Why I am an atheist – Ed Cara

Much like any child with a loving mother, I was often lulled to sleep by her gentle and comforting voice as she read me a story. Unlike most mothers though, she rarely read from the newest selections of the public library, instead delighting me with tales of Samson, King David and of course Jesus Christ himself. I was a young Hispanic Catholic boy and she was smart enough to sprinkle the adventure-laden stories and parables in with the more philosophical readings to tug at my boyish tendencies. Not that she needed to trick me into belief in a God, Hispanic culture being one of the last enduring bastions of Catholicism. And being a 1st generation immigrant from Ecuador, for her belief was simply the default option.

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Creationist FUD refuted

If you’re looking for a meaty weekend read, look no further than Paul McBride’s thorough dismantling of Science and Human Origins, the new bad book from the Discovery Institute, by Gauger, Axe, and Luskin. It’s in 6 parts, taking on each chapter one by one: Part 1, Part 2, Part 3, a prediction about what will be in chapter 4 before reading it, Part 4 (prediction confirmed!), and Part 5.

The creationists are howling. McBride’s evisceration, with Carl Zimmer’s detailed description of the evidence for chromosome fusion, all discrediting what they thought would be a hot new text on the scientific evidence for creation, has made them so furious that they’re even lashing out at me in email — I just linked to the evidence, so I imagine Zimmer and McBride must be seeing some entertaining spectacles in their inboxes. I do so love to see the creationists dancing in the flames of their own immolation.

I will say this, though: I did get one very polite email from a creationist, who told me that he was not a scientist, but that he’d read a couple of articles that sounded impressively sciencey to him, and asked if they didn’t represent a legitimate criticism of the chromosome fusion idea? And he very nicely sent along the two papers for me to read. Here they are:

Bergman J, Tomkins J (2011) The chromosome 2 fusion model of human evolution—part 1: re-evaluating the evidence. Journal of Creation 25(2):106-110.

Tomkins J, Bergman J (2011) The chromosome 2 fusion model of human evolution—part 1: re-evaluating the evidence. Journal of Creation 25(2):111-117.

Two things jumped out at me: it’s by batty Jerry Bergman, no credible source at all, and it’s published in the inbred in-house journal of the Institute for Creation Research. These are not legitimate science papers, although they do throw around enough science terms and techniques, and follow the form of a real science paper, to generate confusion in the mind of the naive reader. They’re beautiful examples of cargo cult science by creationists. Would you like to read them, or use them as bad examples? Here you go, download it for entertainment purposes only.

I read them anyway. I’m not going to bother with a detailed refutation, but I’ll give you the gist. The fundamental confusion in both papers is the nature of the evidence for an ancestral chromosome fusion, and a focus on irrelevant details that are not central to the argument.

The story is this. At some time after the separation of the human and chimpanzee lineages, two ancestral chromosomes, #12 and #13 in the chimpanzee, fused end-to-end to form a single chromosome, #2, in humans. Chimpanzee chromosome 13 forms the short arm (2p) and part of the long arm (2q) of human chromosome 2, while chimpanzee chromosome 12 forms most of the long arm (2q) of chromosome 2.

The primary evidence for this fusion is the comparative genetic content of these chromosomes. That is, most of the genes in chimpanzee chromosome 13 are found in human 2p, and most of the genes in chimpanzee chromosome 12 are in human 2q. The chromatin binding patterns line up, the sequence analysis confirms, and there have been some lovely FISH studies that show the correspondence.

What has since been done is that a prediction was made that there ought to be fragments of telomeres (the end caps of chromosomes) in the middle of chromosome 2, at the fusion site. Which has been examined. And the prediction has been confirmed.

Bergman and Tomkins ignore every single bit of that. Instead, what they do is focus on just the region of the fusion, and complain that it is a tangled mess and hard to interpret — that it is a degenerate telomeric region, rather than a complete and intact telomere, which is what they demand be present. This is an unrealistic expectation, given that every paper on the structure of the fusion region makes the point that it is degenerate.

An analogy: imagine a red Ford Mustang and a blue BMW X6 are in a head-on collision, and both have totally wrecked front ends, with bumpers and radiators and headlights interlocked and everything about their grilles in tangled confusion, and with bits and pieces torn loose and flung about. You’d be able to look at the crash and still tell by everything in and behind the engine compartment that Car #1 was a Mustang and Car #2 was an X6.

Bergman and Tomkins are the bewildered and incompetent investigators who ignore every other factor in the crash, look at a few particularly mangled bits of the wreckage, and declare that they can’t identify it, therefore…the two vehicles were assembled at the factory in this particular configuration, and no crash occurred. But they use lots of sciencey language to explain this at tendentious length, which is sufficient to convince non-scientists that the interpretation of an obvious historical event has been refuted. And that’s all they need to do to accomplish their goals: fling about unfounded fear, uncertainty, and doubt to win over the ignorant.

Why I am an atheist – Don from Delaware

Why am I an atheist?  A year or two ago I had to find a concise answer to this question when my wife mentioned my atheism in passing at a family gathering.  I haven’t hidden my non-belief, but I haven’t invited trouble by going out of my way to bring it up, either.  My mother was in the room, though, and apparently she had never even suspected.  (Apparently my refusal to send the kids to church with her and the “Blessed are the Lesbians” speech she’s heard me launch into in the presence of a homophobe were not sufficient clues.)
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Forever disappointed

I always have unwarrantedly high expectations of creationists. I know that there are some flamingly ignorant nutjobs out there, all your Hams and Hovindses and Luskins, but lurking in my mind is always this suspicion that somewhere there has to be one or two biologically competent ideologues on their side of the fence. And I am always disappointed.

For example, there’s this one fellow, Douglas Axe, who has a legitimate and well-earned doctoral degree in chemical engineering, and several published papers in real science journals (not the fake journals creationists create). The Discovery Institute tapped him to head their Biologic Institute, their attempt to create an organization that would do genuine biological research (it hasn’t, so far). And I thought, hey, maybe this guy at last is a worthy opponent.

But let’s be honest here. I have no illusions that I’m a super-mega-genius, or that I have high standing as a researcher in my field. I’m a grunt in the army of biology, not an officer. So I can imagine someone smarter than me in opposition; I certainly know many on my side who are far more accomplished and intelligent than I am. So you can imagine my disappointment at looking over Axe’s ideas and seeing that he, too, is an incompetent twit.

I was really shocked when he revealed that he didn’t understand coalescence theory at all. It may be a bit esoteric for the lay public, but if you’re a critic of genomics and population genetics, you must at least comprehend the basics. And he doesn’t.

And now he lets me down again. The Biologic Institute is putting out some fresh horror of pseudoscience, a book called Science and Human Origins, in which they presumably bring all their scientific guns to bear in order to question human evolution. And what do they do? They question the evidence of a fusion of chromosome two, something I’ve hammered on Luskin before. And they bumble it up completely.

This stuff isn’t that hard. I’ve explained the basics of synteny, or conserved linkage blocks; fragments of chromosomes are constantly getting shuffled about, inverted, duplicated, and deleted, and we can compare chromosome structure between two species and see exactly how they’ve been juggled. These movements leave traces, and are mechanically well understood; we can see the evidence right therein the sequences.

So Carl Zimmer engaged the Biologic Institute ideologues on their facebook page. They denied that a fusion had occured, and claimed that the evidence was actually against such an event. So Zimmer hit them right where they’re weakest: he asked them to cite that evidence. And what did they do? You know it, it’s familiar. They went dumb and stopped answering. They couldn’t answer the basic question. And this is why I’m vaguely disappointed. Even their self-proclaimed science stars can’t explain something a small-town teaching professor in the Midwest can see laid out plainly in the data.

One benefit, though, is that Carl Zimmer summarized the whole affair in a must-read post. He explains step by step with simple cartoons every event that occurred in the chromosomal fusion, and what the molecular evidence for the phenomenon is. And he shows up the creationists for frauds who won’t address a simple question of sources.

For added hilarity, David Klinghoffer of Evolution News & Views, the DI’s dishonest propaganda organ, has challenged Carl to debate the issue. I don’t know what there is to debate; Gauger, Axe, and Luskin claim there is evidence against a chromosome fusion in human history, Carl asked what it was, and they refused to give it.

So he flatly turned them down, as was sensible to do. Debating creationists is a waste of time. Now that refusal is getting trolled by creationists, accusing him of being ‘afraid’ to debate…and I still don’t know what he’s supposed to argue about. Did the Discovery Institute refuse to cite any evidence supporting their claim? Yes. We’re done.

And my quest for an honest, scientifically competent creationist continues, fruitlessly.

Why I am an atheist – Dave H

When I was nine or ten I asked my Dad what caused the universe and he bought me Carl Sagan’s book Cosmos. It was a wonderful book that answered some questions and got me wondering about a whole lot more. Sagan conveyed the majesty of the real world(s), the world(s) we can observe, with such dazzling eloquence that I could not help but embark immediately on a lifelong journey of discovering the  secrets of the cosmos through the books, TV programmes, and (eventually) blogs of astronomers and cosmologists.  It was only natural that my interest should then extend to all of science (and so eventually lead me to Pharyngula).

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Are you an English major looking for work?

I know, you all are. But here’s a job opportunity for a godless, well organized editor.

Atheist Alliance International (AAI, atheistalliance.org) will be launching a new magazine in 2013 and we are looking for an Editor to plan and implement a fresh layout and format! AAI has gone through many changes in the last year or so – including its re-launch as a genuinely global organisation in 2011 and the adoption of new branding earlier this year. Now we are contemplating another major change and we want to find the right person to work with us to restructure and re-launch AAI’s flagship magazine.

This is a contract, self-managed position that involves securing content for each issue, cover design and management of advertising and production.

Secular World magazine is currently published quarterly and available to AAI Members only, but AAI would like to consider broadening publication options to a range of electronic media. Based on quarterly publication the Editor will be paid US$1,250 per issue plus a share of any advertising revenue secured by the Editor and a share of external sales revenue. AAI is willing to discuss the elements of the payment package with applicants.

Burzynski is still bilking dying children

And credulous newspapers are helping that quack. The latest case is a little girl in Ireland with a disfiguring and deadly rhabdomyosarcoma who is trying to raise money to get the useless and totally fraudulent Burzynski antineoplaston treatment … and this article makes the good point that newspapers are helping to defraud sick people. Both the Irish Times and the Irish Independent reported on the poor girl’s struggle, and they called the fake treatment “pioneering” or “advanced”.

Each uncritical article published about clinics like the Burzynski clinic amounts to free advertising for a treatment which is at best, as yet unproven, and at worst, much more damaging than it is claimed. Though articles about individual patients and families must tread a careful line between criticism of the clinic and the feelings of those involved, the current standard of reporting on these clinics ultimately helps no one. It’s time to stop hiding the controversy, and sweeping it under the carpet. Patients deserve information, not infomercials.

It’s a shame. If you google Burzynski, the first page is full of bullshit promoting the fake treatment — one thing his clinic is good at is SEO — but still, there’s quackwatch and Orac and Larry Moran buried in the muddle, pointing out that this is flaming quackery. You’d think a reasonably intelligent journalist would notice that there’s some controversy here. And even better, you’d expect a reasonably intelligent journalist to pick up a phone, call an oncologist, and ask what they thought of antineoplaston therapy.

But they don’t.

And Burzynski gets free advertising for his $200,000 urine treatments.

Why I am an atheist – Charles Gulledge

When this series first started, my answer to why I am an atheist was pretty simple: I read the Bible.  It’s a quick 2 second answer I can give any time.  And so I have, at least occasionally getting a laugh in return.  But after several weeks of reading others’ responses to the question, and reflecting on root causes, I’ve come to realize that my reasons are much more complex.  Ultimately, however, I’d have to say that I’m an atheist because of my father.

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A pox on all of their houses

I hate this article from the very first paragraph.

Public discussion of evolution often turns into a nasty debate between young-earth creationists on one side and atheists who believe science disproves the existence of God on the other. But it doesn’t have to be that way.

It’s a dishonest setup. It’s a game: let’s pretend that scientists only criticize young earth creationists, and then we’ll set up a bunch of Christian absurdity as the moderate position! Scientists never think of attacking the positions of reasonable Christians, you know.

It’s a lie. We criticize the follies of soft and fuzzy Christianity and old earth creationism all the time, as well as that young earth creationist nonsense. And do you know why we so often have to jump on young earth creationism?

Because the ‘moderate’ Christian jackasses won’t do it.

The article is an excellent example of that: it describes a discussion and joint publication of a book via Biologos between a diverse group of Christians, including young earth creationist Baptists, the Intelligent Design creationist Bill Dembski, and the gang of mushy apologists from Biologos…and how is their interaction described? As “gracious dialogue”. Please. If you’re going to sit there with a bugnutting freaky cultist with a literalist interpretation of every word of the Bible, and not be strongly critical of their freakin’ idiocy because you both believe in Jesus, then yes, I’m going to lump you all together.

Yes, it has to be that way. I see no point in regarding intellectual cowards with greater respect than I do the total fruitloops they associate with.

And further, it is no saving grace that the Biologos crowd can believe in an old earth, when at the same time they are arguing for the existence of a literal Adam and Eve, for the logic of salvation from original sin, for the blood pseudo-sacrifice of a god-man as somehow freeing me from guilt about a disobedient distant ancestor. It’s all garbage, through and through.

We get a succession of bullshit claims that we’re supposed to regard respectfully.

Keathley also points out that for some Christians, evolution presents a problem because it implies that suffering and death have been with the world from the beginning, rather than resulting from rebellion against God.

Right. Reality is a problem for some Christians. So?

“I think everybody recognizes this is an important topic and it’s not going to do any good to simply yell at each other across the fence,” he said. “They need to hear from us on the nature of Scripture, the nature of the fall and of salvation. And we need to hear from them on the nature of modern science.”

The only thing that makes it important is that it is a set of delusions held by powerful and influential people. Otherwise, the “nature of scripture”, the “fall”, and “salvation” are simply incredible and absurd concepts given weight by repetition and dogma.

I don’t just despise the blatant stupidity of young earth creationism. I also despise the equally blatant stupidity of Christian dogma and ‘sophisticated theology’.