Science & Faith
11/14/13 at 09:52 AM 18 Comments

Intelligently Designed in the Lab: Biotech Guru Craig Venter Asks "What is Life?"

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Apple Maps (Mavericks) 3D rendering of the Venter Institute (showing early construction)

What is life? How did it originate? If we could build a simple organism artificially in the lab, would we better understand the answers to these questions? Craig Venter thinks so, and he often speaks in public as if he and his scientific team were striving to do just that, and much more.

Biotech guru Craig Venter addressed such pressing issues in his October 2013 book, Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life. Meanwhile his new San Diego biotech facility celebrated its grand opening on November 9, 2013. Former Vice President Al Gore graced the event with a speech (see the party pics here). "We cannot think of a more appropriate person to commemorate the opening of our net zero carbon, ultra green genomics lab than Al Gore," announced Venter. (Venter is probably unaware that sea ice in the Antarctic has increased inconveniently by about one percent per decade since 1979, despite Al Gore's Nobel-Peace-Prize-winning expectations to the contrary).

What is Venter promoting at his institute? More than just science and technology.

Founded by J. Craig Venter, Ph.D., the [multi-site] JCVI is home to approximately 250 scientists and staff with expertise in human and evolutionary biology, genetics, bioinformatics/informatics, information technology, high-throughput DNA sequencing, genomic and environmental policy research, and public education in science and science policy.

While in Seattle on October 23 promoting his new book, Venter described life at the cellular level using the language of information technology. He said, as Casey Luskin reports, that the cell is a "biological machine," full of "protein robots" which are "not simple robots." DNA is "software" that contains "digital information" or "digital code." He even announced to the audience at Seattle's Town Hall that "life is a DNA software system." That's one influential man's answer to the much debated question: what is life?

Wired Magazine's November 7 interview of Venter (2 days before that wild JCVI San Diego party with Al Gore) revisited the "life" question.

Wired: So you view DNA as the software of life?

All the information needed to make a living, self-replicating cell is locked up within the spirals of DNA's double helix. As we read and interpret that software of life, we should be able to completely understand how cells work, then change and improve them by writing new cellular software.

The software defines the manufacture of proteins that can be viewed as its hardware, the robots and chemical machines that run a cell. The software is vital because the cell's hardware wears out. Cells will die in minutes to days if they lack their genetic-information system. They will not evolve, they will not replicate, and they will not live.

Despite failing to mention epigenetic biological information that is beyond DNA, Venter does express an otherwise correct understand of the central role of DNA's code to construct living organisms. The software of life can build its own hardware, which is more than just proteins. Biological information is also needed to tell the cell how to arrange proteins and other molecules into various cellular subsystems (molecular machines), and yet higher layers of biological hardware systems, from the cellular level on up. As to the evolution of life, Venter avoids mentioning the extensive evidence for natural limits to biological change, which Stephen Meyer explores in Darwin's Doubt.

Wired continues the interview with Venter:

Of all the experiments you have done over the past two decades involving the reading and manipulation of the software of life, which are the most important?

I do think the synthetic cell is my most important contribution. But if I were to select a single study, paper or experimental result that has really influenced my understanding of life more than any other, I would choose one that my team published in 2007, in a paper with the title Genome Transplantation in Bacteria: Changing One Species to Another. The research that led to this paper in the journal Science not only shaped my view of the fundamentals of life but also laid the groundwork to create the first synthetic cell. Genome transplantation not only provided a way to carry out a striking transformation, converting one species into another, but would also help prove that DNA is the software of life.

Wired: What has happened since your announcement in 2010 that you created a synthetic cell, JCVI-syn1.0?

At the time, I said that the synthetic cell would give us a better understanding of the fundamentals of biology and how life works, help develop techniques and tools for vaccine and pharmaceutical development, enable development of biofuels and biochemicals, and help to create clean water, sources of food, textiles, bioremediation. Three years on that vision is being borne out.

In 2010 a BBC reporter summarized the steps that Venter's team of scientists took to make a "synthetic cell" that they called "JCVI-syn1.0."

  1. The scientists "decoded" the chromosome of an existing bacterial cell - using a computer to read each of the letters of genetic code.
  2. They copied this code and chemically constructed a new synthetic chromosome, piecing together blocks of DNA.
  3. The team inserted this chromosome into a bacterial cell which replicated itself. Synthetic bacteria might be used to make new fuels and drugs.

Because Craig Venter in late 2013 is still trumpeting his biotech team's 2010 "synthetic cell" laboratory creation as if it were one of the greatest breakthroughs in modern science, we should pause to reflect on just what they did in 2010 and its implications for the origin of the first life.

In the original research paper that reported the work of Venter and his colleagues, we learn how they copied to a computer the information stored in the DNA of the bacterial species Mycoplasma mycoides, and then chemically (artificially) reconstructed that bacterial DNA to form a "synthetic" chromosome that housed the genome of the original wild bacterial species (with some modifications explained below). This synthetic chromosome created outside of a living cell had the genomic (DNA) information (transferred by computer) from the original bacteria. They then inserted this synthetic chromosome into another closely related species of bacteria whose own DNA had been artificially removed. Basically they hijacked the cellular system of another bacterial species (Mycoplasma capricolum minus the DNA of that bacteria) to bear the genome (DNA) of the original bacterial species Mycoplasma mycoides. The abstract of their paper reported:

We report the design, synthesis, and assembly of the 1.08–mega–base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including “watermark” sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.

The “watermark” sequences that they inserted into the synthetic chromosome included names of project scientists, famous quotations, etc. (spelled out in DNA code), as Luskin explains at the end of his commentary below:

And note also that they had to import the code into a pre-existing bacterial cell [i.e., from the species Mycoplasma capricolum]. That means that any epigenetic information that exists outside of the DNA was borrowed from the bacterial cell [of Mycoplasma capricolum] that they inserted the chromosome into -- not created from scratch. As Elizabeth Pennisi's newspiece in Science on the research observed:

"That's a pretty amazing accomplishment," says Anthony Forster, a molecular biologist at Vanderbilt University in Nashville, Tennessee. Still, he and others emphasize that this work didn't create a truly synthetic life form, because the genome was put into an existing cell.

Even Craig Venter (to his credit) acknowledges, "We didn't create life from scratch." That's an understatement.

The Science newspiece also observed, "So that the assembled genome would be recognizable as synthetic, four of the ordered DNA sequences contained strings of bases that, in code, spell out an e-mail address, the names of many of the people involved in the project, and a few famous quotations." If these bugs are let loose and then rediscovered in 1000 years, will researchers be unjustified in inferring intelligent design when they find e-mail addresses, names, and famous quotes encoded into the genome of this bacteria?

Jim Collins, professor of Biomedical Engineering, Boston University is quoted in the journal Nature with a realistic assessment of what Venter's team accomplished:

This is an important advance in our ability to re-engineer organisms, not make new life from scratch. Frankly, scientists don't know enough about biology to create life. Although the Human Genome Project has expanded the parts list for cells, there is no instruction manual for putting them together to produce a living cell. It is like trying to assemble an operational jumbo jet from its parts list — impossible. Although some of us in synthetic biology have delusions of grandeur [e.g., Venter], our goals are much more modest.

Running with the airplane analogy, we could roughly say that Venter's team copied the assembly instructions for all the airplane parts of one model of airplane (stolen from a factory that made that airplane), and then inserted that information into the information processing center of another airplane assembly factory that was designed to construct a slightly different model airplane. The result: the second airplane factory began to output airplanes of the other model airplane, except for sneaky watermarks like "Craig Venter did this" that would appear on various screens in the cockpit.

Venter and colleagues did not create "artificial life" from non-living chemicals. Rather, they plagiarized the genome of one species of bacteria, digitized it on a computer, then chemically reconstructed that genome (with watermarks added to document their achievement) and inserted it into another DNA-vacated bacterial cell. It would take an immensely larger knowledge base and techological innovation to create a single celled organisms from scratch (from non-living materials). Even if one day scientists accomplish such an amazing achievement, it would only reinforce what Stephen Meyer argued in his book Signature in the Cell: how the transition from non-life to life requires the guidance of intelligent agency.

Even Venter admitted in his November 2013 inteview with Wired Magazine that the most rigorous sense of creating life "from scratch" in the laboratory would mean the following:

If we apply the same strictures to creating life "from scratch", it could mean producing all the necessary molecules, proteins, lipids, organelles, DNA and so forth from basic chemicals or perhaps even from the fundamental elements carbon, hydrogen, oxygen, nitrogen, phosphate, iron and so on.

But even this futuristic biotech scenario is only part of what is required to create life artificially from scratch. It imagines how scientists might get all the parts of a minimally complex living cell together in one place at one time. However, these future scientists would have to know and control much more than that to get the job done. They would have to known all the biologically encoded higher level assembly instructions that tell those molecular parts how to get coordinated into an actual working-living cell. We are very far from accomlishing this breathtaking feat of nanotechnology. Visionaries like Venter are gifted at raising support for these dreams, but Venter needs to more accurately assess what we can and cannot accomplish in the near future.

Recommended further reading:

1. Casey Luskin's analysis of Venter's Seattle talk. Especially note this paragraph:

Venter discussed his research creating such a "synthetic chromosome," and thinks it's important to insert watermarks into them so as "not to confuse evolutionary biologists." I found this curious, and I guess he said it because he knows evolutionary biologists assume nothing is designed, and would therefore assume that even a synthetic chromosome wasn't designed if you don't include the watermark thus evidencing its non-natural origin.

2. What are Darwinian Evolutionists to Make of Craig Venter? 

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