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Saturday, 9 July 2005

Regular readers will know that The Git funds this place through a link to DOMAI (Dirty Old Men Association International) where you will find pictures of pretty young girls. If you like looking at pretty young girls, here are some free samples to view. Payment arrives every time a certain, quite nominal sum is reached. The last two cheques amounted to $US26.61 and $US31.61 respectively. The company that issues the cheques will not allow a higher trigger point for issuing the cheques, which is quite unfortunate. The bank charges The Git $AU10 for each cheques deposit. Thus these two cheques will that are equivalent to ~$AU78 will cost $AU20 (~26% of the value) to deposit. Income tax on the remainder amounts to ~$AU27, leaving a residue of $AU31 (40%) for The Git's use.

 Even though the cheques clear within a week (slow electrons?), the bank won't clear the cheques for 28 days, while Australian cheques clear within 5 days. Worse, the bank won't clear the cheques unless The Git stands in a queue to get to the counter and requests that the cheques to be cleared! Each deposit consumes as much as 40 minutes of The Git's valuable time.

The obvious solution would be to open a bank account in the US, but that's not an available option. Another option would be for a kind reader to receive these cheques, deposit them in their account (where the interest rate is likely a lot higher than the 0.025% The Git receives) and periodically send a cheque for a larger amount after deducting expenses. An alternative would be for The Git to just throw the cheques away, leaving CC Bill richer and the bank and the Australian Taxation Commissioner a little poorer. Frankly, The Git doesn't think they will notice.

Intelligent Design

The Git hasn't footnoted, or referenced this very well, but that's due to the "irreducible complexity" of his personal life :-) So there's a bunch of reading at the end that you might find handy if you want to pursue some of this.

First, what the Former Editor in Chief of the Encyclopædia Britannica has to say on the issue.

At Tech Central Station, Robert McHenry writes:

"The ID party holds that certain aspects of the world, especially details of the anatomy and biochemistry of living beings, are simply too complex to have evolved without guidance. The approved phrase is "irreducible complexity," a "concept" to which we will return. 

ID partisans have trained themselves not to be too specific about the Designer, either, for they have learned the lesson left by the political failure of their predecessors, the Creation Scientists, namely, that too much frankness in the matter of Who the Intelligent Designer is does not pay. So, carefully avoiding anything that sounds like theology, while all the time the butter remains quite firm in their mouths, they simply aver that there is a Design and that it prima facie evidences Intelligence. "God? Oh, heavens, we're not talking about God. It might just be his next-door neighbor Wilson."

Philosophically this is old ground, of course. William Paley's argument for the existence of a watchmaker, given a watch, is the best known example of the type. Not surprisingly, Paley assumed in his analogy that the watch in question was well made and actually kept time. So the naturalist's response to this form of theism has taken a standard form. He points to the very considerable amount of relevant contrary evidence: black flies, killer asteroids, the vermiform appendix, acne, tsunamis, hiccups, and Jerry Springer, not to mention death and disease and a hundred other varieties of human depravity, all of these suggesting if they do not prove that ours is perhaps not the very best of all possible worlds.

But -- correct me if I'm wrong -- this is creation as we actually know it. Any objective observer must report that the universe, if it is the product of conscious design, is clear proof that the designer is incompetent, a blunderer, an all-thumbs amateur who should not be allowed back into the workshop. (As a lad I read a science fiction story whose premise was that the universe is the product of a young Being-in-training, a kind of test piece by an apprentice not yet ready for journeyman status. For the life of me I can't recall the title or author of the story.) Unfortunately, however well Not-Quite-Bright Design might fly as an intellectual position, it lacks market appeal. 

The duplicity of the ID party as to theology is all quite transparent. What seems to be less so, at least to some, is the violence the ID party does to the work of the intellect. Consider "irreducible complexity." What does it mean to say that a given degree of complexity is irreducible? And who gets to say it? Has the ID party discovered a scale by which this question can be answered? Up (or down) to a certain point complexity is open to naturalistic explanation, but beyond that point it is not? "We don't know this yet, therefore it is unknowable." And further, "If you do happen to find it out anyway, don't tell me, because if you do I'll stick my fingers in my ears and go La-la-la-la-la really loud." The "debate" whose current installment is playing out in Kansas is a debate in just that sense and no other. 

Then there is the simple fact that the "theory" of ID is no theory at all, not in the sense that the word is used in science. It is not based on the best available evidence; it enables no predictions; and it is thus not testable. It is, at best, a paltry substitute myth that incorporates some of what actual science has learned or theorized but spurns not only scientific rigor but any intention to perform science. It is not, as claimed, a legitimate criticism of a scientific theory but a criticism of having such a theory at all. No less than the Creation Scientists, and no less than dear Bishop Wilberforce in 1860, though far less forthrightly, the proponents of ID wish to draw an arbitrary line and use the force of the state to declare that science shall not cross it.

Had that watch been found, not by the good Rev. Paley -- equipped as he was by culture and training not only to recognize in it the work of a human artisan but to judge his competence according as it got him to tea on time or not -- but by, say, a mud man of New Guinea, the conclusion drawn would have been quite different. The mud man instantly recognizes what could only be the work of a god, its materials unfamiliar, its intricacy beyond imagining, and its purpose utterly occult.

The difference between the mud man, gazing in awe at the watch, and the ID man, coolly regarding the bacterial flagellum, is that the mud man acts in good faith. The ID man is heir to a culture of knowledge-building that has evolved over millennia, and, for quite private reasons that have nothing to do with the rest of us, he declines the legacy. To be sure, he has every right, for himself, to decline whatever, and however far, he chooses. It only remains for the rest of us decline to decline with him. That would be intelligent."

Robert McHenry seems to abhor "intellectual violence", but only in others. Presumably he manages to excuse his own "intellectual violence" because it's in a Good Cause: Evangelical Atheistic Materialism. Quite rightly, McHenry points out that he is covering old philosophical ground. He manages to mention "Pigeon" Paley and Wilberforce, but omits such notable violators of intellect as Galileo Galilei and Sir Isaac Newton. Both of these intellectual giants believed in the Christian God and saw their scientific work as supporting their theistic beliefs; to use physicist Paul Davies' words, discovering "The Mind of God". Closer in time are Albert Einstein and Max Planck. They too are members of what McHenry calls "the ID Party" and he accuses them of intellectual dishonesty because they "carefully [avoid] anything that sounds like theology". This is manifestly untrue.

McHenry goes on: "Then there is the simple fact that the "theory" of ID is no theory at all, not in the sense that the word is used in science. It is not based on the best available evidence; it enables no predictions; and it is thus not testable." From the Wikipedia:

Proponents of ID study objects in an attempt to isolate what they call signs of intelligence -- physical properties of an object that necessitate design. Examples being considered include irreducible complexity, information mechanisms, and specified complexity. Many design theorists believe that living systems show one or more of these signs of intelligence, from which they infer that life is designed. This stands in opposition to naturalistic theories of evolution, which attempt to explain life exclusively through natural processes such as random mutations and natural selection.

Let's take the opposition first and test the alternative theory: the Received View of Darwinian Evolution (hereafter Neo-Darwinism). McHenry doesn't explicitly state that he is pushing Neo- Darwinism, but since his polemic is clearly aimed at Creation Scientists, we can safely take that to be so. 

1. Neo-Darwinism states that life originated on Earth from simple physical processes completely explicable by physics. The evidence for this is at best circumstantial and there is at least one example of this theory being false. The circumstantial evidence in favour is that simple physical processes can produce some of the complex molecules that we find associated with life. The explanation for the apparent lack of ability to "create life in a test tube from the primordial soup" is that the natural process took a very long time. This is apparently falsified by the rapidity of life appearing on Earth. The counterargument is that even something with a very small likelihood of occurring might well occur sooner, rather than later. It's worth pointing out that there is no fossil primordial soup; the soup's assumed to have been present at life's beginning. This part of the theory also appears to be falsified by the existence of fossils in meteorites. The NeoDarwinists wave their arms and assert that they are not really fossils. In GitSpeak: If it looks like dogshit, smells like dogshit and tastes like dogshit, then it's probably dogshit.
2. Evolution from simple prokaryotes to eukaryotes that evolved from single cells to multicellular life and eventually humans is not so much a theory as observation. Apart from a lunatic fringe, the Creation "Scientists" that McHenry wants us to confuse with the likes of Einstein, nobody doubts the fact that evolution has occurred.
3. Natural Selection, the part of the Received View that Darwin provided, is a mechanism for the expression of existing variability in a race of organisms. It explains how an existing phenotypic characteristic can disappear through breeding. It does not explain how totally new phenotypic characteristics arise. It does explain how man's achievement of breeding many races of dogs, or pigeons from a common wild stock can also occur through natural processes. It is inferred from this that speciation will eventually occur, given sufficient time and isolation.
4. Mendelian genetics is an explanation for the perpetuation of a phenological characteristic. The garden pea is either magenta/pink, or white and never some intermediate shade.
5. The explanation of the evolution of completely novel phenotypic characteristics is random mutation of the genes. A number of problems arise here. Despite the continual announcements in the press for discovery of a "gene for X", there is no widely agreed definition for a gene. Many phenotypic characteristics are related to nucleotide sequences in genomes, but the relationship for most is not one to one, but many to many. While nucleotide sequences are observed to mutate, the deleterious mutations are discarded by natural selection. Those not deleterious all appear to fulfil a similar function to the unmutated sequence. Perhaps the most impressive aspect of genome replication is the variety of error-correcting mechanisms that mitigate against mutations arising.
6. When The Git was first taught genetics, we learned that the nucleotide sequences all coded for proteins. Since the 1960s, we have learned that there are nucleotide sequences with no apparent function, so-called "silent" DNA. The "silent" DNA lacks the error-correction routines that protein forming DNA has. Despite this, it is even better conserved. There has been almost no variation whatsoever for approximately 4 billion years! [Pause for arm-waving and the word "mystery" from the Neo-Darwinists, the same word the Creation Scientists love to use about their God!].
7. In Climbing Mount Improbable, John Dawkins refutes Sir Fred Hoyle's calculation of the probability of a particular sequence of amino acids occurring as being at least 10²⁰. He does this by pointing out that the sequence must have been formed one step at a time, each step being of some benefit to the organism possessing the amino acid sequence (else it would have been deleted by natural selection). Two of the tenets of Neo-Darwinism are that genetic information does not ever pass between separate species and there are no "hopeful mutations" (evolution is not teleological). John Dawkins as the paradigmatic atheistic materialist has always been particularly adamant on this point. While the stepwise gradual accumulation of the changes necessary is plausible, the fact that the identical C4 photosynthetic process arose separately in more than 40 species by pure chance is not.

Let's tease some more out of that last point. Despite the C4 process being vastly more efficient than the C3 process it supplanted in some plant species, both processes continue to co-exist. This is readily explained by the fact that the C4 process shows its advantages in arid conditions when CO2 levels are lower. When the climate is wetter and  CO2 levels are higher, much of the efficiency difference disappears. We might suppose from the Dawkins gradualist explanation above that intermediate genotypes between the C3 and C4 variants would continue to exist. For the theory to be correct, they must have existed. The Git is unable to find any documentation of intermediate genotypes; that is, evidence for gradualism at the genomic level. This is assumed from the existence of different forms at the phenotypic level and that the phenotype [what an organism looks like as a consequence of its genotype] is entirely dependent on the genotype.

A number of alternative explanations to the Neo-Darwinist view exist. Since McHenry brought up the Creation "Science" viewpoint, we can deal with that first. Their view is that evolution never occurred (no evidence), there are no examples of intermediate phenotypes (untrue) and God created each individual by hand as it were. This gives rise to the "Not-Quite-Bright Design" observation McHenry made as if it were the only alternative.

One viewpoint is that absent any evidence for intermediate genomes, but ample evidence for shared genomes among species, then movement of packages of genomic information between unrelated species must occur. This also explains the existence of considerable shared genomic information between corals and vertebrate mammals, but not with any of the supposed intermediate organisms. This forms part of a wider theory called Panspermia, the roots of which go back at least as far as Kant. The packages of genomic information arrive from outside planet Earth, either in bacteria, or viruses, probably borne by comets. Think of the packages as software utilities, being directed by a master application and OS that resides within the "silent" code of the genome. This would explain why the almost identical genomic information regulates eye formation in wasps and humans, but arose in the presumed eyeless common ancestor of both.

Most of the IDers The Git has read seem to accept that the Intelligent Designer, to use "Pigeon" Paley's metaphor, wound up the clock of the Universe and then let it run its own course. God's intelligent design was limited to choosing precise physical parameters that allow this particular unique Universe to exist and produce the fruit called mankind. Several philosophers have pursued this "fine-tuning" argument for the existence of God.

However, The Git is fresh from reading Phil Kitcher's The Lives to Come, an entrancing read about the advances in modern science that not only allow us to design tomatoes that incorporate pigs' genes, but promise they will modify the human genome for the benefit of mankind. Yes Dorothy, eugenics is alive and well; not merely extermination, or selective breeding this time, but 100% pure Intelligent Design. Unless of course we can come up with an argument that humans are incapable of designing things intelligently. 

It seems to The Git that the Evangelical Atheistic Materialists are saying out of this corner of the mouth: "We are going to intelligently redesign humanity" and out of the other: "Intelligent design is impossible". Can we trust people who deny the existence of Intelligent Design while contemplating doing what they deny the existence of? Especially given the track record of past eugenicists.

The Git as ever remains agnostic. No religious group, the Evangelical Atheistic Materialists, nor the Creation "Scientists", nor even the Deists to whom he is drawn rather more than the atheists can claim his unquestioning adherence.

It is interesting to note the rather sudden and extreme hostility to Intelligent Design. Until recently, most proponents were, like Albert Einstein and Sir Fred Hoyle, cosmologists and physicists. Their arguments for belief in an Intelligent Designer hinged on the Fine-Tuning argument. If the laws of physics were ever so slightly different, then the ensuing chemistry that allows life to exist and evolve could never have happened. It is quite unfair of McHenry to say that the ID theory is "unscientific" when it was so firmly based in science. The thought experiments of the ID theorists went along the lines of "what would be the the effects on the universe of changing the various physical constants, such as the strong and weak forces, gravitation, Planck's constant and so forth?" The answer was that only a very tiny subset of all possible universes would allow life to exist.

However, as The Git just noted, these speculations beginning about 50 years ago failed to arouse the kind of ire that the likes of McHenry are now expressing. The answer is that it's probably because the IDers are now extending their speculations to the Sacred Cow of NeoDarwinism. Funnily enough, NeoDarwinism fails the very test that McHenry accuses ID Theory of failing; that is, it's not scientific because it makes no testable predictions. As Sir Karl Popper pointed out decades ago, NeoDarwinism is more in the nature of a research program than a scientific theory. And as physicists are wont to point out to their financiers: "If we could predict the outcome of our research, it wouldn't be research!"

Sir Karl Popper also pointed out that our science improves when theories are subject to criticism. The NeoDarwinists' reaction to criticism appears to be to mostly be of the form of ad hominems, rather than acknowledging that there are considerable unresolved  difficulties with their theories. Popper also pointed out that the best way to argue against a point of view was not to merely refute the opposing arguments, but to bring up better opposing arguments and refute those also. This is a lesson the McHenrys of the world could well emulate, rather than emulating the religious bigotry they claim to oppose.

To wrap this all up, it might be fun to extract some quotes from scientists about recent discoveries regarding the unusually rapid evolution of the human brain.

According to graduate student Eric Vallender, a coauthor of the article, it is entirely possible by chance that that two or three of these outlier genes might be involved in controlling brain size or behavior. "But we see a lot more than a couple -- more like 17 out of the two dozen outliers," he said. Thus, according to Lahn, genes controlling the overall size and behavioral output of the brain are perhaps places of the genome where nature has done the most amount of tinkering in the process of creating the powerful brain that humans possess today.

Here we see once again special "against the odds" events. And does Nature really tinker? The Git thought that Intelligent Designers might, but not unintelligent physical processes! "Hey, lookee here Maw! That cake in the oven's tinkering with the stove controls again!"

One of the study's major surprises is the relatively large number of genes that have contributed to human brain evolution. "For a long time, people have debated about the genetic underpinning of human brain evolution," said Lahn. "Is it a few mutations in a few genes, a lot of mutations in a few genes, or a lot of mutations in a lot of genes? The answer appears to be a lot of mutations in a lot of genes. We've done a rough calculation that the evolution of the human brain probably involves hundreds if not thousands of mutations in perhaps hundreds or thousands of genes -- and even that is a conservative estimate."

This is only surprising because it conflicts with the Received View. It's what you might expect from a designed system. The data appears to contradict NeoDarwinism's belief in very rare, tiny chance mutations over long periods of time.

It is nothing short of spectacular that so many mutations in so many genes were acquired during the mere 20-25 million years of time in the evolutionary lineage leading to humans, according to Lahn. This means that selection has worked "extra-hard" during human evolution to create the powerful brain that exists in humans.

Selection, Dawkins' "Blind Watchmaker", suddenly decides to "work extra-hard"? Why would a standard, uniform, undirected physical process do that? Once more, the argument to best explanation would appear to be Intelligent Design. The Git's not saying he's entirely convinced that is "the" explanation, but it sure beats the hand waving and attribution of intelligence to low-level physical processes we are reading about here.

Conclusion

It's one thing to adopt a particular philosophical position, in McHenry's case that of Atheistic Materialism. It's another to be evangelical about it and declare, as Dawkins has, that anyone who disagrees with you is "ignorant, stupid or insane, or wicked". There is not just one theory of evolution, there are many theories, even within the received Darwinian tradition. Like Kim Sterelny, The Git is a pluralist. Many of those theories are useful viewpoints, but they are not the absolute showstoppers their proponents often wish that they were. More on this next week...

Sources

The Evolution Wiki where some of the jargon is explained.

Several of Richard Dawkins' books are worth reading for the most reductionist view of evolution: The River Out of Eden, The Selfish Gene, The Blind Watchmaker, Climbing Mount Improbable. Dawkins tends to recycle pretty much the same way in a very readable style, so you don't really need to read them all.

Most of what Stephen Jay Gould wrote for his view on the "random" nature of the underlying mechanism of evolution and how though it appears teleological, it isn't. More readable than Dawkins and entertaining as he uses many stories from a wide range of sources to illustrate his points. There are many collections of his monthly Nature essays, but his magnum opus for the ordinary reader has to be Wonderful Life, the story of the Burgess Shale.

Sterelny and Griffiths Sex and Death is a must read if you want to uncover (almost) all of the philosophical issues raised by Neo Darwinian theory. It is not a particularly easy book to read; The Git paused many times to absorb the information presented. A solid background in biology would help, but there are plenty of references with assessments of what to expect from them at the end of each chapter. The authors seem to take particular delight in demolishing standard adaptationist explanations. Parrots are colourful in order to attract mates. Starlings are drab to avoid predators. So parrots fail to avoid predators and starlings fail to find mates?

Does Science Point to God? The Intelligent Design Revolution by Benjamin D. Wiker. The Git chose this piece on a quick Google search as probably typical of what's being written on the issue for popular consumption.

On The Origin of Species by Means of Natural Selection, or The Preservation of Favoured Races in the Struggle for Life by Charles Darwin where you can read what the man actually wrote rather than what everyone else says he wrote.

Cosmic Ancestry where you will find many links and abstracts to scientific papers supporting panspermia.

Email Notification

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Thoughts for the week:

An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going. -- Sir Francis Crick

-oOo-

It is absolutely safe to say that if you meet someone who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I'd rather not consider that). --Richard Dawkins

Current Listening:

Johnny Winter -- Second Winter

Neil Young -- Landing on Water

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