Welp, guess Harun Yahya just disproved the existence of gods

This is a bit of an own goal, sent to me by the Islamic creationist, Harun Yahya.

Darwinists never realize that even though it’s impossible for them to copy out a text consisting of billions of letters without errors creeping in, enzymes combine together millions of units of information as they copy DNA, without making a single mistake. This is simply more proof of the existence of God.

Except that DNA polymerase, the enzyme that copies DNA, makes errors at a rate of about 10-8 mistakes per base pair (error correction processes bring that down to about 10-10 errors per base pair). Whoops. God makes mistakes! Also, while the DNA in the background of the image is correctly exhibiting a right-handed twist, the large orangeish fragment in the foreground seems to have a left-handed coil, in addition to being drawn with a strange and incorrect stick-and-ball arrangement. Tsk, tsk. Wrong and inconsistent. Does he really think this kind of crap will persuade a biologist? Why is he sending it to me?

Although, to be fair, I don’t think most people think chemistry has to be flawless to be compatible with gods, and obviously evolution depends on variation produced by errors, so this whole line of argument is irrelevant.

Musk and Trump belong together

Not again. Elon Musk babbles about a half-assed idea on his twitter account, and suddenly everyone gasps and declares, “HE’S SUCH A VISIONARY.” So now, on top of SpaceX, Hyperloop, Neuralink, electric cars, and being an advisor to Donald Trump, he wants to dig tunnels for cars to alleviate traffic. This scheme is insanely stupid.

We already have these. They’re called subways. They reduce traffic by providing mass transit, which gets around the problem of surface buildings and roads by tunneling underground. The Musk Scheme does nothing to reduce traffic that wouldn’t already be done by increasing the number of lanes or adding more freeways.

Hey! I just had an idea! We could reduce traffic if we just built flying cars! Quick, someone make a flashy concept video for me so the tech press will fawn all over me and people will give me money.

I guess vaccines really do work

The evidence is rather vivid.

Also timely. The Somali community in Minnesota has had an outbreak of 24 cases of measles recently.

Even though the case count has doubled this week, health investigators say the outbreak’s development isn’t presenting them with any surprises. All of the cases involve unvaccinated Somali children from the age of 10 months to 5 years. Fifty percent of the current cases have been hospitalized.

Get those kids their MMRs!

Bill Nye is doing science just fine

Let’s look at a painfully naïve understanding of science.

Science. The word denotes logic. Reason. Cold, hard facts. Measurable data and observable phenomena. Objectivity.

There is a germ of truth in that: scientists use reason, we hope, to interpret data, “facts”, to arrive at a conclusion, but it’s more complicated than that. Science is a process, not the “cold, hard facts” themselves, and it is a process that is supposed to place a check on the subjectivity of scientists. It’s odd, though, to see science reified to the point that we can assign human values like “objectivity” to it.

I’ll use a couple of examples to explain why that understanding of science is wrong.

This is a fist-sized rock. It’s real. You can measure its dimensions, weigh it, break down its chemical composition, determine its location in space and time. It is a “cold, hard fact”. But as far as science is concerned, it’s not very interesting, and wouldn’t warrant a museum exhibit or a paper being written about it.

Where it gets interesting is in the context of a theory or explanation. This is a rock found in association with a recently excavated mastodon skeleton. What provokes discussion is that it is proposed to have been a hammer used by hominins to help butcher the mastodon.

Is that a “cold, hard fact”?

It’s an explanation that is in dispute. Most anthropologists are dubious. Of course, if it’s just a random, eroded rock it becomes a pointless, unsurprising “fact”, because rocks are mundane and common; if it’s confirmed as a stone tool, it becomes a career-making discovery.

Here’s another “fact”. We have some “measurable data” on the age of the mastodon.

Since 1993, the team, including lead author Steven Holen, have repeatedly tried to date the mastodon fragments, using techniques like carbon-dating. They repeatedly failed. They only succeeded when they turned to uranium-thorium dating, which looks at the decay of two radioactive elements. That gave an age of 130,700 years, give or take 9,400 in either direction.

130,700±9,400. Sure sounds measured and specific and sciencey. It’s also a radical surprise — we don’t think people were living in North America 130,000 years ago! Most anthropologists still don’t. That number is in question.

“There are a small number of uranium-thorium dating specialists who think bone can be dated,” says John Hellstrom from the University of Melbourne—who isn’t one of them. “The problem is that uranium moves around in bone, which invalidates the dating unless you can use a mathematical model of that movement to compensate. That is exactly what the authors of this study have tried to do.” Coupled with other evidence about the surrounding rock layers, the bones are “likely to be something around the age the authors claim,” he says, “but I would not give these dates hard-evidence status. More correctly, they indicate the bones are most likely at least tens of thousands of years in age.”

So what is it? A hammer, or a stone? Is it 130,000 years old, or just something over 10,000 years old?

See, this is where we disagree on the meaning of science. Some want to say it’s about absolute truths, crystal-clear facts laid out in the grand Book of Nature. Some of us think instead about complexity and context, that we’re trying to use evidence to reduce uncertainty and converge on models that best explain reality. The scientific meaning of that rock will change as we gather more evidence, develop more tools for examining it in greater detail, look at other sites of similar age, and work to confirm or disconfirm the idea that it is an ancient hammer. Science will change its interpretation, because it is a process that constantly evaluates and re-evaluates the data, and gathers new data that requires modification of our understanding.

And we’re cool with that. That’s how it’s supposed to work. We don’t deal in absolutes.

I think it’s extraordinarily unlikely that it’s an ancient hammer ten times older than any other artifacts we’ve found on the continent, and I’m OK with that. If more evidence emerges of people living in North America 100,000 years ago — which I wouldn’t bet on occurring — then I’m also OK with that. A good scientist should be a leaf on the wind.

Here’s another example of “measurable data and observable phenomena”: digit length ratios and gender. Women are supposed to have a shorter ring finger, relatively, than men, and subtle variations in the ratio of the length of the ring finger to the index finger are supposed to be indicative of everything from sexual orientation, to sperm count, to aggressiveness, to adult hormone concentrations.

I’ve seen people present that difference as a “cold, hard fact”, too. It’s not. It’s a smear of ratios, with only a rough statistical correlation, and no predictive power at all.

That’s the danger of that quote at the top of this article. When you treat science as a collection of facts, you shut down questioning and exploring the complexity of reality — you short-circuit the process, which means you aren’t doing science any more. That doesn’t mean there are no truths in science — evolution is a fact, as is global climate change — but that those facts are more subtle and fluid than most people imagine, and all of them are provisional and subject to re-evaluation.

But there are even more errors at that link. The purpose of the article is to criticize Bill Nye’s new show, Bill Nye Saves the World, which is fine. There is much to criticize in it — I found it a bit superficial and with a style I find annoying, but the thing is…it’s a show intended to reach people other than already-confirmed science educators like me, so it’s fine that I’m not the target. It’s more than fine — I think diverse approaches are necessary, and applaud the blooming of a thousand flowers, which are not all old, white, and male.

But once again, this critic approaches it with his own flawed biases. He watched the show about “The Sexual Spectrum”, and was horrified.

The only “science” mentioned in the episode about sex comes during the first segment when we are informed about sex chromosomes and their function. If you are XX you are female, and if you are XY you are male. Most all of us learned this in school. But Nye is quick to point out that this binary way of looking at things is outdated. Some people have more than two sex chromosomes. Some have only one. Indeed, he instructs us, people don’t really fall into binary categories of male or female, but exist somewhere on a sexual spectrum with male at one end and female at the other.

That is a very revealing paragraph. What constitutes science, to him? Descriptions of chromosomes. He’s already narrowed the slit he views the world of science through to a remarkable degree, because at the very least his reductionist perspective should include endocrinology, and molecular biology, and cellular responses (I understand how many narrow scientists would exclude such things as psychology and sociology from the domain of science, but at least he’s got to understand that there’s more to sex than just chromosomes, right?).

But then he goes on to get the one allowed piece of science wrong!

If you are XX you are female, and if you are XY you are male.

Nope. Not always true. You could argue that if you’re XX, you won’t be able to produce sperm, and if you’re XY, you won’t be able to produce ova, and that if you’re aneuploid you probably won’t produce either. You can kinda sorta limit your understanding of sex to the gametic definition, but there are far too many circumstances where that is irrelevant.

Then it gets worse.

Nye mentions that there are abnormalities in the sex chromosomes in 1 in 400 pregnancies, which he calls “quite a lot.” Calling it a “spectrum” suggests that most of us would be neither XX or XY but something in between. Generally the extreme ends of the spectrum represent the minority with most people somewhere in the middle.

Yes, 1 in 400 is “quite a lot”. It means that at my university, there are probably about 4 students with a chromosomal abnormality of the sex chromosomes, and that’s probably a low estimate. You probably know people with this kind of variation, but the thing is, it usually doesn’t jump out at you as some easily visible phenotype. A surprising number of people show up at fertility clinics with problems in reproduction that only then are discovered to be due to a sex chromosome abnormality.

But here’s how that writer deals with the “cold, hard fact” that a significant number of people in our population have a variation in chromosome number: by trying to argue that the percentage is even lower, as if that matters, and trivializing the existence of the minority.

The fact that abnormalities occur does not negate the norm or render the idea of the norm meaningless. What is more telling, that 399 out of 400 children are born with typical XX or XY chromosomes or that 1 out of 400 is not?

So…what do you propose we do with that 1 out of 400? Ignore them? Pretend they don’t exist? Allow the self-righteous Norms to persecute them? They are real, they exist, they have just as much right to exist as someone with an XY chromosome pair. Their existence is also not a rebuke to the 399 out of 400. It just is. If you’re a scientist, accept that.

There’s another weird thing in his comments.

Generally the extreme ends of the spectrum represent the minority with most people somewhere in the middle.

He seems to have confused a bell curve with a spectrum. No, that is not true. If it were, since the middle of the visible light spectrum is about 570 nm, rainbows would be mostly yellow-green. That the human sex chromosome distribution is strongly bimodal with large peaks at XX and XY does not mean there cannot be a spectrum of intermediates. But then, his approach to refuting the idea of a spectrum of sexuality is to a) minimize the existence of known intermediates, and b) then pretend that they don’t count as a “spectrum”, because they don’t fit his predefined and incorrect understanding of what a spectrum is.

He ends similarly with his biased interpretation of the purpose of sex.

Surprisingly, for someone who supposedly champions reason, not once in this episode did Nye even raise the question What is sex for? Why are human beings sexual? There is no mention of children; no mention of marriage; no mention of love. No mention, in fact, of any sort of consequences for our sexual behavior. Bill Nye speaks in this episode of how things are “in the real world” but one gets the impression that he hasn’t lived there in quite some time.

Well, gosh. If he’s going to reduce sex to his narrow “scientific” interpretation of “cold, hard facts”, why is he bringing up love and marriage? Yeast have sex, you know, but they tend not to bother with religious rituals, and I rather doubt that love is involved.

If Nye had brought up the topic of the purpose of human sex, I’m sure it would have been even more offensive to a Catholic minister.

Sex is for reproduction.

Sex is for pair-bonding.

Sex is for fun.

Sex is for sale.

Sex is for political alliances.

Sex is for entertainment.

Sex is for demonstrating submission.

Sex is for conformity.

Sex is for psychological release.

Sex is for trading for favors.

Sex is for religious celebrations.

Sex is for dominance displays.

Sex is for consolation.

Sex is for whatever you feel like.

I’ve noticed that the “real world” seems to have a lot of people and behaviors who aren’t exactly like me and mine. That doesn’t offend me at all. I think I’d rather encourage everyone to be themselves and be happy, than to arbitrarily decide to be like me and be miserable (I’m happy as I am, but wouldn’t expect others to be).

Likewise, you don’t have to like Bill Nye’s new show. I’m neither into gay sex or Bill Nye Saves the World, and that’s just fine. If it opens up a better perspective on science than too many self-identified “science” advocates have, then more power to it.

You can fake peer review?

I’d never even considered the possibility of faking peer review, but it turns out that it’s possible, if you have a sufficiently sloppy journal.

It’s possible to fake peer review because authors are often asked to suggest potential reviewers for their own papers. This is done because research subjects are often blindingly niche; a researcher working in a sub-sub-field may be more aware than the journal editor of who is best-placed to assess the work.

But some journals go further and request, or allow, authors to submit the contact details of these potential reviewers. If the editor isn’t aware of the potential for a scam, they then merrily send the requests for review out to fake e-mail addresses, often using the names of actual researchers. And at the other end of the fake e-mail address is someone who’s in on the game and happy to send in a friendly review.

But this makes no sense! At least with real peer review, you’re kinda sorta somewhat guaranteed that two people will read your paper — the reviewers. If you’re using fake peer review, sending your paper to the kind of crappy journal that can allow it, it may mean no one will ever read it. It’s a notch on your CV, I guess.

I do appreciate the error made that allows them to be caught, though.

Fake peer reviewers often “know what a review looks like and know enough to make it look plausible,” said Elizabeth Wager, editor of the journal Research Integrity & Peer Review. But they aren’t always good at faking less obvious quirks of academia: “When a lot of the fake peer reviews first came up, one of the reasons the editors spotted them was that the reviewers responded on time,” Wager told Ars. Reviewers almost always have to be chased, so “this was the red flag. And in a few cases, both the reviews would pop up within a few minutes of each other.”

So now all the fake scientists with the fake reviewer email addresses will know to wait a week or two before sending in their two thumbs up reviews. Or, for added verisimilitude, they’ll hold the reply for six months or more. Now we’ll never catch them!

Congratulations, Chuck Kimmel

I entered Chuck Kimmel’s lab at the University of Oregon in the summer of ’79 — 38 years ago (I know, time flies when you’re living your life). It was a rather miserable summer, because I was trying to do physiological recordings of Mauthner cell activity, and nothing worked. Stupid fish. They were so inconsistent and annoying. I’d thump them in the ear one time and get a lovely extracellular spike, and then I’d spend days whacking them some more and they’d just lie there, as inert as the gelatin they were imbedded in, near as I could tell.

But I lucked out, because Chuck was a sympathetic and usually patient advisor, and I got through that summer and onto projects that actually did work. And now he’s won a Major Award.

Chuck Kimmel, a UO professor emeritus in the Department of Biology and the Institute of Neuroscience, recently was honored for his contributions to the field with the International Zebrafish Society’s first-ever George Streisinger Award.

Streisinger, the late UO biologist, is widely considered the founding father of zebrafish research. Kimmel helped establish the foundation of modern zebrafish research.

“Without Chuck working very hard to promote the field, the whole enterprise could have just dwindled,” said Judith Eisen, a UO professor in the Department of Biology and the Institute of Neuroscience whose lab uses zebrafish to study neuron diversity during development. “It’s fair to say Chuck was absolutely instrumental in bringing us from where we were, with just a few labs at the UO, to where we are today, with well over 1,000 labs worldwide.”

He’s the right person to win the first George Streisinger Award. To drop names again, I also knew George fairly well.

“To get an award named for George is a special privilege,” Kimmel said. “George and I go way back and I feel very honored.”

Zebrafish research is now thoroughly ingrained in the culture at the UO, where about 100 researchers in 11 labs use zebrafish to study medical issues and answer fundamental questions about development. But that wasn’t always the case.

Kimmel said he was not thinking about zebrafish research when Streisinger recruited him to come to the UO in 1969. At the time, he was more interested in questions about biological specificity and was drawn to the UO by the Institute of Molecular Biology, one of the first interdisciplinary university research centers.

But by the late 1970s, Kimmel was working closely with Streisinger on several collaborative research projects involving zebrafish. Kimmel zeroed in on developing neurons in the zebrafish brain and embarked on a decade-long research quest to illuminate the developmental steps that led to different tissue types in the zebrafish embryo.

In 1984, Streisinger died while scuba diving. Kimmel and others who worked alongside Streisinger — including UO biologist Monte Westerfield and Streisinger’s assistant, Charline Walker — did their best to pick up where Streisinger left off and fill the void left by his sudden passing.

“George was a wizard of a person,” Kimmel said. “He was perfectly honest, perfectly brilliant, perfectly sharing. He just had a lot of positive attributes, which we all tried to emulate.”

Everyone who knew George loved the guy — he was passionate and enthusiastic about everything. Now I’m realizing that everyone involved in zebrafish is a good person. It must be something about the soothing bubbling of the tanks and the gentle, hypnotic schooling of the fish. It just fills you with calm and love of humanity.

Also in that news announcement, a fellow I do not know, Adam Miller, has won the Chi-Bin Chien award. I will go out on a limb and predict that he is also a nice guy, since he’s a zebrafish person. I did know Chi-Bin Chien, who I mainly remember as always laughing and helpful.

You are now thinking “hey, aren’t you, PZ Myers, also a zebrafish guy?” And yes, that is true, but I’m the exception that proves the rule. Everyone else is wonderful, I’m just here to provide a little contrast.

Add ‘light bulbs growing on trees’ to ‘flying cars’ on your list of things Science didn’t bring you for Christmas

There once was a kickstarter that raised half a million dollars with the idea of genetically modifying trees to glow in the dark, thereby replacing the need for street lights. It failed. I’m not surprised. They are citing technical difficulties in getting the needed genes inserted (it looks like they were using the luciferase reaction, which is the enzyme used by fireflies).

To get the plant to glow well, the research team had to insert six genes. But they never could get all six in at once. At best, some plants glowed very dimly. (The photo above of the glowing plant is a long exposure, making it appear much brighter than it actually is.) Evans says that he realizes now trying to insert six genes into a complex organism like a plant—rather than single-celled bacteria or yeast—was premature.

That’s why TAXA, the company that Evans set up to work on glowing plants, eventually pivoted to creating genetically modified moss that smells like patchouli to subsidize continuing glowing-plant research. Moss is a simpler organism. They got the scented moss growing, but the last bunch was contaminated and could not be shipped to customers. Without the moss, there was no way to keep funding the company. That’s when Evans realized that glowing plants weren’t happening.

I don’t even…yes, this is harder than the popular press sometimes makes it sound. Keep that in mind when you hear some transhumanist wackaloon speak blithely of modifying human genes to increase intelligence or longevity or whatever. The tools keep getting better, so maybe someday it’ll be easy to spritz in any number of genes into any organism we want, but the hard part is always going to be figuring out what genes do what we want, and don’t do what we don’t want.

That’s not what made me instantly doubt the project, though. It was wondering what fantasy world they were living in to think bioluminescence would have adequate output to come even close to the illumination we can produce with street lights. Consider the amount of light you can get from a jar of fireflies, if you’ve ever caught them; they’re pretty, but it really isn’t enough to read by, or to compete with a cheap flashlight. I’ve seen seas lit up with swarms of bioluminescent organisms, but even there it was only bright in contrast to the total darkness of the night. Right away I’m questioning how effective even a “tree” that was a solid cylinder of bioluminescent molecules would be.

Another problem: your tree cells are busy making light, like a collection of glow sticks inside…but they’re surrounded by bark. Trees aren’t transparent, you know, so only the thin outer layer of living cells will count for light production.

So just make the bark the glowing part, you say. Can’t. The outer layer of bark is dead, the luciferase reaction requires constant consumption of ATP and O2. This is an energy-intensive reaction, even if the enzyme is remarkably efficient at converting chemical energy into photons. So you’re basically trying to engineer a plant with an alternative pathway to compete with the Calvin cycle, subverting the whole process of absorbing photons to produce chemical energy to instead throw away that energy by emitting photons. And you’re simultaneously expecting the plant to grow into a massive tree.

Yeah, it’s a hard problem alright.

You now may be thinking but wait — we’ve made glow-in-the-dark fish, and you can buy them for five bucks down at the pet store. That’s a whole different process. Glofish don’t make light, and don’t require internal energy to produce photons. They absorb light and re-emit it at a different wavelength, causing a color shift, a process called fluorescence. I’ve worked with a lot of fluorescent molecules (and even with luciferase), and it takes some non-trivial optics to separate out the shifted color signal. That light is also faint — it takes further non-trivial electronics to amplify it into a useful signal.

The dodge of producing patchouli-scented moss is a transparent fake-out, too. Nothing about that solves any of the problems of introducing a complex and energetically expensive set of genes into a plant. It’s also remarkably pointless. There’s an herb, Pogostemon, that grows naturally and already produces the scent, so why not just go with that? Also, I may have fond memories of patchouli perfume everywhere in the hippie culture of the 1970s, but there seems to be a lot of people who don’t care for it or its associations, so it’s an odd choice for a replacement. When I go to the store to buy a light bulb, I’m not going to be satisfied if the clerk “pivots” and sells me Axe body spray instead.

Bottom line: if you invested in this, you got taken.

More criticism of Neuralink

Antonio Relagado, senior editor for biomedicine for MIT Technology Review, isn’t too impressed with Elon Musk’s claims for Neuralink. In particular, he explains that the 8-10 year time line for the first available implants is absurd and impossible.

Let’s deal with Musk’s time line first. A brain implant is a medical device that requires neurosurgery. Proving that it works requires a stepwise series of experiments that each takes years, starting in rats or monkeys.

Here’s a time line from the real world: a company called NeuroPace was started in 1997 to develop an implant that controls epileptic seizures. It actually senses a seizure coming and zaps your brain to stop it. The device got approved in 2013—16 years later. And that was for a very serious medical condition in which brain surgery is common.

Putting an implant in healthy people? That would require extraordinary evidence of safety. And that’s hard to picture, because as soon as you open someone’s head you put that person’s life at risk. We at MIT Technology Review know of only one case of a healthy person getting a brain implant: a crazy stunt undertaken in Central America by a scientist trying to do research on himself. It caused life-threatening complications.

Musk doesn’t seem to be considering the ethical problems at all. It’s cool tech, but I wouldn’t let anyone stick wires in my brain unless it was to treat a serious medical problem with tested procedures.

So it’s not crazy to believe there could be some very interesting brain-computer interfaces in the future. But that future is not as close at hand as Musk would have you believe. One reason is that opening a person’s skull is not a trivial procedure. Another is that technology for safely recording from more than a hundred neurons at once—neural dust, neural lace, optical arrays that thread through your blood vessels—remains mostly at the blueprint stage.

So what facts am I missing? What makes it even remotely okay that Musk and Facebook are promising the public telepathy within a few short years?

We criticize religions for making false promises without evidence; we imprison people for bilking people out of money on false pretenses; so yes, I agree, why do we give billionaire industrialists a pass when they make secular claims that don’t stand a chance in hell of coming true, and when they do it on behalf of profit-making companies?