Freeman Dyson On Open Source Biology

kripkenstein sends us an article by Freeman Dyson in the NY Review of Books, in which the eminent physicist and big thinker takes on the possible end to the Darwinian era of speciation that has endured 3 billion years on this planet. He discusses the history and future of biology in terms that many in this community will find familiar: "[We can speculate about] a golden age... when horizontal gene transfer was universal and separate species did not yet exist. Life was then a community of cells of various kinds, sharing their genetic information... Evolution could be rapid... But then, one evil day, a cell resembling a primitive bacterium happened to find itself one jump ahead of its neighbors in efficiency. That cell, anticipating Bill Gates by three billion years, separated itself from the community and refused to share... [But] now, as Homo sapiens domesticates the new biotechnology, we are reviving the ancient... practice of horizontal gene transfer, moving genes easily from microbes to plants and animals, blurring the boundaries between species. We are moving rapidly into the post-Darwinian era, when... the rules of Open Source sharing will be extended from the exchange of software to the exchange of genes. Then the evolution of life will once again be communal, as it was in the good old days before separate species and intellectual property were invented."

Comments

Just great

[Anonymous Coward]

If you think that penis-enlargement spam is bad now, just imagine when how bad it will be once "open source biology" takes off

The future

[MyLongNickName]

Ahhhh, I love when these discussions that come up. The "Luddites" come out against this, claiming we are playing god. The "Technophiles" come out and tell us how we must embrace this. Both sides yell so loud that the moderate (and correct) "proceed with caution" crowd gets drowned out.

Re:The future

[Elemenope]

Agreed. 'Proceed with caution' is the best method for approaching technological progress. I must say though that on this one I sympathize much more with the technophobic instinct than usual, as it might not be possible to gauge just how cautious a truly cautious approach would need to be. Ecosystems (and gene sharing within them) are vastly more complicated than we can at present hope to model down to the probable impact of the introduction of a new or altered phenotype. I would say that proper caution would be to wait until computer science has yielded robust enough modeling algorithms and badassed enough machines to run them on to have a better handle upon what exactly we might be monkeying with.

Of course, human curiosity and human greed will outstrip any sense of caution quite quickly if these technologies become as prolific as Dyson predicts.

Re:The future

[HiThere]

The problem is, with the invention of the atomic bomb, et. seq., we have entered an unstable state. Though my instinct is to play conservative, given my reading of the current geo-political state we have a expectable duration as a species measurable in a small finite number of years. I put it at on the close order of two decades (with large error bars).

Given this, it becomes urgent to do SOMETHING that will move us to a state that has a longer expected duration. This means taking risks that would, in other circumstances, be quite reckless. This means pushing AI, nano-technology, space-travel, and experimental biology. Space travel seems like the most likely solution, once we achieve it. The problem is that it's a very difficult problem, as there is a need for self-sufficient colonies to avoid the existential risk problem. Preferably mobile self-sufficient colonies that can subsist in areas with very poor sunlight (i.e., starlight) for multiple centuries. (We're talking about a SLOW rate of dispersion, to save energy.) They would probably need to move slowly enough to scavange from bodies in the Oort cloud and beyond. How this could be financed is a real question.

Nano-technology would be an enabling technology here, as well as a constant threat. But it's potentially so useful, that I can't imagine avoiding it.

AI is a potential alternate way of surviving. If large organizations were controlled by AIs that had socially benevolent goals, then the existential risks would decline VERY significantly. Unfortunately, AIs that had goals taht were not socially benevolent could be another quick route to extinction.

Biology here is a bit of a question mark. It could certainly pose an existential risk, but it already does. And it might be necessary for self-sufficient space colonies. So it might be that you can't get to your desired destination without passing this goal post.

As such, I must say that:
1) We are already in a state of existential risk
2) Advanced biology might make things more threatening, but it may be a necessary step to advancing past the heightened existential risk.

Re:The future

[Elemenope]

I don't know about you, but I'm not in the general practice of putting out fires by dousing them with gasoline. Rushing headlong into further destabilization in the hopes we might collectively trip and fall into a technological singularity seems to me like a very slip-shod way to approach the future.

I agree that for the first time probably in human history we are presented with a significant species existential risk factor. However, I think that rampant garage-and-basement biotechnology for profit is a step in the wrong direction, likely introducing more serious risks and further destabilizations, without much promise of lowering other risks or minimizing existing systemic instabilities. I think, as I stated in my original post, that computer science (and by extension, probably AI) provide the least risky course to pursue, because the tools they provide would enable a better predictive model for planned changes in other areas. I think it best to understand the nature of the systems we are messing with before we start monkeying around with the really fun stuff (like redesigning ourselves and our biosphere).

Re:The future

[DogDude]

The overarching problem with the human race is simple overpopulation (not enough food, not enough medicine, not enough energy, not enough fresh water, etc.).

If the human species doesn't wise up and voluntarily stop the population growth, some "force of nature" will take care of things. I'm leaning towards either a massive anti-biotic resistant bacteria outbreak, or simple and stupid war.

Either way, things aren't dire for the planet or even the species. Things may be dire for a lot of individuals, though.

Re:Open Source != Gene Hacking

[Aladrin]

You've obviously never seen the work of a bad programmer or a good biohacker. Reserve your judgement until you have. (It may be some years, though, as the latter doesn't exist yet, just as programmers didn't exist at one point, either.)

Dyson's predictions with a grain of salt, please!

[microsoft_hater]

He also denies human induced global warming. Great scientists are, of course, always great scientists... But, I think it is time for Freeman to go back to church.

Finally!

[Colin Smith]

the possible end to the Darwinian era Finally the Intelligent Designers will be right.

Relevant to some sectors of computing

[Anonymous Coward]

This communal hippy bullshit does not belong on Slashdot.

Actually it does, but perhaps you don't.

Because those of us engaged in genetic programming research find it relevant to stuff that matters to us.

Information Technology

[mcrbids]

At its heart, the science of Information Technology will grow and consume all other industries. Biology is a form of information technology - the information contained in the DNA/RNA and mitochondria define the outcome of the biological organism - they are the software that comprises us.

It's not written in a language easily understood by humanity, but once the concepts of how things really work together are clearly understood, it won't be long before a high-level language can be developed to define the requested behavior and structures can then be "compiled" into an organism.

This is the fusion of biology and information technology commonly called the technology singularity and which, I'm convinced, is happening all around us.

Slow at first, growing towards advancing rapidly. I see it in software, networks, information technology, science, medical technology, and manufacturing. It's amazing, exciting, and thrillingly dangerous all at once. I honestly thing that we'll either pull it off, and move beyond evolution to create an entirely new form of life, or destroy ourselves and regress to bacteria, rodents, insect life.

Either way, we aren't in Kansas, anymore.

Re:Information Technology

[Colin Smith]

The future of "the technological singularity":

http://hardware.slashdot.org/article.pl?sid=07/06/ 30/1247249

HTH

Re:Information Technology

[naoursla]

Funny thing about exponential curves: It always looks like you are always on the 'flat' part when you are looking towards the future. It is only when comparing to the past while ignoring the future that it looks like you are on the steep part, and that is true at any point in time. Unless "progress" ends up being a sigmoid curve, we will always be wondering if the Singularity has happened and if so when was the point it occurred.

The characters in Charles Strauss's novel Accelerando wonder this very thing even after the Earth has been dismantled for computation parts and the character have uploaded their brains into computers capable of simulating an entire human existance in a fraction of a second.

Re:Information Technology

[Guppy]

Funny thing about exponential curves: It always looks like you are always on the 'flat' part when you are looking towards the future. It is only when comparing to the past while ignoring the future that it looks like you are on the steep part, and that is true at any point in time. Unless "progress" ends up being a sigmoid curve, we will always be wondering if the Singularity has happened and if so when was the point it occurred. There's one factor that keeps the curve from being completely scale-free though, the (relatively) fixed scales of the human observer. The spans of our lifetimes, reproductive cycle, the speed at which we learn and adapt have changed at linear rates (at best) that haven't kept up with the exponential expansion of our technology. Thus far we have been unable to effect substantial changes in our own selves -- human biology simply wasn't "designed" with upgrades in mind. More importantly, I don't think human psychology was either, and from watching popular and political reactions, further advances may merely change the previous statement from unable, to unwilling.

Re:Information Technology

[naoursla]

That is a fair response and suggests that the singularity happens at the point that humanity is unable to successfully adapt to the change.

As Long As...

[flight_master]

This "Freeman" fellow doesn't inspire Gordon Freeman-like expirements, we should be ok.

He's got it backwards

[Colin Smith]

He seems to think that genes exist to serve species.

Deep deep flaws in the analogy

[G4from128k]

This summary would leave any biologist apoplectic for its flaws:

1. Sex IS sharing. It's the ultimate cross-fertilization (literally). Almost all organisms, including humans, openly and enthusiastically share DNA via this mechanism.
2. Horizontal gene flow is terribly terribly limiting in its utility. Once organism becomes more complex, you can't plug-and-play like you can with a bacteria.
3. Horizontal gene flow does not foster rapid evolution in the same way that sex does. Picking up snippets and fragments from another organism is not as powerful as cross-over in sex (which does a far far better job of doing a controlled recombination of complete plans)
3. No organism in the world can resist "sharing its genome." If pirating the DNA of others was really that great an idea, then the human digestive track would contain tools for pulling DNA out of hamburger. It really would not take much cellular machinery to engulf a target cell, deconstruct it, and co-opt its DNA. The fact that horizontal gene transfer doesn't occur outside of simple organism should be an strong evidence of its limitations.

As much as I enjoy Freeman Dyson, he really lost me on this one.

Re:Deep deep flaws in the analogy

[dfetter]

Good points here, but you've left out one really important one: there already
is horizontal gene flow. Cross-breeding does it, and it's more common
that you usually think.

Viruses reproduce by "horizontal gene flow."

Re:Deep deep flaws in the analogy

[rachit]

1. Sex IS sharing. It's the ultimate cross-fertilization (literally). Unfortunately, its not that easy to get women to share their source. And when they go completely open-source, you don't want to use the software anyway, probably viruses lurking in there somewhere.

Re:Deep deep flaws in the analogy

[Anonymous Coward]

It's not necessarily flawed in its suggestions for what the post-darwinian era actually means to the deepest extent. sex between humans is only sharing between homo sapiens, not genes from other species, meaning your second point (2.), is incorrect as HGT would allow us to import genes from other species for gene therapy in parts of our bodies that need it to treat a disease, or cosmetically like something genetically Botox, etc. The difference here is that bio-engineers would aim to insert genes in live tissues rather than correcting a teratogenic offspring, much like bacteria pick up genes during their lifetime and use it for their benefit, as opposed to implementing its "gene updates" in the next generation, where both HGT and "vertical" (?) gene transfer proponents benefit.

3. HGT might not foster rapid evolution- in the traditional sense. time is measured different for humans. Here, applying HGT by humans instead of bacteria is different because we have far more components and resultingly, a very small (or big) specific goal (i.e. an in vivo genetic vaccine against a flu, for example) when using HGT. Evolution for humans becomes much more subjective as our issues and desires in society become the direction (of many choices) of WHAT and HOW fast we're evolving. bacteria don't talk and go on the internet, and a microenvironment of thermophiles' HGT activity in Yellowstone probably will have very little relevance to ones in hydrothermal vents on the sea floor, while humans all over the world are much closer and our survival issues are all much more connnected when there's a flu and there's airplanes. So, picking up fragments of DNA might not be "fast/expedient" by synthesizing it in a lab, but it could be faster than waiting a generation or 9 months to get its in vivo in effect.

4. I think the reason we don't have a DNA extracting kit in our digestive tract is simply because it wasn't extremely required for our survival, but we could later engineer a use for one (enter a post-darwinian era). there are other organisms that do. http://en.wikipedia.org/wiki/Agrobacterium_tumefac iens has examples of plasmids from a bacteria that is inserted into a plant genome. to me, it's more of a technical obstacle than an ideological one to create an organelle in humans in one or a few places of the body to make use of HGT (but regulated of course).

Re:Deep deep flaws in the analogy

[xy]

Y'all should go read the original material by Woese (& Goldenfeld) before making asinie statements about science you clearly don't understand. Though, a large part of that is because Dyson's explanations of the stuff really aren't that good; or more accurately, they aren't very deep, and these are complex issues that require a deep reading to understand. The couple paragraphs Dyson presents are a reasonably good summary, but if you're not inclined to take what he says at face value there's no depth there to convince you.

The "New Biology" article by Woese is brilliant and a much, much better exploration of the nature of evolution and the origins of life.

Dyson needs to stick to physics

[quixote9]

That's funny, which is how I assume he meant it. As a serious statement, it would be totally laughable except that a few people who know even less are going to say, "Ooh, Freeman Dyson. Must be good."

Like the commenter above said, biologists are just mixing and matching from organisms and hoping for the best. A simple regulatory cascade involves around sixty (60) proteins, and biologists have only the vaguest ideas about how to manipulate the process. And that's a big step up from even three years ago. Really. They have barely a clue. As a biologist who's taught college for decades, really, it's true.

Life was never "open source" in Dyson's sense. Horizontal gene transfer is always a rare event, even more so in multicellular eukaryotic organisms like, say, vertebrates or trees. Natural selection has always and will always operate because in order to survive, creatures have to be able to produce lots of offspring. However, there's not enough resources for all of them, and the ones less able to use the resources die. This would be true of any life, anywhere. It's not limited to Earth. Kind of like the speed of light is the same everywhere, and gravity operates everywhere.

Sure, people will get better and better at genetic engineering and biotech. And a good thing, too. Paralysis will become a thing of the past, as will blindness and failing organs. That's great. But it's not going to change life itself.

Re:Open Source == Gene Hacking

[Anonymous Coward]

"The biohackers struggle with how their code will impact their systems in terms of "gene expression" and generational interactions. "

Well, nowadays, with huge operating systems like Vista, nobody knows anymore what impact their code will have, from security breaches to DoS to unexplainable bugs. Couple this with bugs in the processors themselves (Intel, anyone?), with constant vendor patches, and you have developers that struggle with how their code will impact their systems in terms of features and interactions.

"Programmers tend to understand the systems on which their code runs."

Those days of happy mathematical proofs on computing systems in paper are gone. Today we have the sad ordeal of testing a system like if it was small modification in a mind-boggling complex beast created randomly. A simple sorting algorithm implementation can fail without any sensible reason, because of an obscure detail of the implementation of your processor or operating system.

It's actually quite a strong analogy

[Morgaine]

>> This analogy is flawed. The Open Source community creates code from ideas to create programs and systems. In the Biohacking world, genetic code is copied from one system into another system

I don't find it flawed at all.

Free and Open Source Software is concerned not with the creation of a bag of abstract ideas, but a bag (or pyramid) of software components of various kinds (libraries, classes, utilities, etc). Those components are copied around from one application to another very freely, and not restricted to just one type of application or system (analoguous to "species"). This is very close indeed to horizontal gene transfer, cutting them out of one sequence and splicing them into another.

The analogy may be little more than a coincidence of course, so one shouldn't read too much into it, but I think that Dyson uses it quite accurately. Moreover, the equivalent to horizontal gene transfer pervades every single one of our fields of technology, so I think it's true to say that speciation is totally dead in all activities of Man, and biotech is just one example.

Re:Dyson's predictions with a grain of salt, pleas

[Anonymous Coward]

He also denies human induced global warming.

That's no surprise at all, because all honest scientists are honour-bound to adhere to the scientific method, which has an extremely strict M.O.. That M.O. prevents them from making handwaving interpretations and supporting what SEEMS to be the right answer, but is in fact not yet substantiated by current GCMs. Short-term predictions mean nothing when they're just ripples on a widely varying curve.

As soon as the GCMs actually start predicting (accurately) the very pronounced 100ky cycles of climate change over the last million years or so, and also explain accurately how the coldest epocs in the history of the planet happened to coincide with CO2 levels many dozens of times greater than the current ones, that's when honest scientists like Dyson will be able to express agreement with the mass hysteria. But not before.

Honest science isn't about being popular.

Re:genetic killswitch

[smallfries]

It all depends on the definition of "meant". There is some evidence that homosexuality is an advantage - the basic idea is that homosexual aunties or uncles improve the odds of offspring surviving. Even though there is not a direct transfer of genes, increasing the survival odds of people who carry some of your genes improves the survival odds from the gene's point of view.

It could be argued (as the original post did) that homosexuality is a kill-switch in some sense. From a biological programming point of view - it is, as it encodes for a behaviour that stops the genes from reproducing directly. Of course, many people would be arguing about "meant" as an ethical or moral judgment. And there, all bets are off, a rational person could argue that if we start designing our own life that its time for us to define morality ourselves rather than $BOOK of $DIETY. But this being slashdot that is what most of the discussion will follow...