But what if I can explain these fossil mysteries?


I was sent this link to Five Fossil Mysteries…That Evolution Can’t Explain. Challenge accepted, sir!

Unfortunately, after reading their list of five, and realizing it was Answers in Genesis, and that their ‘unexplainable’ mysteries were trivial and stupid, I felt a bit deflated. It was like being invited to a battle, showing up in my +5 armor and +3 Vorpal Sword of Fireballs and discovering my opponents were a bunch of preschoolers in diapers, armed with sippy cups. Undaunted, though, I wreak carnage upon them.

One: Life’s Unexpected Explosion
Forty major animal groups appear out of nowhere at the bottom of the fossil record. Where did this “Cambrian Explosion” come from?

This one is built on a lie by Kurt Wise: But the ancestors of the Cambrian animals have never been found. Yes, they have. The pre-Cambrian biota, however, were small and softbodied — it is totally unsurprising that the transition from small multicellular eukaryotes to large, hard-shelled metazoans would involve smaller creatures without hard body parts, and also that the evolution of hard body parts might be piecemeal. So we find pre-Cambrian trace fossils, trackways and burrows, for instance, and later we find the small shellies, an assemblage of tiny fragments — partial bits of armor, mouthparts, an occasional spike and spine — all of which were once mounted on gooey soft wormy bodies that did not fossilize.

Wise is wrong. The Cambrian is not the bottom of the fossil record, and we have traces of precursors to Cambrian forms.

Two: Those Not-So-Dry Bones
If dinosaurs died millions of years ago, how can their fossils still contain soft tissue?

Question your assumptions, Marcus Ross! What would happen chemically to proteins isolated in sealed, thick mineralized chambers, away from the atmosphere and from degrading bacteria, for millions of years? I don’t know. Apparently they’ll persist in some form for far longer than I would have expected. The fossils are known by strong physical methods to be 70 million years old; finding rare scraps of peptides imbedded deep inside them doesn’t challenge their age, since we didn’t know exactly what happens to totally isolated proteins, but should make us think harder about molecular taphonomy.

Three: Without a Leg to Stand On
Birds are vastly different from dinosaurs, even in the way they walk. How could one come from the other?

Another lie! This one cites a single article, which does not claim that birds are vastly different from dinosaurs — instead, it makes a single, narrower claim about respiration in dinosaurs. It points out that modern birds have basically immobilized the upper leg, the femur, in the body wall, and explains that the reason for that is that movement of that part of the limb would impair the function of abdominal air sacs. They look at fossil dinosaurs, and found that the femur was clearly used in walking, and therefore argue that they almost certainly lacked those abdominal air sacs, although there is evidence that they may have had air sacs elsewhere. Here, read the paper for yourself. It concludes,

We conclude that there are few data supportive of there having been an avian style lung air-sac system in theropods or that these dinosaurs necessarily possessed cardiovascular structure significantly different from that of crocodilians. These conclusions are reinforced by previously cited evidence for crocodilian-like lung ventilation in theropod dinosaurs.

Isn’t it interesting how they present a piece of the scientific literature as supporting their anti-evolution crusade, when it actually does nothing of the kind?

Four: Amazingly Preserved Leaves

When leaves die, they shrivel up and crumble. So why is the fossil record full of well-preserved, flat leaves?

But…but…not all fossil leaves are flat or well-preserved! And leaves don’t always “shrivel up and crumble” — if you’re not zealous about raking your lawn (I can’t imagine who wouldn’t be), it’s pretty easy to get damp, matted piles that preserve the leaves for a few years. You can dig in a peat bog and find preserved plant material that is hundreds or thousands of years old. Anoxic environments can do somewhat surprising things.

Here’s another paper you can read: The Taphonomy of Plant Macrofossils. This is a non-problem. Here’s the conclusion from that paper:

Experiments with individual plant organs and modern vegetation have demonstrated that the leaf-rain potentially contributing to plant fossil beds reflects trees within only short distances of the area of deposition. Separate sedimentary facies in fluvial, paludal and lacustrine environments preserve plant macrofossil assemblages which reflect varying biases in the level of transport (autochthonous to allochthonous deposition) and hydrodynamic sorting (Figure 7 .5).Different vegetation types within any landscape will have a varied proportional representation in these sedimentary facies, reflecting proximity to depositional sites, the mode of deposition of both plant parts and sediment, and the energy of transport. Each ‘flora’ present within an exposure of particular facies will represent a subsample of the total vegetational mosaic, in some cases strongly biased towards individual plant communities, in other cases containing elements from several communities.

In consequence of these observations, plant macrofossil studies of palaeovegetation must (where possible) sample from within discrete bedding planes and consider sedimentary facies when attempting floristic reconstructions of palaeovegetation. While the potential sources of bias are great, observations of modern plant fossil sedimentary analogues allows predictive models to be constructed that allow palaeovegetation reconstructions to account for sedimentary facies, biofacies and differential dispersal (and small-scale variation through seasonal effects?). Such applications of taphonomy are reliant on careful and systematic stratigraphic sampling and result in a finer resolution of the palaeocommunity. Previous approaches of treating single plant fossil localities as a ‘flora’ must be abandoned in favour of such an approach.

Kurt Wise thinks that finding all the leaves neatly flattened (they aren’t) is compatible with the idea that they were fossilized in a catastrophic, world-destroying flood 4000 years ago. He’s an idiot.

Five: Tracks But No Trilobites

Why do we find lots of trilobite tracks in lower rock layers, but we don’t find any trilobite fossils until higher up?

This one is hilarious. I will quote Kurt Wise directly. Why do older rock layers have only trace fossils (trilobite tracks), while more recent Cambrian layers feature whole preserved exoskeletons (see also One: Life’s Unexpected Explosion)?

Such a worldwide pattern of fossil layers suggests that a global catastrophe, such as the Bible describes, once struck the world. What if, when the “fountains of the great deep were broken up” (Genesis 7:11), the spreading waters surprised the trilobites living on the ocean bottom? As the water became muddy, trilobites scurried about in terror, leaving their tracks behind them. Then as a layer of mud covered their tracks, they climbed through the mud and left tracks on the next layer—repeating this process until they finally succumbed in exhaustion and were themselves buried and preserved.

Ah, hydraulic sorting and differential mobility, those familiar old canards. This also explains why clams are found in more recent layers than Kimberella — they were better at climbing. We also have insight into trilobite culture: they must have held great reverence for their ancestors, since while scurrying about in terror, they still found time to excavate all of the bodies of their dead and haul them to higher ground with them. Clearly, they were god’s creatures.

Sorry for all the slaughtered toddlers. Also clearly, I am not one of god’s creatures, since I have so little reverence for religious idiocy.

Any biologists looking for a job?

My university is hiring for a full-time, tenure-track biology position. Take a look at our job ad:

Duties/Responsibilities: Teaching undergraduate biology courses including cell biology, genetics, electives in the applicant’s areas of expertise, and other courses that support the biology program; advising undergraduates; conducting research that could involve undergraduates; and sharing in the governance and advancement of the biology program, the division, and the campus.

We’re looking for a cell biologist who can also teach genetics…hey, hang on there. Those are the courses I teach! Are the other faculty conspiring to replace me?* It’s a cunning plan they had, then, to put me on the search committee to find a new person to bump me off. They probably thought I’d never expect it if it was happening right under my nose.

Oh, well, I’ll accept my fate gracefully. If you think you’d fit in at a liberal arts university where teaching is your primary responsibility, and you know your cell biology and genetics, apply! We’ll be reviewing applicants starting on 10 November, and will be doing initial phone interviews in early December.

*Actually, it’s more about flexibility. With a small department, everyone needs to be able to wear multiple hats, and I’m the only guy teaching genetics right now, and have been the only guy for over a decade. We like to have a backup for everything. So it’s more like I’m a potential single point of failure.

Silicon Valley creationists

There’s a wave of irrationality sweeping through the over-privileged, ridiculously wealthy world of coddled millionaires and billionaires of Silicon Valley. Some of them seem to think The Matrix was a documentary, and that we’re code living in a simulation, so they like to get together and wank over this idea.

That we might be in a simulation is, Terrile argues, a simpler explanation for our existence than the idea that we are the first generation to rise up from primordial ooze and evolve into molecules, biology and eventually intelligence and self-awareness. The simulation hypothesis also accounts for peculiarities in quantum mechanics, particularly the measurement problem, whereby things only become defined when they are observed.

No, that makes no sense. It exhibits a lack of awareness of modern biology and chemistry; “primordial ooze” is a 19th century hypothesis that did not pan out and is not accepted anymore. This guy is ignorant of what would have to be simulated, and thinks that if we were just created with the appearance of having evolved, he wouldn’t have to understand biochemistry, therefore it would be simpler for him.

And where have I seen that “created with the appearance of X” phrase before?

If we are simulated, it doesn’t make the problems go away. This would have to be such a complete simulation that it includes all of physics and chemistry and biology; that models quantum chemistry and the mechanics of all the chemical reactions that produced us; that includes viruses and bacteria, and includes all the evolutionary intermediates; that has such a rich back story that it would be easier to have it evolve procedurally than to have some magic meta-universe coder generate it as some kind of arbitrary catalog. It just doesn’t work. It definitely isn’t a simpler explanation — because it would require all of the complexity of the universe plus an invisible layer of conscious entities running the whole show.

I’ve also heard that phrase that “creation is a simpler explanation than evolution” somewhere before.

I hesitate to say this because I’m no physicist myself, but I don’t think this Terrile fellow understands physics any better than I do, either. The observer effect does not imply a conscious, intelligent, aware observer, as he claims. The observer effect does not mean that there had to be some super-programmer watching over every physical process in order for it to occur.

I don’t think these yahoos even understand what a simulation is.

According to this week’s New Yorker profile of Y Combinator venture capitalist Sam Altman, there are two tech billionaires secretly engaging scientists to work on breaking us out of the simulation.

I think there must be some scientists somewhere who are milking a couple of gullible billionaires out of their cash.

This makes no sense. If we are, for instance, code programmed to respond to simulated stimuli and emit simulated signals into an artificial environment, how can you even talk about “breaking us out”? We are the simulation. Somehow disrupting the model is disrupting us.

If you don’t think this sounds like febrile religious crapola, let’s let Rich Terrile speak some more:

For Terrile, the simulation hypothesis has “beautiful and profound” implications.

First, it provides a scientific basis for some kind of afterlife or larger domain of reality above our world. “You don’t need a miracle, faith or anything special to believe it. It comes naturally out of the laws of physics,” he said.

Second, it means we will soon have the same ability to create our own simulations.

“We will have the power of mind and matter to be able to create whatever we want and occupy those worlds.”

I’ve written some simulations myself — I have some code lying around somewhere that models the interactions between a network of growth cones. We already have the ability to create our own simulations! These guys are all gaga over increasingly complex video games; those are simulations, too.

The NPCs in World of Warcraft do not have rich inner lives and immortality. They do not have an ‘afterlife’ when I switch off the computer. My growth cone models are not finding meaning in their activities because they are expressions of a higher domain of reality.

I, however, am wondering why the Great Programmer in the Sky filled my virtual reality with so many delusional idiots and oblivious loons. The NPCs in this universe are incredibly stupid.

I’m sure there’s a connection between Trump and fossilized soft tissue

I went down the rabbit hole for a little while this morning. It started here: I was sent a link by Trey Smith about the TRUMP: the COMING LANDSLIDE. ~Ancient Prophecy Documentary of Donald Trump. With a click-bait title like that, I had to start watching the video. And then Trey Smith is mesmerizingly weird: his technique is to stick half his face right into the camera, and make lots of hand gestures with a computer screen in the background. It was effective at first just because his tics and odd movements and emphatic phrasing were engrossing, but I didn’t last long, because there’s no substance there. He seems to think Trump is destined to be president, but his main argument is numerology and ‘because the Bible’ with lots of finger stabbing at the video screen behind him.

So I switched to some of his other videos, and of course he’s a Young Earth Creationist, and he’s very impressed by something that has become a veritable obsession with YECs in the last decade or so: preserved soft tissue in fossil dinosaur bones. And that led him to Mark Armitage.

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If everyone from Yong to Zimmer says it’s true, it must be

You must have already read the tragic news: scientists have determined that I am doomed to die by 2072, when I turn 115, if not sooner. This was figured out by analyzing demographic data and seeing that people seem to hit a ceiling around age 115; the mean life expectancy keeps shifting upwards, but the maximum age seems to have reached a plateau. Carl Zimmer gives the clearest explanation of the methodology behind this conclusion, and Ed Yong gives a good description of the phenomenon of death in the very old.

The ceiling is probably hardwired into our biology. As we grow older, we slowly accumulate damage to our DNA and other molecules, which turns the intricate machinery of our cells into a creaky, dysfunctional mess. In most cases, that decline leads to diseases of old age, like cancer, heart disease, or Alzheimer’s. But if people live past their 80s or 90s, their odds of getting such illnesses actually start to fall—perhaps because they have protective genes. Supercentenarians don’t tend to die of major diseases—Jeanne Calment died of natural causes—and many of them are physically independent even at the end of their lives. But they still die, “simply because too many of their bodily functions fail,” says Vijg. “They can no longer continue to live.”

I agree with all that. I think there is an upper bound to how long meat can keep plodding about on Earth before it reaches a point of critical failure. But I’m going to disagree with Yong on one thing: he goes on to explain it in evolutionary terms, with the standard story that there hasn’t been selection for longevity genes, because all the selection has been for genes for vigor in youth, which may actually have the side effect of accelerating mortality.

This is true, as far as it goes. But I think it’s a different phenomenon, that we’re seeing a physico-chemical limitation that isn’t going to be avoided, no matter how refined and potent ‘longevity genes’ become.

When organized pieces of matter are stressed or experience wear, their level of organization decreases. You simply can’t avoid that. Expose a piece of metal in a car to prolonged periods of vibration and it will eventually fail, not because it was badly designed, but because its nature and the nature of its activity dictates that it will eventually, inevitably break.

Likewise a soap bubble is ephemeral by its nature. The same fluid properties that enable it to be blown doom it — the film will flow over time, it will tend to thin at the top, and eventually it will pop. There’s no way to suspend the physics of a soap bubble to let it last significantly longer, shy of freezing it and defeating the whole point of a soap bubble.

In people, we have a name for this wear and tear and stress: it’s called “living”. All these different things we do that make it worth existing are also fundamentally damaging — there’s no escaping the emergence of an ultimate point of failure.

115 years sounds like a reasonable best estimate from the current evidence. I’d also point out that this does not imply that we won’t find a common critical failure point, and find a way for medical science to push it up a year or five…but every such patch adds another layer of complexity to the system, and represents another potential point of failure. We’re just going to asymptotically approach the upper bound, whatever it is.

That’s OK. I’ll take 115 years. It also helps that it’s going to really piss off Aubrey de Grey and Ray Kurzweil.

I hear that women are made of exotic matter

The Nobel in Physics has been awarded for research on exotic matter, but I think you’d be better off looking for a physicist to explain it. I’m sure it’s good work and that the three scientists are deserving, but I just have to leave this fact on the table.

No Nobel Prize has come close to being equitably distributed by gender, but physics has the worst record of them all. Zero women have won it in the past 50 years. Exactly two women have won it ever.

Again, this does not detract from the accomplishments of Thouless, Haldane, and Kosterlitz, but it does make one wonder how much further physics would have progressed if it didn’t have a culture that discouraged half of humanity from participating.

Can I come in and tell you about the cult of Danio?

Now I know how a Mormon or Scientologist or Baptist feels when some heathen tries to earnestly explain their religion. This video is well done, but gives me a bit of the heebie-jeebies.

I started working on zebrafish in 1979 (I wasn’t the first, or even particularly close — that honor goes to the crew in George Streisinger’s lab), and all through the 80s our lab group had a reputation: at every meeting in every talk, we’d recite what was called the Zebrafish Litany, a listing of all the virtues of this quirky new model organism that nobody else knew much about. In fact, at the Friday Harbor lab meetings in developmental biology there was a kind of tradition where the students would linger in the auditorium late at night and mock the speakers and professors with imitations on the podium, and one year a group made fun of us by having a series of students march robotically to the lectern and recite the exact same series of words. And those words are in this video. How dare the unbelievers speak our catechism!

The video doesn’t quite capture the true nature of the Cult of Danio, though. Everything in it is about how zebrafish research contributes to the study of human diseases, which is a nice perk of the system, but we study the fish because the fish are fascinating, not because we are wannabe human disease researchers. Also, the part where he explains the flaws of the zebrafish, that they have many duplicated genes (so do we) and that they have unique genes not found in humans? Those aren’t flaws.

It is nice to see, though, that our orison is now part of the general public awareness of the zebrafish. That’s why we were saying it so often. Soon, you too shall be a believer. All praise George!