it would be better to call the concepts in that paper CSI v2.0 since, like windows 8, it has some radical differences from its predecessor and will come up with different results. Some end users of the concept of CSI prefer CSI v1.0 over v2.0.

It was very easy to estimate CSI numbers in version 1.0 and then argue later whether the subjective patterns used to deduce CSI were independent and not postdictive. Trying to calculate the CSI in v2.0 is cumbersome, and I don’t even try anymore. And as a matter of practicality, when discussing origin-of-life or biological evolution, ID-sympathetic arguments are framed in terms of improbability not CSI v2.0. In contrast, calculating CSI v1.0 is a very transparent transformation going from improbability to taking the negative logarithm of probability.

I = -log2(P)

In that respect, I think MathGrrl (who’s real identity he revealed here) has scored a point with respect to questioning the ability to calculate CSI v2.0, especially when it would have been a piece of cake in CSI v1.0.

For example, take 500 coins, and suppose they are all heads. The CSI v1.0 score is 500 bits. The calculation is transparent and easy, and accords with how we calculate improbability. Try doing that with CSI v2.0 and justifying the calculation.

Similarly, with pre-specifications (specifications already known to humans like the Champernowne Sequences), if we found 500 coins in sequence that matched a Champernowne Sequence, we could argue the CSI score is 500 bits as well. But try doing that calculation in CSI v2.0. For more complex situations, one might get different answers depending on who you are talking to because CSI v2.0 depends on the UPB and things like the number possible primitive subjective concepts in a person’s mind.

The motivation for CSI v2.0 was to try account for the possibility of slapping on a pattern after the fact and calling something “designed”. v2.0 was crafted to try to account for the possibility that someone might see a sequence of physical objects (like coins) and argue that the patterns in evidence were designed because he sees some pattern in the coins somewhat familiar to him but no one else. The problem is everyone has different life experiences and they will project their own subjective view of what constitutes a pattern. v2.0 tried to use some mathematics to create at threshold whereby one could infer, even if the recognized pattern was subjective and unique to the observer of a design, that chance would not be a likely explanation for this coincidence.

For example, if we saw a stream of bits which some claims is generated by coin flips, but the bit stream corresponds to the Chapernowne sequence, some will recognize the stream as designed and others will not. How then, given the subjective perceptions that each observer has, can the problem be resolved? There are methods suggested in v2.0, which in and of themselves would not be inherently objectionable, but then v2.0 tries to quantify how likely the subjective perception can arise out of chance and then it convolves this calculation with the probability of the objects emerging by chance. Hence we mix the probability of an observer concocting a pattern in his head by chance and then mixing it with the probability an event or object happens by chance, and after some gyrations out pops a CSI v2.0 score. v1.0 does not involve such heavy calculations regarding the random chance an observer formulates a pattern in his head, and thus is more tractable. So why the move from v1.0 to v2.0? The v1.0 approach has limitations witch v2.0 does not. However, I recommend, that when v1.0 is available to use, use v1.0!

The question of post diction is an important one, but if I may offer an opinion — many designs in biology don’t require exhaustive rigor as attempted in v2.0 to try to determine if our design inferences are postdictive (the result of our imagination) or whether the designed artifacts themselves are inherently evidence against a chance hypothesis. This can be done using simpler mathematical arguments.

For example, consider if we saw 500 fair coins all heads, do we actually have to consider human subjectivity when looking at the pattern and concluding it is designed? No. Why? We can make an alternative mathematical argument that says if coins are all heads they are sufficiently inconsistent with the Binomial Distribution for randomly tossed coins, hence we can reject the chance hypothesis. Since the physics of fair coins rules out physics as being the cause of the configuration, we can then infer design. There is no need in this case to delve into the question of subjective human specification to make the design inference in that case. CSI v2.0 is not needed to make the design inference, and CSI v1.0, which says we have 500 bits of CSI, is sufficient in this case.

Where this method (v1.0 plus pure statistics) fails is in questions of recognizing design in a sequence of coin flips that follow something like the Champernowne sequence. Here the question of how likely it is for humans to make the Champernowne sequence special in their minds becomes a serious question, and it is difficult to calculate that probability. I suppose that is what motivated Jason Rosenhouse to argue that the sort of specifications used by ID proponents aren’t useful for biology. But that is not completely true if the specifications used by ID proponents can be formulated without subjectivity (as I did in the example with the coins)

The downside of the alternative approach (using CSI v1.0 and pure statistics) is that it does not include the use of otherwise legitimate human subjective constructs (like the notion of motor) in making design arguments. Some, like Michael Shermer or my friend Allen MacNeill, might argue that we are merely projecting our notions of design by saying something looks like a motor or a communication system or a computer, but the perception of design is owing more to our projection than to an inherent design. But the alternative approach I suggest is immune from this objection, even though it is far more limited in scope.

Of course I believe something is designed if it looks like a motor (flagellum), a telescope (the eye), a microphone (the ear), a speaker (some species of bird can imitate an incredible range of sounds), a sonar system (bat and whale sonar), a electric field sensor (sharks), a magnetic field navigation system (monarch butterflies), etc. The alternative method I suggest will not directly detect design in these objects quite so easily, since the pure statistics are hard pressed to describe the improbability of such features in biology even though it is so apparent these features of biology are designed. CSI v2.0 was an ambitious attempt to cover these cases, but it came with substantial computational challenges to arrive at information estimates. I leave it to others to calculate CSI v2.0 for these cases.

Here is an example of using v1.0 in biology regarding homochirality. Amino acids can be left or right handed. Physics and chemistry dictate that left-handed and right-handed amino acids arise mostly (not always) in equal amounts unless there is a specialized process (like living cells) that creates them. Stanley Miller’s amino acid soup experiments created mixtures of left and right handed amino acids, a mixture we would call racemic (a mix of right and left-handed amino acids) versus the homochiral variety (only left-handed) we find in biology.

Worse for the proponents of mindless oirgins of life, even homochiral amino acids will racemize spontaneously over time (some half lives are on the order of hundreds of years), and they will deanimate. Further, when Sidney tried to polymerize homochiral amino acids into protoproteins, they racemized due to the extreme heat and created many non-chains, and the chains he did create had few if any alpha peptide bonds. And then in the unlikely event the amino acids polymerize, in a soup, the amino acids can undergo hydrolysis. These considerations are consistent with the familiar observation that when something is dead, it tends to remain dead and moves farther away from any chance of resuscitation over time.

I could go on and on, but the point being is we can provisionally say the binomial distribution I used for coins also applies to the homochirality in living creatures, and hence we can make the design inference and assert a biopolymer has at least -log2(1/2^N) = N bits of CSI v1.0 based on N stereoisomer residues. One might try to calculate CSI v2.0 for this case, but me being lazy will stick to the CSI v1.0 calculation. Easier is sometimes better.

So how can the alternative approach (CSI v1.0 and pure statistics) detect design of something like the flagellum or DNA encoding and decoding system? It cannot do so as comprehensively as CSI v2.0, but v1.0 can argue for design in the components. As I argued qualitatively in the article Coordinated Complexity – the key to refuting postdiction and single target objections one can formulate observer independent specification (such as I did with the 500 coins being all heads) by appeal to pure statistics. I gave the example of how the FBI convicted cheaters of using false shuffles even though no formal specifications for design were asserted. They merely had to use common sense (which can be described mathematically as cross or auto correlation) to detect the cheating.

Here is what I wrote:

The opponents of ID argue something along the lines: “take a deck of cards, randomly shuffle it, the probability of any given sequence occurring is 1 out of 52 factorial or about 8×10^67 — Improbable things happen all the time, it doesn’t imply intelligent design.”

In fact, I found one such Darwinist screed here:

Creationists and “Intelligent Design” theorists claim that the odds of life having evolved as it has on earth is so great that it could not possibly be random. Yes, the odds are astronomical, but only if you were trying to PREDICT IN ADVANCE how life would evolve.

http://answers.yahoo.com/question/index?qid=20071207060800AAqO3j2

Ah, but what if cards dealt from one random shuffle are repeated by another shuffle, would you suspect Intelligent Design? A case involving this is reported in the FBI website: House of Cards

In this case, a team of cheaters bribed a casino dealer to deal cards and then reshuffle them in same order that they were previously dealt out (no easy shuffling feat!). They would arrive at the casino, play cards which the dealer dealt and secretly record the sequence of cards dealt out. Thus when the dealer re-shuffled the cards and dealt out the cards in the exact same sequence as the previous shuffle, the team of cheaters would be able to play knowing what cards they would be dealt, thus giving them substantial advantage. Not an easy scam to pull off, but they got away with it for a long time.

The evidence of cheating was confirmed by videotape surveillance because the first random shuffle provided a specification to detect intelligent design of the next shuffle. The next shuffle was intelligently designed to preserve the order of the prior shuffle.

Biology is rich with self-specifying systems like the auto correlatable sequence of cards in the example above. The simplest example is life’s ability to make copies of itself through a process akin to Quine Computing. Physics and chemistry makes Quine systems possible, but simultaneously improbable. Computers, as a matter of principle, cannot exist if they have no degrees of freedom which permit high improbability in some of its constituent systems (like computer memory banks).

We can see the correlation between a parent organism and its offspring not being the result of chance, and thus we can reject the chance hypothesis for that correlation. One might argue that though the offspring (copy) is not the product of chance, the process of copying is the product of a mindless copy machine. True, but we can further then estimate the probability of randomly implementing particular Quine computing algorithms (that makes it possible for life to act like computerized copy machines). The act of a system making copies is not in-and-of-itself spectacular (salt crystals do that), but the act of making improbable copies via an improbable copying machine? That is what is spectacular.

I further pointed out that biology is rich with systems that can be likened to login/password or lock-and-key systems. That is, the architecture of the system is such that the components are constrained to obey a certain pattern or else the system will fail. In that sense, the targets for individual components can be shown to be specified without having to calculate the chances the observer is randomly formulating subjective patterns onto the presumably designed object.

That is to say, even though there are infinite ways to make lock-and-key combinations, that does not imply that emergence of a lock-and-key system is probable! Unfortunately, Darwinists will implicitly say, “there are infinite number of ways to make life, therefore we can’t use probability arguments”, but they fail to see the errors in their reasoning as demonstrated with the lock-and-key analogy.

This simplified methodology using v1.0, though not capable of saying “the flagellum is a motor and therefore is designed”, is capable of asserting “individual components (like the flagellum assembly instructions) are improbable hence the flagellum is designed.”

But I will admit, the step of invoking the login/password or lock-and-key metaphor is a step outside of pure statistics, and making the argument for design in the case of login/password and lock-and-key metaphors more rigorous is a project of future study.

Acknowledgments:
Mathgrrl, though we’re opponents in this debate, he strikes me a decent guy

NOTES:
The fact that life makes copies motivated Nobel Laureate Eugene Wigner to hypothesize a biotonic law in physics. That was ultimately refuted. Life does copy via a biotonic law but through computation (and the emergence of computation is not attributable to physical law in principle just like software cannot be explained by hardware alone).