Good work by CFI Vancouver Skeptics

Deepak Chopra visited Vancouver, BC…and CFI was prepared with flyers and volunteers handing them out to people going to the talk. It’s an excellent example of how to effectively and informatively deal with pseudoscientific nonsense. Oh, and they actually had Chopra come out and talk with them, although it sounds like he didn’t say much of substance. But then, he never does.

One thing I’d like to see, though, is that they make copies of their flyers available on the web. Chopra isn’t going to vanish, and having more material that other groups can use when engaging wacky quantum woo artists would be useful.

The Catholic Church: Master of Public Relations

Sadly for them, someone told them it meant relations in public.

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It’s hard to believe that no one at the magazine looked at that cover and noticed that it might have some unfortunate associations, especially given recent church history. Either they are extraordinarily naive, rather stupid, or somebody on the inside was engaging in a little media sabotage.


It’s a conspiracy. I was sent another magazine cover.

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Yeah, the Catholic church is full of mass debaters.

The junk just grows

I keep telling people there’s junk in them thar genomes, and lots of it. ERV has a nice summary of some recent work in which a detailed comparison of the distribution of LINE retrotransposons (selfish DNA that does nothing but insert copies of itself into your DNA; they make up about 20% of your genome) was made — and what they found was that variations were common, new insertions were relatively frequent, and that they can be used to map out human relatedness (although we’ve known that one for a while).

  • LINEs are super useful for determining/tracing human ancestry. As Im sure you all have heard me mention before, new bits of junk that arent ‘supposed’ to be there make excellent connect-the-dots pictures for ancestry (this isnt new, but its still neat).

  • Any two people had ~285 differences in human-specific LINEs (148 minimum, 422 maximum). I have some you dont have, you have some I dont have.

  • They did not check to see whether these LINEs were homozygous (in both copies of your genome). There is probably even more diversity here– I have some LINEs you dont have, but some of them are just on one of my two copies of DNA in each cell. Since we only pass on one copy of our DNA to our offspring, this has an effect on how fast/whether new LINEs are fixed in a population or not. Genetic drift, w00t!

  • The older the LINE, the more likely we all have it in common (we are all related!).

  • Brand spanking new LINEs pop up in ~1/140 births. So, of the ~6 billion people alive today, there are ~30 million new LINEs between us all. If all of these junk LINEs are precious and specially created by Teh Designer, all of us without the new sacred LINEs should be dead. We aint. So…

Cool stuff. There’s a lot of churning over of these things, which is one indication that they’re non-essential junk.

More creationist misconceptions about the eye

Jonathan Sarfati, a particularly silly creationist, is quite thrilled — he’s crowing about how he has caught Richard Dawkins in a fundamental error. The eye did not evolve, says Sarfati, because it is perfectly designed for its function, and Dawkins’ suggestion that there might be something imperfect about it is wrong, wrong, wrong. He quotes Dawkins on the eye.

But I haven’t mentioned the most glaring example of imperfection in the optics. The retina is back to front.

Imagine a latter-day Helmholtz presented by an engineer with a digital camera, with its screen of tiny photocells, set up to capture images projected directly on to the surface of the screen. That makes good sense, and obviously each photocell has a wire connecting it to a computing device of some kind where images are collated. Makes sense again. Helmholtz wouldn’t send it back.

But now, suppose I tell you that the eye’s ‘photocells’ are pointing backwards, away from the scene being looked at. The ‘wires’ connecting the photocells to the brain run over all the surface of the retina, so the light rays have to pass through a carpet of massed wires before they hit the photocells. That doesn’t make sense…

What Dawkins wrote is quite correct, and nowhere in his refutation does Sarfati show that he is wrong. Instead, Sarfati bumbles about to argue against an argument that no biologist makes, that the eye is a poor instrument for detecting patterns of light. The argument is never that eyes do their job poorly; it’s that they do their job well, by a peculiar pattern of kludgy patches to increase functionality that bear all the hallmarks of a long accumulation of refinements. Sarfati is actually supporting the evolutionary story by summarizing a long collection of compromises and odd fixes to improve the functionality of the eye.

There’s a fundamental question here: why does the vertebrate eye have its receptors facing backwards in the first place? It is not the best arrangement optically; Sarfati is stretching the facts to claim that God designed it that way because it was superior. It ain’t. The reason lies in the way our eye is formed, as an outpocketing of the cortex of the brain. It retains the layered structure of the cortex, even; it’s the way it is because of how it was assembled, not because its origins are rooted in optical optimality. You might argue that it’s based on a developmental optimum, that this was the easiest, simplest way to turn a light-sensitive patch into a cup-shaped retina.

Evolution has subsequently shaped this patch of tissue for better acuity and sensitivity in certain lineages. That, as I said, is a product of compromises, not pre-planned design. Sarfati brings up a series of odd tweaks that make my case for me.

  1. The vertebrate photoreceptors are nourished and protected by an opaque layer called the retinal pigmented epithelium (RPE). Obviously, you couldn’t put the RPE in front of the visual receptors, so the retina had to be reversed to allow it to work. This is a beautiful example of compromise: physiology is improved at the expense of optical clarity. This is exactly what the biologists have been saying! Vertebrates have made a trade-off of better nutrient supplies to the retina for a slight loss of optical clarity.

  2. Sarfati makes the completely nonsensical claim that the presence of blood vessels, cells, etc. in the light path do not compromise vision at all because resolution is limited by diffraction at the pupil, so “improvements of the retina would make no difference to the eye’s performance”. This is clearly not true. The fovea of the vertebrate eye represents an optimization of a small spot on the retina for better optical properties vs. poorer circulation: blood vessels are excluded from the fovea, which also has a greater density of photoreceptors. Obviously, improvements to the retina do make a difference.

    It’s also not a condition that is universal in all vertebrates. Most birds, for instance, do not have a vascularized retina — there is no snaky pattern of blood vessels wending their way across the photoreceptors. Birds do have greater acuity than we do, as well. What birds have instead is a strange structure inside their eye called the pecten oculi, which looks kind of like an old steam radiator dangling into the vitreous humor, which seems to be a metabolic specialization to secrete oxygen and nutrients into the vitreous to supply by diffusion the retina.

  3. Sarfati also plays rhetorical games. This is a subtly dishonest argument:

    In fact, cephalopods don’t see as well as humans, e.g. no colour vision, and the octopus eye structure is totally different and much simpler. It’s more like ‘a compound eye with a single lens’.

    First, there’s a stereotype he’s playing to: he’s trying to set up a hierarchy of superior vision, and he wants our god-designed eyes at the top, so he tells us that most cephalopods have poorer vision than we do. He doesn’t bother to mention that humans don’t have particularly good vision ourselves; birds have better eyes. So, is God avian?

    That business about the cephalopod being like a compound eye is BS; if it’s got a single lens, it isn’t a compound eye, now is it? It’s also again pandering to a bias that our eyes must be better than mere compound eyes, since bugs and other lowly vermin have those. Cephalopods have rhabdomeric eyes, meaning that their photoreceptors have a particular structure and use a particular set of biomolecules in signal transduction, but that does not in any way imply that they are inferior. In fact, they have some superior properties: the cephalopod retina is tightly organized and patterned, with individual rhabdomeres ganged together into units called rhabdomes that work together to process light. Their ordered structure means that cephalopods can detect the polarity of light, something we can’t do at all. This is a different kind of complexity, not a lesser one. They can’t see color, which is true, but we can’t sense the plane of polarity of light in our environment.

    I must also note that the functions of acting as a light guide (more below) and using pigment to shield photoreceptors are also present in the cephalopod eye…only by shifting pigments in supporting cells that surround the rhabdome, rather than in a solid RPE. Same functions, different solutions, the cephalopod has merely stumbled across a solution that does not simultaneously impede the passage of light.

    Color vision, by the way, is a red herring here. Color is another compromise that has nothing to do with the optical properties of the arrangement of the retina, but is instead a consequence of biochemical properties of the photoreceptors and deeper processing in the brain. If anything, color vision reduces resolution (because individual photoreceptors are tuned to different wavelengths) and always reduces sensitivity (you don’t use color receptors at night, you may have noticed, relying instead on rods that are far less specific about wavelength). But if he insists, many teleosts have a greater diversity of photopigments and can see colors we can’t even imagine…so humans are once again also-rans in the color vision department.

  4. Sarfati is much taken with the discovery that some of the glial cells of the eye, the Müller cells, act as light guides to help pipe light through the tangle of retinal processing cells direct to the photoreceptors. This is a wonderful innovation, and it is entirely true that in principle this could improve the sensitivity of the photoreceptors. But again, this would not perturb any biologist at all — this is what we expect from evolution, the addition of new features to overcome shortcomings of original organization. If we had a camera that clumsily had the non-optical parts interposed between the lens and the light sensor, we might be impressed with the blind, clumsy intricacy of a solution that involved using an array of fiber optics to shunt light around the opaque junk, but it wouldn’t suggest that the original design was particularly good. It would indicate short-term, problem-by-problem debugging rather than clean long-term planning.

  5. Sarfati cannot comprehend why the blind spot would be a sign of poor design, either. He repeats himself: why, it’s because the eye needs a blood supply. Yes, it does, and the solution implemented in our eyes is one that compromises resolution. I will again point out that the cephalopod retina also needs a blood supply, and they have a much more elegant solution; the avian eye also needs a blood supply, but is not invested with blood vessels. He gets very circular here. The argument is not that the vertebrate eye lacks a solution to this problem, but that there are many different ways to solve the problem of organizing the retina with its multiple demands, and that the vertebrate eye was clearly not made by assembling the very best solutions.

Sarfati really needs to crawl out of his little sealed box of creationist dogma and discover what scientists actually say about these matters, and not impose his bizarre creationist interpretations on the words of people like Dawkins and Miller. What any comparative biologist can see by looking at eyes across multiple taxa is that they all work well enough for their particular functions, but they all also have clear signs of assembly by a historical process, like evolution and quite unlike creation, and that there is also evidence of shortcomings that have acquired workarounds, some of which are wonderfully and surprisingly useful. What we don’t see are signs that the best solutions from each clade have been extracted and placed together in one creature at the pinnacle of creation. And in particular — and this has to be particularly grating to the Genesis-worshipping creationists of Sarfati’s ilk, since he studiously avoids the issue — Homo sapiens is not standing alone at that pinnacle of visual excellence. We’re kinda straggling partway down the peak, trying to compensate for some relics of our ancestry, like the fact that we’re descended from nocturnal mammals that let the refinement of their vision slide for a hundred million years or thereabouts, while the birds kept on optimizing for daylight acuity and sensitivity.

The wisdom of crowds is sometimes the prejudice of the majority

The folks over at the Urban Dictionary have battened upon the word “atheist”, and much hilarity follows. There is one reasonable definition in the bunch, and the rest are mostly indignant complaints by theists.

A worshipper of the self or the god of science, often unknowingly religious.

An atheist can speak of moral relativism, but not live it.

A person who denies the reality of God (particularly Jesus Christ, despite historical proof of His otherworldly being), and lives life ‘free’ trusting in science and ‘logic’. This despite the fact that may be able to point out when and how the universe was created, but are unable to state WHY. Stephen Hawking himself made this point. Despite so much being unknown about what reality actually is, how it came into being, how colours, morality, love, the fabric of space and time ‘happened’, they consider themselves smarter than any faith bearing person, and pretty much anyone else they happen across. God loves atheists. Despite what they make think. Ironically, they are usually more militant about their lack of belief than faith bearing people are about their faith.

Stevie the atheist: "There is no God"

John the Faith-nut: "How did the universe happen?"

Stevie- "The big bang you idiot!"

John- "What caused that to happen?"

Stevie- "Pressure…eh…gasses…eh…"

John- "What caused the ‘pressure’ and ‘gasses’ to exist?

Stevie- "Eh…eh…"

John- "In fact, what caused existence to exist?"

Stevie-"Eh…eh…Darwin said that…"

John- "Who designed the tongue, instrument of Darwin’s speech?"

This goes on for awhile. Atheists have nothing and no faith.

Until they’re on their death bed.

The Urban Dictionary might be a useful site for looking up current slang, but established terms with clear meanings…not so much.

Scientists making creationists cry

The Discovery Institute is getting so politely eviscerated by a couple of people right now — you ought to savor the destruction.

Richard Sternberg, the wanna-be martyr of the Smithsonian Institution, made a stupid mathematical mistake in explaining alternatively splicing, and then, after it was explained to him, did it a second time, revealing that it wasn’t just an unfortunate slip, but a complete failure to grasp the basic concept. Even that wouldn’t be so bad, except that Sternberg has been yammering away about how alternative splicing represents a serious problem for evolution.

Steve Matheson continues his deconstruction of the DI’s poor performance in a recent debate. The creationists are constantly cheesed off about the whole idea of junk DNA, that there are great stretches of sequence that have no specific functional role, and seize upon every little example of non-coding DNA shown to have an effect on the phenotype to claim that all of it does. They don’t understand junk DNA. Again, it’s embarrassing that they even strain at this topic when they are so clueless.

My objection to Meyer’s references to introns and “junk DNA” is more than just a quibble about the molecular biology of introns. I’ve explained before why I find the whole “junk DNA” mantra to be utterly duplicitous, and I referenced my previous writing in the critique of Meyer. The basic story told by DI propagandists and other creationists is that non-coding DNA was ignored for decades, during which it was thought to be completely functionless (due to “Darwinist” ideas), only to be dramatically revealed as centrally important to life. That story is false. The real story is more interesting and complex (of course) and has been explained in detail several times.

Really, T. Ryan Gregory’s short and sweet post on the history of the concept is essential reading. If only the ID creationists would read it…

And finally, Matheson has a far too charitable letter to Stephen Meyer. He assumes that Meyer is a smart guy, honestly interested in science, who has gotten sucked into the inbred and self-deluding folly of creationism, urging him to get out and talk to actual scientists, where he’d learn what they really think, rather than these fallacious myths creationists tell themselves. It’s a nice idea, but I think the premise is incorrect. Meyer is a creationist first, who has been trying to learn little bits of science that he can use to rationalize his preconceptions.

It’s still a very nice letter, though, and a scathing denunciation of the Discovery Institute. They’ll ignore it, I’m sure, except to move Matheson a few notches higher on their list of enemies.