Hey, history sure is easy!

giant

There’s a study that identified a mutation relatively common in Ireland that can lead to acromegaly.

They undertook an ambitious and widely collaborative study, enlisting the invaluable help of patients and the general public to set the study up in Northern Ireland and Republic of Ireland. They identified a particular mutation in Irish patients and now searched for carriers of this gene in Ireland. The frequency of the AIP mutation (R304*) was found to be surprisingly high in Mid-Ulster, Northern Ireland. The data suggest that all Irish patients with this particular mutations (18 families and 81 carriers) are descendants from the same ancestor, who lived in the area 2,500 years ago. Out of the identified 81 carriers 31 had developed acromegaly and over half of these had gigantism (18 patients, 58%). The clinical importance of this study is that we can now screen family members and carriers can be followed to pick disease up early. Our larger study has showed that 24% of seemingly unaffected gene carriers in fact have early signs of acromegaly, and some were immediately operated as a result of the genetic screening process.

Sure. That’s interesting, and also, as they point out, useful.

But this is nonsense.

This study may also give a scientific explanation for the numerous Gaelic myth of giants in Ireland, where the Giant causeway and the legend of the creation of a lake is strongly linked to giants. In modern history, famous Irish giants include Charles Byrne whose skeleton in the Hunterian Museum, London was studied and DNA sample showed he also carries the same mutation. There is data available of numerous giants living in this area over the last centuries such as Mary Murphy (the ‘Portrush Giantess’) and James Kirkland (one of the ‘Potsdam Giants’) making this data support a colourful story.

Professor Sian Ellard, of the University of Exeter Medical School, who collaborated on the research said: “Irish folklore has numerous stories regarding Irish giants and the remains of some of these giants have been studied in the past. Our data provides an explanation for the observation made by the pioneering anthropologist James C. Prichard in 1826.”

Do no other cultures have folklore about giants? Scandinavian mythology is full of giants, and dwarves, too. The Chinese have a creator-god named Pangu, who was a giant. Greek myths have Titans. Do they all have associated mutations? Are AIP mutations the only source of giants in our species?

Why would you take a perfectly legitimate scientific explanation for a specific genetic abnormality and patch an unsupported pseudo-historical just-so story onto it unless you thought history was so trivial that you didn’t need evidence to make that kind of association?

Whoa, I know that guy!

I was reading about the ongoing climate change debate in Australia, and a name from my past came up: Alan Finkel. I used to do contract programming for his company, Axon Instruments (all the neuroscientists out there know that name — it’s pretty much the premier company for making essential neurophysiology gadgets). I had to look up what Finkel has been doing in the last 20 years, since I last worked with him (I was one of the people working on his foray into cellular imaging, of which he says “we didn’t make a successful play in the market”, which is true).

Anyway, he was caught explaining climate change to that idiot, Malcolm Roberts. It’s an excellent explanation.

Across all the countries of the planet we’ve been burning fossil fuels for a rapid rate. It’s clear that by doing that we are emitting ever-increasing carbon dioxide into the atmosphere. The natural systems can’t absorb that. There’s a clear hypothesis, then there’s clear evidence. The thing that I find most compelling, senator, is that when you have a combination of a hypothesis and evidence.
When it comes to carbon dioxide it’s clear what would be driving increases in carbon dioxide, then you go out and measure it. Carbon dioxide goes up every year. Last year carbon dioxide went up 3.05 ppm which is more than any other time.

So the carbon dioxide is going up. Does that create warming? The theory is that carbon dioxide does trap heat, so ultraviolet light comes through the atmosphere without interruption, or almost without interruption, hits the ground, warms the ground and you get an infrared radiation from the ground which is then to some extent trapped by the carbon dioxide.

That theory goes back to 1896, Swedish physical chemist Svante Arrhenius did the initial work on that. He subsequently got a Nobel prize for other work and he identified that back in 1896 that carbon dioxide in the atmosphere, for basic physical reasons will trap heat.

So you’ve got the carbon dioxide, you’ve got the physics that says carbon dioxide would trap heat coming off the ground being radiated from the surface and from the water as well.

Do you have the evidence? Yes!

The temperature is going up and up and up. It was just yesterday that NASA declared that the last 12 months, yet again have been the hottest on record. So in both cases carbon dioxide is going up and it’s trapping heat, you’ve got evidence and theory. The second case is that that trapped heat will lead to an increase in temperature, you’ve got the theory and the evidence. That’s steps one and two.

The third step is the impact. The temperatures going up, what will that do to climate? That’s where it gets very, very difficult now you’re into the world of modelling.

I’m impressed. When I worked with him, he was sharp, talked very fast, and was incredibly focused and enthusiastic. It looks like he still is.

Oh, no…not another debate

Is there any point? Isn’t this whole thing over now?

Anyway, tonight the competent, experience woman is going to have to share the stage with the ignorant, egocentric man, and give him unearned equal time. The topics that Hillary Clinton will discuss have been announced:

  • Debt and entitlements
  • Immigration
  • Economy
  • Supreme Court
  • Foreign hot spots
  • Fitness to be President

Note that I said these are what Clinton will discuss. Trump will be off in argle-bargle land, ranting about how great he is and how his enemies will face his wrath and vengeance. One thing I’ve noticed about these debates, though, is that they don’t discuss…science. I think the politicians are afraid of the subject.

But here’s something brilliant: Gaius Publius explains how every one of those topics could be turned into specific questions about climate change. All it would take is some intelligence and willingness to dig a little deeper on the part of the moderator…

Oh, crap. The moderator is Chris Wallace? Fuck it, he’s a schmuck.

How about that big storm, Seattle?

wastorm

I have friends and family in the Seattle area, so I’ve been following the news about the impending doom-storm that was supposed to strike the Pacific Northwest with some interest. There was a little worry, but mainly I figured it would give my mom something exciting to talk about on the phone. At least I heard about all the pre-storm rush to stock up on candles and flashlight batteries and food, and how Fred Meyer shelves were getting cleaned out; I told them it wasn’t anything to worry about until they were selling out of big sheets of plywood.

And then it just fizzled out. I hear that all you Seattleites got was some gusty blustery rainfall, and then it was over.

How can weather forecasting fail so badly? Here’s a helpful summary of how the models got tricked. Weather is still pretty darned complicated.

It also includes my favorite meme for the non-event.

graysharborstrong

Of course, it could have been much, much worse — the consequences are far more dire if a major storm materializes that was not predicted. Read this account of the Armistice Day Blizzard of 1940 to get some perspective — hundreds of people died because back then, they didn’t have the tools to predict the weather as well as we do today, so people went cheerfully off to hunt ducks and walked and boated their way right into catastrophe.

It is easy to forget that there was a time — not so very long ago, really — when there was no Gore-Tex, no Thinsulate, no neoprene, and no polypropylene. There was a time when outboard motors, far from the sleek and powerful marvels of today, were crude, cumbersome beasts, unreliable under the best circumstances and all but useless under the worst. There was a time when there were no cell phones, no emergency beacons, no Flight for Life helicopters.

There was a time, too, when there were no weather satellites, no telemetry to provide data that could be plugged into sophisticated formulas and fed into supercomputers for timely forecasts. Indeed, that the weather could be predicted with any degree of accuracy then — November, 1940, to be precise — seems almost miraculous, meteorology in those days being one part science and two parts the divination of omens, signs, and portents.

I think a few false alarms are an OK price to pay.

But what if I can explain these fossil mysteries?

challenge-accepted-meme

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.