My dad used to recite an old doggerel about 19th century Boston:

And here's to good old Boston
The land of the bean and the cod
Where Lowells talk only to Cabots
And Cabots talk only to God.

But it could easily have been written about the sciences:

And here's to graybearded physics,
the greek trade in -inos and -ons
where astros talk only to cosmos
and cosmos the pantheon.

Once upon a time, nearly every physicist had a right to talk about God, or perhaps, the limitations of God. Newton the opticker spent 10 years writing commentaries on Revelation. Maxwell the electromagnetician gave lectures on the matter God created. But in recent years, the mantle of high priesthood has fallen on cosmologists, who bear their responsibility gravely.
 
I will never forget the 1992 cover of Scientific American showing a photograph of the Doppler shift in the cosmic microwave background radiation (CMBR) taken with NASA's COBE satellite that George Smoot had entitled "The Face of God".  At first I groaned, thinking that he was pulling a bad PR stunt. Then I got upset, thinking he was criticizing Christianity. Now I feel pity, because I think he was serious. That is the face of his god--a cold, inscrutable, empty gaze that he poured 30 years of his life achieving. His 2006 award of the Nobel prize for this picture makes me even sadder, thinking of the thousands whom he has converted.

What is it about Cosmology that makes it the high priest of physics? Why are most cosmologists so eager to hypothesize about God, the Universe, and Theories of Everything? (Richard Feynman viewed it as a curse afflicting physicists in middle age.)

It probably has to do with beginnings. Every religion has its stories of beginnings that explain "Why Things Are The Way They Are", and cosmologists feel the heavy burden of explaining "The Real Nature of the Universe"  in their airy tales, for night skies aflame with stars and primeval world beginnings have always been intertwined. The Psalmist writes "The heavens declare the glory of God, and the firmament proclaims His handiwork." St Paul writes, "For what can be known about God is plain to them, because God has shown it to them. For his invisible attributes, namely, his eternal power and divine nature, have been clearly perceived, ever since the creation of the world, in the things that have been made."

It is just that today's cosmologists seem to have lost all faith. The late Stanley Jaki took them to task in his book "God and the Cosmologists" for having mangled their science solely to reject their God. For example, the ancient Greek idea of a universe of eternal atoms was constructed in 500BC simply to avoid the necessity of a Creation and a Creator God. For 2000 years such a view was ridiculed, not only because it was atheistic, but also because it could not explain the data. As Heinrich Olbers pointed out, if there are an infinite number of stars in the sky, and an infinite time to observe them, the night sky should be white, not black. Likewise, as Isaac Newton understood perfectly, even if there be only two stars in the sky but an infinite time for gravity to work, they should have all clumped together by now.

These are listed in the textbooks as "paradoxes", which suggest that rather than being taken as support for a beginning, they are taken as removing support for the obvious solution of an eternal cosmos. This is exceeding strange, for over the past 4000 years, godless "eternal" creation myths have dominated less than 10% of the time.

Nevertheless, it was a big shock when the discovery of the CMBR in 1962 destroyed all hope for an eternal "steady-state" universe, and cosmologists grudgingly admitted a beginning to space and time. Robert Jastrow's book "God and the Astronomers" chronicles this upsetting period in modern cosmology.

But the atheist need not have worried. Forty years of theoreticians have gone to work to recover the eternal (and therefore atheist) universe. Two theories that collide and morph continuously like clashing armies in the night (or is that M-branes in higher dimensions?) are Andrei Linde's "multiverse" of Big Bangs occurring everywhere and continuously, and Lee Smolin's "landscape" of 10^500 ways for string theory to roll up.

The peculiar thing about "landscapes" and "multiverses" is that by definition they are impossible to observe. Like debates about "how many angels can dance on the head of a pin", these are proxy wars of metaphysics, these are creation myths that cannot be either proven or disproven. And this fragile state of the myth has led to heated debates between Smolin and Susskind over whose unprovable theory is superior.

This debate would be a yawner were not the scientists, in their eagerness to prove their point, grasping at the weapons of theology and philosophy. So it was with interest that I read Lee Smolin's argument why a timeless _meta-universe makes no sense. That is, Linde's multiverses pop up from somewhere, and likewise a string landscape has to have a location, which turns out be be a "_meta-place" without time or physics or dreams so various, so beautiful, so new,  but only some sort of mathematical Platonic austere existence. And guess who Smolin blames for this state of affairs?

The separation [by Newton] of scientific explanation into law and initial conditions leads to one of the most universal and powerful notions in physics — the notion of configuration space. This is the space of all possible configurations, or states, of the system. In classical and quantum physics we assume that this space exists a priori and outside of time, and that it can be studied independently of the laws of motion. These laws then specify the rules for how the point that describes the initial conditions in configuration space evolves in time. We call this the Newtonian schema for explanation.

And what is Smolin's evaluation of Newton?

The Newtonian schema is the basis for the claim that time is not fundamental in cosmology....This argument is faulty for two reasons....By discarding the Newtonian schema for cosmology and dispensing with the notion of the multiverse, we also no longer have any reason to suspect that time is an illusion.

But now Smolin has a different problem. Rejecting Plato's eternal realm brings us back to Aristotle's inductive science and Lessing's Ditch. Here's Smolin's take:

This alternative metaphysical framework has im­plications for the nature of physical law. Since nothing is true or real outside of time, there is no possibility of speaking of eternal laws. Laws are regularities that we discover hold for very long stretches of time, but there is no reason for laws to be true timelessly — indeed, there is no way to make sense of that notion. This opens the door to the possibility that laws evolve in time,...

Well I'm all for making time real, but I'm also all for universal laws. Is it really true that we can have one or the other but not both? Smolin seems to be ditching Kant for Hegel, he's abandoning Parmenides for Heraclitus. As I mentioned earlier, we keep rehashing the one-and-the-many problem, this time in cosmology. But the worrisome part for modernists raised on the concept of absolute truth, is that Smolin is drifting off into pantheism, where god is truth, and truth is the universe, and the universe is evolving, so god is evolving.

Leonard Susskind isn't ready to give up on either absolute truth or Newton, or for that matter on Darwin either. He credits both of them for having solved this serious metaphysical problem. In his response to Smolin he writes,

Darwin was not particularly interested in astronomy or physics, yet his impact on cosmology was enormous but in a way subconscious. In successfully explaining the origin of species, he eliminated superstition and set a new standard for what an explanation of nature should be like. As I wrote in my book The Black Hole War (Little Brown, 2008), Darwin’s masterstroke was to have “ejected God from the science of life”. True, Darwin was not the first scientist to cast out supernatural beliefs. Two centuries earlier, Newton — another great Cambridge scientist — had done so more than anyone before his own time...
In other words, before Darwin, even the greatest physicists had little alternative to a supernatural explanation of the origin of life, and therefore of nature itself. It was the success of Darwinism that forced the issue and set the standard for future theories of origins, whether it be it of life or of the universe. Explanations must be based on the laws of physics, mathematics and probability — and not on the hand of God.

It seems odd that Susskind is crediting a scientist for proving a metaphysical belief, as if Darwin provided some sort of evidence of the spontaneous origin of life. But notice what Susskind replaces God with--physics, math and more math. And as he explains, the "physics" of choice is string-theory, which many have called pure mathematics with no experimental basis or proof. So as Smolin warned in his earlier exchange, Susskind's timeless multiverse landscape is all math. What then is Susskind's bottom-line defense against Smolin?

Whether string theory with its huge landscape, and eternal inflation with its reproducing pockets of space, will prove to be correct is for the future to decide. What is true is that as of the present time, they provide the only natural explanation of the universe that lives up to the standard set by Darwin.

So there you have it. If you don't want to be a Christian pantheist, you'd better side with Susskind. What better proof of cosmology do you need?

Alas, neither is appealing to me.  As Jaki was always quick to say, neither the atheism of Greece nor the pantheism of India produced the science of the Enlightenment. Rather, the metaphysics of a Christian God who can be both transcendent and immanent, both absolute and particular, both promise-keeping and prayer-answering, both eternal and temporal, is necessary for cosmology to exist. Smolin and Susskind alike are squandering their borrowed capital, and the more they display their riches, the clearer their paupery appears.

Below is an essay that my now favorite religious scholar wrote.
"Is Immortality Important?" by Karen Armstrong.

Now I have read Armstrong, and understand, I think, why you like her writing. She is very clear and includes much learning from other major religions. She does a good job trying to find the common threads in all of them.

But as you well know, all generalizations are false. This is especially true as she shifts from her personal recollections of Roman Catholicism into a general description of these other religions. The parts of RCC she dislikes are very particular, localized, and not typical of the broader church teaching, whereas what she likes about other religions are broad, general features which are in direct conflict with the particulars of Hinduism or Buddhism or Confucianism.

That is if I were to go into the street, interviewing Buddhist monks, Hindu brahmins, Muslim imams, Confucian scholars, I would find two handfuls of anecdotes every bit as objectionable as her stories about first Friday masses. My Sri Lankan friend tells me of the superstition and witchcraft practised by their Buddhist country. My Brahmin Indian student tells me of the dangers of Hindu meditation. My wife tells me of the cruelty of Confucian duty in a Korean family. My Zoroastrian friend (Iranian wife of a German physicist) told me of the persecution endured in Iran. And as for Islam, let me direct you to the Middle East quarterly that asks whether Christianity and Judaism are as equally violent as Karen Armstrong maintains?

So do we judge a religion by the writings of its most learned sages, or by the practices of the majority of its adherents? A case can be made for both. But under either method of evaluation, Christianity uniquely stands out. (I could say Judaeo-Christian to be more inclusive, but given the 12 million or so practising Jews in the world, it doesn't merit "major religion" status.)

The only way to make Christianity look equally bad, is to compare its anecdotal, particular, uneducated folk practices with the textbook, generalized, non-specific philosophers of other major religions, which is what Karen Armstrong does. It isn't an apples-to-apples comparison, as if Pat Robertson is on a par with Lao Tzu, or with the rich, educated, prince Buddha, or the royal philosopher Confucius. But even though it is an unfair comparison, I would argue that she still had to cherry-pick to get an unfavorable comparison. The point being that Robertson is still a "good" man, an honest man, a man you can do business with, whereas none of that would be true of Buddha or Confucius. To say it another way, familiarity breeds contempt, and we condemn our brother for the splinter in his eye, yet admire the foreigner with a log in his. I have no doubt that were you able to interview Buddha in the flesh, you would be treated far worse than you expected, whereas the opposite would be true for interviewing Robertson.

Okay, let me address the proper comparisons.

a) Folk religion

How do the folk religions of Confucianism, Taoism, Buddhism, Hinduism, Islam, and Christianity stack up? Let's make the assumption that income is correlated in some way to work ethic and general morals. Christianity wins that one hands down, though only in the past 3 centuries. Before that Taoism and Confucianism reigned supreme for 10 centuries. So that may be an unfair comparison. But perhaps diachronic or historical comparisons are complex, perhaps one could ask, how do two very close societies that convert to different religions fare? Singapore and Kualalumpur for example? Christianity wins again. There are lots of reasons for this, one of the better books I read on the subject was Rodney Stark, who preceded the book with this essay in the Chronicle of Higher Education (reprinted here)

We could look for other comparisons: child survival rates; attitudes toward the disabled or retarded or elderly; elderly survival rates; support for the arts and literature; development of science; military-civilian discipline. These are all characteristics of the non-professionally religious who make up the majority of any major religion. And once again, Christianity comes out on top, especially in the sanctity of human life category. For when life is sacred, then the investment in life reaches it maximum potential.

b) Professional religious philosophers

Here I will part company with Armstrong. All the things about Christianity that Armstrong likes are actually heresies of the Christian church, and much more aligned with what I would call the Bronze Age religion. I have a lengthy blog on the subject,  in which I contrast some of the characteristics of pre-Jewish Bronze Age religions.

The truly remarkable fact is that atheism has been so dominant in the past 100 years. This has almost never been the case in the history of the world, for the simple reason that historically atheists have been the most despised religion of all, fit only for thieves and murderers. (Stalin, Pol Pot, Mao ...) But what has been the most common religion is what I call homeostasis, the maintenance of cultural survival. From Gilgamesh to Hitler's 3rd Reich, the production of the right kind of babies has always been central to homeostasis. Any religion that advocates birth control and abortion will de facto, not be around for very long.

Imagine that culture is a living beast with a lifetime of centuries, and that you and I are merely transient red blood cells that are born in the marrow, fulfill our duty in the veins, and get recycled in the liver. How then does one red cell pass on this knowledge to the next crop of cells? By talking of a life external and eternal to our short lives.

In just such a way eschatology points to something bigger than ourselves, for whose purpose we were created, and whose duty brings fulfilment, and whose existence subsumes ours. Then Karen Armstrong's seething against "spiteful fantasies" of the afterlife misunderstands everything important about eschatology. Her search for "enlightenment of nirvana" becomes just another selfish attempt to attain a private eschatology. There is no escaping the accusation of selfishness unless there is a recognition of something greater than ourselves, something more eternal than ourselves, something that will continue upon our death. In other words, the very thing she condemns as selfish is the only thing that can rescue us from a selfish, self-absorbed destiny.

Like GWF Hegel, like process theology, like Hindu and Buddhism, like Bronze Age religion, she is putting a lot of sugar-coated philosophical god-talk on a central core of selfish, homeostatic religion. Conversely, no matter how legalistic, uneducated, childish, or primitive it may have been presented, an eternal destiny is the only escape from a selfish absorption with our own existence. Pantheism and polytheism are alike in their need for self-importance and the focus on the now. Which is probably why Islam was so successful in conquering the polytheistic Arabs and Hindus, but failed with the Christians.

And I haven't even gotten to the unique message of Christianity, that which separates it from the absolutist monotheism of Islam and Atheism that which Armstrong rejected along with her vows. But that would take me far beyond Armstrong's thesis.

In responding to an email about "front-loading" as a Deistic solution to the universe that does not require an interventionist (theist) God, I replied that I have some philosophical problems with the phrase "front-loading". It is a concession to Deism that doesn't have to be made. Trying to describe a "front-loaded algorithm" highlights the problem with the philosophical solution.

Historically, the argument for front-loading came from Laplacian determinism based on a Newtonian or mechanical universe--if one could control all the initial conditions, then the outcome was predetermined. First quantum mechanics, and then chaos-theory has basically destroyed it, since no amount of precision can control the outcome far in the future. (The exponential nature of the precision required to predetermine the outcome exceeds the information storage of the medium.)

But "front-loading" permitted Deists to say that God designed the Universe, and then stepped back and let "natural" forces operate, thereby removing any "supernatural" interference of the sort that Lucretius fumed about in 50BC. So if Newtonian determinism was now impossible, perhaps there could be some sort of algorithmic determinism (which I'll call Turing determinism) which could step in and permit a Deist to avoid the supernatural. That is, God doesn't have to create the oak from the acorn anymore, but the biological program He inserted in the acorn can handle all the intermediate steps. So perhaps, God didn't have to create humans, but the biological program in the first living cell He created, started the ecosystem that eventually evolved humans.

This remains, of course, the principle argument of theistic evolutionists, and was Howard Van Till's favored method before he stopped teaching at Calvin College and gave up on theism.

But this argument assumes that one can separate algorithms from the machinery that executes them, the information from the storage medium, the supernaturally contingent from the naturally necessary. The Newtonian revolution was to view the universe as a complicated machine where "natural" laws were the function of the machinery, and "supernatural" interference was information not incorporated into the gears. The fact that a watch tells time was "natural", whereas the setting to Eastern Standard Time was "supernatural" because it was contingent.

ID (Intelligent Design) makes the argument that the gears are just as supernatural as the time zone, because they are designed to function in a certain way. But such an argument doesn't escape the TE (Theistic Evolutionist) defense that the time zone setting is just as "natural" as the gears, because there were no laws of nature broken. This would all be semantics, if it were not for the corollary, that ID claims to probe the character of the designer by studying the design, whereas TE claims that front-loading is indistinguishable from chance, making the designer inscrutable. (Which keeps his faith transcendentally Kantian, and science a-theistically independent of God.)

But is it true that algorithmic front-loading can be naturalistic, independent of God, Turing-deterministic, and thus incapable of revealing anything about a living God?

I'd like to make the argument that Turing determinism is impossible for several reasons, and therefore front-loading is indistinguishable from the supernatural, from the actions of God intervening in history.

a) The Turing problem

Alan Turing himself addressed a number of algorithmic dilemmas with the thought experiment of the deterministic computer now called a Turing machine. He asked if the outcome of such a computer can always be predicted, and demonstrated several examples of completely unpredictable behavior. Applying this to our biological example, it says that some organisms may act/evolve unpredictably, though perhaps not the ones God programmed.

But Turing went beyond this existence proof, and demonstrated necessity--a computing machine with feedback, where the output tape went into the input, was always unpredictable. In our biological example, we have to define the input and the output. TE tells us that the input is an organism, and the output is more organisms, and the computer is the organism too. In other words, the type of algorithmic determinism required by TE is not weakly, but strongly recursive, and therefore doubly unpredictable.

Even should God have infinite knowledge of the outcome of such a biological algorithm, the information regarding its outcome cannot be contained within the system itself. Therefore if the system is determined, it must be determined externally, with constraints outside of biology, which is exactly the definition of the supernatural that the TE "front-loading" was intended to remove!

b) The Functionalism Dilemma

Let us pretend for the moment, that the feedback between the output and the input doesn't exist, that DNA is a code that is itself independent of the cell that houses it. This is similar to the argument that consciousness is just the program running on the computer of the brain with no ability to change the brain circuits. Also note the similarity to Darwinist evolution, where the evolving critter has no ability to modify his genes or plan his progeny (unlike, say, Larmarckian evolution). Why do we have to pretend there is no feedback when there is plenty of scientific evidence for it? Because otherwise the output becomes unpredictable, or more accurately, purposeful. That is to say, contingent indeterminate things allow for will, for consciousness, for decisions in a way that necessary determined things do not.

So ignoring the feedback, or better, disallowing the feedback, means that we must keep the software and the hardware distinct. But this is difficult for a cell, since the DNA software is a subset of the cellular hardware. In physics lingo, we might try to separate the contingent initial conditions from the determined physical laws. Or in computer science lingo, we might try to make a distinction between the arbitrary data and the fixed algorithmic code. The DNA is the contingent data, whereas the RNA and ribosomes are the fixed machinery for transcribing it.  Then TE Turing-determinism would consist of God creating this cellular duplication hardware aeons ago, and feeding it a long tape of DNA instructions that eventually result in us. Presto, theistic evolution with entirely natural development from a long-forgotten supernatural initial condition!

Now the problem with this scenario is not that the one-celled amoeba has little of the DNA that make up humans (the storage problem), nor even that many inter-dependent organisms are needed for humans to exist (the irreducible complexity problem), but that it is impossible to keep the data and code separate.

For example, many computer viruses operate on the principle of "buffer overflow" where a program expects data--say, a last name--and the hacker gives it a program instead which overflows the memory space allocated for it and ends up in the part of memory allocated for code. Voila, the hacker has taken over the program. In just such a way, the DNA encodes not just copies of itself, but for making changes to the copying machinery. Viruses multiply in biology as they do in computers, by hijacking the system machinery. The only safe system is one that is never networked, has no USB port, no floppy or DVD slot, and does only what the factory loaded into it. Since that would be a pretty useless system, I cautiously network my laptop, but spend countless CPU cycles on anti-virus programs, just as much of the cellular DNA machinery is dedicated to making sure it is not hijacked.

Which is to say, because there cannot be any clear separation of data and code, there must exist mechanisms for eliminating hackers. By definition, such systems span the interface between data and code, looking for "foreign" code and "bad" data. But who tells the machine what is "foreign" and what is "bad"? My anti-virus files get updated periodically, but who updates the DNA? How does the cellular immune response recognize itself? If it is not accomplished externally (supernaturally!), then we are acknowledging a process that "contaminates" the determinate code with the contingent data.

Now we begin to recognize the hatred Darwin felt toward Lamarck. For the slightest amount of contingent data (hacker) destroys all determined (legitimate) code. Determinacy is a fragile state, intolerant of any amount of contingency, whereas contingency is robust, absorbing large amounts of determinacy while still remaining contingent.

But the problem is bigger than the need for an immune system. There is information stored in the computer operation, in the motion of the cellular machinery. A computer with a robust immune system, impeccable data storage, and factory-fresh operating system can still hang, "blue-screen" or crash. The system is inoperable until it is "rebooted", which involves taking it back to a known state and starting forward again, and you may still have lost that document you were working on. Every level of hierarchy in a computer has information, from the code, to the data, to the state it was in just before it crashed. And if, God forbid, you were installing the latest operating system service pack from Microsoft when your colleague impatiently pulled the power cord out, you may never be able to recover the system without asking Microsoft to send the system disks and wiping the disk.

So not only is the code indistinguishable from the data in principle, but the operation of the computer, the dynamical state of the system is in principle indistinguishable from the code and the data. The only escape from viruses and incompetent colleagues is an external system fixer, which is precisely the "supernatural" interference that Turing-determinism was intended to avoid. It is even worse than this, for disallowing any external influence means that the code and data get progressively damaged, until they are inoperable; what John Sanford called "Genetic Entropy".  It would appear that without God, our race is doomed.

c) Intelligent Design

Having made the argument that Turing-determinism is not possible, have we fallen into the accursed "God-of-the-Gaps" pitfall which is so reviled by TE? Have we argued that Genetic Entropy will require God to continually tweak the genome to keep it on track? If so, then we have reduced God to a lowly grease-monkey, whose main job is running around defending ID from TE entropy? Surely this is too demeaning a job description for the Creator of the Universe!

Well actually, I think "God of the Gaps" is a very good way to describe God, if you take "gaps" to be fractal. Georg Cantor proposed the Cantor Set, constructed by taking a line and removing the middle third. Then take the two remaining lines and remove their middle thirds. Repeat this process ad infinitum, and what do you have left? Well, we can write a mathematical series of what we have taken from the interval (0,1) and sum the infinite series--e.g. 1/3 + 1/3 (2/3) + 1/3 (4/9) ... and when we are done the series = 1. That is, there is nothing left. Yet something remains, because the number 1/4 still is there! In fact, there are an infinite number of fractions still left in the interval. Cantor described this as a "perfect set that is nowhere dense". It is a set where everything is a gap, yet something remains. It is often used as an early example of a fractal, which I think of as mathematical foam, looking the same no matter how microscopically you examine it.

So once we define a "God of the Gaps" as a "God at every time and spatial scale," then I am quite comfortable with this solution. For if a "gap" represents something we don't know, then we are saying our knowledge is 0% of interval, while God's is 100%. Which is not to say that we have no knowledge, but rather that God's knowledge is infinite compared to ours. (Cantor would have said "trans-finite", and took a lot of grief for suggesting that some infinities are bigger than others, so that there are an infinite number of infinities.)

But we can take the idea of a fractal in another direction altogether. Something that is everywhere the same is homogeneous and boring, lacking information. Something everywhere the same with repetitive structure, say, a salt grain with a face-centered cubic crystal, has very little information.  But if it has a complex structure it contains abundant information, yet if the structure looks the same at every magnification, then not only does it have information, but the information is non-local. The only way that point A far from point B can look like the same structure, is if there is a global requirement imposed on it. Mathematically, a fractal is the solution to a non-local equation. In William Dembski's terminology, it is specified complex information, or CSI.

So paradoxically, when we find that microscopes with higher and higher magnification give us more of the same, we are witnessing something much bigger than our microscope. When whales and elephants and people and shrews and mites and rotifers and bacteria are all made out of cells, we are observing something bigger than the Earth. When stromatolites and trilobites and dinosaurs and mastodons and people are all made out of cells, we are observing something older than the Earth.

In contrast, TE argues that naturalist processes are purely local, indistinguishable from chance and law. But such processes can never produce fractals in either space or time, for like Democritus' atoms, they have no spatial or temporal memory, knowing only themselves and the violent blows of hitting others in their way. But the fractal properties of nature indicate that non-local or global processes are at work, which by definition are external to the individual ignorant participants. In other words, the naturalist understanding of fractal space-time requires a supernatural explanation.

Conclusion

"Front-loading" is the TE attempt to stretch a Newtonian concept of determinism into an algorithmic form to avoid the collapse of Laplacian determinism. We have tried to show that algorithmic or Turing-determinism is incapable of describing biological evolution, for at least three reasons: Turing's proof of the indeterminancy of feedback; the inability to keep data and code separate as required for Turing-determinancy; and the inexplicable existence of biological fractals within a Turing-determined system.

Life is full of challenges, no one can avoid them. It is just a question of which challenges one accepts. My car mechanic brother tells me this one should be avoided at all cost.

Ever since the '94 Suburban rolled on the Interstate, we've been needing a new vehicle that can (a) seat 8+; and (b) pull a trailer. So the wife and I went up to the auto auction that is held every Tuesday and Friday just over the line in Limestone county. It's an interesting location, with a mix of cars from wealthy Madison county and the much poorer environs. We've bought 2 cars there, and discovered that the average mileage is 150,000, and average price around $2000, unless its  Japanese in which case the mileage is closer to 250,000. They've been serviceable cars, though I've spent more than I bid for them, since evidently the buyer is obligated to buy what he bid, but the seller isn't obligated to sell for that.

But both of those cars came from the $300 deductible guarantee lot--if it requires more than $300 in repairs than it can be returned. Today the only vehicle that met our criteria was an old '92 Suburban in the "as is" lot. Now Suburbans hold their resale value much longer than most both because they are reliable and because there isn't much competition, even from the crop of modern SUV's. When's the last time you saw one with 9 kids packed into it? And this Suburban had only 160,000 miles. Low mileage for a 17 year old truck, I thought as I watched it being driven around the lot. The paint was peeling on the hood, the interior was dirty, the A/C didn't cool, and at that age, required the Montreal-protocol-banned Freon propellant, so it couldn't be recharged. "That's probably why it is in the as-is lot", I reasoned as I bid on it and got it for $850. "We'll clean, sand and paint the car, and maybe get some black-market Freon from Mexico" I said to my wife, as I pulled out of the lot and she followed behind me.

That's when I discovered the real reason for the "as is" lot, it had no third gear. The engine shifted up twice and then the power vanished as the tachometer raced wildly. I made an emergency stop at the auto store and bought transmission fluid, oil and radiator anti-freeze. The engine was hot, having been driven 50 miles to the auction in 2nd gear. But no joy, the transmission refused to find 3rd. I bought a Haynes manual.

When I got home I parked the vehicle where it could be jacked up, opened the manual, and read that automatic transmissions were beyond the ability of home repairmen. I went on the internet and discovered that rebuilt transmissions were going for $1100. Ouch. But a rebuild kit with new "steels"--the clutch bands--could be had for $130. This is where I e-mailed my brother, "which kit should I get?"

His advice was immediate. Drive it back to the auction and sell it as fast as possible.

Alas, some things can only be learned by experience. I ignored his advice, got my 16-yr old son off the couch, and jacked up the car. While Haynes may not have instructions on rebuilding transmissions, they did have instructions on removing them. (Installation, as they always say unhelpfully, is the reverse of removal. Would that life were that symmetrical!)  So we got out the wrenches and proceeded to drain the transmission fluid, take off the bolts, and got to the stage where we had to remove the driveshaft.

It wouldn't budge.

"Maybe we should jack the back wheels off the ground," I said while rereading the manual for the fifth time. Strangely, the screw jack in the Suburban was unused. Did they never have a flat tire in 17 years?  But as I soon discovered, this was because the jack was useless. Oh it operated properly and lifted the truck, but the leaf springs were so big, the tires never came off the ground.

"We'll put some boards under the jackstands and the jack," I told my son, "we'll get it off the ground." Three boards and four feet later the truck teetered precariously on the jack stands. Looking around, I found an old log that my son had rolled from a neighbor with the intention of using it as an anvil for making plate armor. "Let's put it under the truck," I said, "we don't want that coming down on us." One tire still had some friction with the ground, so we placed some more boards under the jack and just as the wheel cleared the ground, there was a groan and the entire truck slid sideways off the stands.

As my son scrambled clear, the log did its job. But the jack was bent and my wife's face had gone pale.

"Enough messing around for the day", I said, "time to put the tools away."

"Can we take it to a mechanic?" my wife asked with pleading eyes.

"We'd have to tow it" I answered.

My e-mailing brother was less sanguine. "I'll give you a Subaru that needs a new clutch fork. Why don't you work on that instead?"

Challenges may be accepted or rejected, but they come unanticipated, as heralds of a unknown future, of an unforeseen war. Yes, we can pick our battles, but we cannot pick our wars.

The Suburban said nothing, but its hulking frame remains a mute gauntlet in my driveway, waiting for me to make up my mind.

I had three conversations about miracles in the last 18 hours, and concluded that it still needed some clarification. So here is my fourth and final installment in what became a soap. (Installment 1 here, 2 here, and 3 here.)

What do miracles say?

To summarize the previous 3 posts, we can state succinctly what they don't say. They don't say that God carefully created the "laws of nature" and then whimsically "breaks" them just because He can. Not only is that some sort of dualism (laws being separate from God), but it also promotes a purposeless nominalism (God can do anything He wants for no reason at all.)

Nor do miracles say that the reporter of miracles is untrustworthy, a good storyteller, overly emotional or uneducated. Nor are miracles merely code for something else, a myth that is "true" in some other manner or universe. Nor are miracles rare, limited to certain time-periods, or restricted to gods, demi-gods and extremely holy prophets. That is, miracles are not valuable objects like diamonds, covetted because their existence is scarce, rather, miracles are more like presidential press conferences, valued for what they communicate.

Looking through the Bible, miracles do not occur for their own sake, but in order to serve another purpose. Moses' first three miracles before Pharaoh included turning his staff into a snake, making his skin leprous, and turning water into blood. These were intended to validate Moses as God's messenger and hence his message to Pharaoh that the Israelites should be freed. Pharaoh didn't deny the reality of the miracles, but tested them against his own magicians. When they reported that these were the genuine article, Pharaoh refused the message. The subsequent 10 plagues or "wonders" were then intended to convince the subjects of Pharaoh, the entire Egyptian nation, that Israel was God's people. In fact, the fear of God preceded Israel as it moved up into the Levant. The message of these most famous miracles was the fear of Israel's God.

The miracles of Elijah and Elishah the prophets are the next most famous ones in the Bible, which do not have this overarching message, but seem to be random, acts of personal desire. They call down fire from heaven at will, run faster than horses, multiply oil and flour to feed a family, raise the dead, or float an axe-head that was lost in the river. What is the message here? Each miracle had a story for which the miracle was the punchline.

The wicked queen Jezebel had introduced worship of the thunder-lightning god named Baal, and when Elijah called down fire from a hard blue sky, he was intentionally demonstrating the superiority of Israel's god to Baal. Or when he fed a family with a jug of oil and a jar of flour, it was a demonstration as much for Elijah as the widow, that God is sufficient widows and orphans even in the midst of famine. Or the axe-head that was borrowed and lost in the river, the miraculous recovery shows a concern for private property and personal responsibility.

But without the context, the miracle is of itself meaningless, reminding me of the late great radio host, Paul Harvey's "The Rest of the Story". I'll never forget the one that began, "At 7:05pm the boiler at a little country church exploded, destroying the sanctuary above. Choir practice began at 7:00pm. But no one was injured." In "the rest of the story" Paul Harvey related in his gravelly voice how everyone in the choir had an unusual reason for being late that night. And suddenly the small-town event became a big-town miracle.

So the first thing that miracles tell us, is that they are the punchline to a story, a very personal story that involves characters who appreciate it most. Those of us who watch from the outside may not feel the impact of the miracle, but like Job's friends or Jericho's citizens, may still feel the awe of the event. Despite the intense personalization of the miracle, its impact can be shared with those who are willing to identify with the actors.

And this is the second thing that miracles say, that participation is required. If we are to understand Paul Harvey's miracle, we have to say "That could have been me!" This is what took Pharaoh so long to grasp, though only temporarily. This is what took a tough, war-hardened sergeant in full gear to fall on his knees before an unarmed, gray-bearded Elijah. This is what the Pharisees never grasped when they schemed to kill the resurrector of Lazarus, but what the Philippian jailor immediately understood when an earthquake unhinged his jail.

That participation isn't always quick or easy. In fact, it sometimes is harsh and demanding. It often forces us out of our comfort zone. When Rahab looked out her tiny window above the massive wall and saw the plains dotted with the tents of the Israelites, she must have wondered if all those miracles in Egypt were possible in her fortress-town of Jericho. To acknowledge that "it could have been me", was to fear that foreign god Yahweh, to submit to the rule of an alien nation, to envision a future without the comforts of her land, her language, her friends. Participation is a commitment that doesn't come easily.

This then is the most important thing that miracles say, because they speak directly to us; they ask us for a decision, no, they demand one. Rahab chose by her action, but the remaining 30,000 inhabitants chose by their inaction. In both cases, they made a choice. Miracles, even miracles in far away Egypt, have a way of judging us.

The eye that is blind to the miracle of life; the heart that is cold to the miracle of love; the hand that is clenched from the miracle of alms; the mouth that is dumb to the miracle of thanks is not just impoverished, it is condemned. For miracles are the message that we are made for a purpose, a purpose not our own. Miracles demand from us submission to the one who really is in charge: "a stumbling block to Jews and folly to Gentiles, but to those who are called, both Jews and Greeks, Christ the power of God and the wisdom of God."

Thermodynamics is not only the pinnacle of 19th century physics, but at the time and lingering into the present, carried a whiff of semi-religious overtones. The field arose with the birth of the Industrial Revolution, whose childhood was the Age of Steam. For the first time, steam engines made it possible for man to triumph over his environment without the mobs of slaves Pharaoh needed to erect his pyramids. It was preceded by several centuries of development of water power, with entire factories or mills, located near fast rivers so as to harness the energy of falling water to drive entire buildings full of leather belts. The only remnant today of this important precursor to the Industrial Revolution is the large number of "Mills" in place names. But steam permitted factories to be built anywhere that coal and water could be delivered, and thermodynamics was the Scottish science that fixed its profitability. Despite having a unit of power named for him, James Watts was not the inventor of the steam engine, but the Scot credited with making it 4 times more efficient.

With such success in improving the efficiency of the engine, fertile minds continued to imagine that equally great improvements in efficiency were waiting to be discovered and provide a steady income from patents. Perhaps it was possible to invent an engine that would run forever without any coal at all! But French engineer, Sadi Carnot, destroyed all these fantasies when he calculated the maximum possible efficiency of a theoretical carnot-cycle steam engine. It seems work is a form of energy, and energy is never free, it isn't even cheap. Rather, energy is conserved, neither increasing nor decreasing, but always changing form and degrading into that least usable of all forms: heat. The laws of thermodynamics describe this universal journey of energy from its birth as work to its long drawn-out heat death, where death is deanthropomorphized (physicalized?) as the mysterious "Entropy".

The mathematics wasn't limited to steam engines, however, and the physicist's wandering eye began to see everything as a disguised power plant: the sun, the hydrologic cycle, chemical reactions, the human body, and of course, the living cell. Soon physicists were claiming that there wasn't an object in the universe that didn't obey these laws. In Sir Arthur Eddington's pop-sci book, "The Nature of the Physical World" (1928) he writes:

If someone points out to you that your pet theory of the universe is in disagreement with Maxwell's equations—then so much the worse for Maxwell's equations. If it is found to be contradicted by observation—well these experimentalists do bungle things sometimes. But if your theory is found to be against the second law of thermodynamics I can give you no hope; there is nothing for it but to collapse in deepest humiliation.

And so thermodynamics, like Einstein's space-time, or Heisenberg's quantum mechanics, became part of the furniture of reality, the geometry of Plato's forms, the law of heaven second only to God himself.

There was just one problem. Living things seem to violate thermodynamics routinely.

Which is to say, they multiply and make complex things out of simple ones. They take carbon dioxide and water and sunshine and make redwood trees and oats from it. Then other living things make rabbits or houses or the Golden Gate bridge from them. Complexity is increasing, and work seems to increase, not decrease. How can living things seemingly violate these inviolate laws of entropy?

As I remarked earlier, physicists dismissed it with a wave of the hand. "Living things are not closed systems", they would say, "they consume fuel and emit carbon dioxide, which more than compensates the Entropy-god for the things they make."

But does it? If we draw a big circle around the Earth or around the solar system, is the entropy really increasing? It would seem that the anti-entropy (negentropy) or the information of the system is growing exponentially with life, and this doesn't seem to fit the three laws of thermodynamics. Have they really nothing to say at all about life?

In recent years, biologists have been getting more physical, and physicists getting more biological, so there has been a resurrection of interest in this philosophical topic. An early effort was to find a "fourth law" of thermodynamics that would explain what life is doing. It has blossomed to no less than 17 different attempts on this web site.

Here is Chris Beling's effort.

Here's my correspondence with Chris, on what I think is the meaning of these 4th law attempts.

The 4th Law has been claimed multiple times, Prigogine's MaxEnt being one of the earlier manifestations. (A recent popular book was "Into the Cool" here's a link to my PPT talk.) What is peculiar, is that it sounds like your formulation and Prigogine's are diametrically opposite. So perhaps you want to either: a) describe yours as a further refinement; or b) describe yours as a 5th law.

> I have looked through your powerpoint. I have some difficulty because I do not know the specifics of many of the systems you study i.e Coronal Heating. I think I would have to take each specific subject one by one - and would need more materials to read.

It isn't your fault for finding it hard to read. I usually annotate my PP slides, but not this one, and even I had trouble remembering what I was talking about three years ago! Coronal heating has been a mystery because the source of the energy is the sun's photosphere at 5500K, whereas the corona is 2,000,000K, which makes it appear that energy flows from colder to hotter, violating Newton's law of cooling, as well as numerous thermo laws.

> But there are some interesting things that come out: (1) That Gibbs Free Energy and Exergy are the same thing. I have read one or two books where Exergy was mentioned and to me it seemed the same as Gibbs Free Energy, but then I thought - why give it a different name?

Well, you must remember that Gibbs was a somewhat obscure AMERICAN physicist, and "exergy" is promoted by Europeans. Also recall that Italian Amedeo Avogadro didn't discover any numbers, but rather German Johann Josef Loschmidt, so that when the British Alfred Nobel prize went to Frenchman Jean Perrin in 1909, he would not acknowledge the prior work of a German, and attributed it to the Italian. I hope that clarifies things.

> (2) MEPP. The first thing of interest is that this is the same thing as "The minimum entropy production rule". I had been confused about the naming (as you may see from my paper). I badly need to read on this subject and I think the reference you give should help me.

MEPP actually stands for "Maximum Entropy Production Principle", though Prigogine gave it the minimum entropy title, thus confusing you. Prigogine's Nobel prize in Chemistry in 1977 has been supplanted by more modern work that prefers to talk of the maximum entropy production, though they are still talking about the same thing. The question addressed, is when a system is far from equilibrium, which process restoring equilibrium will dominate? The answer is the one that increases entropy the fastest. So large convection cells will be favored over small ones in a boiling pot, simply because they increase entropy faster than little convection cells.

> Question: Is the MEPP what you would refer to as the 4th law?

Yes, this is the MEPP that I refer to as the 4th law.

> (3) Telos: According to the law of "information decrease" = entropy increase - a law that only works if there is some sort of configuration space (real of imposed) then it is indeed true that the fireball of the BB must be low entropy. This certainly points towards an origination of information (and thus intelligence).

I'm not sure I understand your statement. The BB fireball was incredibly dense as well as incredibly hot. If S=Q/T, then Q (heat) goes as the density, T (temperature) is inversely proportional to density (PV/nR = T), so S was very high in the BB. So it is counter-intuitive that a high entropy BB could produce a low-entropy universe that included us.

> Comment: I don't see in your work mention of information. I think the definition of information is critical for the 5th law (if we call it this).

I'm not entirely sure what happened to the slide on Shannon information. Perhaps I merely said the words when I gave the talk. But in any case, Shannon information is the negative of the log of S ==> -ln(S) = I or "negentropy".

> (4) Do you know of any other good accessible book on MEPP and NET?

My introduction to the topic was "Into the Cool" which I think I referenced at the end of the talk. The original talk I heard was by a remote sensing specialist who demonstrated that the temperature of a field of peas or grassland was an indication of the health of the ecosystem because living things attempt to maximize their exergy. Then the figures in my talk were extracted from lengthy Google searches on the topic, several PP were found. There were also several good Wikipedia entries.

The connection between "telos" and information, is that life uses MEPP to maximize exergy, thereby avoiding heat death. As long as there is a flow of energy, then it is possible to stay far from equilibrium making use of structure to produce MEPP. That structure while not always spontaneous (like Benard convection cells) nevertheless demonstrates order and information. Thus information arises out of heat flow as a 2nd order process (relying on derivatives of the basic quantities), whereas everything in the 1st order (direction of heat flow, equilibrium thermo) removes information. To paraphrase, everything in the first 3 laws destroys information, whereas the 4th law restores information. For the sake of symmetry, perhaps we should have the 5th and 6th laws restoring information as well. I would guess, though haven't done anything in the field for 3 years, that the complexity of 2nd order, non-equilibrium thermo will parallel the transition from electrostatics to plasma physics.

You should download Prigogine's 1977 Nobel lecture. I don't know whether I referenced it or not in my talk. Prigogine was criticized for getting too philosophical (as in Bergsonian) and abandoning physics (a crime Feynman once said was endemic among middle-aged physicists, and I might add, especially those who have become famous). You might think of him as the intellectual grandfather of the Sante Fe Institute and Stuart Kauffman's attempts to find self-organized, emergent phenomena. That is, the everlasting Darwinian hope of life crawling out of the slime. The recent Vatican conference on evolution had a bunch of these guys lecturing the Church on why they don't need no stinking teleology.

The following critical review of Prigogine suggests that his mathematical insights were singularly unfruitful (but then again, that's exactly what you would expect a critic to say), though it is peculiar that the critic doesn't mention Kauffman at all.

Here at seminary, I've finally understood the connection between Whitehead, Bergson, Barth, Milic Capek, scads of modern theologians, Stuart Kauffman, and good 'ole GWF Hegel. There really are only a half dozen metaphysical constructs possible: the One, the Many, the Dual, the Trinity, and various Dialectic dynamical equilibria (think of them as the NET of metaphysics).

I think it was George Gamow who published a book "One, Two, Three, Infinity" about physics, but it could easily have been about philosophy. So also Prigogine and Hegel want to put information into the dynamical regime, which removes it from the static eternity of Augustine. This Hegelian desire attempts to solve the dualist paradoxes introduced by various solutions to the pre-Socratic one vs many problem. However, as my seminary prof attempted to demonstrate, Hegel and his 20th century progeny really can't solve the problem either, rather they just use a sophisticated shell game that keeps moving the problem around. This is Dembski's critique of Darwinism, that it plays a shell game with information. In the end, both Darwinism and Hegel put all the information into the boundary conditions, whose eternality is implied but rarely stated. My prof is trying to convince me that a founding faculty at WTS, Cornelius Van Til, solved the problem with a Trinitarian metaphysic that has been extended by WTS faculty John Frame and Vern Poythress. I've sort of come to the same view in a wide circle that includes some math and physics examples. Here's a paper I wrote last winter for a course I had hoped would get credit, that calls it the "holy grail" of post-modernism.

The point of the paper, is that information is part of the process that it describes, and therefore cannot be separated from it. Such circular loops are particularly pernicious when they deal with definitions. God, people and words are all things whose definition is inclusive of the class, and therefore can be said to be sui generis. Information, then, can only be metaphysically defined in a system that includes one of those three basic categories. E.g, God as information, man as information, or words as information. Otherwise, it becomes an idol, a substitute G/M/W whose definition decimates itself, whose existence denies itself, whose operation eats itself.

After an absence of a month, I apologize to my regular readers who may have given up waiting for the conclusion to the "Miracles for the 21st Century" series. Finals month finally arrived, and I drove the 850 miles home to be with my family while I wrote my papers. This was probably not the speediest solution, though my children thought it the only one. When I arrived, I immediately found plumbing, electrical and yard maintenance problems that had been postponed for 8 months. Then there was a daughter's engagement among other pressing personal issues, so I beg your indulgence.

This is not to say that I was idle. My seminary paper for "hermeneutical foundations" considers the development of the 21st century philosophy and its impact on interpretation of the Bible, aka "Hermeneutics". This Hegelian philosophy turns out to be ubiquitous, as the next discussion of "4th Law of Thermodynamics" suggests, as well as a recent column by a theoretical physicist/cosmologist who thinks he has cut the Gordian knot on multiverse. So stay tuned for a series on "Science for the 21st Century".

  
  Procrustes --
   serving you all the data that fits.

Hidden Messages within the Genetic Code

Since ancient times, astronomers have stared up at the night sky (once thought to be a tent canopy), hoping for clues that would allow them to learn something about the universe. The Search for Extraterrestial Intelligence (SETI) uses radiotelescopes to listen for signals transmitted by intelligent alien beings. This sort of work involves searching through a vast amount of data, hoping to find a discrete signal in the noise.
Now we have entered the genomics era, which has lead to an entirely new group of gazers--the sequence gazers. There is undoubtedly much to be learned through careful analysis of sequence data, and likely, there may be discrete signals that can be pulled out of the vast amount of sequence. These signals, or hidden messages, are encoded by the DNA, just waiting to be discovered. On 23 March 2004, the GenBank nonredundant database was analyzed in hopes to discover a hidden message. The abundances of five different combinations of proline, histidine, alanine, glycine, and glutamate were examined in 2,707,913 sequences. As shown below, “PHAGE” was recovered much more frequently (P<0.001) than the other combinations of amino acids tested.
PHAGE 515
PAGEH 203
PAHGE 196
PAGHE 146
HPAGE 133
Coincidence?
We think not. The chances for each of these combinations to occur is equal. Given that, why does PHAGE occur so frequently? This simply must be one of those occasions where a signal is decoded from all the sequence. We truly are entering “The Age of Phage.” Phage are the most abundant biological entities on the planet, and apparently, they are trying to tell us something…
Rob Edwards
University of Tennessee at Memphis--Memphis, Tenn.
Mya Breibart
Forest Rohwer
San Diego State University--San Diego, Calif.

...TED winner and well known SETI personality Jill Tarter was asked whether she's considered looking at the information signal/information in DNA since it defies all current explanations. She responded with "coding in our DNA has been considered, but not for a while. So why would wet biology be preferable to electromagnetic signals?"

I've tried to make this argument before, though it hasn't gained much traction. Here's the parabolic storyline roughly following Arthur C. Clarke's "2001" and "Childhood's End" plot.

Suppose that the SETI project was begun in the year 1880 before Hertz discovered electromagnetic waves and before Marconi harnessed them for radio. How would SETI look for alien intelligence trying to communicate with us? Why with the telegraph of course! They'd be looking for telegraph lines on Mars, analyzing photographs for evidence of telegraph lines in space... IOW, we always think that our most recent technology is the technology that aliens would use to communicate with us, when in fact, it is the most transient part.

But now suppose that aliens have mastered quantum mechanics, and use quantum teleportation to do their communicating. It means they can cover the galaxy with almost zero wattage without suffering from noise, and signals are observable the moment a civilization leaves behind the childhood of Newtonian mechanistic marbles and understands the power of wavefunctions and non-locality. Then the goal for SETI is building a quantum teleportation antenna / receiver. What would it look like?

Well, it would possess a wavefunction that can be entangled with the transmitter, as well as a consciousness that can detect and collapse the wavefunction. Roger Penrose thinks that the brain has just such an entangled wavefunction that permits consciousness. Perhaps putting a lot of brains together, e.g, an institute or global culture, will increase the signal strength, as all the brains overlap and entangle their wavefunctions simultaneously. Maybe the World President can decree one hour of "thinking positive thoughts" that can be beamed across the galaxy.... IOW, why not wetware? It's the future. EM signals are getting as stale as telegraphy.

Now, suppose that this alien race has already contacted us, but found us not ready for prime time. So it wanted to leave a bunch of receivers lying around for our use when we are ready to talk. Where would it put them? In the phage DNA of course! (Sorry Clarke, monoliths are sooo Mesolithic.)

Now if SETI-types can swallow the idea of a "beneficent alien", as Dawkins proposed in Stein's movie Expelled, then it would seem a small step to a "beneficent designer" and thence to "God". Which perhaps, is the reason Dawkins can't make himself take the step.

A response to Roddy Bullock's post:
Life: (More Than) Some Assembly Required
 
When I took college physics in the 70's from Howard Claussen, who co-invented Teflon (and we whispered in the halls, deserved the Nobel prize), he used to ask us "what is the entropy difference between a live cow and a dead cow?"

None of us knew how to answer that question. Nor did any of my graduate school profs. The problem is that physics did not have a very good handle on the entropy of anything, much less the entropy of life. Oh sure, we could calculate the entropy of mono-atomic ideal gases, but even diatomic gasses became a challenge, much less a living organism. Reductionism, as any biologist will tell you, is the sin of physicists. So when you asked about cats, I couldn't help but think of my esteemed professor's question. In the 30 years since, I think I have the beginning of an answer.

Entropy, as the textbook would say, is proportional to the logarithm of the number of states of the system: S=k ln Ω. "The system" being the 6-dimensional phase space for (mono-atomic gas) particles f(x,y,z,vx,vy,vz). But then it is illustrated with marbles in a shoebox, and we are led to believe that only (x,y,z) are important. If instead we try keep track of (vx,vy,vz) of the particles, we end up with a LOT more states because each particle can be going in just about any direction! Just for fun I argue, lets take the Fourier transform of phase space, F, and note that here the position "disappears" but the velocity comes into focus. Then a good approximation to the total entropy of the (mono-atomic ideal gas) is

S_total = S(f(x,y,z)) + S(F(vx,vy,vz)).

I like to think of it as the sum of space-entropy and time-entropy.

The consequences for cats and cows, is that the elements of the dead cat are all in the same places as the live one, but the velocities are all different. That is, when a cat is alive, everything in it is in motion, the blood through the heart, the electricity through the brain, the ATP through the cells; but when it is dead, everything stops.

The consequences for scientists who want to make "life from scratch", is that they not only have to get all the right ingredients together, but they have to get all the motion too. Getting Frankenstein's monster to sit up takes more than electricity, but a heart-lung machine, a alpha-wave machine, (cellular bots?) etc.

If they think that "just add water" is proof of artificial life, then bacterial spores have been continuous proof of spontaneous generation for 200 years despite Pasteur's miserable failure to convince us otherwise. Which perhaps is the only good thing to come out of this hopeless religiously-driven research: that perhaps we can understand how bacterial spores can go into suspended animation, seemingly without time-entropy, and yet come to life with water.

I had three conversations about miracles in the last 18 hours, and concluded that it still needed some clarification. So here is my third installment in what may become a soap. (Installment 1 here, and 2 here.)

3) This morning, a request came into the library for an interlibrary loan, but for periodicals, they only Xerox the article and mail off a copy. The librarian asked me if I was interested in the topic, and I quickly scanned them. They were all from journals in the past year.

  i) The first one was a theologian defending against Hume's critique of miracles. Seems that there are still people who find Hume convincing.
  ii) The second was a philosopher defending miracles against the claims of methodological naturalism, which defined miracles as impossible events, so of course there can't be any scientific proof for their existence.
  iii) The third was a Frenchman defending the miracle of extraterrestrial life as a prediction of Pierre Teilhard de Chardin, and the evolution of religion.

So the first two articles were stuck firmly in the 20th Modernist Century with its faith in progress and the rejection of God. And the last is the characteristic of the 21st PoMo Century with its faith in process and the emergence of God. Either God doesn't exist or He's still arriving. Why do we swing from one extreme to the other? Why do we go from Atheism to Pantheism, from the absence of God to the ubiquity of gods? Can't we camp out in Theism for a while, after all, isn't that where Science lives? That's the question this blog is addressing.

The librarian started talking to me about a book he was reading that had the NYT writing effusive reviews and Al Mohler not-so-effusive, The Shack.   Guess what the answer to the problem of evil is? Nope, not atheism, try again. Nope, evil isn't just in your head, one more try. Yup, God is emerging. Seems we are on a roll here with Hegel.

Hegel?

Yes, the study of 200 year-old GWF Hegel explained a lot of things I didn't understand about PoMo. Such as why PoMo wants God to be always changing, when frankly, I thought it was one of God's better points, that He never changed. But it seems that this either makes God unapproachable or outdated, take your pick. Recall how we arrived at this impasse: first we made the world a watch, then we made God the watchmaker, then we complained that good watches don't need repairmen, and finally we said that watches have always been around without watchmakers. But since this conclusion led directly to the Holocaust, everyone is now looking for an exit.

Hegel provided exactly the wide sort of exit everyone wanted. He said that the world isn't a watch, but filled with God. In fact, God needs the world to explain Himself, since without the world He'd be that unapproachable heavenly watchmaker that caused so much trouble before. Now Hegel prided himself on being a civilized German, and didn't want to be confused with Hindu pantheists, so he preferred Greek terminology. God was the Absolute, and represents the Ideal.  In this century Heidegger likens God to "Being", and Tillich is famous for calling God "the ground of Being". Whitehead, about 100 years after Hegel, was a no-nonsense Brit who called his his philosophy "panentheism", meaning God is of the world but the world is bigger than God. (You will notice that the more vague the term, the more popular it is with philosophers.)

What all these philosophers are trying to do is make God accessible. Or as they say in seminary, to make him immanent. They all feel that the danger of Kant and Christianity is that God is so transcendent he has no interest in us or in our time frame. And a God who isn't there expires, in Nietzsche's words "God is dead."

But there are real consequences with having a God who is only of the world. It means that God really is stuck in time like you and I.  Long before The Shack, Conservative Rabbi Harold Kuschner wrote a bestseller "When Bad Things Happen to Good People" on the problem of evil, concluding that God is entirely good and knows our pain, but just can't do anything about it either. A bit of a letdown, if you ask me. Which is worse, a God who is powerful but never around, or a God who is always around but can't fix anything?

"Oh, but he can," say the Bergsons and Tiplers and the de Chardins, "in the last day, at the Omega point, when everything reaches perfection, then it will all come out alright.  You'll see, we are all getting better and better until that unity with the Absolute Mind will remove all imperfection."

I think you are getting the drift. There isn't a dime's worth of difference between all these versions of Hegelian dogma and Hindu pantheism or even Buddhist nihilism. You might even start drawing parallels: since the world is all deception and all these varieties of truth a part of the One Big Truth, we can celebrate our diversity, our local gods, our Gaias and Earth Days, our Easters and Ramadans, for they are all part of the web of being, the dance of life, the destiny of time. We are just motes in the eye of God, molecules in the ocean of love, etc etc.

With a half hour of practice and a few websites for material, you could probably spin this sort of thing for a lifetime. Hegel, with more German circumspection, called this process "dialectic", and  convinced everyone that with the destination fixed in the final dissolution in the Absolute, the only thing we needed to worry about was the journey. And in fact, debate was to be encouraged, for thesis would lead to antithesis and thence to synthesis in a never ending argument of history inexorably drawing us higher and higher to that final ecstatic union with the borg.  History resolved all problems. History lead inevitably to Hegel's own philosophy (why am I not surprised?). The History of man is the history of God.

So to recap, we were appalled by atheism and its excesses, so we rejected the Newtonian view of the world as a machine. At first we found refuge in a separationist dualism along with the Romantics, hiding behind the Kantian wall, but physics and history has not been kind to the wall; it is cracking and the barbarians are at the gates. Making the best of a rather desperate situation, we are ready to sally forth, reclaiming the burnt-over lands of time and space for the God who needs circumstances and people to realize Himself.  Rather than languishing in an artsy ghetto, we are now emboldened to recognize that God is revealing Himself through us. Everybody's special now.

Just one little problem. To quote the Incredibles, if everyone is special, then nobody's special.

Unless, to quote Napoleon, "some are more equal than others."

Karl Marx took Hegel seriously and said if history is our destiny, then let us change it! Let us accelerate the progress of mankind by forcing everyone to improve. We'll all arrive at the endpoint so much faster that way. And those who are hindering history will just have to be removed as efficiently and speedily as possible.  All for Progress and Progress for All!

So strangely enough, both atheistic monism and pantheistic monism, despite claiming to be complete opposites, end up in exactly the same place and with the same slogans: WWII, with atheist Hegelian communism and pantheist Hegelian racism in the battle of Berlin.  Rather like today where the diversity slogans that were meant to encourage tolerance are now punishing speech for being intolerant, even when it consists of revelation or miracles.

What then do we do with revelation, with miracles, with God's messages to us today?

"Well, honey, if you want to believe in miracles, that's just fine with us, so long as you get with the program. Just don't go saying embarrassing things about anyone else. No criticism, just positive energy. We're all in this together. Understand?"

We have gone from an Atheist "miracles don't exist", to a Kantian "miracles are myths," to a Hegelian "all miracles are equal", or, "miracles all say the same thing".  Either nothing is a miracle or everything is a miracle, since either nothing is God or everything is God. So the one thing a miracle can't be is the one thing it must be: something special. It may be true, as GK Chesterton pointed out, that the sun rising every day is a miracle, but for most of us, the regularity has erased its unique message. On the other hand, when the EMT pulled 6 unbelted but undamaged children out of my wrecked Suburban, there was little doubt they had witnessed a miracle.

The Atheist says miracles are dumb, the Kantian that they are lies, and the Hegelian that they are garrulous. None of them let miracles say what they are shouting for all to hear.

In the next and last installment, we'll look at what miracles say.   To be continued...

I had three conversations about miracles in the last 18 hours, and concluded that it still needed some clarification. So here is my second installment in what may become a daily soap. (Part 1 is here.)

2) On the way home from the panel, I had a long conversation with Drs. Poythress about the significance of the other panelists response. When the moderator asked how they combined their science with their faith,  one replied that "I just do science", and the other opined that "my faith isn't shaken by science", amplifying with a disturbing scientific discovery that they just accepted. In other words, there appears to be no connection between science and faith.

"Two Kantians versus one VanTillian!" I said.

But despite the claim that science has not shaken their faith, both of the other panelists made the statement that the Bible contains myth. It was the only time I saw Dr Poythress agitated; it was all he could do to keep from interrupting, waiting for the moderator to acknowledge him before blurting out "I don't believe there is any myth in the Bible!"  One of the panelists was not so reserved, shaking her head and restating her opinion.

Now what is peculiar, is that 50 years ago in their member churches, "them's fightin' words". What was unreconcilable, unadulterated "liberalism" for their grandparents, has become mainstream conservatism today. How did "myth" creep into this Kantian wall of separation between church and state?

To answer that question, we'll have to do some history.

Before Christ, at the dawn of Greek civilization, pre-Socratic philosophers were trying to understand how the world could be both beautiful and true, both varied and understandable, both changing and always the same. On the one hand, every person you meet is a unique, different, distinct, person, yet on the other hand they are all people, intelligent, recognizable human beings. Different but also the same. 

Parmenides thought that at the foundation we all exist, and all existences are one, so it is change and variety that is the deception. He had a great influence on Plato, and echoes of his philosophy can be seen right down to the present. Heraclitus took the opposite view, that change was the characteristic of life, that we "cannot step in the same river twice." Leucippus (and later Democritus) tried to find a compromise, that the atoms are unchangeable, but they are ever moving and combining in new ways that lead to change. And there, at the beginning of the classical world, you have the problem of "the one and the many".

Socrates, Plato and Aristotle gave an answer to the one-and-many problem that dominated the entire classical world, and indeed, the medieval world so much so that a classical education, whether of Platonic or Aristotelian flavor, saw Truth as a unitary goal of educational Trivium: Grammar, Logic and Rhetoric. Whenever any of these disciplines sought a different goal, they were roundly criticized. Both Plato and Aristotle seemed to reserve their greatest invective for the Sophists, who valued Rhetoric for its social and political benefits rather than its spiritual and unifying benefits.

With the Christianization of the Roman world, all of these techniques came over into Christendom, merely by exchanging the goals of Greece with the goals of Christ. Although there was much development throughout the Medieval period, the first major crisis came with the Enlightenment, and the breakdown of the Medieval synthesis.

Inductive truth competed with deductive truth, and rhetoric lost its pre-eminent position in the Trivium since argumentation could easily be trumped by experimentation. (eg, Aristotle's arguments that heavy objects fall faster than lighter objects could be disproved in 15 seconds with an experiment in Pisa.)

In other words, the pre-Socratic dilemma of the one-and-the-many had resurfaced, and philosophers were at a loss to reconcile the new sciences with the old synthesis. Just as in classical Greece, skeptics proliferated in this now uncertain environment with the most famous being the apostate David Hume. Later on his analysis would be called an epistemological critique, but the Medieval synthesis did not so compartmentalize its philosophy; it was equally a critique of ethics, theology, and metaphysics, which is what made it attractive to atheists.

In this environment, Immanuel Kant's 1781 Critique of Pure Reason marks a watershed, solving the confusion of skepticism (as well as rescuing theology from the atheists, he believed) with an essential duality between Science and Thought. That is, the world of science and experiments was irrevocably separated from the world of mind and logic by the untrustworthy senses that mediated between the two. Notice the parallels between the pre-Socratic materialist solution of Democrites and that of Kant.

But Kant's solution was not universally admired, and this led to GWF Hegel's development of idealism (~1816) and his lectures on history (1822-23), that inverted the role between the mind and the sciences, arguing that there was a dialectic of Mind working through time that ever produced dualities and braided their syntheses back together again. You might also note the parallels to both Heraclitus, the change being part of the essential unity of Mind.

Therefore by the middle of the 19th century, we had three basic solutions to the problem of the one-and-many,  (which can also be analyzed as metaphysics and/or epistemology): an Enlightenment faith in Science (subsuming Mind); a Kantian Dualism (separate but equal); and Hegelian faith in Mind/Process (subsuming Science). We might also stereotype these views with respect to religion as: atheist monists, theist dualists, and pantheist monists.

This intellectual history neglects what was going on politically. As any historian will tell you, they are not unrelated events. For the Enlightenment view dominated France in 1789 and directly led to the Reign of Terror. This caused a lot of theologians (and politicians like Edmund Burke) to reconsider how best to handle this overzealous faith in Science that abolished God. Kant's dualism suggested that we should let them both live in peace, doing what each does best.

If France was an aberration, it was only that it was a century ahead of its time. Napolean's wars and the rise of the Prussian state set the stage for a reenactment in the 20th century wars of Modernism. Thus throughout the 1800's as Enlightenment though became more and more pervasive, theologians were turning to Kant for a way to reconcile the Church and State. 

The basic conclusion was that morality was a matter of the heart, which the Church could teach best, whereas civility was a matter of the brain, which the state could teach best. Overlapping areas like Miracles were addressed with a compromise: the brain knows they aren't true, and for matters of state we don't allow them to exist, but the heart needs them to be true, so for matters of morality we allow pious belief in their importance. This schizophrenic approach was hard to sustain, and therefore many bright scholars attempted to resolve again this hoary "one-and-many" problem.

In 1921, Rudolf Bultmann published a careful account of how Kant could "de-mythologize"  the Bible without losing its importance, and for the next 50 years, this was the reigning paradigm in theology circles. The idea was that "myth" was something not scientifically true, but morally true, and thus to make the Bible acceptable to an Enlightenment world, which would be of great help restraining their immoral behaviour, one should go through the Bible with a pink highlighter, separating the myth from the facts. 

Now that we have a properly highlighted Bible, we can immediately see which parts are meant for our moral development, and which for our mental development. Bultmann, like Kant before him, saw this as a vast improvement over immoral atheism that would slaughter men as if they were animals. Miracles, as Bultmann carefully explained, were myths that could not possibly be scientific, but were meant for our edification.

This was the view of the two other panellists that night. There is just one problem with it. The Resurrection is highlighted in pink.

Can one disbelieve in Miracles and still believe in a resurrected Christ? And if Christ was not resurrected, was one still a Christian? St Paul, an otherwise unmythological favorite of Bultmann's, thought differently. But then, St Paul didn't have Kant. Could we achieve today what Paul could not achieve in the classical world? What does history tell us?

History has not been kind to Bultmann; first the evangelicals attacked him, and later the liberals. But in a peculiar way, physics attacked him first. In 1924 De Broglie began the deconstruction of Democritean materialism with his thesis on electrons as waves. In time this became the weird world of Quantum Mechanics that destroyed Kant's separation between mind and matter.

It has been, however, a long, slow death. As we noted earlier, politics seems to precede philosophy in these areas. Just as evangelicals became more politically involved in the 1980's, so also they found their rigid separation of church and state was too confining. The realignment of the Republican party under Ronald Reagan, which recombined church and state was preceded by a realignment of the Democratic party in 1968 with the atheist monists, which bore fruit in the election of 2008. The Kantian respect between the natural sciences and the liberal arts had vanished, so that by 2006 the Nobel laureate and president of Harvard could be ejected for "disrespecting" the liberal arts faculty.

But as usual, reactionary evangelicals are the last to hear the news, hence the reliance on poor dead Kant at the panel last night. No, that's unfair to them. They rely on Kant because they are scientists trying to maintain the mutual respect that keeps them their jobs.

Unfortunately, it is a losing battle.  One way of understanding the movie "Expelled", the documentary of academic persecution, is to view it as the result of the Kantian wall crumbling along with the Berlin wall.

How can we then live? If there is no respect between science and faith, we are at the mercy of the one with power? Are the wars of religion next? How do we resolve the problem of the one-and-many, of miracles for the 21st century?

The answer takes us to Hegel, and the next installment.

To be continued...

I had three conversations about miracles in the last 18 hours, and concluded that it still needed some clarification. So here is my first installment in what may become a soap.

1) Last evening, we had a "Writers Group" meeting, where I brought my blog "The Physics of Miracles". They all liked the story-telling, but struggled with the philosophy. "What do you mean by miracles?" they asked me, "And why do you say there are no scientific laws?"

Then last night at Princeton University, I attended a panel discussion on "Faith and Science", where the question came up about miracles as violations of scientific laws. One of the panelists, my advisor Dr Vern Poythress, had written an entire book on the subject "Redeeming Science". (You can support this amazing man by buying his book, but if you have good reasons for being a skinflint, he also makes the PDF available for non-commercial use.) In his book, as well as at the panel, he makes the point that "scientific laws" reflect an outlook on Nature that sees it as an impersonal, mechanical machine, in contrast, say, to a stone-age animist who sees Nature as anthropomorphic spirits, or a Christian who sees Nature as the actions of a personal God.

But isn't Nature impersonal?

The impersonal machine metaphor for Nature (and yes, everything we know is analogous and metaphorical) only arose in the Enlightenment. Some historians of science argue that it was the public awe and admiration of the invention of the pocket watch, (exemplified in William Paley's famous 1801 book on ID and ridiculed by Richard Dawkins in "The Blind Watchmaker") that made everyone think of the universe as  God's pocket watch. Newton's calculus explained the orbits of the planets as precisely as a watch kept time, and thus he was credited with causing the paradigm shift in the view of the cosmos. Realize that for 1000 years before Newton, planetary motion was calculated with circles inside circles, epicycles that looked vaguely machine-like, but without a motive force, without gears or laws or design, so it was considered merely a description of God's actions, not a prescription of a mechanism. Also notice that a century earlier, Descartes had failed in an attempt to find a motive force for the orbits of the planets as vortices of liquid, but since machines aren't made out of liquids, the paradigm shift had to wait for Newton.

So it really has been for a little more than 2 centuries that science can talk about discovering "laws". And these have been very fruitful centuries of scientific progress. Make no mistake, treating Nature as a machine is tremendously productive.

Nevertheless, it comes at a price. We have separated God from His creation, making the machine independent of Him. The 19th century opened with Deists like William Paley, who proposed that God made the Universe as a really complicated watch, wound it up and stepped back. Then the 20th century opened with Atheists like Russell and Einstein who kept the watch, but did away with the Watchmaker, or at least, made Him so distant that He's out of calling range. Then followed the most devastating and global wars in human history, merging with the most deadly and genocidal purges in human history: WWI, WWII, Korea, Cold War-Gulag, VietNam-Cambodia, Rwanda, Sudan. It was and remains a steep price to pay for banishing God.

But we need not become Atheists or even Deists; we can give God a job running Nature. We just have to shed the idea that the universe is a machine.

Does this mean adopting an animist or pantheist view that God = Nature?

No. That was the pagan view supplanted by Christianity. It is as much a deadly snare as the materialist machine. There is a reason, after all, that Science arose only in the West, and only after 1000 years of educating the pagan mind. Because paganism or pantheism prohibits science. We can't go back to that view no matter how attractive a Hindu or a Wiccan religion might appear without destroying the progress of three centuries.

But you will notice that science did not arise in a mechanistic Enlightenment world, it arose in a medieval Christian world, and was appropriated by people like Newton. That is, all those great minds of the Enlightenment were educated in a pre-scientific world at universities that taught Greek and Hebrew and the classics. It took two or three centuries before atheism finally expunged the last remnants of Christianity and attempted their grand experiment of the Atheist State. So contrary to what you may have read, it was not the Enlightenment that produced Science, but medieval Christianity that produced the science that brought the Enlightenment.

Therefore after the abject failure of the Modernist Century, perhaps we should reconsider the elixir that produced the Newtons and Boyles and Pasteurs and Maxwells of the Enlightenment.

That elixir is purpose.

The laws of Nature then, are not impersonal rules of an intricate machine. Nor are they the material embodiment of an emergent will. Rather they are the regularities of a personal God. It is God's transcendent faithfulness that makes them regular. It is God's imminent concern that makes them purposive. So a miracle is not a violation of an impersonal machine, but a loving response to a personal request.

But GK Chesterton, in his wide-ranging critique of materialism published in 1911, said it all so much better!

The modern world as I found it was solid for modern Calvinism, for the necessity of things being as they are. But when I came to ask them I found they had really no proof of this unavoidable repetition in things except the fact that the things were repeated. Now, the mere repetition made the things to me rather more weird than more rational. It was as if, having seen a curiously shaped nose in the street and dismissed it as an accident, I had then seen six other noses of the same astonishing shape. I should have fancied for a moment that it must be some local secret society. So one elephant having a trunk was odd; but all elephants having trunks looked like a plot. I speak here only of an emotion, and of an emotion at once stubborn and subtle. But the repetition in Nature seemed sometimes to be an excited repetition, like that of an angry schoolmaster saying the same thing over and over again. The grass seemed signalling to me with all its fingers at once; the crowded stars seemed bent upon being understood. The sun would make me see him if he rose a thousand times. The recurrences of the universe rose to the maddening rhythm of an incantation, and I began to see an idea.

All the towering materialism which dominates the modern mind rests ultimately upon one assumption; a false assumption. It is supposed that if a thing goes on repeating itself it is probably dead; a piece of clockwork. People feel that if the universe was personal it would vary; if the sun were alive it would dance. This is a fallacy even in relation to known fact. For the variation in human affairs is generally brought into them, not by life, but by death; by the dying down or breaking off of their strength or desire. A man varies his movements because of some slight element of failure or fatigue. He gets into an omnibus because he is tired of walking; or he walks because he is tired of sitting still. But if his life and joy were so gigantic that he never tired of going to Islington, he might go to Islington as regularly as the Thames goes to Sheerness. The very speed and ecstacy of his life would have the stillness of death. The sun rises every morning. I do not rise every morning; but the variation is due not to my activity, but to my inaction. Now, to put the matter in a popular phrase, it might be true that the sun rises regularly because he never gets tired of rising. His routine might be due, not to a lifelessness, but to a rush of life. The thing I mean can be seen, for instance, in children, when they find some game or joke that they specially enjoy. A child kicks his legs rhythmically through excess, not absence, of life. Because children have abounding vitality, because they are in spirit fierce and free, therefore they want things repeated and unchanged. They always say, "Do it again"; and the grown-up person does it again until he is nearly dead. For grown-up people are not strong enough to exult in monotony. But perhaps God is strong enough to exult in monotony. It is possible that God says every morning, "Do it again" to the sun; and every evening, "Do it again" to the moon. It may not be automatic necessity that makes all daisies alike; it may be that God makes every daisy separately, but has never got tired of making them. It may be that He has the eternal appetite of infancy; for we have sinned and grown old, and our Father is younger than we. The repetition in Nature may not be a mere recurrence; it may be a theatrical encore. Heaven may encore the bird who laid an egg. If the human being conceives and brings forth a human child instead of bringing forth a fish, or a bat, or a griffin, the reason may not be that we are fixed in an animal fate without life or purpose. It may be that our little tragedy has touched the gods, that they admire it from their starry galleries, and that at the end of every human drama man is called again and again before the curtain. Repetition may go on for millions of years, by mere choice, and at any instant it may stop. Man may stand on the earth generation after generation, and yet each birth be his positively last appearance.

Chesterton then makes the point that Dr Poythress made on the panel. If regularities are personal, then even more so are the irregularities.

This was my first conviction; made by the shock of my childish emotions meeting the modern creed in mid-career. I had always vaguely felt facts to be miracles in the sense that they are wonderful: now I began to think them miracles in the stricter sense that they were wilful. I mean that they were, or might be, repeated exercises of some will. In short, I had always believed that the world involved magic: now I thought that perhaps it involved a magician. And this pointed a profound emotion always present and sub-conscious; that this world of ours has some purpose; and if there is a purpose, there is a person. I had always felt life first as a story: and if there is a story there is a story-teller.

Chesterton wrote that in 1911, at the pinnacle of Modernism, and on the brink of two devastating global wars of atheism. As the world reeled back from the nihilism of mustard gas and Zyklon B, it searched for an answer to the onslaught of atheism. In the next post, I'll relate the next two conversations on this search. 

To be continued...

Could you explain what you mean about 'denying common descent'? I'm not sure what you mean by denying that - do you mean that different species/creatures are technically related, but because of things like horizontal gene transfer (and possibly introduce of 'new' genes via asteroids/comets and such) it isn't common descent in the way typically pictured?

I'll try to summarize the SPIE 2008 paper, where I attempt to develop this concept just a wee bit, though didn't spell it out explicitly at the time.

The idea is that horizontal gene transfer (HGT) is occurring some 81% of the time. This means that the entire field of "cladistics", which attempts to construct a genetic genealogy tree (pre-genetic trees were based on body shape or morphology with many problems, not least is that they couldn't do bacteria) or DNA is just plain wrong. This is because you can get genes from totally unrelated organisms by viral infection of gametes, the germ-line cells.

That is, in lower organisms, there is no difference between germ-line and somatic cells, the entire bacterium splits in half, or the yeast "buds" when it multiplies. Accordingly, any foreign DNA has the potential to get passed on to descendants. In higher organisms, somatic cell infections do not get passed on to the descendants, only gamete cells do that. Think of this as protection against viral DNA infections.

But what if the virus infects the gamete cells? How can the organism tell if its in danger of being permanently altered?

Well, think of the entire elaborate protocols involved in sexual reproduction. Not only is there a special behavior that can filter out infected individuals, but there are numerous "stress tests" for the gametes to filter out infected or damaged gamete cells. All of this makes it highly unlikely that there will be viruses that can co-opt a species. I also believe this is why most reproductive technologies are damaging to the baby (IVF, GIFT etc) because they apply the wrong kinds of stress test to the gametes.

Despite all this protection, viruses do get through, and infect the gametes. We know this by the presence o in the human genome (and I assume, in all the genomes we have transcribed to date), of "disabled" viral DNA as much as 8% of the total! However, the identification of viruses that have made it into the genome is based on "disabled" viruses, which means the really successful ones aren't so easily identified! The PNAS paper tried to use another algorithm to detect HGT, and concluded that 81% of the genome showed evidence of HGT.

So what does this mean for common descent?

Well, it means that a new species can appear when suddenly a new gene gets inserted into the genome of the mother, and the baby looks nothing like its mother. Or more likely, many genes get transferred but perhaps "disabled" until something "enables" them all, and a speciation event occurs. This "turning on" and "turning off" of genes is the latest hot topic in genetics and goes by the moniker "epigenetics". For example, many people have Herpes infections (cold sores), viruses that have inserted their viral RNA into the cell and lay dormant until stress "turns them on" and they break out in a cold sore. Another common one is CMV, or cytomegalovirus that is endemic to some 80% of the population, but only manifests itself when the immune system is suppressed, e.g. AIDS patients.

But doesn't this look just like Darwin's hypothesis of common descent?

No. Darwin was looking for random diffusion of genes, for small changes that accumulate. What we're saying is that due to HGT, there are rapid, discontinuous changes, perhaps triggered by an environmental stimulus.

But just as Neo-Darwinian theory (NDT) replaced Darwin's fuzzy inheritance with discrete Mendelian genes, couldn't we just reformulate evolution to include *random* HGT as the mechanism of speciation? Couldn't we adapt NDT to this new paradigm and still call it Evolution?

No. HGT and "turning on" the disabled genes by environmental factors means that suddenly, and for a purpose, speciation events occur in large populations. It is the "purpose" part that is non-Darwinian. The speciation event occurs in response to a stimulus, which means that Evolution is directed, it has a pre-planned function.

Let's give a hypothetical example. For 250,000 years, Neanderthals chased mega-fauna around the boreal forests of Eurasia. From isotope analysis, we know that they ate nothing but meat. But along comes the Eemian warming event that makes the Al Gore movie look tame. The glaciers retreat, the boreal forests are replaced by savannah, and the mega-fauna vanish. Your basic Neanderthal is suffering from malnutrition. This puts stress on his immune system and his gametes. One day he wakes up with the mumps, the virus infects his gonads, and nearly all his friends get the same infection. This goes on for a few centuries, and then one year it is so unbearably hot, that Neanderthals are dropping from heat exhaustion like flies. The few that make it through this event have progeny that are born hairless (the better to handle the heat) and seem to be nearly helpless for 5 or 10 years, but then as adolescents, start covering the cave walls with graffiti. And this isn't just him, but lots of wandering tribes seem to suddenly have these kinds of kids. Enough for them to meet each other and start their own tribe. So in this hypothetical example, a speciation event has occurred driven by an infection followed by a triggering event, or generally speaking, global climate change.

The point I'm trying to make, is that random viral infections should degenerate the population, not improve it. But this isn't a random viral infection, it is a purposive viral infection. It transferred a specific gene that lay latent until the environment demanded that it be "turned on". And while my Neanderthal scenario is totally fictional, we are close to having an entire Neanderthal genome transcribed, while simultaneously discovering how epigenetic switches can activate what was previously thought to be non-functional or "junk" DNA. In the very near future, we will have a good handle on the "hidden" information in our genome or in the Neanderthal genome that is waiting for an environmental trigger that can epigenetically turn it on.

Yet if that "hidden" information is not being expressed, then there is absolutely nothing in Darwin's Natural Selection that can select for or against it. So what is it doing there?

Anticipating a future need, otherwise known as purpose, design, intelligence, or planning. Therefore the actual data of Evolution show that Common Descent with Modification cannot explain these environmentally triggered speciation events. There's just way too much planning involved.

But where did the HGT virus get the gene in the first place?

Ah, that is the question isn't it? I tried to answer it in my spie08.pdf paper, but really only answered where the gene came from in the 2nd place -- from comets.

The 1st place is a much more profound question whose potential location(s) now expands to fill the entire galaxy. (And if my dark matter hypothesis is correct, see "Dirty Dozen" post, then the number of locations may expand to fill the entire universe.)

Someone asked me recently "what is the best evidence for Intelligent Design"? I know that may sound like an oxymoron to many of you, who think that ID is a philosophy or a religion and therefore cannot use evidence, its a matter of belief. [Recent FAQ on ID answers many of these Q.]

But if you are a long-time reader of this blog, you will know that I reject the Kantian divide between religion and science. To quote Albert Einstein, "Science without religion is lame; religion without science is blind." That doesn't sound like strict separation to me, though if anything, I would say lame is too weak a word, "terminal" or "metastasized" might be more appropriate. And likewise blind is also too weak, "heretical" or "apostate" might be better.

Why such strong language? Because St Paul ties the whole point of Christianity to the scientific proof of a historical fact. And Science, whether it wants to admit it or not, only arose in the Christianized West, was founded by Christians, whose practitioners continue to use Christian metaphysics, and who only make progress when they functionally operate as if there is a Christian God. Sure, Einstein may say to the Princeton students that he barely believes in a Spinoza (pantheistic) God, but when he is in the heat of argument with Gnostic Niels Bohr, he insists "God doesn't play dice", which is a peculiar thing for a Spinozan to say (especially to a Gnostic!)

So yes, I do believe that ID can be both a philosophy/religion and use evidence, just as much as I believe that Darwinism can be a scientific theory and depend on philosophy/religion. The truth of the matter is that they are both, perhaps not in equal measures, but certainly in essential importance. For example, there are many books that say the best evidence for Christianity is the Resurrection. And perhaps equally many books that say the best evidence for Darwinism is evolution--the observation of change in species over time (as distinguished from capital "E" Evolution--the theory.)

Then what is the best evidence for Intelligent Design?

I think one defines by saying what it is not. So when ID is defined, it is "not chance". You can look at Dembski's "The Design Inference" and that's basically how it works.

Darwinism has two basic tenets: chance (natural selection), and common descent. I am inclined to say that the best argument for ID comes not from denying chance, but by denying common descent. That is, ID accepts as given that there has been evolution/change/development over time. Some have said "front loading" is the best way to describe this change, sort of like watching a seed sprout and flower from the "front-loading" of the DNA program in the germ of the seed. So common descent is not controverted, but the chance part is, so that species and speciation become like the development of a plant, with all life descending from the divine seed.

My argument is that speciation doesn't follow the analogy of a seed. Rather, it is more like the construction of a building. Carpenters are called in to do the framing, and then they leave and stonemasons do the the facing, and roofers do the roof, and electricians come in and do the wiring. Nothing about the half-finished building tells anyone what it will be, only the architect's blueprints in the hands of the main contractor. The blueprints do not build themselves, nor do they operate autonomously or by chance, but everything is semi-hierarchically arranged toward the goal. Everybody doesn't get the same subset of blueprints, or even know what the details of subsequent contractors jobs. The roofers probably have little concern for the electricians. But if a problem arises, say, an roofers truck is blocking the access to an electrical box, the solution doesn't involve referencing the original blueprints. [Aerospace engineering has a entire speciality devoted to this "systems engineering" problem.]

If one were to use a metric like "volume of enclosed space" or "density of enclosed space" or even "complexity of enclosed space" and then chart this metric for the evolution of the building, it would be very far from linear, in contrast to a growing seed.

So speciation and change are part of a grand plan, though individual parts may have no real idea what will come after them. The front-loading, if you will, is non-obvious to many participants. So how do we know or could we know that the Earth and its ecosystem and evolutionary history is a building and not a sprout?

a) Finding the partial blueprints and reconstructing the master ==> which to a certain extant, we have started to make progress on: typeing the genomes of many organisms, doing the historical development of organisms, etc.

b) Fractal distribution of information in the genome or in ecology or in time, indicate that the system has long-range space/time interactions. Long-range interactions are indicative of information, since random space/time events are diffusive and highly local.

c) Another indication is particularity of species and niches and adaptations. For diffusive information (see Dembski's "No Free Lunch" book) the potential species in "parameter space" must be dense, but when they are sparse, there is no diffusive, random solution. Sparse particularity is the characteristic of very low entropy systems, which are high information systems.

d) I'm not sure how significant this one is, but super-linear growth in information density, or even exponential growth would seem to be indicative of long-range temporal organization. That is, not just information, but information flow is significant for planning. During WWII this was the field of "Operations Research", which addressed the problem of getting the men and material to the front. Likewise, in evolution, how does one get the information to the lifeforms that need it?

All of this means that the "organic" paradigm of life multiplying itself into more and more varied niches as a continuum of evolution from a common ancestor can't explain the actual distribution in space and time.

I've used the analogy of a PC booting up Windows XP as an example of a recursively programmed, non-linear evolution of complexity. Life on Earth and its history are so far from being smooth, that the very thing Darwin set out to explain, cannot be explained by his method: change over time. The best evidence for ID then, is not the inability of the chance hypothesis to explain current information (design inference), but the distribution of information over space and time (e.g. "evolution") which cannot be attributed to a diffusive or even "organic" growth from a common ancestor.

Evolution is the best evidence for ID.

Two months ago, I blogged on Michael Brooks quitting his job at New Scientist and writing his "13 biggest scientific mysteries", which have been suppressed by the science establishment. This has generated a flurry of reviews, and now the New Scientist finally carries their review (though it might also be an abstract written by Brooks, I can't tell.) In any case, the list of items is now different.

For reference here is the table of contents from Brooks' book:
1: The Missing Universe (Dark Matter problem)
2: The Pioneer Anomaly (Pioneer spacecraft deflecting from Newtonian trajectory)
3: Varying Constants (physics constants seem to vary over geologic timescales)
4: Cold Fusion (is back and with more data)
5: Life (materialism vs intelligent design)
6: Viking (on Mars in 1976, the labelled release experiment found life)
7: The Wow! signal (radio telescope detected monochromatic beam)
8: A Giant Virus
9: Death (evo/devo debate in evolution)
10: Sex (seems overly complicated, and not at all Darwinian)
11: Free will (materialism doesn't allow it)
12: The Placebo Effect (swallowing sugar pills, injecting saline solution works like a drug)
13: Homeopathy (diluted medicine still works)

In looking over the list, I can see that the earlier blog addressed issues  1,2,7,9,10,11. My treatment of #1 was somewhat cursory, so let me address it at greater length.

1. The Missing Universe
The problem is simple, the Andromeda galaxy (and all other galaxies examined) should be flying apart because the gravity from stars is about 10% of the needed mass to hold everything together. Is there something we can't see (hence, dark) which is providing the gravity to hold the galaxy together?

Well, there has been no shortage of suggestions. The problem is whether any of them make sense. If they were, say, Jupiter sized planets, there would have to be 10-100X more of them than the stars. Many of them would be in orbit about stars, on average some 5-10 per star. We should see both "wobbling" of the star, as well as eclipsing of the star. And while we are up to about 100 extrasolar "Jupiters", it is nowhere near the number needed. The recently launched Kepler mission is designed to monitor 100,000 stars for this eclipsing behavior, and by all accounts should detect 1000's of such Jupiters at the current concentration, but far below the concentration needed to explain the dark matter problem.

Well, could it be hiding in Earth- or Moon-sized objects? Once again, the sheer quantity needed, some 1000-10,000 for each star, is daunting. But Kepler can certainly find even the small guys if they are there.

How about a gas, could the missing matter be hiding in clouds of cold hydrogen gas, the famous HI regions?  Well space is a pretty good vacuum, and the density of even these "dense" clouds would make vacuum-pump manufacturers envious. At 3 or even 10 atoms/cc, we're talking of galactic sized clouds to hold the necessary mass. And even at this low density, starlight passing through parsecs of hydrogen gets absorbed and re-emitted, causing the HI regions to glow, and also stamping the starlight with "absorption band" fingerprints. If the missing matter were gaseous, we would have lots of evidence of it.

What about those dark nebula that only absorb light? That's because they aren't gaseous, but dusty. And once again, there's enough dust there that its presence can be detected by blocking the light behind it. If the dust gets above a micron in size, then it collapses into the stars, if it is below a micron, it gets pushed around by starlight. So not only do we need more dust than is presently observed, but it won't stay put for the 12 billion year lifetime of the galaxy.

The problem is one of cross-sections. If we make the missing matter in small enough pieces to spread it evenly around, then it has such a large optical cross-section we can see it. If we make the missing matter in big chunks, then it has such a large gravitational cross-section we can see it.  This has led theorists to propose MACHOs and WIMPs, or massive compact halo objects and weakly interacting massive particles.

MACHOs are usually thought of as neutron stars, black holes, brown dwarfs, and other very faint stars. This is possible, though all of these have huge gravitational cross sections and should be observable by the things that get attracted to them. For example, black holes may not emit radiation, but when they pull gas from a neighboring star, they end up with an accretion disk that is extremely bright in the X-ray sky.

WIMPs are speculative subatomic particles like neutrinos that have some mass, yet don't emit or absorb light and have almost no interaction with matter. The problem is that neutrinos are thought to be about 10-15ev in mass, and there just aren't enough of them produced by stellar activity to account for the missing mass.  Furthermore, if 10X the mass of the sun is present in a gravitational halo around the sun of trapped WIMPs, we'd have noticed it by now.

A recent astronomical discovery of two galaxies passing through each other gave a whole new perspective on the problem. High optical cross section corresponds to high collision cross section, so if the missing matter were dust or smaller, the two galaxies should have had lots of hot matter at a bow shock. Well they had some, but when they mapped the gravity they found most of the mass was ahead of the shock, the dark matter of the two galaxies had interpenetrated without slowing down. So here is the mystery, the dark matter has both a small collision cross section and a small gravitational cross section. How can it be both?

The answer is deceptively simple. It is bigger than dust, smaller than planets, and "hot" enough to survive 12 billion years without coalescing. Fast-moving, black-crusty comets fit the bill perfectly (though Lou Frank's data don't). But to make all that ice would mean that big bang nucleosynthesis models, which predict the ratios of H/He/Li and very little O, must be off, or early universe star formation was much faster than expected. Both subjects are now getting re-examined (plasma physics was ignored in BBN models, and "cold flows" ignored in early universe cosmologies), and I suspect the hypothesis will be strengthened rather than weakened in coming years. And it would also provide another factor of a billion in the locations for life.

#2 we dealt with before.

#3 Varying Constants
 Physical constants are ratios that science can't explain, and therefore take as givens, boundary conditions, universal constants. Brandon Carter is famous for a 1974 neologism that explained how sensitive our universe is to those inexplicable constants, for if they had been any different, we wouldn't be here to observe it. This "fine-tuning argument" has been taken up by Intelligent Design and Creationists as evidence of a Creator, while the counter-arguments have been either
(a) Carter's original "Anthropic Principle", that since we couldn't observe any set of constants that exclude us, it is mere observational bias, and not evidence of "fine tuning"; or (b) there are gazillions of unobserved universes with different constants, which when combined with (a) allow pure chance to have provided our universe.

Now Eliot Sober is a U. Wisc at Madison philosopher  who really would like to support chance as the explanation of humans, but even he has trouble with argument (a). If you are inclined toward that argument, you should take a look at this paper using Baysean statistics. And despite the NYT suggesting that a multiverse theory doesn't exclude God, it implicitly requires that each baby universe in the set of multi-verses will have a different set of physical constants, which is no more supported than the idea of baby-universes in the first place. So breath-taking are these assumptions, that it is almost impossible to spoof, but Rob Bryanton has managed it, which is a funnier version of my "borg" disproof.

In any case, discovering that physical constants vary over geologic time would wreak havoc with both the "fine tuning" argument, as well as bolster the "multiverse" hypothesis. But mostly it would give cosmologists headaches. And my gut feeling is that it can't be true, that physical constants are tied up in the character of God, "in whom there is no shadow due to changing".

#4 Cold Fusion
This was one of those discoveries 15 years ago that everyone wanted to be true, but no one could duplicate. Consequently, the discoverers were branded charlatans, and run out on a rail. But nevertheless, a small core of true believers kept working on it, and 15 years later, there are repeatable results, albeit no theory to explain them. Historically this isn't so unreasonable, the discovery of superconductivity took 40 years to explain, and likewise spectroscopy took 100 years to explain the discrete lines. In our modern hubris, we think mysteries that last more than 4 years are like wars that last longer than 4 years: a complete and utter disaster. (I have also hypothesized that there are observational QM effects that may cause the results to depend on whether you believe in them.)

So I think Michael Brooks includes this mystery more because of the animosity that it generates than for the delay in theoretical understanding. Perhaps because it has been a devilishly difficult experiment to replicate. But then again, so was Michelson-Morely, so perhaps it is the anger engendered that is the greatest mystery.

5: Life--you might see my somewhat speculative papers about comets.

6: Viking-- I have blogged on earlier and even earlier.

7: The Wow! signal-- I discussed earlier.

8: A Giant virus
(haven't seen anything from his book on this)

9: Death
I've discussed in my booklet on Viruses, Genes and Sin, how death solves the parasite load problem. Thus death is a gift of God to counter the curse of sin. Think of it as a Sleeping Beauty fairytale, that the curse of the evil aunt is blunted by the blessing of sleep. That's why death is planned, not accidental. If we are puzzled by this, thinking that eternal life should be the goal of a Darwinian evolutionary model, then we need only read Genesis 1-3 to understand the purpose of death.

10: Sex--discussed earlier.

11: Free will -- discussed earlier.

12: The Placebo effect
This one is really only a problem for materialists. That is, people who believe that all communication must occur by transfer of particles, and that there are no long range correlations in space and time. I have earlier written on the correlations of space-time, but here I would only point out that repetitive actions will often achieve "muscle memory", which is somehow faster and less conscious than "brain memory". I watch my wife practising Chopin etudes, and over time her fingers become a blur of notes that she could not possibly be remembering in realtime, with the 250ms latency of the nervous system.

Thus the continued application of a medicine does not itself cure the pain, but rather initiate a series of dominos that result in amelioration of symptoms. If injection of morphine for 5 days triggers the endomorphins of the body to eliminate pain, what is to prevent the bodies "muscle memory" from releasing endomorphins even before the needle penetrates the skin or when replaced with saline? Such adaptive behavior has many beneficial consequences, not least is the playing of Chopin etudes, and it would be well within the bodies capabilities to have multiple triggers for certain responses. The only mystery about placebos is that it has taken this long to understand that the body can learn sub-conscious ways to control homeostasis.

12: Homeopathy
I have little sympathy for this practice, though I do understand its philosophy. If one can cure without dangerous chemicals, I am all for it. But were it reliably true, then Chinese medicine would be a whole lot more successful. For when I am sick, I and my pathogens lack the patience to try a hundred lesser treatments, and therefore I find it marginally to deadly dangerous as a proposed cure.

No doubt there are new things being discovered about water every year, and perhaps many of the homeopathic effects will find their explanation in future physics. Indeed, I consider myself the first to have discovered the work function of water exposed to UV light. But life is too precious to experiment on people with novel theories of water. Why have not homeopaths proved their case on a mouse model, like all the other drug companies? With regard to human treatments, the question is not qualitative (does a treatment work) but qualitative (how reliably does it work). Until homeopathy answers that question, it is not a treatment I would willingly undergo.

The New Scientist abstract now lists the 13 top items differently. Here's their new list:

NS 1. The placebo effect (same as #12)
NS 2. The horizon problem (new)
NS 3. Ultra-energetic Cosmic Rays (new)
NS 4. Belfast Homeopathy results (same as #13)
NS 5. Dark Matter (same as #1)
NS 6. Viking's Methane (same as #6)
NS 7. Tetraneutrons (new)
NS 8. The Pioneer Anomaly (same as #2)
NS 9. Dark Energy (new)
NS 10. The Kuiper Cliff (new)
NS 11. The Wow signal (same as #7)
NS 12. Not-so-constant constants (same as #3)
NS 13. Cold Fusion (same as #4)

NS 0. Not one to shirk my duty, here are my thoughts on the new list, as well as vague surprise that Michael has removed all his biology mysteries. I suppose the Darwinistas were upset that he would call an established fact "a mystery". Once again, it is the scientists who are the biggest mystery.

NS 2. The horizon problem is one of cosmological statistical-mechanics. If parts of the Big Bang have been incommunicado for 12 billion years, how did they all end up within millikelvins of each other, as if they were in some sort of equilibrium exchanging energy?

Well there are several ways to solve this problem. The "inflation" scenario has exchange through a "faster-than-light" expansion that solves the problem, but introduces another. It is one specific example of a tertium quid. That is, if A-->C, and C-->A, but A and C have never met each other, we have correlation without causation. This can be accounted for if there is a third object B, such that B-->A and B-->C. For example, lipstick and breast cancer are highly correlated, but not causal, because they are both things causally antecedent to both, namely, women. Therefore if it looks like the universe is in thermal equilibrium, though parts haven't spoken to each other in 12 billion years, perhaps it is because they are both causally connected to a third thing. It could be the physics below the Planck time, it could be a new force field (responsible for inflation), or even God. Given the freedom to pick any correlation one desires, such as inflation, the real mystery is why we think cosmology is such an exact science.

NS 3. Ultra-energetic Cosmic rays.
I've actually given talks on this before, where I propose a galactic (Milky Way) source for the cosmic rays below the "ankle". Michael is concerned about sources above the "ankle", which data suggest must have a source within our galaxy. I have proposed a more hypothetical "DC" accelerator for these particles, produced in cosmic jets. Since our Milky Way is thought to have a massive black hole at the center, it seems reasonable to assume a jet associated with our own galaxy that can make these TeV cosmic rays.

NS 6. Viking's Methane. This is just a rehash of Gil Levin's experiment, but apparently the ESA mission has remotely detected methane on Mars, now confirmed with Earth-based HST measurements. The reason Viking didn't directly detect methane with its atmospheric mass spectrometer, is that mass channel 16 was intentionally "blocked" in the design. Why? They didn't think there would be any methane to see.

 NS 7. Tetraneutrons
Not being a particle physicist, this one takes me by surprise. Given the ability of Los Alamos bomb codes to calculate nuclear reactions to the sub-percent level, I would have thought that all subatomic particles and forces were accounted for to great detail, barring some high energy stuff like the TeV Higgs Boson. But neutrons at 940MeV are so mundane, one would have thought that any binding force (or virtual particle E < 940MeV) would have been well researched by now. Then again, when the helioseismologists tested stellar interior models also derived from bomb codes, the mistakes were at the 10% level rather than the advertised sub-percent. So perhaps nuclear physics isn't so cut-and-dried as I had been led to believe.

 NS 9. Dark Energy
I've blogged on this earlier, as well as in the earlier Brook's review.

 NS 10. The Kuiper Cliff
This one hasn't been a mystery very long, simply because we haven't long possessed the ability to look for planetismals outside the orbit of Neptune where the light is so dim. So chalk one up for new technology:  high quantum efficient CCD's and robotic telescopes.

Since we haven't been looking for very long, this mystery might be solved tomorrow, and I would hesitate to include it with more venerable mysteries. Nevertheless, there is a peculiar correlation with my work. Seems that several of the Kuiper objects are comets, or as some would like to say, water-bearing asteroids. I looked at the distribution of comets in a earlier paper, and concluded that there was enhanced radial diffusion occurring from the Kuiper belt. I attributed this to the effect of "steam jets" whenever a comet came within the orbit of Mars. This would change the apogee distance of the comet, appearing as enhanced diffusion. Now most of the objects that Michael is talking about are on circular, not elliptical orbits, though given their short observation times, there may be some difficulty telling the two types of orbits apart. It would be my hypothesis that the absence of orbits on the outer edge of the Kuiper belt, is in part due to enhanced radial diffusion of comets that spend large portions of their time in this region.

If Michael reads this blog, I hope it sets his mind at rest; for the science is far less surprising than the scientists.