Why my dad is pretty fucking cool, part 783.

[LMNO]

From a commencement speech he recently gave (yes, it's really long; I've redacted the non-essential bits):

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My choice for the cultural event of the millennium is the discovery of the quantum mechanical world view.

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It is very important to understand that what was discovered with quantum mechanics was not what the world is made of. We still do not know that. And in 1925, the year the quantum picture finally became clear, no one had the slightest inkling of quarks and gluons, or even of neutrons.

What Bohr, Heisenberg, Born, Jordan, Dirac, and others discovered was an entirely new way of looking at how nature must be described. They forged a new language in terms of which all future theories and all future discoveries must be expressed. Scientists who continued to use the old language, Einstein tragically among them, produced nothing further of value to the next waves of discovery.

The quantum language is not a neutral language. It has consequences that are so extremely non-intuitive that Einstein, Podolsky, and Rosen tried to use them as evidence that the quantum picture was absurd. The "weirdness" offended Schrödinger from the very beginning, but Bohr and his school embraced it, exposed it, and used its consequences to destroy the old world view.

[edit]

I said the discovery of this new way of looking at things was the most important cultural event of the millennium. What lessons does it have for us today? Of what possible relevance is this difficult theory to non-scientists?

Today I am not speaking to non-scientists, but to an audience who can appreciate the metaphors and the meanings of quantum mechanics, and for you I will note three lessons for life it teaches us.

1. It is highly likely that no one knows what they are talking about. ("Trust no one.")
This is a wonderfully liberating idea. If you have the impression that everyone else knows more than you do, just remember the history of quantum mechanics. Even Einstein and Schrödinger got it wrong. When you are in one of those huge physics conferences with everyone buzzing around talking about concepts that seem incomprehensible, remember that there is a good chance none of them is right.

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2. We cannot even trust our own direct observations. ("Don't even trust yourself.")
Quantum mechanics, of course, tells us that the relation between the theoretical structures that tie all phenomena together in a beautiful pattern, and the events that we observe in nature, is essentially statistical. You cannot infer the significance of events from a single observation.

If, for example, the observed system is not in an eigenstate of what you choose to measure, you will get different results, randomly, each time you observe. Measure the polarization of linearly polarized light with a circular polarization detector, and you will definitely measure circular polarization, about half the time left, and about half the time right circular polarization – just like tossing a coin.

It requires multiple encounters with reality, and an open mind, to piece together a coherent picture. The lesson of quantum theory is that we will always get an answer consistent with the picture we bring to an event. But that answer has everything to do with our preconceived notion of what to measure, and almost nothing to do with "the reality out there".

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3. Persistence pays off. ("Don't give up.")
In the quantum world view, it is possible through many measurements to piece together the wave function of a system and therefore to relate observations to a well
defined underlying conceptual structure that gives meaning to events. The lesson of the history of quantum theory itself is even more instructive. Out of the chaos of apparently contradictory experimental observations and the patently incompatible theories put forward to explain them, emerged a wonderful new way of seeing the world.

This new picture came into existence as the result of an encounter between people who believed there must be some order in the world, and Nature herself. A continual, stubborn persistence epitomized by Bohr's insistent attitude, and Einstein's loyal and lucid opposition, did finally pay off. Even Einstein admitted the logical consistency and usefulness of the statistical theory.

That these men of great talent (and some women too) expended so much effort on the quantum puzzle during the worst social conditions ever experienced in Europe is astonishing to me.

[edit]

Nature has always justified efforts to understand, as long as we remain in partnership with Her.

[Mangrove]

This is great.

I went to two graduations in a week and endured:

a) overlong commencement speech outside on a cold overcast day
b) overlong commencement speech inside a baking hot auditorium complete with screaming children (and minus air conditioning).

Why didn't I get a speech on Quantum Mechanics!??

[Cain]

We got one on Iran, from Prof Ali Ansari. 

Quantum mechanics would've worked too though, I suppose.

[Jenne]

Your dad is an intellectual powerhouse.  Wow.

[Honey]

It requires multiple encounters with reality, and an open mind, to piece together a coherent picture. The lesson of quantum theory is that we will always get an answer consistent with the picture we bring to an event. But that answer has everything to do with our preconceived notion of what to measure, and almost nothing to do with "the reality out there".
-LMNO's Dad

Those people were very lucky!  Your Dad must be a brilliant man.  I liked the whole speech but especially liked the above, it made me think of the Tao Te Ching

27
A good traveler has no fixed plans         
and is not intent upon arriving.
A good artist lets his intuition
lead him wherever it wants.
A good scientist has freed himself of concepts
and keeps his mind open to what is.

Thus the Master is available to all people
and doesn't reject anyone.
He is ready to use all situations
and doesn't waste anything.
This is called embodying the light.

What is a good man but a bad man's teacher?
What is a bad man but a good man's job?
If you don't understand this, you will get lost,
however intelligent you are.
It is the great secret.

Your Dad is very cool.

[Honey]

Hi LMNO et al,

I was re-reading Proust was a Neuroscientist by Jonah Lehrer, & came across this & it made me think of your Dad's speech.  Different fields but somehow simpatico.

"In 1989, Elizabeth Gould, a young postdoc working in the lab of Bruse McEwen at Rockefeller University, in New York City, was investigating the effect of stress hormones on rat brains.  Chronic stress is devastating to neurons, & Gould's research focused on the death of cells in the hippocampus.  But while Gould was documenting the brain's degeneration, she happened upon something completely miraculous: the brain also healed itself.

Confused by this anomaly, Gould went to the library.  She assumed she was making some experimental mistake, because neurons don't divide.  Everybody knew that.  But then, looking through a dusty 27 year old science journal, Gould found a tantalizing clue.  Beginning in 1962, a researcher at MIT, Joseph Altman, published several papers claiming that adult rats, cats & guinea pigs all formed new neurons.  Although Altman used the same technique that Rakic later used in monkey brains – the injection of radioactive thymidine – his results were ridiculed, & then ignored.

As a result, the brand-new field of neurogenesis vanished before it began.  It would take another decade before Michael Kaplan, at the University of New Mexico, would use an electron microscope to image neurons giving birth to new neurons.  Kaplan discovered these fresh cells everywhere in the mammalian brain, including the cortex.  Yet even with this visual evidence, science remained stubbornly devoted to it's doctrine.  After enduring years of scorn & skepticism, Kaplan, like Altman before him, abandoned the field of neurogenesis. 

Reading Altman's & Kaplan's papers, Gould realized that her mistake wasn't a mistake: it was an ignored fact.  The anomaly had been suppressed.  But the final piece of the puzzle came when Gould discovered the work of Fernando Nottebohm, who was, coincidentally, also at Rockefeller.  Nottebohm, in a series of remarkably beautiful studies on bird brains, showed that neurogenesis was required for bird song.  To sing their complex melodies, male birds needed new brain cells.  In fact, up to 1 percent of the neurons in the bird's song center were made fresh every day.  "At the time, this was a very radical idea," Nottebohm says.  "The brain was thought to be a very fixed organ.  Once development was over, scientists assumed that the mind was cast in a crystalline structure.  That was it; you were done."

Nottebohm disproved this dogma by studying birds in their actual habitat.  If he had kept his birds in metal cages, depriving them of their natural social context, he would have never observed the abundance of new cells that he did.  The birds would have been too stressed to sing, & fewer new neurons would have been created.  As Nottebohm has said, "Take nature away & all your insight is in a biological vacuum."  It was only because he looked at birds outside of the laboratory's that he was able to show that neurogenesis, at least in finches & canaries, had a real evolutionary purpose.

Despite the elegance of Nottebohm's data, his science was marginalized.  Bird brains were seen as irrelevant to the mammalian brain.  Avian neurogenesis was explained away as an exotic adaptation, a reflection of the fact that flight required a light cerebrum.  In his Structure of Scientific Revolutions, the philosopher of science Thomas Kuhn wrote about how science tends to exclude its contradictions.  "Until the scientist has learned to see nature in a different way, the new fact is not quite a scientific fact at all."  Evidence of neurogenesis was systemically excluded from the world of "normal science."

But Gould, motivated by the strangeness of her own experimental observations, connected the dots.  She realized that Altman, Kaplan & Nottebohm all had strong evidence for mammalian neurogenesis.  Faced with this mass of ignored data, Gould abandoned her earlier project & began investigating the birth of neurons. 

She spent the next eight years quantifying endless numbers of radioactive rat brains.  But the tedious manual labor paid off.  Gould's data shifted the paradigm.  More than thirty years had passed since Altman first glimpsed new neurons, but neurogenesis had finally become a scientific fact.

After her frustrating postdoc, during which time her science was continually attacked, Gould was offered a job at Princeton.  The very next year, in a series of landmark papers, she began documenting neurogenesis in primates, in direct contradiction of Rakic's data.  She demonstrated that marmasets & macaques created new neurons throughout life.  The brain, far from being fixed, is actually in a constant state of cellular upheaval.  By 1998, even Rakic admitted that neurogenesis was real, & he reported seeing new neurons in rhesus monkeys.  The text books were rewritten: the brain is constantly giving birth to itself.

Gould has gone on to show that the amount of neurogenesis is itself modulated by the environment, & not just by our genes.  High levels of stress can decrease the number of new cells; so can being low in a dominance hierarchy (the primate equivalent of being low class).  In fact, monkey mothers who live in stressful conditions give birth to babies with drastically reduced neurogenesis, even if those babies never experienced stress themselves.  But there is hope: the scars of stress can be healed.  When babies were transferred to enriched enclosures – complete with branches, hidden food, & a rotation of toys – their adult brains began to recover rapidly.  In less than four weeks, their deprived cells underwent radical renovations & formed a wealth of new connections.  Their rates of neurogenesis returned to normal levels.  What does this data mean?  The mind is never beyond redemption, for no environment can extinguish neurogenesis.  As long as we are alive, important parts of the brain are dividing.  The brain is not marble, it is clay, & our clay never hardens. 

Neuroscience is just beginning to explore the profound ramifications of this discovery. ... "   

- Jonah Lehrer, Proust was a Neuroscientist
from Chapter 2 George Eliot: The Biology of Freedom (the whole chapter is interesting, also Walt Whitman: The Substance of Feeling, Marcel Proust: The Method of Memory, Paul Cezanne: The Process of Sight, Igor Stravinsky: The Source of Music, Gertrude Stein: The Structure of Language, Virginia Woolf: The Emergent Self, Auguste Escoffier: The Essense of Taste)

[Kai]

The above story reminds me how much I really HATE the way many scientists attack every new idea that might change their paradigm. Its as bad as the opposite, taking up every "new finding" as true.

[Honey]

Also from Proust was a Neuroscientist by Jonah Lehrer:

The Blessings of Chaos

"How does our DNA inspire such indeterminacy?  After all, Middlemarch had an author; she deliberately crafted an ambiguous ending.  But real life doesn't have an intelligent designer.  In order to create the wiggle room necessary for individual freedom, natural selection came up with an ingenious, if unnerving, solution.  Although we like to imagine life as a perfectly engineered creation (our cells like little Swiss clocks), the truth is that our parts aren't predictable.  Bob Dylan once said, "I accept chaos, I'm not sure whether it accepts me."  Molecular biology, confronted with the unruliness of life, is also forced to accept chaos.  Just as physics discovered the indeterminate quantum world – a discovery that erased classical notions about the fixed reality of time & space – so biology is uncovering the unknowable mess at its core.  Life is built on an edifice of randomness.

One of the first insights into the natural disorder of life arrived in 1968, when Motoo Kimura, the great Japanese geneticist, introduced evolutionary biology to his "neutral theory of molecular evolution."  This is a staid name for what many scientists consider the most interesting revision of evolutionary theory since Darwin.  Kimura's discovery began with a paradox.  Starting in the early 1960's, biologists could finally measure the rate of genetic change in species undergoing natural selection.  As expected, the engine of evolution was random mutation:  double helices suffered from a constant barrage of editing errors.  Buried in this data, however, was an uncomfortable new fact: DNA changes way too much.  According to Kimura's calculations, the average genome was changing at a hundred times the rate predicted by the equation of evolution.  In fact, DNA was changing so much that there was no possible way natural selection could account for all of these so-called adaptations.

But if natural selection wasn't driving the evolution of our genes, then what was?  Kimura's answer was simple: chaos.  Pure chance.  The dice of mutation & the poker of genetic drift.  At the level of our DNA, evolution works mostly by accident.  Your genome is a record of random mistakes.

But perhaps that randomness is confined to our DNA.  The clock-like cell must restore some sense of order, right?  Certainly the translation of our genome – the expression of our actual genes – is a perfectly regulated process, with no hint of disarray.  How else could we function?  Although molecular biology used to assume that was the case, it isn't.  Life is slipshod.  Inside our cells, shards & scraps of nucleic acid & protein float around aimlessly, waiting to interact.  There is no guiding hand, no guarantee of exactness.

In a 2002 Science pare entitled, "Stochastic Gene Expression is a Single Cell[/i], Michael Elowitz of Caltech demonstrated that biological "noise" (a scientific synonym for chaos) is inherent in gene expression.  ..." 
- Jonah Lehrer, Proust was a Neuroscientist

[Captain Utopia]

Just awesome.

[Bebek Sincap Ratatosk]

Eris K Discordia, responsible for it all... AGAIN.

So random chance, chaotic mutation, random genetic drift... all come together to create species as we know it.

Meanwhile, Black Swan events, random chance, accidents, mutations within the environment etc all come together to bring a species to extinction.

It's like Eris' own planned obsolescence. 

[Kai]

Eris K Discordia, responsible for it all... AGAIN.

So random chance, chaotic mutation, random genetic drift... all come together to create species as we know it.

Meanwhile, Black Swan events, random chance, accidents, mutations within the environment etc all come together to bring a species to extinction.

It's like Eris' own planned obsolescence. 

But what about completely nonrandom natural selection? O.o

~Kai,

Thinks you forgot something there.

[Bebek Sincap Ratatosk]

Eris K Discordia, responsible for it all... AGAIN.

So random chance, chaotic mutation, random genetic drift... all come together to create species as we know it.

Meanwhile, Black Swan events, random chance, accidents, mutations within the environment etc all come together to bring a species to extinction.

It's like Eris' own planned obsolescence. 

But what about completely nonrandom natural selection? O.o

~Kai,

Thinks you forgot something there.

I was commenting on the above:

But if natural selection wasn't driving the evolution of our genes, then what was?  Kimura's answer was simple: chaos.  Pure chance.  The dice of mutation & the poker of genetic drift.  At the level of our DNA, evolution works mostly by accident.  Your genome is a record of random mistakes.

Is there natural selection that isn't based on the random expressions of DNA or Black Swan events in the environment?

[LMNO]

And what about positive Black Swans?


Remember, it doesn't have to be catastrophic, it just has to be completely unexpected.

[Bebek Sincap Ratatosk]

And what about positive Black Swans?


Remember, it doesn't have to be catastrophic, it just has to be completely unexpected.

That doesn't seem out of line with what I mentioned... but its a good point. Black Swan events could push species to evolve as easily as they could push them to extinction.

[Kai]

Eris K Discordia, responsible for it all... AGAIN.

So random chance, chaotic mutation, random genetic drift... all come together to create species as we know it.

Meanwhile, Black Swan events, random chance, accidents, mutations within the environment etc all come together to bring a species to extinction.

It's like Eris' own planned obsolescence. 

But what about completely nonrandom natural selection? O.o

~Kai,

Thinks you forgot something there.

I was commenting on the above:

But if natural selection wasn't driving the evolution of our genes, then what was?  Kimura's answer was simple: chaos.  Pure chance.  The dice of mutation & the poker of genetic drift.  At the level of our DNA, evolution works mostly by accident.  Your genome is a record of random mistakes.

Is there natural selection that isn't based on the random expressions of DNA or Black Swan events in the environment?

Yes. Actually, natural selection as it's defined is a nonrandom process.

As I've said before, the biggest argument in Evolutionary Biology is what is more important: random events of catastrophy and genetic drift, or natural selection, a nonrandom process. Biologists don't even agree which is more important.

Perhaps I need to be more clear. Natural selection as a process is the selective forces of the environment nonrandomly acting upon the organism. For example, a flood that kills a population of beetles would be considered a random event, or a small isolated population of butterflies that randomly drifts in wing pattern coloration from orange to red due to random mating (genetic drift).

Natural selection would be a particular population of a species of grass is resistant to disease and over time replaces the other populations, or a tree with higher sugar content in the fruit attracting more birds for transportation thus dispersing over a wider area, or an invasive plant which takes over a region causing many other plants to be displaced or go extinct due to the invasive's vigor and immunity. Natural selection does not cover how variation comes about, only how it continues (or discontinues) by nonrandom effects of the environment. Read the previous sentence again. Mutation is not a part of natural selection, as the whole premise starts with "there is variation".

You could say that everything is reducible to random processes and that any order we impose on the world is illusory, but I think thats a major copout to actually understanding what goes on in this universe.



This all isn't even getting into the argument of gradualism vs saltationism vs punctuated equilibrium. That's a whole 'nother can of worms.