Science

Digital to Biological Printer

by on June 16, 2017 at 12:14 pm in Science | Permalink

In Nature Biotechnology Gibson, Venter et al. describe a biologic printer that can take instructions from the web and without human intervention “print” a variety of biologics:

…DNA templates, RNA molecules, proteins and viral particles were produced in an automated fashion from digitally transmitted DNA sequences without human intervention.

Motherboard has a good writeup:

“If you had [a DBC] hooked up to your desktop computer, we could email you insulin or a vaccine, and the device would produce it for you ready-to-go,” Venter said. “If you think about all the protein-based drugs that are out there… If you can get those by email instead of getting them from the pharmacy, is conceptually going to be a very different world.”

And what is the ultimate goal?

Right now, it prints proteins. In the far future, it could print human babies on Mars.

Hat tip: Martin Laurence.

Boston-based DNA sequencing company is offering to decode the complete genomes of newborns in China, leading some to ask how much parents should know about their children’s genes at birth.

Veritas Genetics says the test, ordered by a doctor, will report back on 950 serious early- and later-life disease risks, 200 genes connected to drug reactions, and more than 100 physical traits a child is likely to have.

Called myBabyGenome, the service costs $1,500 and could help identify serious hidden problems in newborns, the company says.

But some doctors say the plan is a huge overstep. “I think it’s vastly premature to peddle a completely unproven set of data, especially to a vulnerable population like neonates,” says Jim Evans, a professor of genetics at the University of North Carolina Chapel Hill.

The problem is that the risk posed by many disease genes remains uncertain. Even if a child has a mutation in a gene, he or she may never be affected, prompting debate among doctors about whether it’s useful to inform parents.

The Veritas test also steps into uncharted territory by making predictions about how children will look and act: how wide their nose will be, whether they will overeat or have a “novelty seeking” personality, and even whether they are likely to go bald decades in the future.

Evans is sharply critical of any effort to predict traits. Especially with psychology, he says, genetic factors aren’t well understood. “You run the risk of predestination based on bad science,” he says. “Frankly, I think it’s a little bit crazy to do genetic tests on your newborn to find out if 40 years from now they are going to be bald.”

Here is the full story, it has further interesting points.

Jason Kottke reports:

On the website for the book, you can browse the solutions in a ranked list. Here are the 10 best solutions (with the total atmospheric reduction in CO2-equivalent emissions in gigatons in parentheses):

1. Refrigerant Management (89.74)
2. Wind Turbines, Onshore (84.60)
3. Reduced Food Waste (70.53)
4. Plant-Rich Diet (66.11)
5. Tropical Forests (61.23)
6. Educating Girls (59.60)
7. Family Planning (59.60)
8. Solar Farms (36.90)
9. Silvopasture (31.19)
10. Rooftop Solar (24.60)

Refrigerant management is about replacing hydro-fluorocarbon coolants with alternatives because HFCs have “1,000 to 9,000 times greater capacity to warm the atmosphere than carbon dioxide”. As a planet, we should be hitting those top 7 solutions hard, particularly when it comes to food. If you look at the top 30 items on the list, 40% of them are related to food.

Here is the background context:

Environmentalist and entrepreneur Paul Hawken has edited a book called Drawdown: The Most Comprehensive Plan Ever Proposed to Reverse Global Warming which lists “the 100 most substantive solutions to reverse global warming, based on meticulous research by leading scientists and policymakers around the world”.

I will however order the book.

China is far and away the global leader in greenhouse gas emissions, and for all of the EU’s stern tone and finger wagging on climate change, the bloc’s latest data show that its emissions actually increased 0.5 percent in 2015. Contrast that with the United States, which saw emissions drop a whopping 3 percent last year as a result of the continuing (shale-enabled) transition from coal to natural gas.

That is from Jamie Horgan at The American Interest, who makes many other good points, including this:

One’s opinion of the new climate course Trump just charted for America will ultimately depend on how much faith one puts in climate diplomacy as the holy grail for addressing climate change. The truth is, climate diplomacy has always been more about preening, posturing, and moralizing—about optics—above all else. What happened today was also all about optics (intentionally so) and that’s why greens committed to finding “diplomatic” solutions are pulling their hair out today.

I still think it was a mistake to pull out, as “bad optics” are one form of “bad.”  Most of all, Trump’s action contributes to the common and growing perception that America simply isn’t reliable.  But have any market prices indicated that the world’s future is now likely to be more carbon-intensive?  I just don’t see it.

Now for the matter of drive. You observe that most great scientists have tremendous drive. I worked for ten years with John Tukey at Bell Labs. He had tremendous drive. One day about three or four years after I joined, I discovered that John Tukey was slightly younger than I was. John was a genius and I clearly was not. Well I went storming into Bode’s office and said, “How can anybody my age know as much as John Tukey does?” He leaned back in his chair, put his hands behind his head, grinned slightly, and said, “You would be surprised Hamming, how much you would know if you worked as hard as he did that many years.” I simply slunk out of the office!

What Bode was saying was this: “Knowledge and productivity are like compound interest.” Given two people of approximately the same ability and one person who works ten percent more than the other, the latter will more than twice outproduce the former. The more you know, the more you learn; the more you learn, the more you can do; the more you can do, the more the opportunity – it is very much like compound interest. I don’t want to give you a rate, but it is a very high rate. Given two people with exactly the same ability, the one person who manages day in and day out to get in one more hour of thinking will be tremendously more productive over a lifetime. I took Bode’s remark to heart; I spent a good deal more of my time for some years trying to work a bit harder and I found, in fact, I could get more work done. I don’t like to say it in front of my wife, but I did sort of neglect her sometimes; I needed to study. You have to neglect things if you intend to get what you want done. There’s no question about this.

That is from Richard W. Hamming, invaluable throughout.  Hat tip is from Patrick Collison.  Here is the book by Hamming.

That is the topic of my latest Bloomberg column, here is one excerpt:

…it is possible to imagine an alternative vision where federal overhead allocations fall and the liberated money allows more scientists to get more (smaller) grants. Would that be a good idea?

If we look to the private sector as a model, maybe so. Private philanthropy is typically more oriented toward specific projects than toward overhead. One view is that makes federal government funding of overhead all the more important to fill in the gaps; an alternative take is that the private sector realizes a lot of overhead funding ends up wasted, and the federal government ought to see the same. There is some truth to both of these stories, but not surprisingly the academic scientific community is stressing the former.

Research funds spent on overhead strengthen the power and discretion of administrators (who capture and allocate the funds), senior scientists, the lab-based sciences and relatively expensive projects. They make universities more hierarchical and less egalitarian places, where the ability to bring in overhead funds yields status and influence.

Spending less on overhead and more on individual projects would favor small-scale research, and would decentralize authority and influence. Lower overhead allocations would give the government more authority over project choice, and the university less discretion, for better or worse. Overall, projects would have to prove themselves more in the broader world of prizes, donors and news coverage, rather than lobbying within the university for support.

A mixed bag of course — there is much more at the link.

This is not my view, but I am happy to present an alternative perspective for your consideration:

Yes, IRB’s sometimes do ridiculous things. But I served a total of 21 years on the IRB’s of two different institutions, and I’m sure I can match you anecdote for anecdote with obviously dangerous study protocols submitted by investigators, or protocols where the associated consent documents were blatantly misleading or so confusing that even professionals couldn’t understand them. It’s a small minority of submissions, to be sure, but it’s a recurring problem.

In my experience, most protocol delays in IRB review boiled down to issues of clarifying ambiguous language or providing additional background information so that the appropriateness of the proposal can be better assessed. I suspect that much of that could be avoided with better training of investigators on how to write their submissions. At one of the institutions where I served, my Department encouraged junior investigators to “pre-clear” their IRB submissions with me or another Department member who also served on the IRB. We were often able to spot the things that would likely catch the IRB’s attention and help those investigators revise their protocols before submitting them so that they would sail through approval without delays on the first try.

In my view, no person should ever be the judge of his/her own cause. There is nothing in the earlier rules, nor in the modified ones, that prevents an IRB from expediting the review of social science projects that plainly involves little or no risk. Such protocols can be turned around by a staff member in a day or two. But it should never be left to the investigators to make those assessments on their own.

Here is the link of origin.

*Face Value*

by on May 25, 2017 at 9:35 am in Books, Political Science, Science | Permalink

The author is Alexander Todorov, and the subtitle is The Irresistible Influence of First Impressions.  Here is one short excerpt:

When Israeli and Japanese women rated these faces on trustworthiness, their impressions were predictably influenced by what they considered typical.  As the face became more similar to the typical Israeli face, Israelis trusted it more and Japanese trusted it less and less.  As the face became more similar to the typical Japanese face, the opposite occurred.  We trust those who look like members of our own tribe.

The book has excellent photos and plates, recommended.

Yes, the Raj Chetty.  Here is the transcript and podcast.  As far as I can tell, this is the only coverage of Chetty that covers his entire life and career, including his upbringing, his early life, and the evolution of his career, not to mention his taste in music.  Here is one bit:

COWEN: Now your father, he’s a well-known economist, and he studied econometrics with Arnold Zellner at University of Wisconsin. At what age did he start talking to you about Bayesian econometrics?

CHETTY: [laughs]

COWEN: Which is one of his fields, right?

CHETTY: That’s right, my dad did a lot of early work in Bayesian econometrics with Arnold Zellner, and the academic environment was something I grew up with since I was a kid. I’m the last person in my family to publish a paper. My sisters are also in academia on the medical and bio side. Whether it’s statistics or thinking about scientific questions or thinking about how to change things in the world, that’s the environment in which I grew up from the youngest of ages.

We also discuss his famous papers on kindergarten teachers, social mobility, and the other topics he is best known for working on, including tax salience and corporate dividends.  My favorite part is where Chetty explains what I call “the Raj Chetty production function,” namely why he has been part of so many very successful papers, but that is hard to excerpt.  There is also this:

COWEN: In music, the group the Piano Guys, speaking of Mormons. Overrated or underrated?

CHETTY: Underrated. I love the Piano Guys.

COWEN: Why?

CHETTY: I think the Piano Guys are great in terms of doing renditions of popular songs.

COWEN: Not too triumphalist? Do you mean the major chords?

CHETTY: Maybe in some cases, but I like them.

COWEN: Bhindi or okra. Overrated or underrated?…

Self-recommending, if there ever was such a thing.

Paul Krugman blogged on that, with initial impetus from Noah Smith.  Here is Noah:

If you and your buddies have a political argument, a vast literature can help you defend your argument even if it’s filled with vague theory, sloppy bad empirics, arguments from authority, and other crap. If someone smart comes along and tries to tell you you’re wrong about something, just demand huffily that she go read the vast literature before she presumes to get involved in the debate. Chances are she’ll just quit the argument and go home, unwilling to pay the effort cost of wading through dozens of crappy papers. And if she persists in the argument without reading the vast literature, you can just denounce her as uninformed and willfully ignorant. Even if she does decide to pay the cost and read the crappy vast literature, you have extra time to make your arguments while she’s so occupied. And you can also bog her down in arguments over the minute details of this or that crappy paper while you continue to advance your overall thesis to the masses.

…My solution to this problem is what I call the Two Paper Rule. If you want me to read the vast literature, cite me two papers that are exemplars and paragons of that literature. Foundational papers, key recent innovations – whatever you like (but no review papers or summaries). Just two. I will read them.

If these two papers are full of mistakes and bad reasoning, I will feel free to skip the rest of the vast literature. Because if that’s the best you can do, I’ve seen enough.

Those are both interesting posts, but my perspective is different, probably more as a matter of temperament than thinking they are objectively wrong.  Here are a few comments:

1. The best two papers on ethics are not very convincing.  Nonetheless people who have worked their way through a good amount of that literature are much better at ethical reasoning than those who have not.

2. The best two papers on global warming are not very convincing.  What is convincing is how many different perspectives and how many different branches of science point toward broadly similar conclusions.  In fact the aggregate effect here is quite overwhelming (don’t debate gw in the comments, not today; I’ll delete).  It is a question of many moats, not all of them being entirely muddy.

3. I see the Smith-Krugman standard as fairly economistic, and fairly MIT-late 20th century at that.  It is one vision of what a good literature looks like, and a fairly narrow one.  It will elevate simple answers in status, whether or not that is deserved.  It discriminates against dialogic knowledge, book-based knowledge, historical knowledge, and knowledge when the answers and methods are not very exact.  There is the risk of ending up too certain about one’s knowledge.

That all said, I do understand that specialized top researchers, including Nobel Laureates, often may do better holding relatively narrow methodological visions.  Look at all the Nobel Prizes that have been awarded to Chicago.  It might be entirely correct to insist that Becker’s treatise on the family pay more attention to anthropology, but that doesn’t mean he should have followed that advicee.

4. The standard seems to discourage reading, and I would not want to teach it to my students.  I teach something more like “always read more, unless you are writing or doing relevant quantitative work.  And one reason you write is to improve the quality of your reading.  Read more and write more, all the time.”  I still think that is better advice for most (not all) people.

5. Isn’t there a lot to be said for deferring to the opinions of those who have read through the “muddy moat”?  By no means are they all partisans, and the non-partisan ones care most of all about the truth.  After all, they did all that reading!  Defer, rather than trust so much in your ability to pick you the right two papers, or have someone pick them out for you.  I have a much more positive view of survey articles than does Noah, while understanding they do often leave you fairly agnostic on major issues.

6. If the truth of the matter is in fact muddy, you may need to dip into the muddy moat to learn that.

7. The difference between total value and marginal value may be relevant.  You might conclude a field literature has low total value, but the marginal value of learning more about that area still could be quite high.  That is in part because muddy fields and results don’t spread so readily, and so dipping into the muck can yield some revelations.  That is another reason why I would not offer the “two paper standard” as practical advice.

8. If anything, I would put the reading pressure on the other side, namely more rather than less.  Rather than encouraging readers to dismiss or downgrade fields, I would urge them to consult different disciplines altogether, including political science, sociology, and anthropology, others too.  This is much easier to do if you take a more positive attitude toward survey articles.

9. This is quite a subjective impression, but I worry that the dogmatic will use the two paper standard to dismiss or downgrade particular lines of investigation.

10. I don’t know if Noah and Paul were referring to my colleague Garett Jones, who frequently tweets “…if only there were a vast empirical literature” when he sees claims that he regards as empirically false.  Now, I am not the Garett Jones oracle, but I always took his use of the word “vast” to be slightly sarcastic.  Usually these are cases where even a fairly cursory knowledge of the literature in question would indicate something is wrong with the claim at hand.  In my view, Garett is not demanding “vastness” of effort, rather he is criticizing those who don’t grasp what the effort space looks like in the first place.

That title made me think of the woodchuck…anyway, here is the abstract:

Fact-checking has gained prominence as a reformist movement to revitalize truth-seeking ideals in journalism. While fact-checkers are often assumed to code facts accurately, no studies have formally assessed fact-checkers’ performance. I evaluate the performance of two major online fact-checkers, Politfact at Tampa Bay Times and Fact Checker at Washington Post, comparing their interrater reliability using a method that is regularly utilized across the social sciences. I show that fact-checkers rarely fact-check the same statement, and when they do, there is little agreement in their ratings. Approximately, 1 in 10 statements is fact-checked by both fact-checking outlets, and among claims that both outlets check, their factual ratings have a Cohen’s κ of 0.52, an agreement rate much lower than what is acceptable for social scientific coding. The results suggest that difficulties in fact-checking elites’ statements may limit the ability of journalistic fact-checking to hold politicians accountable.

That paper (pdf) is by Chloe Lim, political science at Stanford.  For the pointer I thank Andrew Hall, some interesting political science papers on his home page.  Here is his very interesting book manuscript on how the devaluing of political offices drives polarization, worthy of a top publisher…

Robert Sapolsky’s *Behave*

by on May 11, 2017 at 8:48 am in Books, Science | Permalink

The subtitle is The Biology of Humans at Our Best and Worst.  Sapolsky is tenured in biology and neuroscience at Stanford, and winner of a MacArthur genius grant.  This book is a very impressive compendium of what we know about the social sciences, as might be rooted in behavioral biology and related fields.  The topics include violence, altruism, cooperation, gene-environment interactions, and many more topics along the usual lines.  It’s not a “here is my big idea” book, but rather “here is how we think about social phenomena.”  In the conclusion, Sapolsky writes: “If you had to boil this book down to a single phrase, it would be “It’s complicated.”  Nothing seems to cause anything, instead everything just modulates everything else.”  Those are two very good sentences.

This is likely to be one of this year’s major social science books, and many of you should buy it, but it’s flaw is that there’s no particular claim you are forced to come to terms with.

That is a splendid 1996 book on mathematics and mathematical researchers, by Gian-Carlo Rota.  I found philosophical, mathematical, and also managerial insights on most of the pages.  It is playful and yet earnestly serious at the same time.  Here is one bit:

He [Alonzo Church] looked like a cross between a panda and a large owl.  He spoke in complete paragraphs which seemed to have been read out of a book, evenly and slowly enunciated, as by a talking machine.  When interrupted, he would pause for an uncomfortably long period to recover the thread of the argument.  He never made casual remarks: they did not belong in the baggage of formal logic.  For example, he would not say “It is raining.”  Such a statement, taken in isolation, makes no sense.  (Whatever it is actually raining or not does not matter; what matters is consistence.)  He would say instead: “I must postpone my departure for Nassau Street, inasmuch as it is raining, an act which I can verify by looking out the window.”

It is full of the sociology of everyday life, in mathematical communities that is, for instance:

How do mathematicians get to know each other?  Professional psychologists do not seem to have studied this question; I will try out an amateur theory.  When two mathematicians meet and feel out each other’s knowledge of mathematics, what they are really doing is finding out what each other’s bottom line is.  It might be interesting to give a precise definition of a bottom line; in the absence of a definition, we will give some typical examples.

…I will shamelessly tell you what my bottom line is.  It is placing balls into boxes, or as Florence Nightingale David put it with exquisite tact in her book Combinatorial Chance, it is the theory of distribution and occupancy.

The author fears the influence of philosophy on mathematics, which led to this paragraph:

Philosophical arguments are emotion-laden to a greater degree than mathematical arguments and written in a style more reminiscent of a shameful admission than of a dispassionate description.  Behind every question of philosophy there lurks a gnarl of unacknowledged emotional cravings which act as a powerful motivation for conclusions in which reason plays at best a supporting role.  To bring such hidden emotional cravings out into the open, as philosophers have felt it their duty to do, is to ask for trouble.  Philosophical disclosures are frequently met with the anger that we reserve for the betrayal of our family secrets.

Definitely recommended, the book also has some of the best and most concrete discussions of Husserl’s philosophy I have seen, along with a meta-account of such, and also there is a discussion of the exoteric and esoteric readings of cosmology and black holes and indeed mathematics too.  Here is further information on Gian-Carlo Rota the author.

For the pointer to the book I thank Patrick Collison.

A number of people have climbed onto Twitter and outlined (correctly) how increased uncertainty about the impact of climate change increases the value of doing something about it.  There is downside risk, and of course we wish to buy insurance against that in the form of a more active climate change policy.  Still, that is not looking deeply enough.  I see some of the relevant uncertainties as embodied in the following scenario, which is more about policy means than climate change science:

Following a Trump debacle, finally the Democrats win all branches of government and pass a climate change bill.  There is a carbon tax, and further anti-coal measures, but it isn’t enough to shift energy regimes in a transformational sense (besides, truly transformational technologies require luck and “the right time” far more than price incentives).  Instead the United States becomes more like Western Europe, with higher levels of conservation but no ground-breaking new energy source.  Solar goes up by ten percentage points, and wind by two or three, given NIMBY opposition.  Fracking becomes more efficient yet, which nudges fossil fuels back a bit onto center stage.  Nuclear is closed down altogether, and hydroelectric also goes in reverse or stagnates.  China is as China does, and they slowly move away from their installed coal base, in the meantime taking steps to control their particulate matter but not so much their carbon, copying America in this regard.  India starts a shift from coal to natural gas but still has rising carbon emissions.  Africa and Vietnam exceed growth expectations, with a lot of solar power to be sure, but not enough to counteract their growing industrialization.  The carbon tax causes a mild recession in America, and environmentalism becomes less popular.  The global boost in temperature continues, unchecked.  The people who die each year from regular air pollution — six to seven million at last count — diminish in number with economic growth, but we react largely with indifference to that problem, because it doesn’t fit into domestic political struggles very neatly.

Now, to me something like that is the single most likely scenario, albeit with a lot of uncertainty.  I am still happy to try remedial policy measures, and to try them now, if only out of non-complacency or perhaps just desperation.  But come on, let’s be honest.  If all you are doing is trying to combat uncertainty about the science, you are unwilling to look the actual problem square in the eye, just like the climate deniers, the very people you so much decry.

That is a new project by Jonathan Haidt and the Heterodox Academy, here is a partial summary:

Heterodox Academy announces a simpler, easier, and cheaper alternative: The Viewpoint Diversity Experience. It is a resource created by the members of Heterodox Academy that takes students on a six-step journey, at the end of which they will be better able to live alongside—and learn from—fellow students who do not share their politics.

It’s a very flexible resource that can be completed by individuals before they arrive on campus, presented in an orientation-week workshop, or expanded into a full semester course that students can take during their first year. (It could also be helpful in high schools, companies, religious congregations, and any other organizations that are experiencing sharp political divisions and conflicts.)

…The site is still under development: we welcome feedback and criticism. We particularly seek out professors, high school teachers, and diversity trainers who will partner with us to develop detailed teaching plans and activities. We will have a larger public launch of the project in August, complete with assessment materials that will allow you to measure whether the curriculum actually increased political knowledge and cross-partisan understanding.

Do click on the site itself for a fuller explanation, and please help out if you can.