The Blog of Scott Aaronson If you take just one piece of information from this blog: Quantum computers would not solve hard search problems instantaneously by simply trying all the possible solutions at once.
So said my brother David (MIT math major), on forwarding me this animation of the inner life of a cell.
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22 Responses to ““Holy sh#t — maybe biology doesn’t suck!””
Just keep in mind, the animation is just a cartoon (although as Shaquille O’Neal famously said, “A person has to controll their own cartoon”) — these structures have never been directly observed with anything like the atomic resolution of the animation.
To observe real biostructures with atomic resolution (necessarily at cryogenic temperature) and dynamically animate the observed structures in real time, you’ll need a quantum microscope and an 80-core teraflop processor.
You’ll also need a much deeper understanding of the Kahler geometry of large-dimension Hilbert subspaces.
Hey, it’s the full employment act for 20th-century mathematicians and physicists!
IIRC, on another blog it was noted that cells really are tightly packed with biomolecules and that the animation also for convenience forgot that once in a while some of the kinetics works backwards to undo an earlier “move”.
Torbjörn, the web page that links to the animation has a description of the process of making it where the animators say that they purposely showed more empty space than exists in reality. If they had shown things as they really are, the frame would indeed be so “tightly packed with biomolecules” that viewers would have been able to distinguish very little.
Agnotology: the “system biology of human cognition,” this emerging discipline embraces cognitive science, sociology, anthropology, politics, economics, ethics, and planetary ecology. Agnotology is super-fun and super-important!
Every human cell containes about 500X as many atoms than there are stars in the galaxy … a resource frontier more vast than anything envisioned in Star Trek, and yet residing within each of us.
Accessing those cellular resources, and integrating them into 21st Century society, will require that we federatively embrace pretty much every mathematical, scientific, informatic, and engineering discipline known to humanity.
This pan-scientific embrace will be super-enjoyable and super-important … agnotology is merely one approach to this “great survival sweepstakes of our age.”
OK, it’s time for a Fermi Question. Which means, all of you science-smarties get to show your stuff by picking the correct answer, based solely on your general knowledge of math, physics, chemistry, and biology:
Every male human is continually producing reproductive DNA in his testes. If the net DNA production of a single human male were unspooled as a single thread, the net linear rate of DNA production would most nearly be:
(a) a snail’s pace
(b) human walking pace
(c) human running speed
(d) the speed of a car
(d) the speed of a jet fighter plane
(e) the orbital velocity of the space shuttle
Bonus Fermi Question: human females have a lifetime net production of a few hundred meters of reproductive DNA. Compare and contrast reproductive strategies of women and men in this light. More broadly, what does it mean to be human?
Golly, only four comments on the biology movie, compared to thirty-seven on “Godel, Turing, and Friends”.
E. O. Wilson in his new book The Creation: An Appeal to Save Life on Earth (Amazon sales rank #172, which is pretty darn good!) approving quotes Ralph Chermock’s pep talk to his biology graduate students: “You’re not a real biologist until you know the names of ten thousand species.”
This metric works well for poets, comedians, and musicians. E.g., here is Annie Liebovitz’ picture of Bob Hope sitting in his joke vault, surrounded by 85,000 pages of jokes. It was said that Mr. Hope knew all of these jokes by heart, and could recall them as needed.
Perhaps biology has a lot in common with these detail-loving professions?
But I dunno if the “ten-thousand metric” works so well for physicists: “You’re not a real physicist until you know ten thousand physical laws … ten thousand approximation methods … ten thousand conserved quantities”?
Or for mathematicians: “You’re not a real mathematician until you know ten thousand theorems … ten thousand complexity classes … ten thousand invariants”?
E.g., here is Annie Liebovitz’ picture of Bob Hope sitting in his joke vault, surrounded by 85,000 pages of jokes. It was said that Mr. Hope knew all of these jokes by heart, and could recall them as needed.
Torbjörn Larsson said … if the cells in a human can learn to cooperate, they may learn us something of handling common resources that can’t be handled by markets.
Yes, this cooperating-cells viewpoint is beautifully described in Douglas Hofstadter’s GEB. This inspires us to regard the scientific enterprise as the embodiment of a rational market of ideas.
Of course, the abstract notion of an rational market sometimes collides with the reality of The Chimp-O-Mat—that’s why humor is an essential feature of human cognition!
Answer to Fermi Problem: human testes synthesize linear DNA at orbital velocity — on the order of 100 terabytes of information is spooled out every second.
Yet on the other hand, this requires only that a few tens of nanograms of DNA be synthesized per second, which is easily handled by rather compact (air-cooled and paired for redundancy) organs.
The error rate of DNA replication is astonishingly low, yet given the thermodynamic limits to DNA replication fidelity, many biologists believe that we are about as complex as we can be … a larger genome would be too error-ridden to be evolutionarily stable.
John Sidles: The error rate of DNA replication is astonishingly low, yet given the thermodynamic limits to DNA replication fidelity, many biologists believe that we are about as complex as we can be … a larger genome would be too error-ridden to be evolutionarily stable.
There are organisms with lower error rates. If you’re trying to say something subtle, could you explain how my claim fits in?
“This inspires us to regard the scientific enterprise as the embodiment of a rational market of ideas.”
Hmm. I think markets inspire the model of a market of ideas, with merits instead of money as currency. I don’t see what currency the cells in the body uses.
“The error rate of DNA replication is astonishingly low”
BTW since you mentioned it, IIRC the air cooling of testes was claimed to lower the error rate, in a blog comment this time. Pairing is default due to the development of a bilateral bodyplan for efficient movement with extremities. The question is rather how the body distinguishes right and left to do that, and why it makes some organs nonpaired. ( http://scienceblogs.com/pharyngula/2006/07/the_evolution_of_deuterostome.php )
Douglas Knight asked if I was trying to say anything subtle …
Heck no … it’s tough enuf to say things that are obvious … there’s no intent to be subtle.
For me, that movie inspires reflection on relations and parallels between quantum computing and evolutionary biology; these include a DNA replication error threshold above which stable evolution is impossible.
Another parallel: if human physiology is ad hoc, error-prone, and ingenious, then isn’t human cognition likely to be similar?
John Sidles said: “Many biologists believe that we are about as complex as we can be [given achieveable DNA replication fidelity].”
Douglas Knight: “There are organisms with lower error rates … please acknowledge that my statement is in direct contradiction to yours.”
Uhhhh …. where’s the contradiction?
Possibility I: maybe the biologists are wrong. Then there’s no contradiction — because I merely noted what many biologists believe; there was no assertion that they are right (this is called a “quibble”).
Possibility II: maybe the biologists are right, but there is no contradiction because the more complex the genome, the less the error threshold. Which is pretty darn plausible (but of course, the opposite is equally plausible).
Possibility III: maybe the biologists are right for a more subtle reason … maybe the non-coding regions of DNA regulate gene expression by modulating the winding-unwinding of DNA on nucleosomes.
This is one of the hottest hypotheses in modern biology, because it would mean that DNA embodies two parallel genetic codes, one of which is non-binary. This would help explain why humans and fruit flies seem to have similar numbers of genes. Holy Shannon information theory, Batman!
I would like to try and impress upon you while I am talking about all of these things on a small scale, the importance of improving the electron microscope by a hundred times.
It is not impossible; it is not against the laws of diffraction of the electron. The wave length of the electron in such a microscope is only 1/20 of an angstrom. So it should be possible to see the individual atoms. What good would it be to see individual atoms distinctly?
We have friends in other fields—in biology, for instance. We physicists often look at them and say, “You know the reason you fellows are making so little progress?” (Actually I don’t know any field where they are making more rapid progress than they are in biology today.) “You should use more mathematics, like we do.”
They could answer us—but they’re polite, so I’ll answer for them: “What you should do in order for us to make more rapid progress is to make the electron microscope 100 times better.”
What are the most central and fundamental problems of biology today? They are questions like: What is the sequence of bases in the DNA? What happens when you have a mutation? How is the base order in the DNA connected to the order of amino acids in the protein? What is the structure of the RNA; is it single-chain or double-chain, and how is it related in its order of bases to the DNA? What is the organization of the microsomes? How are proteins synthesized? Where does the RNA go? How does it sit? Where do the proteins sit? Where do the amino acids go in? In photosynthesis, where is the chlorophyll; how is it arranged; where are the carotenoids involved in this thing? What is the system of the conversion of light into chemical energy?
It is very easy to answer many of these fundamental biological questions; you just look at the thing! You will see the order of bases in the chain; you will see the structure of the microsome. Unfortunately, the present microscope sees at a scale which is just a bit too crude. Make the microscope one hundred times more powerful, and many problems of biology would be made very much easier. I exaggerate, of course, but the biologists would surely be very thankful to you—and they would prefer that to the criticism that they should use more mathematics.
Note: the above passage is interesting because in it, Feynman and his audience (and his entire generation of physicists) completely overlook the possibility of resonant imaging, which allows high-resolution images to be obtained with long-wavelength (hence nondestructive) quanta. This was an easy Nobel prize that a whole generation missed (until Lauterbur, Mansfield, Damadian, etc.).
Hopefully, there are other easy pickin’s still available!
We in the quantum computing field have audio-visuals too! Once he hears my recording of a quantum computer (shh! it was recorded at a top secret US government facility), Scott’s brother will surely exclaim, after so many years of vacillating on the issue: “Holy Shirt, quantum computing and my brother don’t suck!”
Thanks to Scott for letting me post this off topic message:
I’ve just released a MacOS X version of my FREE, GRATIS, pedagogical program, Quantum Fog, that simulates a quantum computer using quantum Bayesian nets. I’ve only tested it on a PPC mac (because I don’t own and cannot presently afford to buy an Intel Mac). The program should work on an Intel Mac (via Rosetta), but I’m not sure. If you test it (especially on an Intel Mac) and find that it malfunctions, please tell me immediately so I can fix it.
Possibility II: maybe the biologists are right, but there is no contradiction because the more complex the genome, the less the error threshold.
This is what I am trying to directly contradict. The organisms with the largest genomes do not have the smallest error rate per base. That shows, pretty conclusively, that error rate is not the barrier to genome size.
I also don’t see what III has to do with information theory. Or even what it has to do with genome size!
Douglas Knight sez: I also don’t see what [nonbinary genomic information] has to do with information theory. Or even what it has to do with genome size!
I agree — it’s pretty clear that at this point in time nobody understands the informatic constraints that act on the messy systems associated with eukaryotic reproduction.
Which makes an important point: physics experiments are designed to be “logically clean” and rigorously analyzable, but this is not surely not true of biology.
Somewhere or other I read that in the second half of the 20th Century, condensed matter experiments evolved to be more like inventions than experiments in the Popperian sense — the goal of solid state physics became the invention of physical systems that embodied ever-more-clever Hamiltonians.
Maybe quantum computing can be viewed as the apotheosis of this trend?
Simultaneously, explaining nature—in the sense of explaining the observed phenomena of “natural” nature—became increasingly less relevant to physics. E.g., it is conceivable that there are no 2D fractional quantum Hall systems anywhere in the universe, except in terrestrial physics labs (I wish I had recorded this article in my database).
Now science is orbiting back to focussing on the natural world … so the good news is, we now get to analyze real-world systems. Oh boy!
And the bad news is, these systems are incredibly complex and ad hoc in their design. Ouch!
Hmmm … in my database, the nearest quote I can find that addresses the evolving focus of physics, with specific relevance to David Goodstein’s remark (quoted in an earlier blog) “It is by no means certain that science will even survive, much less flourish, in the difficult times we face“, is the following passage written by George C. Marshall, given in 1939 to the National Association of Manufacturers.
I have taken the liberty of substituting “scientific community” for “country”:
We citizens of [the scientific community] have been fortunate in the bountiful state of our natural resources, in the freedom for expansion, and in the strong individuality of our people.
… We are a highly favored people, and yet the march of time, of invention, and of mechanical perfection have brought us for the first time into very close relationship with all the world.
… I will not trouble you with the perplexities, the problems, and requirements for the defense of [the scientific community], except to say that the importance of this matter is so great and the cost, unfortunately, is bound to be so high, that all that we do should be planned and executed in a business-like manner, without emotional hysteria, demagogic speeches, or other unfortunate methods which will befog the issue and might mislead our efforts.
(The database has an essay by John von Neumann to similar effect, but this I will spare you.)
For me, this is what 21st Century science and technology are all about — planetary survival in combination with (dare we hope) prosperity, equity, and freedom. This definitely means tackling messy systems!
Just to close out this wonderful (for us medical researchers/engineers) thread on the interface between biology and informatics.
Scott sez: Hmm. I think markets inspire the model of a market of ideas, with merits instead of money as currency. I don’t see what currency the cells in the body uses.
Ah yes … money and merit … the quintessential linear measures of rank.
(And speaking of rank, the cover of George Smoot’s book leaves amazingly little doubt about Prof. Smoot’s opinion of his own rank!)
For sure, rank measures are dearly cherished by economists, tenure review committes, and the Nobel Institute … and they are instinctively grasped by chimpanzees.
But biologists—especially field ecologists—are much less fond of rank measures. For example, it just doesn’t make sense to ask whether raccoons are more important than coyotes.
From an agnotological point of view, constellations of ideas are like ecosystems — groups of ideas have to support each other … just like cells in the body!
So Scott, you are correct to say “I don’t see what currency the cells in the body uses” — there is no linear measure that describes cellular ecology.
And if you think about it, a rank-order of ideas does not really capture the functional ecology of human cognition, does it? Doesn’t rank-order rather serve to provide academia with a useful abstraction of the primate instinct for well-posed dominance relations?
Don’t answer this until you’ve sat on an Academic Appointments and Promotions Committee! And here I’m not being cynical. IMHO, it’s a wonderful miracle that the existing science and technology infrastructure works as well as it does.
As we teach our medical students, “Don’t take away a patient’s illusions, until you can offer them a better illusion!”
That’s another way to state the challenge of 21st Century biology’s impending information overload — it’s going to force humanity to develop better illusions.