# Warda/Han and Well-Hung Tongues

The story so far:

As January gave way to February, several bloggers called attention to a puzzling review article in the journal Proteomics, available online and slated for publication in the paper version. Mohamad Warda and Jin Han’s paper was entitled, “Mitochondria, the missing link between body and soul: Proteomic prospective evidence.” As PubMed and Proteomics now note, that paper has been retracted, but not, surprisingly, because it offered no actual evidence for its stated claim — that some grandfalutin’ higher power had been at work inside mitochondria, designing the ways their proteins worked together. Instead, the paper was retracted due to “substantial overlap of the content of this article with previously published articles in other journals” — in plain language, plagiarism.

The story is still unfolding. What concerns the scientific community now is not so much the transparently flawed allegations of Warda and Han themselves, but the sloppy practice of the journal Proteomics in letting those claims get through peer review into publication. Now, nobody expects peer review to be perfect — like any human institution, it’s not going to be — it’s just a procedure for telling, as Cosma Shalizi says, that “a paper is not obviously wrong, not obviously redundant and not obviously boring.” Still, this incident is rather beyond the pale.

While the Warda and Han paper was itself obviously wrong, the developments from it have been far from boring. The Korean newspaper The Hankyoreh picked up the story, and in consequence machine translation gave us the delightful phrase, “OK, the power of science blog!” More recently, Fabienne Gallaire wrote it up in the French publication Rue89. Gallaire’s piece describes how these shenanigans have played out, from the beginning until now. Of particular interest is its accurate description of how the plagiarism was first discovered:
Continue reading Warda/Han and Well-Hung Tongues

# Misplaced Obscenicons

It’s time to take the names of human actions in vain! The following post will contain the sort of language which, if you cared, would have made you stop reading my website already. Consider this item from sportswriter John Donovan:

Joe Torre met with George Steinbrenner for a nice lunch in Tampa the other day, and I’m sure at some point the subject probably turned to the Yankees. And George, I’d bet, at some point looked at his manager and said, “#$!&@* the heck?” The Yanks should be better. Can they win some close games? Now, I don’t really give a flying$!%!#% about sports, unless there’s a chance that Boston will erupt in a riot. Then, I’m interested. However, linguistic peculiarities always get me perked up. Let’s look at that “#$!&@* the heck?” little remark. Everyone who grew up with comic strips knows about the convention of replacing swear words with punctuation symbols. Sometimes, the word being replaced is obvious to those familiar with modern slang; on other occasions, there’s a moderate ambiguity in the decoding. More unusual, however, is the case of an innocent word being obscured. Following comics convention, one would expect to see “What the #$!&@*,” but that’s not what we’ve got here. So, presumably, the proper decoding for Donovan’s remark would have to be. . . .

# Dawkins and Myers on Being Expelled

Josh Timonen has filmed a dialogue between PZ Myers and Richard Dawkins. The clip below describes what happened when the two of them went, with friends and family, to see the creationist propaganda flick Expelled: No Intelligence Allowed. Many people have already observed that the movie’s subtitle is a blazing beacon of irony, but gosh darn it, that observation gets truer every day: the makers of Expelled are bound and determined to drive home their lack of acumen.

The Harvard/XVIVO animation to which the biologists refer, one which creationists have plagiarized before, is available on Harvard’s website.

# A Word from the Cuttlefish

Only the rarest of authors can demolish the “Two Cultures” divide within a single phrase, conjoining a scientific education with the “classical” like two strands of DNA (or like Baucis and Philemon, take your pick). One such author is The Digital Cuttlefish.

When reinventing history
Itâ€™s best to keep the mystery;
If witnesses are noticed, it is best to take them out.
And although the act is telling,
Youâ€™d be better off expelling
Doctor Myers, if you see him, just because the manâ€™s a lout.
You see, PZ is a witness
To the movieâ€™s lack of fitnessâ€”
He is one selection pressure that would render it extinct.
So, with â€œWANTED!â€ posters printed,
To the cinema they sprinted,
And they passed around the mugshots just as soon as they were inked.
While they watched with eyes like eagles for the devil in disguise.
Yes! They spotted Dr. Myers,
Looking just like in their fliers!
The policemen, quite correctly, gave the doctor a surprise.
When they said heâ€™d be arrested
If their actions he protested,
He complied at once (that should have raised suspicions, donâ€™t you think?)
Once his actions had been thwarted
And he left the line, escorted,
Looking back to his companion in the line, he gave a winkâ€¦.
So this little movie trip is
Like a Trojan Eohippus
That delivered Richard Dawkins deep within the fortress walls
I canâ€™t wait to read the story
Of the battle and the gloryâ€”
Cos the trailer to this feature shows the heroâ€™s got some balls!

(Source.)

It’s a good thing we’ve got the Cuttlefish, because a world which has gone this mad deserves a poet.

# Gas

I’m taking off for a few days — got to finish writing some other things, and all — so here’s a poem.

“DULCE ET DECORUM EST,” BY WILFRED OWEN

Bent double, like old beggars under sacks,
Knock-kneed, coughing like hags, we cursed through sludge,
Till on the haunting flares we turned our backs
And towards our distant rest began to trudge.
Men marched asleep. Many had lost their boots
But limped on, blood-shod. All went lame; all blind;
Drunk with fatigue; deaf even to the hoots
Of tired, outstripped Five-Nines that dropped behind.

Gas! GAS! Quick, boys! — An ecstasy of fumbling,
Fitting the clumsy helmets just in time;
But someone still was yelling out and stumbling
And flound’ring like a man in fire or lime . . .
Dim, through the misty panes and thick green light,
As under a green sea, I saw him drowning.

In all my dreams, before my helpless sight,
He plunges at me, guttering, choking, drowning.

If in some smothering dreams you too could pace
Behind the wagon that we flung him in,
And watch the white eyes writhing in his face,
His hanging face, like a devil’s sick of sin;
If you could hear, at every jolt, the blood
Come gargling from the froth-corrupted lungs,
Obscene as cancer, bitter as the cud
Of vile, incurable sores on innocent tongues, —
My friend, you would not tell with such high zest
To children ardent for some desperate glory,
The old lie: Dulce et decorum est
Pro patria mori.

# Specific and the General

TR Gregory finds a particularly egregious and galling mismatch between the headline of a press release and the story itself. He asks, “Do the people who determine headlines not even read the stories?” One more entry in the file of evidence that science journalism isn’t working right. . . and on that note, Brian Switek has some general observations, leading to the following conclusion:

We all bitch and moan about how inaccurate news reports are, but unless we actively become engaged in this sort of reporting (infiltrating the “system,” as it were) our complaints will essentially make little difference outside our own little circles of science enthusiasts. Science bloggers are starting to change this and may play a bigger role in the future, but if we’re to ultimately improve science communication in the media more people with a solid grasp of science are going to have to get involved in the active generation and promulgation of stories rather than just complain about the result.

I always get a Life of Brian vibe when the discussion turns in this direction. “We could sit around here all day talking, passing resolutions, making clever speeches. It’s not going to shift one Roman soldier!”

# Tending to the Sophomoric

I’ve got a simulation cranking away in the background. Once it’s finished, I’ll be able to poke over the results and do science things, but in the meantime, I crave amusement.

Luckily for me, Writerdd finds a review of John Allen Paulos’s Irreligion (2008) in the New York Times. Writer Jim Holt is not pleased:
Continue reading Tending to the Sophomoric

# Henry V, Act 4, Scene 1

But if the cause be not good, the king himself hath
a heavy reckoning to make, when all those legs and
arms and heads, chopped off in battle, shall join
together at the latter day and cry all 'We died at
such a place;' some swearing, some crying for a
surgeon, some upon their wives left poor behind
them, some upon the debts they owe, some upon their
children rawly left. I am afeard there are few die
well that die in a battle; for how can they
charitably dispose of any thing, when blood is their
argument? Now, if these men do not die well, it
will be a black matter for the king that led them to
it; whom to disobey were against all proportion of
subjection.

(Source.)

# Software Quirk of the Day

Suppose you want to know the skewness of a list of numbers, and luckily enough you have Python close at hand. The skew() function in the SciPy stats library returns a single-element array instead of a floating-point number. Why, I have no idea, but at least the developers seem to know about it. Trying to get the value out by a sensible method like, say, indexing the array returns the error message “0-d arrays can’t be indexed.” To get the value itself, subtract 0:

result = scipy.stats.skew(list_of_values) - 0

Just one more way life has found to make itself interesting.

# My Cheap Shot of the Day

This is the Archbishop of Canterbury trying (and failing) to speak about science:

Dr Williams admitted that Neo Darwinism, a theory supported by Atheist Professor Richard Dawkins, is “most problematic” to theology, but he called it “a pseudo science” and “deeply vulnerable to intellectual challenge because it is trying to be a theology.”

And here I thought Richard Dawkins’s professorship was endowed by Charles Simonyi, not Bob Atheist!

# News for Those Still Content

Rebecca Watson wonders why the big news media aren’t covering the Anonymous protests of Scientology which occurred this past weekend, and she notes that the next event, “Operation Reconnect,” will occur the twelfth of April. On the good chance that you won’t be able to see it on TV or read about it in your daily paper, your best bet to find out what’s going on might be to don a mask and attend in person.

Next, Jacques Distler takes a quantitative look at which political party here in Etats-Unisia has really been “the party of business.” Yes, Virginia, claims can diverge from reality now and then — and to drive that point home, check out Steve Novella‘s description of a recent case where uncritical acceptance of “facilitated communication” caused a Colorado family great and completely unnecessary suffering.

# Two Slashdottings In One House

I got a little blip of a Slashdotting when I wrote about the Stuart Pivar incident, but my friend Brian Neltner — expert in genetically engineering viruses to his bidding, and black belt in a martial art which teaches eyeball extraction as a standard “defensive” move — has got the real deal. He designs LED artwork, you see, incorporating UV lights and other extra goodies to create colors which can’t be captured in a camera or reproduced on a computer screen. Imagine a room bathed in smoothly shifting wavelengths of vivid color, changing the appearance of everything they touch as pigments vanish or merge only to arise again in new, deceptive patterns.

That’s our living room.

The total effect of these LED fixtures is a combination of both additive and subtractive color mixing. Oh, and if you look directly at the UV LEDs without the protective diffuser screen installed, well, you better not look again with your remaining eye. Normal people, when we tell them this, back away, but for some reason, MIT students always need to check for themselves.

What do you do with an Ultraluminous Illuminator of Doom? Well, you shine it on artwork! Brian and his mother Janet went to great lengths to find pigments which work well under polychromatic precision light:
Continue reading Two Slashdottings In One House

# Sagan on Flatland

You’re tuned to Radio Sunclipse, first on your RSS dial. It’s Monday morning in our local reference frame, and it’s time for a golden oldie: here’s Uncle Carl himself explaining how we can do geometry in different numbers of dimensions:

You know, his voice does sound a little like Agent Smith.

# SUSY QM: The 1D Dirac Hamiltonian

Whew! We spent a considerable amount of wordage developing the Dirac Equation. Now, it’s time to tie this development back to the supersymmetry material we studied earlier in the non-relativistic context. The result will be a surprising mapping between relativistic and non-relativistic quantum mechanics. Today, we’ll just get the gist of it, and to get started, we’ll begin with the final equation we had before,

$(i\displaystyle{\not} \partial – m)\psi = 0.$

Recalling Feynman’s notation of slashed quantities,

$\displaystyle{\not} a = \gamma^\mu a_\mu,$

we can unpack this a little to

$\left(i\gamma^\mu\partial_\mu – m\right) \psi = 0,$

which we can elaborate to include an electromagnetic field as follows:

${\left[i\gamma^\mu(\partial_\mu + iA_\mu) – m\right] \psi = 0.$

The Dirac Hamiltonian $H_D$ has a rich SUSY structure, of which we can catch a glimpse even having pared the problem down to its barest essentials. To take the simplest possible case, consider a Dirac particle living in one spatial dimension, on which there also lives a scalar potential $\phi(x^1)$. (We could call this a “1+1-dimensional” system, to remind ourselves of the difference between time and space.) The SUSY structure can be seen most clearly when we look at the limit of a massless particle; this eliminates the $m$ term we had before.
Continue reading SUSY QM: The 1D Dirac Hamiltonian

# Excuse Me, We’re From the Net

Both Joshua and I found ourselves passing by the Anonymous people protesting the Church of Scientology today:

At a rough estimate, there were probably a little over a hundred people present at noon — pretty good turnout for a Stand Alone Complex. (And I’ll have you know I thought of that comparison independently.) As Joshua says,
Continue reading Excuse Me, We’re From the Net