Three puzzles that are real – A response to a skeptic
|August 3, 2011||Posted by vjtorley under Cambrian explosion, Intelligent Design|
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
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):
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.
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!