Cambrian explosion Intelligent Design

Three puzzles that are real – A response to a skeptic

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In his latest post on Uncommon Descent, “Evolution” is a Political Controversy? (Or, am I Living in an Alternate Multiverse?), Gil Dodgen shot down claims by author Alan Rogers that the controversy over the theory of evolution is a political controversy.

It’s not a political controversy. It is:

1) An evidential controversy (for example, the fossil record, especially the Cambrian explosion).

2) A logical and computational controversy (the insufficiency of random errors producing highly complex, functionally integrated, self-correcting computer code).

3) A mathematical controversy (clearly insufficient probabilistic resources for anything but the most trivial changes based on Darwinian mechanisms).

Politics have nothing to do with any of this. It’s just basic reason, logic, and evidence.

Yesterday, I came across the following response by a skeptic who wasn’t terribly impressed:

1. The Cambrian “explosion” took many millions of years. It was originally called an “explosion” because research and information about it were limited at that time and it appeared that many species arose very quickly (geologically speaking). It is now usually called the Cambrian radiation.

2. Biological entities are not computers and do not contain “computer code”.

3. The probabilistic resources crap (sic) is based on made up numbers that mean absolutely nothing.

My message to the Skeptic (that’s what I’ll call him for the rest of this post) can be summed up in one sentence: you’ve got a lot of reading to do. Where to begin? Let’s address one point at a time.


Puzzle Number 1. The Cambrian Explosion

First, the Skeptic’s claim that the Cambrian explosion is now usually called the Cambrian radiation is simply rubbish. A quick search over on PubMed revealed 39 science papers with the phrase “Cambrian explosion” in the title, and only 7 with the phrase “Cambrian radiation” in the title. A Google search on the phrase “Cambrian explosion” brought up 342,000 hits, while “Cambrian radiation” brought up only 36,600 results. In scientific circles, as well as common parlance, the phrase “Cambrian explosion” is several times more common than “Cambrian radiation.”

Second, the Cambrian explosion took about 25 million years, by a fairly generous estimate. That is not “many millions of years”; compared to the age of the Earth (4,540 million years), it’s a geological eyeblink. The online brochure, Questions about the Cambrian Explosion, Evolution, and Intelligent Design lists several estimates of the length of the explosion, varying from 5 or 6 million years up to 20 million years.

Third, most of the thirty or so phyla of animals alive on Earth today arose during this narrow window of time, so the skeptic’s statement that it only “appeared that many species arose very quickly (geologically speaking)” (italics mine) during the Cambrian explosion is flat wrong.

Even scientists who have no sympathy for Intelligent Design acknowledge that it poses a real puzzle for evolutionists. In a science journal article entitled MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion (BioEssays 31:736-747, 2009. DOI: 10.1002/bies.20090003), authors Kevin J. Peterson, Michael R. Dietrich and Mark A. McPeek argue that the term “explosion” is an apt one:

One of the most interesting challenges facing paleobiologists is explaining the Cambrian explosion, the dramatic appearance of most metazoan animal phyla in the Early Cambrian, and the subsequent stability of these body plans over the ensuing 530 million years…

Beginning some 555 million years ago the Earth’s biota changed in profound and fundamental ways, going from an essentially static system billions of years in existence to the one we find today, a dynamic and awesomely complex system whose origin seems to defy explanation. Part of the intrigue with the Cambrian explosion is that numerous animal phyla with very distinct body plans arrive on the scene in a geological blink of the eye, with little or no warning of what is to come in rocks that predate this interval of time…

Darwin’s explanation for the Cambrian explosion was that the fossil record was incomplete, but since Darwin penned his hypothesis over 150 years ago, we have learned two immutable facts about the late Precambrian fossil record. First, although chock full of organic forms, the Ediacaran [the period preceding the Cambrian – VJT] is remarkably reticent with its animal ancestors — besides sponges only Kimberella has received broad acceptance as a metazoan, possibly a molluscan metazoan. And second, the geologic fossil record is a fairly accurate representation of biotic evolution such that both molecular clock analyses and paleoecological considerations agree that mobile macrophagous animals are no older than about the Ediacaran itself. Thus, elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself, and cannot be explained away by coupling extinction of intermediates with long stretches of geologic time, despite the contrary claims of some modern neo-Darwinists. (Emphases mine – VJT.)

The authors are not Intelligent Design theorists; they propose that “miRNAs [microRNAs] might play an important role in shaping metazoan macroevolution, and might be part of the solution to the Cambrian conundrum.” Time will tell whether their proposal has any scientific merit; however, the authors deserve full credit for at least facing up to the problem.

It would appear that the skeptic has not acquainted himself with the Intelligent Design movement’s literature on the Cambrian explosion, so I’d like to point him to some online resources that may whet his appetite:

Easy reading on the Cambrian explosion

The Cambrian Explosion: Biology’s Big Bang by blogger Wintery Knight.

Does the Cambrian Explosion disprove Darwinian evolution? by blogger Wintery Knight.

Questions about the Cambrian Explosion, Evolution, and Intelligent Design (brochure at the Darwin’s Dilemma Website).

More advanced reading

Stephen C. Meyer, Marcus Ross, Paul Nelson & Paul Chien, The Cambrian Explosion: Biology’s Big Bang in Darwinism, Design, and Public Education (John A. Campbell and Stephen C. Meyer eds., Michigan State University Press, 2003).

Stephen C. Meyer, The origin of biological information and the higher taxonomic categories, in Proceedings of the Biological Society of Washington, Vol. 117(2):213-239 (2004).

Puzzle Number 2. The Origin of Computer code in organisms – yes, it’s real!

As far as I am aware, no Intelligent Design proponent has ever claimed that biological organisms are computers. What ID proponents do claim is that there is digital code in the cells of living things. That’s not a metaphor. That’s real. In the words of Microsoft chairman (and agnostic) Bill Gates:

Human DNA is like a computer program but far, far more advanced than any software we’ve ever created. (The Road Ahead, Penguin: London, Revised, 1996 p. 228.)

Or as the evolutionary biologist Professor Richard Dawkins puts it:

“The machine code of the genes is uncannily computer-like. Apart from differences in jargon, the pages of a molecular biology journal might be interchanged with those of a computer engineering journal.” (River Out of Eden: A Darwinian View of Life, New York:Basic Books/Harper Collins, 1995, p.17.)

Here’s another quote from Professor Dawkins:

“Physics books may be complicated, but … the objects and phenomena that a physics book describes are simpler than a single cell in the body of its author. And the author consists of trillions of those cells, many of them different from each other, organized with intricate architecture and precision-engineering into a working machine capable of writing a book… Each nucleus … contains a digitally coded database larger, in information content, than all thirty volumes of the Encyclopedia Britannica. And this figure is for each cell, not all the cells of the body put together.” (The Blind Watchmaker: Why the Evidence Reveals a Universe Without Design. New York, Norton, 1987, pp. 2-3.)

In the interests of scientific accuracy, I should point out to readers that DNA itself is not a program. Neither would it be accurate to say that the suite of programs running within the cell are simply written on its DNA. Instead, DNA could be better described as a data storage device, used by the programs running the cell.

ID proponent Dr. Don Johnson, who has both a Ph.D. in chemistry and a Ph.D. in computer and information sciences, has made an even stronger case for the reality of computer code in living organisms. On April 8, 2010, Dr. Johnson gave a presentation entitled Bioinformatics: The Information in Life for the University of North Carolina Wilmington chapter of the Association for Computer Machinery. Dr. Johnson’s presentation is now on-line here. Both the talk and accompanying handout notes can be accessed from Dr. Johnson’s Web page. Dr. Johnson spent 20 years teaching in universities in Wisconsin, Minnesota, California, and Europe. Here’s an excerpt from his presentation blurb:

Each cell of an organism has millions of interacting computers reading and processing digital information using algorithmic digital programs and digital codes to communicate and translate information.

On a slide entitled “Information Systems In Life,” Dr. Johnson points out that:

  • the genetic system is a pre-existing operating system;
  • the specific genetic program (genome) is an application;
  • the native language has a codon-based encryption system;
  • the codes are read by enzyme computers with their own operating system;
  • each enzyme’s output is to another operating system in a ribosome;
  • codes are decrypted and output to tRNA computers;
  • each codon-specified amino acid is transported to a protein construction site; and
  • in each cell, there are multiple operating systems, multiple programming languages, encoding/decoding hardware and software, specialized communications systems, error detection/correction systems, specialized input/output for organelle control and feedback, and a variety of specialized “devices” to accomplish the tasks of life.

But wait, there’s more! The following quotes, which are taken from reputable scientific sources, establish the scientific legitimacy of using terms like “instructions,” “code,” “information” and “developmental program” when speaking of the development of animal embryos (emphases are mine):

“We know that the instructions for how the egg develops into an adult are written in the linear sequence of bases along the DNA of the germ cells.” (James Watson et al., Molecular Biology of the Gene, 4th Edition, 1987, p. 747.)

And from a more recent source:

“The body plan of an animal, and hence its exact mode of development, is a property of its species and is thus encoded in the genome. Embryonic development is an enormous informational transaction, in which DNA sequence data generate and guide the system-wide spatial deployment of specific cellular functions.” (Emerging properties of animal gene regulatory networks by Eric H. Davidson. Nature 468, issue 7326 [16 December 2010]: 911-920. doi:10.1038/nature09645. Davidson is a Professor of Cell Biology at the California Institute of Technology.)

Here’s another recent quote, from an article by Schnorrer et al., on the development of muscle function in the fruitfly Drosophila:

“It is fascinating how the genetic programme of an organism is able to produce such different cell types out of identical precursor cells.” (Schnorrer F., C. Schonbauer, C. Langer, G. Dietzl, M. Novatchkova, K. Schernhuber, M. Fellner, A. Azaryan, M. Radolf, A. Stark, K. Keleman, & B. Dickson, Systematic Genetic Analysis of Muscle Morphogenesis and Function in Drosophila. Nature, 464, 287-291 (11 March 2010). doi:10.1038/nature08799.)

And finally, here is another quote from Professor Richard Dawkins, in The Greatest Show on Earth (Transworld Publishers, London, Black Swan edition, 2010, p. 217):

“…[T]here is a mystery, verging on the miraculous (but never quite getting there) in the very fact that a single cell gives rise to a body in all its complexity. And the mystery is only somewhat mitigated by the feat’s being achieved with the aid of DNA instructions. The reason the mystery remains is that we find it hard to imagine, even in principle, how we might set about writing the instructions for building a body in the way the body is in fact built, namely by what I have just called ‘self-assembly’, which is related to what computer programmers call a ‘bottom-up’, as opposed to a ‘top-down’, procedure.

Dawkins goes on to say that “local rules” make it plausible that this process was accomplished naturally, over a period of one billion years. Whether he is right on this point or not, what I find interesting is that he nevertheless feels the need to employ terms like “instructions” and “rules,” in order to describe the process whereby an embryo is put together.

In short: talk of codes and instructions is not anthropomorphic; it’s a perfectly accurate description of the way each cell works.

The Case for the Intelligent Design of the Cell in a Nutshell:

What accounts for the information in DNA? Part 3 of Stephen Meyer’s Series on the John Ankerberg Show (Skip the first three minutes, if you like.)

Or if you prefer a short 86-second video (a picture is worth 1,000 words):

The ATP Synthase Enzyme. Here’s my short commentary on the video: The video that proves Intelligent Design. I defy anyone to watch this and then tell me the cell wasn’t designed!

Puzzle Number 3. Insufficient Probabilistic Resources to Account for the Origin of Life

The Skeptic claimed that “the probabilistic resources crap (sic) is based on made up numbers that mean absolutely nothing.” I strongly suggest that he peruse Dr. Douglas Axe’s scientific papers at his leisure.

Recent Papers by Dr. Douglas Axe

The Case Against a Darwinian Origin of Protein Folds, Bio-Complexity, Vol. 2010.

Abstract

Four decades ago, several scientists suggested that the impossibility of any evolutionary process sampling anything but a miniscule fraction of the possible protein sequences posed a problem for the evolution of new proteins. This potential problem—the sampling problem —was largely ignored, in part because those who raised it had to rely on guesswork to fill some key gaps in their understanding of proteins. The huge advances since that time call for a careful reassessment of the issue they raised. Focusing specifically on the origin of new protein folds, I argue here that the sampling problem remains. The difficulty stems from the fact that new protein functions, when analyzed at the level of new beneficial phenotypes, typically require multiple new protein folds, which in turn require long stretches of new protein sequence. Two conceivable ways for this not to pose an insurmountable barrier to Darwinian searches exist. One is that protein function might generally be largely indifferent to protein sequence. The other is that relatively simple manipulations of existing genes, such as shuffling of genetic modules, might be able to produce the necessary new folds. I argue that these ideas now stand at odds both with known principles of protein structure and with direct experimental evidence. If this is correct, the sampling problem is here to stay, and we should be looking well outside the Darwinian framework for an adequate explanation of fold origins.

Here’s a short non-technical summary of Dr. Axe’s latest paper by blogger Wintery Knight:
Doug Axe publishes a new peer-reviewed paper on protein folding.

Earlier papers by Dr. Douglas Axe

(1) Douglas D. Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors,” Journal of Molecular Biology, Vol. 301:585-595 (2000). See here for the abstract.

(2) Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, 1-21 (2004). See here for the abstract.

Here’s Dr. Stephen Meyer’s summary of Douglas Axe’s article in his 2004 paper, “The Origin of Biological Information and the Higher Taxonomic Categories”:

“Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 10^77. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 10^77.”

Here’s Casey Luskin’s summary of Douglas Axe’s article in an essay entitled, Responding to the Youtube Challenge to Discovery Institute: Does Any Critic Out There Understand Intelligent Design? Anyone? …Anyone?:

Doug Axe’s research likewise studies genes that it turns out show great evidence of design. Axe studied the sensitivities of protein function to mutations. In these “mutational sensitivity” tests, Dr. Axe mutated certain amino acids in various proteins, or studied the differences between similar proteins, to see how mutations or changes affected their ability to function properly. He found that protein function was highly sensitive to mutation, and that proteins are not very tolerant to changes in their amino acid sequences. In other words, when you mutate, tweak, or change these proteins slightly, they stopped working. In one of his papers, he thus concludes that “functional folds require highly extraordinary sequences,” and that functional protein folds “may be as low as 1 in 10^77.”

Here’s a comment by blogger Wintery Knight in a post entitled, Doug Axe explains the chances of getting a functional protein by chance:

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.

An Important Update by Dr. Douglas Axe:

Correcting Four Misconceptions about my 2004 Article in JMB by Douglas Axe (May 4, 2011).

What is the relevance of all this for Intelligent Design?

The Skeptic may be wondering, “Does all this support Intelligent Design?” Dr. Douglas Axe certainly thinks so. John G. West reports that back in late 2006, Dr. Axe was asked via e-mail by New Scientist reporter Celeste Biever to respond to the charge

[t]hat you have neither confirmed nor denied claims by William Dembski (in his book “Debating Design: From Darwin to DNA” and in several articles he has written) that a paper you published in 2000 (J Mol Biol, 2000 Aug 18; 301(3):585-95) is evidence for ID, or by Stephen Meyer, in his paper “The origin of biological information” (PROCEEDINGS OF THE BIOLOGICAL SOCIETY OF WASHINGTON 117(2):213-239. 2004), that your 2004 paper (J Mol Biol. 2004 Aug 27;341(5):1295-315) is evidence for ID.

Dr. Axe wrote back the following, which New Scientist declined to quote:

I have in fact confirmed that these papers add to the evidence for ID. I concluded in the 2000 JMB paper that enzymatic catalysis entails “severe sequence constraints”. The more severe these constraints are, the less likely it is that they can be met by chance. So, yes, that finding is very relevant to the question of the adequacy of chance, which is very relevant to the case for design. In the 2004 paper I reported experimental data used to put a number on the rarity of sequences expected to form working enzymes. The reported figure is less than one in a trillion trillion trillion trillion trillion trillion. Again, yes, this finding does seem to call into question the adequacy of chance, and that certainly adds to the case for intelligent design.

Finally, here’s an excerpt from a short essays by Dr. Douglas Axe, entitled, Breaking News from the Academy: There’s Plenty of Time for Evolution!:

In the end, whether evolution has plenty of time or not depends on what you want to ascribe to it. It copes well with the most favorable adaptations conceivable (those offering substantial benefit after a single nucleotide substitution), but even slightly more complex tasks involving just two or three mutations can easily stump it [3,4]. The key question, then, is this: What, of all life’s marvels, can be accounted for in terms of the single-change adaptations that Darwinism explains? And the answer, if we take Dawkins’ illustration seriously, is: Nothing that approaches the complexity of a six-word sentence.

You don’t need a biology degree to see that this leaves Darwinism in a difficult position. In fact, oddly enough, it seems that biology degrees only make it harder to see.

The Skeptic charged that “the probabilistic resources crap (sic) is based on made up numbers that mean absolutely nothing.” I hope he’ll eat his words now.

Perhaps, at this point, the Skeptic will repeat his mantra that “Goddidit is a science stopper.” Any explanation, he will argue, has to be better than that one. So here’s my challenge to the skeptic: show me ONE alternative naturalistic explanation for the origin of the cell and for the rise in complexity that took place at the Cambrian explosion, which does NOT require any intelligent foresight. Show me calculations, demonstrating at least in principle that your mechanism is capable of generating the complexity found in living things. Go on – let’s see you do it!

62 Replies to “Three puzzles that are real – A response to a skeptic

  1. 1
    David W. Gibson says:

    I’ll try to interpret “skeptic” a bit differently. We may be agreeing violently here.

    First, the Skeptic’s claim that the Cambrian explosion is now usually called the Cambrian radiation is simply rubbish

    I admit I had not encountered the “Cambrian radiation” label. But how the label is spelled seems quite beside the point. What exactly WAS it, when is it reasonable to say that it started and ended, and what changes happened in the interim? Aren’t these the important questions?

    And I would say 25 million years is a fairly long period of time, far more than an eyeblink. I’m presuming the argument is being put forth that it’s simply not a long enough time for the observed changes (either explosion or radiation, take your pick or use some other word) to take place.

    Third, most of the thirty or so phyla of animals alive on Earth today arose during this narrow window of time, so the skeptic’s statement that it only “appeared that many species arose very quickly (geologically speaking)” (italics mine) during the Cambrian explosion is flat wrong.

    Not at all! Consider a huge tree, with many massive branches off the main trunk. But at one time, that huge redwood was only a few inches tall, and those massive branches were nothing more than twigs or even buds. Yes, with today’s hindsight, we can know that each of those twigs BECAME massive branches. But at the time, they were both tiny and very close together on the newly sprouted tree.

    And so it it is with the phyla. If any biologist today were transported back to (say) sometime early in the Cambrian, lacking knowledge of today’s phylum divisions and the radiation they’ve undergone in half a billion years, what he’d see would be a whole lot of critters essentially similar in size, with various body plans. He might even classify them into only two or three orders.

    Nonetheless, it does appear from our hindsight to be a period of fertile experimentation in body plans and life styles. Part of this is probably the advent of “hard parts”, so that we see records of proliferating forms that left no records before they developed these hard parts, but it was still a time of rapid radiation. Was it more rapid than evolutionary processes could possibly account for? That seems the key question here.

    (And I agree that HOW this occurred is worth studying. We should remember that evolution ITSELF was evolving rapidly.)

    The central issue with Problem #2 is, just how far can the computer analogy be pushed before it begins to break down? As vjtorley says, organisms are not computers. At some point they work differently. The metaphor of organisms as products of computer code can be quite useful in genetic engineering. Without question, DNA contains the instructions for building organisms. But this doesn’t ipso facto make those instructions externally designed and inserted, anymore than an intelligent designer pushes water into a sphere in microgravity. Instead, this is a practical, efficient way to facilitate replication of anything complicated.

    So here’s my challenge to the skeptic: show me ONE alternative naturalistic explanation for the origin of the cell and for the rise in complexity that took place at the Cambrian explosion, which does NOT require any intelligent foresight. Show me calculations, demonstrating at least in principle that your mechanism is capable of generating the complexity found in living things. Go on – let’s see you do it!

    This seems an odd challenge. Nearly all evolutionary biologists feel it has long since been fully adequately answered, at least to the satisfaction of anyone who doesn’t start from the non-negotiable position that it’s wrong.

    But even if they’re all wrong, we must beware of dichotomous thinking – that if 2+2 is not 5, therefore it MUST be 17! There’s no crime in saying that there IS such a mechanism, it MIGHT be the evolutionary processes biologists investigate, it MIGHT be external design, and it MIGHT be some other process entirely. It MIGHT be multiple designers. And they MIGHT have been competing and sabotaging one another’s work, producing phyla in the process.

    I’ll admit that my personal bias is for a TESTABLE hypothesis, and I haven’t been able to operationalize any good test for design beyond “It looks designed to me, and I can’t imagine any other possible mechanism.” I can presume God did it, but His imagination is surely so far beyond mine as to be incomprehensible. So most likely He contrived a mechanism that will require considerable inspiration to ferret out at this late date. But it should be possible to do so, even if slowly, tentatively and usually incorrectly. Sure, the Cambrian era “designed” lots and lots of new critters. But HOW? It’s not entirely fair to say “If you don’t know, then MY explanation must be right.”

  2. 2
    NickMatzke_UD says:

    Re: calculation — Rates of change can be measured, in units of Haldanes or Darwins. They can be measured in the present day, and they can be measured in the fossil record. It has long been known that rates of change observed in the fossil record are much lower than rates of change observable when directional selection is going on today.

    So actually, change in the fossil record is much slower than the maximum allowed by observed evolutionary processes.

    There is some famous work on this:
    http://www-personal.umich.edu/...../Rates.htm

    The idea that the Cambrian “phyla” are as impressively different as the “phyla” today, 530 million years later, is just wrong. Most of the early Cambrian critters were very small (a few centimeters or less) and resembled worms/slugs much more than they do now. Back then, early “vertebrates”, echinoderms, molluscs, arthropod relatives, etc. all look like worms/slugs with some spiffy new features (legs, shells, swimming, depending).

    There are all sorts of problems with the “phylum” concept:
    http://pandasthumb.org/archive.....yla-1.html

    …which any well-informed treatment of the Cambrian would have to address.

    So: Do we *really* have to drag God down from Heaven to gradually fiddle with worm diversity over *millions* of years? Because that’s what you IDists are proposing.

  3. 3
    nullasalus says:

    Do we *really* have to drag God down from Heaven to gradually fiddle with worm diversity over *millions* of years? Because that’s what you IDists are proposing.

    Hey Nick. Do you ever get tired of lying?

    I mean, you know that ID isn’t about ‘dragging God down from Heaven to gradually fiddle with worm diversity’. Yet you repeat this sort of crap over and over, despite being corrected repeatedly, despite having it pointed out to you that ID is silent on the nature of the designer, and despite it being noted that the range of possible designers could far beyond ‘God in Heaven’.

    What you said just known is a lie. It’s flat out dishonest, and you clearly should know better. And really, anyone looking on at this conversation should ask “If Nick is willing to lie about this, where else is he lying? Can I trust him when he gives an interpretation of scientific data?”

    So please, Nick. Give honesty a try for a change.

  4. 4
    GilDodgen says:

    VJ,

    I am somewhat humbled that you have used my post as the source for this essay. I consider you to be one of the most articulate, insightful, intelligent, and well-informed ID apologists on this forum, or anywhere else.

    I’m just a lowly classical concert pianist, artificial-intelligence and aerospace R&D software engineer, and former Dawkins-style atheist, who, after reading Michael Denton’s first book declared, “Unholy crap, I’ve been conned! This Darwinism stuff makes no sense.”

    Michael Behe had the same reaction after reading Denton’s book.

    There were two real kickers that finally convinced me that Darwinism is not only junk pseudoscience, but even worse, a philosophical apologetic designed to do away with any inference to design, even when design screams at us with ear-shattering decibels from every corner of modern science, whether biological, computational, mathematical, or cosmological.

    The first kicker is the trajectory of the evidence. If Darwinism is true, the more we learn, the more Darwinian theses should be validated. But the exact opposite is the case. The more we learn, the more the fossil record looks profoundly and consistently discontinuous, and the more excuses must be made for this transparent disconnect between the evidence and the theory. The more we learn about the complex information-processing systems of the cell, the more excuses must be made for how random processes could have engineered this incredible technology.

    The second kicker is the reaction of Darwinists to the ID challenge, especially those with irretrievable investments in their careers and materialistic worldviews. They get the vapors. Go apoplectic. Claim that ID will destroy all of modern science, science education, and rationality. People will die because we won’t be able to invent antibiotics. A theocracy is impending!

    This kind of reaction to thoroughly rational challenges to a reigning “scientific” orthodoxy is a sure sign that the orthodoxy is on the verge of collapse.

  5. 5
    vjtorley says:

    David W. Gibson

    Thank you for your post. I’d like to address your key points. You write:

    If any biologist today were transported back to (say) sometime early in the Cambrian, lacking knowledge of today’s phylum divisions and the radiation they’ve undergone in half a billion years, what he’d see would be a whole lot of critters essentially similar in size, with various body plans. He might even classify them into only two or three orders.

    I have to respectfully disagree. From my reading of the paper I cited by Peterson, Dietrich and McPeek, it seems that the authors of that paper would disagree with you. The authors write of “the dramatic appearance of most metazoan animal phyla in the Early Cambrian, and the subsequent stability of these body plans over the ensuing 530 million years,” and they add that “numerous animal phyla with very distinct body plans arrive on the scene in a geological blink of the eye, with little or no warning of what is to come in rocks that predate this interval of time.” That doesn’t sound like your evocative image of ” tiny and very close together on the newly sprouted tree.” Nor does it sound like “a whole lot of critters essentially similar in size,” whom a biologist “might even classify … into only two or three orders” if he were judging by appearance alone. On the contrary, the authors of the paper argue that there was more disparity in living things back then than there was today.

    You also write:

    Without question, DNA contains the instructions for building organisms. But this doesn’t ipso facto make those instructions externally designed and inserted, anymore than an intelligent designer pushes water into a sphere in microgravity.

    Well, why does water form a sphere in microgravity? According to this How Come? Website, the answer has to do with the laws of Nature:

    This surface tension is the key to the shape of liquid water spilled in microgravity. Water is free to leave an open container in microgravity, since gravity isn’t keeping it pinned to the bottom. As a parcel of water free-falls in the space station, surface tension pulls the water into a sphere. How come? Since the parcel is free-floating blob, it has one smooth surface exposed on all sides. All molecules on the surface tend to be tugged down and sideways with equal tension by their fellow molecules. And so the blob of water pulls into a compact sphere — the most efficient shape in nature, with the smallest possible surface area.

    But as Dr. Stephen Meyer explains in the program, What accounts for the information in DNA? Part 3 of Stephen Meyer’s Series on the John Ankerberg Show, we know that there is nothing about the chemistry of DNA that dictates the sequence of bases. Necessity can account for the shape of water droplets in microgravity, but not the specified complexity of the DNA molecule, to use a term coined by Leslie Orgel.

    That leaves us with chance and agency. Biologists have long given up on the latter as an adequate mechanism to explain the origin of living cells.

    Concerning my “Let’s see you do it!” challenge, I was mystified to read your response:

    Nearly all evolutionary biologists feel it has long since been fully adequately answered, at least to the satisfaction of anyone who doesn’t start from the non-negotiable position that it’s wrong.

    I find this mystifying because while I’ve seen plenty of qualitative attempts to account for the origin of life, no-one, to the best of my knowledge, has submitted a paper with numerical, quantitative calculations showing that over a period of one billion years, the emergence of a simple bacterium from a soup of amino acids (or an alkaline vent, if you prefer) would be a reasonably probable event. That’s all I want – just a proof of concept, supported by some figures. Some time ago, I composed a post entitled, The 10^(-120) challenge, or: The fairies at the bottom of the garden in which I wrote that my faith in Intelligent Design was falsifiable, and I listed two criteria by which it might be falsified. One was:

    An empirical or mathematical demonstration that the probability of the emergence of life on Earth during the past four billion years as a result of purely natural processes, without any intelligent guidance and starting from a random assortment of organic chemicals, is greater than 10^(-120). [Note: when I wrote “life,” I meant “cellular life.”]

    This wasn’t the first time I had issued this challenge, as you’ll see when you read my post. Concerning my previous challenge, I wrote:

    I didn’t ask for a detailed step-by-step pathway. I didn’t ask for a calculation of the number of steps involved. I didn’t ask for a detailed description of the starting point or end point of these evolutionary transformations. I didn’t ask for a detailed description of the evolutionary mechanism. All I wanted was a feasibility demonstration – what we might call a “proof of concept.” And I wasn’t asking for proof that the proposed mechanism (commonly dubbed “random mutations plus natural selection”) would work. All I wanted was a rigorous mathematical or empirical argument that there was a probability greater than 1 in 10^120 that it could work, over a four-billion-year time period. A back-of-the-envelope calculation would have satisfied me, had it been to the point. A scientific model of the changes involved, which allowed a rough calculation of the probability of their occurrence as a result of “random mutations plus natural selection” over a specified time-period, would have been even nicer.

    I was rather disappointed that nobody took me up on the challenge I issued, or even referred to a paper in which the challenge had been met.

    The complete lack of quantification in scientists’ discussion of mechanisms for the origin of life has sadly disillusioned me, and it makes me suspect that there’s a whole lot of obfuscation going on. Whatever it is that the scientists are doing when they write about their speculative hypotheses, it’s not science. Real science has lots of numbers in it. I’ve had to really dig and delve to get the numbers that matter when modeling the origin of life.

    Total number of carbon atoms in an E. coli bacterium: about 7,000,000,000. Minimum number of base pairs in the genome of any living thing that we know of: about 500,000. Minimum number of proteins required by any living thing that we know of: about 500. Length of an average protein: about 300 amino acids. Odds of just ONE SMALL protein forming by the best unguided natural mechanism we know: about 10^-77. How would you account for the first cell, given data like that?

    You write:

    There’s no crime in saying that there IS such a mechanism, it MIGHT be the evolutionary processes biologists investigate, it MIGHT be external design, and it MIGHT be some other process entirely.

    Fair enough. Personally, I’m quite happy to let a hundred hypotheses bloom, as long as no-one tells me that the obvious one (Intelligent Design) isn’t science.

    You also write:

    I’ll admit that my personal bias is for a TESTABLE hypothesis, and I haven’t been able to operationalize any good test for design beyond “It looks designed to me, and I can’t imagine any other possible mechanism.” I can presume God did it, but His imagination is surely so far beyond mine as to be incomprehensible. So most likely He contrived a mechanism that will require considerable inspiration to ferret out at this late date. But it should be possible to do so, even if slowly, tentatively and usually incorrectly.

    I wholeheartedly endorse your quest for a testable hypothesis. I’d very much like to know how God made the first living cell, and I think He meant us to find out. In the meantime, I have a very simple testable hypothesis: in the organic world, there should be a clear divide between molecules that we can affirm must have been designed (on probabilistic grounds) and molecules that need not have been designed. A blurry boundary would seriously weaken the case for ID, in my opinion: instead, there should be a very sharp divide between the two.

    In the meantime, the research of Dr. Douglas Axe makes me feel confident on purely probabilistic grounds that the millions of different kinds of proteins found in various species of living things were all designed. That much appears certainly beyond reasonable doubt.

  6. 6
    junkdnaforlife says:

    “If (B)Nick is willing to lie about this, where else is he lying? (A)Can I trust him when he gives an interpretation of scientific data?”

    P(A|B)=0%

  7. 7
    Matteo says:

    So: Do we *really* have to drag God down from Heaven to gradually fiddle with worm diversity over *millions* of years? Because that’s what you IDists are proposing.

    So, do we *really* have to make theological statements about how God shouldn’t behave in order to bolster our scientific biases?

  8. 8
    bornagain77 says:

    Nick how many novel proteins do you think arose in the Cambrian explosion???

    Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
    Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.
    http://www.ncbi.nlm.nih.gov/pubmed/15321723

    Correcting Four Misconceptions about my 2004 Article in JMB — May 4th, 2011 by Douglas Axe
    http://biologicinstitute.org/2.....le-in-jmb/

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010
    Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.”
    http://bio-complexity.org/ojs/.....O-C.2010.1

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe, Jay Richards – audio
    http://intelligentdesign.podom.....9_03-07_00

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://biologicinstitute.org/2.....t-collide/

    Stability effects of mutations and protein evolvability. October 2009
    Excerpt: 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,,
    http://www.ncbi.nlm.nih.gov/pubmed/19765975

    “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.”
    Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    Nature Paper,, Finds Darwinian Processes Lacking – Michael Behe – Oct. 2009
    Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites)
    http://www.evolutionnews.org/2.....hes_t.html

  9. 9
    vjtorley says:

    Nick Matzke,

    Thank you for your post. I’d just like to address your comment:

    The idea that the Cambrian “phyla” are as impressively different as the “phyla” today, 530 million years later, is just wrong. Most of the early Cambrian critters were very small (a few centimeters or less) and resembled worms/slugs much more than they do now. Back then, early “vertebrates”, echinoderms, molluscs, arthropod relatives, etc. all look like worms/slugs with some spiffy new features (legs, shells, swimming, depending).

    This comment reminds me of a conversation I had at the Australian National University back in 1979 (I was 18 then), with a pro-choice advocate who told me that a human fetus looks “rather like a frog” up until the fourth month. The proper response is: appearances can be very superficial. What lies beneath? I would want to look at things like cell types. Are the various cell types of living phyla today any more distinct than the corresponding cell types in their ancestors 500 million years ago, shortly after the Cambrian explosion? That’s what I would want to know.

    I had a very quick look at the Panda’s Thumb essay on phyla, and I’ll have a closer look later. It looks interesting.

    As I understand it, currently, there is a vigorous and ongoing debate in the scientific community as to whether a phylum should be defined morphologically or phylogenetically. However, a definition of phylum based on an organism’s body plan has recently been championed by paleontologists Graham Budd and Soren Jensen, who are both thorough-going evolutionists. As Professor Michael Behe writes in his book, “The Edge of Evolution” (2008, Free Press, paperback edition, p. 197):

    Animals are divided into a number of groups according to their general “body plan.” For example, one group of animals, chordates (which includes vertebrates like us), have a nerve chord arranged in the back of their bodies, whereas arthropods, the group that includes insects and crustaceans, have a nerve chord in the front. Biologists count dozens of fundamentally different body plans. Types of animals that have the same body plan are generally grouped together in the same phylum, which is the biological classification right under kingdom (kingdom divides organisms into bacteria, plants, animals, and a few other categories).

    It is a well-known fact that extinct organisms belonging to a phylum are often difficult to classify, because they may have diverged from a phylum’s history before the characters that define the modern phylum were all acquired. However, this fact in no way invalidates phyla as natural anatomical categories. It simply means that some of the characters that characterize the modern phylum are not truly essential traits, but specializations. And of course, extinct organisms may have specializations of their own. In other words, identifying the truly essential traits which define a phylum may require some detective work on the part of scientists. But I guess that’s hardly surprising news.

    I’ll be back later.

  10. 10
    David W. Gibson says:

    vjtorley,

    Thank you for your thoughtful response. I wonder how far apart we might actually be here.

    I have to respectfully disagree. From my reading of the paper I cited by Peterson, Dietrich and McPeek, it seems that the authors of that paper would disagree with you. The authors write of “the dramatic appearance of most metazoan animal phyla in the Early Cambrian, and the subsequent stability of these body plans over the ensuing 530 million years,” and they add that “numerous animal phyla with very distinct body plans arrive on the scene in a geological blink of the eye, with little or no warning of what is to come in rocks that predate this interval of time.”

    In light of today’s half a billion year perspective, I’d agree with you entirely. So I tried to be careful to deprive my hypothetical biologist of this information. And I agree with Nick that what he’d see, for the most part, would be variations on small worms. But we KNOW, with our hindsight, that those small variations BECAME distinctly different body plans.

    My reading (of Valentine and others) is that we examine each fossil through today’s eyes, trying to determine which of today’s phyla each might have been predecessor of. Of course, part of the problem is that the “varied worms” represent the ediacara entering the Cambrian, and not radiation exiting that period. Clearly, diversity branched in many directions relatively quickly. These were new critters, of course, faced with a vast vista of available niches. One would expect rapid radiation at some point in eukaryote evolution, a Big Idea with plenty of space to explore.

    we know that there is nothing about the chemistry of DNA that dictates the sequence of bases. Necessity can account for the shape of water droplets in microgravity, but not the specified complexity of the DNA molecule, to use a term coined by Leslie Orgel.

    What I was talking about was finding an efficient way to replicate complex patterns. DNA, as a program, is a superb packing mechanism. And I would speculate that MANY different packing mechanisms were tried. What we’re seeing now is the ones that worked best.

    (And incidentally, I try to approach this stuff with an open if not entirely blank mind. I notice that ALL your references and sources are creationist publications and materials. But the question we’re considering is, how did the Cambrian explosion come about? What drove it, and did it have enough time for natural processes to do it? Yes, we agree that the creationist answer, determined beforehand, is that ordinary natural processes would not have been sufficient. But what if the creationist orientation is wrong, or incomplete? This comes across very much like someone investigating the “best” form of government, and consulting ONLY Marxists!)

    I find this mystifying because while I’ve seen plenty of qualitative attempts to account for the origin of life, no-one, to the best of my knowledge, has submitted a paper with numerical, quantitative calculations showing that over a period of one billion years, the emergence of a simple bacterium from a soup of amino acids (or an alkaline vent, if you prefer) would be a reasonably probable event. That’s all I want – just a proof of concept, supported by some figures.

    I understand what you’re asking, and I don’t feel it is formulated usefully. I envision a global laboratory, performing billions of experiments simultaneously. AND I envision each successful experiment being widely adopted extremely rapidly. So if each experiment takes one minute, and there are 10 billion experiments going on at once, and the probability of some useful accident is one in a billion, then we have ten useful results per minute but the useful results are retained, all else is discarded. And the retained results spread through whole populations rapidly. The results are explosive, geometric.

    As a comparison, if I shuffle a deck and take the top 5 cards, what are my odds of (that is, how many trials will I require to get) a straight flush? It would surely take a long while. But what if I get to keep the cards I want, and keep drawing? Not only are my odds unity, but it will happen FAST. And to me, this seems so obvious I don’t understand the demand for a quantitative model.

    Let’s say life takes a billion separate required factors before we’d consider it life at all. According to my above speculations, we’re getting ten of those factors adopted per minute. At that rate, life would take 100 million minutes. Which is something less than 200 years! Now, my ex-rectum numbers are probably far from the actual reality, but hopefully the point is clear – if each success is retained, required timescales contract enormously. I get my straight flush within a couple of minutes.

    The complete lack of quantification in scientists’ discussion of mechanisms for the origin of life has sadly disillusioned me, and it makes me suspect that there’s a whole lot of obfuscation going on.

    Hopefully, you understand that there is no way to travel back in time to sample the success rate or the retention rate of successes. These numbers can at best be very hairy estimates. Are you disillusioned because scientists are unwilling to fabricate fictional data? All they can do is plug in not-unreasonable numbers into models, and see the results. Which very clearly allow a Cambrian explosion.

    Total number of carbon atoms in an E. coli bacterium: about 7,000,000,000. Minimum number of base pairs in the genome of any living thing that we know of: about 500,000. Minimum number of proteins required by any living thing that we know of: about 500. Length of an average protein: about 300 amino acids. Odds of just ONE SMALL protein forming by the best unguided natural mechanism we know: about 10^-77. How would you account for the first cell, given data like that?

    Iteratively, of course. Clearly, no modern cell is going to happen by spontaneous generation! But it seems rather, uh, misguided to even bother calculating the odds against it. Nobody I’m familiar with would suggest any such process. Instead, it’s suggested that a cumulative process started with some kind of self-replicating molecule. Once you have that, AND some error rate in the replication (to introduce variation) AND some resource shortage, you have a very small snowball at the top of a very long hill. Replication consumes resources, which quickly deplete. Variation rewards those varieties best at acquiring those resources – generation by generation ad infinitum Give this process a billion years (even a couple hundred million), and these molecules are going to be getting VERY sophisticated. At what point they might be considered alive is a judgment call.

    In the meantime, I have a very simple testable hypothesis: in the organic world, there should be a clear divide between molecules that we can affirm must have been designed (on probabilistic grounds) and molecules that need not have been designed. A blurry boundary would seriously weaken the case for ID, in my opinion: instead, there should be a very sharp divide between the two.

    While I understand this, again I suspect you have not formulated your conditions very usefully. You are requiring (on probabilistic grounds) something I do not think any biologist would accept as remotely reasonable. I think you are looking at the end product of a very very long feedback loop, which very slowly and cumulatively increased in sophistication over thousands of millennia. And you are saying “what are the odds that this product happened ALL AT ONCE, just at random? Too low to bother with. Therefore, design!”

    In the meantime, the research of Dr. Douglas Axe makes me feel confident on purely probabilistic grounds that the millions of different kinds of proteins found in various species of living things were all designed. That much appears certainly beyond reasonable doubt.

    Maybe I am unreasonable (wouldn’t surprise me at all). But I read Axe as spending his efforts proving the impossibility of events nobody ever suggested WERE possible. If we assume the only way to produce a complex protein is by “all at once and nothing first” accident, then yes, we should most reasonably conclude design. But it we assume a very long iterative development process, where proteins started out simple, most didn’t work well enough, those that did became more complex, most of THEM didn’t work well enough and “lost out” to those that did, and we continue this process through Deep Time, then today’s proteins need no external designer at all. They MAY need a designer to create the chemical and physical rules, to create the raw materials, and even to create the vast periods of time required. But I suggest Axe would spend his valuable expertise more fruitfully investigating what IS proposed, rather than disproving what nobody believes anyway.

  11. 11
    Arthur Hunt says:

    What ID proponents do claim is that there is digital code in the cells of living things. That’s not a metaphor. That’s real.

    Of course it’s a metaphor.

    To illustrate, readers and commenters here can try to answer the question – in a cell, what does the string AAAAAAAAAAAA code for?

    Please be specific, and make sure you keep your answer limited to things that the concept of a “digital code” allows.

    (Stephen Meyer answered this question in a manner of speaking in May 2010 at Biola, and his answer clearly made my point. Maybe someone here can do better.)

  12. 12
    David W. Gibson says:

    bornagain77:

    One difficulty with your presentation, at least from my point of view, is that your sources (all both of them) present a very narrow and clearly biased picture of this material. EVERY ONE of your sources, with maybe one exception, is either Douglas Axe or Michael Behe.

    As a comparison, let’s say I was presenting material in support of global warming, and EVERY SINGLE ONE of my sources came from the Sierra Club. Yes, if you were a member of the Sierra Club, you’d find this convincing. But if you disagreed with their view, how credible and objective would you find my selection of sources?

    You seem to be approaching this material like a trial lawyer, hired to win an adversarial proceeding no matter what the underlying fact situation! But at least we know the trial lawyer is PAID to have his mind made up despite the facts, that’s his job. And if the real perp he’s defending gets off, he wins. If an innocent person he’s prosecuting is punished, he wins!

    I really don’t like this legal model applied to science.

  13. 13
    nullasalus says:

    David Gibson,

    EVERY ONE of your sources, with maybe one exception, is either Douglas Axe or Michael Behe.

    Isn’t that a catch-22 setup? Anyone who agrees with Behe or Axe is going to get categorized with ID proponents anyway. At which point the complaint will be, what – you’re only quoting scientists who agree with you to bolster your point. What’s the alternative? “Quote someone who disagrees with your view to support your view”?

    But it we assume a very long iterative development process, where proteins started out simple, most didn’t work well enough, those that did became more complex, most of THEM didn’t work well enough and “lost out” to those that did, and we continue this process through Deep Time, then today’s proteins need no external designer at all.

    Or maybe they did, even assuming that process. The ‘long iterative development process’ may have been a development process. Or maybe it was purposefully tweaked at points. Or maybe the process’ outcome was known in advance.

    Either way, why should that assumption reign from the outset – especially when we know of an alternative “mechanism” in the form of design?

  14. 14
    vjtorley says:

    David Gibson,

    Thank you for your post. I just have time for a very quick comment before I go out. You write:

    I notice that ALL your references and sources are creationist publications and materials.

    Would you call Professor Michael Behe a creationist? He accepts common descent and has acknowledged in his latest book, The Edge of Evolution, that he doesn’t require supernatural intervention to get life started – he’s happy with front-loading at the time of the Big Bang.

    I quite understand your concept of a global laboratory, but my point is that if (as Dr. Axe has shown) we can’t even build a single functional protein, what hope is there of building DNA, let alone a cell?

    As for your suggestion that proteins started out small and gradually grew bigger, Dr. Stephen Meyer discusses that very proposal in his book, Signature in the Cell, in the footnotes on page 527. Very briefly: short proteins require a hydrophilic exterior. To build a larger structure round them, at least some of this hydrophilic exterior would have to become interior to thee larger structure. But this requires that a region of hydrophilic surface becomes hydrophobic, which in turn requires many simultaneous amino acid changes. Thus having a short protein contributes little or nothing to building a larger one.

    I’ll type up the whole passage for you later.

    Actually, Dr. Axe addresses the very same objection in his 2010 paper, The Nature of Protein Folds: Quantifying the Difficulty of an Unguided Search through Protein Sequence Space on page 412 of The Nature of Nature. You might also like to have a look at his other paper, The Case Against a Darwinian Origin of Protein Folds which I referenced above: http://bio-complexity.org/ojs/.....O-C.2010.1

    The overall point he makes here is that useful proteins of any sort – short or long – are so rare that getting to a long one by gradual steps would be a bit like getting to Saturn by jumping from Earth to Mars, and then on to Jupiter and then to Saturn. It’s not feasible.

    Incidentally, find it extremely hard to believe that in the 11-plus years that Dr. Axe has been researching the origin of proteins, no-one has ever approached him and said, “Dr. Axe, if we assume a very long iterative development process, where proteins started out simple, most didn’t work well enough, those that did became more complex, most of THEM didn’t work well enough and ‘lost out’ to those that did, and we continue this process through Deep Time, then today’s proteins need no external designer at all!” That’s just not credible.

  15. 15
    Eocene says:

    vjtorley:

    “The overall point he makes here is that useful proteins of any sort – short or long – are so rare that getting to a long one by gradual steps would be a bit like getting to Saturn by jumping from Earth to Mars, and then on to Jupiter and then to Saturn. It’s not feasible.”
    =====

    That’s why it’s called FAITH. All you have to do is believe. Just like Agent Mulder.

  16. 16
    bornagain77 says:

    David Gibson, perhaps some Darwinian sources??

    Proteins Did Not Evolve Even According to the Evolutionist’s Own Calculations but so What, Evolution is a Fact
    Excerpt: For instance, in one case evolutionists concluded that the number of evolutionary experiments required to evolve their protein (actually it was to evolve only part of a protein and only part of its function) is 10^70 (a one with 70 zeros following it). Yet elsewhere evolutionists computed that the maximum number of evolutionary experiments possible is only 10^43. Even here, giving the evolutionists every advantage, evolution falls short by 27 orders of magnitude.
    http://darwins-god.blogspot.co.....d-not.html

    ===================

  17. 17
    Mung says:

    Are there any honest skeptics?

  18. 18
    vjtorley says:

    FYI David W. Gibson, Nick Matzke

    Why a short protein couldn’t have been modified ste-by-step into a longer one

    Taken from Signature in the Cell by Dr. Stephen Meyer (HarperOne, New York, 2009), pp. 527-528.

    Dr. Meyer writes:

    “Sometimes after I explain the odds against producing a protein of even modest length by chance, someone will ask why a shorter functional protein couldn’t have arisen by chance and then gradually evolved into a larger one. Sometimes critics point out that some functional acid chains, such as peptide hormones, have fewer than 150 amino acids. Critics ask me, “Couldn’t such molecules have arisen by chance and then evolved into longer functional molecules?”

    “There are a number of problems with this scenario.

    “First, functional proteins (including all enzymes) depend upon complex folds, or ‘tertiary structures.’ Attaining tertiary structures in proteins requires about 50 properly sequenced amino acids for the simplest structures and many more (typicaly hundreds) for more typical structures. Moreover, these thresholds of minimal function vary from protein to protein. Just because one protein fold or tertiary structure may need ‘only’ 50 specifically sequenced amino acids does not mean that another can form with that few. Most of them can’t. The protein equivalent of a ruler may form with only 50 amino acids, but the hammer and saw may need 150, the wrench 200, and the drill 300. Many of the functions that a minimally complex cell requires depend on these longer proteins. Thus, the presence of some shorter proteins or peptide hormones in living systems does nothing to obviate the need for many longer proteins in the origin of life.

    “Moreover, as protein chemist Doug Axe explains in more detail in a forthcoming article (‘The Nature of Protein Folds: Quantifying the Difficulty of an Unguided Search through Protein Sequence Space’) there are physical reasons that short proteins with small tertiary structures can’t be gradually transformed into larger tertiary structures. Short proteins typically exhibit a hydrophilic exterior. To build a larger structure around them, at least some of this hydrophilic exterior would have to become interior to the larger structure. But this requires, among other things, that a region of hydrophilic surface become hydrophobic, which in turn requires many simultaneous amino acid changes. Having a short protein to start with contributes little or nothing to building a larger one. The same probabilistic hurdles have to be overcome in sequencing.

    “In any case, it is important to distinguish between peptides that function without a folded structure at all, and proteins that function only with a folded structure. The former (which includes the shorter peptide hormones) are functional only by virtue of binding to larger folded protein structures. But this implies that these shorter molecules have no function – and no selective advantage – apart from the prior existence of much larger protein molecules. Thus, citing functional peptides as a starting point in evolution begs the question as to the origin of the larger protein molecules that give them functional significance. It only pushes the problem back to where it started – to the problem of explaining the orogin of large functionally specified proteins by chance. Indeed, absent long-functional protein molecules – and realistically, a minimally complex self-reproducing cell – there would be no content to confer functional significance or advantage on either unfolded peptide hormones or shorter proteins (for that matter).”

  19. 19
    Mung says:

    David w. Gibson:

    As a comparison, if I shuffle a deck and take the top 5 cards, what are my odds of (that is, how many trials will I require to get) a straight flush? It would surely take a long while. But what if I get to keep the cards I want, and keep drawing? Not only are my odds unity, but it will happen FAST. And to me, this seems so obvious I don’t understand the demand for a quantitative model.

    Let’s say there is one, and let’s call it CSI.

    Out of all possible 5 card combinations drawn from the 52 card deck there are only 4 that constitute a royal flush.

    If you’re able to beat the odds and come up with a royal flush FAST I’d say that’s a pretty good indicator intelligent causation.

    Why do you think some other process could do the same thing without any intelligence involved?

    Are you sure you WANT a quantitative model? Isn’t it easier to pretend that the impossible is possible without one?

    In a deck of 52 cards there are 20 that can be used to contribute to a royal flush. Not bad odds of getting one on the first attempt.

    20:32

    But then say you got one.

    Now you have only four more cards left in the deck that can contribute to your royal flush.

    4:51, then 3:50, then 2:49, then 1:48

    How much time do you plan to spend on this little project of yours?

  20. 20
    David W. Gibson says:

    nullasalus:

    Isn’t that a catch-22 setup? Anyone who agrees with Behe or Axe is going to get categorized with ID proponents anyway. At which point the complaint will be, what – you’re only quoting scientists who agree with you to bolster your point. What’s the alternative? “Quote someone who disagrees with your view to support your view”?

    Well, this is why I spoke of an adversarial orientation. To me, the question is, HOW did this happen. And if there is legitimate disagreement among experts, then the answer to this question probably (usually) is some combination of views, and (since science relies on reality as an arbiter, and eventually there IS agreement based on the sheer weight of research results) relying on only one view is a way of kidding ourselves.

    If someone disagrees with my view, to me this is valuable. It might very well mean that my view is incomplete or poorly informed, and that I have more to learn. Which I won’t do if I simply tune out everything I disagree with. Especially if I’m not very knowledgeable in this field, and “my view” is based largely on ignorant preference and emotional comfort.

    The ‘long iterative development process’ may have been a development process. Or maybe it was purposefully tweaked at points. Or maybe the process’ outcome was known in advance.

    Yes, exactly so! Thank you. Of course that would have been a development process. And could easily have been tweaked constantly, by means we aren’t capable of detecting, to produce some target result. At best, we can study what LOOKS like natural processes, even if we can never know just how natural they are.

    ———————————-

    vjtorley,

    I quite understand your concept of a global laboratory, but my point is that if (as Dr. Axe has shown) we can’t even build a single functional protein, what hope is there of building DNA, let alone a cell?

    As far as I can tell, Dr. Axe has shown that we can’t ‘build’ a single functional protein (1) using the building method he has proposed, and (2) to perform a modern function, billions of years of development from the earliest proto-proteins, whatever they were or whatever they did.

    (Also, you may find yourself persuaded that proteins can’t possibly develop out of predecessor similar molecules, but I’m not quite so willing to simply dismiss a history I can’t know as impossible. What Meyer seems to have done here is to ASSUME some prior form, show that his assumed form can’t work, and conclude that there could have been no prior form of any kind. I don’t think this conclusion follows properly.)

    Again, maybe I’m being unreasonable here, but as far as I can tell, Axe isn’t asking the same question I would. I would ask, HOW did proteins actually develop? Was there any conceivable pathway for which we can find evidence? How would we look for such a pathway?

    In contrast, Axe seems to be asking “How can I show that proteins must have been designed?” And THAT is a very different question. If I asked myself that question, I would quite naturally propose development paths highly unlikely to be followed, and then demonstrate that they could not have been followed. In other words, my methodology would rest solidly on the conclusion I set out to support. I know from my own experience that confirmation bias is easy to build in, at every level starting with the formation of the basic hypotheses themselves.

    Sometimes after I explain the odds against producing a protein of even modest length by chance, someone will ask why a shorter functional protein couldn’t have arisen by chance and then gradually evolved into a larger one.

    But why assume that the first functional protein’s predecessor was a simpler protein? The only real requirement for evolutionary processes is that they be incremental, but this hardly constrains what those increments must be. The world of biology (at least as I understand it) is thick with functional structures “stolen” from similar structures performing very different functions.

    Meyer seems to be saying that the predecessor of the first functional protein couldn’t have been a protein, and THEREFORE there couldn’t have been any predecessor at all! And this conclusion could follow ONLY if there’s an unstated premise that there IS NO evolutionary pathway that could end up resulting in the first simple protein. Meyer takes that premise for granted, but it may not be correct.

    To me, this is like saying that today’s Chevrolet couldn’t possibly have reached the Pacific coast in 1830, because there were no roads. And no matter how simple we make our Chevy, it STILL couldn’t have got there. And even if there HAD been roads, there were no McDonalds stands, so the people would have starved before they got there anyway. And therefore people must have reached the Pacific by supernatural means!

  21. 21
    Mung says:

    20*4*3*2*1 = 480

    52*51*50*49*48 = 311,875,200

    480/311875200 = 1.539 x 10^-6

    Check my math?

  22. 22
    Mung says:

    David W. Gibson:

    At best, we can study what LOOKS like natural processes, even if we can never know just how natural they are.

    How do we decide what LOOKS like a natural process and what DOES NOT look like a natural process?

  23. 23
    David W. Gibson says:

    Mung:

    Let’s say there is one, and let’s call it CSI.

    Out of all possible 5 card combinations drawn from the 52 card deck there are only 4 that constitute a royal flush.

    If you’re able to beat the odds and come up with a royal flush FAST I’d say that’s a pretty good indicator intelligent causation.

    Well, I gave a procedure which would have done the same thing very quickly – just permit yourself to discard and keep drawing. That is, instead of trying for the royal flush all at once and nothing first, go for it incrementally, drawing one card at a time, keeping only the ones you need. This is how feedback processes tend to work.

    In a deck of 52 cards there are 20 that can be used to contribute to a royal flush. Not bad odds of getting one on the first attempt.

    20:32

    But then say you got one.

    Now you have only four more cards left in the deck that can contribute to your royal flush.

    4:51, then 3:50, then 2:49, then 1:48

    How much time do you plan to spend on this little project of yours?

    I’m not sure I’m following you here, so bear with me. Let’s say you decide to keep the first card that qualifies. In that case, AT MOST you’d need to draw 52 cards to complete your royal flush.

    But messy biology might work very differently (my understanding is that it does). The analogy would start by saying, you get to keep as many cards as you can hold provided you can see them all at once without dropping any. There is, after all, no limit on the size of the genome. And you get to draw and discard as many cards as you wish each turn. There is, after all, no strict limit on the number of new mutations per generation, or the number that are discarded or lost. NOW how long to get that royal flush? Not nearly as long.

    But real world biology is even simpler than that, because you do not NEED a royal flush, you need only a better hand than your competitors. Even a single pair might be a winner. NOW how long does it take?

    One of the errors I’ve seen (or at least I consider it an error) is for people to calculate the odds of getting the particular bridge hand they were dealt, rather than the odds of being dealt a bridge hand of any kind. And so people kind of assume that whatever we see today “must have been” evolution’s target. And then they calculate that hitting that particular target is highly unlikely. But evolution is a “whatever works” approach.

    In other posts here, people have gone to great lengths to calculate the odds against a functional, modern protein happening “by accident” or “at random”. But not once do I see any recognition of the idea that proteins themselves might be something an iterative feedback process just stumbled across, because something else mutated into something useful as a protein. But SOME life, perhaps not at all life as we know it, may just as easily have arisen by blundering onto something else entirely.

    I would regard life as we know it as an extremely unlikely outcome of a process capable of producing nearly an infinity of outcomes, ALL of which are extremely unlikely. Just like (after a good shuffle), your odds of being dealt SOME bridge hand are unity. Your odds of being dealt THAT bridge hand are so small you might be tempted to dismiss it as impossible, and look for some external agency who must have stacked the deck to produce anything that improbable!

  24. 24
    Upright BiPed says:

    Mr Gibson, perhaps you would be better off not telling yourself how card tricks can do what has to be done, and try a little harder to observe the actual evidence itself.

  25. 25
    SCheesman says:

    David W. Gibson

    But not once do I see any recognition of the idea that proteins themselves might be something an iterative feedback process just stumbled across, because something else mutated into something useful as a protein.

    Wow, no wonder you see no recognition. Is any of what you say more than a wild-ass shot in the hopeful dark?

  26. 26
    David W. Gibson says:

    Upright Biped,

    The card discussion was meant as an illustration of certain principles. The actual evidence seems open to many different interpretations, which is always the case. And that means, things hinge on testing. But what should be tested, and which tests are meaningful and appropriate? These are good questions. I wouldn’t presume any definitive answer.

    SCheesman,

    No, I wouldn’t say it’s a shot in the dark, so much as an attempt to interpret what evidence I’m aware of, which indicates that evolution as a process, whatever the detailed mechanisms, is entirely contingent and largely arbitrary. So I compared this with a card player. Each card that you draw, changes both your probabilities, and even your strategy. And the NEXT card will change them again.

    Evolution is said to work like this, with each mutation opening up new possibilities that might have been unlikely before, and closing off what looked most probable. Highly contingent, always subject to change without notice.

    But if this IS how the process works, it’s not a hopeful shot in the dark to recognize it. Even if we would prefer a FAR more predictable and organized system.

  27. 27
    Mung says:

    David W. Gibson:

    The card discussion was meant as an illustration of certain principles.

    As such it should actually illustrate the principles.

    Well, I gave a procedure which would have done the same thing very quickly – just permit yourself to discard and keep drawing. That is, instead of trying for the royal flush all at once and nothing first, go for it incrementally, drawing one card at a time, keeping only the ones you need. This is how feedback processes tend to work.

    Oh, I see now. You have one deck and you just iterate through that deck one single time, retaining all the cards that can be used to make a royal flush and discarding any cards 2 – 9.

    And this is how you imagine evolution to work?

    Puhleeze.

  28. 28
    Upright BiPed says:

    Gibson, as I said…perhaps spend a little time with the evidence itself.

  29. 29
    mike1962 says:

    David Gibson: But real world biology is even simpler than that, because you do not NEED a royal flush, you need only a better hand than your competitors. Even a single pair might be a winner. NOW how long does it take?

    You can show me how a targeted search thru a deck of card can give me a royal flush. Now, you show us how incremental adaptation and selection can create a novel cell type, tissue type, organ or body plan.

    (crickets)

  30. 30
    material.infantacy says:

    Is there any point in daydreaming about OOL scenarios that might account for some sort of protein synthesis while disregarding the need for the simultaneous presence of DNA, with the protein sequence codes already present?

    Also, unless protein sequences could exhibit the property of “differential reproductive success,” wouldn’t invoking “evolutionary mechanisms” be absurd?

    Is there any reason to believe that we could do with less than fully functional enzymatic protein sequencers and replicators, simultaneously present with the DNA that codes for them, in which the CODES ARE ALREADY PRESENT?

  31. 31
    material.infantacy says:

    mike1962, indeed, in all these proposed scenarios, the presence of a mind is assumed, which beyond blind search is the only thing to account for the recognition faculty required to make appropriate selections from the deck.

    Imagination is a search mechanism.

    m.i.

  32. 32
    mike1962 says:

    The Skeptic: 2. Biological entities are not computers and do not contain “computer code”.

    Really? Try counting from one to 10. Congratulations, you are a computer!

    Try following any list of instructions. Congratulations, you are a computer!

    Fascinating that encoded within DNA (and other epigenomic factors no doubt) are the instructions to build a biological computer in the form of you. And a self-replicating one at that. These fancy biological computers can build skyscrapers, compose music, philosophize, speak, learn, and study the very DNA that made it. And read the text you are reading right now.

    You’re right, Skeptic. We’re not computers. Or I should say, we’re not computers. And in the areas where we lack, such as fast counting and mathematical computing, we build machines as slaves and make them do our computing work for us! We’re a hell of a lot more than computers.

  33. 33
    mike1962 says:

    EDIT: ^^ “Or I should say, we’re not computers.”

  34. 34
    mike1962 says:

    EDIT EDIT: ^^ “Or I should say, we’re not MERELY computers.”

    Why is there no edit feature here for typing slobs like me?

  35. 35
    material.infantacy says:

    Blame it on your robot slave. xp

  36. 36
    mike1962 says:

    I’m afraid the fault is all mine for the mal entry.

  37. 37
    Mung says:

    David W. Gibson:

    So I compared this with a card player. Each card that you draw, changes both your probabilities, and even your strategy. And the NEXT card will change them again.

    So back to our original example.

    First card drawn at random, 20 cards can be the start of a royal flush. Approx 3:2 against but we’ll be generous and give you this one and say you get a needed card on the first draw.

    Now that we have our first card, there are only four cards left which can complete it.

    So while we have removed one card, and while it is in fact the case that there is 0 probability that we’ll draw that same card again,

    A: How is evolution like that?

    B. How does it change the fact that now the odds for getting the next card we need is 4 out of 51?

    IOW, you claim it changes the odds in your favor, but how? You’ve just reduced your options to 4.

    So if this is how evolution works, after each outcome the next outcome is even less probable, that’s pretty much backwards from the way it’s taught.

    Once you’ve drawn your second card, now your odds are reduced to 3 in 50.

    Not looking good for evolution!

    Time to find a different analogy. This one shows the exact opposite of what you wanted it to show, lol.

  38. 38
    material.infantacy says:

    xp

  39. 39
    vjtorley says:

    David W. Gibson,

    I don’t mind people suggesting alternative pathways for the origin of proteins or DNA. But if they want their proposals to be taken seriously at a scientific level, then they have to be quantifiable and falsifiable. One of the reasons why I like Intelligent Design is that it is both.

    Now let’s go back to your example.

    I envision a global laboratory, performing billions of experiments simultaneously. AND I envision each successful experiment being widely adopted extremely rapidly. So if each experiment takes one minute, and there are 10 billion experiments going on at once, and the probability of some useful accident is one in a billion, then we have ten useful results per minute but the useful results are retained, all else is discarded…

    Let’s say life takes a billion separate required factors before we’d consider it life at all. According to my above speculations, we’re getting ten of those factors adopted per minute. At that rate, life would take 100 million minutes. Which is something less than 200 years!

    Given the numbers you assume, then I’d certainly agree that the origin of life is inevitable, in a fairly short time.

    The problem with your scenario is that if Dr. Axe’s calculations are correct, then the probability of a useful accident is 10^-77, not one in a billion. I think you’ll agree that that puts a dampener on things.

    You have also proposed that proteins might have been built by an iterative process. The real problem here is that functions do not come in halves or tenths; a molecule either has one or it doesn’t.

  40. 40
    David W. Gibson says:

    Hard to keep up here, but I’ll do my best.

    Mung:

    How do we decide what LOOKS like a natural process and what DOES NOT look like a natural process?

    You have asked a very central question here. Some things look designed by aren’t (false positive), while other things look natural but are designed (false negative). Is there any FOOLPROOF way to make such determinations, eliminating ALL false positives and negatives? Hopefully, whatever method we use will produce the same results no matter who is doing the classification.

    And this is probably important. Even archaeologists are frequently unable to say definitely whether or not something was a tool. We could adopt the policy position that EVERYTHING is designed, of course. But such a position can render useful discriminations impossible.

    Upright Biped:

    Mr Gibson, perhaps you would be better off not telling yourself how card tricks can do what has to be done, and try a little harder to observe the actual evidence itself.

    This is an excellent recommendation in principle, but beyond my competence in practice. You are like the convention of mice deciding that the cat needs to wear a bell. Now, how does one implement this policy?

    Certainly I am not a biologist, not even close. So I see the vast majority of the world’s biologists largely in agreement. Should I agree with them? If not, on what basis? Not on the merits – I’m not qualified to judge the merits. I admit I find it difficult to accept that many thousands or tens of thousands of highly intelligent and educated people have devoted their life to real-world experimental research, producing a cumulative body of knowledge for well over a centurhy, and nearly ALL of them have missed the boat. And not just missed it, but COMPLETELY, TOTALLY missed it. Not even in the same time zone! For me, this is beyond my suspension of disbelief.

    Now, let’s take this a step further and note that those who disagree, besides being a very tiny minority, do almost no research at all. And the one or two who DO research, seem to be trying to demonstrate that claims nobody has made are without merit. This doesn’t mean they’re wrong, of course. But to me it means one must look at the usefulness of the research results, to see if applications based on it work.

    If I had the research money, I could shoot a bullet into the air, discover where it came down, and calculate the odds of it coming down in that precise location and nowhere else. And I could show that the odds were unacceptably low to the point of near-impossibility, without even breathing hard. So have I proved that bullets fired into the air DO NOT fall to earth? Have I proved that the research bullet performed a miracle? Most cogently, if I started out to ‘prove’ that bullets don’t land, would my experimental methodology reflect confirmation bias? If I shouldn’t be looking at the probability of landing exactly there, what SHOULD I be loking at? Might you suspect that my entire research program was created from the ground up to grind an Axe.

    Mung:

    And this is how you imagine evolution to work?

    Puhleeze.

    In some important ways, yes, that does reflect my understanding. I’ve tried to explain my understanding as clearly as I can. I may be all wrong, but “puhleeze”, as a counter-argument, is hard for me to extract anything helpful out of. All I know is that you disagree with my understanding, but I am no wiser as to why, or how to improve it.

    You can show me how a targeted search thru a deck of card can give me a royal flush. Now, you show us how incremental adaptation and selection can create a novel cell type, tissue type, organ or body plan.

    And if I can’t do it, do you seriously conclude it can’t be done? I also showed how a NON-targeted NON-search through a deck of cards could produce an IMPROVED hand. Even if the improvement is along entirely different lines.

    I think you underestimate how creative complex adaptive processes can become given enough time. I think you expect every experiment to be a breakthrough, and don’t allow for the situation where 99% of your trials can be errors, and you STILL come out ahead simply by keeping the few successes.

    Is there any reason to believe that we could do with less than fully functional enzymatic protein sequencers and replicators, simultaneously present with the DNA that codes for them, in which the CODES ARE ALREADY PRESENT?

    Probably not. But conversely, is there any reason to believe that no conceivable natural process, operating over billions of years, could have produced this or something equally complex? Personally, I find it as difficult to reject design, as I find it difficult to reject the existence of a process I’m not aware of yet, and may never be.

    So while we have removed one card, and while it is in fact the case that there is 0 probability that we’ll draw that same card again, A: How is evolution like that?

    It isn’t. The only point of the card analogy was the retention of helpful results, so that every iteration is not starting from scratch.

    B. How does it change the fact that now the odds for getting the next card we need is 4 out of 51?

    Because you have already selected a target! The next card may be one of the 51 unhelpful for THAT target, but not necessarily unhelpful for ANY useful target. And hopefully we understand that each generation IS the target. If it works, we’re there. If something new works next generation, no matter how differently it works, so long as it WORKS we are “there” again, except it’s somewhere else.

    So if this is how evolution works, after each outcome the next outcome is even less probable, that’s pretty much backwards from the way it’s taught.

    So your understanding of the analogy pushes it beyond the intent. The intent was only to show that unlikely or complex outcomes can arise from simple processes, PROVIDED useful results are retained with each iteration.

    Time to find a different analogy. This one shows the exact opposite of what you wanted it to show, lol.

    I have tried to create an analogy that illustrates one simple principle. It was not intended to BE evolution, only to illustrate the amazing power of retention of results. I wonder that you find it so difficult to understand this, or that you seem so compelled to misunderstand.

    After each outcome, the next outcome in the biological world cannot be predicted. There is no organism that is incomplete, halfway between A and B. Every organism is complete and successful if it survives, no matter what comes next. If evolution is a drunkard’s walk without a destination, then no particular place the drunk passes through is a “goal”, and the path he took to get there is byzantine, astoundingly inefficient, stupefyingly improbable. Yet the PROCESS is simple – a drunk staggering around mindlessly.

    mike1962:

    Really? Try counting from one to 10. Congratulations, you are a computer!

    Try following any list of instructions. Congratulations, you are a computer!

    Or more accurately, you are capable of doing something a computer is doing as well. And if you prevent a door from closing, you are a doorstop!

    The original complaint was that at some point, the analogy between computer code and DNA breaks down, as any analogy does. Nonetheless, I’d say its pretty accurate to compare DNA to computer instructions, in the sense that we can manipulate both with analogous means.

    I have no difficulty imagining myself as running the biological equivalent of machine code (I’m a retired firmware programmer). NOT a high level code, DNA is not even slightly abstract. But machine code actually IS what the CPU does – each bit represents a state change. The analogy to DNA is very close.

  41. 41
    material.infantacy says:

    David Gibson, nobody expects you to answer every objection at lightning fast pace, so take your time. We would ask that you at least consider them. I recommend focusing primarily on vjtorley’s responses, since it’s his OP; and it’s really tough for any of us kids to rival his knowledge or reasoning.

    There’s a fundamental problem with chance and necessity though, and that’s neither can be invoked as a cause for living systems, based on what we know about either one.

    The possibility that nature could eventually arrive at a solution can never be ruled out, so appealing to what could possibly happen, in that the probability is not zero, seems inappropriate, when we have an empirically vindicated causal “mechanism” that would better account for it.

    Take it easy, this thread’s likely to go on for days.

    m.i.

  42. 42
    material.infantacy says:

    I’d also like to add that admitting the astonishing similarity between DNA and machine code doesn’t much help your case.

    You can explain the operation of a computer system in entirely physical terms without any regard for Intelligent Design. However you get into real trouble when you try to explain its origin in those same terms.

  43. 43
    Mung says:

    After each outcome, the next outcome in the biological world cannot be predicted. There is no organism that is incomplete, halfway between A and B. Every organism is complete and successful if it survives, no matter what comes next. If evolution is a drunkard’s walk without a destination, then no particular place the drunk passes through is a “goal”, and the path he took to get there is byzantine, astoundingly inefficient, stupefyingly improbable. Yet the PROCESS is simple – a drunk staggering around mindlessly.

    Well put.

    If follows that your card analogy has nothing whatsoever to do with evolution.

    Yet you think it does. Why?

    Because the drunk falls down a set of stairs and that’s where he finds himself, that does not increase his chances of swimming the Atlantic.

    Throw as many drunks as you like at the problem.

  44. 44
    material.infantacy says:

    Is there any reason to believe that we could do with less than fully functional enzymatic protein sequencers and replicators, simultaneously present with the DNA that codes for them, in which the CODES ARE ALREADY PRESENT?

    Probably not. But conversely, is there any reason to believe that no conceivable natural process, operating over billions of years, could have produced this or something equally complex? Personally, I find it as difficult to reject design, as I find it difficult to reject the existence of a process I’m not aware of yet, and may never be.

    There’s always reason to believe that given, not billions of years, but maybe 10^300 years, we might see a little something, if only we knew that it was EVEN FEASIBLE to construct a proto-self-replicator from simpler precursors by just waiting around that long. You better bring a book or two.

    That’s the thing here, the numbers we’re dealing with are not in the billions, or in the billions of billions of billions. They’re well off into the category of INCONCEIVABLY LARGE NUMBERS for which there are no names, nor any picture you could draw.

    So to just conclude that “wow, billions of years is, like, a lot, so I’m sure just about anything could happen,” is just not reasonable given what we know about the ASTOUNDINGLY SOPHISTICATED composition of a single cell.

    And appealing to processes we have yet to discover is likely to make the problem more difficult, not simpler. Given the track record, every new discovery adds to the list of problems that need to be overcome for a viable OOL scenario. Not to mention, appealing to “unknown processes” to avoid inferring design is transparently self-deceptive, if not just plain deceptive.

  45. 45
    junkdnaforlife says:

    David: What you are describing in you royal flush analogy seems to be a foreword looking intelligent process with a target.

    For your analogy to work via blind process, you would have show that each card selected had an initial function of its own.

    If your opponent held a royal in hearts, then you would need a royal in spades to win. So you begin peeling through the deck and quickly come across the ten of spades and select it. But the ten of spades serves no initial function, as a ten high does not beat a royal in hearts. And since there is no mechanical or chemical process dictating that spades are more likely to stick to your finger than non spades, then you must make a choice to hold the functionless ten of spades. And now you are acting as an intelligent agent working towards a functional target with a purpose.

    As far as your bridge analogy goes, stating that a specific bridge being dealt may have a high probability against, but any bridge hand being dealt is inevitable, is true. But this is not analogous to folding proteins. If it were, then any chemical combination would inevitably fold some protein. But I do not think this is the case.

  46. 46
    Upright BiPed says:

    David Gibson,

    This is an excellent recommendation in principle

    I notice here that you start your response with the implicit suggestion that there are times when it’s not a good idea to understand for yourself, or apparently even to attempt to. You (no doubt) are about to tell me I need to hand it off to experts. Quite frankly, I am a little repulsed by that kind of position. I think history is full of factions, and individuals, and governments, and gurus who just love people like you. But I’ll tell you right now that I think you are lying about that in your own life, and that you only say it now to serve your current purposes. At least, that is my hope.

    Of course, don’t get me wrong; I respect experts for the same reasons as anyone else. They’ve earned their position, and I gain from their journey. If I was sitting in a Doctor’s office being diagnosed with a condition, I would certainly rely on that physician’s expertise. But if that same physician tells me that I’m being punished for something I’ve done – I would have a problem with that. I would not feel the slightest bit obligated by his physician’s license to think he had one wit of sense. By that same token, if that physician tells me that “I” am just an inner delusion amongst the matter and the death, then don’t ask me to turn it over to him, because he is full of shit (for the same reason as the first). I’m not so stupid as to think that his practice of biological science requires him to choose between either idea (they have nothing whatsoever to do with it) and it certainly doesn’t give him any authority over questions I already know he has no answers for. If I find a practitioner who is an expert on everything, I’ll adopt a different position.

    You are like the convention of mice deciding that the cat needs to wear a bell. Now, how does one implement this policy?

    My ‘o my. In the space of one sentence you’ve gone from suggesting I give up thinking for myself, and before I can step in line with the other cattle, I’ve become a mouse who needs to fear the cat. I am sure you are a very fine propagandist, with an inexhaustible supply of things to say, but honestly, I am not so certain this is your forum. The people around here actually read the data.

    Perhaps you are subject to a little propaganda yourself. The position espoused by your opening remark would certainly provide that opportunity.

    Certainly I am not a biologist, not even close. So I see the vast majority of the world’s biologists largely in agreement. Should I agree with them? If not, on what basis?

    Who is it that you are kidding here? You didn’t come to UD to find out if anything valid was going on here; you came here for one reason and one reason only. You came here to fight. You have culture battle dripping from every post you make.

    I’m not qualified to judge the merits.

    The only thing you’re disqualified from is knowing what the merits are to begin with, so don’t fool yourself otherwise. And that disqualification is something you’ve done to yourself. If you take the stance you’re promoting here, then it just goes with the territory.

    I admit I find it difficult to accept that many thousands or tens of thousands of highly intelligent and educated people have devoted their life to real-world experimental research, producing a cumulative body of knowledge for well over a century, and nearly ALL of them have missed the boat.

    You ‘admit’ this huh? It’s good that you can talk about it. It might help you to know that every time the consensus was wrong about something, they were first right about it, and usually for a long time. History says it only takes one person to be right. That’s the way science works, so don’t feel bad. There is something else you might want to realize, given that it is of profound importance within empirical pursuits such as science: 1) ID breaks no physical law, and 2) ID has never been refuted on the merits.

    For me, this is beyond my suspension of disbelief.

    I suggest a history book, or two.

    Now, let’s take this a step further and note that those who disagree, besides being a very tiny minority, do almost no research at all.

    A tiny minority? Over what scale shall we measure this? Quality of the science? The ability to demonstrate answers? The sheer numbers within the human enterprise of study?

    Why not just spit in Newton’s face, David? Spit in Maxwell’s. Spit in Pasteur’s. Spit in Galileo’s while you at it. Put on your cape and park a lugie right on Faraday’s forehead; one for the team.

    Or, are all those old fogies past their prime in your eyes? Did they not live in your time of enlightenment, so they cannot be held accountable for their tired old beliefs? Is that your rationale? And your contemporaries like Behe or Denton, or Abel, and the others? What about someone like Polanyi? You ignore them anyway, so what’s the point. One group you disregard, while you ignore the others. You’ve stuck the perfect balance to be exactly who it is you suggest you are.

    And the one or two who DO research, seem to be trying to demonstrate that claims nobody has made are without merit.

    Claims that nobody has made? Do you need medication? That’s just hilarious.

    This doesn’t mean they’re wrong, of course. But to me it means one must look at the usefulness of the research results, to see if applications based on it work.

    Tell me, what is the scientific applicability of the biologist’s claim that the universe is a place of pitiless indifference? What was the test that confirmed this result with such profound conclusion, that forevermore it should be taken as an unassailable fact, unassailable regardless of the evidence against it? Unassailable to the point that we shall redefine the science of Newton and Maxwell and Faraday and Galileo around it?

    If I had the research money, I could shoot a bullet into the air, discover where it came down, and calculate the odds of it coming down in that precise location and nowhere else. And I could show that the odds were unacceptably low to the point of near-impossibility, without even breathing hard.

    Unfortunately, this mental exercise has nothing to do with anything in ID. It’s just that, a mental exercise, and it’s meaningless. Would you like to know why? Well there are many reasons, but one in particular jumps out at me. The act of shooting a bullet in the air (to have it return to the earth) has physical principles in operation that explain what is taking place. Yet, within the evidence for biological design, there is no such physical principle in operation. Quite to the contrary, all the physical principles in operation work diametrically opposed to what is observed. One must simply take the biological phenomena as a given, then explain how it staves off the entropy which all other systems are subject to. Or, did you not know that?

    Perhaps you wouldn’t breathe too hard by reading a book or two.

    So have I proved that bullets fired into the air DO NOT fall to earth? Have I proved that the research bullet performed a miracle?

    This, again, is utterly meaningless. In fact, it’s quite silly. I get what you were going for, but you missed it. I suggest to you again, this is not the forum for such baseless analogies.

    Most cogently, if I started out to ‘prove’ that bullets don’t land, would my experimental methodology reflect confirmation bias?

    If you only knew how utterly disconnected this line of thinking is from the issues, you would be ashamed to have made this remark.

    If I shouldn’t be looking at the probability of landing exactly there, what SHOULD I be looking at?.

    Gawd. You should be looking in the mirror. After that, you should be looking at a book that argues the evidence on their actual merits. I promise it won’t hurt. Your airy, swirling, mystical smoke analogies just aren’t cutting it.

    Might you suspect that my entire research program was created from the ground up to grind an Axe

    Ba-dump-bump! All that for a cheap shot that missed so badly that you made yourself a fool?

    But you can always learn something, then decide. You certainly wouldn’t be the first.

  47. 47
    junkdnaforlife says:

    “If I had the research money, I could shoot a bullet into the air, discover where it came down, and calculate the odds of it coming down in that precise location and nowhere else.”

    This type of analogy is used often. The measuring of the distance and calculating the odds is something that an intelligent agent is injecting into a routine chance and necessity outcome after the fact. The calculations are independent of the phenomenon. The phenomenon itself is inevitable. There is nothing improbable about shooting a gun into the air. There is nothing improbable about the bullet being subject to gravity. And there is nothing improbable about a the bullet landing back somewhere on earth. Landing back on earth is an inevitable outcome. OOL is not analogous to this. Using your analogy correctly, it would be as if the shooter fired several bullets into the air, and they all landed back on earth and spelled out his first and last name in the sand. This outcome would not have been considered inevitable. This is more analogous to OOL.

  48. 48
    Ilion says:

    DWG:Certainly I am not a biologist, not even close. So I see the vast majority of the world’s biologists largely in agreement. Should I agree with them? If not, on what basis? Not on the merits – I’m not qualified to judge the merits.

    Then, you are not qualified to entertain *any* opinion on the matter, whatsoever. For, if you are not qualified to reject, as being false, the assertions of “vast majority of the world’s biologists [who are assertedly] largely in agreement” in what they assert, then neither are you qualified to accept these assertions as being true. Nor are you qualified to disagree with, nor judge, some other person who rejects the assertions.

    Yet, here you are.

  49. 49
    mike1962 says:

    David Gibson: mike1962: Or more accurately, you are capable of doing something a computer is doing as well. And if you prevent a door from closing, you are a doorstop!

    Indeed. DNA (and whatever other epigenetic factors are involved) produce things that are computers and doorstops. Except these particular doorstops can design and create other doorstops. And computers. And much more.

    The original complaint was that at some point, the analogy between computer code and DNA breaks down, as any analogy does.

    I would say DNA is more like a CNC code. And the product that is built is a computer and a hell of a lot more.

    And that is my point to the original skeptic. I don’t remember who he was or what thread it was on. While DNA might not be analogous to a Turing tape, it creates “devices” that not only can act like Turing machines, but can understand them and design them. The effect of his point was quite pointless.

  50. 50
    mike1962 says:

    Because the drunk falls down a set of stairs and that’s where he finds himself, that does not increase his chances of swimming the Atlantic.

    I can testify from personal experience this is true! 😀

  51. 51
    Mung says:

    …this is not the forum for such baseless analogies.

    I sense another analogy coming!

  52. 52
    Mung says:

    David W. Gibson:

    As a comparison, if I shuffle a deck and take the top 5 cards, what are my odds of (that is, how many trials will I require to get) a straight flush? It would surely take a long while. But what if I get to keep the cards I want, and keep drawing? Not only are my odds unity, but it will happen FAST. And to me, this seems so obvious I don’t understand the demand for a quantitative model.

    What is the relevance of this analogy?

  53. 53
    lastyearon says:

    Material.infancy

    There’s a fundamental problem with chance and necessity though, and that’s neither can be invoked as a cause for living systems, based on what we know about either one.

    Your assuming your conclusion in your argument.

    If I understand you correctly, you’re saying that (a) we know that chance and necessity are not capable of producing certain things. And (b) we know that intelligent agents are capable of producing those things. Therefore, since life is one of those things, only intelligent agents could have produced them.

    But how do you already know that chance and necessity are not capable of producing those things? If chance and necessity produced life, then it is capable of producing those things.

  54. 54
    material.infantacy says:

    Hi lastyearon, here’s that quote again with some added emphasis:

    There’s a fundamental problem with chance and necessity though, and that’s neither can be invoked as a cause for living systems, based on what we know about either one.

    This is really a statement regarding what we know about chance and necessity.

    There may indeed be some unknown phenomena or laws which govern the spontaneous generation of living systems, and it will always remain a possibility that we’ll discover exactly that.

    But we can’t invoke the unknown in order to explain what we observe. I’m not saying that we could never invoke chance and necessity — certainly if it could be empirically demonstrated that such are capable, we would be obligated to defer to such causes.

    However based on what we observe, and what we “know,” there are only two potential causes for it: 1) chance and necessity, that is, physical law; 2) design.

    Any materialistic scenario which must generate a minimum proto-self-replicator, i.e., a living cell with DNA and the proteins which process it, exposes staggering odds, in the realm of the utterly inconceivable.

    So based on what we know today, design appears to be the best explanation, though it’s apparent we have a lot more to learn.

    If I understand you correctly, you’re saying that (a) we know that chance and necessity are not capable of producing certain things. And (b) we know that intelligent agents are capable of producing those things. Therefore, since life is one of those things, only intelligent agents could have produced them.

    I’m saying that we don’t know any chance and necessity scenarios which allow for its efficacy. That’s different from saying that we know that chance and necessity are incapable.

    And we know design is. So I’m insistent that design is a valid provisional explanation, pending the discovery of some new force or process which allows complex specified systems to come about in a “petri dish” of sorts.

    Chance and necessity could never be ruled out entirely; but it’s entirely reasonable, based on what we know, to avoid attributing what we observe in a living system, to chance and necessity at this point in our discoveries.

  55. 55
    lastyearon says:

    Ok. So, if I understand you correctly, you are saying that we don’t know how chance and necessity can create things like life. And that as long as we don’t know, it is reasonable to suggest that life was designed by an intelligent agency.

    Many ID proponents, including Stephen Meyer in his recent book, would argue otherwise, saying that we know that chance and necessity cannot create complex things like life. My argument above stands in that case.

    To your argument, I would say that it sounds a lot like god-of-the-gaps.

  56. 56
    material.infantacy says:

    But LYO, neither is chance-of-the-gaps reasonable.

    If we don’t know of any chance scenario which could possibly account for what we observe, then what does the insistence that it must’ve come about by chance amount to?

  57. 57
    material.infantacy says:

    I’m suggesting a corollary to what we observe. What is chance suggesting?

    Back later…

    m.i.

  58. 58
    lastyearon says:

    m.i.

    If we don’t know of any chance scenario which could possibly account for what we observe, then what does the insistence that it must’ve come about by chance amount to?

    Why did you omit necessity? Let me restate the above, this time including necessity.

    If we don’t know of any scenario driven by chance and necessity which could possibly account for what we observe, then what does the insistence that it must’ve come about by chance and necessity amount to?

    And let me rephrase it a little further, this time by substituting “chance and necessity” with “nature”. (And if this isn’t a valid substitution, let me know why)

    If we don’t know of any natural scenario which could possibly account for what we observe, then what does the insistence that it must’ve come about naturally amount to?

    Doesn’t this sound like a god-of-the-gaps argument to you?

  59. 59
    Mung says:

    lastyearon:

    If we don’t know of any scenario driven by chance and necessity which could possibly account for what we observe, then what does the insistence that it must’ve come about by chance and necessity amount to?

    Could you perhaps make any less sense?

  60. 60
    material.infantacy says:

    lastyearon,

    I didn’t intend anything cheeky by omitting necessity. I’ll try and be more careful.

    Doesn’t this sound like a god-of-the-gaps argument to you?

    No, I can’t say it does. Because god-of-the-gaps is a straw man used in an attempt to discredit ANY observation which might suggest design. In other words, there is no inference to design which can be made, that will satisfy the criticism that it’s god-of-the-gaps reasoning. That’s a criticism leveled by default against any invoking of an intelligent cause. It’s lost all its punch in the overuse.

    Let me try this.

    The event we observe, a living system, has one of two explanations: 1) it’s designed; 2) it’s not designed (chance/necessity, aka physical law, natural processes, etc).

    If we can demonstrate that intelligent intervention (design) is not required, then we’ve demonstrated the efficacy of c/n to account for it. No design required, IDists go home.

    If invoking everything we know about physics, chemistry, and probability doesn’t produce a single viable explanation in over fifty years, it seems reasonable that design, at the very least, is on the table — that it is a viable explanation, NOT a REQUIRED one.

    I mean that’s the minimum, that design should be considered reasonable even if some consider it unsatisfying.

    However the game is, as it stands, to rule out design at all cost, and give it no quarter, nor anyone who promotes the idea. I think that’s deeply flawed, and depends on a severe ideology.

    Invoking design does neither of these: 1) halt the progress of science; 2) prevent anyone from continuing the search for strictly material explanations.

    I don’t know how to say it any other way. The only reason I can see for rejecting the design hypothesis out of hand, is that the idea is seriously offensive to some.

    I really have no explanation for why that is.

    Do you have any objections to scientists following evidence that allows for the possibility of a living system being designed?

    Is there any good reason to believe that a designer of living systems is not required? I don’t mean philosophical reasons, but scientific ones.

    Is there anything that you would consider evidence of a designer of life?

    If you can answer those questions, there may be more to discuss.

    In the meantime, thanks for the discussion.

    m.i.

  61. 61
    ScottAndrews says:

    “God of the gaps” is a misleading expression first because it implies a nearly or partially completed continuum, as if nearly everything had been figured out. If a person has a space between their teeth we call it a gap. If they have one tooth or none, we don’t call that a gap.

    It’s an inapplicable expression unless someone is explicitly filling the “gaps” with God.

    It translates to ‘Don’t use your fantasies to fill in the “gaps.” You may only use our fantasies.’

  62. 62
    ScottAndrews says:

    I neglected to mention the second reason why the expression is misleading. It causes one to visualize a gap between two things, giving the impression that “gap” is somehow quantified. Like when you’re missing a piece of a puzzle – you know exactly what that piece will look like.
    The subtle suggestion is that solving these mysteries is as simple as finding a piece that fits.

    The truth is that no one knows what that piece is shaped like because they are missing most of the pieces. All they have is the picture on the box.

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