Friday, March 7, 2014

Fish, Extremophiles, and the Emperor's New Clothes

We're learning more about life's limits, learning that there's more to learn and re-learning very old lessons. Proverbs 20:17, and all that.
  1. High-Pressure Fish
  2. Finding Life
  3. Grand-Sounding Claptrap

Empty Looms and Faulty Generalizations

(From Vilhelm Pedersen, via Wikimedia Commons, used w/o permission.)

Maybe you know the story: "two rogues, calling themselves weavers," tell a vain emperor that they've got special cloth, and will make the emperor the finest clothes.

They explain that the cloth can't be seen by anyone who "was unfit for the office he held, or who was extraordinarily simple in character."

The emperor gave these "weavers" large sums of money, so they could start work immediately.
"...So the two pretended weavers set up two looms, and affected to work very busily, though in reality they did nothing at all. They asked for the most delicate silk and the purest gold thread; put both into their own knapsacks; and then continued their pretended work at the empty looms until late at night...."
("The Emperor's New Clothes," Hans Christian Andersen, via Project Gutenberg)
The emperor says that he sees the cloth, since he didn't want to seem unfit for office. His ministers pretend to see the cloth, too.

Finally, a child who hadn't learned the importance of ignoring reality says: "But the Emperor has nothing at all on!"

If someone said Hans Christian Andersen's story shows that emperors always get duped, that would be one sort of faulty generalization: making a sweeping assumption from too little data.

Assuming that a few examples are typical is easy, and may partly explain why so many folks take it for granted that religious people are crazy; or science is a fraud; or religion is at war with science.

Some scientists have deliberately lied, more have made whacking great mistakes. But that doesn't show that all scientists are frauds or fools: or that science is bogus.

Hoaxes, even popular ones, don't last forever. Given time, someone's going to notice a disconnect between objective reality and what the emperor wants to believe.

Dawson's Dawn-Man, the Piltdown Man — or — the Importance of Being British

(From John Cooke, via WikiMedia Commons, used w/o permission.)
("Dawson's dawn-man," before the hoax was exposed: a group portrait by John Cooke, 1915.)

The Piltdown Man, or "Dawson's dawn-man," had a pretty good run: from December of 1912,  to November of 1953.

I gather that the hoax lasted so long partly because so many folks desperately wanted to believe that the first man came from a prehistoric Merrie olde England.

It didn't hurt that Dawson's Piltdown Man, with an ape-like jaw and not-quite-human-size brain, looked like the missing link some scientists had imagined.

Not everyone thought that Charles Dawson's "discovery" made sense. The Royal College of Surgeons, using copies of the skull fragments Dawson had, put them together: and found that the brain was about the size of a modern human.

A Little Bit of This, a Little Bit of That —

As it turns out, the Royal College of Surgeons were right. The part of "Piltdown Man" they reconstructed was from a human skull: someone who had lived in the medieval era.

The lower jaw came from a Sarawak orangutan that had died about five centuries previously. The bones looked older than they were, since they'd been stained with an iron solution and chromic acid.

The teeth really were fossils: from a chimpanzee. Microscopic file marks hint that someone had whittled them down to look like they'd come from a critter with a human diet.

The Piltdown Man hoax did quite a bit of damage: encouraging scientists to look for more evidence of an early human who had never existed, wasting time and effort in discussion of the fraud.

Some folks who don't like science, or want an 17th century Calvinist to be right about humanity's origins, love the Piltdown Man. The Piltdown hoax encourages the notion that scientists are liars. Never mind that scientists exposed the fraud.

Then there's Nebraska Man and the Cardiff giant, and those are other topics.

Archaeoraptor Angst

Dust is still settling from a more recent forgery, Archaeoraptor: which, again, scientists exposed as a fraud.

National Geographic announced Archaeoraptor as a "missing link" in October of 1999. A few months later, the magazine issued a press release saying that the fossil might be a composite.

They'd gotten it right the second time. Archaeoraptor really is a fossil: three, actually. The head and upper body are from Yanornis; a bird; the tail comes from a Microraptor; the legs and feet are from a third, still-unidentified, animal.

Besides wasting time with another fraud, the Archaeoraptor scandal involves illegal export of fossils from China. And, of course, the usual folks can use it as "proof" that scientists lie, and evolution is a fake.

Studying the Universe

I'm not terribly surprised that some professors decided to try passing computer-generated nonsense text as scholarly papers.

What's remarkable is that more than a hundred have been found so far: all published by outfits that should have known better. I'll get back to that.

Folks who want science to be a lie will probably add this scandal to their list of arguments: along with the Piltdown Man and a few other high-profile hoaxes.

Me? I'll go on, worshiping God and learning about this wonder-filled creation.

The universe is beautiful, good, and there for us to study. Honest research cannot hurt faith, because faith comes from God; God is making the universe; God is truth; and truth cannot contradict truth. (Genesis 1:1-2:9; Catechism of the Catholic Church, 31-32, 105-108, 159, 279, 282-289, 301, 341)

(image courtesy NASA/JPL-Caltech)

Bottom line? Truth is important. (Exodus 20:16; Deuteronomy 5:20; Psalms 119:90; John 14:6; 1 Timothy 2:4; Catechism of the Catholic Church, 159-160; 2464-2503)

1. High-Pressure Fish

(From Oceanlab, via BBC News, used w/o permission.)
"At more than 7,000m down, these snailfish are among the deepest fish known to science"
"Fishy molecule 'sets depth limit' "
Jonathan Amos, BBC News (March 3, 2014)

"Scientists say it is unlikely that any fish can survive in the oceans deeper than about 8,200 metres.

"No fish has ever been seen living beyond this limit, but the researchers point to good physiological reasons why it should not be possible, also.

"It rests on the particular molecular mechanism they use in their tissues to withstand crushing pressures.

"To go deeper would require fish to evolve some other mechanism, the team tells the journal PNAS.

"The all-important molecule is a so-called osmolyte called trimethylamine N-oxide (TMAO). It is what gives fish their 'fishy smell'.

"TMAO acts to stabilize the proteins fish use to build and maintain their cells.

"Without its presence, the proteins would be distorted by the high pressures found at depth and stop functioning...."
Molecules have shapes which make a difference in how they act: like the benzene ring. Depending on who you listen to, a scientist who was trying to understand how benzene works daydreamed about a snake biting its tail, or dancing monkeys, and that's another topic.

An osmolyte is a compound affecting osmosis.

No Fish Beyond This Point?

These scientists noticed that fish species living at different depths had different amounts of TMAO. The deeper the species, the more TMAO. They plotted a curve from several species, then tested hadal snailfish from the bottom of the Kermadec Trench. The animals, living more than 7,000 meters below sea level, had as much TMAO as predicted on the curve.

So — that means that animals can't live deeper than these fish?

More to Learn

Some fish have been dredged up from greater depths than this study's snailfish: but none have been observed swimming in the deepest parts of Earth's ocean.
"...But extending that line forwards moves TMAO concentrations to a point where they would inhibit cell function, at about 8,000-8,500m's depth.

"Life's limits

" 'We know that if TMAO is too high, it makes proteins so stable they can't work,' explained Prof Yancey.

" 'The myosin protein in muscle, for example, needs to flex for muscles to move, and too much TMAO would stop this happening.'..."
(Jonathan Amos, BBC News)
Single celled critters, like archaea, bacteria, and foraminifera, live in deeper places: like the Marianas Trench. So do animals like sea anemones and sea cucumbers. Amphipods, crustaceans with a remarkable tolerance for pressure, and for compression and decompression.

It may help that these crustaceans seem to have five osmolytes, where fish only have two.

Since some animals can live at depths that apparently would kill fish, why can't fish?

The authors of this study think that maybe it's because fish haven't had time to evolve pressure-resistant cells.

Crustaceans like amphipods have probably been around since the Carboniferous, a third of a billion years ago; both sea cucumbers and sea anemones date back to the Middle Cambrian, about a half-billion years back.

But fish, with and without jaws, go back to the Cambrian, too. It looks like we still have more to learn: which is no surprise.


2. Finding Life

(From BBC, used w/o permission.)
"The last place on Earth… without life"
Rachel Nuwer, BBC (March 3, 2014)

"In the Atacama Desert in northern Chile, it looks as if nothing could ever survive. It is one of the driest places in the world, and some sections of the Mars-like expanse can go 50 years without feeling a drop of rain. As poet Alonso de Ercilla put it in 1569: 'Towards Atacama, near the deserted coast, you see a land without men, where there is not a bird, not a beast, nor a tree, nor any vegetation.'

"Yet Atacama is not devoid of life. Microorganisms called endoliths have found a way to cling on, by hiding themselves inside the pores of rocks, where there's just enough water to survive. 'They support a whole community of organisms that eat the byproducts of their metabolism,' says Jocelyne DiRuggiero, a microbiologist at Johns Hopkins University. 'And they're all just sitting right there in the rocks – it's quite fascinating.'

"Life, it seems, has an incredible knack for finding ways to persist. Indeed, microorganisms have been around for nearly four billion years, giving them ample time to adapt to some of the most extreme conditions in the natural world. But are there places left on Earth so harsh that they are rendered sterile?..."
Heat around sea hydrothermal vents, where water temperature is 122° centigrade (252° Fahrenheit), would kill a human, and many other plants or animals.

According the Rachel Nuwer, most scientists put 150° centigrade, or 302° Fahrenheit, as an upper limit for life. That's the point where proteins start breaking down, so we probably won't find anything living in those hydrothermal vents.


(From Philippe Crassous/SPL, via BBC, used w/o permission.)
"A deep ocean worm, which lives on the edge of a hot 'black smoker' vent on the floor of the Atlantic Ocean. ... feeds off mineral-eating bacteria...."
"...This means that microorganisms can thrive around hydrothermal vents, but not directly within them, where temperatures can reach up to 464C (867F). The same is true for the interior of an active volcano on land. 'I really think temperature is the most hostile parameter,' says Helena Santos, a microbial physiologist at the New University of Lisbon and president of the International Society for Extremophiles. When things get hot enough, she says, 'It's impossible – everything is destroyed.'

"High pressure, by contrast, appears to be less of a problem for life. This means that heat rather than depth probably limits how far below the surface of the Earth life occurs. The centre of the Earth's 6,000C (10,800F) temperature certainly precludes all life, although the depth at which the cut-off occurs is still under investigation. One microorganism called Desulforudis audaxviator was discovered nearly two miles (3.2km) below the Earth's surface, in a South African gold mine. It has not been in contact with the surface for potentially millions of years, and survives by siphoning nutrients from rocks undergoing radioactive decay...."
(Rachel Nuwer, BBC)
That deep sea worm reminds me of Ed "Big Daddy" Roth's grotesque cartoon characters, and that's another topic.

Some extremophiles, critters that live in extreme environments, live in Siberian permafrost, where "normal" temperatures are -10° centigrade (14° Fahrenheit); or in a hypersaline subglacial Antarctic lake where the water is -20° centigrade (-4 Fahrenheit).

Some microbes live in radioactive waste, some depend on arsenic, mercury, or other heavy metals to survive: and some live with cyanide. The hot springs of Kamchatka, Russia, are home to microbes that need sulphur or carbon monoxide.

Researchers found traces of microbes in Antarctica's Don Juan Pond, but aren't sure if the critters were living there, or got blown in from elsewhere. Salinity in Don Juan Pond is 40%, compared to the Dead Sea's 33%: so we may have found an environment that's too salty for life.

Then again, maybe not.

Life as We Know It: And Otherwise, Maybe

Back in the '60s, a former professor at Boston University put together a pretty good argument for life chemistries that might plausibly work in temperatures ranging from near red-hot to near absolute zero:
  • Fluorosilicone in fluorosilicone
  • Fluorocarbon in sulfur
  • Nucleic acid/protein (O) in water
  • Nucleic acid/protein (N) in ammonia
  • Lipid in methane
  • Lipid in hydrogen
    ("View from a Height" Isaac Asimov (1963), Lancer Books (p. 63))
Isaac Asimov's grasp of ecology and physics was a trifle shaky, at least in his fiction: but this time he was speculating in his professional field, chemistry.

I think he's probably right: that life-as-we-know-it isn't necessarily the only sort. We're #3 on that list, by the way.
(Adapted from Apathetic Lemming of the North (March 24, 2010))

3. Grand-Sounding Claptrap

"Publishers withdraw more than 120 gibberish papers"
Conference proceedings removed from subscription databases after scientist reveals that they were computer-generated. Richard Van Noorden, Nature (February 25, 2014)

"The publishers Springer and IEEE are removing more than 120 papers from their subscription services after a French researcher discovered that the works were computer-generated nonsense.

"Over the past two years, computer scientist Cyril Labbé of Joseph Fourier University in Grenoble, France, has catalogued computer-generated papers that made it into more than 30 published conference proceedings between 2008 and 2013. Sixteen appeared in publications by Springer, which is headquartered in Heidelberg, Germany, and more than 100 were published by the Institute of Electrical and Electronic Engineers (IEEE), based in New York. Both publishers, which were privately informed by Labbé, say that they are now removing the papers...."
Apparently the erudite-sounding drivel was good enough to get past a peer-review process.

This is a serious problem, both for the reputation of the publications that blundered: and for honest scientists whose papers were pushed out of the publications to make room for the claptrap.

All the Gibberish That's Fit to Print

(From, used w/o permission.)
"Over 100 published science journal articles just gibberish"
Maxim Lott, (March 1, 2014)

"Do scientific papers ever seem like unreadable gibberish to you? Well, sometimes they really are.

"Some 120 papers published in established scientific journals over the last few years have been found to be frauds, created by nothing more than an automated word generator that puts random, fancy-sounding words together in plausible sentence structures. As a result they have been pulled from the journals that originally published them.

"The fake papers are in the fields of computer science and math and have titles such as 'Application and Research of Smalltalk Harnessing Based on Game-Theoretic Symmetries'; 'An Evaluation of E-Business with Fin'; and 'Simulating Flip-Flop Gates Using Peer-to-Peer Methodologies.' The authors of those papers did not respond to requests for comment from"
Those papers weren't submitted by college kids after an evening of beer pong. The authors were professionals: college professors who had presumably sobered up from their undergraduate daze.

In their defense, sort of, the computer scientist Cyril Labbé says that professors are under a lot of pressure to publish. I believe it. "Publish or perish" was an unofficial motto in academia, a half-century back, and I haven't noticed much change in the halls of ivy since.

It's not just professional pride or social pressure. Apparently quite a few colleges and university pay professors on a piecework basis: the more papers a prof pushes out, the higher the prof's pay.

I see how paying someone a set amount for every widget coming off the bench makes sense: providing that there's a widget inspector. For the computer science and math fields, at least, the widget inspector seems to have been sleeping on the job.

"... Free From any Dependence on ... Objective Truth ..."

"...This is not the first time nonsense papers have been published.

"In 1996, as a test, a physics professor submitted a fake paper to the philosophy journal Social Text. His paper argued that gravity is 'postmodern' because it is 'free from any dependence on the concept of objective truth.' Yet it was accepted and published.

"But how could gibberish end up in respectable science papers? The man who discovered the recent frauds said it showed slipping standards among scientists....

"...But he [Cyril Labbé] has no explanation as to why the journals published meaningless papers.

" 'They all should have been evaluated by a peer-review process. I've no explanation for them being here. I guess each of them needs an investigation,' he said.

"The publishers also could not explain it, admitting that the papers 'are all nonsense.'..."
(Maxim Lott,
My guess is that these ersatz papers were evaluated by a peer-review process. I'm closing in on retirement age, so most folks working for these learned publications are probably younger than I am.

Although I think that accumulating experience, and perhaps wisdom, is an option as one ages: I don't assume that younger folks are dull-witted.

However, I started college when "relevance" was still in fashion: and checked out when political correctness was in bloom.

I'm not surprised that folks trained to loathe male-dominated hierarchical authoritarian systems of oppression, racism real or imagined, and incidentally some academic skills, let the occasional bit of magniloquent balderdash slip by.

Particularly when it has a nifty title, like these; all of which are nonsense:
  • "Application and Research of Smalltalk Harnessing Based on Game-Theoretic Symmetries"
    2009 International Joint Conference on Artificial Intelligence
  • "Investigation on E-Commerce based on Suffix Trees and Moore's Law"
    2009 International Conference on Environmental Science and Information Application Technology
  • "Implementation of Workflow Engine Based on Petri Nets"
    2010 International Conference on e-Education, e-Business, e-Management and e-Learning
  • "An Optimal Method for Assessing Information System Risk Decision-Making on Common"
    2010 Second International Conference on Computer Engineering and Applications
  • "Random Archetypes and Their Influences on Networking"
    2012 International Conference on Computer Science and Electronics Engineering
    (From "Articles IEEE have removed from their database")
What's sad is that this news will probably encourage at least some folks who don't like science to assume that all scientists are conniving liars. It's a faulty generalization, but perhaps an understandable one.

More about published gibberish:
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What's That Doing in a Nice Catholic Blog?

From time to time, a service that I use will display links to - odd - services and retailers.

I block a few of the more obvious dubious advertisers.

For example: psychic anything, numerology, mediums, and related practices are on the no-no list for Catholics. It has to do with the Church's stand on divination. I try to block those ads.

Sometime regrettable advertisements get through, anyway.

Bottom line? What that service displays reflects the local culture's norms, - not Catholic teaching.