Another tiresome apologist

Please, please, all you critics of the “New Atheism”: get some new arguments, or at least avoid the ones that are trivially ridiculed. Damon Linker is complaining about those darned New Atheists, prompted by the criticisms of Kevin Drum of a pretentious essay by David Hart (I also wrote a criticism of Hart; I’ve also criticized the dreary Mr Linker before).

Linker seems to be offended that Hart’s superficial and poor argument was rejected; he calls the essay “powerful” — I found it ridiculous — and also claims, to my surprise, that Hart was atempting to show that Christianity was true. We must have read two different essays, because what I saw was a lot of verbiage bitterly complaining about the New Atheists, singling out Dawkins and Hitchens in particular, and not one word in support of any particular faith. The whole essay was about belittling and ridiculing atheists, nothing more…which makes it particularly ironic that Linker then turns around and expresses his irritation at all those rude, ridiculing New Atheists.

Linker’s essay focuses primarily on two issues he has with the New Atheists. They confuse truth with goodness, thinking that we’ll achieve some kind of Utopian society by simply rejecting falsehood, and in a related point, we just aren’t sad enough about the death of god. How dare we be godless and glad of it!

What’s most disappointing is Drum’s failure to grasp the culminating point of Hart’s essay, which, as I take it, is this: the statements “godlessness is true” and “godlessness is good” are distinct propositions. And yet the new atheists invariably conflate them. But a different kind of atheism is possible, legitimate, and (in Hart’s view) more admirable. Let’s call it catastrophic atheism, in tribute to its first and greatest champion, Friedrich Nietzsche, who wrote in a head-spinning passage of the Genealogy of Morals that “unconditional, honest atheism is … the awe-inspiring catastrophe of two-thousand years of training in truthfulness that finally forbids itself the lie involved in belief in God.” For the catastrophic atheist, godlessness is both true and terrible.

Let’s deal with that first point first. Linker is wrong, and he’s eliding his own rather troubling implications about religion. We are saying godlessness is true, sure enough, but we aren’t making the leap he is claiming: we’re next saying that truth is good. Truth is a neccesary but not sufficient prerequisite for goodness. We obviously cannot say that godlessness inevitably leads to an ideal society — there are enough examples to show that is wrong — but that building a society on a false premise is even more disastrous.

Linker avoids that argument, because he knows it will require backing himself into a corner. I presume he doesn’t want to try to argue that truth is irrelevant to Christianity (but you never know…apologists can get very weird), but he also doesn’t even try to justify the validity of his religious beliefs — not when he can just gripe, gripe, gripe about atheists.

His second argument is even worse — it’s pathetic and goofy and wrong. He idolizes “Old Atheists”, what he calls “catastrophic atheists”, because they at least had the manners to grieve a little bit over abandoning the old superstitions. And from the fact that we’re forthright and enthusiastic about embracing secular ideals, he assumes that we must be unthinkingly optimistic.

The point is not that atheism must invariably terminate in a tragic view of the world; another of Hart’s atheistic heroes, David Hume, seems to have thought that it was perfectly possible to live a happy and decent life as a non-believer. Yet the new atheists seem steadfastly opposed even to entertaining the possibility that there might be any trade-offs involved in breaking from a theistic view of the world. Rather than explore the complex and daunting existential challenges involved in attempting to live a life without God, the new atheists rudely insist, usually without argument, that atheism is a glorious, unambiguous benefit to mankind both individually and collectively. There are no disappointments recorded in the pages of their books, no struggles or sense of loss. Are they absent because the authors inhabit an altogether different spiritual world than the catastrophic atheists? Or have they made a strategic choice to downplay the difficulties of godlessness on the perhaps reasonable assumption that in a country hungry for spiritual uplift the only atheism likely to make inroads is one that promises to provide just as much fulfillment as religion? Either way, the studied insouciance of the new atheists can come to seem almost comically superficial and unserious. (Exhibit A: Blogger P.Z. Myers, who takes this kind of thing to truly buffoonish lengths, viciously ridiculing anyone who dares express the slightest ambivalence about her atheism.)

(Awww, he noticed me.)

No, I have no sense of loss in giving up religion, so he’s right there. He seems to regard religion as we would cigarettes — a nasty habit, but one ought to at least have the common decency to suffer when giving them up, because he’s got that monkey on his back, and it’s not fair that others might not. But that’s no argument for keeping the habit, and it’s also fallacious because not everyone is as comfortable as I am.

Everyone has a different story about leaving faith behind. Some suffered greatly; they had this belief dunned into them from an early age, and it was all tangled up in threats of damnation and betrayal of family, and for many, it hurt painfully and even now, they may feel regrets and concerns.

But, you know, once you get past the fears, once you realize that it’s certainly no worse to be free of superstition than to be afflicted with it, and there’s a wonderful clarity once you sweep away those pointless old cobwebs of faith. I can’t go back to the delusions — truth is far more interesting. But Linker gets it all completely wrong.

So by all means, reject God. But please, let’s not pretend that the truth of godlessness necessarily implies its goodness. Because it doesn’t.

You tellin’ me? Of course it doesn’t! What we godless folk know is that the universe is a heartless place, almost entirely inimical to our existence, and that there is no guiding father figure with our best interests in mind who is shaping our destiny. There is no god. There is no absolute good. We’re free to struggle to make a better world for ourselves, with no illusion of an all-powerful superman to help us out.

Mr Linker has obviously confused us with the theists who do believe in an ultimate omnipotent goodness and a set of beliefs that will lead all the faithful in a path of righteousness that will culminate in paradise. It’s almost amusing how much projection there is in these people who despise atheists by accusing them of the sins of the godly.

Physiology explains it all

That Indian yogi who claims to never eat has a page on EsoWatch, the wiki of irrational belief systems, and it has some interesting content. Some of the actual medical data from observations of crazy yogi have been published — nothing as blatant as catching him in the act of eating, but the signs are all there. Sonograms showed urine in the bladder and feces in the colon that later disappeared, somehow. And the blood work taken by the credulous MD, Sudhir Shah, show changes symptomatic of starvation.

Some (if not all ?) blood parameter of the november 2003 examination are shown on the webpages of Sudhir Shah. The values presented show an increase in serum urea, and a drop three days after the examination. The same is true for serum sodium, serum chloride and serum potassium. The hematocrit is also increasing. This is a clear sign of dehydratation and hemoconcentration, compatible with a period of starvation and thirst. Blood sugar is decreasing, and serum acetone is increasing. This is also a sign of starvation. At the beginning and three days after the test, values are normal.

But, instead discussing such a starvation period (and not a long lasting esoteric inedia) as a very plausible source for the blood values shown, these are explained by neurologist Sudhir Shah to be amazing and to show a sort of medicine wonder. But in fact they show a normal behaviour of a subject, compatible with actual knowledge in physiology and bioenergetics. Examinator Shahs words sound different: “We have reached a hypothesis which confirms that Jani’s body has certainly undergone a biological transformation due to yogic kriyas. And he can control his inner organs’ functions, which itself is intriguing.”

No, it’s not. It’s obvious. I can change my “inner organs’ functions”, too, just by fasting for a day or strolling down to Dairy Queen and pigging out on fats and sugars. It isn’t magic, it’s physiology.

It is rather appalling that this doctor can’t tell the difference, though.

Another volley in the battle

This essay on the accommodationists vs. the ‘new atheists’ gets off to a bad start, I’m afraid, and I had some concern it was going to be another of those fuzzy articles.

There is a new war between science and religion, rising from the ashes of the old one, which ended with the defeat of the anti-evolution forces in the 2005 “intelligent design” trial.

That’s incorrect. The anti-evolutionists have not been defeated — they got smacked in the nose with a rolled-up newspaper, and that’s about it. The creationists are still thriving, and in some places (like Texas) getting even bolder and noisier.

It gets better from there, though. It’s a polite framing of the arguments between the apologists for religion and the opponents of religion, and the author favors the latter.

Neandertal!

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You don’t have to tell me, I know I’m late to the party: the news about the draft Neandertal genome sequence was announced last week, and here I am getting around to it just now. In my defense, I did hastily rewrite one of my presentation to include a long section on the new genome information, so at least I was talking about it to a few people. Besides, there is coverage from a genuine expert on Neandertals, John Hawks, and of course Carl Zimmer wrote an excellent summary. All I’m going to do now is fuss over a few things on the edge that interested me.

This was an impressive technical feat. The DNA was extracted from a few bone fragments, and it was grossly degraded: the average size of a piece of DNA was less than 200 base pairs, much of that was chemically degraded, and 95-99% of the DNA extracted was from bacteria, not Neandertal. An immense amount of work was required to filter noise from the signal, to reconstruct and reassemble, and to avoid contamination from modern human DNA. These poor Neandertals had died, had rotted thoroughly, and the bacteria had worked their way into almost every crevice of the bone to chew up the remains. All that was left were a few dead cells in isolated lacunae of the bone; their DNA had been chopped up by their own enzymes, and death and chemistry had come to slowly break them down further.

Don’t hold your breath waiting for the draft genome of Homo erectus. Time is unkind.

We have to appreciate the age of these people, too. The oldest Neandertal fossils are approximately 400,000 years old, and the species went extinct about 30,000 years ago. That’s a good run; as measured by species longevity, Homo sapiens neandertalensis is more successful than Homo sapiens sapiens. We’re going to have to hang in there for another 200,000 years to top them.

The samples taken were from bones found in a cave in Vindija, Croatia. Full sequences were derived from these three individuals, and in addition, some partial sequences were taken from other specimens, including the original type specimen found in the Neander Valley in 1856.

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Samples and sites from which DNA was retrieved. (A) The three bones from Vindija from which Neandertal DNA was sequenced. (B) Map showing the four archaeological sites from which bones were used and their approximate dates (years B.P.).

The three bones used for sequencing were directly dated to 38.1, 44.5, and 44.5 thousand years ago, which puts them on the near end of the Neandertal timeline, and after the likely time of contact between modern humans and Neandertals, which probably occurred about 80,000 years ago, in the Middle East.

Just for reference: these samples are 6-7 times older than the entire earth, as dated by young earth creationists. The span of time just between the youngest and oldest bones used is more than six thousand years old, again, about the same length of time as the YEC universe. Imagine that: we see these bone fragments now as part of a jumble of debris from one site, but they represent differences as great as those between a modern American and an ancient Sumerian. I repeat once again: the religious imagination is paltry and petty compared to the awesome reality.

A significant revelation from this work is the discovery of the signature of interbreeding between modern humans and Neandertals. When those humans first wandered out of the homeland of Africa into the Middle East, they encountered Neandertals already occupying the land…people they would eventually displace, but at least early on there was some sexual activity going on between the two groups, and a small number of human-Neandertal hybrids would have been incorporated into the expanding human population—at least, in that subset that was leaving Africa. Modern European, Asian, and South Pacific populations now contain 1-4% Neandertal DNA. This is really cool; I’m proud to think that I had as a many-times-great grandparent a muscular, beetle-browed big game hunter who trod Ice Age Europe, bringing down mighty mammoths with his spears.

However, it is a small contribution from the Neandertals to our lineage, and it’s not likely that these particular Neandertal genes made a particularly dramatic effect on our ancestors. They didn’t exactly sweep rapidly and decisively through the population; it’s most likely that they are neutral hitch-hikers that surfed the wave of human expansion. Any early matings between an expanding human subpopulation and a receding Neandertal population would have left a few traces in our gene pool that would have been passively hauled up into higher numbers by time and the mere growth of human populations. In a complementary fashion, any human genes injected into the Neandertal pool would have been placed into the bleeding edge of a receding population, and would not have persevered. No uniquely human genes were found in the Neandertals examined, but we can’t judge the preferred direction of the sexual exchanges in these encounters, though, because any hybrids in Neandertal tribes were facing early doom, while hybrids in human tribes were in for a long ride.

Here’s the interesting part of these gene exchanges, though. We can now estimate the ancestral gene sequence, that is, the sequences of genes in the last common ancestor of humans and Neandertals, and we can ask if there are any ‘primitive’ genes that have been completely replaced in modern human populations by a different variant, but Neandertal still retained the ancestral pattern (see the red star in the diagram below). These genes could be a hint to what innovations made us uniquely human and different from Neandertals.

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Selective sweep screen. Schematic illustration of the rationale for the selective sweep screen. For many regions of the genome, the variation within current humans 0 is old enough to include Neandertals (left). Thus, for SNPs in present-day humans, Neandertals often carry the derived -1 allele (blue). However, in genomic regions where an advantageous mutation arises (right, red star) and sweeps to high frequency or fixation in present-day humans, Neandertals will be devoid of derived alleles.

There’s good news and bad news. The bad news is that there aren’t very many of them: a grand total of 78 genes were identified that have a novel form and that have been fixed in the modern human population. That’s not very many, so if you’re an exceptionalist looking for justification of your superiority to our ancestors, you haven’t got much to go on. The good news, though, is that there are only 78 genes! This is a manageable number, and represent some useful hints to genes that would be worth studying in more detail.

One other qualification, though: these are 78 genes that have changes in their coding sequence. There are also several hundred other non-coding, presumably regulatory, sequences that are unique to humans and are fixed throughout our population. To the evo-devo mind, these might actually be the more interesting changes, eventually…but right now, there are some tantalizing prospects in the coding genes to look at.

Some of the genes with novel sequences in humans are DYRK1A, a gene that is present in three copies in Down syndrome individuals and is suspected of playing a role in their mental deficits; NRG3, a gene associated with schizophrenia, and CADPS2 and AUTS2, two genes associated with autism. These are exciting prospects for further study because they have alleles unique and universal to humans and not Neandertals, and also affect the functioning of the brain. However, let’s not get confused about what that means for Neandertals. These are genes that, when broken or modified in modern humans, have consequences on the brain. Neandertals had these same genes, but different forms or alleles of them, which are also different from the mutant forms that cause problems in modern humans. Neandertals did not necessarily have autism, schizophrenia, or the minds of people with Down syndrome! The diseases are just indications that these genes are involved in the nervous system, and the differences in the Neandertal forms almost certainly caused much more subtle effects.

Another gene that has some provocative potential is RUNX2. That’s short for Runt-related transcription factor 2, which should make all the developmental biologists sit up and pay attention. It’s a transcription factor, so it’s a regulator of many other genes, and it’s related to Runt, a well known gene in flies that is important in segmentation. In humans, RUNX2 is a regulator of bone growth, and is a master control switch for patterning bone. In modern humans, defects in this gene lead to a syndrome called cleidocranial dysplasia, in which bones of the skull fuse late, leading to anomalies in the shape of the head, and also causes characteristic defects in the shape of the collar bones and shoulder articulations. These, again, are places where Neandertal and modern humans differ significantly in morphology (and again, Neandertals did not have cleidocranial dysplasia — they had forms of the RUNX2 gene that would have contributed to the specific arrangements of their healthy, normal anatomy).

These are tantalizing hints to how human/Neandertal differences could have arisen—by small changes in a few genes that would have had a fairly extensive scope of effect. Don’t view the many subtle differences between the two as each a consequence of a specific genetic change; a variation in a gene like RUNX2 can lead to coordinated, integrated changes to multiple aspects of the phenotype, in this case, affecting the shape of the skull, the chest, and the shoulders.

This is a marvelous insight into our history, and represents some powerful knowledge we can bring to bear on our understanding of human evolution. The only frustrating thing is that this amazing work has been done in a species on which we can’t, for ethical reasons, do the obvious experiments of creating artificial revertants of sets of genes to the ancestral state — we don’t get to resurrect a Neandertal. With the tools that Pääbo and colleagues have developed, though, perhaps we can start considering some paleogenomics projects to get not just the genomic sequences of modern forms, but of their ancestors as well. I’d like to see the genomic differences between elephants and mastodons, and tigers and sabre-toothed cats…and maybe someday we can think about rebuilding a few extinct species.

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PL, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. (2010) A draft sequence of the Neandertal genome. Science 328(5979):710-22.

Andrew Wakefield and the great autism fraud

If any one person is responsible for the current anti-vaccination hysteria, it’s Andrew Wakefield, the surgeon who cobbled up a very bad study of vaccination and autism. For a good overview, read this summary of a talk by Brian Deer, a reporter who also has a very thorough summary of the Wakefield affair. It’s amazing how sloppy the work was, and how lavishly Wakefield was paid for perpetrating it. I guess it’s easy and lucrative to carry out medical fraud, as long as your conscience will let you overlook the little matter of dead children.

Alabama suffers some more

The other day, I posted about the smear campaign in Alabama against Bradley Byrne, which tried to impugn the man by saying, “Byrne supported teaching evolution…said the Bible was only partially true”. Byrne won a speck of sympathy from me, despite the fact that he’s a Republican, for at least standing up for the evidence.

That sympathy is gone now. Byrne has come back with a rebuttal.

• I believe the Bible is the Word of God and that every single word of it is true. From the earliest parts of this campaign, a paraphrased and incomplete parsing of my words have been knowingly used to insinuate that I believe something different than that. My faith is at the center of my life and my belief in Jesus Christ as my personal savior and Lord guides my every action.

• As a Christian and as a public servant, I have never wavered in my belief that this world and everything in it is a masterpiece created by the hands of God. As a member of the Alabama Board of Education, the record clearly shows that I fought to ensure the teaching of creationism in our school text books. Those who attack me have distorted, twisted and misrepresented my comments and are spewing utter lies to the people of this state.

Well, screw you, too, you rednecked ignorant yokel. It’s a real shame that the people of Alabama are being served by fools and pandering morons. Now the Alabamans know who to vote against, I just hope there’s somebody sensible left in the field to vote for.

What a waste of a fine May day

The wingnuts had a party in DC! It was called May Day: A Cry to God for a Nation in Distress, and consisted of a small mob of prayerful crazies listening to people at the microphone beg God to force Hollywood to make more movies like Gibson’s Passion, and by the way, make sure that hussy Dakota Fanning isn’t in them. It’s an odd way to help a nation in distress, by asking for more torture porn.

Alas, a Minnesotan was also there, and she embarrassed us with this little speech:

And father, we repent that we have not used godly wisdom when we have elected officials into elected positions in our state and nation, father, and that it has opened the door, that Minnesota holds the responsibility for placing the first Muslim in Congress, and Father, for that we repent.

It’s true. Not only did Minnesota elect Michele Bachmann, but we also elected Keith Ellison. Unlike Bachmann, though, Ellison seems to be more interested in getting his secular job done in Washington, and doesn’t wave his religion like a bloody flag.

Maybe Crazy Minnesota Lady should have asked forgiveness for electing an incompetent right wing loon to office, instead.

Violence is not free speech

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Lars Vilks, the cartoonist who drew Mohammed as a dog, has been attacked while lecturing on free speech. He was not seriously harmed. There is a video clip showing the attack, the chanting spectators, and the police quelling the mob.

That’s ugly. Muslims everywhere should be embarrassed, and should be repudiating the behavior of those thugs. Peaceful protest is one thing, but there is no offense in a cartoon that justifies leaping up and punching someone.

Here’s something even uglier:

An al-Qaeda front organisation then offered $US100,000 ($A110,730) to anyone who murdered Vilks – with an extra $US50,000 ($A55,365) if his throat was slit – and $US50,000 ($A55,365) for the death of Nerikes Allehanda editor-in-chief Ulf Johansson.

I think it’s only appropriate that Vilks’ sketch of Mohammed as a mangy cur should receive wider circulation because of the vileness of their response.