Has Life Been Made From Scratch? by Joe Deweese, Ph.D.

http://apologeticspress.org/APContent.aspx?category=9&article=3597

Has Life Been Made From Scratch?

by	Joe Deweese, Ph.D.

Some news sources are making the claim of creating life from scratch. They assert that scientists have been able to make life from “four bottles of chemicals” (Sanders, 2010). The statements are made in reference to the work of Dr. Craig Venter and colleagues at the J. Craig Venter Institute (JCVI) when the team announced the success of efforts to replace the chromosome of a bacterial cell with a “chemically synthesized genome” (Gibson, 2010). The transplantation of a bacterial genome is an impressive accomplishment, one that may mean very little to most people, but did the scientists truly make life from scratch?
In order to answer the central question, it is important to understand the process for design, synthesis, and assembly of the genome. First, the DNA sequences that encode the genome of the bacterium Mycoplasma mycoides were manipulated on a computer. The changes made in the genome included deleting some nonessential DNA sequences, inserting a few extra genes, and inserting “watermark” sequences that would be used to verify that the transplant was successful and DNA in the organism was the modified DNA. Interestingly, these watermarks include coded sequences with names and e-mail addresses, a creative step that provided a unique tracking capability for the procedure.
Second, the team partnered with a company to synthesize the DNA in ~1080 base-pair sequences. (DNA consists of two complementary strands of bases that “pair up” to make a double-stranded or duplex molecule.) It took 1000 of the sequences to make the entire set of DNA that ultimately would be required to provide the instructions for asexual reproduction of the bacteria. Additionally, the scientists were challenged with the complex task of assembling the DNA fragments into a much larger one million base-pair (Mbp) synthetic chromosome. (By comparison, there are three billion base pairs of DNA in one copy—23 chromosomes—of the human genome). The ~1000 fragments of ~1000 base pairs each were “stitched” together inside yeast cells through a process of DNA recombination which is inherent to the cell. The team first constructed ~10,000 base pair DNA sections and then ~100,000 base pair sections before stitching the final ~1 Mbp chromosome together. Clearly, the recent publication chronicles a complex series of events that results in the reporting of the design, synthesis, and assembly of the requisite information for controlling continuous self-replication.
The assembly of the final artificial bacterial chromosome with the imbedded natural genes and the “watermark” sequences was confirmed using several molecular techniques, and the chromosome ultimately inserted into a bacterial cell of a closely related yet distinctive species (Mycoplasma capricolum) where the original DNA had been expunged. The recipient bacterial cell (M. capricolum) had intact proteins and RNA molecules, which included all of the required, preformed, and functional enzymes to support self-replication once the new chromosome was inserted. Researchers grew the cells through a number of cell divisions, which eventually diluted out, degraded, and replaced the original M. capricolum proteins. Thus, the researchers were left with a “synthetic” cell from M. capricolum that was now producing proteins from a “synthetic” DNA molecule coding for genes originally from M. mycoides.
Overall, the technical expertise demonstrated in the report is quite an impressive accomplishment. DNA synthesis, cloning, and recombination techniques are frequently used but have never been applied on the scale of millions of base pairs. Furthermore, the experiment demonstrated that there is a minimal set of genes that can be used to run a basic bacterial cell. The researchers from JCVI had previously demonstrated that there is a “minimal gene complement” that would sustain the life of another bacterium, Myscoplasma genitalium (Fraser, 1995). In the Fraser report, the researchers deleted ~100 of M. genitalium’s ~480 genes one at a time and found it could still survive (but could not survive when multiple genes were deleted simultaneously). The recent work of JCVI helps to support the concept that there is a minimal set of genes that can support life resulting in the interesting question: how could “simpler” life exist (much less develop) with fewer genes than the “minimal gene complement”? A question that is controversial—and, to say the least, has enormous implications for whether life could develop from nonlife.
There are several important considerations to bear in mind when considering the impact of the study, namely: 1) the DNA sequences for all of the genes were already designed and synthesizers were used to generate the actual DNA; 2) the recipient cell contained preformed enzymes and other factors needed to support life—the cell was not “made from scratch”; 3) the sole replaced component in the recipient cell was the “instructions,” that is, the DNA; and 4) the researchers relied on living systems to help assemble the chromosome into its final form through the stitching process in yeast described above.
The JCVI experiment is similar to what happens when an egg is fertilized. The proteins and other factors are already present in an unfertilized egg, just as they were in the recipient bacterial cell. Upon fertilization, the DNA from the mate is joined together with the DNA already in the egg, allowing growth and development to begin. The important thing in both cases is that it is not simply the DNA alone that is needed. Instead, a new living cell requires many preformed proteins and RNA molecules in order to support and sustain life.
One overly simplistic yet accurate analogy compares the JCVI process to that of taking the hard drive out of one computer and replacing it with a second hard drive that was set up separately (“News to Note,” 2010). In the hard drive analogy, the computer and all of its components already exist, and only the hard drive is replaced. In the case of the JCVI experiment, the cell and its components already exist, and only the DNA is replaced. While simple in its description, it is important to note that the experiment overcame numerous technically difficult steps before finding success. Moreover, it is important to remember that even the DNA was adapted from a living organism. In other words, the “hard drive” was “programmed” using pre-existing “software.”

CONCLUSION

It is true that this experiment is very impressive, and the challenges that were overcome should not be dismissed lightly. In fact, the results provide evidence for the complexity of life. The JCVI researchers started with the genome of an organism that is among the smallest known to man. It contains as few genes as possible to sustain life. Yet, it was a long (over 10 years) and very expensive (~$40 million) process to copy the genome of this simple organism, assemble the copy into an intact chromosome, and insert this chromosome into an already living cell (Pennisi, 2010). It is fascinating how much effort went in to this procedure—which really did not create new life; rather it simply modified existing molecular machinery that is required for life.
While there are many who fear that the JCVI process may open the door to great and terrible power in the hands of scientists, it is likely an unwarranted fear for what will happen with the technology. Similar to all of nature, in the right hands and with pure motives, it may at some point be used for good or, at the whim of corrupt goals, could generate evil results. Ultimately it must be acknowledged that God is in control, and the evidence of His handiwork is apparent in even the simplest of microorganisms.

REFERENCES

Gibson D.G., Glass J.I., Lartigue C., Noskov V.N., Chuang R.Y., Algire M.A., Benders G.A., Montague M.G., Ma L., Moodie M.M., Merryman C., Vashee S., Krishnakumar R., Assad-Garcia N., Andrews-Pfannkoch C., Denisova E.A., Young L., Qi Z.Q., Segall-Shapiro T.H., Calvey C.H., Parmar P.P., Hutchison C.A. 3rd, Smith H.O., Venter J.C (2010), “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome,” Science, May 20, http://www.sciencemag.org/cgi/content/abstract/science.1190719.
Fraser C.M., Gocayne J.D., White O., Adams M.D., Clayton R.A, Fleischmann R.D., Bult C.J., Kerlavage A.R., Sutton G., Kelley J.M., Fritchman R.D., Weidman J.F., Small K.V., Sandusky M., Fuhrmann J., Nguyen D., Utterback T.R., Saudek D.M., Phillips C.A., Merrick J.M., Tomb J.F., Dougherty B.A., Bott K.F., Hu P.C., Lucier T.S., Peterson S.N., Smith H.O., Hutchison C.A. 3rd, Venter J.C. (1995), “The Minimal Gene Complement of Mycoplasma Genitalium,” Science, October 20, 270(5235): 397-403.
“News to Note” (2010), Answers in Genesis, May 22, http://www.answersingenesis.org/articles/2010/05/22/news-to-note-05222010.
Pennisi, E. (2010), “Synthetic Genome Brings New Life to Bacterium,” Science, May 21, vol. 328, http://www.sciencemag.org/cgi/content/summary/328/5981/958.
Sanders, Laura (2010), “Genome from a Bottle,” Science News, May 20, http://www.sciencenews.org/view/generic/id/59438/title/Genome_from_a_bottle_.