“First cell controlled completely by a synthetic genome”

_{William Dembski

May 20, 2010

Genomics, Intelligent Design}

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Big news at Craig Venter’s Synthetic Genomics:

Summary: Link 1

Press Release: Link 2

The rhetoric is interesting. What they’ve done is stuck a synthetic genome inside a nonsynthetic cell. Nonetheless, they’ve slipped into talking of a “synthetic bacterial cell.” Indeed, one headline reads “The First Self-Replicating Synthetic Bacterial Cell.” This is hype.

If something is going to be called “synthetic,” shouldn’t the whole of it be synthesized and not merely a minuscule portion of it? Also, does such a cell knowably signal design and, if so, why wouldn’t cells untouched by Synthetic Genomics do the same, i.e., implicate design?

Comments

Looks to me like Venter's achievement merely understates the obvious; that creation of life requires intelligence. The Bible described this long before Venter's tinkering.Bantay_{May 20, 2010
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barb, you state: "by replacing its genome with one they wrote themselves," if you can call plagiarizing a already existing genome and very selectively editing the preexisting information of that genome within very tight constraints, then I guess it may fairly be said that yes they "wrote" the genome themselves. The search space for them to find even a single novel gene, or protein, that would do anything at all, much less one that would accomplish a specific task they wanted, is beyond the 1 in 10^150 universal probability bound of Dr. Dembski. Thus they will never ever write a synthetic genome that they have truly created themselves from scratch, they will forever be "borrowing" already written material. Plagiarism: Don't Do It http://www.youtube.com/watch?v=gC2ew6qLa8Ubornagain77_{May 20, 2010
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"To make the synthetic cell, a team of 25 researchers at labs in Rockville, Md., and San Diego, Calif., led by bioengineer Daniel Gibson and Dr. Venter essentially turned computer code into a new life form. They started with a species of bacteria called Mycoplasma capricolum and, by replacing its genome with one they wrote themselves, turned it into a customized variant of a second species called Mycoplasma mycoides, they reported." So they didn’t create life. When a group of scientists manages to make a complete membrane, cytoskeleton, nucleus, ribosome, golgi apparatus, nucleus, and the hundreds of other cell components from basic non-living chemicals and slap it all together and make it start up from total inactivity, *THEN* they can say they created life. In the meantime, this is just a step towards that goal.Barb_{May 20, 2010
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Is this kind of like gene patenting where they claim intellectual property rights on already existing information?Phaedros_{May 20, 2010
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What about cotton/polyester blends?JT_{May 20, 2010
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Bill asks, “If something is going to be called “synthetic,” shouldn’t the whole of it be synthesized and not merely a minuscule portion of it?” Great achievement, sure, but diminished if overhyped. Visiting a relative in rehab recently, I observed several people with prosthetic legs, rehabbing on the double bar or the training steps. Also, there were old gentlemen and ladies learning to cope with hip replacements (by artificial stuff), and young people, mad as stink at fate, because they needed knee replacements (more artificial stuff). Are they all synthetic now?O'Leary_{May 20, 2010
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The level of sensationalism and overstating of the claims of any piece of work is directly proportional to the arrogance and egos involved. Venter is notorious for his lack of humility, and the press is willingly complicit in over-hyping the "synthetic" aspect of this work.Gage_{May 20, 2010
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If something is going to be called “synthetic,” shouldn’t the whole of it be synthesized and not merely a minuscule portion of it?
You could say that the cell into which the DNA was inserted wasn't a fully synthetic cell, but that its descendants - especially its indirect descendants in the second and later generations - have been "bootstrapped" away from the hybrid organism and so are fully synthetic. And indeed Synthetic Genomics talks about "boot[ing] up" in the linked announcements. But see "Reflections on Trusting Trust" for a famous illustration of the limits of bootstrapping. And Synthetic Genomics' knowledge and understanding of the phenotype produced by the reproduction of a bacterium containing its artificial genome is much less detailed and complete than the insight a programmer has (or thinks she has) into the workings of the C compiler produced when she compiles her C source code for a C compiler using an existing C compiler whose object code she hasn't studied exhaustively. So the claim that Mycoplasma mycoides is a fully synthetic organism is much further from the mark than the corresponding claim about a C compiler produced by the mechanism described above, even though there are surely no Trojans in M. capricolum specifically intended to hoodwink Synthetic Genomics. (In any case it's not clear that 'synthetic' is the mot juste here.) "WHAT I CANNOT UNDERSTAND" ...anonym_{May 20, 2010
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lars, I agree it is a breathtaking step forward, I just have a huge problem with Venter's "sin of omission" in clarifying just how constrained he was in following strict protocol, nor in his lack of admission that he did not actually create any new genes (or proteins). Shoot even for the larger pieces of DNA they had to use yeast for the final steps of assembly. As Dr. Dembski asked: "If something is going to be called “synthetic,” shouldn’t the whole of it be synthesized and not merely a minuscule portion of it?"bornagain77_{May 20, 2010
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Interesting too that even the synthetic genome is mostly copied from a natural one, so most of the design in it is not Venter's. Nevertheless, this does sound like a significant step to me: If they can consistently get cells to reproduce "normally" after a synthetic genome is inserted, they have a lot more power to then tweak the genome according to design goals.lars_{May 20, 2010
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What a sham. The grand claim that they started with 4 bottles of chemicals and WAA LAA a synthetic genome popped out leaves out quite a few important steps: Just the first step of assembly is as such: The capacity to affect the chemical synthesis of DNA has been a long time in the making. This process refer to the nonbiological, chemical production of small segments of DNA, called oligonucleotides.,,,,,,,,,,,,,, The specific steps for the chemical synthesis of oligonucleotides include: 1. Attaching the first nucleotide to a solid support after deblocking the appropriate group. 2. Removing the appropriate protecting group from the attached nucleotide in the first position to allow it to react with the next nucleotide in the oligonucleotide sequence that has had the appropriate blocking group removed from it. 3. Allowing the nucleotides to react under carefully controlled conditions. 4. Adding a chemical cap to any unreacted oligonucleotides. (This step is necessary because a small percentage of the nucleotides don’t react with the attached oligonucleotide chains.) 5. Stabilizing the linkage between the two nucleotides with an oxidizing agent 6. Washing away unreacted nucleotides. 7. Repeating steps 2 through 6 until the entire oligonucleotide has been made. 8. Cleaving the oligonucleotide from the solid support. 9. Removing all the blocking groups. 10. Purifying the oligonucleotide. This step is absolutely critical to ensure the accuracy of the biochemical recombination steps during the whole genome assembly process. Because the technology to chemically synthesize oligonucleotides has been in place for several decades, it’s easy for scientists to take it for granted. Today, the chemical production of oligonucleotides is virtually an automated turnkey process. Yet, it’s important not to overlook the remarkable technical accomplishment this capability represents. If it wasn’t for the dedicated efforts over the course of the last half century of some of the best scientists in the world (including Nobel Laureates), to develop and improve methods to chemically make DNA, Venter’s team would have no hope of affecting the complete synthesis of the M. genitalium genome. http://www.reasons.org/tnrtb/2009/01/29/ http://www.reasons.org/tnrtb/2009/02/05/a-case-for-intelligent-design-part-3-of-4/bornagain77_{May 20, 2010
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I found this quote from Craig Venter interesting: "When we look at life forms, we see fixed entities, ... But this shows in fact how dynamic they are. They change from second to second. And that life is basically the result of an information process. Our genetic code is our software." I write software for a living. I wonder how much the original genetic "coder" got for making life?Protagonist_{May 20, 2010
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Venter said: it's the first species on our planet to have it's parent being a computer He implies that it's the 1st intelligently designed species. It's more like the 1.5 millionth. Quote is from video in the BBC's report: http://news.bbc.co.uk/1/hi/science_and_environment/10132762.stmhalo_{May 20, 2010
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Bill, Glad to see you are making the point. It seems to me that it is like saying because I have added a new software program I have built a new computer. The genome may be a library of instructions, but a living cell is still necessary to read and act on those instructions, just as I need a pre-existing intelligently designed computer to read the new program I uploaded. Without the computer (cell), the software (genome) is lifeless. I fail to see what the big deal is. Humans have been manipulating the genome through mate selection, selective breeding, etc. etc. for as long as we have been alive. So now we can change the program library more directly, but we are still dependent on the existing living cellular machinery to read and implement the program.idchild_{May 20, 2010
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