I thought the whole thing was excellent. Like many people, I’ve been trying to withhold judgment on Snowden’s motivations. But after reading this, I’m strongly inclined to believe that his motives are pure, and that he is displaying the type of heroism that our country desperately needs.

Or, if he is actually a villain with some sort of mysterious ulterior motive, he is the sort of charismatic genius supervillain you never see outside of the movies, and I look forward to seeing the schematics for his secret volcanic undersea lair.

I’ve posted a few of the highlights below. If you’re really short on time, here are the highlights of the highlights:

the public needs to know the kinds of things a government does in its name, or the “consent of the governed” is meaningless.

Our founders did not write that “We hold these Truths to be self-evident, that all US Persons are created equal.”

Ask yourself: if I were a Chinese spy, why wouldn’t I have flown directly into Beijing? I could be living in a palace petting a phoenix by now.

Being called a traitor by Dick Cheney is the highest honor you can give an American

This country is worth dying for.

And here are the more extended highlights

Q (Glenn Greenwald): Why did you choose Hong Kong to go to and then tell them about US hacking on their research facilities and universities?

A: First, the US Government, just as they did with other whistleblowers, immediately and predictably destroyed any possibility of a fair trial at home, openly declaring me guilty of treason and that the disclosure of secret, criminal, and even unconstitutional acts is an unforgivable crime. That’s not justice, and it would be foolish to volunteer yourself to it if you can do more good outside of prison than in it.

Second, let’s be clear: I did not reveal any US operations against legitimate military targets. I pointed out where the NSA has hacked civilian infrastructure such as universities, hospitals, and private businesses because it is dangerous. These nakedly, aggressively criminal acts are wrong no matter the target. Not only that, when NSA makes a technical mistake during an exploitation operation, critical systems crash. Congress hasn’t declared war on the countries – the majority of them are our allies – but without asking for public permission, NSA is running network operations against them that affect millions of innocent people. And for what? So we can have secret access to a computer in a country we’re not even fighting? So we can potentially reveal a potential terrorist with the potential to kill fewer Americans than our own Police? No, the public needs to know the kinds of things a government does in its name, or the “consent of the governed” is meaningless.

Q (Gabrielaweb): Why did you wait to release the documents if you said you wanted to tell the world about the NSA programs since before Obama became president?

A: Obama’s campaign promises and election gave me faith that he would lead us toward fixing the problems he outlined in his quest for votes. Many Americans felt similarly. Unfortunately, shortly after assuming power, he closed the door on investigating systemic violations of law, deepened and expanded several abusive programs, and refused to spend the political capital to end the kind of human rights violations like we see in Guantanamo, where men still sit without charge.

Q (MonaHol): Ed Snowden, I thank you for your brave service to our country.

Some skepticism exists about certain of your claims, including this:

I, sitting at my desk, certainly had the authorities to wiretap anyone, from you, or your accountant, to a federal judge, to even the President if I had a personal email.

Do you stand by that, and if so, could you elaborate?

A: Yes, I stand by it. US Persons do enjoy limited policy protections (and again, it’s important to understand that policy protection is no protection – policy is a one-way ratchet that only loosens) and one very weak technical protection – a near-the-front-end filter at our ingestion points. The filter is constantly out of date, is set at what is euphemistically referred to as the “widest allowable aperture,” and can be stripped out at any time. Even with the filter, US comms get ingested, and even more so as soon as they leave the border. Your protected communications shouldn’t stop being protected communications just because of the IP they’re tagged with.

More fundamentally, the “US Persons” protection in general is a distraction from the power and danger of this system. Suspicionless surveillance does not become okay simply because it’s only victimizing 95% of the world instead of 100%. Our founders did not write that “We hold these Truths to be self-evident, that all US Persons are created equal.”

Q (Spencer Ackerman): Edward, there is rampant speculation, outpacing facts, that you have or will provide classified US information to the Chinese or other governments in exchange for asylum. Have/will you?

A: This is a predictable smear that I anticipated before going public, as the US media has a knee-jerk “RED CHINA!” reaction to anything involving HK or the PRC, and is intended to distract from the issue of US government misconduct. Ask yourself: if I were a Chinese spy, why wouldn’t I have flown directly into Beijing? I could be living in a palace petting a phoenix by now.

Q (@KimberlyDozier): US officials say terrorists already altering TTPs because of your leaks, & calling you traitor. Respond?

A: US officials say this every time there’s a public discussion that could limit their authority. US officials also provide misleading or directly false assertions about the value of these programs, as they did just recently with the Zazi case, which court documents clearly show was not unveiled by PRISM.

Journalists should ask a specific question: since these programs began operation shortly after September 11th, how many terrorist attacks were prevented SOLELY by information derived from this suspicionless surveillance that could not be gained via any other source? Then ask how many individual communications were ingested to acheive that, and ask yourself if it was worth it. Bathtub falls and police officers kill more Americans than terrorism, yet we’ve been asked to sacrifice our most sacred rights for fear of falling victim to it.

Further, it’s important to bear in mind I’m being called a traitor by men like former Vice President Dick Cheney. This is a man who gave us the warrantless wiretapping scheme as a kind of atrocity warm-up on the way to deceitfully engineering a conflict that has killed over 4,400 and maimed nearly 32,000 Americans, as well as leaving over 100,000 Iraqis dead. Being called a traitor by Dick Cheney is the highest honor you can give an American, and the more panicked talk we hear from people like him, Feinstein, and King, the better off we all are. If they had taught a class on how to be the kind of citizen Dick Cheney worries about, I would have finished high school.

Q (Ryan Latvaitis): What would you say to others who are in a position to leak classified information that could improve public understanding of the intelligence apparatus of the USA and its effect on civil liberties?

A: This country is worth dying for.

Anyway, with that as prelude, here, for your Sunday morning reading pleasure, is a sequence of Google poems (the latest hot nerd trend in found poetry). This sequence, if it were to be titled, would be titled something like “How long until . . . ”

If there are any screenwriters out there reading this, those last two could form the basis for an awesomely horrible romantic comedy.

If you’re not familiar, these two genes are important because genetic variation in their DNA sequences has been linked to breast cancer. So, the sequence of your DNA in these two genes can reveal if you have a higher-than-average risk of developing breast cancer. It was exactly this sort of test that prompted Angelina Jolie to undergo a preemptive double mastectomy.

The problem is that the tests were really, really expensive, because of Myriad’s patents. So, the immediate consequence of the ruling should be that the prices for these tests should come way, way down.

The opinion (PDF here, if you’re interested) focuses on the difference between “discovering” something — like the sequence or location of a gene — and “creating” something — like a thing that can be patented. So, a gene is a naturally occurring thing that can not be patented. However, if you take the mRNA from a gene and reverse-transcribe it to make cDNA, this new thing might still be patentable. But, the ruling explicitly notes that the cDNA would be a creation because of the removal of introns. So, cDNA from a single-exon gene might not be patentable.

The ruling explicitly states that it offers no opinion on the patentability of genes that have had their DNA sequences deliberately altered — leaving that question for another day.

It also points out limitations of the ruling with respect to plants. The goal here seems to be to ensure that this ruling is not interpreted as invalidating any plant patents covering plant strains that have been developed through selective breeding.

That all seems pretty straightforward. The ruling does seem to leave a number of issues surrounding the patenting of genetic material unresolved, but it is quite clear about which issues it is kicking down the field.

But then there’s this bit of weirdness at the end.

The opinion is pretty much unanimous, which is always nice. Except for a little, tiny bit of dissension from Antonin Scalia. Here is the complete text of his dissenting opinion:

I join the judgment of the Court, and all of its opinion except Part I–A and some portions of the rest of the opinion going into fine details of molecular biology. I am unable to affirm those details on my own knowledge or even my own belief. It suffices for me to affirm, having studied the opinions below and the expert briefs presented here, that the portion of DNA isolated from its natural state sought to be patented is identical to that portion of the DNA in its natural state; and that complementary DNA (cDNA) is a synthetic creation not normally present in nature.

I actually thought Part 1-A of the ruling was a little weird when I first read it. Not because it said anything strange or controversial, but because it read sort of like a Wikipedia entry on basic genetics, and contains a lot of details that don’t seem particularly relevant?.

Here’s the full text of the part of the ruling about which Scalia says, “I am unable to affirm those details on my own knowledge or even my own belief.”

Genes form the basis for hereditary traits in living organisms. See generally Association for Molecular Pathology v. United States Patent andTrademark Office, 702 F. Supp. 2d 181, 192–211 (SDNY 2010). The human genome consists of approximately 22,000 genes packed into 23 pairs of chromosomes. Each gene is encoded as DNA, which takes the shape of the familiar “double helix” that Doctors James Watson and Francis Crick first described in 1953. Each “cross-bar” in the DNA helix consists of two chemically joined nucleotides. The possible nucleotides are adenine (A), thymine (T), cytosine (C), and guanine (G), each of which binds naturally with another nucleotide: A pairs with T; C pairs with G. The nucleotide cross-bars are chemically connected to a sugar-phosphate backbone that forms the outside framework of the DNA helix. Sequences of DNA nucleotides contain the information necessary to create strings of amino acids, which in turn are used in the body to build proteins. Only some DNA nucleotides, however, code for amino acids; these nucleotides are known as “exons.” Nucleotides that do not code for amino acids, in contrast, are known as “introns.” 

Creation of proteins from DNA involves two principal steps, known as transcription and translation. In transcription, the bonds between DNA nucleotides separate, and the DNA helix unwinds into two single strands. A single strand is used as a template to create a complementary ribonucleic acid (RNA) strand. The nucleotides on the DNA strand pair naturally with their counterparts, with the exception that RNA uses the nucleotide base uracil (U) instead of thymine (T). Transcription results in a single strand RNA molecule, known as pre-RNA, whose nucleotides form an inverse image of the DNA strand from which it was created. Pre-RNA still contains nucleotides corresponding to both the exons and introns in the DNA molecule. The pre-RNA is then naturally “spliced” by the physical removal of the introns. The resulting product is a strand of RNA that contains nucleotides corresponding only to the exons from the original DNA strand. The exons-only strand is known as messenger RNA (mRNA), which creates amino acids through translation. In translation, cellular structures known as ribosomes read each set of three nucleotides, known as codons, in the mRNA. Each codon either tells the ribosomes which of the 20 possible amino acids to synthesize or provides a stop signal that ends amino acid production.

DNA’s informational sequences and the processes that create mRNA, amino acids, and proteins occur naturally within cells. Scientists can, however, extract DNA from cells using well known laboratory methods. These methods allow scientists to isolate specific segments of DNA — for instance, a particular gene or part of a gene—which can then be further studied, manipulated, or used. It is also possible to create DNA synthetically through processes similarly well known in the field of genetics. One such method begins with an mRNA molecule and uses the natural bonding properties of nucleotides to create a new, synthetic DNA molecule. The result is the inverse of the mRNA’s inverse image of the original DNA, with one important distinction: Because the natural creation of mRNA involves splicing that removes introns, the synthetic DNA created from mRNA also contains only the exon sequences. This synthetic DNA created in the laboratory from mRNA is known as complementary DNA (cDNA).

Changes in the genetic sequence are called mutations. Mutations can be as small as the alteration of a single nucleotide—a change affecting only one letter in the genetic code. Such small-scale changes can produce an entirely different amino acid or can end protein production altogether. Large changes, involving the deletion, rearrangement, or duplication of hundreds or even millions of nucleotides, can result in the elimination, misplacement, or duplication of entire genes. Some mutations are harmless, but others can cause disease or increase the risk of disease. As a result, the study of genetics can lead to valuable medical breakthroughs.

So, what do you think Scalia is objecting to? Is he just signaling that he thinks that the details of the molecular biology are not important here? Is it the claim that “Genes form the basis for hereditary traits in living organisms”? Is he unable to affirm with his own belief that G pairs with C? That uracil substitutes for thymine in RNA? That humans have 23 pairs of chromosomes?

Please share your most outlandish conspiracy theories in the comments!

Bazelon’s article includes the best Freudian typo I’ve seen in a long time. Near the end of the article, she takes on President Obama’s reassurances that there is really nothing to worry about. In addition to the fact that “it’s nothing to worry about” is a bald-faced lie, she notes that

it is depressing to watch this president become a misleading parser of words in the service of arrogating authority.

I don’t know if that was intentional, but I love it.  ”Aggrogating” is probably just an innocent typo, but it is a fortuitous one, as it invokes “aggro”, which is slang for aggressive.

It was in common use a while ago — I want to say maybe the 90s? — as in “Dude, I’ll give back your Nirvana CD. No need to get all aggro about it!”

Today, I think it is primarily used in the context of online gaming to describe NPCs (non-player characters) who will attack characters without provocation. And this, of course, is exactly the danger inherent in giving unlimited surveillance abilities to the government.

For the record, I personally find it extremely concerning that the NSA is scooping up all of this data, whether or not it is technically legal. In fact, most concerning is the fact that all is that the decisions about what, exactly, is legal have been, and continue to be secret (see, e.g., this piece by Noah Feldman).

A new poll suggests that most Americans are actually okay with government surveillance and loss of privacy (at least when the polling question includes the word “terrorism”). Now, personally, I disagree with most Americans on this one (because there is too much potential for abuse, because systems put in place to deal with terrorism invariably get applied to other things, and because I think that most people’s cost-benefit analysis goes haywire as soon as you say “terrorism”).

However, let’s say for the moment that most Americans would justifiably allow government surveillance of their online activity for the sake of protection against possible terrorist attack. Well, in that case, why the need to lie to people about it? Why has the legal interpretation of the Patriot Act been done in secret?

“You don’t need privacy if you’re not doing anything wrong” cuts both ways, Mr. President.

And I, for one, am not at all reassured that this sort of surveillance system is not going to lead to the aggrogation of authority.

Every year, Barnes & Noble runs a program to encourage kids to read (and, presumably, to purchase books from Barnes & Noble). Here’s how it works, you pick up (or print out) a copy of their summer reading kit (available here), which includes a summer reading journal. You read eight books of your own choosing over the summer (which may or may not have been purchased from Barnes & Noble). Then you write down what you read, whom you would recommend each book to, and why. (Yes, kids, that’s “whom.”)

Then, you return your completed summer reading journal to a Barnes & Noble store before September 3, and they’ll give you a FREE BOOK. Not ANY free book. For instance, you can’t choose Leonardo da Vinci’s 30.8 million dollar Codex Leicester. No, you have to select your free book from the following book list:

So why am I shilling for Barnes & Noble here? Because one of the books you can select as your free book is Remarkable, by Elizabeth “Lizzie K.” Foley, which, as discussed previously, is the single greatest novel in the history of the English language.

Do not be distracted by the My Little Pony: Meet the Ponies of Ponyville. The ponies can wait. Read your eight (8) books, and then run, don’t walk (but stop and look both ways before crossing any streets — also, take a responsible adult with you) to your nearest Barnes & Noble and pick up your free (FREE!) copy of Remarkable.

How is that like capitalism, you ask?

The central economic myth of America is that it is a frictionless meritocracy. If you work hard, you’ll get ahead, no matter who you are, no matter where you come from. The corollary of that is that the people who are ahead got there through hard work, that they have earned everything they have.

In fact, the right-wing version of the myth goes further. It says that the rich have become rich in spite of the obstacles that have been put in their way, like the minimum wage, a (barely) progressive tax structure, organized labor, and government regulation.

In that version of the myth, wealth flows towards the top, just like those balls in the gif roll towards the center. This somehow magically happens, in spite of the fact that those ramps are clearly pitched down away from the center, in spite of the fact that those greedy redistributionists are continually trying to steal the hard-earned money of millionaires and billionaires to pay for their “roads” and their “education.”

What is revealed when the structure is rotated is that, no, actually, those ramps are pitched down towards the center. The ramps are just cleverly constructed so that, when viewed from just the right angle, it looks like they slope the other way, and that the balls are rolling uphill.

What the 2008 financial crisis, and the various more recent events — from interest rate manipulation (LIBOR) to money laundering for terrorists (HBSC) to the impotence/complicity of government regulators (too big to fail / too big to prosecute) — have shown is just how sharply the ramps of our economic system slope towards the center, despite the protestations of the plutocrats who sit at the bottom of that well gobbling up all of the wealth that falls in.

At the moment, the battle over the future of our economy and of our civilization is focused on this issue of perception. The people who benefit from the current rigged system are working as hard as they can to ensure that you keep on looking at our economic system from that one special perspective, the one where the rich are miracle workers who can make balls roll uphill.

So do yourself a favor. Take a walk around our economy. Look at it from a variety of different angles. Sure, look at it from the point of view of the investment banker, of the white-collar professional, of the successful small business owner. But also look at it from the point of view of the recent immigrant with poor English, of the college graduate with $100,000 of student debt and an offer of an unpaid internship, of the single parent of a child with a crippling developmental condition, of the victims of predatory lending schemes, of the third-generation homeless.

You’re going to discover that the economic playing field really is not very level. But I think you’ll discover that if you look at it from anything other than a position of extreme privilege, the slope of that playing field is not necessarily in the direction we are taught to think it is.

In 2013, Rutgers basketball coach Mike Rice received a $475,000 severance after video footage surfaced showing Rice pelting his players with basketballs, grabbing and shoving them, and shouting obscenities at them.

What do these two stories have in common? The stories reveal how Universities are not motivated by their stated missions (truth, education, etc.), so much as by a drive for money and prestige. As a friend of mine recently put it, “Pursuing truth is great, just don’t let it get in the way of your careerism.”

Now, you may be wondering how you can get a job at a University where you get to abuse students, and if you get caught and fired, you still walk away with nearly half a million dollars. I mean, you probably thought you could only get a job like that in an S & M dungeon, or maybe the CIA.

Here’s what pisses me off about the whole thing. Rice did not lose his job for abusing his players. He lost his job for embarrassing the University. When the video first surfaced, everything was handled in house. Rice was given a three-game suspension and a $50,000 fine — secretly. Then, when the video showed up on line, he was fired, along with an assistant coach and the athletic director (who received a $1.25 million severance package). (Here‘s one version)

Some players have argued that Rice’s behavior was not as bad as it appears on the video, and David Plotz argued in Slate that this type of behavior from his own high-school coach made him “a better player and a better man.” Maybe they’re right. Maybe we would all be better off if we were berated regularly for our shortcomings. There’s a balance in there somewhere between “preventing bullying” and raising a generation of hothouse flowers, and I’m not always convinced that we, as a society don’t veer too far in the direction of kid gloves.

The point is, you can imagine defending having a coach like Mike Rice. Likewise, you can imagine arguing that behavior like Rice’s is absolutely unacceptable in a University setting. What is bullshit is internally saying, yes, Mike Rice is great, he just needs to tone it down a notch, and then, when the public finds out, being all, “Oh my god! I can’t believe this was happening!” Basically, the sense you get is that no one was interested in figuring out what the right thing to do was. Everyone was motivated by protecting their own careers, and deflecting embarrassment away from the University.

So how does this relate to dancing teenagers in Jamaica?

The 2005 paper had seven co-authors, but the three key players are Robert Trivers and Lee Cronk, both from the Rutgers Anthropology Department, and William Brown (a postdoc at the time, now in the Psych department at University of Bedfordshire).

A couple of years after the paper came out, Trivers started to suspect that Brown had manipulated the data to make the results more compelling than they actually were. He went on to detail his analysis in a book published in 2009.

So what happens when one of the authors of a high profile paper comes out and claims that the results presented in the paper were not just wrong, but fraudulent? A news piece just out at Nature notes that Trivers approached Nature in 2008 about retracting the paper, but they were not interested. After all, why would they be? Nature’s business plan hinges on publishing studies that are exciting — studies that will be cited by a lot of other papers, and that will attract a lot of attention from the popular press.

This means that Nature (and other high-impact journals like Science) are particularly prone to a few types of bad papers. One is the shocking result that would lead to a major paradigm shift if it were true — but it is not true. One is the paper that seems to represent a huge advance, but is a modest advance that seems bigger than it is because it fails to cite much of the relevant literature. And one is the type we’re potentially talking about here, where a paper presents some really beautiful results, which are beautiful because the data has been manipulated in some way.

The problem is that this business model works great. The upsides of citations and press coverage apparently far outweigh the downsides of publishing incorrect, or incorrectly presented results. In general, there is not that much effort that goes into replicating results in science (arguably, a lot less than there should be). And even if a study fails to be replicated, and is shown to have been wrong, this typically happens years later, when no one is paying attention to the original study anymore.

That means that Nature and Science tend to have this funny status. In biology, anyway, everyone dismisses them as “magazines” or “tabloids.” At the same time, everyone is desperate to publish there.

So what do you do if you’re one of these journals? Well, if you are driven by a moral principle of promoting truth and spreading the best information possible, you put more effort into vetting papers up front, and when a paper is shown to be wrong, you actively try to correct the misperceptions stemming from the fact that people are saying, “Well, this was published in Nature, so it must be right.” On the other hand, if you are driven by the financial health of your corporation, you continue to publish things that will attract attention, and you retract or correct only when you absolutely have to, and you do it as quietly as possible, so as not to harm your brand.

Similarly, what do you do if you are a University associated with publishing a fraudulent paper? Again, if your guiding principles are truth and honest scholarship . . . oh, who am I kidding, those have not been the guiding principles of Universities for decades. As a University, your guiding principle is to maximize your money and prestige (to the extent that prestige begets money). That means that you will promote truth to the extent that you are required to do so, in order to maintain your brand as an important “research” and “education” institution. But what you really want is to keep the accusations of fraud as quiet as possible.

According to Trivers’s account of events, his going public with his book detailing the case for fraud, Rutgers was forced to undertake an investigation, since the work was supported in part by a grant from the NSF. Had they failed to do so, they might have become ineligible for NSF funds. When they completed their investigation in 2012, the University refused to make the results public. Trivers has posted the report on his own site (here). In brief, the report says that, yes, there is evidence for fraud in the paper (although the Nature news piece notes that Brown still denies having manipulated the data).

There’s another part of the story, though, that is much more disturbing. Trivers tells of an incident where he went to confront co-author Lee Cronk in his office about the situation. Trivers felt that Cronk had backed Brown’s version of events, and that the Rutgers report had vindicated his position over theirs, and he called Cronk a “punk.” Cronk then reported the incident to the campus police, and Trivers wound up getting banned from campus for alleged violation of the University’s anti-violence policy.

Now, clearly, I was not there, and so I have no independent source of knowledge about what happened that day. However, the version of event related by Trivers (read the whole thing here), sounds completely consistent with my own interactions with him. His version of the story suggests motivations and actions on the part of others:

It suggests that Cronk overreacted / acted punitively when Trivers confronted him. Maybe he was embarrassed and angry, and pretended to have felt physically threatened by Trivers in order to get back at him. Maybe he really did feel physically threatened, because, maybe, like most academics, he’s sort of a wuss. Maybe he overreacted in the heat of the moment, later wishing that he had not gotten the police involved. I don’t know. I’ve never met him, but this does pass the sniff test as the type of thing I can imagine a lot of Professor types doing.

It suggests that Rutgers sided against Trivers in the incident, perhaps out of retaliation for his original whistleblowing about the paper and the embarrassment and financial cost his actions imposed on the University. After all, if he had kept his mouth shut, they would not have had to undertake the whole fraud investigation, which I’m sure cost a bundle, and they would not have had the embarrassment of national press coverage. Again, clearly, I have no privileged details here, but this sounds like something you would do if you were a University that

I don’t want to pick on Rutgers in particular here. I think that this is the course of action that would have been taken by any University. That does not make it right, though.

I also don’t want to pick on Brown and Cronk, both of whom I suspect are perfectly bright and competent researchers. Even if Brown did actively manipulate the data, I see that as a pathology of the system, where getting a Nature paper can mean the difference between getting a job and not getting a job. If we didn’t hand out jobs and funding and promotions based on numbers of publications and citations — but rather on the quality and rigor of people’s research — there would not be incentives to manipulate or fabricate data. Even if Cronk maliciously got the Rutgers police to ban Trivers from campus, he did so in the context of a system that almost never rewards standing up and saying, “You know what, I was wrong.”

I know a lot of great scientists, people who are their own harshest critics, who are reluctant to publish results until they are 100% certain, who view even critical reviews of their manuscripts as good opportunities to make their work better. I also know a lot of scientists who are happy to cut corners, exaggerate the significance and importance of their results, and promote themselves, even, sometimes, at the expense of the truth.

Unfortunately, the way the current incentive system works, the latter group tend to have much better jobs than the former.

Until we can fix that, everything is going to conspire to encourage researchers to exaggerate, manipulate, and even fabricate their data. And everything is going to conspire to discourage Universities and journals from addressing and correcting fraudulent and erroneous results.

We have to reward honest, serious work that is not necessarily flashy. And we have to reward people who are willing to admit and correct mistakes.

Most of all, we have to reassert the principle of “truth” as our highest value in academia, and fight against its erosion by the secondary values of fame, prestige, and, most importantly, funding.

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Disclosure statements.

Since 2011, I have had an unpaid adjunct / visiting scholar position at Rutgers in the Genetics Department. During that time, I have gotten to know Trivers a bit, and we, in fact, have plans to work on a project together. In my experience, he is brilliant, boisterous, foul-mouthed, politically incorrect, and honest to a fault — exactly the sort of person all academics should aspire to be. Unfortunately, in their current incarnation, Universities much favor mediocre minds and personalities who will toe the corporate line, and who will bring funding to the University without inconvenient things like “truth” get in the way.

In elementary school, I was once on the losing side of a full-length, YMCA-league basketball game that ended 6 to 5. In junior high, I once attended a week-long basketball camp at the end of which I received the Orwellian “Most Improved Player” award.

Here’s the thing. How does the FBI know, or think it knows, that it has recovered “Female DNA”? Well, there aren’t a lot of details available yet, but there are a couple of possibilities.

First, let’s start with the basic genetics. Humans normally have 46 chromosomes, which come in 23 pairs, as well as some mitochondrial DNA. From the mitochondrial DNA, and 22 of the 23 other chromosome pairs, there is nothing to tell you whether the DNA came from a male or a female. The genetic difference between males and females resides in that last chromosome pair, the sex chromosomes. At the sex chromosomes, women have two X chromosomes, while men have one X chromosome and one Y chromosome.

So, if you have a discrete source of your DNA sample, like a hair, you could do a couple of things. You could test it for the presence of Y-chromosome genetic material. If the DNA source was female, you should not find any. Of course, that requires basing your conclusion on a negative result (the absence of a Y chromosome), which is not ideal, since it is possible that you could miss the material for technical reasons (e.g., failure of a particular chemical reaction).

The real thing you would look for to indicate that you had DNA from a female is the presence of two different X chromosomes. That means you need to identify the DNA sequence on part of the X chromosome. You can do this by actually sequencing a region of the chromosome, but this is probably unnecessarily expensive. After all, the vast majority of sites on the chromosome are going to be identical, not just in the X chromosomes in your sample, but in every X chromosome in every human being in the world.

What you can do instead is use tools that focus on specific sites that are already known to be variable in the population. Maybe there’s a particular site where it is known that some people have a C in their DNA sequence, while other people have a G. (This is referred to as a “polymorphic” site.) You simply ask whether that site in your particular sample has a C or a G, while simultaneously asking the analogous question about thousands of other sites.

If your DNA sample came from a male, you might find that the answer is C, or G, or whatever, at a particular site. What the answer is is not as important as the fact that there will be a single answer. If your DNA sample comes from a woman, you should find that sometimes you have a mixture of C and G. Of course, at a given site, you could still get a single answer, say, G, if both of the woman’s X chromosomes had a G at this position. However, if you look at a whole bunch of sites, you should find that a decent number of them indicate a mixture of two sequences — revealing the presence of two distinct X chromosomes, and therefore, a female.

But what if you don’t have a discrete genetic sample, like a hair, to work from? There’s not a lot of detail in the original article, so we have to speculate a bit here. (I’ve reached out to the reporters from the original piece, to see if there was some genetics-dork-relevant information that did not make it into the article. I’ll post an update if and when I hear back.) It seems likely that the bombs would also have carried DNA from one or both of the Tsarnaev brothers. Thus it is possible that the DNA collected by the FBI could contain a mixture of cells from multiple different individuals — like, say, they swabbed all around the bomb’s remains to collect their samples. What would they need to do then?

Well, first of all, let’s consider the case where you had a mixture of the two brothers’ DNA. The Y chromosomes from Dzhokhar and Tamerlan would be (virtually) identical, having both been copied from single the Y chromosome of their father. The two would have distinct X chromosomes, each of which would be a patchwork of pieces copied from their mother’s two X chromosomes.

So, the X chromosomes present in this sort of sample would look similar in some ways to the X chromosomes you would get from a female DNA sample: there would be some polymorphic sites where you would find a mixture of DNA sequences in your sample. However, we would not expect to find as many of these mixed sites as in a sample from a female. On average, half of the X chromosome sequence inherited by one brother would be (virtually) identical to the sequence inherited by the other brother. Although, depending on how, exactly, recombination plays out, the identical fraction of their X chromosomes could range anywhere from nearly none to nearly all of it. It is possible, just by chance, that the X chromosomes inherited by Dzhokhar and Tamerlan would be as different from each other as the two X chromosomes present in their mother. Of course, at this point, DNA samples have almost certainly been collected from both brothers, so that investigators would know exactly what sequences to expect.

But what if there was an even messier mixture of DNA, say with samples from both brothers as well as one or more additional people? Well, at some point, the procedure of just looking for mixed sites in the DNA sequence is going to run into trouble. At most of these polymorphic sites, there are just two variants circulating at any frequency in the population. So, simply identifying sites that are polymorphic within your sample will let you distinguish between one X chromosome and more than one, but will not necessarily do a good job of telling you exactly how many different X chromosomes are present.

One approach to deal with this situation would be to look at a different type of polymorphism, one where there are more than two sequence variants present in the population. The polymorphisms most commonly used in this sort of context are short tandem repeats (STRs). These are stretches of DNA where a short sequence, maybe four or so nucleotides long, is repeated over and over again. Due to the nature of the process by which DNA is copied, these sequences are prone to a particular type of mutation, where the number of repeats increases or decreases. So, I might have a stretch of 19 copies of the sequence TCTA at a particular site in my genome, while you might have 23 copies of TCTA at the same location in your genome.

By looking at a whole bunch of these STR sites, the FBI could probably tell if the DNA they collected contained two, three, four, or more distinct X chromosomes. And, these are most likely the sorts of sites they will be using to see if the DNA collected from the bomb matches the DNA collected from Katherine Russell.

Although the focus of this post has been on genetics, and specifically what it means for the FBI to say that they recovered some “female DNA,” I would be remiss if I did not include the caveat (emphasized in the original WSJ article) that there are a lot of different ways that someone’s DNA might have gotten onto one of the bombs without that person having been involved in the bombing — even if that person winds up being Tamerlan Tsarnaev’s widow.

Q: What’s the difference between E. O. Wilson and a stopped clock?

A: A stopped clock does not have unlimited access to a national media platform to push its ridiculous ideas on the public.

Bazinga!

A couple of weeks ago, E. O. Wilson published a piece in the Wall Street Journal, where he argued that you don’t need math to be a great scientist. There are two parts of the argument. First, that science is more about conceptual thinking that does not require mathematical formalism to get at great ideas. Second, that when it comes time to mathematize, you can always find a mathematician to collaborate with.

He has already been taken to task in places like Slate and Huffington Post. The criticism in these pieces and most of the grumbling I’ve heard around the internet has been something along the lines of, “Nuh uh! Math is too important!” More specifically, that the era of math-free scientific discovery is over. That to operate at the frontier of science in the twenty-first century, you have to be able to grapple with the mathematical and statistical concepts required in the days of big data.

There’s something to that.

On the other hand, I’m sympathetic to what Wilson is trying to do here. I would hate to see anyone drop out of science because they don’t feel that they can keep up with the math. Of course, that’s partly because I think most people can do more math than they think they can, if you know what I mean.

But what I want to focus on here is Wilson’s view of collaboration. This, even more than math, is going to be the must-have talent of the twenty-first-century scientist. The thing about science is, an awful lot of it has been done. To get to the frontiers of human knowledge requires years of study, and, for those of us without super powers, a lot of specialization. At the same time, the most interesting and important problems often lie between areas of specialization, and require contributions from more than one area. Those most interesting and important problems are going to be solved by teams and networks of people who bring different skills to the table, and who are able to integrate their skills in a way that leads to a whole that is greater than the sum of the parts.

It’s that integration bit, I think, that Wilson does not really get. Wilson’s view of collaboration seems to go something like this: you make some observations about some biology, come up with some ideas, then you go find someone who can translate those into the language of mathematics.

Here’s the thing about translation, though. It can’t be unidirectional, or rather, it shouldn’t be unidirectional. At the risk of something or other (obscurity? pretentiousness?), I’m going to dip into poetry here. Robert Haas (Poet, Berkeley Professor, and Occupy hero), in addition to writing a bunch of his own extraordinary verse, has translated seven volumes of poetry by Czech Nobel laureate Czesław Miłosz. Or, more accurately, he collaborated with Miłosz to produce those translations.

After Miłosz’s death, Haas included their translation of Czesław Miłosz’s poem “O!” in his own volume Time and Materials. The poem is prefaced with this note about the translation process:

In his last years, when he had moved back to Kraków, we worked on the translation of his poems by e-mail and phone. Around the time of his ninetieth birthday, he sent me a set of poems entitled “Oh!” I wrote to ask him if he meant “Oh!” or “O!” and he asked me what the difference was and said that perhaps we should talk on the phone. On the phone I explained that “Oh!” was a long breath of wonder, that the equivalent was, possibly, “Wow!” and that “O!” was a caught breath of surprise, more like “Huh!” and he said, after a pause, “O! for sure.”  Here are the translations we made:

Now, if you’re not a writer and/or avid reader of poetry, it may seem strange to fuss over the difference between “Oh!” and “O!” But worrying about the difference between “Oh!” and “O!” is precisely the sort of thing that differentiates poetry from other forms of writing. Robert Frost famously defined poetry as “what gets lost in translation.” One way to unpack that statement is to say that translation can typically capture the basic meaning of words and phrases, but the part of writing that is poetry is the part that goes beyond that basic meaning. Poetry is about subtle differences in meaning. It is about connotation and cultural resonance. It is about the sounds that words make and the emotional responses that they trigger in someone who has encountered that word thousands of times before, in a wide variety of contexts.

These things almost never have simple one-to-one correspondences from one language to another. That means that a good translation of poetry requires a back-and-forth process. If you have a translator who is truly fluent in both languages — linguistically and culturally — this back-and-forth can happen within the brain of the translator. But, if your translation involves two people, who each bring their expertise from one side of the translation, they have to get on the phone every so often to discuss things like the difference between “O!” and “Oh!”

Doing mathematical or theoretical biology is exactly like this.

The theories and observations that build up in the biological domain exist in a language that is profoundly different from the language of mathematics. For theory in biology to be both accurate and relevant, it has to stay true to both of these languages. That means there has to be a vibrant, even obsessive, back-and-forth between the biological observations and concepts and the mathematical representations that attempt to capture and formalize them.

As in the poetry case, if you, as an individual scientist, have a deep understanding of the biology and a fluency in the relevant mathematics, that back-and-forth can happen in your own brain. Where E. O. WIlson is right is in his assertion that, if you don’t have the math, you can still make a contribution, by focusing on building your deep understanding of the biology, and then by finding yourself a mathematician you can collaborate with.

But there’s a trick.

If you’re going to follow this route, you have to sit down with your mathematician, and you have to walk through every single equation. You have to press them on what it means, and you have to follow the thread of what it implies. If you’re the mathematician, you have to sit down with your biologist and say, “If we assume A, B, and C, then mathematically that implies X, Y, and Z.” You have to understand where, in the biology, A, B, and C come from, and you have to work together to discover whether or not X, Y, and Z make any sense.

Basically, each of you has to develop some fluency in the other’s language, at least within the narrow domain covered by the collaboration. If you’re not willing to put in this level of work, then yes, you should probably consider a different career.

Now, maybe you think I’m being unfair to Wilson here. After all, he doesn’t explicitly say that you should hand your ideas over to the mathematicians and walk away. And obviously, I don’t have any privileged access to the inner workings of Wilson’s brain or the nature of his collaborations.

But let’s go back to a couple of years ago, when he collaborated with Martin Nowak and Corina Tarnita to write a controversial paper in which they argued that modeling the evolution of social behaviors based on “kin selection” was fundamentally flawed. That paper elicited a response from the community that is rare: multiple responses criticizing the paper on multiple fronts, including one letter (nominally) co-authored by nearly 150 evolutionary biologists.

I won’t go into the details here, as I have written about the paper and the responses multiple times in the past (here and here, in particular, or you can just watch my video synopsis of the criticism here).

Briefly, the controversial article (published in Nature, arguably the most prestigious journal for evolutionary biologists), completely misinterprets, misrepresents, and/or ignores the work done by other people in the field. It’s a little bit like if you published a physics paper where you said, “But what if the speed of light is constant in different frames of reference? No one has ever thought of that, so all of physics is wrong!” That’s an exaggeration, of course, but the flaws in Wilson’s paper are of this general type.

The weird thing about the paper is that it includes an extensive supplement, which cites much of the literature that is disregarded by the main text of the paper. It is exactly the sort of error that happens when you have something that is written by a disconnected committee, where the right hand does no know what the left hand is doing. Basically, it is hard to imagine a scenario in which someone could actually have understood the papers that are cited and discussed in the supplementary materials, and then turned around and, in good faith, have written that paper.

That leaves us with a few possible explanations. It could be that the authors were just not smart enough to understand what they were talking about. Or it could be that they deliberately misrepresented prior work to make their own work seem more original and important. For the purposes of our discussion here, let’s assume that neither of these explanations is accurate.

Instead, let’s assume that everyone involves is fundamentally competent, and was acting in good faith. In that case, perhaps the problem came from a failure of collaboration. E. O. Wilson probably knows more than just about anyone else in the world about the biology underlying the evolution of social behavior — especially among eusocial insects. Martin Nowak is a prominent and prolific mathematical biologist. Corina Tarnita was a postdoc at the time, with a background primarily in mathematics.

Wilson, as he acknowledges, lacks the mathematical skills required to really understand what the models of kin selection do and do not assume and imply. Tarnita, I imagine, has these skills, but as a young researcher coming out of math, perhaps lacked the biological knowledge and the perspective on the field to understand how the math related to the prior literature and the state of the field. Nowak, in principle, had both the mathematical skills and the biological experience to bridge this gap. He’s a curious case, though, as he, rather famously in the field, is interested in building and solving models, and has little interest in what has been done by other people, or in chasing down the caveats and nuanced implications of his work.

Among the three of them, Wison, Nowak, and Tarnita have all of the skills and knowledge required to write an accurate analysis of models of kin selection. But if assembling the requisite skills was all that was necessary, that Nature paper would have been very different — in much the same way that you could dump a pile of gears, shafts, and pistons in my driveway, and I could drive away in a Camaro.

The challenge of interdisciplinary collaboration is to combine your various skills in a way that creates something greater than the sum of the parts. If you can master this, you’ll be able to make great contributions to whatever field you apply your skills and interests to.

In the case of Wilson’s disastrous paper, what we got was a situation where the deficits that each of the researchers brought to the table combined to create something greater than the sum of the parts. Sadly, I get the feeling that Wilson does not understand this difference, that he thinks collaborating with mathematicians means explaining your intuition, and then waiting for them to “prove” them.

So, yes, you can be a great scientist in the twenty-first century, even if you don’t have great mathematical skills yourself. But, just as Robert Haas called up Czesław Miłosz on the phone to discuss the difference between “O!” and “Oh!” maybe you’re going to have to call up your mathematician collaborators to talk about the difference between O(x) and o(x). You don’t necessarily have to understand the difference in general, but you do need to understand the difference and its implications in the context of the system you’re studying, otherwise you’re not really doing science at all.