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J. Craig Venter,  Digital Life and Intelligent Design

Sometimes, when you read a book by a great scientist, there are some special paragraphs, that are really intelligible by the layperson, like myself. And it is these few special paragraphs that make it all worthwhile.

Such is the case with J. Craig Venter's new book, "Life at the Speed of Light, from the Double Helix to the Dawn of Digital Life."

http://m.indigo.ca/product/books/life-at-the-speed-of/9780670025404?ikwid=life%20at%20the%20speed&ikwsec=Home

Here are a few quotes from the book, that for the layperson, are some of the "Ah Ha" moments, that can really teach us something new. And I might add ties in to some great arguments for intelligent design.

From the beginning of Chapter 4, Digitizing Life, Venter writes:"This is now the era of digital biology, in which the proteins and interacting molecules in a cell can be viewed as its hardware and the information encoded in its DNA as its software. All the information needed to make a living, self-replicating cell is locked up within the spirals of its double helix. As we read and interpret that code, we should, in the fullness of time, be able to completely understand how cells work, then change and improve them by writing new cellular software. But, of course, that is much easier to say than to do in practice: studies of this DNA software reveal it to be much more complex than we had thought even a decade ago."

From the beginning of chapter 7, Venter writes:"If I were to select a single study, paper, or experimental result that has influenced my understanding of life more than any other, I would without any doubt choose one above all others: "Genome Transplantation in Bacteria: Changing One Species to Another." The research that led to this 2007 paper in Science not only shaped my view of life but also laid the groundwork that made it possible to create the first synthetic cell. Genome transplantation not only provided a way to carry out a striking transformation but would also help prove that DNA is the software of life."

After being one of the scientists at the forefront of the Human Genome Project, Venter wanted to, as a "proof of concept", sequence the genome of a bacterium, so accurately, that the code now residing digitally on his office computer, could be artificially recreated in the laboratory, as a new DNA molecule. Now it was a matter of "Genome Transplantation in Bacteria" and getting the "artificial" genome to be "booted up" by the waiting laboratory prepared bacterium.

It is a truism, that world views "change the world" and Mr. Venter "takes sides" by suggesting that anything other than atheism is "vitalism." Mr. Venter writes, "Our experiments did not leave much room to support the views of vitalists or those who want to believe that life depends on something more than a complex composite of chemical reactions." (Chapter 7, Page 109.)

Not so Mr. Venter! For many Christians, it is like your extreme sports, this extreme logic; that obviously human beings did not write the DNA software of life; some other intelligence did. And this extreme logic, for many of the reasons you yourself have discovered in the lab - Even if the genome was simple, the fact that it uses many computer programming methods, such as a gene in biology is similar in function to a code object in computer programming (both accomplish a specific task and help make code reusable. ) - is good scientific evidence that the genome was designed, by an intelligence, "at least beyond our pay scale." Keeping in mind, that the DNA software, together with the coordinated complexity of the design of the computer hardware (the ribosomes etc.) to read it, is the hallmark or "watermark" of intelligent design.

http://m.indigo.ca/product/books/signature-in-the-cell-dna/9780061472794?ikwid=signature%20in%20the%20cell&ikwsec=Home

Always keeping an open mind, that this other intelligence could be coding in parts, using some laws of nature we have not even discovered yet. But nothing "vitalistic" about this, just the humility to assume that human intelligence is probably not the only source, or even the best source, of intelligence in the universe.

But enough of this "philosophy stuff" (important as it is) and let's get back to the lab, and the drama of "booting up" the first "proof of concept" - taking from the office computer a digitized copy of a working bacterial genome, and recreating it chemically in the lab as "bootable chromosomes" that can drive the waiting hardware of existing bacteria.

From chapter 8, Venter writes:

"In retrospect it's clear that we were very close to success, though it did not feel so at the time. After running all the controls we were convinced that a design or sequence error must have managed to slip past the various checks we had made during genome synthesis. Because we had sequenced the DNA we assumed that the error must have occurred in one of the original sequences that we had used in the genome design. In order to check our code we had to create the biological equivalent of what the developer of a computer application would recognize as debugging software. The operating system of a modern computer is vast, running to tens of millions of lines of code, and over the decades engineers have developed smart debugging programs to aid in finding faults.

Vladimir Noskov, a staff scientist in the Synthetic Biology & Bioenergy Group at the JCVI, Maryland, was our resident yeast guru. Noskof had graduated from St. Petersburg State University, Russia, and then went on to a doctorate there in yeast genetics. After spending five years in Japan studying chromosomal DNA replication and a "checkpoint" in the yeast cell cycle, where DNA surveillance and repair is carried out, he worked at the National Institutes of Health, Bethesda. There, in the Chromosome Structure and Function Group, Noskov invented several applications for a technique to manipulate large pieces of DNA in yeast, known as transformation-associated recombination (TAR) cloning, which offers advantages over an older method that relies on what are called yeast artificial chromosomes, or YACs.

For our biological debugger we decided to start by verifying the eleven 100,000-base-pair segments. Noskof, using TAR cloning, constructed equivalent-size segments from the native M. mycoides genome so that we could independently substitute each one with a synthetic segment to see if they would support life. From these complex experiments we found all but one of the eleven 100kb synthetic segments was compatible with life. For final proof Dan Gibson constructed a hybrid genome with ten synthetic segments and one native segment and obtained successful transplants.

Having established which segment contained an error or errors that did not support life, we sequenced the DNA once again, this time using the highly accurate Sanger sequencing method, and found that there was a single base-pair deletion. If this sounds as trivial as writing "mistke" instead of "mistake," equating nucleotides to individual letters is slightly misleading, in the sense that DNA code is read three nucleotides at a time, so that each three-base combination, or codon, corresponds to a single amino acid in a protein. This means that a single base deletion effectively shifts the rest of a genetic sentence that follows, and hence the sequence of amino acids that the sentence codes for. This is called a "frameshift mutation"; in this case, the frameshift occurred in the essential gene dnaA, which promotes the unwinding of DNA at the replication origin so that replication can begin, allowing a new genome to be made. That single base deletion prevented cell division and thus made life impossible.

Once we had found the critical error, we were able to reassemble the 100kb segment correctly and used yeast to reassemble the entire genome. We were now ready once again to attempt the genome-transplantation experiment.

(Note: The synthetic genome had been modified so that a bacterial colony run by this genome would turn bright-blue.)

... Finally, very early on Monday morning, (the petri dishes were removed from the incubator) ...There, a little off the center of one plate, was one-and only one- bright-blue colony of cells...

We had come such a long way, suffered so many failures, so many years of efforts of trial and error, of problem-solving and invention. At last, it seemed that all the effort had finally paid off."

Let's enjoy and note, two more computer programming methods used by the genome as mentioned in the above quote. Keeping in mind the central thesis of this intelligent design argument is that even if the DNA software of life were simple, the fact that this software uses many computer programming methods, is good scientific evidence that the genome was designed. One is the built in code debugging routines or EDAC (Error Detection and Correction) of DNA repair enzymes to insure that the code, when copied, remains intact. And that not even one base pair is dropped, causing the rest of the three letter codons, to code for gibberish. The other computer coding method is "simply" the use of "file headers" and "end of file marks" to ensure the cellular hardware, begins and ends, reading the gene codons, at the right spot.

I want to say to Mr. Venter that I greatly respect the work and achievements in the lab, of great scientists like himself and his team, and I take it as seriously as he does, as proof of concept.

What makes a computer? An intelligence makes a computer, whether electronic, biological, or otherwise.

P.S. Actually, Mr. Venter at least hints at intelligent design when he writes (from Chapter 9, "Inside a Synthetic Cell"), "Whether or not (the first cells) came from another planet, through the process known as panspermia, or were spread by intelligent life forms via what Francis Crick called "directed panspermia," the ultimate origin of the first cells remains a mystery." The point is, even great scientists like Mr. Venter and Francis Crick, when analyzing the coordinated complexity of the DNA software and the many machines of the first cellular hardware, consider other than purely natural causes for the design and proliferation of the first life.

Why then do we not include the above as evidence for intelligent design in the curriculum of high school biology science class? I guess because it would mean the National Center for Science Education

 http://ncse.com/

capitulating that the design view is good science, and based on good scientific evidence, after all.

P.P.S. Ok, back to the "philosophical stuff," (it is important.) Mr. Venter refers to the classic book "What is Life" by the physicist Erwin Schrodinger. The DNA software of our life sets in motion a process that is anything but static. What is Life? Life is a fountain. And I can imagine some great intelligence somewhere, taking the "hard drive" of our memories, and "booting it up" as individual persons, children of God, Fountain II. Note, my optimism is based on science, not despite science, and I know, this is what all the young people in high school deserve too. An optimism based on science. And that is what teaching the evidence for intelligent design in the curriculum of high school biology science class can achieve. What makes a computer? An intelligence makes a computer.

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