Yet more bacteria found where they weren't expected

Gee, it seems like every week there's a story about bacteria being found in parts of the body where they weren't expected.  (It was the placenta last week.)

This week - it's the healthy male urogenital tract:

Much like the vaginal microbiome differs among women and changes over time, the penis is home to a variety of bacteria that vary with a man’s age, sexual activities, and whether he is circumcised, among other things. And it’s not just the skin that envelops the male sexual organ that’s inhabited by microbes: researchers continue to identify bacteria that dwell within the urogenital tract, a site once considered sterile in the absence of infection.

David Nelson, an associate professor of microbiology and immunology at Indiana University in Bloomington, was investigating Chlamydia infections when he and his colleagues found evidence to suggest that the sexually transmitted pathogens in the urogenital tract were obtaining metabolites from other microbes. “There was a signature in the chlamydial genome that suggested this organism might be interacting with other microorganisms,” said Nelson. “That’s what initially piqued our interest. And when we went in and started to look, we found that there were a lot more [microbes] than we would have anticipated being there.”

The researchers found that some men pass urine containing a variety of lactobacilli and streptococci species, whereas others have more anaerobes, like Prevotella and Fusobacterium. In terms of overall composition, “we see a lot of parallels to the gut,” said Nelson, noting that there doesn’t seem to be a standout formula for a “healthy” urogenital tract. Commensal microbes within the urethra could make a man more susceptible to infection by supporting colonization by pathogens like Chlamydia, whereas bacteria that consume the environment’s nutrients could help prevent it. “We just don’t know at this point,” said Nelson.

I would presume that men who partake of a particular activity without condoms might generally have a larger number of bacteria to be found there, for obvious reasons. 

Amusing article about cranky academic

Slavoj Zizek calls students stupid and boring. Stop worshiping this man!

What Clive Palmer should have said

Yes, Clive Palmer was in error in claiming Tony Abbott wanted the PPL for Peta Credlin, because she is already covered by a generous public service leave plan (not to mention that it was extremely tacky because Credlin had gone public about her attempts to use IVF - unsuccessfully - to have a baby.)

No, what he should have said is that Abbott is wanting to look after his daughters.  (Or at least those of them, like Frances, who are in the private sector.) 

I've always thought that this was the most likely explanation for Abbott's weird adoption of this pet policy. 

Confirmation that ocean acidification is a scary experiment without precedent

Modern ocean acidification is outpacing ancient upheaval, study suggests

 I'm sure we've seen this conclusion about the comparative rate of ocean acidification from previous studies, but still:

Some 56 million years ago, a massive pulse of carbon dioxide into the atmosphere sent global temperatures soaring. In the oceans, carbonate sediments dissolved, some
organisms went extinct and others evolved.

Scientists have long suspected that ocean acidification played a part in the crisis—similar to today, as manmade CO2 combines with seawater to change its chemistry. Now, for the first time, scientists have quantified the extent of surface acidification from those ancient days, and the news is not good: the oceans are on track to acidify at least as much as they did then, only at a much faster rate.

In a study published in the latest issue of Paleoceanography, the scientists estimate that surface ocean acidity increased by about 100 percent in a few thousand years or more, and stayed that way for the next 70,000 years. In this radically changed environment, some creatures died out while others adapted and evolved. The study is the first to use the chemical composition of fossils to reconstruct surface ocean acidity at the Paleocene-Eocene Thermal Maximum (PETM), a period of intense warming on land and throughout the oceans due to high CO2.

"This could be the closest geological analog to modern ocean acidification," said study coauthor Bärbel Hönisch, a paleoceanographer at Columbia University's Lamont-Doherty Earth Observatory. "As massive as it was, it still happened about 10 times more slowly than what we are doing today."

 And the oceans do not fix themselves quickly:

The study confirms that the acidified conditions lasted for 70,000 years or more,
consistent with previous model-based estimates.

"It didn't bounce back right away," said Timothy Bralower, a researcher at Penn State who was not involved in the study. "It took tens of thousands of years to recover."

Krugman on the history of inequality

That Old-Time Inequality Denial - NYTimes.com

 This short, sharp post by Krugman on the Piketty/Giles controversy is well worth reading in full.  Heck, it's short, so let's just cut and paste it (please forgive me Paul):

Brad DeLong links to the now extensive list of pieces debunking the FT’s attempted
debunking of Thomas Piketty, and pronounces himself puzzled:

I still do not understand what Chris Giles of the Financial Times thinks he is doing here…

OK, I don’t know what Giles thought he was doing — but I do know what he was actually doing, and it’s the same old same old. Ever since it became obvious that inequality was rising — way back in the 1980s — there has been a fairly substantial industry on the right of inequality denial. This denial didn’t rely on any one argument, nor did it involve consistent objections. Instead, it involved throwing many different arguments against the wall, hoping that something would stick. Inequality isn’t rising; it is rising, but it’s offset by social mobility; it’s cancelled by greater aid to the poor (which we’re trying to destroy, but never mind that); anyway, inequality is good. All these arguments have been made at the same time; none of them ever gets abandoned in the face of evidence — they just keep coming back.

Look at my old article from 1992:  every single bogus argument I identified there is still being made today. And we know perfectly well why: it’s all about defending the 1 percent from the threat of higher taxes and other actions that might limit top incomes.

What’s new in the latest round is the venue. Traditionally, inequality denial has been carried out on the editorial page of the Wall Street Journal and like-minded venues. Seeing it expand
to the Financial Times is something new, and is a sign that the FT may be suffering from creeping Murdochization.

It's interesting to note his complaint that the right wing arguments against worrying about equality involved throwing up everything and seeing if anything would stick.

What other matter has been dealt with by the Right (particularly the American Right) in a similar way?   Climate change, of course.  (See the Skeptical Science list of 155 failed arguments against climate change and its effects.)

Yet, hilariously, the same Right wing which is attacking Piketty slapped themselves on the back last week about how they thought that Giles had shown that Piketty was "cherry picking" and fabricating his way to a position - just like those damn climate change scientists at the IPCC!  (See the country's wingnuttiest of all economists Steve Kates on that.)

Of course, they had gone off completely prematurely about Giles (see here for details) just as they did with the meaning of the "Climategate" emails, and the current atmospheric temperature record of the last decade or two.   And anyone with common sense could see that they were grasping at these things without thinking about it in any depth at all.

They continually claim that ideological motivation in others is overriding proper analysis, while being blind to their own ideological blinkers causing the outright error of refusing to believe detailed, repeat scientific analysis.

We live in very frustrating times.

There's much to be said for not being an artistic prodigy

As I always say, those of us who have no particular artistic talent at least have the consolation that we don't share the personal foibles that so often seem to accompany artistic prodigies.

I don't think I have ever read much about Beethoven's personal life before, but this review of a new book that concentrates on it indicates he was (yet another) eccentric and difficult artistic genius.  Some extracts:

In truth, Beethoven thrived as a strong-willed but socially adept virtuoso pianist and composer for his first 25 years or so. As he developed hearing problems in his late 20s, however, and moved toward the realization that the malady was irreversible, he began to turn inward. As he descended into deafness in his 30s and 40s, he grew increasingly mercurial, irritable, and paranoid. At times, he appeared to be fully irrational. He wrote emotional confessionals and fought with members of his family. He flirted with numerous women but was unable to sustain a lasting relationship. He moved restlessly from dwelling to dwelling, changing residences in Vienna more than 30 times in 35 years. A smart dresser in his youth, he appeared increasingly unkempt and disheveled. In his final decade, he became so dissipated that he was once mistaken for a vagabond and thrown into jail. By any measure, Beethoven’s personal life was bizarre....

The Beethovenian paradox of “crisis and creativity”—to use the phrase coined by Solomon—has been well described in the past. But no one before Suchet has focused quite so intensely, and so eagerly, on the crisis part—and the composer’s melodramatic highs and lows: stopping the orchestra during an already overly long performance and insisting that the players start again from the beginning; refusing to bow before passing royalty when walking in the park with Goethe; receiving a distinguished visitor with an unemptied chamber pot under the piano. Such stories, well known to historians, are too good to make up.

The review also touches on a huge fight over guardianship of a nephew Karl (with poor Karl attempting suicide at the age of 20), fights with his patron, and more.  But seeing this blog always likes to note gastrointestinal problems of the famous (well, Hitler in particular), it's interesting to note that Beethoven was also a sufferer:

Suchet also presents ongoing reports regarding Beethoven’s gastrointestinal issues, which run through the book like an idée fixe. These begin with a description of the stomach pains and diarrhea that Beethoven experienced before his first concert at the Burgtheater in Vienna in 1794, followed by periodic updates on his irritable bowel syndrome, bad digestion, irregularity, acute constipation, colic, distended stomach, and more. While these disorders have been noted elsewhere, they are presented in unusual detail here, so much so that one begins to wonder whether the book might have been more aptly titled The Inner Beethoven. This may be more information about Beethoven’s bodily functions than we want to know.

Yet another candidate for an episode of the TV series concept I'm trying to sell to HBO about time travelling doctors delivering fecal transplants!   (Oddly, they're not returning my emails.)

Gun fantasies of the NRA

Of course, the NRA is continuing to run a "good guy with a gun" line about how the answer to mass shootings is to arm everyone.   I had not heard of this look at recent American mass shooting before, though:

Last year Mike Bloomberg's group issued a comprehensive study of mass shootings covering 2009 through 2013. Using a combination of law enforcement and media reports, the researchers were able to identify 43 mass shootings, using the FBI's definition of "mass shooting" as any incident in which at least four persons were killed by someone using a gun. Of these shootings, 40 percent arose out of domestic disputes, and at least 6 of the 17 shooters had been named in previous domestic assaults. In only 10 percent of the shootings was there evidence of prior contact between the perpetrator and a mental health professional, although friends and relatives of other shooters expressed some awareness that mental health issues might have precipitated the attacks.

Now let's get down to Colion's real nitty-gritty, the issue of multiple shootings in gun-free zones. The report states that, at maximum, one-third of these shootings took place in what might have been considered gun-free zones. But other than four school shootings, the Aurora movie theater and Fort Hood (the report was released before the Navy Yard shooting), it's not clear that any of the other 37 mass shootings took place in specific gun-free zones, although the researchers probably assumed that the two multiple shootings in Chicago and one in DC also took place in gun-free zones. And how many of the 43 multiple shootings ended with a "good guy" pulling out a gun? None. In every incident except one, the shooter either shot himself or was arrested by the police. The bystanders who subdued Jared Loughner after he shot Representative Giffords were unarmed. The recent Santa Barbara shootings took place in off-campus locations where anyone was legally able to carry a gun.

High intensity rain and English floods expected to increase

BBC News - Climate change to boost summer flash floods, says study

And once again, I see, Andrew Bolt demonstrates that he cannot get his brain around the concept that you can have a climate change which means (for some parts of the world) generally drier summers, interspersed with more intense rain and therefore sudden floods.  

The BBC article notes that this is indeed the expectation for at least part of England:

Both models found that summers in the future would be drier overall.
However, when it came to intense downpours, defined as more than 28mm per hour, the higher resolution model saw a significant increase.

Piketty: the response

I see that Piketty has made a detailed response to the Financial Times claims of errors, and it seems to have gone over well with most side line commentators.   Giles himself is still muttering.

Of most interest to me, though, has been that FT has really copped quite a pasting from many of its readers in comments for the way it handled this.  (See the comments to the two links above.)  Clearly, the opinion of a large number of their readers is that they really exaggerated the criticisms made by Giles in a very unwarranted fashion.

The fear of Piketty continues amongst the Right wing economists, though, with Steve Kates bloviating at Catallaxy about how Piketty "is an economic illiterate" over the weekend.

I also see that one response to Piketty that is being increasingly used as a fall back by free market types is to say "so what if he's right?  What does inequality matter anyway now that even the poor can afford a big screen TV?"  In fact, it was JC from Catallaxy (a very comfortably rich trader, who did a stint on Wall Street some years ago)  who brought to my attention this piece at Barrons which argues that position strenuously.  Who knew that a rich man would come out swinging for the position "inequality - it's always great!"?

In fact, I thought there had been a very large amount of economic commentary on the matter of inequality over the last few years that had most economists acknowledging problems for an economy if inequality gets too out of control.  As the readers of Catallaxy are notoriously disdainful of The Economist, perhaps they had missed it?   I suggest they go to the website and do a search.

As it happens, someone in comments to that Barrons article points out the author has come out with some surprising opinion in the past:

 Boudreaux argued in October 2009 that insider trading “is impossible to police and helpful to markets and "investors....Far from being so injurious to the economy that its practice must be criminalized, insiders buying and selling stocks based on their knowledge play a critical role in keeping asset prices honest—in keeping prices from lying to the public about corporate realities.

In a January 2013 article for the Wall Street Journal, Boudreaux and Mark Perry argued that the “progressive trope ... that America's middle class has stagnated economically since the 1970s” is “spectacularly wrong"".

But apart from the economics reasons for not wanting it, there has been much commentary regarding the social effects of inequality, and most reviews point out that Piketty spends a fair of time talking about these  in a historical context by reference to the stories of Austen and others.   Yet I see that Graham Young, the long time operator of Online Opinion (and at least formerly a part of the Liberal Party) make this recent criticism of the book:

I’m a third of the way through Piketty’s book and so far he hasn’t made a very good case at all – lots of graphs and correlations, but no reason to suppose that any particular level of inequality brings good or bad results. Perhaps he brings this together in the next two-thirds, but at this stage I’m not too worried if we have the same level of inequality as we had in the 20s.

 I responded in the thread:

You want an economist to tell you precisely when a certain level of inequality becomes problematic?
I would have thought that the matter is a question answered by an application of morality and common sense, not by a graph.

And I made that comment before reading this blog entry in The Economist which basically said the same thing, although I can't find the link right now.

It's pretty clear that Piketty is all the talk of the town because inequality was already a hot topic, and his work has provided something like a physicist's Grand Unified Theory about it, based on new and valuable data collection and interpretation.

But some ideologically committed people (many of them quite well off, of course) don't want to hear about it. 

Magnets and brains

Opposites attract and help repel depression

Magnetic stimulation is providing relief from severe depression after
only three treatments, providing an alternative to electroconvulsive
therapy for seriously ill patients.

The finding by researchers at The Alfred hospital means the
treatment can now be offered to patients needing rapidly effective
treatment, for example those who are suicidal or refusing to eat or
drink.

Transcranial magnetic stimulation involves applying a strong
magnetic field to particular areas of the brain, causing neurons to fire
and strengthening connections with other areas of the brain.

I'm not sure if they have any clear idea why it works, but it seems a big advance.

Urban rats discussed

How Portland Lives With, Not Against, Its Rats - Merilee D. Karr - The Atlantic

The article is mainly of interest for its discussion of rat behaviour when they are are not overcrowded.  (As contrasted with when they live in cities with heaps of food.)

Excellent Android news / expert evidence

I was disappointed when I got the Samsung tablet that the ABC iView service was not available as an app on Android, even though it was on iPads.  (The problem being the difficulty in making sure such an app will work across a range of devices running different versions of Android.)  The ABC did say they were working on it.

I didn't realise til this morning that it's now out, as is SBS's similar service.

Both seem to work well on my (now pretty basic) Samsung Tab.

I used it to watch Friday night's excellent show on SBS:  "Medieval Lives - Birth, Death and Marriage".  This episode on marriage was very interesting, and I recommend watching on any format you can.

It was particularly amusing to hear this part about what the Church courts would consider in deciding whether to annul a marriage (as someone else who watched the show summarizes):

Records from the 14th and 15th century York archives show that prostitutes were called in by the court to examine the man and to physically test him. The prostitutes would then report back to the court. There are rather graphic testimonies in the records.

 Here's a bit more detail on this bit of medieval history from a book, Regional Variations in Matrimonial Law and Custom in Europe, 1150-1600 :

Give it a rest, Clive

I'm not sure that it's a good look for a 74 year old to continue to play up to his long standing, self created, joke letch image long after we've learnt that it wasn't a joke after all and virtually ended his marriage:

James began by joking about why he’d made the effort to travel from Cambridge where he’s usually confined due to the need for thrice-weekly hospital visits.

“As with every other red-blooded Australian male I’m doing it to impress Tony Abbott’s daughters,’’ he told a sold-out crowd of 400 fans.

For next weekend

I don't normally go to the Wall Street Journal for cooking suggestions, but via Zite (still a very enjoyable source of randomness on my Samsung tablet) I found an article there about spatchcocking chicken.  It included this recipe, which I think I'll try next weekend, if I can remember to start on Friday evening:

Italian Lemon-Garlic Marinade

Mix together zests and juices of 1 lemon and 1 orange, 4 cloves garlic, peeled and sliced, 1 coarsely chopped onion, several sprigs each of fresh rosemary and fresh thyme or 2 teaspoons of each herb dried, a pinch of red pepper flakes, 1 teaspoon salt, ½ teaspoon freshly ground black pepper and 1/3 cup extra-virgin olive oil.

Place marinade in a large Ziploc bag with 1 spatchcocked chicken. Place bag on a plate and refrigerate at least 24 hours and up to 48, turning bag over occasionally.

Maybe this is where the aliens have gone

Pair of researchers suggest black holes at center of galaxies might instead be wormholes

What an interesting suggestion:

The supermassive black hole candidates at the center of every normal galaxy might be wormholes created in the early Universe and connecting either two different
regions of our Universe or two different universes in a Multiverse model. Indeed, the origin of these supermassive objects is not well understood, topological non-trivial structures like wormholes are allowed both in general relativity and in alternative theories of gravity, and current observations cannot rule out such a possibility.

A good idea for science fiction, too.

Weird signalling

Quantum Collect Calling

I have no idea if this any potential practical application, but it is certainly a curious result that it appears a signal can be sent with no energy from the sender arriving:

 We show that it is possible to use a massless field in the vacuum to
communicate in such a way that the signal travels slower than the speed of
light and such that no energy is transmitted from the sender to the receiver.
Instead, the receiver has to supply a signal-dependent amount of work to switch
his detector on and off. This type of signalling is related to Casimir-like
interactions and it is made possible by dimension ---and curvature--- dependent
subtleties of Huygens' principle.

A tale of 2 economics writers

Two takes on the university fee de-regulation this morning.

The first by the condescending hater of anyone other than company directors in business class, Judith Sloan, who slips this in early on: 

And no doubt the revolting students will continue to revolt for their selfish reasons.

Her charming tendency to throw in bitchiness continues unabated, then.*

Of course everything will be fine, she writes; universities won't up fees so much, these pathetic students complaining about a policy that descended out of the sky have nought to complain about.  (Even though she then goes on to identify a way it may still be problematic for government funding.)

The second is by Ross Gittins, who the economic dries of Catallaxy don't care for.

Whereas Sloan's analysis is (at heart) based on her confidence that free markets in everything always works out for the good, Gittins actually thinks deeper about what sort of "market" tertiary education is, and gives us some reasons why he thinks universities will charge higher, quite quickly:

In the early noughties, the Howard government allowed unis to raise their fees by 25 per cent. One small uni decided not to do so. It found its applications from new students actually fell. So the following year it put its fees up like all the others and its applications recovered.

In Britain, the Cameron government allowed unis to raise the £3000 annual fee they charged local students up to a limit represented by the £9000 fee charged to foreign students. Almost all of them took the opportunity to raise their fees to the maximum allowed.

Applications dropped by 9 per cent in the first year, but rose in subsequent years.
On the basis of all this, my guess is the sandstone unis will raise their fees a long way and the less reputed unis won't be far behind them.

Their notion of competition will be to make sure no one imagines a lesser fee than the big boys is a sign of their lesser quality.

I had actually heard from a former private high school teacher at one of Brisbane's major schools tell me that this happened when he was there -  the teachers were told that as the competing school was increasing their fees, of course they would be putting up there's too (with no costs justification, but just to make sure people didn't think their school was lesser quality.)

Guess which analysis I find more convincing?

*  Judith read the Gittins column, and starts off her criticism of it in what has now become pretty much her default snide, bitchy style.  

If you ask me, the announcements made over the weekend of the type of fee rises from a couple of the big universities sounded more supportive of Gittins than Sloan.  

I also part heard someone from Melbourne University this morning explaining that the reason that the VC's who wanted fee deregulation are now sounding hesitant about the government's policy is because they didn't plan on the government funding cut that is accompanying it.   (I think that was the gist of it, anyway.)

Lenore and Michelle are right

Lenore Taylor points out that if Tony Abbott is now frustrated that he has lost the allegiance of a heap of pensioners, even when their pension is actually still going to increase, it is a case of being hoist upon his own petard:

The important difference between an absolute cut and a reduction in a predicted future increase was often lost on Tony Abbott in opposition.

He would, for example, warn of catastrophic job “losses” due to the carbon tax, using as evidence modelling that in fact showed employment would continue to grow strongly, but slightly less strongly than had the carbon price not been there.

He accused the former government of “cutting” the health budget when it had in fact pared back future projected increases in the health budget because of some statistical thing that no one could ever really understand.

But now, in government, he’s right on to the difference. It’s like a miracle, or something. And it’s Labor who are suddenly having trouble with the absolute cut versus lower future increase thing.

So when Bill Shorten accuses him of “cutting” or “ripping off” pensions, Abbott responds, quite correctly, that pensions will continue to increase every six months, imploring Labor to just have the decency to tell the truth.

 And Michelle Grattan is also pretty on the mark in her column today too:

Tony Abbott seems to have fallen into the same trap as Paul Keating in 1993. Keating refused to accept that John Hewson had handed him that win; he insisted on believing it was an endorsement of him and his philosophy.

Like Keating, Abbott triumphed on negatives. But now he and his colleagues think they have a mandate to transform dramatically the society and its culture, going far beyond what people expected.

There’s little sign, however, that the government has the political skills to match its ambition, or that the community shares its often uncompromising, black-and-white view of the world.

The point is, as I'm sure many have already suggested, people voted out a chronically dysfunctional Labor Party, rather than voting with any great enthusiasm for Tony Abbott personally.   And you can  hardly argue that there was any evidence that they were ready for a great change in governmental philosophy when Abbott slid in by promising to follow most key Labor policies.

Abbott, being a professional opportunist weathervane, thereby set himself up for failure.

Couldn't happen to a more deserving politician.

Just stop giving him money

I see that Jonah from Tonga is rating very poorly:  240,000, compared to 331,000 for Spicks and Specks, which won't be made again because of low ratings.  (I wouldn't mind betting that S&S is a lot cheaper to make than Lilley's projects.)

So is this finally the end of the ABC funding Lilley?   I hope so...

Next on my hit list:  the appalling looking Housos on SBS.  Perhaps I should gird my loins and watch it first, though.   (Do I have to?)

More on the miracle (berry)

I recently posted about the taste changing "miracle" berry we bought in Canberra, and noted that there had been hopes it could be used as non sugary sweetener.  The Atlantic has an article about how that dream is still alive.