Author Archive for PharyngulaPage 4 of 41

Mary’s Monday Metazoan: The pressure to perform

My wife sent me this photo, and was intrigued. The water boatman sings through its penis, and sings very loudly — 105 decibels from an animal that's only a few millimeters long (no word on the length of its penis). I have received subtle signals that I am…inadequate. Does anyone have any suggestions? Should I get an implant of one of those mini-iPods? Or perhaps even an iPod Touch?

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(via National Geographic)

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How good is American health care?

A study in the Journal of the Royal Society of medicine has assessed the effectiveness of health care in 19 western countries and come up with a simple ranking system: a measure of the the number of lives saved relative to expenditures proportional to the GDP. One parameter, called the GDPHE, or GDP Health Expenditure was a measure of how much money the country was sinking into health care per citizen; by dividing this by the mortality rates, they got a measure of the effectiveness of the health care system.

This is a ranking system, and I have mostly a hyper-competitive American audience, so you all want to know whether you win or not, right? You want the data that shows that the US is #1! And here it is, the one result that shows us at the top of the ladder, our average health care as a function of GDP.

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Look at that: we don't just win, we win big, leaving our closest competitor, Germany, in the dust. We spend 125% of the money Germany does per person. Does it feel good, America? We are tossing bigger buckets of money into health care than anyone else.

But now for the number that really matters, the GDPHE ratio. How many lives are we saving with all that money? Here's the answer. Look at the last column, which is the ratio of money spent to lives saved.

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Oops. We're…#17. We're almost the worst — thanks, Portugal and Switzerland, for neglecting the medical needs of your citizenry more than we do.

Our health care is miserably inefficient, and we pour extravagant sums of cash into it, but you might ask whether it works at all. And the answer is a bit of good news, yes, it does. This study also compared death rates over time and came to the conclusion that, in the US, more than half a million people are alive today who would not have been with the medical care we offered 25 years ago. Medicine in the US is good, it's just far more economically wasteful than it ought to be.

I'm still thinking I ought to retire to Ireland.

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Live by the science, die by the science

This is a wonderful video debunking the Kalam Cosmological Argument. What I really like about it is that it takes the tortured rationales of theologians like William Lane Craig, who love to babble mangled pseudoscience in their arguments, and shows with direct quotes from the physicists referenced that the Christian and Muslim apologists are full of crap.

(via Skepchick.)

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Happy birthday, Randi!

Hey, look, James Randi has seen an integral number of orbits around the sun! Everyone congratulate him today.

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Also note that I actually have a t-shirt with his face on it.

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Anti-matter! In space!

Science fiction dreams may come true: a small, thin band of stable anti-matter has been discovered near Earth. It was predicted theoretically, but now emissions from the annihilation of these particles has been observed.

The existence of a significant flux of antiprotons confined to Earth's magnetosphere has been considered in several theoretical works. These antiparticles are produced in nuclear interactions of energetic cosmic rays with the terrestrial atmosphere and accumulate in the geomagnetic field at altitudes of several hundred kilometers. A contribution from the decay of albedo antineutrons has been hypothesized in analogy to proton production by neutron decay, which constitutes the main source of trapped protons at energies above some tens of MeV. This Letter reports the discovery of an antiproton radiation belt around the Earth. The trapped antiproton energy spectrum in the South Atlantic Anomaly (SAA) region has been measured by the PAMELA experiment for the kinetic energy range 60-750 MeV. A measurement of the atmospheric sub-cutoff antiproton spectrum outside the radiation belts is also reported. PAMELA data show that the magnetospheric antiproton flux in the SAA exceeds the cosmic-ray antiproton flux by three orders of magnitude at the present solar minimum, and exceeds the sub-cutoff antiproton flux outside radiation belts by four orders of magnitude, constituting the most abundant source of antiprotons near the Earth.

I had to laugh my cynical, evil laugh at the BBC report on this discovery, though.

The team says a small number of antiprotons lie between the Van Allen belts of trapped "normal" matter.

The researchers say there may be enough to implement a scheme using antimatter to fuel future spacecraft.

Bwahahahahaha! Space travel? Foolish, optimistic journalists. You know the first use of these things, once the means to harvest and maintain them is found, will be anti-matter bombs.

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How am I going to fit an MRI in the bedroom?

Maybe you've seen this before: it's a diagram of the sensory and motor cortex of the brain, with a little man or homunculus drawn over it to illustrate the somatic areas associated with each region. You see where the little man's knee is on the left image of the sensory cortex? Stick an electrode in there and zap it, and a patient/victim will feel a sensation in his knee. Put the patient in an MRI and tickle his knee, and that region of the brain will light up. Cool, huh?

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Another cute feature: look in the medial longitudinal fissure. You see the homunculus's toes, and right down there, located beyond the toes, is where the genital sensory area is located. Poke at that with an electrode and…we're talking happy time at the Mad Scientists' convention. But notice, though, that in the diagram of the homunculus, the poor creature's genitals are drawn, and they're male. It's a bit sexist, don't you think?

This bias has now been corrected.

a team led by Lars Michels at University Children's Hospital in Zurich, Switzerland, used functional magnetic resonance imaging to confirm that the position of the clitoris on the homunculus was in approximately the same position as the penis in men. Barry Komisaruk at Rutgers University in Newark, New Jersey, and his colleagues have now used the same method to map the position of the clitoris, vagina and cervix on the sensory cortex as women stimulated themselves.

I read these things, and I think to myself that I really went into the wrong research field. Oh, well.

They also discovered something else.

Komisaruk also checked what happened when women's nipples were stimulated, and was surprised to find that in addition to the chest area of the cortex lighting up, the genital area was also activated. "When I tell my male neuroscientist colleagues about this, they say: 'Wow, that's an exception to the classical homunculus,'" he says. "But when I tell the women they say: 'Well, yeah?'" It may help explain why a lot of women claim that nipple stimulation is erotic, he adds.

Now, as a true nerd and as a typical male who has always been mystified by the female sexual response, I feel a deep craving to plumb the mysteries with my own personal fMRI scanner. It'll also be a research project that will go over well at the next Mad Scientists' convention.

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Simple rules for folding a gut

I learned something new today, and something surprising. I've opened up my fair share of bellies and seen intestines doing their slow peristaltic dance in there, and I knew in an abstract way that guts were very long and had to coil to fit into the confined space of the abdominal cavity, but I'd always just assumed it was simply a random packing — that as the gut tube elongated, it slopped and slithered about and fit in whatever way it could. But no! I was reading this new paper today, and that's not the case at all: there is a generally predictable pattern of coiling in the developing gut, and it's species-specific.

The midgut forms as a simple linear tube of circular cross-section running down the midline of the embryo, and grows at a greater rate than the surrounding tissue, eventually becoming significantly longer than the trunk. As the size of the developing mid- and hindgut exceeds the capacity of the embryonic body cavity, a primary loop is forced ventrally into the umbilicus (in mammals) or yolk stalk (in birds). This loop first rotates anticlockwise by 90° and then by another 180° during the subsequent retraction into the body cavity. Eventually, the rostral half of the loop forms the midgut (small intestine) and the caudal half forms the upper half of the hindgut (the ascending colon).

The chirality of this gut rotation is directed by left-right asymmetries in cellular architecture that arise within the dorsal mesentery, an initially thick and short structure along the dorsal-ventral axis through which the gut tube is attached to the abdominal wall. This leads the mesentery to tilt the gut tube leftwards with a resulting anticlockwise corkscrewing of the gut as it herniates. However, the gut rotation is insufficient to pack the entire small intestine into the body cavity, and additional loops are formed as the intestine bends and twists even as it elongates. Once the gut attains its final form, which is highly stereotypical in a given species, the loops retract into the body cavity. During further growth of the juvenile, no additional loops are formed, as they are tacked down by fascia, which restrict movement and additional morphogenesis without inhibiting globally uniform growth.

That is just plain awesome. Now I want to open up a zebrafish and look at the curling of its intestines, or better yet, peer into a larva and see if there are any predictable rules of formation. Oh, jeez, I want to look inside my own belly, although that would be a kind of self-defeating experiment.

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Morphology of loops in the chick gut. a, Chick gut at embryonic day 5 (E5), E8, E12 and E16 shows stereotypical looping pattern. b, Proliferation in the E5 (left) and E12 (right) gut tubes (blue) and mesentery (red). Each blue bar represents the average number of phospho-H3-positive cells per unit surface in 40 (E5) or 50 (E12) 10-mm sections. Each red bar represents the average number of phospho-H3-positive cells per unit surface over six 10-mm sections (E5) or in specific regions demarcated by vasculature along the mesentery (E12). The inset images of the chick guts align the proliferation data with the locations of loops (all measurements were made in three or more chick samples). Ant., anterior; post., posterior. Error bars, s.d. c, The gut and mesentery before and after surgical separation at E14 show that the mesentery shrinks while the gut tube straightens out almost completely. d, The E12 chick gut under normal development with the mesentery (left) and after in ovo surgical separation of the mesentery at E4 (right). The gut and mesentery repair their attachment, leading to some regions of normal looping (green). However, a portion of the gut lacks normal loops as a result of disrupting the gut-mesentery interaction over the time these loops would otherwise have developed.

So how do species-specific coiling patterns emerge? A naive expectation might be that there are specific genes associated with the process that selectively impose bends at specific locations along the length of the intestine — that there is genetically determined spatial information along the tube that defines how it should coil. This is not the case. Instead, the reproducible pattern of coiling is an emergent property of some general parameters of the tissues.

You do need to know some very elementary anatomy to know what's going on here. The gut begins embryonically as a simple, straight tube, fixed at both ends at the mouth and anus. Initially, the gut is the same length as the body, and is suspended from the back of the body cavity by a continuous sheet of tissue, the mesentery, that is also the same length as the gut. But then what happens is that the gut elongates, while the mesentery grows much more slowly. This difference in growth rates means that the gut is under compression along its length, restrained by the mesenteries, which causes it to periodically buckle.

One way to test the role of the mesentery is to remove it. If you carefully cut it away from the gut, as is shown in (c) and (d) of the figure above, it straightens out — in a fully relaxed state, without the compression of the mesenteries, the gut is straight and linear. You can do partial cuts, too, and wherever a stretch of gut is released from the mesentery constraint, it uncoils.

Take it another step. Is this how generic tubes and sheets interact? The authors took a rubber tube of length Lt, and a rubber sheet of length Lm, where Lm is less than Lt. They stretched the rubber sheet to length Lt, stitched it to the rubber tube, and then let it go. Voila, it spontaneously coiled into a configuration (b) that closely resembles the chicken gut (c).

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Rubber simulacrum of gut looping morphogenesis. a, To construct the rubber model of looping, a thin rubber sheet (mesentery) was stretched uniformly along its length and then stitched to a straight, unstretched rubber tube (gut) along its boundary; the differential strain mimics the differential growth of the two tissues. The system was then allowed to relax, free of any external forces. b, On relaxation, the composite rubber model deformed into a structure very similar to the chick gut (here the thickness of the sheet is 1.3 mm and its Young's modulus is 1.3 MPa, and the radius of the tube is 4.8 mm, its thickness is 2.4 mm and its Young's modulus is 1.1 MPa. c, Chick gut at E12. The superior mesenteric artery has been cut out (but not the mesentery), allowing the gut to be displayed aligned without altering its loop pattern.

This is qualitatively convincing — they do look very similar, and at this point I'm willing to believe that mechanical forces are sufficient to explain the coiling pattern. The authors take another step, though: they bring out the math and get all quantitative. This is a reasonable idea; from the model above, it does look like the shape is reducible to a small number of parameters, so it's a manageable problem. So brace yourself: a little math coming right up.

We now quantify the simple physical picture for looping sketched above to derive expressions for the size of a loop, characterized by the contour length, λ, and mean radius of curvature, R, of a single period. The geometry of the growing gut is characterized by the gut's inner and outer radii, ri and ro, which are much smaller than its increasing length, whereas that of the mesentery is described by its homogeneous thickness, h, which is much smaller than its other two dimensions. Because the gut tube and mesentery relax to nearly straight, flat states once they are surgically separated, we can model the gut as a one-dimensional elastic filament growing relative to a thin two-dimensional elastic sheet (the mesentery). As the gut length becomes longer than the perimeter of the mesentery to which it is attached, there is a differential strain, ε, that compresses the tube axially while extending the periphery of the sheet. When the growth strain is larger than a critical value, ε* the straight tube buckles, taking on a wavy shape of characteristic amplitude A and period λ>A. At the onset of buckling, the extensional strain energy of the sheet per wave- length of the pattern is Um∝Emε22, where Em is the Young's modulus of the mesentery sheet. The bending energy of the tube per wavelength is Ut∝EtItκ2λ, where κ ∝ A/λ2 is the tube curvature, It ∝ ro4-ri4 is the moment of inertia of the tube and Et is the Young's modulus of the tube. Using the condition that the in-plane strain in the sheet is ε* ∝ A/λ and minimizing the sum of the two energies with respect to λ then yields a scaling law for the wavelength of the loop:

gut_form.jpeg

Did you get all that? If not, don't worry about it. What it all means is that we can measure general properties of gut tissues, plug the parameters into these formulas, and ask a computer to predict what the gut should look like in a numerical simulation. And it works!

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Predictions for loop shape, size and number at three stages in chick gut development. a, Comparisons of the chick gut at E16 (top) with its simulated counterpart (bottom). b, Scaled loop contour length, λ/ro, plotted versus the equivalently scaled expression from equation (3) for the chick gut (black squares), the rubber model (green triangles) and numerical simulations (blue circles). The results are consistent with the scaling law in equation (1). c, Scaled loop radius, R/ro, plotted versus the equivalently scaled expression from equation (4) for the chick gut, the rubber model, and numerical simulations (symbols are as in b). The results are consistent with the scaling law in equation (2). Error bars, s.d.

At this point, you should be saying enough — that's more than enough awesome to convince you that they've determined the rules that shape the gut. But no, they go further: all the above work is in chickens, so they reach out and start disemboweling other species, and ask if their formulas work to describe their gut coiling, too. Would you be surprised to learn that it does?

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Comparative predictions for looping parameters across species. a, Gut looping patterns in the chick, quail, finch and mouse (to scale) show qualitative similarities in the shape of the loops, although the size and number of loops vary substantially. b, Comparison of the scaled loop contour length, λ/ro, with the equivalently scaled expression from equation (3) shows that our results are consistent with the scaling law in equation (1) across species. Black symbols are for the animals shown in a, other symbols are the same as in Fig. 4b. c, Comparison of the scaled loop radius, R/ro, with the equivalently scaled expression from equation (4) shows that our results are consistent with the scaling law in equation (2) across species (symbols are as in b). In b and c, points are reported for chick at E8, E12 and E16; quail at E12 and E15; finch at E10 and E13; and mouse at E14.5 and E16.5. Error bars, s.d.

What makes this a beautiful result is that it's a perfect illustration of the principles D'Arcy Wentworth Thompson laid out in his book, On Growth and Form (and even the title of the paper is a nod to that classic of developmental biology). Sometimes, simple mathematical rules govern the patterns we see in developing systems, whether it's the Fibonacci spirals we see in the head of a sunflower or the coils of a nautilus shell, or tangled loops of our intestines. The form is not laid out in tightly-coded, case-by-case specification in the genome, but by the genetic definition of only a few parameters, in this case the relative rates of growth of two adherent tissues and the compression they impose on an elongating tube, from which a lovely arrangement flowers elegantly.


Savin T, Kurpios NA, Shyer AE, Florescu P, Liang H, Mahadevan L, Tabin CJ (2011) On the growth and form of the gut. Nature 476:57-63.

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Anti-Caturday post

Have you ever witnessed a cat in heat? Yowling, hissing, screaming, tearing at each other…or at best, moping about the house, trying to get intimate in unseemly ways with you, pressing their butts up against everything and responding to every touch with lordosis. They are tacky and obnoxious. It's no wonder that pet owners get the randy little beasts neutered — it's not just to prevent them spawning more of their creepy kind, but to suppress their repulsive sexual demonstrations.

Now molluscs, on the other hand — if we had them as pets, we'd be putting hormones in their food to induce more frequent balletic copulations. We'd want a pair elegantly and silently writhing in a corner of the living room all the time, and we'd applaud in wonder and stroke them when they were done, murmuring "Beautiful boy/girl, lovely boy/girl, well done."

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Hey, Norway!

I have more imminent travel plans. I'll be at the World Humanist Conference in Oslo this coming weekend, and then on Monday the 15th I'll be doing this:

Paul Z. Myers er en amerikansk biolog som jobber ved University of Minnesota Morris, og forsker på zebrafisk innen området evolusjonær utviklingsbiologi. Mest kjent er han for sin populære blogg Pharyngula, hvor han blant annet kommer med harsk kritikk mot intelligent design og kreasjonistmiljøet generelt. Kort sagt er han en aktivist innen den amerikanske kreasjonisme-/evolusjons-debatten. I august er PZ i Oslo i forbindelse med World Humanist Congress 2011, og tar i den forbindelse selvsagt turen innom puben for å slå av en prat med Oslo-skeptikerne!

Skeptikertreffene er uformelle, sosiale treff for skeptikere i Oslo-området. De er ment som en mulighet til å diskutere skepsis, vitenskap og alt mulig annet med likesinnede, og bli kjent med andre skeptikere. Man trenger ikke å være medlem av foreningen Skepsis.

Denne gangen samles vi nok en gang på Asylet, i bakgården dersom det er fint vær. Hvis du ikke har vært med før, så se etter bordskiltet vårt med logoen på, eller spør i baren.

I do not know what that means. If I'm now committed to doing burlesque in Norwegian, let me know soon. When I was a wee little kid, I could recite the Lord's Prayer in Norwegian, but I think I've forgotten it all now.

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Somebody doesn’t understand basic genetics

Oh, boy. Look at these quotes from a recently published magazine article, and try to guess where they came from.

Scientists had also implicitly assumed that the X chromosomes in all women were identical.

We had? When?

The first comprehensive study of gene activity in the X chromosome of women reveals an unexpected level of variation among individual females. This extensive variation means there is not ONE human genome, but TWO - Male and Female.

This does not follow. There's also individual variation in chromosome 7, and every other chromosome in the genome. Allelic and expression variation do not make for calling every variant a different genome.

Chromosomes are the set of genetic instructions that guide the creation of an organism. Every human embryo begins with two X chromosomes, but in order to be a male, one of the X chromosomes turns into a Y chromosome.

Wait, how? Could this happen even now? Watch out ladies: if you watch too much football, one of your X chromosomes might turn into a Y.

Depending on the gene, having two active copies can matter very little or very much. When genes on the second X chromosome that escape inactivation are expressed, this can create a stronger overall concentration of particular genes.

That started out just fine, and then degenerated into gobbledygook.

Have you figured it out? You're probably thinking it's some wacky creationist journal, because they are always written by people who don't understand science and get the facts all wrong.

But no: it's from Health & Wellness magazine, written by Angela Hoover. The editor of the magazine.

The title of the magazine is a clue. What the heck is "wellness", and how is it different from "health"?

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The pain will soon end

The new site is suffering — the poor thing is just dying and struggling and screaming, trying to cope with the traffic. Say goodbye, Ed Brayton is going to put a bullet in its brain tonight, and it'll be dead.

But good news! A brand new dedicated server is being installed tonight as well! There will be a brief transition in which all commenting will be shut down, and then the existing content will be whisked out of the old, clunky server and transferred to the swift and gleaming hard drives of a brand new machine. Then there will be a period of confusion as a new IP address must propagate out over the network, but within hours for some lucky few and a day or two for others, we'll be back in action, and hopefully not the limpy wimpy kind of action we've been getting lately.

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Chutzpah!

Some people are planning to make a sequel, another 13 part series, to Carl Sagan's Cosmos. This may be a greater heresy than giving Star Trek a reboot with a time-travel movie, or turning Star Wars into Jar Jar Binks land, but there is one glimmer of sunshine: it's going to star Neil deGrasse Tyson. He's our only hope.

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Friday Cephalopod: And a quirky cheery good morning to you, too!

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(via Aquaviews)

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I guess I’m going to have to get a new tie

I've got a lovely crocoduck tie, but maybe I need a new pigbird tie. Look! Evolution is impossible! It's like a flying pig!

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This is some new awful short video from Answers in Genesis. It's slick and fast and just babbles rapid-fire lies at the viewer — don't stop, don't think, you might catch on to the nonsense!

It makes precisely two discrete claims that it claims disprove evolution. All you have to do is watch this video and yay, you're done, you can forget that science stuff and move on to loving Jesus. Here are the arguments:

  1. There is no known observable process by which new genetic information can be added to an organism's genetic code.

    Except mutations and gene transfer, of course. Oh, hey, they forgot those! That does sort of scuttle their whole point. I'm afraid we do know of observable processes that add measurable, quantitative genetic information to an organism (not to its code, though: that's stupid. Whoever created this thing is one of those common ignoramuses who can't tell the difference between a genome and a genetic code). Geneticists have seen this happen: look at copy number variants in humans, for instance, and geneticists have seen novel mutants in flies in which a segment of the genome is duplicated; parents don't have it, progeny does. We also have evidence from gene families. We have five α globin genes and six β globin genes (some of which are dead pseudogenes), for instance, and they're clearly derived by duplication and divergence.

    So sorry, guys, this one is simply a lie. I'd be happy to be confronted by a creationist peddling this bit of misinformation, since it is so patently bogus.

  2. Life has never been observed to come from non-life.

    Ooh, better. This claim is literally true and not a flat-out lie. It's also irrelevant. One of the things you'll discover as you get deeper and deeper into biology is that it's chemistry all the way down. There are no vital agents working away inside a cell, adding intelligent guidance: it's all stoichiometry and reaction kinetics and thermodynamics. In a sense, all life is built of non-life and denying it is like seeing the Lego Millennium Falcon and arguing that it couldn't possibly be made of little tiny plastic bricks. Yeah, it is.

    But it's true that we haven't seen life re-evolving from simple chemicals now, and there's a good reason for that: this planet is now crawling with life everywhere, and life's building blocks that form nowadays don't last long — they're lunch. We also have only rudimentary ideas of what prebiotic chemicals were reacting in ancient seas, so we can't even simulate early chemistry in an organism-free test tube, yet. Scientists are busily tinkering, though, and we do have protocols that spontaneously produced complex organic chemicals from inorganic sources, we just haven't found the formula for a chemical replicator yet.

    But it's an irrelevant objection, anyway. Nobody has shown me god conjuring people out of mud, either. Creationists have their own problem of demonstrating origins, and they aren't even trying to puzzle it out — goddidit, they're done.

The conclusion is, of course, to claim that they have now disproven evolution (they haven't), and therefore…Jesus. Faulty premises and ludicrous leaps of logic make this one a pathetic foray into addressing evolution. It's slick, though — maybe they should have used a picture of a greased pig as their header image.

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My successful ancestors

This is an excellent comic at Abstruse Goose that illustrates the depth of our evolutionary history. The ending is a downer, though; shouldn't the protagonist have been enlightened and encouraged by this information?

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I broke it

I was afraid this would happen. Trying to shift the bulk of the traffic from here to freethoughtblogs has not gone well: the server can't handle the load, so it's currently grinding away glacially to serve everyone and serving no one in the process.

Everything will be moved to a sniny new server by this weekend, though, which should fix things. I hope.

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