Ignorance and dependency make for excellent shackles

Here’s a story of a remarkable woman, Eudocia Tomas Pulido, also known as Lola. She was the Filipino house slave of a Filipino immigrant family, in the late 20th century. She was given to the family as a gift by a local warlord in the aftermath of WWII, and was brought along when they emigrated to the US; they didn’t pay her a salary, didn’t even give her a room of her own, and she cooked and cleaned and raised their kids for practically her entire life. The author of the story is one of those kids, and was trying to make amends for the injustice, but still…she never went to school, had little money of her own, spoke English poorly, and was stranded in America. Even with the best intentions in the world, it’s hard to overcome the deficits imposed by an impoverished upbringing and adulthood.

The only answer is to treat every child as deserving of opportunity and autonomy, and raise them without those shackles. It’s a disgrace that a major American political party seems to be in the business of making new improved coffles for everyone.

We don’t need conspiracy theories to explain Trump

I don’t believe there is a conspiracy, or that our president is a Russian mole. Instead, I accept the “he’s a stupid man” theory. It explains everything without demanding remarkable planning and conscientious effort, which I don’t think the guy at the top is capable of. Trump can’t tell fact from fiction, and neither can the Republicans in congress, or a big chunk of the electorate.

That’s quite the racket

Nature Biotechnology published a rather startling paper: DNA-guided genome editing using the Natronobacterium gregoryi Argonaute. It claims “that the Natronobacterium gregoryi Argonaute (NgAgo) is a DNA-guided endonuclease suitable for genome editing in human cells,” which would make it an alternative to CRISPR/Cas9, and would make the authors rich.

I don’t know any of the details, though, because it’s behind a paywall, and my university doesn’t have an institutional subscription (universities don’t automatically get every journal, and the ones we do get cost the institution an arm, a leg, a pound of flesh, and a bucket of blood). I could pay for it personally, but Nature would charge me $32 for a pdf. If you think about it, it’s quite the deal: the authors do all the research work and then pay for the privilege of publishing in a Nature journal, and then Nature charges readers to see it. The last part would be understandable if they charged a reasonable fee, but of course they don’t.

Imagine if the New York Times worked that way. They fire all their journalists, and tell them that their new model is that if they’re very, very good they can continue to be published in the NYT if they pay Arthur Sulzberger for the privilege. Also, Arthur will change subscription policies: it’ll cost you $10,000/year to subscribe, but you could also just pay for individual articles. Yeah, you’ll pay $32 each week to read David Brooks.

But it’s all moot anyway! The paper has been retracted — no one could replicate the results. Or, at least, there’s an editorial expression of concern.

Guess what? I can’t read that one either. $32. Both the article and its ‘retraction’ are still available for a fee.

This is an amazing business model. Publish a tantalizing paper that is crap, charge people to read it. Publish an announcement that said tantalizing paper is crap, charge people to read it. What we need next is an editorial justifying the science journal’s predatory exploitation, charge people to read it.

(via Neuroskeptic)

Matt Herron sent along the paper and the “expression of concern”, if you were curious about the 3 paragraphs you could get for $32.

Editorial Expression of Concern: DNA-guided genome editing using the Natronobacterium gregoryi Argonaute

Feng Gao, Xiao Z Shen, Feng Jiang, Yongqiang Wu & Chunyu Han

Nat. Biotechnol. 34, 768–773 (2016); published online 2 May 2016; addendum published after print 28 November 2016

The editors of Nature Biotechnology are issuing an editorial expression of concern regarding this article to alert our readers to concerns regarding the reproducibility of the original results. At this time, we are publishing the results of three groups (http://dx.doi.org/10.1038/nbt.3753) that have tried to reproduce the results in the critical Figure 4 in the original paper by Han and colleagues, which demonstrates editing of endogenous genomic loci in mammalian cells. None of the groups observed any induction of mutations by NgAgo at any of the loci or under any of the conditions tested above the sensitivity of the assays used. Similar results have been recently reported by a different group of authors in Protein & Cell (doi:10.1007/s13238-016-0343-9).

We are in contact with the authors, who are investigating potential causes for the lack of reproducibility. The authors have been informed of this statement. While the investigations are ongoing, Chunyu Han and Xiao Z. Shen agree with this editorial expression of concern. Feng Gao, Feng Jiang and Yongqiang Wu do not feel that it is appropriate at this time.

We will update our readers once these investigations are complete.

Our Modern Media at Work

Chris Cillizza of CNN thinks it is awesome that Donald Trump won the dirt vote.

Someone needs to tell Cillizza, and the demented graphic designer who put all the effort into making a constellation of 50 irrelevant pie charts, that dirt doesn’t vote. Also that pie charts suck.

I would like to see Cillizza try and articulate why he thought that noise was awesome, though.

Those rocks belong to everyone

If you’ve ever been to a national park (or to most state parks), there are strict restrictions on what you are allowed to do as a visitor: you can’t back a pickup truck in and load it up with petrified wood, or an assortment of cactuses, or harvest a crop of squirrels. There are all kinds of rules to protect the status of the park from predatory hordes of visitors — if you go rafting through the Grand Canyon, for instance, get used to pooping into a can because you have to haul out everything you bring in.

This is true for everyone. You don’t get to say “Back off, man, I’m a scientist” to excuse going at the Grand Canyon walls with a rock hammer. You have to get a scientific collecting permit, and it’s no rubber stamp process — your application actually gets reviewed by qualified peers.

You know what’s even less effective? Saying Back off, man, I’m a creation scientist.

Creationists regularly run tours through the Grand Canyon, pointing at the rocks and misinterpreting them and using the lens of the Bible to lie about the science, and that’s OK. They’re hurting themselves with ignorance, but as long as they don’t wreck the experience for others, that should be their right. But Andrew Snelling, the Answers in Genesis geology wackaloon who thinks the canyon is only about 4,000 years old, wants to chip away at the rocks and haul away samples, which he will abuse to support his pet thesis. The National Park Service turned him down.

The NPS is awesome.

One of the many things that bug me about creationists is their dishonesty. Snelling had applied for a collecting permit, but avoided saying anything about what he intended to do and minimized his affiliations, pretty much the opposite of what real scientists do.

After conducting three other research projects in the Grand Canyon and guiding 30 river tours of the canyon, he filed a research proposal in Nov. 2013 seeking to collect 60 half-pound rock samples, the suit states. The 24-page proposal only once mentioned his role at Answers in Genesis and contained no other references to religious motivation or creationism.

Snelling claims park officials asked Snelling for two peer reviews evaluating his research proposal, something that hadn’t been asked for in his previous projects. He provided three, which court documents show were written by other academics who have participated in creationist research.

He was turned down. The reviews of his proposal are amusing.

Karl Karlstrom, Ph.D. with the University of New Mexico said Snelling proposal, in part, was not “well written, up-to-date or well referenced” and “I suspect his research application… is motivated by his faith that the Cambrian strata were deposited during Noah’s flood, which is the creationist (and certainly not the scientific) explanation for Grand Canyon strata.”

Peter Huntoon, a former professor at the University of Wyoming, said the park should adhere to “your narrowly defined institution mandate…that ours is a secular society as per our constitution” and argued creationists have already decided the answers to their proposed questions.

“Your internal screening processes should include an examination of the credentials of the submitters so that those who represent inappropriate interests should be screened out,” Hutton wrote and suggested a history of creationist research pre-dating Answers in Genesis.

The third peer-review from Ron Blakley of Northern Arizona University simply said, “it is difficult to review such an outlandish proposal.”

Huntoon’s remark is particularly apropos. Snelling has determined what the “answer” will be (it’s in Genesis!), and there is literally no purpose at all to collecting physical evidence that will be ignored in favor of a collection of ancient myths. That isn’t science.

So of course Answers in Genesis is suing the NPS, and is invoking the Holy Name of Donald Trump to do so.

The suit cites President Donald Trump’s executive order signed May 4 which states all executive departments and agencies shall, to the greatest extent practicable and to the extent of permitted law, respect and protect the freedom of persons and organizations to engage in religious and political speech.

In a press release, Ken Ham, president of Answers in Genesis said this will be a test case of Trump’s order.

Since when is breaking up bits of a park “free speech“?

Hey. I’ve got a rock hammer. I’m also going to visit the Answers in Genesis Ark Park next month. Donald Trump says I get to collect a few bits and pieces in the name of my inviolable religious rights. Do you think that will fly?

Scott Adams embarks on the Johnny Hart road

I don’t normally read Dilbert — I’ve seen far too much of the benighted ignorant psyche of its creator — but this one was just laid out on a table at the coffee shop yesterday, and I knew I’d have to deal with it. In this one, Dilbert goes full climate science denialist. This might be fun, to dissect Dilbert, because even though it will kill what little humor is present in it, at least we’ll have a good time laughing at Scott Adams. Let’s dissect the shit out of this thing.

Here’s the setup.

OK, this is sort of fine. I think it’s a good idea for companies to think about what impact climate change will have on them, and how they affect the environment. I’m at a green university, and we’ve had these sorts of discussions. Still do, all the time.

It is definitely true that human activity is warming the Earth. It will lead to a global catastrophe, depending on how you define catastrophe: it will cause acute economic disruption, resource wars, and the death of millions. Is that catastrophic enough for you?

By the way, I notice that the scientist is a goateed and balding white man in a lab coat. It’s either unconscious bias (that’s how scientists are supposed to look!), or, I can’t help but notice a weak resemblance to Michael Mann.

Next panel, Dilbert asks Scott Adams’ idea of a smart question.

On the face of it, yes, that is a good question. I’d encourage students to ask that every time an instructor told them something. But consider the context. The answer to that question is readily available — google it. You can read the papers. You should have the answer to that from your high school earth science class. So why is Dilbert being made to ask this trivial question right at the start of this meeting? I can tell right away that this is not a sincere question, this is a derailing tactic to justify a software engineer speaking out of his ass to the scientific expert. Sound familiar?

Then we get the eternal dilemma of the science popularizer. Do you just scorch this ass with contempt because you can see right through him, or do you try to take the question seriously and give the primer in kindergarten climatology he’s asking for?

You can’t win, you know. The game is rigged. If you do the former, you’ll be accused of being hostile and mean. If you do the latter, you’re patronizing and people will write scornful blog posts about how you think raw data dumps will cure all the scientific misunderstandings in the world.

So what do you do? Most of us will take the generous view and try to explain exactly what the questioner is asking for, like our Michael Mann surrogate here:

And that’s also fine. So far, the strip has been true to the characters, and the nature of their interactions. It’s denialist vs. scientist, familiar territory, and now it’s time for the funny, clever twist…but Adams can’t deliver. He has to resort to sticking words in the mouth of the scientist that are not at all true to the character.

That’s just wrong. It’s not what climate scientists say or even think. It’s what Scott Adams, who is no scientist of any kind, says and thinks. And with that betrayal of the premise of the joke, it abruptly falls flat and dies. If all you can do to discredit a point of view is to lie and make puppets say falsehoods, it’s your position that fails. Adams does this because he lacks any insightful response to the honest arguments of scientists.

I guess there’s supposed to be a punchline of some sort next. Once again, Adams fails to meet the minimal standards of his medium.

I think the punchline is supposed to be implying that science supporters can only defend their position by calling True Skeptics mean names. Of course, the entire point of the two panels just above that is to call climate scientists conscious liars.

The only people who will find this at all funny are the denialists who see the panels in which the climate scientist openly maligns his methodology as affirmations of their beliefs. That’s OK, it’ll finally be the death of Dilbert — I skimmed the comments and noticed several people were shocked that Scott Adams endorse an anti-scientific claim. Apparently they’ve never read his blog before.

I shouldn’t claim it’ll kill Dilbert, though. Nothing kills syndicated comics. Johnny Hart went full-blown creationist/evangelical Christian/anti-Muslim bigot, and newspapers just kept right on buying up the strips. Hart died in 2007, and B.C. is still going.

And people think tenured professors have it easy.

Creationists need better evidence than that

I found this claim by Mark Armitage that had determined that a triceratops fossil was only a few thousand years old to be ridiculous. He has a defender, Jay Wile, who disagrees with me. He has two main points.

First, I said that carbon dating a dinosaur fossil is absurd — the 14C levels will be too low to get a reliable ratio. Wile thinks that you can, and that being able to cite a number makes it true.

Well, had Dr. Myers bothered to click on the link given in my post, he would have seen that an age was reported: 41,010 ± 220 years. As I state in that link, this is well within the accepted range of carbon-14 dating, and it is younger than many other carbon-14 dates published in the literature. In addition, the process used to make the sample ready for dating has been spelled out in the peer-reviewed literature, and it is designed to free the sample of all contamination except for carbon that comes from the original fossil. Now as I said in my original post, it’s possible that the reading comes from contamination. However, I find that unlikely, given the process used on the sample, the cellular evidence that Armitage found, and the fact that such carbon-14 dates are common in all manner of fossils that are supposedly millions of years old or older.

There are two sources of 14C we have to be concerned with. The bulk of it is cosmogenic, formed in the upper atmosphere from cosmic ray bombardments of ordinary, stable 14N. This 14C decays at a geologically rapid rate, with a half-life of 5730 years. Living things respire and tend to equilibrate their 14C levels with the environment. Another source, though, is the radioactive decay of other elements that generate high energy particles that can also bang into atoms to generate unstable radioactive isotopes. This is a much rarer event, though, so objects that are dead and buried and isolated from the atmosphere tend to equilibrate to a much lower concentration of 14C.

In carbon dating, the 14C to 12C ratio is measured. If it’s close to that of the atmosphere, it was recently exchanging carbon with the atmosphere. If it’s somewhere above the level of dead carbon buried deep in rocks (which has a non-zero level of 14C), it’s older, and we can estimate how much older from the ratio. You can always calculate a ratio. You can always measure a date. However, it will hit a ceiling of about 50,000 years, because of the limits of precision and because the ratio can converge to a value indistinguishable from the background level of 14C. Date a carbon sample that’s a hundred thousand years old; it will return an age of 50,000 years. Carbon date a chunk of coal from the Carboniferous, 300 million years ago, and it will return an age of 50,000 years.

That an “age” was reported is meaningless. An age of 40,000 years means that about 7 14C half-lives had passed, or that less than 1% of the atmospheric levels of 14C were present in the sample. Wile doesn’t understand this at all. He doesn’t seem to comprehend that there could be another source of 14C than from equilibration with the atmosphere. He thinks it is significant that ancient carbon can have non-zero amounts of 14C.

However, creation scientists have carbon-dated fossils, diamonds, and coal that are all supposed to be millions of years old. Nevertheless, they all have detectable amounts of carbon-14 in them. For example, this study shows detectable levels of carbon-14 in a range of carbon-containing materials that are supposedly 1-500 million years old. Surprisingly, the study includes diamonds from several different locations! Another study showed that fossil ammonites and wood from a lower Cretaceous formation, which is supposed to be 112-120 million years old, also have detectable levels of carbon-14 in them. If these studies are accurate, they show that there is something wrong with the old-earth view: Either carbon dating is not the reliable tool it is thought to be for “recent” dating, or the fossils and materials that are supposed to be millions of years old are not really that old. Of course, both options could also be true.

Or that there are underground sources of radioactive decay that can generate low levels of 14C, and that Jay Wile doesn’t understand basic principles of radiometric dating.

Wile also dismisses the possibility of an inclusion of recent biological material in the sample that might skew the date earlier, which is unjustifiable. Armitage himself writes about Soft, moist, muddy material can be seen surrounding pores of bone vessels on inner horn surfaces and rootlets penetrating lower, interior surface of samples where he claims to spot intact Triceratops cells.

But contamination can’t possibly be a confounding problem, oh no.

The second main point Wile makes is that gosh, those cells sure look like osteocytes, which have a distinctive shape with many branching processes. How would osteocytes have gotten in there?

Armitage did not compromise his own results. He simply wrote truthfully about his fossil. In addition, anyone with a basic understanding of histology would know why plant roots, fungal hyphae, and insect remains do not compromise his results in any way. Based on all the visual evidence, the cells he found are osteocytes. They are not only the shape and size one expects from osteocytes, they have the filipodial extensions that are characteristic of osteocytes. They also have the cell-to-cell junctions one expects in groups of osteocytes. Thus, they cannot be the result of contamination, since plants, fungi, and insects do not have osteocytes.

My answer to that is…I don’t know. It’s weird. And Armitage doesn’t know either, and everything he says about the sample is incompatible with these being intact, preserved osteocytes.

The fact that any soft tissues were present in this heavily fossilized horn specimen would suggest a selective fossilization process, or a sequestration of certain deep tissues as a result of the deep mineralization of the outer dinosaur bone as described by Schweitzer et al. (2007b). As described previously, however, the horn was not desiccated when recovered and actually had a muddy matrix deeply embedded within it, which became evident when the horn fractured. Additionally, in the selected pieces of this horn that were processed, soft tissues seemed to be restricted to narrow slivers or voids within the highly vascular bone, but further work is needed to fully characterize those portions of the horn that contained soft material. It is unclear why these narrow areas resisted permineralization and retained a soft and pliable nature. Nevertheless it is apparent that certain areas of the horn were only lightly impacted by the degradation that accompanied infiltration by matrix and microbial activity. If these elastic sheets of reddish brown soft tissues are biofilm remains, there is still no good explanation of how microorganisms could have replicated the fine structure of osteocyte filipodia and their internal microstructures resembling cellular organelles. Filipodial processes show no evidence of crystallization as do the fractured vessels and some filipodial processes taper elegantly to 500 nm widths.

So…

  • The tissue is not isolated or protected in any way. It’s wet, unmineralized, and filled with a “muddy matrix”. Some of the soft tissues, the “vessels”, are crystallized.

  • The “osteocytes”, though, are perfectly preserved down to the level of organelles, ultrastructural junctions, and delicate processes.

Doesn’t anyone else have a problem with this? I’ve had to struggle with fixative cocktails to get good preservation of single-cell levels of detail; I’ve had animal tissue bathed in a soothing, perfectly balanced medium under my microscope, and seen bacterial infections turn them into disintegrating, collapsing blobs of blebbed out fragments of decaying cells within minutes.

Yet somehow Armitage finds picture-perfect “osteocytes” in tissues that have been soaking in mud, perforated by plant roots, and presumably have been lying there rotting since, by his measure, some time around the Great Flood, a few thousand years ago.

I’m just curious. As an experiment, if we killed a cow and then left it to rot in a damp field for just a month, would that be a good way to make useful histological samples of bone tissue?

How about if we left it there for a year? Or 40,000 years?

The Schweitzer papers on preserved cells in dinosaur bone at least demonstrate careful technique to minimize contamination and artifacts. They also don’t include comments that reveal the author doesn’t understand the basic principles of radiometric dating. The Armitage papers, on the other hand, are sloppy, get improbable results, and reveal a lot of biased reasoning.

I don’t know how cells that look like osteocytes got there, but I’m very suspicious.