When not to trust scientists

Forensic DNA evidence is not infallible : Nature News & Comment

Given that it infuriates me that a substantial slab of people do not believe that those who work in the physical sciences are competent when working out things like a temperature record, or the effects of a gas in an atmosphere, I suppose I give the impression much of the time that I never question scientists of any stripe.

But when it comes to the biomedical sciences:  yes, there are many examples of scientists leaping in when they should be more cautious.

And when they get caught up in a court case, they are particularly prone to giving up caution, presumably  because they think they are promoting a good outcome.

This article in Nature shows the danger:

The term 'touch DNA' conveys to a courtroom that biological material
found on an object is the result of direct contact. In fact, forensic
scientists have no way of knowing whether the DNA was left behind
through such primary, direct transfer. It could also have been deposited
by secondary transfer, through an intermediary. (If I shake your hand
then I could pass some of your skin cells onto something that I touch
next.)

Contamination from secondary DNA transfer was raised as a possible problem in Nature in 1997 (R. A. H. van Oorschot and M. K. Jones Nature 387, 767; 1997).
It is known to happen, but has largely been dismissed by legal experts
as being rare outside the conditions of a laboratory. Experiments done
in real-world conditions seemed to support this, and concluded that
secondary DNA transfer would have little impact on interpretation of the
genetic profile.

It is important to recognize that DNA amplification kits have become
much more sensitive than they were in the past. As a result, the types
of samples being analysed have expanded. Investigators no longer need to
identify and request analysis of body fluids such as blood, semen and
saliva. They can swab surfaces for otherwise invisible cells left
behind, on the handle of a weapon or on a windowsill, perhaps, and ask
labs to generate a DNA profile from them. The new kits can generate a
full genetic profile of a suspect from as little as 100 picograms
(trillionths of a gram) of DNA.

These subtleties are not usually explained in court. Instead, a jury is told
that there is a one-in-a-quadrillion chance that the evidence retrieved
from the crime scene did not come from a defendant. Naturally, the
jurors assume that the defendant must have been there.

Given  the power of modern forensic techniques to pull a DNA profile from a
smudge of cells, secondary DNA transfer is no longer a purely
theoretical risk. In California in 2013, a man called Lukis Anderson was
arrested, held for four months and charged with murder after his DNA
was found under the fingernails of a homicide victim.

Anderson had never met the victim and was severely intoxicated and in hospital
when the man was killed. The same paramedics who took Anderson to
hospital responded to the murder. Most likely, the paramedics were
covered in Anderson's DNA, which they then inadvertently transferred.
The charges were dropped.

Experiments in our labs, under the supervision of forensic anthropologist Krista Latham,
show how easily DNA can be transferred to an object.

We asked pairs of people to shake hands for two minutes and then each
individual handled a separate knife. In 85% of cases, the DNA of the
other person was transferred to the knife and profiled. In one-fifth of
the samples, the DNA analysis identified this other person as the main
or only contributor of DNA to the 'weapon' (C. M. Cale et al. J. Forensic Sci. http://doi.org/8j2; 2015).

How significant is the result of a single study? Other analyses have shown
that DNA transfer can be unpredictable and can depend on environmental
conditions. We need more research on when and how secondary transfer can
occur.

Republican hopelessness

So, Ohio Governor John Kasich recognizes the complete policy nuttiness of Trump and Carson:

"I've about had it with these people," Kasich said at the rally in Westerville, Ohio. "We got one candidate that says we ought to abolish Medicaid and Medicare. You ever heard of anything so crazy as that? Telling our people in this country who are seniors, who are about to be seniors that we're going to abolish Medicaid and Medicare?"
Retired neurosurgeon Ben Carson has acknowledged that he would like to gut Medicare.
Kasich went on, saying, "We got one person saying we ought to have a 10 percent flat tax that will drive up the deficit in this country by trillions of dollars" and there's another challenger in the field who "says we ought to take 10 or 11 [million] people and pick them up — I don't know where we're going to go, their homes, their apartments — we're going to pick them up and scream at them to get out of our country. That's crazy. That is just crazy."
Donald Trump has expressed support for deporting immigrants living in the country illegally.
"We got people proposing health care reform that's going to leave, I believe, millions of people without adequate health insurance," Kasich says. "What has happened to our party? What has happened the conservative movement?"

But his own plans for tax and finances?  (my bold):

Mr. Kasich’s tax plan -- which would cut the top individual income-tax rate to 28% from 39.6% and provide more relief for lower-income people through the Earned Income Tax Credit -- is the latest offering in an array of tax cuts proposed by Republican presidential candidates.
Mr. Kasich’s proposal isn’t the largest or most radical reduction on the GOP table, but it is being offered as part of one of the most specific plans to eliminate the deficit. It is still short on many details about how the budget would be balanced but calls for drastic policy changes such as transferring responsibility for Medicaid, welfare and highway-construction funding to the states.

The old "we must cut taxes on the rich to make the budget balance" line, hey?  (And let other governments work out how to raise money for services and infrastructure.)

Sorry, he may be less nuts than the populist leaders (who no one expects to last), but his views still show all the deficiencies that have been plaguing the Republican Party for years.

And how's that Laffer endorsed Kansas going:

“These things take some time,” Brownback said not long ago when asked whether his king-size income tax cuts have had the desired effect.
The key, he said, is patience.
Arthur Laffer wants more time too. He’s the philosophical architect of the Kansas income tax cuts.
“You have to view this over 10 years,” Laffer said. “It will work in Kansas.”
But that’s one point of view. As Kansas struggles with higher sales taxes and slashed budgets, I wondered what economists who focus on this stuff would say.
It’s been nearly three years since the state slashed income tax rates and took scores of businesses off the tax rolls. To be exact, it’s been two years, nine months and 23 days.
How much time do we have to wait for the promised “shot of adrenaline into the heart of the Kansas economy” that Brownback promised?
I randomly called half a dozen economists from around the country. They’re at major think tanks and major universities far from Kansas, and they don’t have any dog in the Kansas dispute. I asked this: Have the tax cuts had enough time to work?
Economists don’t agree on much, but they agreed on this, and they were unanimous: Yes, the tax cuts have had plenty of time. No question about it.

Ha!   Will Laffer still be around in 10 years to claim victory?

Update:  just noticed this from a live blog of the 3rd GOP presidential candidate debate:

Nobody is doing better on the debate stage tonight than Ted Cruz. He won the biggest applause of the night with his attack on the press, and now he gets an appeal to Ron Paul libertarian voters by professing himself in favor of a return to the gold standard and a call to audit the Federal Reserve.

 As I said, how utterly hopeless...

Update 2:  Vox has a good piece about Ted Cruz's attack.  The key points:

Cruz's attack on the moderators was smart politics — but it was almost precisely backwards. The questions in the CNBC debate, though relentlessly tough, were easily the most substantive of the debates so far. And the problem for Republicans is that substantive questions about their policy proposals end up sounding like hostile attacks — but that's because the policy proposals are ridiculous, not because the questions are actually unfair.

The Republican primary has thus far been a festival of outlandish policy. The candidates seem to be competing to craft the tax plan that gives the largest tax cut to the rich while blowing the biggest hole in the deficit (a competition that, as of tonight, Ted Cruz appears to be winning). And the problem is when you ask about those plans, simply stating the facts of the policies sounds like you're leveling a devastating attack....

 Cruz's strategy was smart, and he was arguably the debate's big winner. But it bespoke a deeper weakness. Republicans have boxed themselves into some truly bizarre policies — including a set of tax cuts that give so much money to the rich, and blow such huge holes in the deficit, that simply asking about them in any serious way seems like a vicious attack. Assailing the media is a good way to try to dodge those questions for a little while, but it won't work over the course of a long campaign.

When is a proof a proof?

The biggest mystery in mathematics: Shinichi Mochizuki and the impenetrable proof 

I don't often post about mathematics, but Peter Woit's blog had a link to this article in Nature about a lengthy proof that hardly anyone in the field can understand:

But almost everyone who tackled Mochizuki's proof found themselves floored. Some were bemused by the sweeping — almost messianic — language with which Mochizuki described some of his new theoretical instructions: he even called the field that he had created 'inter-universal geometry'. “Generally, mathematicians are very humble, not claiming that what they are doing is a revolution of the whole Universe,” says Oesterlé, at the Pierre and Marie Curie University in Paris, who made little headway in checking the proof.

The reason is that Mochizuki's work is so far removed from anything that had gone before. He is attempting to reform mathematics from the ground up, starting from its foundations in the theory of sets (familiar to many as Venn diagrams). And most mathematicians have been reluctant to invest the time necessary to understand the work because they see no clear reward: it is not obvious how the theoretical machinery that Mochizuki has invented could be used to do calculations. “I tried to read some of them and then, at some stage, I gave up. I don't understand what he's doing,” says Faltings.

Fesenko has studied Mochizuki's work in detail over the past year, visited him at RIMS again in the autumn of 2014 and says that he has now verified the proof. (The other three  mathematicians who say they have corroborated it have also spent considerable time working alongside Mochizuki in Japan.) The overarching theme of inter-universal geometry, as Fesenko describes it, is that one must look at whole numbers in a different
light — leaving addition aside and seeing the multiplication structure as something malleable and deformable. Standard multiplication would then be just one particular case of a family of structures, just as a circle is a special case of an ellipse. Fesenko says that Mochizuki compares himself to the mathematical giant Grothendieck — and it is no
immodest claim. “We had mathematics before Mochizuki's work — and now we have mathematics after Mochizuki's work,” Fesenko says.

But so far, the few who have understood the work have struggled to explain it to anyone else. “Everybody who I'm aware of who's come close to this stuff is quite reasonable, but afterwards they become incapable of communicating it,” says one mathematician who did not want his name to be mentioned. The situation, he says, reminds him of the Monty Python skit about a writer who jots down the world's funniest joke. Anyone who reads it dies from laughing and can never relate it to anyone else.

 All rather odd.

A sad McDonalds story

The night time 'McRefugees' of Hong Kong - BBC News

Management never asks the sleeping customers to leave?

Ridley wrong

Countering libertarian arguments against science funding | Science | The Guardian

Matt Ridley ran a bank into the ground, chose to blame "regulation", and now is a major player in the lukewarmer field, associating with wrongologist economist Richard Tol.

His latest book is not a hit with the reviewer from (of course) The Guardian, but also not even the one at The Spectator.

He is, generally speaking, a bit of a pillock who is best ignored.  

Dumb and on the wrong side of morality

I see that the IPA, Sinclair Davidson and his blog are promoting heavily a new book by the zero credibility Ian Plimer that insists the only way to help the global poor is to burn more coal - lots more coal:

Catallaxy is full of hilarious hyperbole from its conservative cohort about how this communist Pope is trying to kill millions by arguing that increased CO2 is not the way to go.

But in all honesty - if an economist can't see through the complete and utter bulldust that an aging geologist has been specialising in for some years now, there's no reason to trust his or her judgement on anything.

Floods and climate change, continued

Just noticed a recent paper:

Severe flooding occurred in Thailand during the 2011 summer season, which resulted in more than 800 deaths and affected 13.6 million people. The unprecedented nature of this flood in the Chao Phraya River Basin (CPRB) was examined and compared with historical flood years. Climate diagnostics were conducted to understand the meteorological conditions and climate forcing that lead to the magnitude and duration of this flood. Neither the monsoon rainfall nor the tropical cyclone frequency anomalies alone was sufficient to cause the 2011 flooding event. Instead, a series of abnormal conditions collectively contributed to the intensity of the 2011 flood: anomalously high rainfall in the pre-monsoon season especially during March; record-high soil moisture content thorough the year; elevated sea level height in the Gulf of Thailand which constrained drainage, as well as other water management factors. In the context of climate change, the substantially increased pre-monsoon rainfall in CPRB after 1980 and the continual sea level rise in the river outlet have both played a role. The rainfall increase is associated with a strengthening of the pre-monsoon northeasterly winds that come from East Asia. Attribution analysis using the Coupled Model Intercomparison Project Phase 5 historical experiments pointed to the anthropogenic greenhouse gases as the main external climate forcing leading to the rainfall increase. Together, these findings suggest increasing odds for potential flooding similar to the 2011 flood intensity.

Not a cent from me

Apple is a ridiculously successful company:

Apple has more than $205bn of cash in the bank, the company revealed on Tuesday as its chief executive Tim Cook said the firm had made more than $234bn in 2015, making it its “most successful year ever”.
The California company now has more money in the bank than the Czech Republic, Peru and New Zealand make in gross domestic product (GDP) a year, according to World Bank statistics. Apple’s cash balances increased by $2.8bn in the last three months alone.

I'm not sure their doing anything really useful with their money, though, apart from throwing it in the air and letting it fall on their head, McDuck style.  I suggest establishing a private air force with which to blow up coal mines or their train lines. (Useful and would annoy Bill Gates, too!)

I trust he dressed appropriately for his big speech...

Diamonds in the sky

Climate scientists ponder spraying diamond dust in the sky to cool planet : Nature News & Comment

The diamonds part sounds a bit wacky.  

Hmmm.

The AFR is being openly gossipy about Tony Abbott and Peta Credlin:

This is going to be pretty hard for some of you to get your heads around, so I guess I better just tell it to you straight:
So, about that Margaret Thatcher lecture that Tony Abbott is delivering in London on Tuesday night – you know, the privately funded trip which, according to the former PM's office, he's being accompanied on with his wife, Margie Abbott?
If only the travelling party was really so conventional. See, there's also a villa in France, where, following the big speech, Abbott will be retiring  for a period of convalescence with his former chief of staff, Peta Credlin, his C-bombing advancer, Richard Dowdy, (aptly named) and his mysterious press office veteran, Nicole Chant.

And you thought Credlin joining the then PM (sans wife Margie, but avec daughter Frances Abbott) skiing at Perisher in July was a little unusual!

We wonder if Margie will be joining the French party or steering well clear? If we're all still talking about Ainsley Gotto nearly 50 years after she ran John Gorton's PMO, Abbott's Last Tango Near Paris will certainly be one for the history books.

I remarked at the time that the publicity given in an Abbott friendly News Ltd paper to Abbott and Credlin skiing together was rather unusual.   Now Fairfax is joining in.

Surely this latest piece should be the cause of some complaint if there is nothing to the Abbott/Credlin relationship?

Update:  I see that on Twitter, The Australian has tweeted that Credlin "became more like a first lady" (as noted in its linked story on the Abbott downfall.)  The full quote in the article:

If there was one overarching, final loyalty from the prime minister, it was to his chief of staff. She had become almost a first lady, accompanying Abbott to everything from private dinners at the New York home of Rupert Murdoch to private snow-skiing holidays with Abbott and his daughter Frances. The chief of staff was the one introduced to foreign leaders. She interrupted to answer questions others put to Abbott, ruled the strategy, and used her power and intellect to barricade his office against the outside. His colleagues came to see their relationship as impenetrable and toxic for the government. But Abbott had empowered Credlin and, in the end, it was Abbott’s call. He gave her free rein. He called his colleagues sexist for challenging her.

Sounds to me like subtle innuendo?  

I can't work out what is  going on here.   Is it that they are emboldened that Abbott or Credlin will not address the innuendo directly, because there is something to it?   And what about the spouses?   If this is just scurrilous gossip, why aren't they making their displeasure known?

I have said before, if something is going to be revealed about the Abbott Credlin relationship that has been known by journalists for years, people should be furious if it is only done now, after the "family man" campaign Abbott ran for years against Gillard (and, in a sense, Rudd, in the last election).  
 

Unliveable desert countries

I'm told by a relative that Doha is already an unbearable place to live for any length of time, but researchers are saying that the Arabian Gulf is going to get much worse and perhaps become virtually unliveable*:

A human body may be able to adapt to extremes of dry-bulb temperature (commonly referred to as simply temperature) through perspiration and associated evaporative cooling provided that the wet-bulb temperature (a combined measure of temperature and humidity or degree of ‘mugginess’) remains below a threshold of 35 °C. (ref. 1). This threshold defines a limit of survivability for a fit human under well-ventilated outdoor conditions and is lower for most people. We project using an ensemble of high-resolution regional climate model simulations that extremes of wet-bulb temperature in the region around the Arabian Gulf are likely to approach and exceed this critical threshold under the business-as-usual scenario of future greenhouse gas concentrations. Our results expose a specific regional hotspot where climate change, in the absence of significant mitigation, is likely to severely impact human habitability in the future.

*  OK, without airconditioning.  Although, it's actually pretty incredible to me that people lived there at all before airconditioning.  Here's the summary from phys.org:

It would still be rare, and cities such as Abu Dhabi, Dubai and Doha wouldn't quite be uninhabitable, thanks to air conditioning. But for people living and working outside or those with no air conditioning, it would be intolerable, said Eltahir and Pal. While Mecca won't be quite as hot, the heat will likely still cause many deaths during the annual hajj pilgrimage, Eltahir said.

Furry Hannibal Lecters

The case against otters: necrophiliac, serial-killing fur monsters of the sea - Vox

Wow.  This article really makes the case for otters having some very surprising, and horrible, behaviours.

Nasty virus tricks

HIV latency: a high-stakes game of hide and seek

It's interesting to read about the devious way HIV, even when people are on treatment, hides itself:

In latent infection, HIV integrates its genetic material into the DNA of the patient and becomes “silent”.

A brilliant added tool is the use of a long-lived critical cell of the immune system, the resting T cell, as its preferred hiding site. These latently infected resting T cells can slowly divide and, given HIV is now part of the patient’s DNA, the HIV is passed down to the daughter cells too.

HIV usually replicates in activated T cells and can efficiently kill those cells in several ways. First, the virus directly damages the outer membrane of the cell. This membrane usually keeps the cell intact.

Following infection of a cell, bits of the virus are quickly revealed to the immune system which, once activated, can zoom in and eliminate the infected cell.

However, if the virus manages to get inside a resting cell, in contrast to an activated T cell, all the machinery needed to produce new viruses is not available and the virus life cycle essentially shuts down.

If things shut down after the virus has already entered the patient’s DNA it gets stuck there – forever.

As the article also notes, people who go off the antiviral drugs quickly get high viral counts - within weeks.


What a nasty virus it remains.

Yet more on climate policy

Here's a very worthy bit of commentary about the Vox article I posted about on Sunday - pointing out that one has to be on the lookout for fatalism in the way the problem is described.   (It's by Michael Tobis, who is doing guest posts at ATTP lately.)

Movie economics

Turns out that Greg Jericho knows a lot about the matter of government subsidy for the movie business. 

I suspect that the benefits of this sort of government support are a bit stronger than Jericho thinks.  I reckon that of the type of industries government can be seen to be helping,  this one has a certain high profile, confidence building factor that others don't share.   All the publicity surrounding a major star staying for protracted periods on the Gold Coast or in Sydney (and saying nice things about these places) must count for something, no?  (Unless, of course, you are Barnaby Joyce and manage to turn a national image of relative youth and vigour into something more resembling a patronising fogey-ness.)

About Gary

I've been reading up a little about Gary Powers, the key figure in Bridge of Spies.

The Smithsonian.com has a short article about him, which contains a couple of surprises (he was allowed a conjugal visit with his wife, but she was an unfaithful alcoholic; and he kept a journal while in prison that indicates he may have had a touch of Stockholm syndrome.) 

His son has a website up, which doesn't have a lot of content, but some of it is interesting.

As for the old poison needle in the coin trick:  yes, this was true and the poison used was saxitoxin, derived from shellfish.  

You can even read an account of his accident on the CIA website, where we get a good description of his dangerous exit from the U2:

The young pilot had been flying for almost four hours when he heard a dull thump, the aircraft lurched forward, and there was a bright orange flash from a nearby surface-to-air missile. The plane’s right wing began to droop and the nose started to go down. Powers tried to correct it, but the plane continued its downward trajectory. Powers was uncertain if the control cable had been severed or if the tail was gone. He was certain, however, that he no longer had control of the plane.

Powers initial reaction was to pull the destruct switches, but he decided he’d better secure an exit plan for himself first. This, however, was proving difficult as the g forces had hurled him to the nose of the plane, which was spinning tail first towards the earth. Powers thought of ejecting but realized, in his current position, he likely would have had both off his legs cut off while trying to escape the plane.  

On the verge of panic, Powers decided he would climb out of the plane. The whirling aircraft had passed thirty-four thousand feet when he removed the canopy. He took off his seat-belt, which sent him flying halfway out of the aircraft. His face plate frosted over rendering him visionless. Powers tried to get to the destruct switches twice but, realizing time was running out, he began kicking frantically and miraculously the oxygen hoses that were holding him hostage in the U-2 broke and freed him from the spiraling plane.

Suddenly, all was silent, except for the rustling of material as the chute opened and settled in the wind. Powers hung in the air desperately trying to comprehend what had just happened and trying to assess his current situation. He was fifteen thousand feet above the Soviet Union and the ground was growing ever closer. As he clutched the straps of his chute, he saw a piece of the plane float down past him.

Maybe not exactly as portrayed in the movie, but pretty close.

Bridge spied

Hmmm.   This is an odd situation.  For once, I think a Spielberg film has been a tad overpraised, collectively, rather than my usual feeling that there are too many critics too cynical about him.

It's not that there's anything wrong with Bridge of Spies:  the acting is fine; the script has witticisms at times; and I don't think anyone now does history with finer and more authentic feel in the art direction than  Spielberg.  

It's just that I missed an element of tension, and had been expecting a bit more, I guess, intrigue in the story.   Out of Spielberg's last few films, I admit, this impressed me less than both War Horse or Lincoln.  (And Lincoln was a bit similar in that we already knew the ending - the interest is in how the movie gets there.)

I am also a little surprised that it hasn't had a wingnut backlash in the US, as it can be read as impliedly criticising the handling of those captured by the US in the war on terror, yet Breitbart gave it a glowing review too. 

Anyway, it's worth seeing, as Spielberg always is.  I just wish I could have been more gushing in praise.

Climate change economic modelling questionned

David Roberts at Vox has a good article up explaining the doubts about how valid any of the long term economic modelling of climate change can really be.

Given that I had noticed those doubts being expressed in some of the quieter corners of the 'net for a year or two now, it's good to see this is  finally getting some broader attention.

I did raise this issue in a thread at John Quiggin's blog recently too, noting Pindyck's criticism of the whole IAM exercise, but he didn't comment on it.

More about that Berkeley study...

The Economist has a good article up giving some more of the background of the Berkeley study that looked at the economic effects of global warming in a new way.  Here's part of it:

A paper published this week in Nature challenges this finding. The authors—Marshall Burke, Solomon Hsiang and Edward Miguel—suspected that economists had been looking for the wrong thing: a linear relationship between temperature and growth. Instead, they looked for an optimal temperature, on the assumption that excessive cold could harm growth as much as punishing heat. That is exactly what they found: hotter-than-usual years benefit countries, rich and poor alike, up to an average annual temperature of 13°C, after which hotter weather begins to sear growth. That allowed them to draw inferences about the likely effect of climate change: for Brazil, for example, an increase in temperature of 3°C will lead to a fall in output of 3% (see chart).

The apparent heat resistance of rich countries, it turns out, is simply because some of them, such as Germany and France, lie on the colder side of the optimum, so grow faster in hotter years, whereas others, such as America and Australia, lie on the hotter side, and so wilt as temperatures rise. Within individual counties in America, for instance, every hot day (with an average temperature over 24 hours of 24-27°C) lowers the average income per person that day by 20%, according to a working paper from the National Bureau of Economic Research by Mr Hsiang and Tatyana Deryugina. Very hot days (over 30°C) lower income per person by 28%. Looking at the average impact of rising temperatures in rich countries as a group had obscured such strong responses.

 David Appel shares my skepticism of (as he puts it) an economic model atop a climate model, but his post extracting some of the material from the paper is worth reading too.  (I added a comment to his post along the lines of what I said here.)