biology – Common Infirmities

The mythical pre-history of plant-based meat

In reading Matthew Cobb‘s fascinating new book on the history of ethics and genetic engineering I came across this quote from Martin Apple, president of the world’s first transgenic plant research institute, the International Plant Research Institute, in 1981:

We are going to make pork chops grow on trees!

Of course, long before the first soy latte was even a twinkling in the woke barrista’s eye, people were concerned with plant-based substitutes for meat and dairy for religious reasons. And this reminded me obliquely of the myth of the barnacle goose.

In the Middle Ages it was widely believed that this bird grew from its snout from trees hanging over the water, or out of a barnacle attached to the bottoms of ships or loose pieces of wood. This raised a conundrum for medieval rabbis: For purposes of kashrut, should these geese be classed as fish, meat, or something else?

Some authorities said they were neither fish nor fowl, but rather like shellfish were impermissible no matter how they were slaughtered. But Rabbi Mordechai ben Hillel Ashkenazi of Regensburg said that, effectively, they are fruits:

Regarding birds that grow on trees, there are those that say that they do not require shechitah [ritual slaughter], because they do not reproduce sexually and are like any wood. (Quoted in Sacred Monsters: Mysterious and Mythical Creatures of Scripture, Talmud and Midrash, Nosson Slifkin, p. 319.)

Truly the world’s first plant-based meat!

Finding the mitochondrial Na’ama

I was having a conversation recently about Biblical ancestry and the antediluvian generations, and it got me to thinking about how scientists sometimes like to use biblical references as attention-grabbing devices, without actually bothering to understand what they’re referring to — in this case, the so-called “mitochondrial Eve”. The expression was not used in the 1987 Nature paper that first purported to calculate the genealogical time back to the most recent common ancestor (MRCA) of all present-day humans in the female line, but it was a central to publicity around the paper at the time, including in academic journals such as Science.

The term has come to be fully adopted by the genetics community, even while they lament the misunderstandings that it engenders among laypeople — in particular, the assumption that “Eve” must in some sense have been the first woman, or must have been fundamentally different from all the other humans alive at the time. The implication is that the smart scientists were making a valiant effort to talk to simple people in terms they understand, taking the closest approximation (Eve) to the hard concept (MRCA), and the simple bible-y people need to make an effort on their part to understand what they’re really talking about.

In fact, calling this figure Eve is a blunder, and it reveals a fundamental misunderstanding of the biblical narrative. Eve is genuinely a common ancestor of all humans, according to Genesis, but she is not the most recent in any sense, and suggesting that she is just confusing. The MRCA in the Bible is someone else, namely the wife of Noah. Appropriately, she is not named, but if we want a name for her, the midrashic Genesis Rabbah calls her Na’ama. She has other appropriate characteristics as well, that would lead people toward a more correct understanding. To begin with, she lived many generations after the first humans. She lived amid a large human population, but a catastrophic event led to a genetic bottleneck that only she and her family survived. (That’s not quite the most likely scenario, but it points in the right direction.) And perhaps most important — though this reflects the core sexism of the biblical story — there was nothing special about her. She just happened to be in right place at the right time, namely, partnered with the fanatic boat enthusiast when the great flood happened.

Achieving transparency, or, Momus among the rotifers

At the recent Evolutionary Demography meeting in Miami there were two talks on the life history of rotifers. One of the speakers praised rotifers as a model organism for their generously choosing to be transparent, facilitating study of their growth and physiological changes. I had never really thought much about transparency as a positive feature of organisms (from the perspective of those wanting to study them) — though I guess the same has also favoured the development of the C. elegans system.

I was reminded of the famous quip (reported by his son Leonard Huxley) of T H Huxley, when he asked a student at the end of a lecture whether he had understood everything:

“All but one part,” replied the student, “during which you stood between me and the blackboard.”

To which Huxley rejoined, “I did my best to make myself clear, but could not render myself transparent.”

Momus would have been pleased.

Schrödinger’s menu

I was just rereading Erwin Schrödinger’s pathbreaking 1944 lectures What is Life? which is often praised for its prescience — and influence — on the foundational principals of genetics in the second half of the twentieth century. At one point, in developing the crucial importance of his concept of negative entropy as the driver of life, he remarked on the misunderstanding that “energy” is what organisms draw from their food. In an ironic aside he says

In some very advanced country (I don’t remember whether it was Germany or the U.S.A. or both) you could find menu cards in restaurants indicating, in addition to the price, the energy content of every dish.

Also prescient!

How odd that the only biological organisms that Schrödinger is today commonly associated with are cats…

Political DNA

As someone who actually works with DNA — or, at least, DNA data — I find the drift of the colloquial use of “DNA” disturbing. It’s impossible for me to avoid the resonances of biological determinism, but I’m not sure how other people understand it. I’ve collected a lot of usages, and it seems to have been used in the past to suggest that individuals are being driven by their training or by the historical imperatives of their organisations. Which is sort of fair. But either the meaning is drifting, becoming more crude, or it’s being appropriated for racist purposes.

In this article in yesterday’s Washington Examiner

That Senate Minority Leader Chuck Schumer, D-N.Y., will politicize everything is a given — it’s in his DNA.

Now, I’m pretty sure that the reference to his DNA is not meant to be an ethnic slur. But not completely sure. Why is it there? What is DNA supposed to be adding? Is it his political DNA, his personal DNA (in which case it’s just a redundant statement that this is his immutable characteristic), his family DNA, or his ethnic DNA (which would make it an antisemitic slur). Impossible to say.

Primary sex ratio, the short version

Five months after our article with Orzack et al. appeared in PNAS, showing that the primary sex ratio (the fraction of boys conceived) is close to 50%, contradicting centuries of supposition that it was substantially higher (more male-biased), Bill Stubblefield, Jim Zuckerman and I have published a popular account of the research in Nautilus. It was an interesting experience, the back and forth with an editor to make something comprehensible and gripping for a general audience.

I didn’t end up exactly as we would have liked, but it was probably better — as an effort to explain the science and the background to a general audience — than what we would have produced entirely on our own. The layout and graphics are also very well done.

It’s now been condensed down to three paragraphs on Gizmodo. They even condensed the illustration.

The biggest genetics-investment opportunity ever!

I was just looking at this paper from 2012, that purports to discover the heritability of economic and political preferences by slightly shady statistical analysis of GWAS data. And then it hit me: We could market

An investment plan tailored to YOUR genotype

Okay, we’ll have to work on the catchphrase. Feel free to send your seed money. (The genotype-based diet is running like gangbusters.) Excuse me while I go off for a moment to write the patent application.

Impact!

Genetics and Democracy in the United Kingdom

What is the attraction of monarchy? According to the BBC headline “Kate Middleton in labour as world waits”. Really? The world? What exactly are they holding off on? Doesn’t the world have important things to do? (On the other hand, I’ve just discovered that The Guardian now has an alternative “republican” versions of its web site, with a report on rock star Morrissey in place of the princess’s labour pains. Just click to toggle.)

In honour of the newly announced maturation of the royal zygote into an air-breathing royal neonate — and its generous decision to head off a constitutional crisis by choosing to make do with only half its potential complement of X chromosomes — who is already predestined to rule over Britain, even while he is likely to be occupied less with affairs of state in the near future than with spitting up curdled royal milk from HRH the DoC’s royal mammary glands, I am reposting my proposal from two years ago, occasioned by the royal wedding. The proposal has been unaccountably ignored, despite its prospects for improving the democratic legitimacy of the monarchy. I can only infer that the neglect is due to a basic discomfort among the British elite with the innovations of modern science (unlike the innovations in, say, tax accounting, of which they tend to be avidly fond).

With the impending union of male and female royalty breeders, there has been increasing tendency to cite Thomas Paine’s evergreen mockery:

The idea of hereditary legislators is as inconsistent as that of hereditary judges or hereditary juries; and as absurd as an hereditary mathematician, or an hereditary wise man; and as ridiculous as an hereditary poet-laureate.

(Paine never got to see the number of statistician children filling posts in some of today’s leading statistics departments, but the point is, in principle, well taken.) Seen as the monarchical version of an election — the keystone of the procedure by which a legitimate head of state is created — a Royal wedding certainly feels a trifle arbitrary. But this opposition to monarchy, though it wears the finery of modernity, has failed to keep up with advancing technology. True, it might formerly have been the case that the hereditary principle made the choice of head of state no different from a lottery (for which, see this suggestion). It seems impossible to unite the hereditary principle with the increasingly popular superstition that rulers should be selected by some non-random process, and that hoi polloi should have something to say about it. But now the following arrangements have been announced by the Palace (a particularly sodden corner of the palace wine cellar, to be precise)*:

Following the wedding, a selection of at least 5 royal spermatozoa** will be extracted and fully sequenced by a specially selected team at the Royal Institution for Genetics Pedigree Studies. The secret method (which, in a nod to popular taste, does use beer as a reagent) has been designed to be maximally non-destructive.
The sequences will published on the website princesperm.gov.uk. The public will have 5 days to register and vote for the one that they prefer be invited to form their new ruler.
The elected sperm will be invited in the first instance to inseminate the royal egg. Should it fail in its attempt, the second-place sperm will be sent in. In the case of a repeat failure, a national referendum will be held to determine the correct voting procedure.

* It may be argued that this election proposal, being purely fictional and even farcical, has no bearing on the justification or not of the British monarchy. A dangerous argument indeed, for those who would dispense with fiction and farce would leave central pillars of the British constitutional order bereft of all foundation.

** Why are the future queen’s eggs not also sequenced? Choice of the ovum is a royal prerogative, cf. Blackstone, Commentaries on the Laws of England, v. 5, section 113 (Oxford 1765-1769).

Who needs math?

According to a study by sociologist Michael Handel, summarised here by Jordan Weissman, 75% of American workers never use any mathematics more complicated than fractions in their work. (It goes without saying that most partake of recreational calculus, at least on weekends…) Writing in the NY Times last year, Andrew Hacker argued that most schoolchildren are wasting their time learning mathematics: They’ll never understand it, and they won’t be any the worse off for it. As for scientists, the great entomologist E. O. Wilson has recently taken to the pages of the Wall Street Journal to argue that

exceptional mathematical fluency is required in only a few disciplines, such as particle physics, astrophysics and information theory.

For that matter, even Albert Einstein famously remarked to a schoolgirl correspondent

Do not worry about your difficulties in Mathematics. I can assure you mine are still greater.

But that was after he’d mostly decamped from physics for sagecraft.

Wilson goes on to portray mathematical biologists as technicians, armed with useful tools and useless ideas. And if you need them, you just hire them. (It’s not like they have anything important to do with their time.) So what’s going on? Are mathematicians scamming the public, teaching algebra and other unnecessaries to justify their existence? I would suggest that there are several important issues that these wise men are ignoring or underplaying:

It may be true (as Hacker argues) that only a tiny techno-elite actually needs to know how a computer works, or how to compute the trajectory of a spacecraft, or how to program a Bayesian network. But when they’re 11 years old you don’t know who will have the interest or aptitude to join that elite. If you start sieving the children out early because they don’t seem like a likely candidate for that track — and let’s be honest, a lot of the tracking is going to be based on parental status and educational attainment — most of them will have no way to change tracks later on, because of the cumulative nature of mathematical understanding. Worth noting, in this context, is Handel’s observation (cited above) that skilled blue collar jobs are actually slightly more likely to require “advanced maths” (algebra and beyond) than skilled white collar jobs. So you can’t decide who needs the advanced maths based on the kinds of work they’re going into. Those without the education are simply more likely to be stuck at the lower rungs of whatever trade or profession they go into. (On the other hand, a larger fraction of white collar workers are in Handel’s “upper” (skilled) category, so an average blue collar worker probably needs less maths than an average white collar worker.)
Mathematics is a language. And what is discussed in that language is, as Hacker recognises, crucial to the fate of everyone in the world. Those who have not learned at least the rudiments of the language are excluded from the conversation. I am reminded of a friend who dismissed the value of learning to speak French, with the argument that “Everyone in France speaks English.” Now, France might have been a bad choice for his claim, but even if it were true, it puts you at a significant disadvantage to be surrounded by people who speak your language, while you can’t decipher their language to understand what it is they’re saying to each other.
Think about that Einstein quote: Everyone finds mathematics difficult when they’re pushing beyond their current knowledge. If we’re going to drop mathematics training when it becomes challenging, we might as well stop counting when we run out of fingers and toesies.
I would suggest that Wilson may be using more sophisticated mathematics in his work than he is aware. To paraphrase J M Keynes, practical biologists who believe their work to be quite exempt from any need for mathematics, are usually the slaves of some defunct mathematician. Modern biologists of bench and field are often quite attached to some mathematical and statistical machinery that happens to be some years old, and seemed impossibly abstruse when it first seeped in from the pure mathematics or theoretical statistics world. Many of the attempts to apply mathematical techniques in biology (or sociology or economics or whatever) will prove more clever than enlightening, but some will stick, and become part of the basic toolkit that the biologists who think they don’t need any sophisticated math do use. Wilson’s arrogant posture really reflects the fact that there are far more trained mathematicians who are intellectually flexible enough to try and figure out what the biologists are doing, and what the connections might be to their own field, than trained biologists willing to work in the other direction.

Genetics and Democracy in the United Kingdom

Solving the democracy deficit through modern science

With the impending union of male and female royalty breeders, there has been increasing tendency to cite Thomas Paine’s evergreen mockery: “the idea of hereditary legislators is as inconsistent as that of hereditary judges or hereditary juries; and as absurd as an hereditary mathematician, or an hereditary wise man; and as ridiculous as an hereditary poet-laureate.” (Paine never got to see the number of mathematician children filling the posts in most of today’s leading mathematics departments, but the point is well taken.) Seen as the monarchical version of an election — the keystone of the procedure by which a legitimate head of state is created — a Royal wedding certainly feels a trifle arbitrary. But this opposition to monarchy, though it wears the finery of modernity, has failed to keep up with advancing technology. True, it might formerly have been the case that the hereditary principle made the choice of head of state no different from a lottery (for which, see this suggestion). It seems impossible to unite the hereditary principle with the increasingly popular beliefs that rulers should be selected by some non-random process, and that hoi polloi should have something to say about it. But now the following arrangements have been announced by the Palace (a particularly sodden corner of the palace wine cellar, to be precise)*:

Following the wedding, a selection of at least 5 royal spermatozoa** will be extracted and fully sequenced by a specially selected team at the Royal Institution for Genetics Pedigree Studies. The secret method (which, in a nod to popular taste, does use beer as a reagent) has been designed to be maximally non-destructive.
The sequences will published on the website princesperm.gov.uk. The public will have 5 days to register and vote for the one that they prefer be invited to form their new ruler.
The elected sperm will invited in the first instance to inseminate the royal egg. Should it fail in its attempt, the second-place sperm will be sent in. In the case of a repeat failure, a national referendum will be held to determine the correct voting procedure.

** Why are the future queen’s eggs not also sequenced? Choice of the ovum is a royal prerogative, cf. Blackstone, Commentaries on the Laws of England, v. 5, section 113 (Oxford 1765-1769).