Sunday, April 30, 2006

Re: this uncertainty confuses me because so many`experts' have so many different viewpoints

AN (copy to CED, with later minor changes)

----- Original Message -----
From: AN
To: Stephen E. Jones
Sent: Sunday, April 30, 2006 8:45 AM
Subject: [...]

[Graphic: "Uncertainty," Marco Roascio, Arte81]

AN>Dear Steve Jones,
Hello. I have e-mailed you once before complementing the work you do on your blog. I read your articles everyday and, I think you have one of the best "intelligent design"/creation websites on the net.

Thanks for your message. I presume you know it is my policy to respond publicly to private messages on creation/evolution/design, after removing the sender's personal details. Also, that it is my policy not to get involved in personal discussions on creation/evolution/ design issues.

AN>I really enjoy how you analyze and break down pro-darwin news articles with complete confidence. I am e-mailing you today because I am very frustrated with this whole debate (creationism vs. evolutionism vs. intelligent design).

Thanks. It is inherently frustrating because most of those active in such debates have well-formed views that are, to a large extent, worldview-driven, and so resistant to opposing evidence and arguments.

AN>I have only been familiar with the current debate since around this past Christmas (after getting to an argument with a classmate ...) and I feel that I am unable to discern much of what is being said concerning evolution or ID ... Before college, I was ... basically kind of a semi-wild hipster type that could care less about school or this kind of debate. I was just content riding around on my skateboard and hanging out around town.

Thanks for the background, some of which I deleted because it might identify you.

AN>I am frustrated because I don't know who to believe anymore. Everyday, I read the debates and comments on various ID web pages from extremely smart people with PhD's in biology, math, engineering, etc.

The main problem is not intelligence, or education, but starting assumptions. For example, if your starting assumption is that there is no God (atheism, materialism, naturalism), or that there is a God but He does not intervene in the world (gnosticism, deism, theistic naturalism), then no evidence for creation by supernatural intervention could be accepted, and some form of evolution would then be the only option. As Christian geneticist David Wilcox observed, "One can be a theistic `Darwinian,' but no one can be an atheistic `Creationist'":

"I conclude that the easy acceptance of neo-Darwinism as a complete and adequate explanation for all biological reality has indeed been based in the metaphysical needs of a dominant materialistic consensus. One can be a theistic `Darwinian,' but no one can be an atheistic `Creationist.'" (Wilcox, D.L., "Tamed Tornadoes," in Buell J. & Hearn V., eds., "Darwinism: Science or Philosophy?, " Foundation for Thought and Ethics: Richardson TX, 1994, p.215)

AN>I am pretty convinced that Dawkins and Dennett are completely wrong mainly because of C.S. Lewis's "argument from reason".

Agreed. I presume you have read Reppert's book:

"When C. S. Lewis presented the argument from reason in his revised third chapter of Miracles, he claimed that what he called `strict materialism' could be refuted by a one-sentence argument that he quoted from J.B.S. Haldane: `If my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true ... and hence I have no reason for supposing my brain to be composed of atoms.' [Lewis, C.S., "Miracles: A Preliminary Study," Macmillan: New York, 1978, p.15; quoting Haldane, J.B.S., "Possible Worlds," [1927]; Transaction Publishers: New Brunswick NJ, 2001). However, Lewis maintains that naturalism involves the same difficulty, but he goes on for nine pages explaining why. I suspect that in Lewis's time the idea of nonreductive materialism was not as prevalent as it has since become, and that what passed as `materialism' was identified with strong forms of reductionism. However, here I will be defining materialism broadly, such that it will be very difficult for someone to argue that some form of nonmaterialist naturalism will escape the difficulties I advance for materialism. Any genuinely naturalistic position requires that all instances of explanation in terms of reasons be further explained in terms of a nonpurposive substratum. For if some purposive or intentional explanation can be given and no further analysis can be given in nonpurposive and nonrational terms, then reason must be viewed as a fundamental cause in the universe, and this strikes me as a huge concession to positions such as theism, idealism and pantheism, which maintain that reasons are fundamental to the universe. Any genuinely naturalistic position will be subject to the same objections that I am presenting against materialism, so I will develop my argument in relation to materialism." (Reppert, V.E., "C.S. Lewis's Dangerous Idea: A Philosophical Defense of Lewis's Argument from Reason," InterVarsity Press: Downers Grove IL, 2003, pp.50-51)

AN>And if Dawkins and Dennett are right (which I highly doubt it), then that is the end of the discussion and pretty renders humanity worthless. It would also make our planet and it's amazing human history and spirit into the cruelest joke ever told.

Agreed. But I presume that they don't care about "humanity", but only about themselves. They are both rich and famous and want the Universe to be indifferent to them (i.e.there is no God who can call them to account):

"Theologians worry away at the `problem of evil' and a related `problem of suffering.' ... On the contrary, if the universe were just electrons and selfish genes, meaningless tragedies like the crashing of this bus are exactly what we should expect, along with equally meaningless good fortune. Such a universe would be neither evil nor good in intention. It would manifest no intentions of any kind. In a universe of blind physical forces and genetic replication, some people are going to get hurt, other people are going to get lucky, and you won't find any rhyme or reason in it, nor any justice. The universe we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil and no good, nothing but blind, pitiless indifference. As that unhappy poet A.E. Housman put it: `For Nature, heartless, witless Nature Will neither care nor know.' DNA neither cares nor knows. DNA just is. And we dance to its music." (Dawkins R., "River out of Eden: A Darwinian View of Life," Phoenix: London, 1996, p.155. Emphasis in original)

AN>I also highly doubt that chance mutations and randomness are capable of creating everything we see today even if large amounts of time are added to the equation. I couldn't leave some Lego blocks (do they have these in Australia) out for millions of years and expect them to assemble in to a Lego city.

Good illustration (and Lego blocks are worldwide-my son is now a computer engineer in the USA and it was probably his vast collection of Lego that helped!).

AN>Anyways, I have read commentary from most of the guys over at ... and they seem to view ID as some sort of curiosity. They don't think it is science or even a theory just yet. They claim to still accept evolution for the most part and think that ID will add to RM+NS to develop a stronger theory of how life developed in its' current state. I think ... at ... believes in macroevolution. Isn't that just the same as accepting Neo-Darwinism? Can macro-evolution be designed?

I don't want to comment on individuals, and everyone is entitled to their view of ID. However, I will say that any claim that "ID is not even a scientific theory" is just a play on the words "scientific" and "theory." ID is a theory in the sense that it makes a testable claim about the real world, namely that some things in nature are best explained as the product of intelligence:

"The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection." ("Top Questions: Questions about Intelligent Design," Discovery Institute - Center for Science and Culture)

If it is a scientific theory to claim that there is no design in nature (as Darwin's theory does):

"Paley's argument is made with passionate sincerity and is informed by the best biological scholarship of his day, but it is wrong, gloriously and utterly wrong. The analogy between telescope and eye, between watch and living organism, is false. All appearances to the contrary, the only watchmaker in nature is the blind forces of physics, albeit deployed in a very special way. A true watchmaker has foresight: he designs his cogs and springs, and plans their interconnections, with a future purpose in his mind's eye. Natural selection, the blind, unconscious, automatic process which Darwin discovered, and which we now know is the explanation for the existence and apparently purposeful form of all life, has no purpose in mind. It has no mind and no mind's eye. It does not plan for the future. It has no vision, no foresight, no sight at all. If it can be said to play the role of watchmaker in nature, it is the blind watchmaker." (Dawkins, R., "The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design," W.W Norton & Co: New York NY, 1986, p.5. Emphasis original)

then it is equally a scientific theory that there is design in nature.

AN>I am confused as to why people that see the plausibility of ID cannot accept it? Hasn't Dembski and Behe done a good enough job of developing this theory? Since ID has not been proven as science, would that mean that Darwinian Evolutionism is true until proven false?

There are no doubt a variety of reasons, mostly to do with confusion about what ID is. Those from the creation side can (and some do) reject ID because it is not Biblical enough and/or does not make it explicit that the designer is the God of the Bible. They don't seem to realise that it is not possible to prove from the evidence of nature alone that the designer was the Christian God, although those IDists who are Christians (like me) assume it is.

Those on the evolution side mostly reject ID because they have a prior committment to naturalism (i.e. strong naturalism: nature is all there is = there is no supernatural = there is no God; or weak naturalism: nature is a closed system of cause-and-effect in which God, even if He exists, would not intervene). While ID does not insist that the designer is supernatural (Michael Denton for example was once a Discovery Institute CSC Fellow and he was not even a theist, and seems to believe in a form of Aristotelian teleology in which the laws of nature are the designer), philosophical naturalists unwittingly confirm Romans 1:18-20 in that they intuitively recognise that there is design in nature and connect that with a Creator.

AN>[...] See above about me generally not commenting on others. If I did so, then that person would rightly expect me to let them put their point of view on this blog, and I have neither the time, nor the inclination to do that. I closed down my list CED, because after 11+ years (1994-2005) debating creation/evolution/design, I regarded that for me it was no longer a profitable use of my scarce time.

AN>Stuff like this depresses me! Argh!

One thing you learn in the creation/evolution/design debate is that you are going to get depressed if you expect that others are going to see your point of view, let alone accept it. The best that you can hope for is: 1) you can see their point of view; and 2) clarify and modify your own position, in the light of any actual facts (as opposed to mere opinions and philosophical preferences) that they present (e.g. as I did with common ancestry).

AN>[...] See above.

AN>Thanks so much for reading this long e-mail and I'd really appreciate a reply (but please take your time because I know you are a busy guy). I am sorry to burden YOU with my problems but I really don't know anybody that is knowledgeable about this kind of stuff that can guide me in the right direction.

In this field of creation/evolution/design, there is no "right direction", in the sense that no one can prove that they are right and all those who disagree with them are wrong. I personally accept (and have said so publicly since 1999) that I would have no problem as a Christan if Darwinian evolution (i.e. its facts, as opposed to its philosophy) were 100% true:

" I would have no problem even if Darwinian evolution was proved to be 100% true, because the God of the Bible is fully in control of all events, even those that seem random to man (Prov. 16:33; 1Kings 22:34). Jesus said that not even one sparrow will die unless God wills it (Mat. 10:29-30), which means that God is fully in control of natural selection. But if the Biblical God really exists there is no good reason to assume in advance that Darwinian (or any form of) naturalistic evolution is true!" (Stephen E. Jones: My testimony of how I became involved in the Creation/Evolution debate, 1999-2005)

All that can be done is come to your own assessment of what position best fits all the evidence. A test of that is a serene confidence that one really has honestly considered all the evidence and one's position adopted is, as best as one can ascertain, the right one. I assume that if one's `body language' is nastiness and attempting to suppress opposing positions (as the Darwinists do):

"In the final analysis, it is not any specific scientific evidence that convinces me that Darwinism is a pseudoscience that will collapse once it becomes possible for critics to get a fair hearing. It is the way the Darwinists argue their case that makes it apparent that they are afraid to encounter the best arguments against their theory. A real science does not employ propaganda and legal barriers to prevent relevant questions from being asked, nor does it rely on enforcing rules of reasoning that allow no alternative to the official story. If the Darwinists had a good case to make, they would welcome the critics to an academic forum for open debate, and they would want to confront the best critical arguments rather than to caricature them as straw men. Instead they have chosen to rely on the dishonorable methods of power politics." (Johnson, P.E., "The Wedge of Truth: Splitting the Foundations of Naturalism," Intervarsity Press: Downers Grove IL, 2000, p.141)

then I assume that one does not really believe in one's heart of hearts, that one's position is correct.

AN>It's just that all of this uncertainty confuses me because so many `experts' have so many different viewpoints from Ken Ham to Richard Dawkins! I don't know who is right and who is wrong for sure. If you don't have time to respond to any of this, could you please forward it to somebody who can?

Join the club! There is inherent and unresolvable "uncertainty" in this field of creation/evolution/design, precisely because it is seen from a variety of mutually exclusive "viewpoints". As Darwin rightly noted, each "fact" is seen and then stored on one's mind along with a "point of view":

"Although I am fully convinced of the truth of the views given in this volume under the form of an abstract, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. ... I look with confidence to the future,- to young and rising naturalists, who will be able to view both sides of the question with impartiality ... for thus only can the load of prejudice by which this subject is overwhelmed be removed." (Darwin, C.R., "The Origin of Species by Means of Natural Selection," 1872, Sixth edition, J.M. Dent & Sons: London, 1928, reprint, p.456)

that gives it its meaning. Therefore, one cannot expect that those with radically different "viewpoints" see the same facts, in the fullest sense of their meaning and weighting.

All one can do is try to understand the "many different viewpoints from Ken Ham to Richard Dawkins" and compare their core claims against the evidence (both scientific and Biblical). It may be helpful to remember Isaac Asimov's point that it is a fallacy to think that "right" and "wrong" are absolutes (at least in scientific matters), there being a "relativity of wrong":

"The young specialist in English Lit, having quoted me, went on to lecture me severely on the fact that in every century people have thought they understood the Universe at last, and in every century they were proved to be wrong. It follows that the one thing we can say about our modern `knowledge' is that it is wrong. ... This particular thesis was addressed to me a quarter of a century ago by John Campbell [a science fiction editor], who specialized in irritating me. He also told me that all theories are proven wrong in time. My answer to him was, `John, when people thought the Earth was flat, they were wrong. When people thought the Earth was spherical, they were wrong. But if you think that thinking the Earth is spherical is just as wrong as thinking the Earth is flat, then your view is wronger than both of them put together.' The basic trouble, you see, is that people think that `right' and `wrong' are absolute; that everything that isn't perfectly and completely right is totally and equally wrong." (Asimov, I, "The Relativity of Wrong," in "The Relativity of Wrong," [1988], Oxford University Press: Oxford UK, 1989, reprint, pp.214-15. Emphasis in original)

Also, Ken Ham and Richard Dawkins can be right and wrong about different things. For example, Ham could be wrong, and Dawkins right, on the age of the Earth. But Ham could be right, and Dawkins wrong, on whether Christianity is true (which it is). And the consequences of Ham being wrong about the age of the Earth, and Dawkins being wrong about Christianity being true, are infinitely different!

AN>I am still looking forward to purchasing your book whenever it is finished.

Thanks. As I have said, I am taking a one-year detour from my "Problems of Evolution" book, to classify my ~10,000 evolution quotes, into an Evolution Quotes Book. I passed my 500th quote the other day, leaving `only' ~8,000 to go (since I have eliminated a lot already and the original estimate of ~10,000 was probably too high). I am hoping that there are going to be a lot of further quotes that I can leave out, as it is going to be difficult to keep the book to about 1,000 quotes. As I also have said, I will probably self-publish it directly as an eBook.

AN>Your Friend in Christ,

As "Your Friend in Christ," I hope you don't mind me saying that if you are a relatively new Christian, you should consider that your higher priority is growing your Christian life (Mt 13:18-23; Col 1:10; 1 Pet 2:22; 2 Pet 3:18), compared with debating on the Internet. If the Internet is taking quality time away from your regular personal Bible study and prayer, and Christian fellowship, then my advice is to either cut the debating back, or abandon it altogether.


Stephen E. Jones, BSc (Biol).
"Problems of Evolution"

Saturday, April 29, 2006

Salvage prospect for 'junk' DNA #1

Salvage prospect for 'junk' DNA: The genome may possess far more complexity than was imagined, BBC, 26 April 2006, Paul Rincon ...

[Graphic: "What is junk DNA, and what is it worth?," Pennsylvania State University]

A mathematical analysis of the human genome suggests that so-called "junk DNA" might not be so useless after all. The term junk DNA refers to those portions of the genome which appear to have no specific purpose. But a team from IBM has identified patterns, or "motifs", that were found both in the junk areas of the genome and those which coded for proteins. The presence of the motifs in junk DNA suggests these portions of the genome may have an important functional role. The findings are reported in Proceedings of the National Academy of Sciences journal. But they will have to be verified by experimenters in the lab, the scientists behind the work point out. Dr Andrew McCallion, who was not an author on the new paper, commented: "Up until not so long ago, we were under the impression that the vast majority of information in the genome, if not all of it, was encoded in those stretches of DNA that encoded proteins. "We now understand there is much more complexity involved," . Lead author Isidore Rigoutsos and colleagues from IBM's Thomas J. Watson Research Center used a mathematical tool known as pattern discovery to tease out patterns in the genome. This technique is often used to mine useful information from very large repositories of data in the worlds of business and science. They sifted through the approximate total of six billion letters in the non-coding regions of the human genome and looked for repeating sequence fragments, or motifs. "One of the things that arises from this paper is that junk DNA may not be junk. But this needs to be verified," Dr Rigoutsos told the BBC News website. Dr Rigoutsos said his team's work suggested, "a connection between a vast area of the genome we didn't think was functional with the part of the genome we knew was functional". He explained that experimental work would be needed to establish this connection: "The average lab does not have the resources to prove or disprove this, so it will need a lot of effort by lots of people," he explained. The paper in PNAS suggests that the actual positioning of the motifs is associated with small RNA molecules that are involved with a process called post-transcriptional gene silencing (PTGS). "A human embryo starts out as a single fertilised cell and rapidly divides into a widely complex series of cells that become a human being," explained Dr McCallion. "Every cell in that human being contains the same complement of genes and what makes each cell different is the precise way that genes are turned on and turned off." PTGS turns genes off after the process of transcription has taken place. One way in which this occurs is through "RNA interference", which involves the introduction of double-stranded RNA molecules. These trigger the degradation of another type of RNA molecule known as messenger RNA (mRNA), "down-regulating" the gene. During transcription, this molecule encodes and carries information from genes to sites of protein synthesis. "These regions may indeed contain structure that we haven't seen before," said Dr Rigoutsos. "If indeed one of them corresponds to an active element that is involved in some kind of process, then the extent of cell process regulation that actually takes place is way beyond anything we have seen in the last decade." ... [As I have said before, I well remember in earlier days debating Darwinists who used to cite it as an argument against design that genomes contained so much "junk DNA." For example, the Darwinist philosopher David Hull, in his 1991 review in Nature of the first edition of Phil Johnson's Darwin on Trial, cited it as an argument against design that "95 per cent of the DNA that an organism contains has no function":

"What kind of God can one infer from the sort of phenomena epitomized by the species on Darwin's Galapagos Islands? The evolutionary process is rife with happenstance, contingency, incredible waste. death, pain and horror. Millions of sperm and ova are produced that never unite to form a zygote. Of the millions of zygotes that are produced, only a few ever reach maturity. On current estimates, 95 per cent of the DNA that an organism contains has no function." (Hull D.L., "The God of the Galapagos." Review of "Darwin on Trial," by Phillip E. Johnson, Regnery Gateway: Washington DC, 1991. Nature, Vol. 352, 8 August 1991, p.486).

In fact my strongly Darwinist genetics textbook as late as 2002 was still using the term "junk DNA":

"This repetitive DNA comprises at least three categories. One is `junk' DNA, DNA that is not useful to the organism, made up of untranscribed and parasitic sequences (selfish DNA). ... Much eukaryotic DNA is junk, apparently doing no harm. In some cases, 97% of the host genome is composed of junk DNA. Recent work seems to indicate that gross differences in DNA content between higher organisms may be due to the differing abilities of different species to rid themselves of this parasitic DNA. If it builds up without being removed, the DNA content of the species can soar. Thus, the wide differences in DNA content among higher eukaryotes mentioned at the beginning of this section have little to do with the complexity of the organism, but rather with the ability of the organism to remove junk DNA as it forms." (Tamarin, R.H., "Principles of Genetics," International Edition, [1996], McGraw-Hill: New York, Seventh Edition, 2002, pp.458-459)

But as Dembski pointed out in 1999 (indeed in a 1998 article in First Things which used virtually identical language), that while "on an evolutionary view we [would] expect a lot of useless DNA," on an ID view we would "expect DNA as much as possible to exhibit function":

"Design is not a science-stopper. Indeed design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term `junk DNA.' Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA as much as possible to exhibit function. And indeed the most recent findings suggest that designating DNA as `junk' merely cloaks our current lack of knowledge about function. For instance, in a 1997 issue of the Journal of Theoretical Biology, John Bodnar and his colleagues describe how `non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development.' [Bodnar, J.W., Killian, J., Nagle, M. & Ramchandani, S., "Deciphering the Language of the Genome," Journal of Theoretical Biology, 189, 1997, p.183] Design encourages scientists to look for function where evolution discourages it." (Dembski W.A., "Intelligent Design: The Bridge Between Science and Theology," InterVarsity Press: Downers Grove IL, 1999, p.150)

As the Discovery Institute's John West responded (presumably referring to Dembski's abovementioned article), "In 1998 an ID theorist, reckoning that an intelligent designer would not fill animals' genomes with DNA that had no use, predicted that much of the `junk' DNA will someday be found to have a function":

"By contrast, said Alan Leshner, chief executive of the American Association for the Advancement of Science, Intelligent Design offers nothing in the way of testable predictions. `Just because they call it a theory doesn't make it a scientific theory,' Leshner said. `The concept of an intelligent designer is not a scientifically testable assertion.' Asked to provide examples of non-obvious, testable predictions made by the theory of Intelligent Design, John West, an associate director of the Discovery Institute, a Seattle-based ID think tank, offered one: In 1998, he said, an ID theorist, reckoning that an intelligent designer would not fill animals' genomes with DNA that had no use, predicted that much of the `junk' DNA in animals' genomes -long seen as the detritus of evolutionary processes - will someday be found to have a function. (In fact, some `junk' DNA has indeed been found to be functional in recent years, though more than 90 percent of human DNA still appears to be the flotsam of biological history.) In any case, West said, it is up to Darwinists to prove ID wrong." (Weiss R. & Brown D., "New Analyses Bolster Central Tenets of Evolution Theory: Pa. Trial Will Ask Whether 'Alternatives' Can Pass as Science, Washington Post, September 26, 2005)

And note the anti-IDist authors responding that "more than 90 percent of human DNA still appears to be the flotsam of biological history"!

The fact that more and more of the genome previously thought to be "junk" is turning out to have, not just a function, but a highly sophisticated function, is more evidence for design and against Darwinism.

I had intended to add, for possible inclusion in my Quotes Book (which will now probably be a self-published eBook), brief quotes, with equally brief comments, in date order, from news articles I had on so-called "junk DNA." But there tuned out to be too many which would make this post too long. Especially as I want also to quote from Dawkins and Dennett, where Dawkins based part (perhaps a large part-since Dennett cites it as evidence) of his "selfish-gene" theory on `junk-DNA' (which he called "selfish-DNA"). So I will split this post into two parts and continue later with just the quotes and my comments in part #2]

Stephen E. Jones, BSc (Biol).
"Problems of Evolution"

Friday, April 28, 2006

Mirecki: No new information in reported beating

No new information in reported beating, The Lawrence Journal-World, Monday, April 24, 2006 ... The trail has gone cold in the investigation of a roadside beating reported late last year by a Kansas University professor. Douglas County Sheriff's Office spokeswoman Lt. Kari Wempe said Thursday that detectives had finished their paperwork related to religious studies professor Paul Mirecki's report that he was beaten by two unknown men on Dec. 5, 2005, on a roadside south of Lawrence. The office has not identified any suspects and, unless any new leads come in, the investigation is finished. At the time, Mirecki was under fire for comments he had posted online critical of organized religion. ... [I presume that the trail has grown cold because there never was a beating! That is, "Mirecki's report that he was beaten by two unknown men" was merely the latest hate crime hoax in academia.

For my reasons, see my post, "Those black eyes." Briefly, Mirecki's minor injuries, evident in the two black eyes in the above photo, are consistent with him falling over and hitting his face on a hard surface, and are not consistent with him being beaten by "two men for about one minute with a metal object, striking him repeatedly on the head, shoulders and back." Evidently Mirecki's colleagues in the University of Kansas religious studies department, thought so too, because instead of supporting him, they recommended he step down from his post as Chairman, which he did.

But, apart from the waste of police resources (although I doubt they ever took it seriously, evidently regarding Mirecki as the culprit), Mirecki has got what he deserved. His blatant attempt to get revenge on the ID movement for the Kansas Board of Education adopting new science standards that allowed evolution to be criticised has backfired spectacularly. By his own admission his career is now ruined.

It is ironic that Mirecki's idea of teaching a course on ID has been taken up by other secular educational institutions, such as Cornell and Knox College. This will no doubt be picked up by other colleges and universities, which will in turn lead to ID literature having to be taken seriously, even if only to critique it!

Since this may be my last post on Mirecki, I have posted below an introduction to the Gnostic `gospel' that is his other claim to fame, the so-called `Gospel of the Savior'. In the light of the money-making hype about another Gnostic `gospel ', the Gospel of Judas, it may be helpful for some to see another example of the Gnostics' dishonest tactic of placing their bizarre teachings in the mouth of Jesus, an apostle, or some other character from the genuine Christian Scriptures.]

Stephen E. Jones, BSc (Biol).
"Problems of Evolution"

"The most recent Gospel to be discovered is called the Gospel of the Savior. It poses real difficulties for translator and reader alike, since so much of its text has been destroyed (i.e., there are numerous holes in the manuscript). Nonetheless, it was obviously once an intriguing account of Jesus' life-or at least of his last hours. For the surviving portion of the text recounts the final instructions of Jesus to his disciples, his prayer to God that the `cup' might be taken away from him, and then a final address-to the cross itself. Whether this Gospel originally contained an entire account of Jesus' life and death cannot be determined. There are numerous differences between the surviving passages of this Gospel and the parallel accounts in the New Testament. One of the most striking is that when Jesus asks his Father to `remove this cup from me,' he does so not in the Garden of Gethsemane, but in a vision in which he has been transported to the throne room of God himself. In addition, this account records God's replies to Jesus' requests. But probably the most intriguing aspect of this hitherto lost Gospel is its ending, where Jesus (who is called `the Savior' throughout the account) speaks directly to the cross: `O cross do not be afraid! I am rich. I will fill you with my wealth. I will mount you, O cross, I will be hung upon you:' It appears that the unknown author of this Gospel made use of earlier Christian texts, including the Gospels of Matthew and, especially, John, and the book of Revelation. He evidently produced his account sometime in the second century, although the Coptic manuscript that contains it dates from the sixth or seventh century. The original language was Greek. We do not know where the text was originally written. The surviving manuscript was discovered in Egypt and acquired for the Papyrus Collection of the Berlin Museum in 1967; but it remained unnoticed there until an American scholar, Paul Mirecki, came upon it in 1991. He and another scholar, Charles Hedrick, published the first edition of the text; an authoritative reconstruction of its narrative with a readable translation was then made by Stephen Emmel. That is the translation I reproduce here, including the places where the translator indicates that the manuscript cannot be read." (Ehrman B.D., "Lost Scriptures: Books that Did not Make It into the New Testament," Oxford University Press: New York NY, 2003, pp.52-53)

Thursday, April 27, 2006

Evolving enzymes

Evolving enzymes: A catalyst uses quantum mechanics to speed chemical reactions, The Economist, April 15th 2006 ...

[Graphic: Wikipedia, "Enzyme"]

IMAGINE hitting a tennis ball against a wall. Time after time, the ball bounces back. But, just occasionally, the ball disappears only to reappear on the other side of the wall. The wall is solid; no bricks are missing. It sounds surreal, but in the weird world of quantum mechanics such occurrences, involving very small objects over very short distances, are an everyday effect known as quantum tunnelling. [Also at Seed Magazine. This could be a very important (perhaps even Nobel prize-winning) discovery, if it turns out to be true.]

Whether such an effect could account for odd behaviour at larger sizes and distances has long been the subject of debate. In particular, it is of interest to chemists, who want to know how a group of proteins called enzymes speedup, or catalyse, chemical reactions at rates that are, in some cases, millions of times faster than the reaction rate in their absence. This is important because, in the absence of enzymes, most chemical reactions in biological cells would occur too slowly to support life. [If it turns out that some enzymes exploit quantum tunnelling, then that would be yet another fine-tuned for life parameter of the Universe.]

The answer, reported in this week's issue of Science, is that enzymes also exploit this quantum-mechanical loophole. Like all catalysts, enzymes work by providing a chemical reaction with an alternative pathway that has a lower energy threshold to get it going. Nature will take the path of least resistance, just as a ball left to roll about in a bowl will settle inert at the bottom of the vessel. The question is: exactly how does the enzyme change the energy barrier for the chemical transformation such that the ball tunnels through the side of the bowl rather than languishing at its bottom? The researchers, based at the University of Manchester and the University of Bristol, both in Britain, studied a compound called tryptamine, which belongs to a group of neurotransmitters and other chemical messengers that contain a nitrogen and two hydrogen atoms connected to an "aromatic" ring by a two-carbon chain. By common convention, an enzyme's name describes what it does, followed by the ending "ase". So an enzyme called aromatic amine dehydrogenase (AADH) removes hydrogen from tryptamine. [It is going to be really interesting if neurotransmission requires quantum tunnelling!

That might then support Roger Penrose's theory that intelligence is not substrate-neutral (as artificial intelligence maintains), but the mind (even of lowly organisms) derives its power from the cellular ultrastructure of neurons:

"Yet there must indeed be a complicated control system governing the behaviour of a paramecium-or indeed other one-celled animals like amoebas- but it is not a nervous system. The structure responsible is apparently part of what is referred to as the cytoskeleton. As its name suggests, the cytoskeleton provides the framework that holds the cell in shape, but it does much more. It is the cytoskeleton's role as the cell's 'nervous system' that will have the main importance for us here. For our own neurons are themselves single cells, and each neuron has its own cytoskeleton! Does this mean that there is a sense in which each individual neuron might itself have something akin to its own 'personal nervous system'? This is an intriguing issue, and a number of scientists have been coming round to the view that something of this general nature might actually be true. ... In order to address such issues, we should first glimpse the basic organization of the cytoskeleton. It consists of protein-like molecules arranged in various types of structure: actin, microtubules, and intermediate filaments. ... The 'control centre' of the cytoskeleton ... is a structure known as the centriole. This seems to consists essentially of two cylinders of nine triplets of microtubules ... The centriole forms the critical part of a structure called the microtubules organizing centre or centrosome. ... the centriole, which seems to be the focal point of the cytoskeleton, a structure that apparently controls the cell's movements and its detailed organization. ... Hameroff and his colleagues have argued, for more than a decade, that microtubules may play roles as cellular automata, where complicated signals could be transmitted and processed along the tubes as waves of differing electric polarization states of the tubulins. Recall that tubulin dimers can exist in (at least) two different conformational states that can switch from one to the other, apparently because of alternative possibilities for their electric polarizations. ... Indeed, if tubulin dimers are the basic computational units, then we must envisage the possibility of a potential computing power in the brain that vastly exceeds that which has been contemplated in the AI literature. Hans Moravec, in his book Mind Children (1988), assumed, on the basis of a 'neuron alone' model, that the human brain might in principle conceivably achieve some 1014 basic operations per second, but no more, where we consider that there might be some 1011 operational neurons, each capable of sending about 103 signals per second . If, on the other hand, we consider the tubulin dimer as the basic computational unit, then we must bear in mind that there are some 107 dimers per neuron, the elementary operations now being performed some 106 times faster, giving us a total of around 1027 operations per second. Whereas present-day computers may be beginning to close in on the first figure of 1014 operations per second, as Moravec and others would strongly argue, there is no prospect of the 1027 figure being achieved in the foreseeable future. ... it is clear that the possibility of 'microtubular computing' (cf. Hameroff 1987) puts a completely different perspective on some of the arguments for imminent human-level artificial intelligence." (Penrose, R., "Shadows of the Mind: A Search for the Missing Science of Consciousness," [1994], Vintage: London, 1995, reprint, p.357-366)]

Hydrogen, the simplest atom, consists of a single proton encircled by a single electron. As electrons are point-like, their quantum mechanical behaviour is well known. But protons are far bigger, and the idea that they might be able to quantum tunnel is more controversial. Yet the AADH catalyses the breakage of the otherwise very stable, carbon-hydrogen bond at ambient temperatures, a feat that would appear to be impossible. Something strange must be going on. The researchers suspect that protons as well as electrons are undergoing quantum tunnelling, that is, hydrogen itself is quantum tunnelling. [The proton has about 1836 times more mass than an electron, so that presumably makes it difficult to see how it could be involved in quantum tunnelling. But maybe part of it (a proton is composed of three quarks) can be?]

The team used x-ray crystallography experiments combined with computational simulations to examine the chemical reactions involved. The researchers caught an intermediate step in the process by which hydrogen is removed from tryptamine, namely the point at which a proton disappears from a carbon atom as the carbon-hydrogen bond breaks. They argue that this happens because the enzymes move in such as way that it becomes possible for protons to quantum tunnel. The work suggests that the motion needed is relatively short-ranged, although other researchers are also looking at whether long-range movement that extends throughout the enzyme plays a role in catalysis through quantum tunnelling. Much of the work that is being done in this area is hotly contested. Indeed, a related article in the same issue of Science by Stephen Benkovic and Sharon Hammes-Schiffer of Pennsylvania State University casts doubt on the findings, describing them as "at variance with other systems" and suggesting that there is more going on than was examined in the study. Nevertheless, the idea that protons as well as electrons can quantum tunnel is a striking one. And, as if that claim were not intriguing enough, the British researchers raise the possibility that short-range tunnelling in enzymes might be the result of evolutionary pressure. [If they mean "evolutionary" in the sense of biological¸ it would seem to have the cart before the horse. If biochemical reactions were not catalysed, there would be no life in the first place. As a Dr. Richard Wolfenden found, uncatalysed biochemical reactions could take millions, indeed up to a trillion years. So As Wolfenden himself pointed out, "Without catalysts, there would be no life at all, from microbes to humans,' . `It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction'":

"All biological reactions within human cells depend on enzymes. Their power as catalysts enables biological reactions to occur usually in milliseconds. But how slowly would these reactions proceed spontaneously, in the absence of enzymes -minutes, hours, days? ... Dr. Richard Wolfenden .... In 1998, he reported a biological transformation deemed `absolutely essential' in creating the building blocks of DNA and RNA would take 78 million years in water. `Now we've found one that's 10,000 times slower than that,' Wolfenden said. `Its half-time - the time it takes for half the substance to be consumed - is 1 trillion years, 100 times longer than the lifetime of the universe. Enzymes can make this reaction happen in 10 milliseconds.' Wolfenden, along with co-authors ... published a report of their new findings ... in the ... Proceedings of the National Academy of Sciences. ... May 13. The report highlights the catalytic power of phosphatase enzymes to tremendously enhance the transformation rate in water of a specific group of biochemicals: phosphate monoesters. Protein phosphatase enzymes acting on these monoesters help regulate the molecular cross-talk within human cells, the cell signaling pathways and biochemical switches involved in health and disease. `We have esters floating around in our cells with all kinds of functions,' Wolfenden said. `Every aspect of cell signaling follows the action of the type of phosphatase enzyme that breaks down phosphate monoesters. Other phosphatases highlighted in the study for their catalytic power help mobilize carbohydrates from animal starch and play a role in transmission of hormonal signals.' As to the uncatalyzed phosphate monoester reaction of 1 trillion years, `This number puts us way beyond the known universe in terms of slowness,' he said. `(The enzyme reaction) is 21 orders of magnitude faster than the uncatalyzed case. And the largest we knew about previously was 18. We've approached scales than nobody can grasp.' ... `Without catalysts, there would be no life at all, from microbes to humans,' he said. `It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction.' ... `The enzymes we studied in this report are fascinating because they exceed all other known enzymes in their power as catalysts. We've only begun to understand how to speed up reactions with chemical catalysts, and no one has even come within shouting distance of producing their catalytic power.'". (Lang L.H., "Without enzyme catalyst, slowest known biological reaction takes 1 trillion years, EurekAlert!, 5 May, 2003. My emphasis)

However, Dr. Wolfenden is a tad confused. Without life, there is no "natural selection". As Theodosius Dobzhansky, co-founder of Neo-Darwinism, pointed out, "Prebiological natural selection is a contradiction in terms":

"One way out of the problem would be to extend the concept of natural selection to the pre-living world of molecules. A number of authors have entertained this possibility, although no reasonable explanation has made the suggestion plausible. Natural selection is a recognized principle of differential reproduction which presupposes the existence of at least two distinct types of self-replicating molecules. Dobzhansky appealed to those doing origin-of-life research not to tamper with the definition of natural selection when he said: `I would like to plead with you, simply, please realize you cannot use the words `natural selection' loosely. Prebiological natural selection is a contradiction in terms.' [Dobzhansky T.G., in Fox S.W., ed., "The Origins of Prebiological Systems and of Their Molecular Matrices," Academic Press: New York NY, 1965, p.310] Bertalanffy made the point even more cogently: `Selection, i.e., favored survival of "better" precursors of life, already presupposes self-maintaining, complex, open systems which may compete; therefore selection cannot account for the origin of such systems' [von Bertalanffy L., "Robots, Men and Minds," George Braziller: New York NY, 1967, p.82]" (Thaxton C.B., Bradley W.L. & Olsen R.L., "The Mystery of Life's Origin: Reassessing Current Theories," [1984], Lewis & Stanley: Dallas TX, 1992, p.147. My emphasis)

After all, if there was such a things non-biological "natural selection" (especially so powerful that it could perform biochemical reactions without enzymes), then biological natural selection (and Darwinism) would be even more unfalsifiable that it already is! How could anyone tell if mutations were random if there was natural selection at the biochemistry level? That would be a case of `out of the frying-pan and into the fire for Darwinism, if it embraced non-biological `natural selection' to solve its origin of life problem!

I have added this quote to a new section of my "Problems of Evolution" book outline, PE 7. 4. 5. "Problems for all naturalistic origin of life theories ... Slowness of reactions without enzymes"]

Whether this suggestion proves to be weirder than quantum mechanics itself remains to be seen. ... [Actually, I don't think this suggestion is "weird" at all. Clearly something amazing is going on that can speed up a biochemical reaction (which is "absolutely essential in creating the building blocks of DNA and RNA") from "78 million years" down to "10 milliseconds"!]

PS: Here below is another quote (by an atheistic evolutionist, despite the title) about the central origin of life "chicken and egg' dilemma", that "all of the enzymes needed to catalyse gene expression are themselves produced by the expression of their genes," that is, "DNA and RNA are needed to make proteins, while proteins are needed to make DNA and RNA"!

Stephen E. Jones, BSc (Biol).
"Problems of Evolution"

"This process of protein synthesis is known as 'translation', since the genetic message is now being translated from the language of DNA and RNA (i.e. from the language of nucleic acids) into the language of proteins. The entire process of decoding a gene into a protein, involving both transcription (the production of the mRNA) and translation (use of the mRNA to make protein) is known as gene 'expression'. And remember that all of the enzymes needed to catalyse gene expression are themselves produced by the expression of their genes; and all the other types of RNA, such as tRNAs and the RNAs found in ribosomes, are produced by the transcription of genes that encode them. So DNA and RNA are needed to make proteins, while proteins are needed to make DNA and RNA, and also to assemble proteins. This presents us with a 'chicken and egg' type of dilemma: how could DNA and RNA (or any similar nucleic acid) have first formed and been replicated without proteins; or how could proteins have first formed without the DNA genes and mRNAs needed to encode them, and without the other proteins needed to catalyse their manufacture? That is really the central issue facing scientists trying to explain the origin of life on earth - how did self-replicating systems of genes encoding proteins that make new genes and proteins ... first arise?" (Scott A., "The Creation of Life: Past, Future, Alien," Basil Blackwell: Oxford UK, 1986, p.39. Ellipses original)

Tuesday, April 25, 2006

Gordon Rattray Taylor on the fish-to-amphibian transition

I have been having fun today revisiting my old quotes (and scanning new ones) for my Quotes Book.

Here are three by Gordon Rattray Taylor from his book, "The Great Evolution Mystery" (1983). First on the fish to amphibian transition, which despite claims like "Darwin Would Have Loved It" (i.e. Tiktaalik roseae), by TIME magazine, the transition, as Taylor (a committed fully naturalistic evolutionist) pointed out, was as un-Darwinian as one could imagine:

"When we survey the evolutionary story, from the first multicellular creatures up to man we soon get the feeling that from time to time there was a dramatic change of plan - and indeed of lifestyle - that is quite inconsistent with the slow accumulation of imperceptible changes upon which Darwin based his theory. Evolutionists call such discontinuities 'saltations' (that is, jumps). The study of evolution in this large sense is sometimes called megaevolution, in contrast with the micro-evolution of species; the term macro-evolution is also used but is ambiguous, since some workers use it for evolution only slightly above the species level. ... The most obvious and striking of these major steps was the step from sea to land, a step taken some 360 million years ago. Suddenly, four-legged air-breathing creatures appeared - quite unlike the scaly, limbless, water-breathing fishes which had been the most prolific creatures up to this time. ... So why did the fishes invade the land? No one knows. The real obstacles to such a move were the massive structural changes needed to make life on land worthwhile. To begin with, the fish would need legs simply in order to relieve the pressure of its body on the ground, which would compress the lungs. Equally importantly, the land animal needs a strong pelvic girdle. The fins of fishes are attached only to bony plates beneath the skin and could not support the weight of the body until a link had been provided to transmit their support to the spine. There were problems with the front suspension too, for in fishes the forward fins are firmly linked to the skull. Turned into legs, the animal would have to move its head from side to side with each step, so a new system of suspension had to be provided. Finally, since the weight of the body was no longer taken by the water, the spine itself needed strengthening. We are all so used to the idea of bone that it is hard for us to realise what a milestone the creation of bone was. Without bone, or something very like it, many terrestrial creatures could not support themselves against the drag of gravity. ... And so on to the next step, because land animals must also protect their body from drying out, by swapping scales for an impervious skin. Actually, the skin of some modern amphibians is quite sophisticated: it admits water when the creature returns to that element, the increased permeability being under hormonal control. We do not know if anything of the kind occurred in primitive amphibians. Land animals also need to protect their eyes from drying by a flow of tears and need an eyelid to protect it from dust particles. Similarly the nose must be protected by a supply of mucus. The land animal must also change its sense organs. It no longer needs the curious organ which runs along its side called a lateral line, and this is converted, by an amazing series of steps which I shall shortly describe, into the ear. The eye, too, changes, since the refractive index of air is different from that of water and no doubt there are modifications in the sense of smell ... And then, of course, there is the problem of the legs themselves. Before ever the fish reached the land the structure of its fins began to change. Instead of rays, a series of bones corresponding to the tibia, radius and ulna of the arm appeared. Digits, tarsals and metatarsals evolved (so it is now generally conceded) as wholly new structures, though the point - unwelcome to Darwinians - was hotly contested in the 1930s. The fish which decided to remain fish very sensibly, converted their lungs into swim-bladders with which they could regulate the depth at which they swam. Though we have this clue in the bone-structure of the crossopterygian fin there are no intermediate forms between finned and limbed creatures in the fossil collections of the world. Once again the critical evidence for gradual evolution is missing. The earliest definitely four-footed creatures known were found in strata some 370 million years old in Greenland, which at that time was not icy but had a mild climate. Known as Ichthyostegids, they possessed a five-toed foot but retained the fishy tail and the lateral line of their fishy ancestors. Their skulls, however, were already typically amphibian and their jaws were equipped with teeth. About three feet long, they probably lived in shallow waters and impaled small fish on their sharp teeth. They are the nearest we can get to a 'missing link' in this context." ... All that need concern us is the larger question of whether such an impressive array of coordinated changes could have taken place by chance, and have done so without leaving in the fossil record a single intermediate form to prove the point. As Darwin complained: 'Where are the infinitely numerous transitional links' that would illustrate the action of natural selection? Not here, at any rate." (Taylor G.R., "The Great Evolution Mystery," Harper & Row: New York NY, 1983, pp.55-57, 59-61. My emphasis)

Just note again those "massive structural changes needed to make life on land worthwhile": 1) "the fish would need legs"; 2) "a strong pelvic girdle" with; 3) "a link provided to transmit their support to the spine"; 4) "a new system of suspension had to be provided"; 5) "the spine itself needed strengthening" (leaving aside the original "creation of bone" - see `tagline' below - which "required not one but a whole burst of mutations, all integrated to a single end "); 6) "protect their body from drying out, by swapping scales for an impervious skin"; 7) "protect their eyes from drying by a flow of tears"; 8) "need an eyelid to protect it from dust particles"; 9) "the nose must be protected by a supply of mucus"; 10) "change its sense organs. the lateral line is converted, by an amazing series of steps into the ear" (see further below).

As for 6) "legs," "Before ever the fish reached the land the structure of its fins began to change. Instead of rays, a series of bones corresponding to the tibia, radius and ulna of the arm appeared. Digits, tarsals and metatarsals evolved (so it is now generally conceded) as wholly new structures (and note there were two pair, i.e. four-arms and legs), rather than just one pair - arms, which would be all that was needed to flop between pools, not that it needed even that-just stiff fins would have done).

And as Taylor rightly noted by his: 'Where are the infinitely numerous transitional links' that would illustrate the action of natural selection? Not here, at any rate," this did (and does) not support Darwin's theory of the natural selection of random micromutations!

As Taylor observes (and I wholeheartedly agree), this "progressive series of changes" to just one part, the conversion of the fish lateral line into the land animal's inner ear "look more like the refinement of a plan than the result of a series of happy accidents" (my emphasis):

"With all this, of course, went improvements in the brain, most notably the power to compare the times at which signals from one source reach each ear, thus providing a method of estimating the direction in which the source lies. ... In contrast with the case of the eye, where undifferentiated cells were specialised into the required forms, here existing structures have been profoundly modified and even shifted to another position in a progressive series of changes which certainly look more like the refinement of a plan than the result of a series of happy accidents. But the insoluble problem is how and why did a balance organ become an organ of hearing? As van Bergeijk pointedly asks: 'What prompts the fish to begin developing a sensory apparatus that will respond to a stimulus about the very existence of which the fish knows nothing?' ... After describing the last part of this process, the adaptation of the bones linking the jaw to the skull into a chain of ossicles linking the eardrum to the inner ear, Ernst Mayr sweepingly remarks: 'Not all the steps in this process are yet entirely apparent, but I think little doubt is left as to the principle involved.' If by 'principle' one means merely progressive remodelling, the statement is a truism. But if 'principle' means that chance selection brought about these elaborate changes, then there must be very great doubt indeed. Like de Beer, Mayr does not seem to appreciate the elementary point that demonstrating the occurrence of a sequence of events does not explain why they happened. But what kind of mutations could bring about the major changes I have described? Could cause a tube to roll up into a helix? Could cause other tubes to form semi-circular canals accurately set at right angles to each other. Could grade sensory hairs according to length? Could cause the convenient deposit of a crystal in the one place it will register gravity? Even more amazingly, some fishes do not trouble to secrete a crystal but incorporate a bit of sand or stone. What kind of mutation could achieve this - when and only when a natural crystal is not formed? The purpose is fulfilled, the means are unimportant. It just doesn't make sense." (Taylor, ibid., 1983, pp.105-106)

I assume that this in fact was "the refinement of a plan" and (as previously posted here and here) this will form part of my `Construction Project' Design Argument (see here; here and here), when I eventually write my book, "The Design Argument."

Stephen E. Jones, BSc (Biol).
"Problems of Evolution"

We are all so used to the idea of bone that it is hard for us to realise what a milestone the creation of bone was. Without bone, or something very like it, many terrestrial creatures could not support themselves against the drag of gravity. ... Bone has a precise, indeed an unique, structure, being composed of mineral and living matter interspersed. The strength of bone comes from the mineral component: crystals of hydroxyapatite; the adaptability from the living collagen. The two are arranged in specific patterns, with spaces reserved for living bone-making cells and for blood vessels. You may be one of those who think of bone as inert, stony, almost eternal. In fact it is highly mobile, almost fluid on the evolutionary scale. Bone-building cells add to it here, bone-destroying cells erode it there, until it is sculptured into a different form, even in the span of a single lifetime. On the evolutionary scale, of course, much bigger changes are possible. If one of the larger bones is sliced in half, it is seen to contain a spongework of criss-crossing sheets, the trabeculae, which align themselves in precisely the best way to absorb the stresses to which that particular bone, in that individual, is being subjected. Like the network of girders which support a bridge or a structure like the Eiffel Tower, this gives strength for a minimum of weight. In addition the major bones contain a cavity, lined with a special sheath, which generates the blood cells needed by the blood. Human blood cells have a life of only 120 days, and you and I rely on our marrow providing a stream of replacements. Another membrane covers the exterior. (It is from the internal and external sheaths that the bone-making cells come.) Then there is the mystery of joints with their capsule of cartilage and their remarkable lubricant, the synovial fluid. It is obvious that the creation of bone required not one but a whole burst of mutations, all integrated to a single end - an incredible thing to happen by chance even if nothing else had been going on." (Taylor, ibid, 1983, p.57. My emphasis)

Sunday, April 23, 2006

Start of the ID movement: Thaxton, et al., "The Mystery of Life's Origin" (1986)

In my last post I mentioned that Thaxton et al.'s "The Mystery of Life's Origin" (1984) is usually (and in my opinion rightly) accepted as marking the start of the modern ID movement. But rather than post quotes from that book there in support, I decided to do that in this separate post.

In the book, Charles B. Thaxton, Walter L. Bradley and Roger L. Olsen most importantly distinguished between "supernatural" and "intelligent" (since unlike creationism ID's contrast is between unintelligent and intelligent, not between natural and supernatural), cause:

"The study of chemical evolution is strikingly similar to forensic science. Consistent with the uniformitarian view that life arose through processes still going on, numerous investigators have reported on laboratory observations and experiments which they offer as circumstantial evidence for the naturalistic origin of life. Though the conditions of the early earth are assumed to have been different from today's conditions, the processes are assumed to have been the same. According to this uniformitarian thinking, if we can reproduce in our laboratories today conditions as they were in the remote past, we should expect to obtain the kinds of changes that occurred then. This is the basis of prebiotic simulation experiments reported in chemical evolution literature. `Implicit in this [uniformitarian] assumption is the requirement that no supernatural agency "entered nature" at the time of the origin, was crucial to it, and then withdrew from history.' [Kenyon D.H. & Steinman G., "Biochemical Predestination," McGraw-Hill: New York, 1969, p.30]. (Actually all that is required for this assumption is that no intelligent-purposive-interruption or manipulation of the workings of natural forces ever occurred at the time of life's origin or since.)." (Thaxton C.B., Bradley W.L. & Olsen R.L., "The Mystery of Life's Origin: Reassessing Current Theories," [1984], Lewis & Stanley: Dallas TX, 1992, Second printing, pp.7-8)

They made the point that biotic enzymes and human intelligence (which are not supernatural) can routinely do things (like produce information) that abiotic processes cannot do (or at least there is no experience of them doing it):

"We believe the problem is analogous to that of the medieval alchemist who was commissioned to change copper into gold. Energy flow through a system can do chemical work and produce an otherwise improbable distribution of energy in the system (e.g., a water heater). Thermal entropy, however, seems to be physically independent from the information content of living systems which we have analyzed and called configurational entropy. As was pointed out, Yockey has noted that negative thermodynamic entropy (thermal) has nothing to do with information, and no amount of energy flow through the system and negative thermal entropy generation can produce even a small amount of information You can't get gold out of copper, apples out of oranges, or information out of negative thermal entropy. There does not seem to be any physical basis for the widespread assumption implicit in the idea that an open system is a sufficient explanation for the complexity of life. As we have previously noted, there is neither a theoretical nor an experimental basis for this hypothesis. There is no hint in our experience of any mechanistic means of supplying the necessary configurational entropy work. Enzymes and human intelligence, however, do it routinely."(Thaxton, et al., ibid., p.183)

What success that prebiotic simulation experiments had, they did so by "the crucial but illegitimate role of the investigator" (i.e. intelligent design):

"Over the years a slowly emerging line or boundary has appeared which shows observationally the limits of what can be expected from matter and energy left to themselves, and what can be accomplished only through what Michael Polanyi has called `a profoundly informative intervention.' [Polanyi M., "Life Transcending Physics and Chemistry," Chemical Engineering News, August 21, 1967, p.54]. When it is acknowledged that most so-called prebiotic simulation experiments actually owe their success to the crucial but illegitimate role of the investigator, a new and fresh phase of the experimental approach to life's origin can then be entered. Until then however, the literature of chemical evolution will probably continue to be dominated by reports of experiments in which the investigator, like a metabolizing Maxwell Demon, will have performed work on the system through intelligent, exogenous intervention. Such work establishes experimental boundary conditions, and imposes intelligent influence/control over a supposedly `prebiotic' earth. As long as this informative interference of the investigator is ignored, the illusion of prebiotic simulation will be fostered. We would predict that this practice will prove to be a barrier to solving the mystery of life's origin." (Thaxton, et al., ibid., p.185. Emphasis original)

Note that they made the first ID prediction above that :"As long as this informative interference of the investigator is ignored this practice will prove to be a barrier to solving the mystery of life's origin". That prediction, made ~22 years ago, still holds good today. In other words, until origin of life research: 1) stops using intelligent design illegitimately (in which case their prebiotic simulation experiments won't work at all); and 2) starts using intelligent design legitimately, (i.e. allows the ID paradigm into science) science will never succeed in solving the problem of the origin of life.

Thaxton et al. note that we know intelligent designers can synthesize proteins and build genes but we don't know that it can be done by "unassisted abiotic means" (my emphasis):

"We cannot disagree that there is need for an alternative to chemical evolution. In recognition of the fact that Panspermia offers no theory of origins, it must implicitly assume chemical evolution on some other locale in the cosmos, where conditions are more favorable than on earth. Many of the objections raised concerning terrestrial chemical evolution must, however, apply to other planets by the principle of uniformity In any setting it comes down to the fact that natural forces acting alone must be capable of supplying the necessary configurational entropy work of building the protein, DNA etc., and then assembling the cell. We know by experience that intelligent investigators can synthesize proteins and build genes. We still have no evidence it can be done by unassisted abiotic means. " (Thaxton, et al., ibid., pp.193-194)

Finally, they pointed out that DNA is not just analogous to a message that in our uniform experience otherwise is produced by intelligent causes. DNA's genetic code is a message, such that the laws of Information Theory apply to it, and SETI would unhesitatingly infer an intelligent source to any signal received that conformed to those laws:

"Consider, for example, the matter of accounting for the informational molecule, DNA. We have observational evidence in the present that intelligent investigators can (and do) build contrivances to channel energy down non random chemical pathways to bring about some complex chemical synthesis, even gene building. May not the principle of uniformity then be used in al broader frame of consideration to suggest that DNA had an intelligent cause at the beginning? Usually the answer given is no. But theoretically, at least, it would seem the answer should be yes in order to avoid the charge that the deck is stacked in favor of naturalism. We know that in numerous cases certain effects always have intelligent causes, such as dictionaries, sculptures, machines and paintings we reason by analogy that similar effects also have intelligent causes. For example, after looking up to see `BUY FORD' spelled out in smoke across the sky we infer the presence of a skywriter even if we heard or saw no airplane. We would similarly conclude; the presence of intelligent activity were we to come upon an elephant-shaped topiary in a cedar forest. In like manner an intelligible communication via radio signal from some distant galaxy would be widely hailed as evidence of and intelligent source. Why then doesn't the message sequence on them DNA molecule also constitute prima facie evidence for an intelligent source? After all, DNA information is not just analogous to a message sequence such as Morse code, it is such a message sequence [Yockey H.P., J. Theoret. Biol. Vol. 91, 1981, p. 13]. The so-called Shannon information laws apply equally to the genetic code and to the Morse code. True, our knowledge of intelligence has been restricted to biology-based advanced organisms, but it is currently argued by some that intelligence exists in complex non-biological computer circuitry. If our minds are capable of imagining intelligence freed from biology in this sense, then why not in the sense of an intelligent being before biological life existed? " (Thaxton, et al., ibid., pp.210-211)

While other books, like Denton's Evolution: A Theory in Crisis (1985), Johnson's Darwin on Trial (1991) and Behe's Darwin's Black Box (1996), had a major influence on the growth of the ID movement, in my opinion (and supported up by the quotes above) Thaxton, Bradley and Olsen's The Mystery of Life's Origin (1984), rather than negatively attack evolution, made the first positive arguments for Intelligent Design itself, and so marked the beginning of the modern ID movement.

That is however not to deny that important arguments for design made by earlier design theorists like Robert E.D. Clark: The Universe: Plan or Accident? (1949) may, and A.E. Wilder-Smith: The Creation of Life (1970) and The Natural Sciences Know Nothing of Evolution (1981) did, influence Thaxton, et al. They included Wilder-Smith's Creation of Life in their Selected Readings (p.220), but his The Scientific Alternative to Neo-Darwinian Evolutionary Theory (1987) was too late.

Stephen E. Jones, BSc (Biol).
"Problems of Evolution"

"Dawkins ... a bully ... does not write good science ... a genius from the wrist down"

It seems the whole world is turning against Dawkins:

Electric Universe, The Australian, David Bodanis has cracked the popular science formula, writes Helen Elliott, April 22, 2006 Electric Universe By David Bodanis Abacus, 298pp, $24.95. ... Yet no one has a patent on fundamentalism. Scientists are as susceptible as anyone else; Dawkins is believed to be writing a book that aims to demonstrate that people who believe in a god are less intelligent than non-believers. Bodanis is critical of those whom he sees as not up to scratch; he does not respect Dawkins. "He's a bully, and he does not write good science," he says flatly. "Remember what George Orwell said about Salvador Dali? 'He's a genius from the wrist down.' That's Dawkins." He acknowledges Dawkins's astonishing rhetoric but loathes his dismissal of anyone who has any belief in a higher spirituality as idiots. Bodanis grew up in an observant Jewish household and although he doesn't call himself traditional, he still observes Friday nights. If Dawkins is right about his views on religion, he adds, "then Einstein, who was quite religious, [was] an idiot". ...

Personally, I assume that Dawkins needs help, his extreme hatred of religion in general, and Christianity in particular, stemming from this sexual abuse incident in his childhood:

"Happily I was spared the misfortune of a Roman Catholic upbringing (Anglicanism is a significantly less noxious strain of the virus). Being fondled by the Latin master in the squash court was a disagreeable sensation for a nine-year-old, a mixture of embarrassment and skin-crawling revulsion, but it was certainly not in the same league as being led to believe that I, or someone I knew, might go to everlasting fire. As soon as I could wriggle off his knee, I ran to tell my friends and we had a good laugh, our fellowship enhanced by the shared experience of the same sad pedophile. I do not believe that I, or they, suffered lasting or even temporary damage from this disagreeable physical abuse of power. Given the Latin master's eventual suicide, maybe the damage was all on his side." (Dawkins R., "Religion's Real Child Abuse," Op-Ed, Free Inquiry, Fall, 2002, Vol. 22, No. 4)

I assume it is no coincidence that it was at the same young age ("a nine-year-old") this tragically happened, when Dawkins rejected the Christianity of his upbringing and "toyed with atheism":

"'I toyed with atheism from the age of about nine, originally because I worked out that, of all the hundreds of religions in the world, it was the sheerest accident that I was brought up Christian. They couldn't all be right, so maybe none of them was. I later reverted to a kind of pantheism when I realised the shattering complexity and beauty of the living world. Then, around the age of 16, I first understood that Darwinism provides an explanation big enough and elegant enough to replace gods. I have been an atheist ever since." (Dawkins R., "You Ask The Questions," Independent, 23 February 2003)

On a more pleasant topic, as for "Who Owns the Term Intelligent Design? No One", I hereby nominate Dawkins as the first person to actually use the term "intelligent Designer" in 1982:

"Biology is the study of the complex things in the Universe. Physics is the study of the simple ones. It is the complexity of life, coupled with the precision of its adaptation, that cries out for a special kind of explanation, and the hunger for such explanation has frequently driven people to believe in a supernatural Creator. Complexity means statistical improbability. The more statistically improbable a thing is, the less can we believe that it just happened by blind chance. Superficially the obvious alternative to chance is an intelligent Designer. But Charles Darwin showed how it is possible for blind physical forces to mimic the effects of conscious design, and, by operating as a cumulative filter of chance variations, to lead eventually to organised and adaptive complexity, to mosquitoes and mammoths, to humans and therefore, indirectly, to books and computers." (Dawkins R., "The Necessity of Darwinism," New Scientist, Vol. 94, 15 April 1982, pp.130-132, p.130. My emphasis)

That is two years before Thaxton et al.'s "The Mystery of Life's Origin" (1984), which is usually (and in my opinion rightly) accepted as marking the start of the modern ID movement (see next post).

Dawkins also used the term "intelligently designing" in this "transparently feeble argument" (by him) from his 1986 The Blind Watchmaker:

"So, cumulative selection can manufacture complexity while single-step selection cannot. But cumulative selection cannot work unless there is some minimal machinery of replication and replicator power, and the only machinery of replication that we know seems too complicated to have come into existence by means of anything less than many generations of cumulative selection! Some people see this as a fundamental flaw in the whole theory of the blind watchmaker. They see it as the ultimate proof that there must originally have been a designer, not a blind watchmaker but a far- sighted supernatural watchmaker. Maybe, it is argued, the Creator does not control the day-to-day succession of evolutionary events; maybe he did not frame the tiger and the lamb, maybe he did not make a tree, but he did set up the original machinery of replication and replicator power, the original machinery of DNA and protein that made cumulative selection, and hence all of evolution, possible. This is a transparently feeble argument, indeed it is obviously self-defeating. Organized complexity is the thing that we are having difficulty in explaining. Once we are allowed simply to postulate organized complexity, if only the organized complexity of the DNA/protein replicating engine, it is relatively easy to invoke it as a generator of yet more organized complexity. That, indeed, is what most of this book is about. But of course any God capable of intelligently designing something as complex as the DNA/protein replicating machine must have been at least as complex and organized as that machine itself. Far more so if we suppose him additionally capable of such advanced functions as listening to prayers and forgiving sins. To explain the origin of the DNA/protein machine by invoking a supernatural Designer is to explain precisely nothing, for it leaves unexplained the origin of the Designer. You have to say something like 'God was always there', and if you allow yourself that kind of lazy way out, you might as well just say 'DNA was always there', or 'Life was always there', and be done with it. The more we can get away from miracles, major improbabilities, fantastic coincidences, large chance events, and the more thoroughly we can break large chance events up into a cumulative series of small chance events, the more satisfying to rational minds our explanations will be." (Dawkins R., "The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design," W.W Norton & Co: New York NY, 1986, p.141. My emphasis)

I would therefore not be surprised if the term "intelligent design" was unconsciously picked up by early ID theorists from their reading of Dawkins? If so, then maybe that will in the long-run turn out to be Dawkins' only lasting achievement!

Stephen E. Jones, BSc (Biol).
"Problems of Evolution"

Breathing space

[Source: "Pulmonary surfactant biology," School of Earth & Environmental Sciences, University of Adelaide]

Last night I found this old New Scientist article, which made a big impression on me at the time, misfiled in my filing cabinet:

"Breathing space: Do lungs work because of a mutation 350 million years ago?," New Scientist, Kurt Kleiner, 11 October 1997 ... AIR breathing developed independently many times in the history of evolution. But a subtle biological mechanism that allows lungs to function seems to have developed only once, and is still used by all air-breathing vertebrates, say researchers in Australia. Lungs need to expand and contract, but if the surface tension of liquid in the lungs is too high, the tissue sticks together and breathing is impossible. So in air-breathing vertebrates, the surface tension is lowered by a coating of proteins and lipids, called the surfactant system, on cells lining the lungs. Christopher Daniels and student Lucy Sulivan of the University of Adelaide compared the surfactant systems of 18 vertebrates, including fish, lizards, chickens and humans, and found that all make use of a key protein called surfactant protein A. They conclude in this month's Journal of Molecular Evolution that the surfactant system developed once in an ocean-dwelling ancestor about 350 million years ago, and has been used again and again as vertebrates developed lungs and crawled out of the water. `It's similar to the insulin system and haemoglobin-it's one of the things you have to have for the organism to do well,' says Daniels. `Since it evolved, it hasn't changed.' Daniels thinks the surfactant system may have developed first in the gut, as a way to regulate surface tension between the organs there. Even today, there are similar surfactant proteins in the guts of rats, he says. Because the lungs and the gut are closely related in the developing embryo, Daniels believes a genetic mutation may have shifted the surfactant to the lungs and made air breathing possible. Allan Smits of Quinnipiac College in Hamden, Connecticut, who also studies pulmonary surfactants, says Daniels's research on the surfactant system is convincing. `Clearly air breathing couldn't have developed without it,' he says. `It is definitely necessary for air breathing.'"

On searching the web for more information about it, I found references to it in News in Physiological Sciences, August 2003, and in Physiological and Biochemical Zoology, September/October 2004.

I also found the following comment I had made (and forgotten) on the New Scientist article, to the Calvin Reflector in 1998 (my added emphasis):

Obviously lungs had to exist before animals could live on land, and so lungs had to be developed in water, before they were needed on land. But that was not enough. It seems that lungs out of water need a special coating called the surfactant system, which stops the lung tissue sticking together in air. So right on cue, 350 million years ago, just before it was needed on land, an ocean-dwelling fish happened to have a special mutation which gave it a surfactant system that it didn't need, so that down the track its descendants could crawl onto the land. But of course that special mutation had to have happened to the same line of fish that also developed legs underwater, before they were needed on land. No doubt it will also be found that special mutations had to appear on cue to provide special land-dwelling eyes, ears, nostrils and eggs, in readiness for the `invasion' of the land later down the track by tetrapods. Not bad going for a `blind watchmaker' process that can't plan ahead!

This, along with other major transitions like the reptilian egg will form part of my `construction project' argument from design, when I write my future book, "The Design Argument." That is, when a series of major changes occur in a line towards a specific long-term end, it is reasonable to infer a designing intelligence is the ultimate cause.

This fits with a Fred Hoyle quote I rediscovered yesterday, while compiling my Quotes Book, in which he makes the same point that Dembski makes in his Explanatory Filter, that design is reliably inferred in the conjunction of : 1) very low probability events; 2) that match an independent external specification.

Hoyle gives the example of if a sequence of numbers generated by a roulette wheel over a year turned out to match the digits of pi:

"It is not at all difficult to formulate examples of events with exceedingly low probabilities. A roulette wheel operates in a casino. A bystander notes the sequence of numbers thrown by the wheel over the course of a whole year. What is the chance that this particular sequence should have turned up ? Well, not as small as 1 in 1040000, but extremely small nonetheless. So there is nothing especially remarkable in a tiny probability. Yet it surely would be exceedingly remarkable if the sequence thrown by the roulette wheel in the course of a year should have an explicit mathematical significance, as for instance if the numbers turned out to form the digits of pi to an enormous number of decimal places. This is just the situation with a living cell which is not any old random jumble of chemicals." (Hoyle, F., "The Universe: Past and Present Reflections," Annual Review of Astronomy and Astrophysics, Vol. 20, 1982, pp.1-35, p.15)

This is the same paper that the atheist Hoyle made his famous statement that, on the basis of the remarkable coincidence between the matching resonance levels of carbon and oxygen, without which there would be a lot less carbon in the Universe and therefore no life, that this was "Another put-up job" and "A common sense interpretation of the facts suggests that a superintellect has monkeyed with physics, as well as with chemistry and biology" (my emphasis):

"From 1953 onward, Willy Fowler and I have always been intrigued by the remarkable relation of the 7.65 Mev energy level in the nucleus of 12C to the 7.12 MeV level in 16O. If you wanted to produce carbon and oxygen in roughly equal quantities by stellar nucleosynthesis, these are the two levels you would have to fix, and your fixing would have to be just where these levels are actually found to be. Another put-up job? Following the above argument, I am inclined to think so. A common sense interpretation of the facts suggests that a superintellect has monkeyed with physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature." (Hoyle, Ibid., p.16).

Hoyle concluded the paper with:

"Taking the view, palatable to most ordinary folk but exceedingly unpalatable to scientists, that there is an enormous intelligence abroad in the Universe, it becomes necessary to write blind forces out of astronomy." (Hoyle, Ibid., p.15. My emphasis)!

Stephen E. Jones, BSc (Biol).
"Problems of Evolution"