Anthropobiota: Tree of Synthetic Life Friday, May 9 2008
biology 1:37 pm
A proposed name for the new kingdom of synthetic life: Anthropobiota.
(This is hardly original… see Anthropocene, but it seems most likely to catch on.)
The first member of Anthropobiota will likely be Mycoplasma laboratorium, at the J. Craig Venter Institute. The group also “hopes to eventually synthesize bacteria to manufacture hydrogen and biofuels, and also to absorb carbon dioxide and other greenhouse gases”, according to the Wikipedia page. This would lead to additional species for specific purposes. The point of Mycoplasma laboratorium is to implement a “minimal bacterial genome”, a jumping-off point for future synthetic species. All of these species would fall under Anthropobiota, as long as the genetic material is entirely synthetic. If not, that’s just genetic engineering.
Anthropobiota would be located outside the root of the Tree of Life. It would be a complementary Tree, at first much smaller than the original. The Tree of Life contains between 10 million and 1 billion bacteria species, between 10 and 30 million animal species, and some unknown quantity of archaea. So quite a few new species would need to join Anthropobiota for it to rival the current Tree.
I seem to remember an accusation in some phylogenetics journal that a group of Archaea was outside the root of the Tree of Life, but I can’t find it for the life of me. Anyway, there could be two or more separate Trees of Life. Anthropobiota will be a new one. The Tree of Synthetic Life.
Two different species within Anthropobiota need not evolve from other species in the same group. Each one could be created from scratch, by scientists in a lab. Once we develop the technology to reliably and inexpensively synthesize long genomes from nucleic acid precursors, and swap them for native genomes, we’re in business. The flood gates for new species — both benign and malign — will open.
The Lifeboat Foundation A-Prize page is a foresightful effort to to put development of artificial life forms in the open, where it should be. It a reward to whoever creates the first life form that “must execute at least one synthetic nonbiological operation in order to complete its life cycle”.
On the A-Prize page, Dr. Alan H. Goldstein, Professor of Biomaterials at Alfred University, creates four classifications of life: Natural Biological, Genetically-Engineered Biological, Synthetic Biological, and Synthetic Nonbiological (Animat). According to his classification system, Mycoplasma laboratorium would fall into the third category: Synthetic Biological. It will not be eligible to collect the A-Prize, because that would require an organism that integrates an entirely nonbiological, consistent (over generation) element into its biological life cycle.
Anyway, I’m looking forward to the creation of Mycoplasma laboratorium later this year. I hope that creating synthetic life stays expensive for at least a couple more decades.
You confused amino acids (building blocks of proteins) and nucleic acids (the building blocks for genomes).
Ah, thx. Also, I welcome an actual biologist to use this idea (of giving synthetic life a classification name) and lend it some credibility.
I find this subject to be extremely interesting. It’s a shame that it is not really talked about in other places or forums. As Michael has stated, Google and Yahoo show almost zero results for this kind of thing.
I also like the whole classification scheme that has been proposed.
Michael, if the new bacteria species falls into the thid category, Synthetic Biological, what would be an example of the fourth category, Synthetic non-biological? Would AI fit into that category?
It occurs to me that the Anthropobiota would have to have a new classification category “Derivation”, consisting of Manufacturae and Iteratiae — referring to how it came into existence (either through human manufacture or through that iterative error process we call evolution). This would be a mandatory sub-species classification.
So, you could have Mycoplasma laboratorium manufacturae and Mycoplasma laboratorium iteratiae; these would refer to those that M. laboratoriums that are as made, and to those that have undergone sufficient genetic drift as to be phenotypically variant from the manufactured example.
Obviously, if left to the wild you’d see a lot more of the M. laboratorium-i.
This seems significant //to me// because it would render the tracking much easier. And perhaps interesting.
Something that used a medium other than DNA/RNA to code its design, for instance. Read the A-Prize page in full for more info. For detailed questions, you can track down Dr. Goldstein. It’s his definition.
Google does have results for this sort of thing… search for “synthetic life”. I meant that it didn’t have results for “anthropobiota”.
Ian, thanks, I was thinking about that as I wrote the post, but was tongue-tied on a name. A very relevant distinction.
Anyone know how long it takes for a bacteria to evolve appreciably in the wild? A few months or years, maybe? It took a while for hospital “superbugs” to emerge.
Timescale is in the month range, that I’m pretty sure on. It all depends on changes in its environment. I forget where I read it, but I recall that evolution isn’t a property of iteration but rather of alterations in environment. (Makes sense when you put it all together, really.) That being said… since bacteria go through a generation once every roughly six hours (depending on species), I feel pretty confident in that months time. It really depends on the pressures involved. Antibiotic resistance can actually take just a single bottle-necked generation to come about.
The only problem with such strains is that generally speaking they can’t outcompete the non-resistant strains in the wild. It’s precisely that same reason which is why I don’t worry too much about the implications of synthetic life. By the time we can generate synthbiomes that can actually outcompete, we’ll have enough experience that we won’t be likely to fuck up the biosphere.
“I seem to remember an accusation in some phylogenetics journal that a group of Archaea was outside the root of the Tree of Life, but I can’t find it for the life of me.”
Originally, life was classified into two broad kingdoms, Animalia and Plantae. When we learned how extensive the microbial world was, that broke down, and so we added three new kingdoms (Monera, Protista, Fungi). Archaea share a common ancestor with all other life, but their biochemistry falls outside of the five-kingdom system entirely, so Woese and others added the domain as another level of organization on top of the kingdom (Woese’s domains were Eukarya, Prokarya, and Archaea). Others added Archaea in as a sixth kingdom, but this seems to be a minority view. Synthetic life would be fundamentally different from everything else we’ve encountered, so we’d need a new level of organization on top of the domain. Perhaps we could have four general categories: non-life, viruses and prions, cellular life, and synthetic life.
“I hope that creating synthetic life stays expensive for at least a couple more decades.”
Any particular reason why?
Except synthetic life would by definition be cellular. And, furthermore, once a sufficient quantity of synthetic genes are introduced into the wild populace, it won’t be very long at all until even traditionally abiotic processes are introduced to the wild — especially as the eight new bases are introduced to wild, as it were, which //will// happen within a century at the very most. I should expect to see humans with synthetic bases in roughly the same amount of time (what with single-celled eukaryotes exchanging genetic information via plasmids which have a habit of inserting themselves into any random eukaryotic cell including germ cells of macroscalar life).
I guess, the first Anthropobiota will be, or already is, are bitstrings. Inside computers.
It will also be by far the most productive line.
I guess so.
Any particular reason why?
Because I suspect that the risks outweigh the benefits, until we have the intelligence to set up a global rapid response system.
Dangerous, deadly, catastrophic, billion dead, etc., these are all phrases that come to mind. Call me crazy, but I’m not.
I just wanted to avoid addressing the danger issue in this post, because it takes so long.
I think “planimals” (planned plants/animals) might be catchier than any tongue-twisting “Anthropo” neologism.
But none of these results are “synthetic” life, since, as C. Sagan said, “If you really want to make an apple pie from ‘scratch’, first you have to create the entire Universe”.
We are simply scrambling pre-existing cellular or amino or even “prion” formulas.
The inherent danger in fiddling with the uncanny fabric of Life is that, unlike learned Nature, we can bypass its self-sterilizing (hybrid) safeguards with our brute ingenuity and may potentially unleash pandemics that the Earth’s organisms (us included) have no inbred immune defenses against.
Treading slowly in the Unknown is always a wiser course than blithely dancing into a molecular minefield, intoxicated with mere power.
Best to explore, first, inside the mind.
Where any unleashed toxins and monstrosities are only theoretically poisonous or exterminating.
While I can see the “prion problem” as somewhat more than vexing, I still fail to see why this is lumped in with synthetic cellular life. The simple fact of the matter is that we won’t be able to produce genomes of sufficient sophistication to even begin to outcompete the native varieties for several decades at the very least. FAI is an easier task than is a synthetic superbug that could wipe out all life. Or even all life on an island or aquatic body. Or even all of a specific species.
Doesn’t need to actively wipe out all life, just reproduce effectively enough to outcompete native species in a short time. Look at the nematode. Simple and everywhere. Replicates every week or two. Even easier would be a bacterium immune to bacteriophages.
Why decades to produce megabase genomes? We’re already almost at 1 Mb , and nematodes are only 30 Mb. The entire space of bacterial diversity is almost within reach, and the space of viral diversity is already within reach today, with enough money.
Changes to a single gene can have big effects. This is well documented. The advantages of synthetic genomes are huge over natural ones. Engineers can modify a series of genes to effect a large fitness jump that would be inaccessible to evolution, which must go through a series of intermediary adaptive steps to reach a fitness peak. Evolution gets stuck in local maxima, etc.
It’s odd that you say we’re far from creating sufficiently complex genomes when we’ve already synthesized viruses from scratch and are about to synthesize a bacterial genome from scratch.
You and I share strongly dissimilar views as to the levels of complexity necessary to produce a genome that can outcompete the “fallow” genotypes.
I could go on more at length, but at this point given the fact that this seems to be a strongly recursive discussion, I’m just going to let it go at that.
We can synthesize megabase genomes, but can we “write” a novel genome for even something as complex as a bacterium? M. laboratorium is all cribbed from existing bacteria.
Frightening to read the author’s concepts within this blog, and to read the viewer’s comments. I just finished the film “I Am Legend” last night, and to think of the futuristic complications that the film touched on, and to then read the ego’s that are pontificating on this site is a mind blower indeed. Science Fiction is reality folks, and yes we have the ability to explore this avenue of scientific exploration due to the Genome and the illustrious scientist’s that cracked the code, but do we have the right to play God and destroy what Nature has created just because we can? Free will is the gauntlet here, and all of us will walk our individual paths that our own personal free will choices will pave for us, and all of us will have to answer for our own personal choices when we die. When science and the scientists making these new discoveries, take it upon themselves that they have the right through their personal free will choices, to make life-changing choices for all of the other life forms in the ecosystem of Planet Earth, because of a drive that Science is exhibiting of personal greed based desires for fame and fortune to feed the industries greed for creating new synthetic life forms to patent and market, shows to me that the evolutionary process of our species has not been guided by an interdependency to the whole and seeing that interdependency but has been guided by a super-ego complex that feels that mankind is separate and in control of Planet Earth. Guess what your base, greedy desires are not going to matter! Earth will be shaking off the “un” evolved humans with the tunnel vision of greed, just like a dog shakes off fleas. Your misguided tunnel vision of “I’m all powerful and will created synthetic life” isn’t going to make evolution’s final cut. Green is the scene and all of you whom are embracing careers in this new field better start thinking interdependently because your ego based, me first, I’m better, than the rest of all life on Planet Earth philosophy is dead archaic energy, and the headset has changed.
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