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It’s alive! A primer on synthetic life

Colby Cosh on Craig Venter’s biotechnology breakthrough


 

I’ve got a neglected heap of notes for weblogging topics, but Craig Venter’s latest biotechnology stunt metaphorically swept them clear from my desk. It is not easy to comprehend by means of plain English what Venter and his research institute have achieved. The title of their paper for Science offers the best possible short summary: “Creation of a bacterial cell controlled by a chemically synthesized genome.” Reactions range from the alarmist—dear God, he’s created synthetic life!—to the dismissive—bah, it’s not synthetic life at all! (The Raelians, for their part, take the view “He’s created synthetic life, and we think it’s awesome!”)

Here’s the strictly technological significance of what Venter has done: he used computers to create a synthetic genome that never previously existed in nature, turned that information into physically existing DNA, replaced the DNA of an existing organism with the new DNA, and successfully showed that his artificial software “worked”—that it could self-reproduce and serve as the design for functioning progeny. It is the production of an all-new life form from human programming. I do not think Scots SF author Ken MacLeod goes too far when he writes “This is a moment in evolution, the origin of a new kingdom: the Synthetica, as artist Daisy Ginsberg has suggested we call it, supplementing nature’s bacteria, eukarya, and archaea.”

Creationists and Catholics are putting on a brave face, and they have a basic point that cannot be gainsaid. Venter had to follow “God’s” existing “literary rules” of genome construction, so to speak; his artificial genome had to contain essential bits of programming plagiarized from nature, some of which are not fully understood. And nobody can yet imitate “God” in building a cell from scratch: an existing bacterium had to have its own chromosomes scraped out to provide a platform for Venter to build upon. It’s a bit like observing that, yes, this sentence I’m writing right now is completely original in the usual sense, but I haven’t made up any of the words in it completely from scratch, and to be understood as a message, it must follow a certain accepted structure.

That being said, once you’ve gone Gutenberg, there is no going back. The key passage in the Venter paper is perhaps this one [emphasis mine]:

We refer to such a cell controlled by a genome assembled from chemically synthesized pieces of DNA as a “synthetic cell”, even though the cytoplasm of the recipient cell is not synthetic. Phenotypic effects of the recipient cytoplasm are diluted with protein turnover and as cells carrying only the transplanted genome replicate. Following transplantation and replication on a plate to form a colony (>30 divisions or >109-fold dilution), progeny will not contain any protein molecules that were present in the original recipient cell. This was previously demonstrated when we first described genome transplantation. The properties of the cells controlled by the assembled genome are expected to be the same as if the whole cell had been produced synthetically (the DNA software builds its own hardware).

If I had a way of putting that last parenthetical in double-bold face, I’d do it. No, we can’t yet build a cell from scratch, but if we can edit the software of an existing cell to any degree we please—although the process described in the paper is still of a crudity that bleeds forth from its every line—it really doesn’t matter. The descendants will reproduce according to our program, and will be indistinguishable from the descendants of a cell created by God, Klingons, or Santa’s elves. The software builds its own hardware. Sixty-seven years after DNA’s role as a genetic information carrier was confirmed, and 57 years after its structure was ascertained, we can now say that there exists, in the parlance of mathematics, a true constructive proof of this.

But then again, no biologist or other sane person really needed such a proof. The best lay summary of Venter’s achievement that I have found is provided by robotics professor Rodney Brooks, a man who has thought a great deal about the operational definition of life.

..the fact that [Venter’s] genome works as a genome is not a surprise to molecular biologists. They have long believed that life is chemistry, and that one string of connected atoms is just as good as another having the same arrangement. They have long ago discounted the idea that there is any sort of specialness imparted to a molecule by its history of production. Molecules have no souls.

But the new cells are also not synthetic life in that the ancestor cell was an existing live cell. It was not built from pieces in the same way that the synthetic genome was built. That is another, perhaps harder technological challenge, but also one that there may be no imperative to try to achieve in the short term; hijacking existing cells may be all that we need to develop all sorts of new synthetic forms.

The press has both overplayed that what has been done is a surprise, and underplayed the interesting challenges that lie ahead, in that their biggest fears do not automatically follow from the current achievement.

Brooks is saying that there are no new theoretical implications from the Venter team’s accomplishment, as there actually were from the Venterian work that preceded the demonstration of synthetic life—namely, paring the smallest genome known to exist in nature down to an even smaller instruction set, and getting humans closer (closer than God or natural selection ever managed) to the theoretical minimum of information needed for a DNA sequence to be meaningful. Playing God? Hell, that’s for amateurs!

That DNA can practically be edited will come as a shock only to those whose anti-materialist or vitalist views depend on clinging to some particular state of human technological ignorance. There are no longer very many biologists in that category. If life can be designed and mass-produced synthetically like machines, there won’t be much ground left on which to argue that living things aren’t machines.

Biologists presented with the Venter news are instinctively contemplating the revival of familiar old forms previously discarded by natural selection, and the synthetic genome adds spice to the ethical debates over whether we would be justified in making a Neanderthal or a woolly mammoth. This is not really a big theoretical deal either. The more important, wider prospect on offer is the ability to recover biodiversity by artificial means, and the eventual end of the rule than “extinction” is the definitive end for a species. The thought of one day being able to see a dodo strut and squawk and lay eggs is romantic (in a way that warms even the stony heart of Darwinian tough-guy Richard Dawkins) and missions of that sort are now one big step closer to fruition.

But the really exciting and scary idea here is the customizability of life, and as Brooks says, we don’t know what limits, other than the obvious physical ones, scientists might ultimately run up against. Let’s note, though, that so-called “genetic modification” in agriculture has already accomplished a lot, even with one hand tied behind its back by trade rules and consumer fears. (What we refer to as “genetic modification” is really just genetic modification 2.0. The hybridization and artificial selection that humans were busily engaged in for several millennia beforehand was 1.0; the stuff we’re talking about in this article is, if you like, version 3.0.) Journalist Quinn Norton offers some wild thoughts about bacteria that “pee out biofuels or Prozac, eat Gulf of Mexico oil, or glow in the presence of melamine, cancer, or anger”. These dreams may transcend what is ultimately feasible. Or they may hint only at a thousandth of a thousandth of the possibilities.


 

It’s alive! A primer on synthetic life

  1. This is about the fifth piece I have read about this and I still don't feel any more enlightened.

    Scientists have created life – they are just tinkering with the process from now on. Is this big deal or not? It seems quite important to me but others seem indifferent.

    " …. bacteria that 'pee out biofuels or Prozac, eat Gulf of Mexico oil, or glow in the presence of melamine, cancer, or anger'. These dreams may …. ”

    My neighbour is old (80 at least) and the other day he was talking about all the technology/society changes he's seen in his lifetime – from what I can tell he was born before everything we rely on now even existed. And it got me thinking about whether changes I would see in my lifetime would be as dramatic as my neighbour's.

    • I think it's a pretty big deal. No, they haven't really created life, but they've been able to completely reprogram it.

      From what Cosh has described (and thanks to him for going through all this), it's basically a de facto creation of life. Technically it hasn't happened, but the end product is the same as if he had, so who cares? Ok, for researchers interested in the actual origins of life, and pretty much anyone else who has a stake in it, this is pretty blah. But for bioengineering, and all of us who stand to use the products of such bioengineering, this is about as huge as it gets, at least for a first step.

    • Probably far more dramatic. The rate of technological change is accelerating.

    • Likely moreso. By the time you die, there will be generations that not only don't recognize the technology you used, but won't recognize the technology their own parents used because they've both been supplanted.

  2. I wonder how Jack Horner's 'breed a dinosaur from a chicken egg' work is going.

  3. Colby's Quote:
    …he used computers to create a synthetic genome that never previously existed in nature, turned that information into physically existing DNA, replaced the DNA of an existing organism with the new DNA…

    Reminds me of this…

    One day a group of scientists got together and decided that man had come a long way and no longer needed God. They picked one scientist to go and tell Him that they were done with Him. The scientist walked up to God and said, “God, we've decided that we no longer need you. We're to the point that we can clone people and do many miraculous things, so why don't you just leave us be.”

    God listened patiently to the man and after the scientist was finished talking, God said, “Very well. How about this? Let's have a man making contest.”

    The scientist, with great arrogance said, “That would be fine.”

    The Lord added, “Now, we are going to do this just like I did back in the old days with Adam.”

    The scientist said, “Sure, no problem,” then bent down and grabbed a handful of dirt.

    God said to the scientist, “No, no, no. You go get your own dirt!”

    Or, get your own "existing organism" to stick your home brewed DNA into…

    • That really ought not to be much of a challenge. On the other hand, for the reasons Colby explained, there is no pressing need to create synthetic cytoplasm, since hijacking an existing cell seems to work just as well.

      I wonder if you realize that there is far greater arrogance in asserting that a particular fairy tale (out of thousands) about how reality came to be is the one true story, rather than trying to explain it through rational observation. But then, there's probably no god. Now stop worrying and enjoy your life.

      • arrogance? fairy tale?

        Are you just trying to get under somebody's skin or are you actually that dimwitted.

        Rational observation leads to assume an intelligent creator. It's really just as simple as that. The singularity, big bang, a gazillion years of evolution? I guess not all "fairy tales" are created equal.

        (p.s. it's arrogant to think that humankind is doing anything but scratching the surface when it comes to our knowledge of the universe. It often seems like a case of infants playing with electricity, or geneticists playing with…)

        • Andrew – I was referencing an (old) joke…and found it rang true with this current situation. Thus, I posted it for all Colby's readers (and Colby) to share a laugh. I assume that Colby got the joke, and that his world view was not threatened by it, as yours seems to be.

          Andrew, please take one half of your own advice (whoops, sorry – not your advice, but that of Richard Dawkins and Ariane Sherine, who you are directly quoting from the UK ad campaign) – stop worrying, and enjoy your life.

          I happen to agree with Colby that the implications of this research are at once full of promise AND full of danger. Most human research is – witness the harnessing of the atom, which can be a tremendous boon or a tremendous boom, depending on how the science is applied (yes, you can use that line if you wish, Colby).

          I have always appreciated Colby's professed respect for his Christian contemporaries (evidenced often in his columns and his past work with the Byfield family), despite his (also professed) disagreement with their world view. I also respect his world view, while maintaining my own Christian viewpoint.

          Thanks to Colby for bringing this topic to us for discussion.

          • Well, it is a very good joke.

  4. Good summary, Colby. But this experiment isn't greatly relevant to the idea of bacteria that "pee out biofuels or Prozac," etc., because you don't need a whole novel genetic code to do that. Scientists have been modifying bacterial genetics and inserting new genes for a long time, and most practical applications of genetics are going to involve a continuation of that rather than trying to make new types of bacteria from scratch.

    IMO, this is a cool development but doesn't really signify a great deal.

    • They used a novel chemical synthesis procedure to assemble viral-sized pieces of bacterium DNA into a complete DNA sequence ("from scratch", as it were). Once inserted into the host cell, the genome was capable of self-replication. It's a major development.

    • It might not be such a big deal if all of the possible genes one might want to insert were already out there. However, nature has only "explored" a tiny fraction of the options for genetic code through evolution. It is not so hard to imagine an automated process for synthetic lifeform creation that would quickly outstrip what nature has accomplished to date.

  5. WOW this was recent.

    AMAZING that they've finally succeeded in creating a programed DNA sequence, I don't think it should be downplayed as "unsuprising" or "nothing new" this is a landmark discovery! I mean, grant it one that we foresaw since forever ago, but isn't that with every discovery? Hypothesis leads to Testing, Testing leads to discovery, Discovery leads to theories that transform our understanding of things and shift paradigms.

    This has never been done before, I am personally thrilled that this has been done and that MY SPECIES did it!

    Gene Modification, does that mean they can transplant healthy il-23 into a patient with nonhealthy il-23 regardless of understanding the cause of said unhealthyness and that person would be cured of, oh idk, crohns? :)

    Curing cancer, yes making biofuel spewing trees would be nice, and my personal favorite making life that's able to grow and sustain on other PLANETS! GOD what a wonderful time I live in. The possibiliities are endless!

  6. That's awesome. It marks the beginning of a whole new field of engineering: genetic software. Rather than writing a program for a computer built of plastic and metal, we can write one for a computer built of proteins, and most importantly: this computer has the means to replicate itself. The possibilities for construction, disaster / waste cleanup, fuel production, etc. are vast. The possibilities for weaponry are also vast and somewhat scary (think "The Day the Earth Stood Still"), but in a world where biological weaponry is already a fact of life this may not be all that much of a difference.

    I don't understand why Cosh keeps going on (a bit insultingly, I might add) about God and the implications for Christians. Is this somehow a threat to Christianity or an ethical problem for Christians (other than the weaponry ? I don't see how. If someone were to engineer a human mind from nothing more than matter, then sure. But cells / bacteria or even macroscale animals….I'm not seeing the problem.

    • Besides weaponry, I worry a bit about whether regulations can keep pace with new biotechnologies like this. I mean, we're still kind of flailing on hard goods, even more on pharmaceuticals, then even more on genetically-modified crops and the like. This has the potential to be like a genetically-modified pharmaceutical that can self-replicate… it's a minefield of social issues and legal challenges.

      I agree though, that the focus on Christians seems unwarranted – this is a very profound development, but it really says little on the origins of life. There are some ethical issues here, sure, but I don't see how they apply specifically to Christians either.

    • I don't understand why Cosh keeps going on (a bit insultingly, I might add) about God and the implications for Christians.

      I think it's a bit of a tradition. Every time there's an advance in genetic engineering, journalists will write some variation of: "How will Christians respond to this latest provocation?"

        • Fair enough. There's no shortage of Christians who view genetic engineering as "playing God".

          • I think that's incorrect. There are a lot Christians who view genetic engineering of humans as "playing God, but genetic engineering of plants/animals? For widespread objections to those I think you have to go to hardcore environmentalists.

          • Of course Gaunilon, some deluded individuals believe that humans are animals. They should watch this

            [youtube swlsqkAyxqYhttp://www.youtube.com/watch?v=swlsqkAyxqY youtube]

            to understand the truth.

        • Sure, Christians will have concerns about the ethical use of this technology as with any other technology…nothing novel about that. It would be foolish not to.

          That, as described in your link, is a pretty far cry from " Creationists and Catholics are putting on a brave face…" Er what? A "brave face"? As though this is some kind of blow to creationism or Catholicism? I don't get it. It sounds like Cosh misunderstands Catholic doctrine on creation, somehow thinking that it attributes immaterial souls to animals. Otherwise the comment seems nonsensical.

          • Catholic doctrine does attribute immaterial souls to animals. Or were you prepared to make the William Jennings Bryan argument that you're not one?

          • …sort of thought it was clear that I was distinguishing "animals" as in "brutes" from "human animals".

            As in my original response: if someone were to engineer a human mind from nothing more than matter, then yes there'd be a conflict. But cells / bacteria or even macroscale (non-human) animals….I'm not seeing the problem.

            Man, in terms of Catholic doctrine, is a rational animal. It's only the "rational" part that implies an immaterial soul, not the "animal" part of the definition.

          • I'd say that's practically the definition of "putting on a brave face" right there. Do Dawkins' Neanderthals present you with a "problem", or will this theoretical "engineered human mind" have to belong to someone with a Queen's MBA and a propensity for purple neckties in order to pose one?

          • Neanderthals were engineered by humans? Who knew?

            Seriously, I don't see the problem with Neanderthals (Dawkins's or anyone else's). If they were rational then Catholic doctrine would hold that they had immaterial souls. If not, then not. "Rational", in terms of Aristotelian/Thomistic/Catholic thinking just means the ability to see universals and deduce conclusions accordingly.

            Incidentally, the train of Aristotelian / Thomistic philosophical reasoning isn't the only basis for concluding that the human mind cannot be replicated by matter alone. The modern Lucas-Penrose argument suggests the same conclusion based on Godel's theorem.

          • And "pop" goes the bubble that is the "soul", as you turn it into an immaterial, unlocatable miasma which can only coexist with the capacity to reason. Jury's out on the Neanderthals until we make one! (Of course your doctrine is several hundred years out of date; nowadays we know, being much smarter than dear old Thomas Aquinas, that the soul instantly penetrates the ovum along with the sperm.)

          • Not sure what you're getting at here. The Catholic understanding of "rational soul" has always been "immaterial" and "unlocatable". That's not a response to modern science; it's exactly what the Church has held for a very long time, and what Aristotle independently deduced.

            As to Aquinas, he (and Aristotle) certainly made their share of mistakes – most notably when they were making guesses as to premises for which they had no data. But anyone who has studied the reasoning of either would be careful about suggesting that we, nowadays, are smarter. Particularly since in many respects modern science is slowly catching up with the conclusions to which they reasoned, after the comparative dark ages that was the Newtonian era.

          • Of course, in Thomistic philosophy there is a vegetative soul, sensitive soul, and rational soul. The vegetative soul is what the Romans would call "anima" and modern doctors would call "signs of life", in other words the very quality of being alive and breathing. The sensitive soul is your capacity to perceive through the senses, and the instincts of being directed by them. The rational soul is the capacity to think and reason.

            Of course, all of these types of the soul aren't really separate from each other, since Aquinas, like Aristotle before him, was a material monist. The purpose of the division of the soul into three parts was a recognition of brain death, and the hope that a rational soul endured when it was clear that signs of life and awareness had fled. A person was not entirely complete however, without a material existence. This was an awareness that reason would pretty impossible without a material life to observe and interact with.

            The idea of the the soul being separate from the body and inhabiting it like a hand in a glove is more of a Platonic/Cartesian ideal of dualism. DeCartes in fact had the idea that the pineal gland was the connection of the soul to the body. A tether in the brain if you will.

          • Ah, you are a bit more of a lefty that you are letting on Colby, with the idea that we are somehow smarter for being born centuries later. Aquinas was ignorant of a great many scientific discoveries (and did not have a proper appreciation for the methodology that would become the Baconian method and the later scientific method), but he wasn't stupid.

            This was a man, after all, who was able to give four different lectures to four groups of students at the same time. If you actually ever bothered to give a glance at his writings, I think you will find many observations which are as sharp and relevant as they were several centuries. I know you won't bother though, because most have been conditioned by society to regard 1500 years of human history as being without value.

          • Meanwhile, the Macleans.ca comments have been totally deaf to sarcasm for approximately the same amount of time.

          • Perhaps.

          • Souls yes, immaterial souls no.

            It is the rational part (that which is in the image of God) which makes us unique (as far as we know).

    • The usual stereotype is that some Christians believe that God is the source of all life and that dinosaurs didn't exist and such.
      Do you honestly think that some fundamentalists won't care that man is "creating life"?

      It's a stereotype, but it is what it is. Just like the endlessly enraging left vs right "debates".

      • I think you're confusing a number of things. First, Christians do believe that God is the source of all life. That's not a stereotype. Where Christians differ is on whether God is the source of all life directly, or whether He is the source of some life indirectly. This case would be the "indirect" variety.

        I've never heard of, much less met, a Christian who believed that dinosaurs never existed. I have met people who believe that dinosaurs coexisted with humans, but that's quite different.

        • I actually met both of these kind of people, the ones who believed that dinosaurs never existed just explained to me that God put fossils on earth to test our faith. Luckily 99% of Christians I have met to do not share this belief.

          • Ha! That's interesting. Just goes to show, there are kinds of folks out there.

          • Ha! That's interesting. Just goes to show, there are all kinds of folks out there.

          • I've heard that before too.

            While we're talking about Aristotle and Aquinas they had observed fossils as well. They had an idea of inorganic generation of fossils, related to the idea of all matter striving towards a teleological end of perfection. Just as metals strived from baser metals to gold, so too did inorganic matter strive towards life. There was even talk in Scholastic circles of creating life through alchemy, and life evolving out of water and mud.

            They weren't biblical literalists you see. That's a relatively modern Christian invention. The protestant reformation stressing a return to the bible was in many ways an anti-intellectual reaction against Aristotelean teachings and scholastic learning.

  7. "It's a bit like observing that, yes, this sentence I'm writing right now is completely original in the usual sense …"

    You say that now, but just wait until we have computer generated lifeforms generating the blogs about comptuer generated lifeforms. ;-)

  8. I love the Raelians! Whatever happened to that little girl they cloned down in Florida ten years ago?

    • She sells oranges on the side of the road.

  9. We have now become gods.

    Time to throw out the old fairy tales.

    • Maybe when we turn amino acids into proteins and turn proteins into cells.

      Oh, and crack that whole "mortality" thing.

      • Except that would be cheating after having been given the blueprint, idea and materials to create amino acids. We'll have become gods when we create fiat ex nihilo. Let me know when you've done that Emily.

  10. We're right to wonder in awe at the achievement and worry about the consequences of it for evil.

    Inevitably there will be evil consequences, because human beings often make mistakes and sometimes make evil choices.

    You don't have to be religious to be skeptical about this laboratory accomplishment.

  11. It is quite a breakthrough (assuming that the experiment is successfully repeated by others). I can see agriculture and medicine being the biggest beneficiaries. For some reason though the common definition of a virus – a piece of bad news wrapped up in protein- was my first thought after reading about Venter's process for creating synthetic life . Too many creepy sci-fi movies, I suppose.

  12. Colby seems to be saying, "this proves we are nothing more than molecular machines — yeah!!!". An odd point to make.

    Second point: life is so chemically simple, dumb-as-a-rock nature can do it. But, when we do a tiny tweak, how great and clever we are!!!

  13. I don't know much about Catholicism, Thomistic Philosophy, or Genetics. But is this the possible answer to male-pattern baldness!?!?! Yes! Yes! I love you Jesus!

    • Just joking, forget Hair Club for Men, this is the idea behind Perfect Superhuman Baby for Asian Billionaires

  14. We have already gone so far without nature, Nature no longer recognize humans as a relative species. We decided to become "better than God" with temptation in the garden of Eden. (which was probably similar to having heaven on Earth). Now we have created Hell on earth. The brightest and most clever or cunning survive. Humans are disposable or we wouldn't have wars. Money replaced god long ago. People are willing to go against their own divine natures to chase the elusive dollar. Everything we own is taxed, where we go, what we do, what we eat is owned by someone of no more superiority to ourselves. Monsanto or Tyson want to own and genetically modify all the seeds of the earth which were free for mankinds own use. Animals if given a choice of G. M. food do not recognize the genetically grown imposters. We oh so great humans have lost the ability to smell evil and recognize bad intentions. The loss of those two key instincts have gotten us tricked into so many countless troubles. People (apes) were playing god long ago and up to now have never thought so highly of themselves. Let's get back to the garden and let Nature show us the way! There's always someone with a devious plan for any profound invention. Don't give it to them. Until you figure out the mystery of life and why we are here we have no business doing any changes to the genome.

  15. And coming soon:

    iLife – the gizmo for billionaires, by billionaires! Who needs people? MAKE YOUR OWN! Soon, either something like the Borg, or the Cylons. (NOTE: They may not have a use for us.)
    And the minute you buy version 2 at WalMart, version iii… will be out on the market the next day!

    Or… if you prefer.
    "*** Microsoft Life has Encountered a Fatal Error. The Planetary Ecology is shutting down.****
    (ERR Code: Cx0000791, SEGMENT: Do700034, Ax7733308, B056230348, MODULE: M00002)

    But then again:
    It is not as if human life has any importance. Nor is the Earth that great a planet anyway.
    "No, Mr. Bond, I expect you to Mutate, and die!"

    We play with VERY dangerous things, we little bags of meat and bone. But we do not seem to know. Or Care.
    After all: Any man…. no matter how smart he thinks he is, no matter how educated the diplomas say he is, no matter that there be 20 years of experience…. is for sale… if the price is right.
    "Alas, poor Yuric, I knew him well….."
    "So you have killed by mad scientist, Mr Bond. I will merely buy or clone another."
    "I felt a great disturbance in the Force. As if 6 billion people, cried out in terror, and were stilled."

  16. It seems to have become our destiny to try to create something "better" than ourselves – free choice can have a way of sneaking up and blindsiding us – all will be corrected to the original plan at the end.

  17. Poor, Colby. You actually think all that 'software' discredits the anti-materialists. If I could wake you from your atheistic wet dream, you might realize the information on a page is not synonymous with the ink that produced it. In your world, apparently, only ink exists.

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