Science

Printing Cancer Killing Viruses

by on December 19, 2014 at 4:50 am in Economics, Science | Permalink

Cell biologist Andrew Hessel of Autodesk is designing viruses in software to attack a specific individual’s cancer and then using DNA Printers to create the viruses as a drug. Here from an interview with New Scientist (gated).

It’s really about making a specific medicine tailored to one person–“N-of-1″ medicine–rather than try to make it a best fit for a whole population. My vision is to create a personalized treatment that can be made in a day by printing bespoke cancer-fighting viruses.

I’m not fully convinced by his economic model but it may be useful as a vision-goal:

I see the business model shifting away from the blockbuster-drug model of the pharma industry–getting the best product for the most people and charging the most for it–to more of a Netflix model, in which you might purchase a subscription for all-that-you-need medicine to manage your cancer.

…I’m pretty sure I can get the virus printing costs down to a dollar a dose. The virus itself is designed by algorithms using diagnostic data from the patient. That info is put into a program that will design the cancer-fighting virus, so the cost of design is cheap. Then there’s testing, and there is no simpler test than on the patient’s own cancer cells in a dish. So that whole process should cost less than $100 end-to-end. If you are on a cancer subscription model paying $100 a month, I see that as ultimately profitable.

Hessel is also far too sanguine about the FDA who he thinks will allow this under “compassionate use.” No way – not today when the FDA prohibits 23andMe from even providing information about DNA and its probable consequences, see my post Our DNA, Our Selves. To make this a reality we will need scientific breakthroughs and also A New FDA for the Age of Personalized Medicine.

In particular, about 57% of the papers accepted by the first committee were rejected by the second one and vice versa. In other words, most papers at NIPS would be rejected if one reran the conference review process (with a 95% confidence interval of 40-75%)

Here is another framing:

If the committees were purely random, at a 22.5% acceptance rate they would disagree on 77.5% of their acceptance lists on average.

That is from Eric Price on the NIPS experiment, there is more here.

For the pointer I thank a loyal MR reader.

Those are the topics of a new paper by Güell, Mora, and Telmer, which is interesting on multiple levels.  The abstract is here:

We propose a new methodology for measuring intergenerational mobility in economic well-being. Our method is based on the joint distribution of surnames and economic outcomes. It circumvents the need for intergenerational panel data, a long-standing stumbling block for understanding mobility. It does so by using cross-sectional data alongside a calibrated structural model in order to recover the traditional intergenerational elasticity measures. Our main idea is simple. If ‘inheritance’ is important for economic outcomes, then rare surnames should predict economic outcomes in the cross-section. This is because rare surnames are indicative of familial linkages. If the number of rare surnames is small this approach will not work. However, rare surnames are abundant in the highly-skewed nature of surname distributions from most Western societies. We develop a model that articulates this idea and shows that the more important is inheritance, the more informative will be surnames. This result is robust to a variety of different assumptions about fertility and mating. We apply our method using the 2001 census from Catalonia, a large region of Spain. We use educational attainment as a proxy for overall economic well-being. A calibration exercise results in an estimate of the intergenerational correlation of educational attainment of 0.60. We also find evidence suggesting that mobility has decreased among the different generations of the 20th century. A complementary analysis based on sibling correlations confirms our results and provides a robustness check on our method. Our model and our data allow us to examine one possible explanation for the observed decrease in mobility. We find that the degree of assortative mating has increased over time. Overall, we argue that our method has promise because it can tap the vast mines of census data that are available in a heretofore unexploited manner.

There are ungated versions here.  For the pointer I thank the excellent Kevin Lewis.

“Something out there is killing everything, and you’re probably next.”

You can view the talk here.  It is called “The Great Filter.”

You can file this one under “Questions that are rarely asked.”  The authors are Bauman, Gale, and Milton and the subtitle is Cross sectional study of political affiliation and physical activity.  It seems, in fact, that the armchair socialists are up out of their chairs:

Objective To examine the validity of the concept of left wing “armchair socialists” and whether they sit more and move less than their right wing and centrist counterparts.

Design Secondary analysis of Eurobarometer data from 32 European countries.

Setting The study emanated from the authors’ sit-stand desks (rather than from their armchairs).

Participants Total of 29 193 European adults, of whom 1985 were left wing, 1902 right wing, 17 657 political centrists, and 7649 politically uncommitted.

Main outcome measures Self-reported political affiliation, physical activity, and total daily sitting time.

Methods Linear models were used to examine the relation between physical activity, sitting time, and reported political affiliation.

Results The findings refute the existence of an “armchair socialist”; people at the extremes of both ends of the political spectrum were more physically active, with the right wing reporting 62.2 more weekly minutes of physical activity (95% confidence interval 23.9 to 100.5), and the left wing 57.8 more minutes (20.6 to 95.1) than those in the political centre. People with right wing political affiliations reported 12.8 minutes less time sitting a day (3.8 to 21.9) than the centrists. It is those sitting in the middle (politically) that are moving less, and possibly sitting more, both on the fence and elsewhere, making them a defined at-risk group.

Conclusions There is little evidence to support the notion of armchair socialists, as they are more active than the mainstream in the political centre. Encouraging centrists to adopt stronger political views may be an innovative approach to increasing their physical activity, potentially benefiting population health.

The full paper is here, and for the pointer I thank Michelle Dawson.

*Do No Harm*

by on December 12, 2014 at 1:35 am in Books, Medicine, Science | Permalink

I loved this book, which is written by a neurosurgeon with a knowledge of behavioral economics (he even has designed a talk  “All My Worst Mistakes,” based on Daniel Kahneman’s work).  The subtitle is Stories of Life, Death, and Brain Surgery and the author is Henry Marsh.  Here is one bit:

…as the brain has the consistency of jelly a sucker is the brain surgeon’s principal tool.

Here is another:

All that really matters is that I am as sure as I can be that the decision to operate is correct and that no other surgeon can do the operation any better than I can.  This is not as much of a problem for me now that I have been operating on brain tumours for many years, but it can be a moral dilemma for a younger surgeon.  If they do not take on difficult cases, how will they ever get any better?  But what if they have a colleague who is more experienced?

And another:

Few anaesthetists believe what surgeons tell them.

How about this one?:

‘There are operations where one really doesn’t know what’s going to happen,’ I muttered to Mike.

Highly recommended, it is already out in the UK, in the U.S. coming out in May 2015.  It has made many best of the year lists in the UK.  Here are some related videos.

Geoengineering

by on December 12, 2014 at 12:20 am in Data Source, Science | Permalink

David Keith, a climate scientist at Harvard University, and author of  A Case for Climate Engineering, is interviewed at re/code.

There’s no question it reduces the global average temperatures; even the people who hate it agree you could reduce average global temperatures. The question is: How does it do on a regional basis?

By far the single most important thing to look at on a region-by-region basis is the impact on rainfall and temperature.

And the answer is, it works a lot better than I expected. It’s really stunning.

A lot of us thought that, in fact, geoengineering would do a lousy job on a regional basis — and there’s lots of talk on the inequalities — but in fact, when you actually look at the climate models, the results show they’re strikingly even.

Now, it’s not perfect and there are some things it won’t do. Turning down the sun does nothing for ocean acidification.

But it looks like it can cut, like, 80 percent of the total variation in climate, which is really stunning.

In some ways we should be singing it from the rooftops. But the scientific community is so painfully scared of talking about it. These papers come out, and people find the best ways to say, well, it sort of works, but it’s really awful.

The fact is, people really appear to have found a way to significantly reduce the climate risk — by more than half, which is a big deal.

Hat tip: Mark Frazier.

Many economists like to dump on their fellow social scientists, and personally I find that reading anthropology is often quite uninspiring.  That said, I would like to say a small bit on the superiority of anthropologists.  I view the “products” of anthropology as the experiences, world views, and conversations of the anthropologists themselves.  Those products translate poorly into the medium of print, and so from a distance the anthropologists appear to be inferior and lackluster (I wonder to what extent the anthropologists realize this themselves?).

Yet anthropologists have some of the most profound understandings of the human condition.  They have witnessed, absorbed, and processed some of the most interesting data, especially those anthropologists who do fieldwork of the traditional kind.

The rest of us are simply (usually) too blind to see this.  It even can be argued that anthropology is the queen and most general of the social sciences, and that economics, as a social science, is simply playing around in one of the larger anthropologically-motivated sandboxes, namely the economy.

We so often confuse “what can be translated into print well” with “what is important and interesting.”  In classical music there have been performers, such as Jorge Bolet, who are incredible but whose genius didn’t translate well in the recording studio.  That does mean anthropology is very often not a highly leveraged means of status and influence.

I believe that travel — when done intelligently — is the most fundamental method of learning.  And yet most travel books are a crashing bore.  Don’t confuse what you — as an outsider — can consume well with what is good and important from an inside perspective.

Skype Translator is on the way

by on December 4, 2014 at 1:38 pm in Education, Science, Web/Tech | Permalink

In May, Satya Nadella and Skype Corporate Vice President Gurdeep Singh Pall unveiled Skype Translator, Microsoft’s breakthrough in real-time speech translation at Re/code’s inaugural Code Conference. Since then, the engineering team has been hard at work to get the technology behind Skype Translator ready for a preview release. Starting today, we are rolling out a Skype Translator preview program sign-up page.

There is more here, the pointer is from Lotta Moberg.

That is the early “computer,” remember?:

Who made the famed Antikythera Mechanism, the astronomical calculator that was raised from an ancient shipwreck near Crete in 1901?

The complex clocklike assembly of bronze gears and display dials predates other known examples of similar technology by more than 1,000 years. It accurately predicted lunar and solar eclipses, as well as solar, lunar and planetary positions.

For good measure, the mechanism also tracked the dates of the Olympic Games. Although it was not programmable in the modern sense, some have called it the first analog computer.

We now learn that the calendar of this mysterious device begins in 205 B.C.  The key point, in my view, is that we have discovered no other comparable machine from antiquity or any other era other than modern times.  It took us until 2006 to even understand what the device was supposed to do, using advanced tomography, and we had been holding it since 1901.

So what to infer?  The first option is that this device was a true outlier, standing sui generis above its time.  Cardiff University professor Michael Edmunds “described the device as “just extraordinary, the only thing of its kind””.

As an artifact that is true, but is that so likely in terms of broader history?  It is pure luck that we fished this thing out of the Mediterranean in 1901.  (By the way, further dives are planned to search for more parts of it.)  The alternative possibility is that antiquity had many more such exotic devices, which have remained unreported, at least in the manuscripts which have come down to us.  That would imply, essentially, that we don’t have a very good idea of what antiquity was like.  In my view that is the more rational Bayesian conclusion.  It is more likely than thinking that we just lucked out to find this one unique, incredible device.  To put it another way, if you found some organic life on a traveling comet, you ought to conclude there is more of that life, or something related, somewhere else.

And to me, the Antikythera Mechanism does not sound like a “lone genius” kind of device: “The gear teeth were in the form of equilateral triangles with an average circular pitch of 1.6 mm, an average wheel thickness of 1.4 mm and an average air gap between gears of 1.2 mm.” (Wikipedia)  That suggests it was made by some kind of regular industrial process.  It also had some sophistications which modern Swiss watches do not.

Given this Bayesian conclusions, which other strange claims stand a decent chance of being true of antquity?  Which other surprises await us?

I find this an interesting passage: “the mysterious device was already pretty ancient by the time it went down some time around 85BC to 60BC with a ship carrying a bride and her dowry, io9 reports…”  You don’t find a lot of people carrying around a lot of ancient PCs today, so might there have been an Antikythera Great Stagnation way back when?  I think maybe so.

Here is a Lego model of the device.  Here is an introductory YouTube video.  Here is Wikipedia on the Antikythera Mechanism, a very good entry.

I owe thanks to Vic Sarjoo for pointers and Robin Hanson for a useful conversation on this topic.

The best-laid plans…

by on November 27, 2014 at 11:32 am in History, Philosophy, Science, Travel | Permalink

Circa 1985:

Merkel, in her early thirties, was looking forward to 2014—when she would turn sixty, collect her state pension, and be allowed to travel to California.

That is from the George Packer profile of Angela Merkel, which I will recommend to you all once again, do note it starts a bit slowly but picks up.

…cetacean brain size, relative to body size, increased substantially about thirty-eight mill years ago when the odontocetes evolved from the ancient archaeocetes…

What drove these changes? It does not seem to have been the transition to an aquatic existence itself as that occurred about fifty-five million years ago and brains stayed at roughly the same relatively small size relative to body weigt as the archaeocetes made their gradual entry into the ocean.  A better hypothesis is that the increased brain size of the odontocetes thirty-eight million years ago was driven by the evolution of echolocation.  The early odontocetes had inner ear bones that were good at picking up high frequency sound, which suggests that they had developed a form of sonar.  Lori Marino thinks “that echolocation came on line and then got co-opted for social communicative purposes.”  In this scenario, the odontocete brains increased in relative size to deal with the acoustic information itself, as well as, perhaps, a new perceptual system based on the data from the returning echoes.  But…the change may have been even more profound: “This may indicate that the large brains of early odontocetes were used, at least partly, for processing this entirely new sensory mode [echolocation] that evolved at the same time as these anatomical changes and perhaps for integrating this new mode into an increasingly complex behavioral ecological system.”

That is from the new and notable The Cultural Lives of Whales and Dolphins, by Hal Whitehead and Luke Rendell, previously covered on MR here.  And here is my earlier post on the economics of dolphins.

Human-dolphin fishing cooperatives

by on November 21, 2014 at 2:37 am in Books, Education, Science | Permalink

1. They have been reported to exist in Australia, India, Mauritania, Burma, and the Mediterranean, but the best known are in Brazil.

2. In parts of southern Brazil, human fisherman have been cooperating with dolphins for many generations (of each species).

3. If fishermen clap just the right way, dolphins will herd fish into the desired areas of fishermen, in muddy lagoon areas.

4. The dolphins perform a distinctive kind of dive to signal to the humans it is time to cast the net for the fish.

5. Only some individual dolphins are able (willing?) to do this well, perhaps the others belong to the forty-seven percent.

5b. The dolphins which cooperate with the fisherman are also more social, more socially connected, and more cooperative with other dolphins.

6. The Brazilian fishermen name the star cooperating dolphins after ex-presidents, soccer players, and Hollywood stars.

7. The names aside, it is not clear whether dolphins benefit from offering this assistance; some commentators suggest the dolphins end up with isolated or injured fish from these exercises.

Here is one blog post report on these practices.  Here is one piece of the original research.  I stumbled upon this while reading the new and excellent Hal Whitehead and Luke Rendell The Cultural Lives of Whales and Dolphins, a new book from University of Chicago Press.

We have some new results, from Maria Victoria Anauati, Sebastian Galiani, and Ramiro H. Gálvez, all consistent with my prior intuitions:

Does the life cycle of economic papers differ across fields of economic research? By constructing and analyzing a large dataset that combines information on 9,672 articles published in the top five economic journals from 1970 to 2000 with detailed yearly citation data obtained from Google Scholar, we find that published articles do have a life cycle that differs across fields of economic research (which we divide into the categories of applied research, applied theory, econometrics methods and theory). Applied research and applied theory papers are the clear winners in terms of citation counts. For the first years after their publication, they receive higher numbers of citations per year than papers in other fields of research do. They also reach a higher peak number of citations per year and apparently sustain those peak levels for longer, in addition to being cited over longer periods of time (i.e., they have a longer lifespan). Citation patterns are much less favorable for theoretical papers, which are the object of fewer citations per annum in the first years following publication, have lower peak numbers and a shorter lifespan. Econometric method papers are a special case; the pattern for most of these papers is similar to the pattern for theory papers, but the most successful papers (as measured by the number of citations) on econometric methods are also the most successful papers in the entire discipline of economics.

The SSRN paper is here.  And via Ben Southwood, here is an interesting new paper on how citation success usually pops up early in the life of a paper: “…citations in the first two years after publication explain more than half of the variation in cumulative citations received over a longer period.”

No one knows for sure, you will find a brief survey of some estimates here.  Let’s start with a few simpler points, however.

First, China is notorious for making announcements about air pollution and then not implementing them.  This is only partially a matter of lying, in part the government literally does not have the ability to keep its word.  They have a great deal of coal capacity coming on-line and they can’t just turn that switch off.  They’re also driving more cars, too.

Second, China falsifies estimates of the current level of air pollution, so as to make it look like the problem is improving when it is not.  Worse yet, during the APEC summit the Chinese government blocked the more or less correct estimates coming from U.S. Embassy data, which are usually transmitted through an app.  A nice first step to the “deal” with the United States would have been to allow publication (through the app) of the correct numbers.  But they didn’t.  What does that say about what one might call…”the monitoring end”…of this new deal?

Third, a lot of the relevant Chinese regulatory apparatus is at the local not federal level (in fact it should be more centrally done, even if not fully federalized in every case).  There are plenty of current local laws against air pollution which are simply not enforced, often because of corruption, and often that pollution is emanating from locally well-connected, job-creating state-owned enterprises.  Often the pollution comes from one locality and victimizes another, especially in the north of the country.   Those are not good local regulatory incentives and it will take a long time to correct them.  Right now for instance Beijing imports a lot of its pollution from nearby, poorer regions which simply wish to keep churning the stuff out.  The Chinese also do not have anything close to a consistently well-staffed environmental bureaucracy.

Fourth, if you look at the history of air pollution, countries clean up the most visible and also the most domestically dangerous problems first, and often decades before solving the tougher issues.  For China that highly visible, deadly pollutant would be Total Particulate Matter, which kills people in a rather direct way, and in large numbers, and is also relatively easy to take care of.  (Mexico for instance has been getting that one under control for some time now.)  The Chinese people (and government) are much more worried about TPM than about carbon emissions, which is seen as something foreigners complain about.  Yet TPM is still getting worse in China, and if it is (possibly) flat-lining this year that is only because of the economic slowdown, not because of better policy.

When will China cap carbon emissions?  “Fix TPM and get back to me in twenty years” is still probably an underestimate.  Don’t forget that by best estimates CO2 emissions were up last year in China by more than four percent.  How many wealthier countries have made real progress on carbon emissions?  Even Denmark has simply flattened them out, not pulled them back.

The Chinese really are making a big and genuine effort when it comes to renewables, it is just that such an effort is dwarfed by the problems mentioned above.

The media coverage I have seen of the U.S.-China emissions “deal” has not been exactly forthcoming in presenting these rather basic points.  It’s almost as if no one studies the history of air pollution anymore.

I understand why a lot of reporters want to “clutch at straws” — it’s good for both clicks and the conscience — but a dose of realism is required as well.  The announced deal is little more than a well-timed, well-orchestrated press release.