The J Curve

Friday, March 25, 2005

Ode to Carbon

I took a close look at the benzene molecular model on my desk, and visions of nested snake loops danced in my head…

Is there something unique about the carbon in carbon-based life forms?

Carbon can form strong bonds with a variety of materials, whereas the silicon of electronics is more finicky. Some elements of the periodic table are quite special. Herein may lie a molecular neo-vitalism, not for the discredited metaphysics of life, but for scalable computational architectures that exploit three dimensions.

Why is the difference in bonding variety between carbon and silicon important? The computational power of nature relies on a multitude of shapes (in the context of Wolfram’s principle of computational equivalence whereby any natural process of interest can be viewed as a comparably complex computation).

“Shape based computing is at the heart of hormone-receptor hookups, antigen-antibody matchups, genetic information transfer and cell differentiation. Life uses the shape of chemicals to identify, to categorize, to deduce and to decide what to do.” (Biomimicry, p.194)

Jaron Lanier abstracts the computation of molecular shapes to phenotropic computation along conformational and interacting surfaces, rather than linear strings like a Turing Machine or a data link. Some of these abstractions already apply to biomimetic robots that “treat the pliability of their own building materials as an aspect of computation.” (Lanier)

When I visited Nobel Laureate Smalley at Rice, he argued that the future of nanotech would be carbon based, due to its uniquely strong covalent bond potential, and carbon’s ability to bridge the world of electronics to the world of aqueous and organic chemistries, a world that is quite oxidative to traditional electronic elements.

At ACC2003, I moderated a debate with Kurzweil, Tuomi and Prof. Michael Denton from New Zealand. While I strongly disagreed with Denton's speculations on vitalism, he started with the interesting proposition that "self-replication arises from unique types of matter and can not be instantiated in different materials... The key to self-replication is self-assembly by energy minimization, relieving the cell of the informational burden of specifying its 3D complexity... Self-replication is not a substrate independent phenomenon." (Of course, self-replication is not impossible in other physical systems, for that would violate quantum mechanics, but it might be infeasible to design and build within a reasonable period of time.)

Natural systems exploit the rich dynamics of weak bonds (in protein folding, DNA hybridization, etc.) and perhaps the power of quantum scanning of all possible orbitals (there is a probability for the wave function of each bond). Molecules snap together faster than predicted by normal Brownian interaction rates, and perhaps this is fundamental to their computational power.

For example, consider the chemical reaction of a caffeine molecule binding to a receptor (something which is top of mind =). These two molecules are performing a quantum mechanical computation to solve the Schrödinger equation for all of their particles. This simple system is finding the simultaneous solution for about 2^1000 equations. That is a task of such immense complexity that if all of the matter of the universe was recast into BlueGene supercomputers, they could not find the solution even if they crunched away for the entire history of the universe. And that’s for one of the molecules in your coffee cup. The Matrix would require a different approach. =)

A simultaneous 3D exploration of all possible bonds warps Wolfram’s classical computational equivalence into a neo-vitalist quantum equivalence argument for the particular elements and material sets that can best exploit these dynamics. A quantum computer with 1000 logical qubits could perfectly simulate the coffee molecule by solving the Schrödinger equations in polynomial time.

Of course this begs the question of how we would design and program these conformational quantum computers. Again, nature provides an existence proof – with the simple process of evolutionary search surpassing intelligent design of complex systems. Which brings us back the earlier blog prediction, that biology will drive the future of information technology – inspirationally, metaphorically, and perhaps, elementally.

Traditional electronics design, on the other hand, has the advantages of exquisite speed and efficiency. The biggest challenge may prove to be the hybridization of these domains and design processes.

27 Comments:

  • Hi Steve,

    Vitalism is much older than the 1600s. It traces back to the earliest written human records. The Sanskrit word and concept of prana and its ramifications are central to the Upanishads and some other early Vedic texts (for an example see the Prasna Upanishad.

    The Sanskrit word "prana" evolved in one linguistic path to the word "pneuma", which in Greek means air, breath or spirit.

    Democritus, who anticipated many findings of modern science and was a scientific genius on the order of Newton and Einstein, predicted a vital life force ("pneuma") distinguishing the animate from inanimate.

    By Anonymous Geordie, at 2:15 PM  

  • "For example, consider the chemical reaction of a caffeine molecule binding to a receptor. These two molecules are performing a quantum mechanical computation to solve the Schrödinger equation for all of their particles. This simple system is finding the simultaneous solution for about 2^1000 equations."

    If Jaron Lanier is correct, the two molecules are not solving the Schrödinger equation, rather the two molecules are running pattern recognition programs with a feedback loop. The information (information = differences that make a difference) that the two molecules are exchanging is very limited.

    If we use Occam's razor we can eliminate the explanation that requires "a task of such immense complexity that if all of the matter of the universe was recast into BlueGene supercomputers, they could not find the solution even if they crunched away for the entire history of the universe."

    By Anonymous Anonymous, at 9:03 PM  

  • Hi Steve:

    Some thoughts:

    * it's an interesting observation (from an experimentalists point of view) that nature chooses to encode information using complex structures (base pairs for example) that are bound in secondary and tertiary structures. If all that one wished to do was to encode a particular pattern one could use a far simpler primary structure such as a polymer chain (using four co-monomers, one could generate ABACDBA... codes). Natural codes contain not only the code but the ability to implement the code, a far greater power.


    * carbon has the ability to bond to a wide variety of elements, as well as to itself in various different configurations. This is driven by the remarkable ability to hybridize orbitals so one has sp3, sp2, and sp hybrids each driving a different geometry. This ability to shift shape gives carbon the ability to readily create stable compounds with complex three dimensional structures (see above) - creating keys to any desired lock if you will. I can't think of any other element that has the flexibility to make rings of three members right up to six plus with relative ease for example.......

    Cheers

    Tony

    By Anonymous tony, at 11:07 AM  

  • ahhh, too much carbon talking... I need some candy. =)

    (Now seriously, I am attempting to write something here I have in my mind but I couldn´t deconstruct it in words yet. Anyway it is a meta-comment, a thought on how does our intelligence affect our understanding of how nature make things work, which may leave us completely out of any competition with her. I suspect that Mother nature made us smart, but not smart enough to duel her. With her own mastery, that is. Be back soon.)

    By Blogger Gisela Giardino, at 8:21 PM  

  • Hey there Anonymous Occam-comic,

    The ideas you’re commenting on are meant, at least by me, to be usefully applied only to big systems with lots of internal state that interact with other big systems with lots of internal state, but if you really want to try to reduce to absurdity, consider the humble prion. That's a simple example of a molecule with memory, and if you really want to, you can apply a pattern recognition/expectation paradigm interpretation to it without being absurd, but probably without gaining anything practical for your efforts, either. There are actually quite complicated receptors in the olfactory system that DO change and for which the pattern recognition paradigm could be theoretically applied, but your average small molecule can't take on memories from chemical interactions, so it would indeed be absurd to talk about it having a pattern sensing expectation.

    The motivations to think broadly about this question are the beliefs that scale matters deeply (that good ideas about simple systems can’t just be repeated many times to usefully explain big systems) and that Moore’s Law by itself will not assure that today’s computer science ideas will remain useful forever. When we think about biological phenomena or artificial systems we might want to build someday that will be able to perform similar tricks we need to find new reductionistic ideas that can be applied generally, and the ideas in play here are simply part of an attempt to adapt what we observe in natural cognition to the structure of large simulations and software architectures.

    By Anonymous Jaron Lanier, at 6:59 PM  

  • Near-simultaneous thinking: I just posted an ode to carbon of my own, from an organic chemist's perspective.

    I spend my days trying to design synthetic molecules that will bind to biological receptors, and I can tell you that it's no picnic. But still, it's doable, given enough time and money. I agree with you that it would be foolish not to take advantage of the power and complexity of molecular biology. A billion years of real-world optimization is not to be sneezed at. . .

    By Anonymous Derek Lowe, at 3:03 PM  

  • It seems our computing paradigm for understanding nature is like a Rube Goldberg machine - it works but it's exceedingly and unnecessarily complex. Maybe the Schrödinger equation is similar. Math is supposed to make our lives easier - in this case, I wonder if the math is more complex than nature itself.

    By Anonymous Anonymous, at 9:10 AM  

  • "Jaron Lanier abstracts the computation of molecular shapes to phenotropic computation along conformational and interacting surfaces, rather than linear strings like a Turing Machine or a data link."

    This sentence makes me think of a new trend in mathematics : higher dimensional algebras (HDA).

    Instead of computing with string of symbols : a+b etc... the formulas are now multidimensional ones and the operators are geometrical objects. I am not talking about fractions where the bidimensional look is just syntactic sugar. A fraction can be expressed as a linear string of symbols.

    Topologically, an operator (like + or /) is equivalent to a point connected to its operands. Operators are 2D, 3D (or more) objects for HDAs and computing is gluing all these shapes together to build new shapes.

    The topological properties of the space are encoding algebraic properties and there are strong links between both domains.

    By Anonymous alpheccar, at 1:40 PM  

  • Jesus Christ, what is all this in aid of? Jurvetson showing he is "Mr. Science"? God it is such a boring WANK-OFF.

    Steve, you need to meet girls.

    By Anonymous Anonymous, at 8:15 PM  

  • Right you are, anon. That's why I post so rarely. Spent the day with my daughter instead.

    The comments here, on the other hand, are fascinating to me.

    Alpheccar: do you have a pointer where I can learn more about HDAs for beginners?

    By Blogger Steve Jurvetson, at 8:40 PM  

  • Carbon. One pillar of life. Water, the other. Both unique.

    Carbon's ability to make unique long, strong chains.

    H20's unique abilities as solvent, expanding when freezing into solid form, about the only such known (one obscure metal supposedly too)

    Life itself, relying on two materials which by the essence of their features have no rivals among moleculs, is on the edge of normal.

    By Blogger Estonia in World Media (Rus), at 3:01 AM  

  • Steve,

    I know of several places where you can download papers about HDA. But most are probably far too complex.

    I think the best is for you to contact me so that we can see what kind of paper would be best for you as an introduction to the topic.

    By Blogger alpheccar, at 10:07 AM  

  • Ode to Carbon

    [ counterpoint to carbon, or why not lowly silicon ? ]

    I took a close look at the benzene molecular model on my desk, and visions of nested snake loops danced in my head…

    [ now that can only be treated by a visit to a licensed medical practitioner ....sorry I cannot help that one ]

    Is there something unique about the carbon in carbon-based life forms?

    [ hmmm, what you mean to ask, is why does carbon when oxidized, go gas phase, and silicon when oxidized not form a gas? ]
    Fundamentally this might have some connection as to why your laptop works with lowly silicon, and why Nantero will be struggling to make single wire pair crossed nanotube memories for quite some time - bottom up Nantero, versus top down silicon (despite the modest successes in CN mat switches ) ]

    Carbon can form strong bonds with a variety of materials, whereas the silicon of electronics is much more fickle.

    [ all relative you might add, as the strength of carbon based chemistry is taken in the perspective of less thermodynamically demanding applications - silicon compounds are plenty strong, but silicon’s propensity to form SiO2, which is a solid, not a gas, causes a variety of interesting things - compared to carbon based chemistry. For one, your glass - drinking glass, is typically SiO2 based. Another is that the manufacturing technology, err process technology, for most practical ( even high performance ) computational elements that are helping you extend the reaches of your thoughts, are critically dependent on the stability of the SiO2 glass, versus the volatility of many Carbon compounds, like many well know carbon bearing gases - C/O and C/H gases. So the “wondrous stability properties” of carbon chemistry for potential application to electronics needs to be taken in a context of greater subtlety than “visions of nested snake loops danced in my head”, as chemical and electronic properties of compounds are considerably more subtle and complex than your visions....even if there are not silicon analogs to hydrocarbon chemistry in life forms. And even the hype of Nanotubes, while it may manifest itself in innovative products, goes back to analogous VLS ( vapor liquid solid ) of silicon whiskers in the late 50’s and early 60’s at Bell Labs. VLS whisker growth of silicon rods / nanorods, is one for one analogous to nanoparticle catalytic carbon nanotube growth which is a graphene form of tube epitaxy. So much for novelty, nano here is just materials science. ]

    Some elements of the periodic table are quite special. Herein may lie a molecular neo-vitalism, not for the discredited metaphysics of life, but for scalable computational architectures that exploit three dimensions.

    Why is the difference in bonding variety between carbon and silicon important?

    [ this statement is preposterous. First bonding comparisons between different members of column 4 elements have more similarities than differences. The shape and nature of bonding orbitals shared between adjacent members of column 4 elements is considerably closer than comparisons to elements in other columns to column 4. Next, the differences you cite, as being hugely different, mostly do not have to do with bonding and stability ( your conclusions as to stability are flat wrong ) but have to do with the characteristics of resultant oxides and hydrogen compounds.... whether the oxide forms is a gas or a solid has HUGE ramifications in the applied chemistry results... you neglect this fact and prefer to talk of dancing hallucinations, which are more appealing in you style of prose. But facts are not visions, even if the prose is less appealing to computational nanoists ]

    The computational power of nature relies on a multitude of shapes (in the context of Wolfram’s principle of computational equivalence whereby any natural process of interest can be viewed as a comparably complex computation).

    [ this is blather ..... flat out poop ]

    “Shape based computing
    [ properly phrased as ....shape based CHEMISTRY - sorry not everything is “computing” despite visions of whatever. ]

    is at the heart of hormone-receptor hookups, antigen-antibody match ups, genetic information transfer and cell differentiation. Life uses the shape of chemicals to identify

    [ BOND --- selectively, for function there is no overt recognition, no ID so to speak. ],

    to categorize, to deduce and to decide [ decide ... where is the thought process hidden ? ]

    what to do.” (Biomimicry, p.194)

    Jaron Lanier abstracts the computation of molecular shapes to phenotropic computation along conformational and interacting surfaces, rather than linear strings like a Turing Machine or a data link.

    [Chemistry is neither, despite whatever Jason might propose ]

    Some of these abstractions already apply to biomimetic robots that “treat the pliability of their own building materials as an aspect of computation.” (Lanier)

    When I visited Nobel Laureate Smalley at Rice, he argued that the future of nanotech would be carbon based, due to its uniquely strong covalent bond potential, and carbon’s ability to bridge the world of electronics to the world of aqueous and organic chemistries, a world that is quite oxidative to traditional electronic elements.

    [ Any microelectronics process engineer with insight into how devices are built will argue quite forcefully this is just wishful thinking. Even Gordon Moore says something to this effect, and Nantero’s harsh realities beyond making the compromise “Carbon Matt” switches (versus Ruecke’s ideal single wire crossed pair per the Nature publication ), will clearly indicate this will remain fact for quite some time to come....Nanotubes will not in the reasonable future make high integration random logic devices requiring high process yield for function, so that designers of complex logic might build your X86 cpu.....carbon ULSI nano electronics will be a long time coming, for a reasonably long time. I am familiar with the Caltech effort to make defect tolerant nanotube logic, this is very similar to the Wafer Scale VLSI effort in the mid 80’s that also went nowhere. It all comes down to device costs.

    I also visited the Smalley lab, but for a whole week, and made a record 100+ Nanotube Atomic Force Microscope tips, in about 3 days of work. Smalley would not speak to me directly since I do not posses a PhD, but he had his top scientists ask me, even grill me for hours on how to make nanotube integrated electronics. I said it will not be practical until you can “grow” the relevant elements in a useful manner at a wafer scale. I still stand by this statement, as spin on polymer dispersed Nantero crossed “wire” mats will not demonstrate the potential promise of electronic mobility seen in individual nanotube's electronic performance. Nor will crossed wire mats approach the performance stated in the vaunted Ruecke’s paper in Nature.

    Cavendish Kinetics will be a more practical mems nano memory, than the nanotube mats, and their success or failure will come down to execution and skills in microfabrication and process integration. The success of a mems crossbar device, nanotube or based on other strategies, is all in the process technology approach, and nano terminology will not change that. Your laptop speaks plenty to this simple fact of the relative importance of process technology vs. nano concepts. I will bet you won’t have a nanotube computational device in a commercial laptop for quite some time. ]

    At ACC2003, I moderated a debate with Kurzweil, Tuomi and Prof. Michael Denton from New Zealand. While I strongly disagreed with Denton's speculations on vitalism, he started with the interesting proposition that "self-replication arises from unique types of matter and can not be instantiated in different materials... The key to self-replication is self-assembly by energy minimization, relieving the cell of the informational burden of specifying its 3D complexity... Self-replication is not a substrate independent phenomenon." (Of course, self-replication is not impossible in other physical systems, for that would violate quantum mechanics, but it might be infeasible to design and build within a reasonable period of time.)

    Natural systems exploit the rich dynamics of weak bonds (in protein folding, DNA hybridization, etc.)

    [ Does this not contradict your statement as to the relative stability of carbon versus “weak silicon” chemistry. QED as we used to say in my Canadian elementary school’s geometry class.... elementary pun intended, for elementary errors of logic ]

    and perhaps the power of quantum scanning of all possible orbitals (there is a probability for the wave function of each bond). Molecules snap together faster than predicted by normal Brownian interaction rates, and perhaps this is fundamental to their computational power.

    [ again it is chemistry - you are projecting the ability to think upon the inanimate .... elementary error even on a good day ]

    For example, consider the chemical reaction of a caffeine molecule binding to a receptor (something which is top of mind =). These two molecules are performing a quantum mechanical computation to solve the Schrödinger equation for all of their particles.

    [molecules “computing?” Nano jargon is not an excuse to confer computational abilities in place of “mere” chemistry ....]

    This simple system is finding the simultaneous solution for about 2^1000 equations. That is a task of such immense complexity that if all of the matter of the universe was recast into BlueGene supercomputers, they could not find the solution even if they crunched away for the entire history of the universe. And that’s for one of the molecules in your coffee cup. The Matrix would require a different approach. =)

    A simultaneous 3D exploration of all possible bonds warps Wolfram’s classical computational equivalence into a neo-vitalist quantum equivalence argument for the particular elements and material sets that can best exploit these dynamics. A quantum computer with 1000 logical qubits could perfectly simulate the coffee molecule by solving the Schrödinger equations in polynomial time.

    [ Qubits are another thing, as the application of quantum encryption requires Human computation via designed circuits .... this is not analogous to the wrongly conferred computational abilities of chemicals “computing”. They don’t compute ever in the course of bonding and reactions, despite whatever you might put in your or Jason’s coffee. Chemicals do CHEMISTRY - no computation involved, never will be ... except by humans modeling chemistry, attempting to understand chemistry ]

    Of course this begs the question of how we would design and program these conformational quantum computers.

    [ good question, simple answer, since these “computers don’t compute, you don’t have to ponder the unponderable.....pretty simple, and it certainly won’t ship as a product in your lifetime or mine ]

    Again, nature provides an existence proof – with the simple process of evolutionary search

    [ “evolutionary search” implies evolution is an active mechanism, while this is thoughtful, evolution is in fact a passive mechanism of selection, not a computational search in the least, it is in many ways akin to a Brownian motion selection ]

    surpassing intelligent design of complex systems

    [Where do you get this? Natural systems have their beauty and complexity that far surpasses man’s attempts to synthesize feeble copies, but in the same light, man’s attempts to design new innovations has its own subtleties that you seem to trivialize. Why? The two are very different, on many levels obvious and non-obvious ] .

    Which brings us back the earlier blog prediction, that biology will drive the future of information technology – inspirationally, metaphorically, and perhaps, elementally.

    [ This will be more for futurist’s metaphors than useful IT products, largely for reasons that relate to I/O and ability to design complex systems in squishy bio ( as a former designer you should understand the importance of viable design rules to manufacturability ). Cambrios may be a stretch, except for materials production methods which may evolve from their truly innovative work. Their motives are all in the right direction, but computation with anything that seems biological, is more than just speculative, even if the prose is appealing to computationally centric futurists. Top down computational fabrication ( ie microchips and derivatives ) will dominate long into the future, for all the right reasons, principally the ability to design complex systems. Horowitz, an experienced designer rather than nanoist, may put this to you more politely, but the concepts are fundamentally correct ...as is his design skills amazing ]

    Traditional electronics design, on the other hand, has the advantages of exquisite speed and efficiency. The biggest challenge may prove to be the hybridization of these domains and design processes.

    [ now that is sensible ... ]

    [ Posted by Mark Andrew Wendman 7:30am June 30th 2005 ]

    posted by Steve Jurvetson at 3:47 PM

    By Blogger Mark Wendman, at 8:23 AM  

  • Hi Mark. Have we ever met before? I like the idea you start with, an Ode to Silicon; perhaps that could be your next posting. The wonder of one material set does not negate the wonder of another.

    You make some interesting points, but they are embedded in rhetoric of a tone that perplexes me. I’ll presume it’s humor, so I can laugh with you…

    A short set of replies:
    1) While carbon nanotubes are interesting, I never mentioned them. Perhaps you assuming that’s what I was talking about, and that you could somehow generalize a conclusion from them. I was not writing about any particular technology or company.

    2) I also make no assertions about stability. I write about the variety of bonds, from strong to weak. Other column 4 elements are interesting too, and let’s not forget the 3-5 compounds.

    3) You assert that the bonding variety of carbon vs. silicon is “preposterous.” Perhaps you should take your debate up with the organic chemists who posted here before you:

    “carbon has the ability to bond to a wide variety of elements, as well as to itself in various different configurations. This is driven by the remarkable ability to hybridize orbitals so one has sp3, sp2, and sp hybrids each driving a different geometry. This ability to shift shape gives carbon the ability to readily create stable compounds with complex three dimensional structures (see above) - creating keys to any desired lock if you will. I can't think of any other element that has the flexibility to make rings of three members right up to six plus with relative ease for example” (Tony)

    “a likely requirement for any kind of chemical-based life is large molecules with structural diversity. Life's bound to be complex, and carbon compounds give you all the complexity you can handle - straight and branched chains, rings, whatever you want. And those bonds come in more than one flavor... Carbon gives you a wonderful 1D / 2D / 3D building set. There's another key thing about the element. More structural (and reactive) diversity comes from all the ways that carbon can form bonds with other elements... We've got solids, liquids, and gases, acids and bases of all strengths, nonpolar compounds and polar ones fitted with all kinds of electron-rich and electron-poor zones, and reactivity all the way from rock-solid to burst-into-flames.” (Derek)

    Your “QED” logic error comment was the funniest of all. That’s a good one. I imagine you doing a happy dance. Your proof is what exactly? Carbon’s ability to form strong double bonds and a variety of bonds contradicts the weak bonds of organic systems?? Are you presuming these are mutually exclusive? Where can we find “elementary errors of logic” in this thread? (the classic hasty generalization and ad hominem come to mind)

    4) As for your eloquent refutation of computational equivalence, as “flat out poop”, I translate this as “does not compute”, and I don’t know if you are unfamiliar with the concept or if you have a refutation that you would like to present. I find the perspective of Wolfram, SFI and complexity theory in general, to be a very useful framework. Personally, I side with Oxford physicist, David Deutsch: “Any physical experiment can be regarded as a computation, and any computation as a physical experiment.” (Fabric of Reality, p.246.)

    5) Reductionism arguments, like “it’s just chemistry” or “it’s all quantum physics” are interesting in certain contexts, but they are not mutually exclusive, nor are they helpful for all layers of emergent abstraction. Chemistry is loosely coupled to information theory, as physics is to psychiatry.

    6) I won’t quibble with your concern over the word choice in the quotes from Janine and Jaron. You can take that up with them (Jaron also posted above). I am not “projecting the ability to think upon the inanimate.” It seems to me that the ad hominems substitute for a counter argument when we discuss quantum mechanics.

    7) We completely agree on the relative difficulty of applying nanotech or bottom-up approaches to logic (x86, complex logic, computational devices, etc.). I have written about that numerous times before, on the blog and elsewhere. I think the near term opportunities are in memory, not logic, and that may lead to a bifurcation of Moore’s law. Moore was very interested in this when I spoke with him about it last month.

    8) Your prediction that a quantum computer “certainly won’t ship as a product in your lifetime or mine” is quite bold for a 50-year time frame. What do you base that on? Well, actually, that could be a long digression here. Why not take your argument to the /. thread where you can see some more optimistic predictions.

    9) I don’t think we have a disagreement on evolution. Evolutionary search is a simple iterative process that is very different from a top down design. I am not trying to trivialize either. Broadly speaking, Daniel Dennett and Richard Dawkins posit that evolution as an algorithmic process distributed over time and space with an accumulation of design, such that life is a systematic series of small-scale reversals of entropy.

    10) I also agree with your closing paragraph, and have written about those same points (the I/O “Interface problem” and the lack of complex systems theory) over the past five years. I agree with your summary on computation, but I think memory is different (and increasingly important).

    You end with Horowitz. Do you have a private message for me there? Is this the Professor Mark Horowitz of Stanford and Rambus? When I saw him last month, he was very much enjoying his sabbatical. What was he doing? He was studying biology and biological metaphors for computing. He became a student in the Bio-X program.

    This one goes to 11) My opening sentence about the benzene model sparking visions of snake loops seems to have really distracted you, prompting multiple retorts. It was a joke, not an argument. I thought it was an obvious allusion. “Every student of Organic Chemistry has heard the story of how the structure [of benzene] appeared to Kekulé in a dream in which he saw chains of carbon atoms dancing in circles like a snake chasing its own tail.” (source) This was a tongue-in-cheek attempt to engage the average reader. Which brings me back to tone. This is a blog, not an academic paper. It is meant to be a playful exploration of ideas in the spirit of brainstorming, not a vituperative debate.

    By Blogger Steve Jurvetson, at 12:48 PM  

  • Oops, Mark. Missed another one. In your closing, you say “computation with anything that seems biological, is more than just speculative, even if the prose is appealing to computationally centric futurists.” If I am parsing this right, and you mean to say that biological systems can’t compute, then I would caution about such sweeping generalizations of what can’t be done. A single existence proof proves the contrary, and a multitude of current ones becomes embarrassing.

    MIT robotics Professor Rodney Brooks at TED this year: “Within 2-3 weeks, freshmen are adding BioBricks to the E.Coli bacteria chassis. They make oscillators that flash slowly and digital computation agents.”

    There is so much still to learn on these frontiers of the unknown. I think we are in a modern Renaissance, a time for open-minded exploration. This is not to negate or belittle the accomplishments of the past. Without them, we could not push forward in new directions.

    By Blogger Steve Jurvetson, at 1:17 PM  

  • Fascinating by nothing: first there is much more money in your surroudings than ideas to let to nurture. Point.

    Second: internal US policy issues should't matter about what the future will be.

    My love to US began whan I was five yerars old, reading Walt's Disney stories.

    Tird: let go off million dollars if you want get another Google, don't let this Google (good run end very profitable)
    do it all.

    It could be dangerous for Google, for me, for everybody.

    One which runs all it's always a
    treat, and a bad way to for who thinks that one way is a solution.
    Ways are many. Don't make them lone. Maybe you earn today, but sure you lose next day.

    Have my greetings, be up.

    "poli" Inc
    a Delaware Corporation

    Franco Cumpeta
    Director

    By Anonymous Anonymous, at 9:25 AM  

  • more on theory / computation vs experiment

    Hi Steve,

    out of deference to your sentiments at present, I posted elsewhere on my blog, a further continuation of the discussion. I understand your wishes.

    Mark Wendman

    By Blogger Mark Wendman, at 12:50 PM  

  • has anyone stopped to think that maybe base pairs are not the smallest unit of information in life? could there be nano-scale structures hidden within the GCAT we all love so much?

    and lastly, could any insights be gained if one approaches the study of biology from a standpoint of intelligent design? (by aliens, not any of that god/jesus garbage)

    after all, we lowly humans have already created hybrids that never existed before. so in a sense, we ourselves are designing life. to dismiss intelligent design outright translates into an absolute belief that no intelligence greater than humans has ever existed in the universe. that seems kind of pompous, dont you think?

    maybe all these complex biological structures operate the way they do not because of billions of years of random chance, but because they were DESIGNED to operate, by someone/something smarter than we can even begin to comprehend.

    and once again, let me make it clear, i am not espousing god or jesus or mary or allah or any of the rest. i loathe religion in all its forms. intelligent design does not have to mean religion.

    By Anonymous Anonymous, at 7:41 AM  

  • hi Steve;
    Since I came up with simplifying carbon's isotopic physics to improve its heat transport- Minsky and Kurzweil suggest we chat ,if you'd care to suggest the email channel. I'm working on a review of current and about to be published nano-books for the WSJ.
    Best
    Russell
    mnestheus@aol.com

    By Blogger Russell, at 1:21 AM  

  • Hey Anonymous: You’re Not Alone! Alien Intelligent Design is a growing movement (let’s call it AID).

    See this open letter to the Kansas School Board. The data is compelling, and the potential PR strategy is sublime… ;-)

    And, strangely enough, if you ponder the graph in that letter, it has implications for software piracy as well. Yar!

    By Blogger Steve Jurvetson, at 11:54 AM  

  • Hi Steve,

    It seems that Mark Wendman's lengthy reply was largely centered on Nantero and their competitor, Cavendish Kinetics. Since DFJ is one of the original investors in Nantero, I was wondering if you would care to comment on your own perspective of the relative merits of the two approaches?

    By Anonymous Anonymous, at 6:46 PM  

  • Anon,

    Word on the street is that nantero is doing much better than expected. I have to eat my words humbly. Early on my guess is that the concept for the Rueckes Nature publication device had to be seriously reworked, and it was. Despite my skepticism I now openly lunch from humble pie. My take is nantero might well do very well indeed, despite the complexity of the novel innovation. I guess that it will come down to whether the frequency of stray tube swithc shorts is adequately low to accomodate a commercially viable cell redundancy ( repair cells and method ).

    I suspect it will ......

    Best Regards,

    the humble pie eater .....

    By Blogger Mark Wendman, at 2:41 PM  

  • I think, I suppose, when a person move with an idea, and bear the pain and the offences just because he's only an owner of it, and nothing other, and when this person shows he's able to turn this idea into a project, and make it running in the world, I think, I suppose, it's time to leave mistakes and to give hime a strong hand, in money, in confidence, sensing it's all right. For the benefit of all. This is me.

    Franco Cumpeta
    "poli Inc."

    By Anonymous Franco Cumpeta, at 3:04 PM  

  • The lock-and-key methods of the immume system, amino acid selection via 3 base keys, enzymes, and hormones are all examples of where mechanical (bulk movement) and thermal activity initiate a lock-n-key "if-then" operation. Once brought into close proximity, that operation proceeds with infinite quantum speed to find a local energy minium. It's really a very complex test statement to see if the current trial is matching the one correct answer out of all the possibilities in the world. A lock and key if-then statement could be as simple as the simplest if-then statement which is a NAND gate. Conversely, a set of properly wired NAND gates could solve the topological lock-n-key problem, but a heck of a lot slower than the method biology uses.

    A properly wired set of NAND gates can perform any boolean operation and create a complete computer and all the resulting memory and logical operations. And so can a series of these biological "if-then" statements operating in parallel (at the same time in different parts of the body). Instead of wires transmitting electrical impulses to the next NAND gates, biology uses blood, water, limph system, and nerves to transmit molecules and ions to perform the next lock-and-key operation.

    Wolfram goes into lots of examples, but he should just back out the argument to NAND operation. A series of "if A and B squares are black, then C is white...." can execute any algorithm given enough squares. You could map out an entire CPU and it's memory as black and white (0 and 1) cellular automata that obey the one rule above, although the page would be very wide and some sections would be reused (e.g. one section would be an adder). I leave it to the reader as an exercise to make a 4-bit adder out of this one operation and graphing it as cellular automata.

    "Chemistry does not compute" is just absurd since, for example, there are labs that use liquid chemistry to solve the traveling salesman problem and other things that require trillions of simultaneous computations or trials.

    So I believe it's completely fair to say biology is an example of a self-replicating, self-programming, classical, statistical, quantum, and parallel computer. But then again, what isn't? With some length, I can show rocks and washing machines to be the same.

    By Anonymous Anonymous, at 1:18 PM  

  • Dear Anon,

    interesting facts, I did google and go over to the 1st (and mostly only true) hit on the search term

    "labs that use liquid chemistry to solve the traveling salesman problem",

    which was
    http://www.kurzweilai.net/articles/art0276.html?m=14

    Reading this indicates an interesting and commercially signifcant but seemingly restricted class of computing problem can be solved by Liquid Chemistry.

    But practically speaking, if it was so significant and so advantageous, why are not more folks solving their compute intensive Travelling Salesman work with this? Some of this is fairly self evident.

    And in strictest terms - since computation generally involves unusual flexibility in algorithmic coding, which this example does not seem to provide, I'd say that the example is quite restrictive in applicability outside of a narrow class of specific algorithms. and not in general programming for certain.

    Is that truly computing as typically described? Well for the travelling salesman problem I'd agree, but for most computation as you and I know it, it is extremely hard to envision more general applications of this specific technique nor derivations thereof.

    BTW - even though it is fairly obvious who you are, it is rather silly to post anonymously.

    By Blogger Mark Wendman, at 1:44 AM  

  • It is not Biology,
    but Physics that will determine future of computation....

    By Blogger Brazilian, at 9:50 AM  

  • hi everyone my name is purple and i realy like this site. it is so ganster yo. power out to the big g on the other side of gansta ville.:) anyway did you hear that pluto is not a planet. so freakin cool dog. see ya peeps lata on the ganster side yo.
    peace ;)

    By Anonymous Anonymous, at 4:47 PM  

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