Clarence Thomas speaks in court! (Four words.)

January 14, 2013 • 5:00 pm

The execrable conservative Supreme Court Justice Clarence Thomas finally said something in a U.S. Supreme Court hearing. He hasn’t spoken during oral arguments (which is how the hearings are conducted) since 2006, and

As the New York Times reports:

Justice Thomas leaned into his microphone, and in the midst of a great deal of cross talk among the justices, cracked a joke. Or so it seemed to people in the courtroom.

The official transcript confirms that Justice Thomas spoke, for the first time since Feb 22, 2006. It attributes these words to him, after a follow-up comment from Justice Scalia concerning a male graduate of Harvard Law School: “Well – he did not —.” That is all the transcript recites.

Thomas’s four words of wisdom followed this exchange, reported by the Los Angeles Times:

Justice Antonin Scalia, taking the state’s side, said Boyer’s lawyers certainly appeared qualified. [The issue is whether a Louisiana inmate had comptent lawyers.]

“She was a graduate of Yale Law School, wasn’t she?” asked Scalia.

Yes, she is a “very impressive attorney,” replied Carla Sigler, an assistant district attorney from Lake Charles, La.

“And another of his counsel, he was a graduate of Harvard Law School,” Scalia continued. “Son of a gun,” he added.

“Well, he did not…” Thomas said, his words mostly drowned out by cross talk.

“I would refute that, Justice Thomas,” Sigler replied, apparently defending the view that a Yale or Harvard law degree is solid proof the attorney is minimally competent.

Thomas is a godawful justice, who simply follows Scalia’s lead, breaks no legal ground, and always takes the part of the wealthy and the Republican. He exemplifies the politicization of the Court, and I fervently wish he would go. No chance of that.

A good day: Uncle Eric sends plaudits

January 14, 2013 • 1:49 pm

Well,  Mondays don’t get much better than this: I’ve become a meme-let and subject of a Facebook exchange, and now, over at Choice in Dying, Uncle Eric MacDonald has written a post about my having finished the Bible: “C0ngratulations, Jerry Coyne!”  Of course being Uncle Eric, he reminds me that I’ve omitted 9 books from the Ethiopian canon and 11 from the Western canon, but for now I’m satisfied with the King James version. I’m going to reread the Qur’an, but somehow I quail at having to read the Book of Mormon.

Eric has read the Bible four times (he was once an Anglican priest), but gave up the last time after reading just the Torah (the first five books of the Old Testament). He adds:

Jerry deserves our congratulations for persevering to the end, though, to be frank, the only reason for doing something like this is to be able to say that you had actually done it.

Well, it’s a bit more than that: I wanted to see for myself what it said rather than taking the word of others, I wanted to be conversant with the most important religious work of Western culture, and, of course, if I’m to continue engaging with religion I need the benefit of being familiar with scripture.  I have learned a lot: including that Jesus’s wisdom was overrated, that the Old Testament God is an arrogant, praise-courting bully, and that the Bible is not a great work of literature.  That much I was told before, but I’m a scientist and wanted to replicate the findings of others.

Eric does, however, find more literary merit than I do in the Bible:

The Bible, though, has some genuine treasures, amongst them the Song of Songs, a lively erotic work of some subtlety, and the book of Job, perhaps the most unrelentingly searching study of the problem of evil ever written. The book ends, of course, on an entirely false note, as though lives can substitute for lives, or wealth for suffering, but the poetic heart of the book is an ageless and so far unanswered challenge to the justice of any imaginable god. Another text of some value is Ecclesiastes, the author of which was almost certainly not a true believer, who provides as convincing a case for atheism as any of the new atheists. It’s fundamental message is that “shit happens.” The world goes on in its accustomed way without any sign of design or purpose, and so one should live stoically, drifting with the tide of change, accepting the goodness that may come one’s way, and enduring the suffering without complaint.

I found Job overly long and oppressive; and the whole point is undercut, as Eric says, by Job’s acceptance of blind obedience to a supposedly loving deity who is really unspeakably cruel. And, to be honest, I found the tale tedious. But yes, the Song of Songs and much of Ecclesiastes has its poetic bits. Literary taste is subjective, of course, but all in all I like the Bhagavad Gita better.

Of course the point of Eric’s post was not to congratulate me, but to use my completed reading as a platform to proclaim his own take on the Bible, which is precisely why his post is so good. It contains, for example, this important point:

Like everything we say about god or gods, its answers largely consist in a suppression of the questions that ordinary people ask, but it does so in such a way as to suggest that real answers have been given. Holy books are illusions that people play with words.

This is something that it took me a long time to recognise. It’s most obvious in the case of the problem of evil, but it is also present in practically everything that religion proposes about itself, and this is where apophatic theology gets its leverage, because, in the end, there are no answers to the kinds of questions that religion asks. The Bible, and religion in general, recognises the mystery of human life, the urgent questions, all unanswered, that most people, in one way or another, are exercised with most of their lives, and it pretends that, by talking about them, by thematising them, they are somehow answered, without noticing that the answers are really questions rephrased as words of worship, praise and adulation, or are simply the same questions asked in the context of worship.

In debating theologians, or any believers, I’d like to ask them, “Precisely how has religion answered any of The Big Questions?”  If they adduce the Golden Rule, one can say that that moral dictum came from Confucius, and probably well before. Any “answer” common to most faiths will have been arrived at with equal ease by secular reason. As for the other Big Questions, like “What is our purpose?” or “How are we saved?”, every religion has a different answer. Faith cannot answer any questions, scientific or otherwise, at least not in a way that holds for all people. (Scientific answers, in contrast, are valid for everyone.)

Eric’s post is much meatier than I can convey here, but go over and see how he defends his claim that the idea of finding truth through revelation is completely incoherent.

Thanks, Uncle Eric!

Quote of the day: Robert G. Ingersoll #6

January 14, 2013 • 11:31 am

This quote, also taken from Ingersoll’s “The Gods” (1872) is an appropriate way to finish my series of excerpts, for it deals with the battle between science and faith (and yes, it is a battle despite accommodationists’ assurance otherwise). This week we’ll be featuring quotes by Walter Kaufmann in a fantastic book I’ve nearly finished, Critique of Philosophy and Religion (read it!). But first the final bit of Ingersoll:

In every age some thinker, some doubter, some investigator, some hater of hypocrisy, some despiser of sham, some brave lover of the right, has gladly, proudly and heroically braved the ignorant fury of superstition for the sake of man and truth. These divine men were generally torn in pieces by the worshipers of the gods. Socrates was poisoned because he lacked reverence for some of the deities. Christ was crucified by a religious rabble for the crime of blasphemy. Nothing is more gratifying to a religionist than to destroy his enemies at the command of God. Religious persecution springs from a due admixture of love towards God and hatred towards man.

. . .For ages, a deadly conflict has been waged between a few brave men and women of thought and genius upon the one side, and the great ignorant religious mass on the other. This is the war between Science and Faith. The few have appealed to reason, to honor, to law, to freedom, to the known, and to happiness here in this world. The many have appealed to prejudice, to fear, to miracle, to slavery, to the unknown, and to misery hereafter. The few have said, “Think!” The many have said, “Believe!”

The first doubt was the womb and cradle of progress, and from the first doubt, man has continued to advance. Men began to investigate, and the church began to oppose. The astronomer scanned the heavens, while the church branded his grand forehead with the word, “Infidel,” and now not a glittering star in all the vast expanse bears a Christian name. In spite of all religion, the geologist penetrated the earth, read her history in books of stone, and found, hidden within her bosom, souvenirs of all the ages. Old ideas perished in the retort of the chemist, and useful truths took their places. One by one religious conceptions have been placed in the crucible of science, and thus far, nothing but dross has been found. A new world has been discovered by the microscope; everywhere has been found the infinite; in every direction man has investigated and explored and nowhere, in earth or stars, has been found the footstep of any being superior to or independent of nature. Nowhere has been discovered the slightest evidence of any interference from without.

These are the sublime truths that enabled man to throw off the yoke of superstition. These are the splendid facts that snatched the scepter of authority from the hands of priests.

Ingersoll could write, and you should read Susan Jacoby’s new biography of him.

LOLzy publicity: 50 Shades of Evolution and a meme

January 14, 2013 • 9:49 am

This is a real Facebook exchange which I have permission to share. A student was reading Why Evolution is True in public and was accosted by a stranger. She recounted the experience on Facebook, with the replies given (identities hidden to protect the evolution-friendly):

50_Shades_of_Evolution

And meme of the day on Facebook’s “Great scientists and inventors“, where I don’t really belong! (But given that, I won’t quibble about “elucidating on”. . . ).

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h/t: ZF, Grania

True facts about the baby echnidna

January 14, 2013 • 8:08 am

Here’s a funny, short, but also semi-informative video about an amazing monotreme, the echidna (there are actually four species in two genera). (There are two forms of monotremes, or egg-laying mammals: the echidnas and the platypus.)

I once got to play with an echidna named Francis at Harvard; it was being used for experiments on locomotion. Although it was too spiny to pet, it was furry underneath and very affectionate, with an amazing snout that was able to insinuate itself between my ring and my finger!

“zefrank 1” has a number of funny videos, including three about animals (all beginning with “true facts about. . “). We saw his clip on true facts about angler fish on January 2.

If you want to see that amazing penis (and you really should unless you’re squeamish about biology, which isn’t good for readers here): go see this video.

We’ll have more on animal genitalia, including Iceland’s amazing penis museum, later this week.

Paul Davies, chemistry, and the origin of life

January 14, 2013 • 6:50 am

How the unique properties of life originated from inert matter is still one of the great unsolved problems of biology. Creationists, of course, claim that our failure to solve it means that God did it: as Ingersoll noted in yesterday’s quote, “Our ignorance is God; what we know is science.”

And perhaps we’ll never know precisely how life began, for it happened in the distant past and involved chemical reactions that could not fossilize.  But I have confidence in three things: life originated naturally and not through God’s fiat; that we will show that this was possible within 50 years or so by demonstrating the evolution of life-like systems in the laboratory under primitive Earth conditions; and that while life may have originated more than once, all living species descended from only a single proto-organism (lots of evidence for that one). If we can demonstrate the origin of life in the lab through realistic experiments, then—although we may not know how it really happened several billion years ago—we can say that it could have happened naturally, and therefore we need not invoke God.

Paul Davies is an astrophysicist who spends a lot of time promoting the comity between science and faith, and who won the Templeton Prize in 1995. As Wikipedia notes:

An opinion piece published in the New York Times,[2] generated controversy over its exploration of the role of faith in scientific inquiry. Davies argued that the faith scientists have in the immutability of physical laws has origins in Christian theology, and that the claim that science is “free of faith” is “manifestly bogus.”[2] The Edge Foundation presented a criticism of Davies’ article written by Jerry Coyne, Nathan Myhrvold, Lawrence Krauss, Scott Atran, Sean Carroll, Jeremy Bernstein, PZ Myers, Lee Smolin, John Horgan, Alan Sokal and a response by Davies beginning I was dismayed at how many of my detractors completely misunderstood what I had written. Indeed, their responses bore the hallmarks of a superficial knee-jerk reaction to the sight of the words “science” and “faith” juxtaposed.[3] While atheists Richard Dawkins[4] and Victor J. Stenger[5] have criticised Davies’ public stance on science and religion, others including the John Templeton Foundation, have praised his work.

I’ve written about Davies’ accommodationism several times on this site; one example, in which he finds God in quantum mechanics, is here (see also his 2007 New York Times article asserting that science rests on faith.) But, to give him credit, Davies is also something of a polymath, and has an interest not just in physics, but in the early Ediacaran fauna and especially in the origin of life (“abiogenesis”). He’s apparently done technical work on the last issue, which I must confess I haven’t read (the literature on abiogenesis is huge). But in yesterday’s Guardian, Davies summarizes his work in a piece called “The secret of life won’t be cooked up in a chemistry lab.”

His basic claim is that science hasn’t solved the origin-of-life problem because it’s been left largely in the hands of chemists, and from-the-ground-up reductionist chemistry is not the way to solve it:

But a more fundamental obstacle stands in the way of attempts to cook up life in the chemistry lab. The language of chemistry simply does not mesh with that of biology. Chemistry is about substances and how they react, whereas biology appeals to concepts such as information and organisation. Informational narratives permeate biology. DNA is described as a genetic “database”, containing “instructions” on how to build an organism. The genetic “code” has to be “transcribed” and “translated” before it can act. And so on. If we cast the problem of life’s origin in computer jargon, attempts at chemical synthesis focus exclusively on the hardware – the chemical substrate of life – but ignore the software – the informational aspect. To explain how life began we need to understand how its unique management of information came about.

Well, he doesn’t mention that many biologists and biochemists have also worked on the problem, including Stanley Miller, Gerald Joyce, and Nobel Laureate Jack Szostak. But never mind. Davies goes on to say that the fundamental problem is not in the purview of chemistry, but in how biological information gets organized hierarchically:

Information theory has been extensively applied to biological systems at many levels from genomes to ecosystems, but rarely to the problem of how life actually began. Doing so opens up an entirely new perspective on the problem. Rather than the answer being buried in some baffling chemical transformation, the key to life’s origin lies instead with a transformation in the organisation of information flow.

Sara Walker, a Nasa astrobiologist working at Arizona State University, and I have proposed that the significant property of biological information is not its complexity, great though that may be, but the way it is organised hierarchically. In all physical systems there is a flow of information from the bottom upwards, in the sense that the components of a system serve to determine how the system as a whole behaves. Thus if a meteorologist wants to predict the weather, he may start with local information, such as temperature and air pressure, taken at various locations, and calculate how the weather system as a whole will move and change. In living organisms, this pattern of bottom-up information flow mingles with the inverse – top-down information flow – so that what happens at the local level can depend on the global environment, as well as vice versa.

. . . Walker and I propose that the key transition on the road to life occurred when top-down information flow first predominated. Based on simple mathematical models, we think it may have happened suddenly, analogously to a heated gas abruptly bursting into flame.

. . . The way life manages information involves a logical structure that differs fundamentally from mere complex chemistry. Therefore chemistry alone will not explain life’s origin, any more than a study of silicon, copper and plastic will explain how a computer can execute a program. Our work suggests that the answer will come from taking information seriously as a physical agency, with its own dynamics and causal relationships existing alongside those of the matter that embodies it – and that life’s origin can ultimately be explained by importing the language and concepts of biology into physics and chemistry, rather than the other way round.

Now I have to say that this is either way above my pay grade, is too abstruse for the general public, or is simply wrong. And I’ll take a chance here and say that the problem is not going to be solved using information theory or “top down” considerations. Yes, of course the environment played a role in the origin of life, but that doesn’t mean that we can’t take a reductionist approach. (As an example of “top down” control, Davies uses the fact that genes can be turned on by environmental factors, but of course that area of research progressed purely through reductionism, not through incorporating “environmental information theory.”)  To me, the problem of abiogenesis involves taking a set of original molecules that didn’t contain any information for a replicator, and then figure out what kind of processes enabled them to gain the ability to replicate. Along with that is the formidable problem of how the replicator became connected with a phenotype, in other words, how that replicator evolved to produce proteins and cells—and that is information.  All this can, I think, be attacked without any importation of “information theory” from the beginning. Information is a consequence of, rather than an a priori requirement for, understanding abiogenesis.

In fact I don’t know what Davies is suggesting here, and maybe his technical work has insights that are fruitful.  The Guardian article, though, is simply opaque, and there are hints from other work that Davies’ approach may not be fruitful.

One of these is a new book by chemist Addy Pross, What is Life? How Chemistry Becomes Biology. (The title, of course, is borrowed from Erwin Schrödinger’s famous book that had such a huge influence on the pioneers of molecular genetics.)

I have just received this book and have only glanced through it, but it’s a short volume describing the latest thought on the origin of life, and Pross’s own speculations on how it started. And it’s pure chemistry: no information theory needed. It does, in fact, what Davies says hasn’t been done: meshing the language of chemistry with that of biology.

I’m told by those who have read it that Pross has an intriguing and possibly correct idea about how a population of molecules can, through a process of biochemical natural selection, become replicators that get hitched to metabolism. The “information” of life then is a result of the process, not something that, as Davies asserts, needs be modeled in from the beginning. As Pross notes on p. 152:

A moment’s thought suggests therefore that the term “information” in its biological context is just “specific catalysis” when considered in a chemical context.

I’ll be reading this book in the next month or so, and will report back, but I wanted to say four things now:

1. If you’re interested in the origin of life, read Pross’s book. It’s written for the curious layperson, and is therefore perfectly suitable for the non-scientist readers of my site.
2. I suspect that Davis is wrong and that the reductionist approach, based on chemistry, is the way to solve the problem of life’s origin.
3. But I may be wrong, too, and somehow, in ways I don’t understand “top down information flow”—whatever that means—may be the key to the problem. But if the history of science is any guide, the problem will yield to chemists starting with a population of molecules existing under realistic early-Earth conditions.
4. The Guardian article is completely opaque to the nonscientific reader (indeed, to me as well), and seems more like p.r. for Davies’ work than a genuine attempt to explain to the layperson how life might have originated.

Picture 1

h/t: Michael

Quote of the day: Robert G. Ingersoll #5

January 13, 2013 • 1:13 pm

Here The Great Agnostic describes the ungodliness of natural selection. The excerpt, like others I’ve given, is from his 1872 essay “The Gods“, and once again, like Jesus, Ingersoll speaks in metaphor.

Would an infinitely wise, good and powerful God, intending to produce man, commence with the lowest possible forms of life; with the simplest organism that can be imagined, and during immeasurable periods of time, slowly and almost imperceptibly improve upon the rude beginning, until man was evolved? Would countless ages thus be wasted in the production of awkward forms, afterwards abandoned? Can the intelligence of man discover the least wisdom in covering the earth with crawling, creeping horrors, that live only upon the agonies and pangs of others? Can we see the propriety of so constructing the earth, that only an insignificant portion of its surface is capable of producing an intelligent man? Who can appreciate the mercy of so making the world that all animals devour animals; so that every mouth is a slaughter house, and every stomach a tomb? Is it possible to discover infinite intelligence and love in universal and eternal carnage?

What would we think of a father, who should give a farm to his children, and before giving them possession should plant upon it thousands of deadly shrubs and vines; should stock it with  ferocious beasts, and poisonous reptiles; should take pains to put a few swamps in the neighborhood to breed malaria; should so arrange matters, that the ground would occasionally open and swallow a few of his darlings, and besides all this, should establish a few volcanoes in the immediate vicinity, that might at any moment overwhelm his children with rivers of fire? Suppose that this father neglected to tell his children which of the plants were deadly; that the reptiles were poisonous; failed to say anything about the earthquakes, and kept the volcano business a profound secret; would we pronounce him angel or fiend?

And yet this is exactly what the orthodox God has done.

According to the theologians, God prepared this globe expressly for the habitation of his loved children, and yet he filled the forests with ferocious beasts; placed serpents in every path; stuffed the world with earthquakes, and adorned its surface with mountains of flame.

Notwithstanding all this, we are told that the world is perfect; that it was created by a perfect being, and is therefore necessarily perfect. The next moment, these same persons will tell us that the world was cursed; covered with brambles, thistles and thorns, and that man was doomed to disease and death, simply because our poor, dear mother ate an apple contrary to the command of an arbitrary God.