Sunday, May 23, 2010

Genetic technology: did scientists play God?

Genetic technology: did scientists play God?

Of course they did: a group of scientists intelligently designed a complex creature and brought it into being. Isn’t that what creationists say that God is supposed to have done? So the answer to this question, which is being raised all over the internet (see here, here, and here, for example), is “yes.

But whether Craig Venter and his colleagues created a synthetic bacterium in order to play God is doubtful., where for some reason Andrew Brown is allowed to continue injecting nonsense into the ether, he sees the synthetic organism as “another triumph of the only major scientific programme driven from the beginning by explicit atheism.“

How a synthetic cell
was created

Thaksin Shinawatra in 2001The scientists "decoded" the chromosome of an existing bacterial cell - using a computer to read each of the letters of genetic code.

Thaksin Shinawatra in 2006They copied this code and chemically constructed a new synthetic chromosome, piecing together blocks of DNA.

A Thai soldier stands guard in front of the Government House in  Bangkok on 19 September 2006The team inserted this chromosome into a bacterial cell which replicated itself. Synthetic bacteria might be used to make new fuels and drugs.

This is remarkably stupid, even for Brown. Yes, Venter is an atheist, and so was Francis Crick, who Brown sees as the father of the synthetic life program. But it’s clear that the work culminating in today’s remarkable paper in Science was driven not by an idea to disprove God, or replace him, but by two other factors.

The first is simple curiosity—to see if we really could synthesize a working genome. H. L. Mencken described this as the strongest motivation of the scientist:

What actually moves him is his unquenchable curiosity–his boundless, almost pathological thirst to penetrate the unknown, to uncover the secret, to find out what has not been found out before. His prototype is not the liberator releasing slaves, the good Samaritan lifting up the fallen, but the dog sniffing tremendously at an infinite series of rat-holes.

And, really, think of what we’ve done: using only the 3 pounds of jelly in our heads, and materials wrested from the Earth and laboriously transformed, we’ve been able to make a genome—one that can completely direct a living organism. This is not the same as creating life, for that’s still a way off. But it’s nevertheless amazing, and we don’t grasp how truly amazing it is because we’re inured to the miracles of biotechnology. But think: how close is a chimp to doing this? They don’t even have PCR machines!

But Venter and his team are no fools, and they know that their methodology, which took a decade to perfect, can have enormous payoffs. We can now make genomes to our desire, and put in them any genes we want, and then use them to build organisms. We’ll have to start with simple ones like bacteria, but even there the social benefits are immense: the use of artificial bacteria to produce biofuels, for example. Accompanying all this must be stringent government and public oversight, of course—even Venter recognizes that. But still, even if this project simply stopped here, it would be a triumph of the human imagination, like putting men on the Moon.

But enough. I won’t go over the technical details of this achievement: the background has been discussed by Carl Zimmer at The Loom (he’ll undoubtedly do a big post today), and the research by Elizabeth Pennisi at Science and P. Z. at Pharyngula.

I’ll just post a Quick Guide (apologies again to Current Biology):

What is Mycoplasma?

Mycoplasma is a type of bacterium that lacks cell walls (thereby rendering it impervious to antibiotics like penicillin, which work by hindering cell-wall synthesis, preventing bacteria from dividing). M. mycoides causes lung disease in cattle and other ruminants.
transformed mycoplasma
Mycoplasma mycoides created at the Venter Institute by swapping a new genome into Mycoplasma capricolum

Colonies of the transformed Mycoplasma mycoides bacterium. Image Credit: J. Craig Venter Institute.

Why did they use this group of bacteria?

Because it’s the creature with the smallest genome that can still grow independently in the lab. A small genome makes synthesis easier, and it has to grow independently in the lab because under all definitions that is a living creature. (There is still a controversy about whether viruses, whose genomes have already been synthesized, qualify as “living” creatures, for they parasitize the genomes of other creatures for replication and coat synthesis, and cannot grow by themselves in the lab.)

What did Venter’s team do?

They synthesized the chromosome of one bacteria, Mycoplasma mycoides, from scratch, and injected that artificial chromosome into dead cells of a related species, Mycoplasma capricolum. The artificial chromosome worked properly, reviving those dead cells and giving them the ability to grow, metabolize, and divide. In effect, they artificially built the entire genome of a species and showed that it could work in a manner similar to that of the naturally-occurring genome.

What’s so great about that?

First of all, it’s a stunning technical achievement. The M. mycoides genome is a million base pairs long, and getting that all correct, and putting the DNA together in the proper linear order, took a decade of work. (A much smaller viral chromosome had been synthesized a few years ago.) The chromosome was assembled in yeast, and in several stages, each of which was fraught with problems. Finally, the assembled chromosome was put into the recipient cell. Each of these steps required developing a new technology. And of course, as I mentioned above, there is the potential of enormous benefits of genetically engineered organisms.

Couldn’t this kind of tinkering cause big problems?

Yes, of course. If this kind of work was done without the proper guidelines and oversights, pathogenic or destructive bacteria could accidentally wreak havoc. Nobody, including Venter, claims that scientists should be allowed to do this kind of work willy nilly. In the case of the Science report, the researchers were careful to disarm all the genes in M. mycoides that were pathological. But clearly new guidelines are in order.

Did Venter’s team create life?

No. They created an artificial genome that was able to direct a living organism. But that stretch of DNA would have been absolutely useless had it not been injected into a cell that already had the proteins and protein-synthesizing system that could take the DNA and use it to assemble new cells and proteins, as well as to allow the DNA to divide and make new cells. (This is a complicated process that requires many enzymes and other proteins.) After a few generations, all the protein-synthetic, metabolic, and DNA-replicating machinery finally derived from the synthetic genome, so in that sense there was now synthetic life. But it could not have started without enzymes, ribosomes, and other biological material from the “dead” recipient species, M. capricolum.

Indeed, this is the whole problem of how life appeared in the first place. The biggest obstacle in understanding how life evolved is that DNA needs proteins in order to build a cell and to replicate itself, but those proteins can’t be made without DNA in the first place. It’s a chicken-and-egg problem. The problem of the origin of life is the problem of how the DNA/protein system coevolved. Venter’s team circumvented this problem by providing the starting materials: the proteins and cellular matrix that helped the artificial DNA start replicating and making proteins.

Is real artificial life around the corner, then?

Probably not for a while. We have to solve the chicken-and-egg problem first. That is, we need to synthesize a DNA or RNA molecule that can, out of a vat of supplied but simple chemicals, construct a cell that has the proteins and other materials necessarily to make the whole thing a self-contained organism that can grow and divide in the lab. That is a long way off. I don’t know if I’ll see it in my lifetime, but I am confident that my students will in theirs.

When we do that, will we then be playing God?

I don’t like this whole notion of “playing God” because I don’t believe in one. If that question means, “Can we create life from off-the-shelf chemicals?” then the answer is “almost certainly yes.” But we must add that this creation of life in a high-tech lab bears no resemblance to how scientists think life originated four billion years ago. That happened in some “warm little pond,” using chemicals much simpler than the ones Venter used. It was a process that took eons, and resulted in an organism much simpler than a Mycoplasma. We should not think that Venter’s group was somehow mimicking the origin of life. They weren’t, and didn’t intend to.

Will we ever be able to figure out, then, how life began?

I don’t think so. The traces of that life are long gone, although remnants exist in things like the genetic code of modern organisms. But those first replicating creatures left no fossils, and there are many ways they could have originated. We’re gradually developing an understanding of how they might have come into being—RNA, for example, seems to be a better candidate than DNA for the first “replicator”—but we’ll never know for sure. There are some questions that science simply can’t answer, because the substrate for our understanding isn’t there. But that does not mean that God did it!

How will creationists react to this achievement?

I predict several responses. First, that it doesn’t mimic the creation of life the way that God did it (either poofing complex species of organisms into being ex nihilo or, if you’re a theistic evolutionist, evolving the first cell). Or, they’ll say that this proves intelligent design because the Venter creature was, after all, intelligently designed. But, as I said, this experiment was not conducted to mimic the evolutionary origin of life.

But what creationists cannot get around is the increasing demonstration that life is merely an immensely complicated chemical reaction. Venter’s team made a genome able to direct and support life using off-the-shelf nucleotides and some other reagents. Eventually, in a few decades, they’ll be able to make a fully living bacterium in the same way. And then we will have played God, at least the way religious people mean it. And maybe, before our own species gets incinerated by the Sun in five billion years, we may even make conscious creatures. That will be the final blow to mind-body duality.

Life is just complex chemicals—nothing more, nothing less. Venter and his team have gone a long way toward showing this. And I’m very glad that I was alive to see it.

UPDATE: This one of the “watermarks” Venter’s group put in the synthetic DNA was a line from James Joyce! Of course I would have preferred the last line from “The Dead,” the finest prose piece ever written in English: “His soul swooned slowly as he heard the snow falling faintly through the universe and faintly falling, like the descent of their last end, upon all the living and the dead.”


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