Posted by jlwile on May 30, 2010
Craig Venter and his team have built the genome of a bacterium from scratch and incorporated it into a cell to make what they call the world’s first synthetic life form.
It’s an amazing feat of biotechnology, and the process he and his team produced might result in some incredible applications down the road. What I find interesting about the process, however, is how well it illustrates that life simply cannot come about as the result of random chemical reactions guided by some sort of selection process. In other words, this stunning achievement really demonstrates the impossibility of abiogenesis.
The scientific report of Venter and his team’s accomplishment can be found on the website of the journal Science1. I finally got around to reading it, and it is truly fascinating. When you look at the details of how they created their “synthetic” life form, you find that Venter and his team relied on already-living systems not once, not twice, but a total of three times. Without relying on these already-living systems, they would not have been able to produce their “synthetic” cell.
So what exactly did they do, and how did they rely on living systems three different times in order to do it? Well, they wanted to build a genome that they knew would work, so they decided to build one that had already been sequenced. They chose a bacterium called Mycoplasma mycoides, which has a small genome, even for a bacterium. Indeed, bacteria from this genus are often studied to determine what the “minimal” genome for life could possibly be. By starting with the sequence of an already-living bacterium, Venter and his team are technically relying on an already-living system, but I won’t count that. After all, they needed to produce a genome that was actually functional, so it makes sense to copy one from a living organism.
How did Venter and his team “make” this genome? That’s where we find the first instance in which they relied on an already-living system to get the job done. They ordered small chunks of DNA (they call them “cassettes”) from Blue Heron Biotechnology, and then they used yeast cells in a three-step process to stitch those chunks together into a full genome. This is actually discussed in a paper previously published in the journal Science.2
Like bacteria, yeast can have DNA in small, circular units called plasmids. These plasmids are separate from the yeast’s chromosomes, and yeast cells have the chemical machinery to allow them to replicate independently of the DNA in the chromosomes. Venter and his team ordered the DNA chunks to have sequences that would force the yeast cells’ chemical machinery to “stitch” the chunks into bigger chunks to form a plasmid.
Now why order DNA in small chunks and then force the yeast cells to stitch them together? Because human science is limited in the amount of DNA it can produce. Currently, human science and technology can produce small segments of DNA artificially, but when the strand of DNA becomes moderately long, it becomes unstable, and the strand breaks. Thus, scientists don’t have the capability of making an artificial genome. They only have the capability to make small chunks of an artificial genome. So Venter and his team employed yeast cells to do what human science cannot do: stitch small chunks of DNA into a complete genome.
Now remember, this technique was published in a previous paper, and that paper was published two years ago. Why didn’t Venter and his team make big headlines back then? Because when they produced their genome this way, it wouldn’t work. In the end, they concluded that the “synthetic” genome they made had too many mistakes in it. In this paper, they figured out a way to avoid making those mistakes. How? That’s where they relied on an already-living system for the second time.
The chunks of DNA were stitched together inside the yeast cells in three separate steps, each time producing a larger strand of DNA. To make sure there were no serious mistakes, they took some of the DNA produced after the second step (strands that were 100-kb long) and mixed it with the DNA from living Mycoplasma mycoides bacteria. As they say in their current paper:
By mixing natural pieces with synthetic ones, the successful construction of each synthetic 100-kb assembly could be verified without having to sequence these intermediates.
In the end, then, they used DNA they knew was functional (because it came from a living bacterium) to test their “synthetic” DNA. This revealed several problems, which they could then go back and fix. This was apparently a painstaking process. At one point, they say they were delayed by many weeks because of the deletion of a single base pair.
So…once they used a living system to stitch together the DNA (because human science cannot do that) and then used a living system to test the stitching after step two, what did they do? They transplanted the “synthetic” DNA into a living bacterium from a slightly different species, Mycoplasma capricolum, whose DNA had been removed.
Why did they do this? Because life is more than just DNA. In other words, a genome is not something that is alive. Think of it as a complex computer program. A computer program can make a computer do some amazing things, but by itself, a computer program can’t do anything. In order to do something, it must be installed in a working computer. In the same way, DNA by itself is not alive. However, it can make a living cell do a lot of great things. Thus, in order to get their “synthetic” DNA to do something related to life, Venter and his team had to put it into an already-living cell.
Of course, they had to do a lot of engineering to accomplish this transplant, because cells recognize foreign DNA. Thus, even though the recipient M. capricolum cell had no DNA, it had the chemical machinery to detect foreign DNA and destroy it. Venter and his team tried to disguise their “synthetic” DNA to look like M. capricolum DNA. To further ensure success, they then destroyed all traces of the enzyme that M. capricolum would have used to destroy foreign DNA.
Now please don’t get me wrong. I am not minimizing what Venter and his team have accomplished. It is a truly remarkable achievement. In fact, part of what makes it so remarkable is how much they relied on living systems to get the job done. In essence, they used living yeast cells to do what no human scientist can do, then they used living bacterial cells to error-check the yeasts’ work, and then they used a living bacterial cell as a recipient for their DNA, because otherwise, it would not have been able to function.
This truly stunning achievement, then, shows just how dependent life is on the existence of life. To make life, you need life. Even the best human science has to offer relied on already-living systems three times in order to “make” a living bacterium.
This just confirms how the concept of abiogenesis is not science. It’s fantasy.