What? The giraffe didn’t get a long neck by stretching?

Next they’ll try telling us the elephant didn’t get its trunk by a crocodile tugging on it.

The genomes of okapi and giraffe have been sequenced, and the signatures of specific genetic changes that are unique to their lineage have been identified. It looks like it wasn’t an act of will after all, but the accumulation of small changes over millions of years. Surprise!

This is an interesting comparison between long-necked mammals, short-necked, related mammals, and mammals as a whole that identified a number of genes that showed evidence of selection. The idea was to find the genes associated with a specific morphological change.

Using the average pairwise synonymous substitution divergence (dS) estimates between giraffe, okapi and cattle as calibrated by the pecoran common ancestor (27.6 mya), the divergence of giraffe and okapi from a common ancestor is estimated to be 11.5 mya.

Using the average pairwise synonymous substitution divergence (dS) estimates between giraffe, okapi and cattle as calibrated by the pecoran common ancestor (27.6 mya), the divergence of giraffe and okapi from a common ancestor is estimated to be 11.5 mya.

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Something in this poster reminded me of home

Except…the text is disturbing. It’s on the wrong side of the continent. Read this story of a common occurrence around Puget Sound.


Douglass Brown was 15 when he saw a giant tentacle emerge from Puget Sound.

He was in Tacoma, walking down the beach with a girl he liked. Then he looked out at the water.

“I see this arm come out of the water. It was 10, 15 feet in the air,” Brown says. “It looked like an octopus or something like that, and I just took off running.”

I can so imagine walking along the beach with my girl when I was that young, and enjoying the aquatic wildlife. Except that I can’t imagine running — that’s the part where you hold each other a little closer, and sigh romantically.

(Also, I think the “10, 15 feet” part is a gross exaggeration. “Inches,” maybe. But then, one does tend to inflate in those situations.)

At last, a sensible perspective on aging


The world is full of naive people who think we’re going to be immortal some day soon, in spite of all the evidence that says no (Kurzweil is a prominent example of such techno-optimism, as is Aubrey de Grey). It’s not just bad biology, it’s also bad physics, as Peter Hoffman explains. We’re all made of parts that are constantly being battered by thermal energy as an essential part of their operation, and damage accumulates until…we break down. This is unavoidable.

If this interpretation of the data is correct, then aging is a natural process that can be reduced to nanoscale thermal physics—and not a disease. Up until the 1950s the great strides made in increasing human life expectancy, were almost entirely due to the elimination of infectious diseases, a constant risk factor that is not particularly age dependent. As a result, life expectancy (median age at death) increased dramatically, but the maximum life span of humans did not change. An exponentially increasing risk eventually overwhelms any reduction in constant risk. Tinkering with constant risk is helpful, but only to a point: The constant risk is environmental (accidents, infectious disease), but much of the exponentially increasing risk is due to internal wear. Eliminating cancer or Alzheimer’s disease would improve lives, but it would not make us immortal, or even allow us to live significantly longer.

The article points out that we can accurately model mortality with only a few general parameters, and they’re rather fundamental and physics-dependent — we can tweak the biology as much as possible, but the underlying physical properties are going to be untouchable.

I would add, though, that while the mortality curves he shows are inevitable, biology can stretch and contract them, and we do have measurable variation in different species that shows that there is a kind of scaling factor to the curves in biological diversity — it’s not as if every species that lives at the same average temperature have identical life expectancies! Even within the human species, there are genetic variants that affect longevity, and clearly different life-style choices influence mortality, even though we’re every one of us ticking along at roughly the same 37°C. So please, yes, we can reduce the incidence of heart disease and cancer, and get a longer average lifespan…but even if we were to eradicate those major causes of mortality, we’re all going to get up around the century mark, and then we’re going to plummet off a cliff because of all the accumulated cellular damage and declining physiological efficiency.

By the way, one odd thing when I tried to find an illustration to accompany this post: I searched on “aging”. Almost all the photos on the web illustrate women by a huge margin. I am forced to conclude that only women suffer from the ravages of age; men simply get mature. But at least it’s one topic that women get to dominate!

It’s still crank science if a teenager does it

You generally want to encourage young people to engage with science, but sometimes that means telling them that their ideas are bad. Take this Canadian boy who was in all the news, for instance: he was claiming to have discovered a method for finding Mayan ruins by basically using Google maps, aligning a star map with the terrestrial map and claiming to find that the Mayans built everything according to the layout of the constellations.

I was suspicious for a couple of reasons.

  • It made no sense. Yes, religion/astrology can persuade people to do foolish things, but you can’t claim that all the cities in the Yucatan peninsula were mapped out by lining them up with constellations. People also do things, like the massive resource investment involved in putting up a city made of stone, for pragmatic reasons.

  • The stars represent a random pattern of dots — and a pretty dense one, at that. Settlements in Mexico were also densely sprinkled about. This sounds like classic pareidolia, fitting noise to an expected pattern.

  • I have a little more respect for anthropology/archaeology than to think you can do it effectively in your armchair in Quebec without ever putting your butt on the ground at the study site.

Then the news reported that using his star hypothesis and satellite imagery, he had found a new ‘lost city’. That sounds like good science — hypothesis testing and all that.

Unfortunately, he hadn’t found a city. He’d found an abandoned cornfield, which, in a densely populated part of the world like that, isn’t at all unusual. His search criteria were so loose and poorly informed that he’s pretty much guaranteed to find a match somewhere near any random spot on the map, which means he’s ‘testing’ a hypothesis with a procedure guaranteed to generate false positives everywhere.

The sad part is that science has some standards for rigor, and everyone is going to tell this teenager that his method doesn’t work. Meanwhile, pseudoscientists have no standards at all, and will be telling this teenager that he’s brilliant and clever and is making a true contribution to their pseudohistory. He’s going to be denied by one and tempted by the other. Which one will he follow?

I’ll be curious to see if he gets mentioned at the Paradigm Symposium this weekend. This is exactly the kind of baloney they love…but then, the kid was smart enough to not say anything about alien astronauts, so maybe it won’t be on their radar.

The sure-fire, simple way to tell if an article about epigenetics is full of crap

It’s easy. If it uses the word “Lamarckian” without boldly prefixing it with “not“, you can just stop reading. Likewise if the word is prefixed with “pseudo-“, “semi-“, or “quasi-“. Just skip it. It’s too confused to bother with.

Epigenetics is in the news again, and in fact, it’s newsworthiness seems to be rising at a fantastic rate. Eight years ago, would you believe, I wrote a short summary of what epigenetics is, driven largely by the fact that a lot of people were writing about epigenetics without acknowledging that it was a grab-bag of mundane regulatory processes. It’s gotten worse. I had to explain the obvious: epigenetics ain’t magic. I tried to explain it last year again, that people have a lot of misconceptions about epigenetics. It’s frustrating because epigenetics encompasses a lot of cool and important stuff — genetic switches and gene regulation and plasticity and environmental responsiveness — but all the popular press wants to talk about is this weird idea that it’s a way break the tyranny of genetics and evolution and modify your genes for future generations, which is just plain wrong.

What it tells me is that there is still a lot of uneasiness about the implications of evolutionary theory. Not among most evolutionary biologists, of course, but in the general population. They wish for a way to believe that their progeny (and themselves) can be enhanced by an act of will, and they think that a poorly understood phenomenon like epigenetics provides a loophole. The whole idea that evolution is a statistical property of populations rather than something they can game to their advantage as individuals leaves them queasy. So they noodle around with the idea that somehow, by practice, they can change their whole genetic legacy using the buzzword “epigenetics”, not even realizing that epigenetic phenomena are a consequence of the properties of proteins, coded by genes, and regulatory sequences imbedded in their DNA, and that even short term cytoplasmic responses in the cell are ultimately derived from information in their genome.

People who use epigenetics as something that is anti-evolutionary remind me of Perry Marshall, the creationist who thinks Barbara McClintock’s work rebuts Darwinism, because he wrongly thinks somehow that it refutes the role of chance in evolution. They hate the whole idea of chance-driven processes, and want a way to shape genetics by an act of will, instead. It’s painful to see the contortions they put themselves through to run away from the implications of evolution and genetics.

Stop! Turn back!

This story about feathered dinosaurs is really good, and it also included the video below.

As the little man was strolling along past the dinosaurs that were getting bigger and bigger, I felt the urge to tell him to stop…starting about 30 seconds in.

It really should have ended with something huge stepping on him. The suspense was building up and up and was not released.