Friday levity: Darwin Myths

There's a hashtag named ‪#‎DarwinMyths‬ going around on Twitter. Here are a few that I made up. Except that they aren't myths, of course.

1. Darwin who was a failed doctor originally planned to write a book titled "The Origin of Sepsis" to make up for his medical school failures.
2. A little known fact about Darwin: He had multiple personality disorder. The other personality's name? Alfred Russell Wallace.
3. Fun fact: The original phrase in the first edition of "The Origin of Species"was "Endless worms, most beautiful".
4. Contrary to popular belief, the main reason why Darwin used to take hot baths in sanitariums was to play with his rubber ducky.
5. Contrary to popular belief, "Darwin's bulldog" was an actual bulldog which threatened Bishop Samuel Wilberforce (Hence Huxley's misquoted quip: "The dog hath delivered him into my hands.")

6. The story goes that Darwin once spied two attractive beetles and then spied another one which he could not bear to lose, so he simply put one of the first two in his mouth so he could catch the third one. The story is actually about madeleines, not beetles. The gluttonous Darwin later asked biographers (one of whom had titled his version "The Last Madeleine") to change that minor detail.

7. Contrary to popular belief, Darwin conned his way on to the "HMS Beagle" not by pretending to be a "gentleman scientist" but by pretending to be part of a dance troupe that was supposed to keep Captain FitzRoy entertained on the long and lonely voyage. Presumably his performances were so forgettable that he could easily transition into his other role without arousing FitzRoy's fury, or attention for that matter.

Placebos can be really complicated

Heisenberg and Dirac in the age of NIH funding

The men who engineered the quantum revolution had some hard tasks cut out in front of them. But as the brilliant Philip Anderson says in his sparkling collection of essays "More and Different", at least they did not have to deal with the exigencies of NIH/NSF funding crunches, tenure pressures, media sensationalism, instant approbation or reprobation from social media, and the dog-eat-dog culture of peer review that has come to plague the upper echelons of science. Tis was a simpler time, and here's what would have happened to poor Werner and his fellow physicists had they tried to practice their trade today...it would be funny if it weren't painful.

A molecular modeler to his beloved (medicinal chemist)

With all apologies to W. B. Yeats

Original: "I BRING you with reverent hands
The books of my numberless dreams;
White woman that passion has worn
As the tide wears the dove-gray sands,
And with heart more old than the horn
That is brimmed from the pale fire of time:
White woman with numberless dreams
I bring you my passionate rhyme." Corrupted: "I BRING you with reverent hands Bioactive among my numberless conformations Unstrained structures that my protein has worn As the slide showcases the top-ranked ligands, And with common sense more than docking score                              That is scraped from the muddy waters of sampling Ascendant among my numberless failures You better now hand me my dime."

If computational recipes were like food recipes...

...the menu at Boston's elegant L'Espalier might look something like this.

Maine beef tenderloin: Carrot tagliatelle al ragù, gorgonzola mornay, sunny side up quail egg, crispy shallots

10 ns molecular dynamics run: Replica exchange, orthorhombic box, embedded sodium ions, 1 fs time step, Nose-Hoover thermostat. Happy water molecules. Smooth trajectory.

West Coast King salmon, lightly smoked, with vanilla and cardamom: faux hazelnut gnocchi and pumpkin juice

New England Induced-fit Docking protocol: Braised loop resampling, 5A residue movement, multicore run with threading. Optional polarized force field (add 10 tokens). Error bars.

Honey glazed duck for two with roasted pumpkin, chestnut, foie jus, smoked chocolate puree and toasted nuts and seeds (add 20)

Multi-ligand conformer search: Seared 10 kcal/mol energy window. Glazed harmonic potential. Monte-Carlo dihedral drive (add 20 tokens). Experimental infusion.

Licorice glazed Hudson Valley foie gras with black trumpet mushrooms, hay ash roasted banana, black sesame and almond-rice milk.

Similarity search: Shape-based scaffold hopper, optionally paired with electrostatics. Statistically validated (add 50 tokens). 

There's a reason they're called computational "recipes".

"In surprise advance announcement, 2013 Nobel Prize in physics awarded to Higgs boson"

In honor of April Fool's day I am posting an old post from Scientific American which I wrote not on April 1st but on September 30th, a few days before the announcement of the Nobel Prize awarded that year for the prediction of the Higgs Boson. The post was an interesting social experiment. First Sci Am panicked and took it down. They put it back up again after I agreed to include a note at the end explaining that it was a spoof (I thought any reasonable person who read it would have realized this by about the third paragraph). As comments on the post indicate, some commenters fretted and fumed but many others were appropriately mirthful.

In a stunning and premature decision that is a first in the 113 year history of the august institution, the Nobel Prize Committee in Stockholm today announced the awarding of the 2013 Nobel prize for Physics to the Higgs Boson. Originally scheduled for October 8, the announcement instead came more than a week in advance. The change in date was guarded with the same secrecy that has always guarded the nominations for the coveted prize. The award has sparked immediate and intense controversy and speculation, both because of its premature announcement and because of the highly unconventional nature of the recipient.

According to Prof. Lars Brink, the chairman of the Nobel physics committee, the decision was driven by a simple reason: to quell the rancorous feelings regarding division of credit and authorship that have suffused the scientific community ever since the particle was discovered in July last year. “We were startled and depressed by how personal the controversy got after last year’s discovery of the boson”, remarked Prof. Brink. “Instead of focusing on the finding itself – which was unanimously regarded as a long sought after breakthrough – both scientists and the media got obsessed with who should deserve the credit, whether one, two, four or six people should win the prize. We found that the beautiful discipline of physics was being torn apart by this constant bickering. It was no longer about the science, it was a beauty contest.”

Confronted with the impossible task of deciding who exactly to award the prize – a decision that would have been controversial regardless of its outcome – and distraught by the incessant obsession with people instead of particles, the committee took the radical but well-considered step of omitting human beings from the prize altogether. “The decision was grueling, but we thought about it a long time and finally reached a consensus. We said, look, it’s not really about the theorists or the experimentalists, it’s really about the particle; this fundamental, all-encompassing particle that underpins the very existence of matter”, explained Prof. Lars Bergstrom, a member of the committee and a particle physicist himself. “Nobody denies the tremendous efforts and creativity contributed by the scientists and engineers who predicted the particle and built the LHC. But since the real hero of the story is the boson itself, why not take human beings out of the equation altogether? We therefore decided to honor the one thing that really matters in this whole story”.

By no means was the radical departure from tradition an easy task; one member of the committee who chose to remain anonymous disclosed that the interminable late-night sessions, shouting matches and the unprecedented interruption of a proud and flawed human decision process by an objective, dispassionate analysis had forced her to see a therapist. Another member confided that “While I realize that science is a very human process, in this case it has been the ‘human’ part of it that has really driven me up the wall.”

The Higgs boson thus becomes the first particle, and the first non-human entity, to be awarded the Nobel Prize in any field. Since interviews with the particle could not be held for obvious reasons, the media was instead shown a graph displaying a bump supposed to indicate its existence. A member of CERN’s PR division also wore a large, squishy Higgs costume, doing his best to mimic the behavior of the fleeting particle as he whizzed from one end of the room to another, hid and emerged from behind a curtain and breathlessly answered questions about gauge symmetry and vacuum fluctuations. Reporters were also treated to a video showing the kind of particle collision that produces the Higgs; however since the effect is statistical, no one can be sure that that particular collision has anything whatever to do with the breakthrough.

The seven human candidates (five theorists and two experimentalists) have had mixed reactions to the surprise announcement. Dr. Peter Higgs who had the most invested in the discovery had the following to say: “I am very happy for my namesake boson. I am very happy that it has been recognized for this singular honor. I agree that it’s not about the people, it’s about the science, and I humbly submit….DAMN IT, I should have won that damn prize”. Others took a more philosophical view. A leading scientist on the experimental team mused out loud, “When I think about it, I realize that we are no more than particles and fields ourselves in this endless and accelerating cosmos. The great black hole at the center of the galaxy beckons us in the spirit of Ulysses’s sirens, and our minds are being seduced and ravaged at this very moment by the very guts of the cosmic leviathan…”. At this point the glassy-eyed scientist was quickly ushered into a waiting car by some family members.

The awarding of the prize to the boson has also made it difficult to nominate a speaker for the traditional Nobel lecture in December. After another round of votes, the decision was taken to simply leave the stage empty for an hour and let the all-pervasive Higgs field around us do the talking. According to Prof. Brink, “During this one-hour period, the audience will be asked to maintain complete silence, close their eyes, and try to imagine how the Higgs bosons in their brains give rise to neural signals that generate thoughts of envy, lust and disappointment. A better tribute to this remarkable particle will be hard to imagine.”

Note: In case it’s not clear, this post is supposed to be satirical and humorous. I don’t see the Nobel Prize being awarded to non-human entities anytime soon. Meanwhile, the brilliant men and women who further our understanding of life and the universe will continue to win well-deserved awards like the Nobel Prize. The real point of this post was to stress the fact – through satire – that what really matters are the discoveries themselves. As Richard Feynman put it after he received the award, “I’ve already got the prize. The prize is the pleasure of finding the thing out, the kick in the discovery….”

Schrodinger and Hawking in the Starbucks line

This list of entries entitled 'literary Starbucks' speculates what different well-known writers and fictional characters would order based on their personalities if they were to suddenly turn consumerist and appear in the Starbucks around the corner. Here's a sample involving "To Kill a Mockingbird" star Atticus Finch:

"Atticus Finch goes up to the counter and orders the one drink on the menu that no one else was brave enough to get. As he walks out, everyone else stands up in solidarity."

Naturally (yes, naturally) this got me thinking about what certain physicists would utter if placed in the same situation.

ISAAC NEWTON

Newton slowly walks up to the counter and is thinking of ordering some biscuits instead of a drink. Before he can say anything he sees a few biscuits in the display window named "Leibniz". He grows red in the face, curses loudly and storms out.

WOLFGANG PAULI

The portly Pauli waddles up to the counter and offers up a precise description of ingredients which he wants in his exclusionary latte. The barista furiously scribbles the order and makes the drink. Pauli takes a sip and screams "This is not even bad". The barista tries to stammer an excuse. Pauli puts both fingers in his ears and runs out.

ERWIN SCHRODINGER

Dressed in his impeccable bow tie Schrodinger elegantly walks up to the counter. First he orders a caramel macchiato, then switches to a green tea latte, then contemplates a pumpkin spice drink, then reverts back to simple coffee, then finally asks that the barista make him a drink with a superposition of all possible ingredients in the coffee shop. When served this drink he takes a sip and throws up.

NIELS BOHR 

Bohr walks up to the counter and mumbles his order. When the barista says she didn't understand, he repeats the order with a different version of mumble. When this happens three times he retreats to the corner and sits there smoking his pipe and mumbling to the stranger next to him.

PAUL DIRAC 

Dirac hesitantly steps up to the counter. The barista asks him what he would like. Dirac asks him what's on the menu. The barista spends about five minutes describing the several offerings. Dirac finally asks for a cup of water and leaves.

ALBERT EINSTEIN 

Einstein orders a tall vanilla latte. When he takes a sip he feels obliged to point out to the barista that it's the worst drink he has ever had, and that includes the "English" tea served at the Institute for Advanced Study. The barista drily points out that taste is a very relative thing. There's not much Einstein can say to this and he retreats to a corner seat, trying to smile and look sage-like but fuming inside at being hoist by his own petard.

RICHARD FEYNMAN 

Feynman walks in with a pair of bongos and makes such a din that he is indignantly asked to leave. Five minutes later he walks out of the cafe with two free macchiatos, and the baristas have no idea what the hell happened there.

LEO SZILARD 

Szilard walks up to the barista and asks her if they have a pastrami sandwich. The barista says they do and quickly realizes it's a bad idea when Szilard likes the sandwich so much that he lodges himself into a comfortable chair and refuses to leave even when the cafe is about to close. He says this is where he is going to live for the next one month. 

ENRICO FERMI 

Fermi walks up to the counter and offers a very precise description of his drink. While the drink is being made Fermi comes up with a theoretical formula to maximize the taste and flavor of an arbitrary caffeine-based beverage as well as a new, cheaper and more efficient design for the espresso machine. He is offered a job as manager on the spot.

STEPHEN HAWKING 

Hawking whirs around to the counter in his electric chair and orders up some English breakfast tea in his digital American accent. For some reason the baristas are all looking very offended and seem reluctant to serve him his drink. It doesn't take long for Hawking to realize the reason - for the last few minutes he has been saying something to his scientific colleague about a "black hole with no hair".

MURRAY GELL-MANN

Looking erudite and self-important Gell-Mann ambles up to the counter. He only seems interested in two qualities of the drinks in the cafe - flavor and color. After picking his favorite combination of the two he proceeds to correct the baristas' pronunciation of every item on the menu as well as their own names.

EDWARD WITTEN 

Witten orders his usual grande chai. And he ends up being the only one among the physicists who offers unadulterated praise for the drink, saying that it excels in every possible dimension.

Frankenstein and his monster in the age of Oprah and NIH funding

Frankenstein and his monster on Broadway
(Image: dvdbeaver.com)

The Nobel Prize-winning physicist Robert Laughlin is one of those rare minds who combines a wide-ranging knowledge of many fields with a wicked sense of humor and a devil-may-care attitude. This combination of gifts is on full display in his wonderful book "A Different Universe", a volume that at its heart is about the limitations of reductionism in physics and the manifestations of emergence but which tends to gambol around a remarkable variety of topics ranging from politics to scientific personality with cheerful barbs and a constant sense of wonder about what we don't know about the human and the natural worlds.

In the book is contained a gem. Laughlin imagines what Mary Shelley's Frankenstein would have been like in the modern age of cut-throat federal funding, media frenzy and winner-take-all economic incentives. The result is in equal parts riotous humor and a capsule of deep insight. Definitely the funniest thing about Frankenstein I have read.

"I find it profoundly ironic that the very fallibility of science that motivated Mary Shelley to write Frankenstein – people’s tendency to believe they understand things when they actually do not – should become mainstream and acceptable for financial reasons. It brings to mind Oscar Wilde’s observation that the lack of money is the root of all evil. One can just imagine what Mrs. Shelley’s novel would have been like had it been written today. Instead of an angst-ridden nerd from Geneva, Victor Frankenstein would have been an enterprising young spam profiteer from the Thomas Jefferson High School of Science and Technology in Alexandria, Virginia. Instead of traveling to Igolstadt to learn his highly creative surgical techniques, Victor would have flown to Boston to attend Harvard Medical School – after a four-year hiatus at Princeton investigating tennis and women.  

Instead of constructing the monster in secret he would have used political connections to obtain a stupendous grant from the National Institutes of Health, then set up shop in Bethesda and floated a massive initial public offering. Instead of reviling his creation he would have plastered it on fliers touting his innovative technical breakthrough and announcing the launch of a new longevity clinic. The monster, meanwhile, forsaking a murder rampage as insufficiently destructive, would instead write a best-selling trash novel, appear on Oprah, and run for governor of California. Victor himself would not seek death on the ice floes of the Arctic but would look forward to a morally and financially untroubled retirement in Palm Springs as soon as his lawyers got rid of those meddlesome do-gooders from the Securities and Exchange Commission."

What happens when chemists have nothing better to do on a Wednesday afternoon?

• This. It started with me posting a link on Facebook to an awesome recent paper describing physicists' efforts to reweigh the electron to an accuracy of one part in a trillion. The great Aaron Finke - of the regretfully dead Carbon-Based Curiosities - then weighed in.

   

  Aaron Finke This is what happens when physicists are bored.
  
  "So... uh... whatcha up to?"
  "Nothin, just Facebooking and eating a Hot Pocket"
  "...cool, cool. Wanna... wanna reweigh the electron?"
  "Yes. Yes I do."

  
  
• 

  Ashutosh Jogalekar Computational chemist version:
  
  "So…uh, whatcha up to?
  "Nothin, just twittering and eating a Hungry Man chicken meal."
  "…Cool…Hey, wanna parametrize that aziridine N-C bond with some stretch-bend cross-terms?
  "You bet!"

  
  
• 

  Ashutosh Jogalekar Synthetic chemist version:
  
  "So…uh, whatcha up to?
  "Nothin, just textin and eating an Amy's frozen teriyaki bowl." (clearly the synthetic chemist is more evolved)
  "…Cool…Hey, wanna repeat Woodward's B12 synthesis, but this time using RCM in some of the steps?"
  "Oh God yes!"

  
  
• 

  Aaron Finke Geologists:
  
  "So, uh, whatcha up to?"
  "Not much, just youtubing and eating taco bell"
  "Cool, cool. Hey, wanna get shitfaced?"
  "I already am"
  "Oh ok"

  
  
• 

  Ashutosh Jogalekar Clearly there's a fine line between being bored and being shitfaced.

  
  
• 

  Aaron Finke that's the nice thing about being a geologist
  
  you never have to be in a hurry

  
  
• 

  Ashutosh Jogalekar At least until the continents start coming together again. Then things get truly shitfaced in a hurry.

  
  
• 

  Aaron Finke "So, uh, whatcha up to?"
  "Nothin, just waiting for the continents to collide together again"
  "Cool, cool... how long will that take?"
  "Probably a couple hundred million years."
  "Cool, cool... wanna get shitfaced?"
  "I already am"
  "Okay"

  
  
• 

  Aaron Finke "Well, have fun. I'm gonna go help weigh that electron with the physicists"

  
  
• 

  Ashutosh Jogalekar *Geologist returns after helping physicists reweigh the electron, computational chemists parametrize every single molecule that can be built from 12 heavy atoms and synthetic chemists make vitamin B12 from a simple, four-carbon compound isolated from bat feces*
  
  "So, uh, whatcha up to?"
  "Nothin, just waiting for the continents to collide together again"
  "Cool, cool... how long will that take?"
  "Probably a couple hundred million years."
  "Cool, cool... wanna get shitfaced?"
  "I already am"
  "Okay"

  
  
• 

  Aaron Finke Why am I not a geologist

  
  
• 

  Ashutosh Jogalekar Because you would rather spend your time much more productively on the 67th synthesis of aquabatguanine using hammer and tong chemistry?

  
  
• 

  Aaron Finke what am I, Chinese?

  
  
• 

  Ashutosh Jogalekar Of course not. The Chinese made aquabatguanosine.

  
  
• 

  Aaron Finke ...again.
  
  well this might be the dumbest conversation on your FB wall ever. You're welcome.

  
  
• 

  Ashutosh Jogalekar Eminently postworthy (with your permission, naturally: I am planning to name it "When chemists have nothing to do on a Wednesday afternoon"). May even help to resurrect the dead CBC.

  
  
• 

  Aaron Finke do it