I, for one, welcome the Internet surveillance state

Well, not really, but I figure I better say so. Google is listening.

Something to consider: the convictions in Steubenville were obtained with the assistance of the flood of data from cell phones. Bruce Schneier considers the implications of constant technological monitoring.

So, we’re done. Welcome to a world where Google knows exactly what sort of porn you all like, and more about your interests than your spouse does. Welcome to a world where your cell phone company knows exactly where you are all the time. Welcome to the end of private conversations, because increasingly your conversations are conducted by e-mail, text, or social networking sites.

And welcome to a world where all of this, and everything else that you do or is done on a computer, is saved, correlated, studied, passed around from company to company without your knowledge or consent; and where the government accesses it at will without a warrant.

Welcome to an Internet without privacy, and we’ve ended up here with hardly a fight.

Are you ready for a world with diminishing privacy? The more difficult question might be…is this a bad thing? The examples given are a little bit on the trivial side — but does it matter if Google, or anyone, knows what sort of porn you like? A little bit more openness might mean an end to shame and sanctimony — but I think the real concern is that selective openness is the danger. If everyone’s porn preferences were known to everyone else, it wouldn’t be a weapon…but if shame continues to fester in the culture at large, then corporations and institutions and individuals with privileged information can use it for unsavory purposes.

Also, I don’t think corporations have porn habits (that we know about!) that could be exploited, so it’s a little asymmetric. Corporations do have extensive financial information that they closet away, though — so if they get to follow our kinks and peccadilloes, do we get access to their shady transactions? That might be a fair trade. Which probably means it couldn’t possibly happen.

Hamza Tzortzis is playing gotcha with Lawrence Krauss now

After that debate between Tzortzis and Lawrence Krauss that was overshadowed by the disgraceful anti-egalitarian exhibition of Muslim misogyny, iERA is now trying a new tactic: they’re releasing tiny snippets of the debate that they believe they can spin into anti-Krauss sentiment. Here’s a perfect example, Krauss’s reply to a question about the morality of incest.

The audience gasped when Krauss said it’s not clear to him that incest is wrong, and then he went on to argue that there are biological and societal reasons why incest is not a good idea, but that he’d be willing to listen to rational arguments for sexual and emotional interactions between siblings, for instance…not that he’d encourage such behavior. It’s a nuanced and complicated reply in too short a time, but otherwise, he’s not wrong.

But you know what Tzortzis is thinking: this is a perfect clip to play to the dogmatic mob, his people, who don’t do complicated and nuanced, and don’t care about rational arguments, only absolute dictates.

I’d add two other arguments that might sink in.

One is that religions also rationalize incest. Here’s the Protestant Christian example:

Since Eve was made from one of Adam’s ribs [Genesis 2:21-22], she would have been a clone of Adam and, had there been any genetic mutation in Adam, this would have been reproduced in Eve and expressed in their offspring. However, we may reasonably conclude that there were no mutations, and the very first commandment given to them was “to be fruitful and multiply” [Genesis 1:28]. However, the business at the tree of the knowledge of good and evil took place long before there were any children.

The account then continues where God confronted the guilty pair at the tree, but they did not confess their guilt or plead for forgiveness [Genesis 3:1-13]. God then cursed the serpent, imposed reproductive difficulties upon Eve and “cursed the ground for [Adam’s] sake” [Genesis 3:17]. From that moment, everything that Adam – and mankind since – ate had grown in the cursed ground. Cell by living cell, Adam began to very slowly change from his initial state of eternal perfection to mortal imperfection, and he finally died at the age of 930 years [Genesis 5:5]. Nevertheless, Adam and Eve’s immediate offspring would have been very close to physical perfection while brother-sister marriages were the only unions possible! Further, according to the genealogies given in Scripture, pre-flood longevity was about the same as that for Adam, so families were very large compared to those of today. Brother-sister unions were not only unavoidable, but they undoubtedly became traditional and expected.

Catholics make a similar argument.

Incest was not a problem for the immediate descendants of Adam and Eve. It became a problem when the deterioration of the gene pool meant that there was an increased likelihood that the offspring of the unions of near relatives would inherit physical or mental problems. Adam’s immediate descendants inherited perfect or nearly perfect genes, so the unions of near relatives were not a problem. Besides, near relatives were the only people who existed.

Muslims, too.

it is a known fact that legislation differs from one Shari’ah to another, while the principles and beliefs remain the same in all of them. So, making of portraits was allowed in the Shari’ah of Sulayman (peace be upon him) but is prohibited in our Shari’ah. Similarly, making prostration of salutation was permitted in the Shari’ah of Yusuf (peace be upon him) but is illegal in ours. Also, war booty was prohibited for nations before us but it is completely legal for us. The Qiblah of people before us used to be towards Bayt Al-Maqdis, but for us it is towards Ka’bah. In a similar way, marriage between brothers and sisters was permitted in the Shari’ah of Adam (peace be upon him) as opposed to those that came afterwards. The following is a clarification on the issue by Haafidh Ibn Katheer, who said:

Allaah allowed Adam (peace be upon him) to marry his daughters to his sons for necessity. Every couple used to have a boy and a girl. Hence, he married the girl of one couple to the boy of another. This is said by Suddi regarding what has been narrated by Abu Maalik and Abu Salih, from Ibn ‘Abbas, by Murrah from Ibn Mas‘ood and by other companions of the Prophet (peace be upon him) that Adam did not have (in his grandchildren) a baby boy unless it was accompanied by a girl, so he married the male of a couple to the female of another, and the female of a couple to the male of another

So apparently their absolute moral prohibition against incest isn’t quite so absolute after all. A good Muslim can fuck his sister if Allah tells him to.

But the other example I’d give is current, and it’s done all the time. Ever looked at a purebred Arabian horse’s pedigree? It’s an incestuous nightmare, and it’s encouraged — it’s even regarded as a good thing to reinforce good stock with a moderate amount of inbreeding.

Here’s an example of a horse pedigree. Notice what’s going on?

horsepedigree

Look at Pie’s Joseph, for instance. He is the product of a breeding between Wood’s Jay and Wood’s Jay’s granddaughter, Wood’s Chili.

Pie’s Joseph was then bred with his own niece, Pie’s Lady I, and they had a daughter, Pie’s Lady II. Pie’s Joseph was than bred to his own daughter to produce a son, Blue Joe, who is also his grandson.

Let’s not even get into cows and pigeons. Here’s a quick glimpse at the sordid sex life of Favorite:

cowpedigree

Are you squicked out yet? You shouldn’t be. This stuff is going on on farms all over the world. The biological prohibition isn’t quite as strong as you might think — if you want extremes of a phenotype, as you might in agriculture, trying to achieve selective homozygosity for specific traits might actually give you an advantage.

We tend to not want that kind of result in human crosses…although, if you think about it, an unscrupulous nation could embark on a breeding program for athletic ability that would benefit from a multi-generation pattern of incest…

But this all highlights a common problem: get into a debate with fanatics and ideologues like the iERA mob, and they will actually hold it against you if you actually consider the complexities of reality. We like both complexity and reality; how can you argue with someone who comes in with a bias that what you regard as virtues are sinful, and demands that the universe fit itself to their false simplicities?

I support the #tooFEW project

Hey, we all know what atheists, gamers, tech people, and scientists have in common: underrepresentation of minority viewpoints and the presence of indignant white male gatekeepers. Now we get to add another category: wikipedia editors. In that great common resource that gets used all over the place as a quick entry to basic concepts, only 15% of the editors are women. The Feminists Engage Wikipedia project sounds like an excellent way to correct that, by educating more women in how to edit wikipedia and increase the range of contributions.

Note that this is a positive effort. No one is proposing to go in and destroy the patriarchal power structure of wikipedia or anything like that — they are simply trying to get more individuals from wider backgrounds to add topics of interest. All good, right? Exactly in the collaborative spirit of wikipedia?

You’d think so, but they’re already getting pushback. A few people are resentful and think that the initiative will lead to lots of inconsequential topics to clutter up wikipedia — how dare someone think a black feminist writer might be worthy, when we’ve got to document every episode of My Mother the Car? The guys are getting busy strategizing.

sinfest_strategizing

Those of you who are interested might follow Moya Bailey on her blog and on twitter…and participate!

(Thanks to Dana for making me aware of this!)

The Genetic Code is not a synonym for the Bible Code

Oh, boy. The Intelligent Design creationists are all excited about a new paper that purports to have identified an intelligent signal in the genetic code.

Here’s a new paper that can be added to the growing stack of intelligent-design articles in peer-reviewed journals. Even though the authors do not use the phrase “intelligent design,” their reasoning centers on the detection of an intelligent signal embedded in the genetic code — a mathematical and semantic message that cannot be accounted for by a natural cause, “be it Darwinian, Lamarckian,” chemical affinities or energetics, or any other.

I’ve read the paper by ShCherbak and Makukov, and by golly, the Discovery Institute flack really has accurately summarized the paper: it does explicitly and clearly claim to have identified evidence of design in the genetic code! That’s newsworthy in itself, that the creationists can accurately summarize a scientific paper…as long as the results conform to their ideological expectations.

Unfortunately, what they’ve so honestly described is good old honest garbage.

Here’s the short summary of what they do: they jigger the identities of the amino acids coded for by each codon into a number, a nucleon sum. What is that, you might ask? It’s determined by adding up the number of protons and neutrons in the amino acid, which is simply the mass number of the compound. Further, you can distinguish the amino acid into it’s R group, and the atoms that make up the peptide chain proper, which he calls the B group, for standard block. The mass number of the B group is always 74, except for proline, so he transfers a hydrogen from the R group to the proline B group to bring it up to 74, and by the way, did you notice that 74 is two times 37, which is a prime number? Now if you take all the three-digit decimals with identical digits (111, 222, 333…999), and sum their digits (111=3, 222=6, 333=9, etc.) you get the quotient of the number divided by…37!!!1!!

Are you impressed yet? This is simply numerology, juggling highly derived quantities that have little to do with functional properties of the molecules to come up with arbitrary numerical relationships, and then claiming that they’re somehow significant. They also play games with the sums of the mass numbers of just the R groups for certain codons, adding or subtracting the B number, finagling things until they get numbers that are evenly divisible by their magic prime number of 37, etc. It’s pure nonsense through and through.

But every once in a while, something sensible emerges out of the murk. Here’s the logic of their argument:

To be considered unambiguously as an intelligent signal, any patterns in the code must satisfy the following two criteria: (1) they must be highly significant statistically and (2) not only must they possess intelligent-like features, but they should be inconsistent in principle with any natural process, be it Darwinian or Lamarckian evolution, driven by amino acid biosynthesis, genomic changes, affinities between (anti)codons and amino acids, selection for the increased diversity of proteins, energetics of codon-anticodon interactions, or various pre-translational mechanisms.

(1) is simply saying that there must be a pattern of some sort — if the code were purely random assignment of arbitrary nucleotides to each amino acid, it wouldn’t be much of a sign — it would suggest that the sequence is noise, not signal. (2) is the really hard part, the one where you’d have to do a lot of work: you’d have to show that natural processes did not contribute to the pattern. They do not do that. They can’t do that. They take a different and curious tack.

They literally argue that because organizing the code by their nucleon sums makes no sense and has no reasonable functional consequences…therefore it must be an artificial and intentional feature. I’ve heard this argument before. It’s called the Chewbacca defense. Ladies and gentlemen, think about it: that does not make sense! If nucleon numbers show a mathematical pattern of any kind in their relationship to codons, you must accept the existence of a designer.

However, if we can show a natural property that leads to the organization of the genetic code, then I’m afraid their argument evaporates. Even more so than building an argument on the Chewbacca defense, that is.

There’s a very good discussion of the genetic code in Nick Lane’s book, Life Ascending: The Ten Great Inventions of Evolution, and I’ll briefly summarize it.

First, there is a pattern to the genetic code! No one has ever denied that; it’s obviously not the case that amino acids are randomly assigned to trios of nucleotides. Here’s the code:

geneticcode

Let’s look at one amino acid, glycine (Gly), down in the bottom right corner. The genetic code is degenerate: that means that most amino acids have multiple combinations of nucleotides that can specify them. Glycine’s codes are GGU, GGC, GGA, and GGG. Do you see a pattern? The code is actually GG_, where the third position has a lot of slack or wobble, and any nucleotide will do. We see similar cases where just the first two nucleotides are sufficient to specify leucine, valine, serine, proline, threonine, alanine, and arginine. Even with the other amino acids, there are some constraints; CA_ can identify histidine or glutamine, but if the third letter is a pyrimidine (U or C), you get histidine, while if it’s a purine (A or G), you get glutamine. There are patterns all over the place here! So of course ShCherbak and Makukov could find evidence of significant organization.

But there’s more. There are other rules associated with this pattern.

In the synthesis of these amino acids, biochemistry typically modifies a raw starting material. The first letter of the codon says something about the biosynthesis of the associated amino acid.

If the first letter is:
• C, then the amino acid is derived from alpha-ketoglutarate.
• A, then the amino acid is derived from oxaloacetate.
• T, then the amino acid is derived from pyruvate.
• G, then the amino acid is derived in a single step from simple precursors.

The second letter of the codon is correlated with chemical properties of the amino acid.

If the second letter is:
• A, then the amino acid is hydrophilic.
• T, then the amino acid is hydrophobic.
• G or C, the amino acid has an intermediate hydrophobicity.

Wait…so there’s a pattern to the genetic code, and that pattern is associated with the physical properties of the amino acids? Why, that makes sense. Chewbacca is routed! The most likely origin of the code lies in likely catalytic properties of dinucleotides; pairs of nucleotides in ancient organisms were initially functioning as proto-enzymes before they were incorporated into strings of coding information. At least that provides a historical physico-chemical route to the particular code we now have that does not require weird numerological masturbation.

It’s rather pathetic that the Discovery Institute thinks this is a beautiful piece of science. It’s not. It’s nonsense. But look how the DI spins this story:

How will evolutionists respond to this paper? It’s hard to see how they could dismiss it. Maybe they will try to mock it as old Arabian numerology, or religiously inspired (since Kazakhstan, which funded the study, is 70% Muslim). Those would be unfair criticisms. The authors have Russian names, certified doctorates, and wrote in collaboration with leading lights in the West. Or perhaps critics could argue that the authors hail from a foreign country whose name has too many adjacent consonants in it to take them seriously.

No, it appears the only way out for Darwinists would be the “Dawkins Dodge.” You may remember that one from the documentary Expelled, where Dawkins admits the possibility of panspermia for Earth, so long as the designers themselves evolved by a Darwinian process.

What’s most notable about this paper is the similarity in design reasoning between the authors and the more familiar advocates of intelligent design theory. No appeals to religion or religious texts; no identifying the designer; just logical reasoning from effect to sufficient cause. The authors even applied the “design filter” by considering chance and natural law, including natural selection, before inferring design.

If Darwinists want to go on equating intelligent design with creationism, they will now have to take on the very secular journal Icarus.

I didn’t even consider the religious or ethnic basis of this study; it didn’t come to mind at all. It is clearly simple stupid numerology, though. Look at the rationale given for all of the conclusions, which consist entirely of mathematical manipulations of arbitrary derived properties of the molecules, to arrive at a claim of prime number significance.

We certainly don’t need to invoke panspermia. Nothing in the genetic code requires design. and the authors haven’t demonstrated otherwise.

I am most amused by the cute parallelism of claiming surprise that the authors of this paper use “design reasoning” similar to that used by American Intelligent Design creationists. They’ve been slinging this slop for decades; why be impressed that another set of Intelligent Design creationists in Kazakhstan are using the same tired tropes?

I’m also not impressed with the failure of implementation of their logic. OK, they have a ‘design filter’ that they apply, but so what? Their methods failed to recognize a well-known functional association in the genetic code; they did not rule out the operation of natural law before rushing to falsely infer design.

And that last bit…I don’t care what journal it was published in. The prestige of a journal does not confer infallibility, and even the best of journals will occasionally publish crap. They will be especially likely to publish garbage when they stretch beyond the expertise of their reviewers. Icarus is a journal of planetary science that publishes primarily on astronomy and geology. This particular paper conveniently falls between the cracks — it’s a weird paper full of trivial arithmetical manipulations for arcane purposes with no scientific justification for any of its procedures. I don’t know how it got accepted for publication, other than by boring the reviewers with its incomprehensible digit fiddling.

One last thing: don’t rush to claim a secular purpose behind this work. It’s already been appropriated by freaky strange religious fanatics and lovers of the bible codes. You can’t blame shCherbak directly for this weirdo’s interpretations, but certainly he isn’t far from his temperament.

The facts presented on this site, when combined with those now revealed to us by shCherbak, constitute invincible evidence of the truth of the Judeo-Christian Scriptures, and of the Being and Sovereignty of their Divine Author.

Yeah, numerology. Nothing but wanking over tables.

Larry Moran has more — it turns out that Uncommon Descent and Cornelius Hunter also liked this paper. Flies are drawn to shit, I guess.

TED Talk: spreading bullshit about the desert

What? TED vectoring pseudoscience? Unpossible! In one recent particular instance, though, a TED talk firmly grounded in bullshit — literal and figurative — is gaining a mortifying amount of traction with people who really should know better.

The lecturer is Allan Savory, who for the last couple decades has been pushing his own brand of Maverick Science despite hidebound opposition from “scientists” with their “peer review” and their “evidence” and their “reproducible results.”

Savory’s thesis: every desert in the world is caused by insufficient grazing. We know this because of reasons. All those desertified former grasslands in Africa and the Middle East that have been turned to dusty parking lots by cattle and sheep and goats just didn’t have enough livestock on them to churn up the soil, shit everywhere, and then move on to the next patch of land in a rotational grazing approach.

Savory’s approach can work in theory, on marginal grassland with very close monitoring and if your management goals do not include protecting species that are intolerant of cattle. Can work.  Doesn’t necessarily. And that’s irrelevant to actual deserts, yet Savory wants to push his approach onto ancient desert landscapes anyway.

The biggest problem for me, as I point out this morning at KCET, is that Savory doesn’t distinguish between actual deserts — stable, diverse yet fragile habitats — and ruined grasslands. He conflates “desertification” — a term that needs to be abandoned — with actual deserts, then misrepresents the basic science  of desert ecology, for instance calling cryptobiotic crusts a “cancer.”

None of this is a surprise to anyone who has followed Savory over the last few decades. Same shit, different day. But TED has helped him go viral, and there are people who are taking him at his word to an embarrassing degree. Even though he says stuff in the talk like “There is no other option” but to follow his program, a phrase that should cause any sane person to back away slowly with her hand firmly protecting her wallet.

But environmentally concerned people, even here in California, show a disturbing willingness to believe any negative shit they hear about the desert. The TED audience laps Savory’s crap up to a disheartening degree.

Anyway, I debunk what I can of Savory’s crap here at KCET. What I can given time and space, that is. It’s only a 13-minute video and one could write a book about the wrongness.

 

Call for an accounting

I have my doubts about the efficacy of the growing welter of petitions for every possible cause, but at least we can express our concerns. There is now a petition to nvestigate psychiatric research misconduct at the University of Minnesota, my place of work, so I feel an obligation to bring it up.

Dan Markingson was mentally ill and committed suicide almost ten years ago. He was in bad shape and was committed for psychiatric care (he was suffering from violent delusions) when he was recruited into a study by AstraZeneca of anti-psychotic drugs. This was not a good idea; running an experimental clinical trial on patients at serious risk of doing physical harm to themselves and others is not recommended.

In fact, the CAFE study also contained a serious oversight that, if corrected, would have prevented patients like Dan from being enrolled. Like other patients with schizophrenia, patients experiencing their first psychotic episode are at higher risk of killing themselves or other people. For this reason, most studies of antipsychotic drugs specifically bar researchers from recruiting patients at risk of violence or suicide, for fear that they might kill themselves or someone else during the study. Conveniently, however, the CAFE study only prohibited patients at risk of suicide, not homicide. This meant that Dan—who had threatened to slit his mother’s throat, but had not threatened to harm himself—was a legitimate target for recruitment.

He was also signed on by his own consent: the consent of a committed mental patient with serious concerns about his competence, and against the wishes of his mother.

The petition does not assign blame, but only asks for an objective examination by external reviewers. You know there’s a problem when the university’s own bioethicists are supporting the call for investigation.

In 2009, the Minnesota state legislature passed “Dan’s Law,” which prohibits researchers from recruiting a patient under an involuntary commitment order into a psychiatric drug study. Media outlets such as Mother Jones, the St. Paul Pioneer Press, City Pages and Scientific American have published accounts of Dan’s story. His story was also featured in the documentary film, Off Label. In 2010, AstraZeneca, the sponsor of the study in which Dan died, settled federal fraud charges for $520 million, and a University of Minnesota psychiatrist was implicated. Last year, the Minnesota Board of Social Work found serious wrongdoing by the study coordinator for the research study in which Dan died.

More recently, evidence of fraud and serious privacy violations in psychiatric studies at the university have emerged. It is possible that other research subjects have died or suffered serious injuries, or that they have been mistreated in other ways. Bioethicists at the University of Minnesota itself have called for an external investigation, yet the university still refuses.

I signed it. I’d like to recommend that more people sign it.

Another scary aspect of this is the possible abuse of science. There’s some funny stuff going on in clinical trials…

A 2006 study in The American Journal of Psychiatry, which looked at 32 head-to-head trials of atypicals, found that 90 percent of them came out positively for whichever company had designed and financed the trial. This startling result was not a matter of selective publication. The companies had simply designed the studies in a way that virtually ensured their own drugs would come out ahead—for instance, by dosing the competing drugs too low to be effective, or so high that they would produce damaging side effects. Much of this manipulation came from biased statistical analyses and rigged trial designs of such complexity that outside reviewers were unable to spot them. As Dr. Richard Smith, the former editor of the British Medical Journal, has pointed out, “The companies seem to get the results they want not by fiddling the results, which would be far too crude and possibly detectable by peer review, but rather by asking the ‘right’ questions.

I’ve been reading Goldacre’s Bad Pharma: How Drug Companies Mislead Doctors and Harm Patients. There really are grounds for more global concern.

What I taught today: molecular biology of bat wings

Hard to believe, I know, but this class actually hangs together and has a plan. A while back, we talked about the whole cis vs. trans debate, and on Monday we went through another prolonged exercise in epistatic analysis in which the students wondered why we don’t just do genetic engineering and sequence analysis to figure out how things work, so today we reviewed a primary research paper by Chris Cretekos (pdf) that teased apart the role of one regulatory element to one gene, Prx1, in modifying the length of limbs. It’s a cool paper, you should read it. It’s kind of hard to replicate the teaching experience in a blog post, though, because what I did most of the hour was ask questions and coax the students into explaining methods and figures and charts.

I’m afraid that what you’re going to have to do is apply for admission to UMM, register for classes, and take one of my upper level courses. I always have students read papers direct from the scientific literature, and then I torture them with questions until they extract meaning from them. It’s fun!

Although…it would also be cool to have a scientific-paper reading and analysis session at a conference, now wouldn’t it? Especially if it could be done over beer.

Yay! Another reservoir of sequestered carbon can now be released into the atmosphere!

Uh, that was a sarcastic “yay”. Japan is planning to extract natural gas from frozen methane hydrates in the deep ocean. It’s good for them in the short-term — they’ll be able to meet their natural gas needs for decades. But, oh boy, wait until everyone starts liberating yet another locked-up carbon source for energy.

I’m sweating already.