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“Creating first synthetic life form”

Question: When Venter and Co. create the first synthetic life form, will it have been by intelligent design? Follow-up question: Will they do it from scratch, i.e., from non-biosynthesized materials as had to have happened when life originated, or by generously helping themselves to enzymes and a host of other biosynthesized materials?

Creating first synthetic life form
By CAROLYN ABRAHAM
Monday, December 19, 2005
Globe and Mail Update

http://www.theglobeandmail.com/servlet/story/RTGAM.20051219.wxlife19/BNStory/specialScienceandHealth

Work on the world’s first human-made species is well under way at a research complex in Rockville, Md., and scientists in Canada have been quietly conducting experiments to help bring such a creature to life.

Robert Holt, head of sequencing for the Genome Science Centre at the University of British Columbia, is leading efforts at his Vancouver lab to play a key role in the production of the first synthetic life form — a microbe made from scratch.

The project is being spearheaded by U.S. scientist Craig Venter, who gained fame in his former job as head of Celera Genomics, which completed a privately-owned map of the human genome in 2000.

Dr. Venter, 59, has since shifted his focus from determining the chemical sequences that encode life to trying to design and build it: “We’re going from reading to writing the genetic code,” he said in an interview.

The work is an extreme example of a burgeoning new field in science known as synthetic biology. It relies on advances in computer technology that permit the easy assembly of the chemical bits, known as nucleotides, that make up DNA.

Several scientific groups are trying to make genes that do not exist in nature, in hopes of constructing microbes that perform useful tasks, such as producing industrial chemicals, clean energy or drugs. Dr. Venter and his colleagues are pushing the technology to its limits by trying to put together an entirely synthetic genome.

“We have these genetic codes that we have been determining, so part of the proof [that they encode an organism] is reproducing the chromosome and seeing if it produces the same result,” he said.

Government and scientific bodies in the U.S. have investigated safeguards for the new technology, given its potential to yield new pathogens as weapons of bioterror. Ethicists have raised concerns about humans altering the “nature of nature.”

But proponents feel the many benefits of redesigning micro-organisms to do human bidding far outweigh the risks.

The Venter team is starting small, working to construct a simpler version of the bacteria known as Mycoplasma genitalium, a common resident of the human reproductive tract. They hope to determine the minimum number of genes required to breathe life into an organism.

M. genitalium is a single-cell bacterium with just one chromosome and 517 genes. But the Venter team is paring the recipe down and believes their version will be able to survive with as few as 250 to 400 genes — each of which they are making themselves, one chemical piece at a time.

“I grew up doing that with cars and clocks and radios and things like that,” Dr. Venter said. “You take them apart to understand them and then you try and see if you can reassemble them.”

But even if the team can assemble all of the bug’s 500,000 DNA chemicals (roughly 35,000 has been the record so far), no one knows if the organism will be viable. Will simply synthesizing a chemical sequence spark life?

“Nobody has ever done it before so absolutely it is a key hurdle,” Dr. Venter said.

Dr. Holt, a Vancouver native who worked in the United States with Dr. Venter until 2002, described it as a “chicken and egg” problem.

“You need an egg to make the chicken, but you also need the chicken to make the egg,” Dr. Holt said.

“So the profound problem is what do you do with this DNA once you get it? How do you turn it into an actual organism? You need the genome to encode and make the organism.

“But the way biology works, you need the organism to make the genome.”

Dr. Holt and his UBC group are tackling that very problem.

One option for sparking life in a lab-made genome, he explained, is to transplant the synthetic DNA into the shell of an existing microbe. But unlike a human cell, the genetic material of bacteria is not neatly contained in one nucleus that can be removed and simply replaced with another.

“Their chromosomal DNA is floating throughout the entire organism,” Dr. Holt said.

So the Vancouver group is researching the use of high-voltage electricity to essentially zap open a host bacteria and slowly infuse it with small pieces of new DNA.

No method exists to insert large DNA fragments. The UBC experiment involves breaking down the DNA of Haemophilus bacteria, a bug common to the upper respiratory tract, into 19 separate pieces and inserting it into the shell of an E. coli, commonly found in the human gut.

“That’s the strategy, though we don’t know if it will work,” Dr. Holt said.

“I thought this was one of the most important problems and one that we should get working on here.”

The problem, Dr. Venter said, is worth solving first with bacteria.

Having launched a company called Synthetic Genomics, Dr. Venter believes “the whole world is open” in terms of the commercial applications of being able to build or redesign micro-organisms for specific tasks.

He insists the main goal of his project to build the first synthetic life form, however, is to understand the essence of life, how it evolved and the essential elements that sustain it.

“Here we are trying to understand the human genome with 24,000 some odd genes and 100 trillion cells and we don’t know how 300 or 400 genes work together to yield a simple living cell,” he said.

“So if we ever have any hope of understanding our own genome, we need to start with something we can actually tear apart, break down and rebuild. So we’re starting with a four-cylinder engine instead of a space shuttle.”

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20 Responses to “Creating first synthetic life form”

  1. It seems that the _only_ thing they are doing is constructing a new genome. That’s a momentus achievement, but as Sternberg argued in several papers, contrary to what Darwinists think, the cell is not exclusively generated by the genome. In fact, if anything, the genome is as much influenced by the cell as the other way around. See:

    Genomes and Form: The Case for Teleomorphic Recursivity
    On the Roles of Repetitive DNA Elements in the Context of A Unified Genomic-Epigenetic System

  2. Generously helping themselves to an entire cell minus the DNA!

    But it’s an just an engineering problem to build the cell too. Nothing that can’t be solved with time and money.

    The ostensible path for this technology is first to completely reverse engineer an existing cell and then develop the technology to reprogram it to build whatever you want with atomic precision. It’s all in the 1987 book “Engines of Creation” by K. Eric Drexler. The first assembler will be a coopted bacteria. The second assembler will be more rugged machine built of carbon instead of protein and will be constructed by the first assembler.

    The rate of technologic progress is accelerating. One of the best explanations for the Fermi Paradox I’ve read is that once intelligent life reaches the point where it’s using radio its rate of technologic progress is nearing the point where the slope goes vertical. They call this a technologic singularity where life becomes so advanced they no longer communicate using radio and are as interested in communicating with radio-stage intelligence as we are in communicating with earthworms.

  3. johnnyb,

    Interesting post. I’m a total layman so I hope you’ll bear with me. It looked to me like the genome project failed to deliver trait-specific sequences as per plan. Thus, it was panned by some as a huge disappointment. However, science tends to uncover things even—or especially—as a direct consequence of its “failures,” and the role of the proteins was thus brought forward in a big way.

    I’m not a member and have no access to these academy papers but I take it that Von Sternberg presents evidence (or at least arguments) that protein operations in the cell directly alter DNA sequences. Since proteins have such varied functions, could you class these for us in any way?

    Also, if cellular proteins alter DNA, then I assume extra-cellular actions must be taken into account.

    Taking it a step further, I have read some guys who argue for heritable environmental effects on DNA, perhaps acting through these proteins.

  4. An experiment like this will not open anyones’ heart to ID. These scientists are just too entrenched in the naturalistic paradigm. They most likely will be till the day they die.

  5. How does one get such a high score on the pandas game? My highest so far has been 18,720.

  6. No matter- even if they are to succeed and build something we could define as living, it still wouldn’t be the same as nature. And it wouldn’t be from scratch either…nowhere near it. They’re using natural products within living things to build simple synthetic genes (which they already do), but it’s not playing God in any real manner.

    They’re taking the parts that nature made and putting them together just like nature does. Doesn’t seem like a very big deal to me, and there are major hurdles as the article points out- and many think that there’s no way these hurdles will ever possibly be overcome. Maybe true, maybe not- I don’t think it matters either way.

    What’s the joke about the man having the conversation with God about building something (life maybe) and God does it in a snap and the man tries to use some dirt that God made and God says- get/make your own dirt. Whatever that joke is…

  7. “How does one get such a high score on the pandas game?”

    Use a slower computer. The slower the better. Everything in the game moves proportionately slower including the Think Tank and the munitions. The advantage is that your brain doesn’t go slower so you end up with more time to react.

  8. Lee Strobel made a joke somewhere about two scientist challenging God saying:

    “God we can do anything you can, even create life from scratch.”

    After taking their challenge, God notices that they are gathering up some dirt to extract from it the essential elements for life and says:

    Wait a minute. Wait a minute. Get your own dirt!

  9. I knew I wasn’t imagining that joke!

  10. Josh Bozeman writes:
    “No matter- even if they are to succeed and build something we could define as living, it still wouldn’t be the same as nature…Doesn’t seem like a very big deal to me…”

    Josh, Dude,
    Bill posted this article as an example of how a non-supernatural designer might actually be able to produce life. He wants them to succeed. The more like nature, the better for Bill, as long as they don’t do it via some “son of Miller-Urey” experiment.

    As Bill asked:
    “Question: When Venter and Co. create the first synthetic life form, will it have been by intelligent design?”

    Stay on your own side of the debate, Josh! :-)

    Kidding aside, I’d love to see them succeed. What a gutsy project (even if Ventner as a person is a bit hard to stomach).

  11. Excuse me… It’s Venter, not Ventner.

  12. I would like to make a prediction. If they stick to the effort of trying to create viable life from chemicals alone, they will fail.
    And I DO believe this prediction is consistent with ID theory but not consistent with macro-evolutionary theory.

    From the article:
    “So the profound problem is what do you do with this DNA once you get it? How do you turn it into an actual organism? You need the genome to encode and make the organism. But the way biology works, you need the organism to make the genome.”

    ID says There are some structures in biological systems (and in physics, but that is not an issue here) that appear to have an Intelligent Cause. In ID theory, such systems are said to be “irreducibly complex”. Irreducible Complexity is the chicken & egg conundrum at the micro-biological level.

    “Irreducible Complexity” implies (in my opinion–please correct me if I’m wrong) there is no way to organize raw chemicals so that “life starts”. Both the life and the complex structure to support life either start together at precisely the same moment or there is no start. Life doesn’t evolve out of non-life.

    These scientists may develop a new microbe (if so, more power to them and perhaps useful technologies will result), but they will not do so “from scratch” using only raw chemicals even if zapped with electricity or whatever else they can think of. To form a new microbe, they will need at least one already-living microbe to start with. If they start with a cell or any part of a cell structure from a previously living microbe, then they will not have started “from scratch”.

    Their failure (using raw chemicals alone) will be consistent with ID theory and inconsistent with evololution theory.

  13. No matter what they do, it will most definitely be by design. They do have a business model, don’t they?

  14. Red

    ““Irreducible Complexity” implies (in my opinion–please correct me if I’m wrong) there is no way to organize raw chemicals so that “life starts”.”

    You’re wrong. Irreducible complexity is achievable, routinely in many instances, with intelligent direction and that includes organizing chemicals so that life starts. IC is not impossible without intelligence, it’s exceedingly improbable. When the probability of chance arrangement into an given IC structure exceeds a certain boundary it is virtually impossible. Dembski places that bound somewhat arbitrarily at 10^150 and calls it the universal probability bound. It is a number ostensibly larger than all the subatomic particles in the observable universe.

  15. DaveScot writes:
    “When the probability of chance arrangement into an given IC structure exceeds a certain boundary it is virtually impossible. Dembski places that bound somewhat arbitrarily at 10^150 and calls it the universal probability bound. It is a number ostensibly larger than all the subatomic particles in the observable universe.”

    Dave,

    Probabilities are always between 0 and 1, inclusive. Dembski’s universal probability bound is not 10^150; it’s 1 divided by 10^150.

    And 10^150 is not just “ostensibly larger” than the number of subatomic particles in the universe, it’s hugely larger, by a factor of some 10^70. The number 10^150 is Dembski’s upper limit on the number of “events” that can happen during the time between the Big Bang and the heat death of the universe (or these days, the possible “Big Rip”), not the mere number of particles.

    The reasoning is that the minimum duration of an “event” is the Planck time, which is roughly 1 over 10^43 seconds (Dembski takes it as 1 over 10^45, presumably to be conservative). That means there can be 10^45 events per particle per second.

    Taking a conservative upper bound of 10^25 seconds in the total meaningful life of the universe, Dembski gets 10^45 times 10^25 or 10^70 events per particle during the lifetime of the universe.

    Finally, multiplying 10^70 by an upper bound on the number of particles in the observable universe, 10^80, he arrives at an upper bound of 10^150 total events during the lifetime of the universe.

    By the way, he is now using a variable UPB because the fixed UPB was not universally applicable. He still maintains that the fixed UPB is fine for most practical purposes. See

    http://www.designinference.com.....cation.pdf

  16. Thanks Dave,
    “Irreducible complexity is achievable, routinely in many instances, with intelligent direction and that includes organizing chemicals so that life starts.”
    Now that you mention it, yes of course I see that IC is achievable with intelligent direction, but to arrange chemicals into a structure so that life starts? I question that, but maybe I’m not questioning it on the right grounds.

    For example, a dead microbe right at the moment of death is a complete arrangement of the chemical structures necessary for life. Perhaps the microbe was killed by just enough heat to rupture its cell wall. Perhaps the laboratory scientist was standing by ready to repair the cell wall with an precision-protein micro patch. He applies the patch. At that instant, we have a complete chemical structure for a living microbe. But I don’t think–once the patch is applied–that the microbe would “start back up” again. Would it?

    That is essentially what the genome scientists appear to be trying to do. Except, what the article indicates is they are trying to build a microbe from scratch. But it is the same thing. Let’s say they succeed in completely duplicating every protein and chemical structure of the microbe. Is the artificial microbe going to “start up”? I don’t think it will.

    If the evidence for design in living systems is evidence of real design as opposed to the “appearance of design”, then to look at a living system is like looking at the finished artwork of a renowned painter. Neither the artist nor the tools used by the painter are seen in the finished work. There is a quality in real art that cannot be duplicated. Forgeries are easily detected by experts.

    To carry this analogy one step further…. Great art is often said to have a “life of its own” in it. That is, there is a quality in the finished art that exists apart from the collection of paints and designs. In living systems–if the design is “real”–the “life of its own” in the collection of chemicals is “life”.

    My prediction about the work in Canada is that the “life” will fail to materialize IF they stick strictly to building the microbe from “scratch”. Now if they remove the DNA from an existing microbe and replace it with their own DNA, the microbe might live and might even reproduce. That’s not from scratch in that case.

    So, maybe I’m using the wrong ground for my argument. I chose IC, but you are right: IC is achievable with directed intelligence. ON THE OTHER HAND… Is it REALLY IC if it is non-functional? OK, probably so.

    Can you see my argument, though? On what ground in ID theory COULD I make my argument?

    Thank you for your comments.

  17. KeithS

    “Probabilities are always between 0 and 1, inclusive. Dembski’s universal probability bound is not 10^150; it’s 1 divided by 10^150.”

    Congratulations on correcting a typo. You finally got something right!

  18. KeithS

    “And 10^150 is not just “ostensibly larger” than the number of subatomic particles in the universe, it’s hugely larger, by a factor of some 10^70.”

    Wow. You counted all the particles. How long did that take you?

  19. Red

    “but to arrange chemicals into a structure so that life starts?”

    Sure. Cells do it all the time when one cell divides into two cells. Why should a single cell be able to do something that scientists and engineers (who are themselves collections of cells) cannot? A very important thing about cells is that they demonstrate the feasibility of some nanometer scale construction that is within the limits of the physically possible. This is the proof that at least some of the things envisioned by nanotechnolists are possible. Read Drexler’s book. It’s online and werry werry good.

  20. Dave,
    “Sure. Cells do it all the time when one cell divides into two cells.”
    A piece of the original cell goes with the two new cells. So each cell is starting with a piece of living cell. I stipulate that scientists MAY be able to replace their artificially constructed DNA into a living microbe and see the “new” microbe reproduce, but that will not be like constructing a microbe from scratch.

    “Why should a single cell be able to do something that scientists and engineers (who are themselves collections of cells) cannot?”
    Well again, if the design is “real” as opposed to “illusory”, then we will have a “quality” of the intelligent designer (whoever, whatever he/she/it may be) stamped on the finished product of design (like the smile of the Mona Lisa) something that cannot be duplicated.)

    When we talk about the intelligence exhibited in the construction of the entire universe(!), I just do not think the scientists in Canada (or anywhere) possess that level of intelligence, the level that is exhibited in that quality of a microbe that we recognize as “life”.

    I think the experiment in Canada is a very good test of the principles of Intelligent Design vs. the principles of both NDE vs. the idea that nature itself possesses some naturally occurring purposeful creativity.

    If all anyone has to do to jumpstart a collection of chemicals into a living organism is arrange the chemicals properly, then the “remote probability” argument does NOT refute natural selection/random mutation. Or it leaves wide open the possiblity of nature itself possessing directed intelligence.

    I think the Canadians will fail because I believe the inference of intelligence separate from nature is real not illusory.

    One other note: it occurs to me that “specified complexity” is the ground of my argument. Besides the complex information system we see in DNA, “life–the quality of living” is also a detail of the specification. Simply arranging the DNA properly does not meet all the specifications.