The J Curve

Thursday, November 25, 2004

Giving Thanks to our Libraries & Bio-Hackers

As I eat a large meal today, I am reminded of so much that we should be thankful for. Most evidently, we should give thanks to the epiglottis, the little valve that flaps with every swallow to keep food and drink out of our windpipe. Unlike other mammals, we can’t drink and breathe at the same time, and we are prone to choking, but hey, our larynx location makes complex speech a lot easier.

Much of our biology is more sublime. With the digitization of myriad genomes, we are learning to decode and reprogram the information systems of biology. Like computer hackers, we can leverage a prior library of evolved code, assemblers and subsystems. Many of the radical applications lie outside of medicine.

For example, a Danish group is testing a genetically-modified plant in the war-torn lands of Bosnia and Africa. Instead of turning red in autumn, this plant changes color in the presence of land mines or unexploded ordinance. Red marks the spot for land mine removal.

At MIT, researchers are using accelerated artificial evolution to rapidly breed M13 viruses to infect bacteria in such a way that they bind and organize semiconductor materials with molecular precision.

At IBEA, Craig Venter and Hamilton Smith are leading the Minimal Genome Project. They take the Mycoplasma genitalium from the human urogenital tract, and strip out 200 unnecessary genes, thereby creating the simplest synthetic organism that can self-replicate (at about 300 genes). They plan to layer new functionality on to this artificial genome, to make a solar cell or to generate hydrogen from water using the sun’s energy for photonic hydrolysis (perhaps by splicing in novel genes discovered in the Sargasso Sea for energy conversion from sunlight).

Venter explains: “Creating a new life form is a means of understanding the genome and understanding the gene sets. We don’t have enough scientists on the planet, enough money, and enough time using traditional methods to understand the millions of genes we are uncovering. So we have to develop new approaches… to understand empirically what the different genes do in developing living systems.”

Thankfully, these researchers can leverage a powerful nanoscale molecular assembly machine. It is 20nm on a side and consists of only 99 thousand atoms. It reads a tape of digital instructions to concatenate molecules into polymer chains.

I am referring to the ribosome. It reads mRNA code to assemble proteins from amino acids, thereby manufacturing most of what you care about in your body. And it serves as a wonderful existence proof for the imagination.

So let’s raise a glass to the lowly ribosome and the library of code it can interpret. Much of our future context will be defined by the accelerating proliferation of information technology, as it innervates society and begins to subsume matter into code.

(These themes relate to the earlier posts on the human genome being smaller than Microsoft Office and on the power of biological metaphors for the future of information technology.)

P.S. Happy Thanksgiving, even to the bears… =)

23 Comments:

  • Another provocative post. Your penultimate paragraph is especially moving. I see your vision here, but given the way living organisms actually develop, outward from the neural tube, I'm wondering where the brain is in this model.

    Innervation extends outward from the brain. For there to be innervation, it would seem a brain must exist. Perhaps I'm wrong about that. But this planetary brain, if it is a brain, ought to produce consciousness as well, consciousness that would presumably guide our developing body in its self-administrations.

    I love science and technology. They are the only real hope we have. We have no choice but to solve our problems, otherwise they will consume us. But I also suspect that creating artificial life forms, such as IBEA's proposed prion(?), might be extremely dangerous. Prions are suspected as the enemy in Mad Cow disease, if I'm not mistaken. And there is compelling evidence that a mycoplasma (fermentans?) is responsible for chronic fatigue and fibromyalgia syndromes. These diseases have long incubation periods. Animal testing might prove inaccurate.

    How can we be optimally certain (i.e., as certain as we can be) that new inventions are indeed innocuous? We need the complete view. We need comprehensive context. It would appear that we need superhuman consciousness, such as a global brain might afford. One hopes such a brain in on its way...

    I hope you're enjoying this as much as I am. As always, thanks for sharing with us.

    By Anonymous Anonymous, at 11:02 AM  

  • So let’s explore this idea, which I might describe as the emergent hive mind, the Gaia/Selfish Biocosm hypothesis, or perhaps competing societal memeplexes. If we are just nodes in the hive, like ants in a colony, would we comprehend the hive’s activity, and would we have any agency or control over its actions, even through conscious collective action?

    The breadth and frequency of communication defines the hive’s operation. With the social insects, the hive will learn lessons over long periods of time – longer than the life span of the members themselves. The hive itself is a locus of learning, not just individual ants.

    For the past 1000 years the pace of human societal change has been glacial. The "clock rate" of an emergent intelligence would be the pace of inter-human communication. That was scattered, intermittent, and topologically clustered. We look back to the 50s and see plenty of change in norms, beliefs and culture, but it's harder to see the changes on the same time scale as our mental activity (as a node).

    Fan-out is also important. The adult brain has an average synaptic fan-out of 1000. 2 year olds (aka "learning machines") have a fan-out of 10,000. Neural network simulations with low fan-outs achieve very little.

    What is the fan-out of human social networks? With modern telecommunication networks, the fan-out broadened and connectivity started to span geography. With the Internet, the fan-out widened considerably (with multipoint communications like this post) and the clock rate increased with IM and email. We have broadcast mechanisms and multi-modal communications. We have the power of dynamic group-forming networks. With agent-based systems, the clock rate would increase further still.

    And compared to the brain, “humans++” are powerful nodes. We have large local and near-line memory stores via our technologies and databases. (How much of the brain’s neurons are functioning as local memory vs. a computational capability?) We also have local agency - perhaps entering the domain of recursion and reentrant mimetic code.

    What is the sensory I/O of a hive mind? The neurons of the brain are not the I/O; they do not interface with the world directly. As nodes in a hive mind, we may be contributing to activities entirely beyond our senses. As Ember and others hook billions of embedded sensors and machines to the network, the potential array of I/O interfaces starts to compound and extend the metaphor beyond human nodes to include other symbionts – much like the body is a federation of cells and cells are a historical endosymbiosis of simpler organisms.

    And lastly, we could take a less anthrocentric, Dawkins-esque approach… If the global brain is analogous to competing memeplexes rather than one Gaia-inspired sentience, then what is the reproduction rate? The competition is among memes. It is no longer coupled to our biological clocks.

    By Blogger Steve Jurvetson, at 1:31 PM  

  • We are not just nodes, as ants are. We are conscious nodes, and consciousness changes everything. It collapses the emergent gap.

    A global brain would aggregate individual consciousness to form superconsciousness, just as the individual brain aggregates action potentials to form consciousness. From superconsciousness should emerge the mechanisms of control.

    The breadth and frequency of communication defines the hive’s operation.You could have written, the hive's consciousness. The breadth and frequency of communication is indeed the issue. So let us consider the modern world. Accelerating change, breadth and frequency increasing exponentially, as we all know... What is the end of it? Where does it crystallize? What is the final form it will assume?

    I am certain it will involve technology, software running on the Internet, filling the air. It will allow us to optimize the breadth and frequency of our communication. At some critical threshold on this path, the hive presumably awakens, an autonomous being. As technology of our own design, we will be able to communicate with this being.

    Teilhard de Chardin saw the global brain 50 years ago. I consider him the first great prophet of the Singularity (he called it the noosphere, among other things), and there have been many since him, some may even be friends of yours;).

    Fan out will be maximized when the technology is right. Yes, humans++ (love it!) are powerful indeed, not like ants at all. And then a gorgeous paragraph. Entirely beyond our senses... Yes, a new symbiont is born, and promptly swallows us. Earth, the human collective, says, "I."

    What an amazing time to be alive.

    By Anonymous Anonymous, at 7:30 PM  

  • Heya!

    I just want to make to comments. No. Three, better. =)

    1) Would "Anon" give a name to us? Don´t need to be real if he/she doesn´t want to reveal his/her ID, but at least a nickname. Those words deserve authorship by far. =)

    Please.

    2) Is it heretic that I bring Isaac Asimov here? Talking about prophets, I consider him one of the best. A modern Julio Verne, or a Leonardo Da Vinci. I always wonder if that brilliant minds precognize the future or induce the way of the present builders of it...

    From The last Question by Asimov:

    "Man considered with himself, for in a way, Man, mentally, was one. He consisted of a trillion, trillion, trillion ageless bodies, each in its place, each resting quiet and incorruptible, each cared for by perfect automatons, equally incorruptible, while the minds of all the bodies freely melted one into the other, indistinguishable."

    (sorry J that once again I come with this tale) |-)

    He visions -as well- the final union of the individuals as a holistic "one". And I celebrate that and I agree with him and Anon that we are walking towards that by the hand of the new technology. Shall nanotech -being the nexus of all sciences, the ultimate eclecticism - produce the final breakthrough to achieve the goal.

    3) Now, my added comment begins with a "however".

    However, all this we are talking about, expecting to happen, trying to calculate when and how... in my opinion, is not about to happen but in the middle term as a tangible phenomena. When you read the voices of people who lived years before huge changes in the world along history, you see the same anxiousness which with we speak here today, and their ability to forsee and expect change -maybe because of our lifespan inner measure- most of times involved little years ahead. Learning from our past revolutions witnesses and visionaries´ words VS. the final unfolding of events is a good excercise to prevent us from anxiety, helplessness, exaggerated hope or escepticism, and the common feeling this is the greatest change to happen to Mankind, and that we are "in the end of times".

    Also, let´s please not forget that we here, blogging, connected to Internet, represent about the 3% of the world population. Billions live below the poverty line. And eventhough changes will happen, I believe that to make real and possible a future "we", a global conciousness, we should have to acknowledge those who also are to be part of the WE and today starve.

    Or is this, one more time, our common Thinker´s Oblivion? We tend to believe all people are in our same conditions and we build our thinking expanding our particularity -a lucky one, to thank for, talking about thanksgiving- to the whole. Unfortunately we are a tiny number. We should have that in mind in order to foresee the pace of change at global scale.

    OK, OK. You will surely want to tell me that I should remember that the Time of things has been accelerated due to the speed of communications technologies and other devices. True. We live *faster* than our Grandpas did, for sure. Also true is that since we are trying to testify about what we are at the same time living, there are great changes that our apreciation of time is very subjective. Our emotions and our interests fill the "Future" canvas with colors that may not there when the time comes.

    But that will be revealed in retrospective. Our grandchildren will tell.



    Besos! or kisses! ou bises! ;-)

    By Blogger Gisela Giardino, at 10:45 AM  

  • Merci Gi^2,

    Re: 2) Visionary entrepreneurs forge the future every day.
    I just offer some oft-quoted thoughts:

    "The best way to predict the future is to invent it."
    — Alan Kay

    Re: 3)
    "More profound is the prospect of humanity dividing into the gene-rich and gene-poor... Bear in mind that forecasters always overestimate effects in the near future, and underestimate the farther future. The farther future, these days, is still in our lifetimes."
    — Stewart Brand (reviewing Remaking Eden)

    "You know, the future has already arrived.
    It's just not evenly distributed yet."
    — William Gibson

    By Blogger Steve Jurvetson, at 6:09 PM  

  • Thank you for the kind words Gisela. Asimov describes Teilhard's noosphere perfectly, and with the addition of automatons. Hmmm... Are all the prophets seeing the same inevitable future? It seems so bright. I can't help but wonder how we get there from here, but try to stay hopeful.

    And thank you Steve for making yourself available for dialogues such as this. The quotes are great. One hopes such an inventor will soon step forward and start distributing. If you know this person, tell them to please hurry up;). Our situation brings to mind one of my own favorite quotes:

    "The Age of Nations is past. The task before us now, if we would not perish, is to build the Earth."
    -- Teilhard de Chardin

    You're right about the name, Gisela. How about... CE? It was an old nickname.

    Peaceful holidays to all,

    -CE

    By Anonymous Anonymous, at 1:55 PM  

  • I nearly forgot to say how much I agree with Gisela's main point. Any global brain worth its silicon must come equipped with a mechanism for truly global innervation, which is to say, rapid expandability into the Third World. Without that mechanism such a brain would not be global. It would not give rise to Earth.

    Having said that, the solution must be economically viable; there must be a compelling business case. It's a tough nut to crack, but essential to do so. Excellent point. One hopes the inventors are listening.

    -CE

    By Anonymous Anonymous, at 2:59 PM  

  • Please pardon my use of the term, 'Third World.' I should have used 'Developing World.' -CE

    By Anonymous Anonymous, at 10:46 AM  

  • My prayers have been heard! Anon has a name. =)

    Hi CE!!! Thank you very much for answering to my request and your words about my comment. Also, thank you Steve, as always. I am not thanking you much lately because I don´t want to spam you. I thanked you already so much in so many discussions that if you search for "thank you" in google probably your blog will be in top 20. ;-)

    I liked very much your quotes, most of them that of the not yet evenly distrubuted future. The most accurate IMO. And that guy Allan, surely he works for HP. =P

    CE, I am happy that you agree with me. About words, "Third world" is oldfashioned, true, but "Developing countries" is a hopeful lie, so, for me they both have the same bad reputation. =) And honestly, I don´t care much about labels... in both ways we know what countries you talk about. Argentina, for -unfortunate- example.

    I want to share this article, which has been widely spread by the time of its publication in 2001, which I find most encouraging and in accordance to this post, Steve, and yours on Nanotech as well. Eventhough is old, its spirit remains. It should.

    The human genome revolution or evolution?And also I like it because it quotes my other favourite -in fact it is my leit motif- short story "The writting of the God" by J.L. Borges. Again, sorry for being recursive with this as well, but isn´t it great that biologists make this liric turns in their writings? Finally I will add here something I wrote in a letter to the most special person in my life, which is related to this all. Hope you find all this interesting. =)

    "In me, passion is when I feel synchronicity. When I experience the whole as one. When there are no points of view, there is only one broad view. When you feel unity. When there is no in and out, no you and me. No frontiers, no distance, only a "we". Jorge Luis Borges, the Master of all argentinian writers wrote a short story called "the writting of the God". I can´t describe to you how do I feel when I read it. It always makes me cry as the result of how deep I feel those words. It is not because it is sad or it puts me down. I translated to English its last two pages if you´d like to read it. It is in my weblog: http://giselagiardino.blogspot.com however I recommend that you read it complete (4 pages total). I couldn´t find a translation on the Internet."

    By Blogger Gisela Giardino, at 1:00 PM  

  • Merci!

    Hey, I finally got a picture of an emerging hive mind. I guess we will recognize it in formation! ;-)

    By Blogger Steve Jurvetson, at 8:41 PM  

  • Great image, Steve. Hopefully we won't have to wait for the actual formation. Something from Gisela's human genome link comes to mind.

    "We can dream, as the prisoner Tzinacan in the novel “The writing of the God” by Jorge Luis Borges who, due to forced isolation and meditation, reaches a point where he understands the whole universe as a single coherent equation, that our efforts, conjugated to the contribution of more fundamental sciences, will lead to a modelisation of a whole cell, a group of cells, or a whole physical body as an equally coherent equation."

    Our putative inventors are undoubtedly moving in this direction. Maybe soon we'll see such a model. I can't wait! Thank you, Gisela, for a great read. I, too, am passionate for synchronicity. Will read your Borges translation soon.

    -CE

    By Anonymous Anonymous, at 11:55 AM  

  • This comment has been removed by a blog administrator.

    By Blogger Franco Cumpeta, at 12:44 PM  

  • I tried to send you a messeage made this way: how do you organize web contents when you get local if not with a map?

    Subsequently, how do you make a map like a book you can read?

    Even, more, aren't you a little getting noise by all this IT so called, so enginereed, plan? Hum.

    By Blogger Franco Cumpeta, at 12:58 PM  

  • And so expensive, plan?

    By Blogger Franco Cumpeta, at 1:06 PM  

  • I am certainly disoriented with sir Cumpeta´s last comments. There is a veil of something I sense like mistery that doesn´t let me undertand his point... Now that I think it resembles the email spam advertising that uses a tone of strange questionings in order to lead you into the trap.

    Please, don´t mean to offend anybody with my words, but I surely would like you sir to be a little more open with your thoughts because we are many who read Mr. Jurvetson´s fine weblog and we try to comprehend each other from other so different levels, ages and living circumstances.

    Thank you.

    By Blogger Gisela Giardino, at 1:18 PM  

  • Steve,

    We are facing the last hours of this 2004 and I wanted to wish you the best of best in the coming year for you and yours. During this year many new things began -as your blog, the Eclectics´... Flickr- and I wish and hope that they continue their expansion, unfolding at this wonderful pace and filled with success, happinness and lots of learning and exchange!

    Having met you is something remarkable that happenned to me this year and I take it as a true gift. And I know many people feel likewise. Thank you for being there. Thank you for openning yourself and sharing your spaces. Thank you for being an example of what is the outcome of a brilliant mind guided by a pure nature. Thank you for honoring me with your friendship. Thank being patient with my questions, my ignorance, my foolishness and my different points of view. Thank you for making me feel that what I think matters, and that is important to express myself as well as it is to hear others.

    The world needs more people like you. Definitely. A great 2005, full of love, peace, learning and fun! Cheers!

    Gisela

    By Blogger Gisela Giardino, at 4:58 PM  

  • Yes, how we solve someway the problem our brain sends to our imagination? There's no any specific memory storage in our brain, anyway we keep record of our memories, sometimes in a so bright mode similar to a printed photographic stuff. Where the memory is stored, or better, maybe, what the like algorhytms are ready to run when we seek for something in our brain? And what these processes move, so to get the final result, at the end?

    Sorry, Mrs Gisela, my aim wasn't to bother. It was maybe a run of drums (Haydn, the concert called "the drum's hit" just because Mr Haydn had to awake sleeping listeners to his music, other way being lost).

    By Blogger Franco Cumpeta, at 1:38 PM  

  • Franco, thank you for giving a further explanation on your point. And I apologise for having not understood you from the beginning. Happy 2005 for you.

    We are discussing about God somewhere else, such a usual topic, and I contributed with a simply translated J.L. Borges quote from its story: "The Immortal". I did remember this conversation we have been having here with CE, aka Anon ;-), talking about the future "One-ness" (hapy new year for you!). So I wanted to share it here. If you have the book The Aleph I strongly recommend it. Here is a cool link with a summary"Being immortal is trivial. All the creatures are immortal but men, because they ignore death. The divine, the terrible, the incomprehensible thing is to acknowledge our own immortality. I have noticed that despite religions, that conviction is very rare. Israelis, Cristians and Muslins believe in immortality, but the veneration they tribute to the first century proves that they only believe in this last, because they destine all the rest, in infinite number, to reward or punish it. The wheel of some Hindustan religions looks more reasonable to me. In that wheel, that has neither a beginning nor an ending, every life is an efect of the previous one and engenders the next one, but none of them on their own determines the whole... Indoctrinated by the excercise of centuries, the republic of the immortal men had achieved the perfection of tolerance, even with disdain. They knew that given an infinite period of time it happens everything to every man. For his past or future virtues, every man is owner of all goodness, but also of all evil, for the infamies of his past or his future. As with gambling, where pair figures tend to even the impair, likewise it is canceled and corrected talent with stupidity, [...].

    I know of those who did evil in order to let goodness result in the future centuries or the past ones... Faced like that, all our actions are fair, but indifferent as well. There are no moral neither intellectual merits. Homer composed The Oddisey, in an infinite period of time, what is impossible is NOT to compose The Oddisey, at least once.

    Nobody is no one, only one immortal man is all men. As Cornellio Agrippa, I am god, I am hero, I am philosopher, I am devil and I am world, which is an exhausting way of saying that I am nothing.

    The concept of the world as a system of precise compensations greatly influenced the Immortals. Firstly, it made them invulnerable to mercy. [...]"

    By Blogger Gisela Giardino, at 9:01 AM  

  • When I write a book, it's like I write a chip, or maybe an architecture. When it's done it's done. When we go to the brain organization, it seems that all is done but at the same time all is on the way.

    I'm always in trouble. The brain organization doesn't "store" something in some place, but is able to "restore" everything when I call the thing.

    How the brain does it? One of the suggestion (not solutions, please) is in the dyanamic structure of our brain. Our brain - supposedly - doesn't stores anything, but dynamycally adds paths over paths like a grid, that's modified by experience day by day.

    The grid of neurons someway "marked" as carriers, keep record of the importance of some simple message that may activate a neuronal connection that then reproduces what we call "memory".

    Grids of relevant importance get more attenction than grids of few. Neurons react not to a single event, but only when a pull of events show to be similar to what the grid informations store as event.

    Not a single fact or thought, but a chain of facts and thoughts that in the whole show to be meaningful.

    Not one key, just to say, but almost seven (just to lift off a number) keys together, move the whole.

    But, Steve, this is a very tangled field, indeed. Walk in a jungle.

    By Blogger Franco Cumpeta, at 1:15 PM  

  • Hi i am totally blown away with the blogs people have created its so much fun to read alot of good info and you have also one of the best blogs !! Have some time check my link to !!Make extra money

    By Blogger lokokid, at 9:11 AM  

  • The 'anonymous' author made some very compelling points regarding prions and mycoplasma which were seemingly dismissed by Mr Jurvetson. would you care to comment on this Steve?

    I've read a little about you this evening and I found you to be a very interesting person.

    People like Venter and yourself are obviously highly intelligient, you have strong visions and you want to change the world.

    What deeply troubles me is that it seems through ego and vanity you are determined that you see the changes in YOUR lifetime with apparent disregard for the implications in the future.

    How ironic is that? =)

    The very fact that you ignored the issues mentioned proves this.

    We need great thinkers, we need innovators.

    But we need people with a heart and soul as well as a brain.

    Ukguy

    By Anonymous Anonymous, at 7:00 PM  

  • Sorry - I ignored the earlier prion comment because I thought it was completely off base (no prions involved).

    The work is very motivated by an eye to the future and trying to find a sustainable way to live on this planet.

    By Blogger Steve Jurvetson, at 9:58 PM  

  • This just in, from Technology Review:

    The ocean hosts a stunningly--and surprisingly--diverse menagerie of microorganisms, according to a massive genetic study published today.

    "We have not understood much about our own planet and our own environment," Venter told Technology Review from his boat, the Sorcerer II, currently in the Sea of Cortez, in Mexico. "We've been missing as much as 99 percent of the life forms and biology out there."

    The first set of results, published this week in three papers in the journal PLoS Biology, revealed six million new proteins, doubling the number of known protein sequences. "Everywhere we sampled, we found new proteins," says Venter.

    In fact, every environment sampled showed high genetic diversity, both within and between samples. The findings are challenging the notion of species in microorganisms. "When you look at microbes, they don't appear to be individual species"

    "Microbial communities are almost like a superorganism, where each microbe is contributing to community as a whole," says Weinstock. "We really need to characterize the metagenome and analyze the genes and protein products as an aggregate."

    Venter and others eventually hope to find proteins that can be co-opted to create novel bacterial machines--proteins involved in hydrogen production or carbon fixation, for example, that could one day be engineered to boost the carbon-fixing capacity of the ocean or to create fuel-producing bacteria. "Genes are the design component of the future," says Venter.

    By Blogger Steve Jurvetson, at 5:02 PM  

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