Craig Venter: A Modern Day Prometheus?

 

 You can include a subtitle too

---

 

Craig Venter: A Modern Day Prometheus?   Introduction: References

 

Introduction:

 

In the summer of 2007, a team of researchers at the J. Craig Venter Institute (JCVI) reported that they had successfully transformed one type of bacteria, Mycoplasma capricolum, into another type, Mycoplasma mycoides.  This transformation was achieved by genome transplantation methods by replacing Mycoplasma capricolum's genome with that of Mycoplasma mycoides.  The species of mycoplasmas were specifically chosen because of their relatively small genomes made them easy to work with and were relatively fast growing mycoplasmas (Lartigue C. et al., 2007).  In 2003, Craig Venter's team had successfully created a synthetic genome of the 5, 386 bacteriophage φX174 (phiX), however, this result is much more significant because mycoplasmas are several kilobases larger, ranging from 0.58-1.38 megabase pairs (Lartigue C. et al., 2007).  This result in itself is revolutionary, but Craig Venter in his usual abmitious self wants more; according to him, the ultimate goal of this research is to entirely create an organism from scratch.  However, as expected, this research has been met with much criticism stemming from the ethical implications associated with it.  This article will delve into the specifics of the research and touch on some of the ethical issues that have arisen.

 

 The Wolbachia Infection:

 

A group of scientists at the University of Rochester and the J. Craig Venter Institute made the fascinating discovery of a parasite transplanting its whole genome into its host species in the summer of 2007.  The parasite Wolbachia is believed to have infected the cells of 70 percent of the world's invertebrates (Dunning Hotopp J. C. et. al., 2007). Recently, researchers discovered that the parasite's entire genome has been integrated into a particular host's genome, in this case, the Wolbachia parasite has 'infected' the fruit fly Ananassae.  The discovery sheds light on the phenomenon of lateral gene transfer; ultimately hinting that lateral gene transfer occurs in nature at a much higher frequency than previously believed.  For Craig Venter and his laboratory, it is an example of one of the steps in creating a synthetic cell, the insertion of an entirely different species' genome, occurring in nature (Dunning Hotopp J. C. et. al., 2007).

 

 

The First Steps:

As a first step to creating a synthetic cell, Craig Venter’s research group successfully replaced the genome of Mycoplasma capricolum with that of Mycoplasma mycoides essentially transforming one bacterial specie into another. The technique they employed was genome transplantation as shown in the below:

 

 Image: NYT June 29, 2007

Transplantation:

 

An antibiotic selectable marker gene was initially added to the M. mycoides LC (large colony type) chromosome to allow for selection of living cells containing the transplanted chromosome. M. mycoides LC chromosome was then transplanted into the M. capricolum cells. After several rounds of cell division, no more M. capricolum genes appeared in the bacterial genome and only M. mycoides genes were present (Lartigue C. et al., 2007).

 

Verification:

 

2D gel electrophoresis and protein sequencing were used to show that all expressed proteins were the ones coded for by M. mycoides LC chromosome. Two sets of antibodies each specific to the cell surface of the two cell colonies were reacted with transplant cells. If the transplantation did indeed occur then only the antibodies specific to M. mycoides cell surface proteins will be bound. The new, transformed organisms show up as bright blue colonies in images of blots probed with M. mycoides LC specific antibody. No bright spots appeared when probed with antibodies to M. capricolum (Lartigue C. et al., 2007).

 

Creating the Synthetic Cell:

 

Ultimately, Craig Venter’s goal is to successfully create synthetic cells that take up carbon dioxide from the atmosphere to produce methane that can be used in other fuels. According to Craig Venter this goal should be realized in the next ten years and possibly half that length of time (New York Times, Jun. 29, 2007). Regardless of when this happens, the The JCVI believes that the existence of these synthetic cells will mitigate the effect of global warming and reduce our dependence on fossil fuels.  However, his first big hurdle will be to device a means of creating this synthetic cell. The general idea behind creating a synthetic cell is depicted in the image below:

 

 

 Image: NYT June 29, 2007

 

 

In January of this year, JCVI reported that they had created the first synthetic bacterial genome (Gibson D. G. et. al., 2008). The bacterial genome created was that of Mycoplasma genitalium which approximately 580,000 base pairs in size. Before this report, the largest genome to be synthesized was only 32,000 base pairs in size known as the polyketide synthase gene cluster. This is largely due to the fact that there are several obstacles to synthesizing large strands of DNA: Synthetically adding the nucleotides, adenine, guanine, cytosine and thymine to any chromosome is incredibly difficult. Moreover, as the size of the artificially synthesized DNA gets longer, it becomes more brittle and is hard to work with (Gibson D.G. et. al., 2008). Nonetheless, using very elaborate techniques, the group of scientists at the J. Craig Venter Institute was able to synthesize the M. genitalium genome in its entirety.

 

 

Detailed Methods of Genome Synthesis:

 

Native M. genitalium genome was resequenced to ensure that the team was starting with an error-free sequence. After obtaining this correct version of the native genome, the team specially designed fragments of chemically synthesized DNA to build 101 “cassettes” of 5,000 to 7,000 base pairs of genetic code. These base pairs were assembled from chemically synthesized oligonucleotides. As a measure to differentiate the synthetic genome versus the native genome, the team created “watermarks” in the synthetic genome. These are short inserted or substituted sequences that encode information not typically found in nature. Other changes the team made to the synthetic genome included disrupting a gene to block infectivity (Gibson D.G. et. al., 2008).

 

From here, the team devised a five stage assembly process where the cassettes were joined together in subassemblies to make larger and larger pieces that would eventually be combined to build the whole synthetic M. genitalium genome. In the first step, sets of four cassettes were joined to create 25 subassemblies, each about 24,000 base pairs (24kb). These 24kb fragments were cloned into the bacterium Escherichia coli to produce sufficient DNA for the next steps, and for DNA sequence validation (Gibson D.G. et. al., 2008).

 

The next step involved combining three 24kb fragments together to create 8 assembled blocks, each about 72,000 base pairs. These 1/8th fragments of the whole genome were again cloned into E. coli for DNA production and DNA sequencing. Step three involved combining two 1/8th fragments together to produce large fragments approximately 144,000 base pairs or 1/4th of the whole genome. At this stage the team could not obtain half genome clones in E. coli, so the team experimented with yeast and found that it tolerated the large foreign DNA molecules well, and that they were able to assemble the fragments together by homologous recombination. This process was used to assemble the last cassettes, from 1/4 genome fragments to the final genome of more than 580,000 base pairs. The final chromosome was again sequenced in order to validate the complete accurate chemical structure. The synthetic M. genitalium has a molecular weight of 360,110 kilodaltons (kDa). Printed in 10 point font, the letters of the M. genitalium JCVI-1.0 genome span 147 pages (Gibson D.G. et. al., 2008).

 

 

Ethical Rumblings

 

Sequencing an entire genome is no small feat.  Yet it may pale in comparison to actually designing, engineering, and then ultimately building one.  Advancing the current state of technology and genetic know-how, Craig Venter and his laboratory are making the idea of designing, engineering, and building a genome a reality.  Such a breakthrough begs an age-old question: What is life?

 

"Are we alive? Yes. Is a virus alive? Maybe. Still, a half-century after the discovery of the double helix, nobody doubts that it is our DNA that determines who we are- in the same way that lines of code determine software or the digital etchings on a CD determine the music you hear.  Etch new signals, and you write a new song.  That, in genetic terms, is what Venter has done." (Time Magazine, Jan. 24, 2008)

 

Craig Venter has been quoted as saying:

 

"What is life? I don't think there are many biologists trying to answer that one...We're...working on a reductionist view of trying to take the smallest genome that we have...and see if we can't understand how those...[genes] work together to create life..."

 

The attempts to cut down an organism to the most essential, bare genes constitutes a reductionist approach that has received much criticism over the years.  Scholars, scientists, and ethicists all argue that a reductionist approach:

 

1. Limits our understanding of living organisms

 

2. A reductionist understanding of human life is unacceptable to those who believe that the human experience cannot be solely explained by physiological definitions

 

Arguments over such points, the haggling over certain definitions- such exercises impact scientific and social issues far beyond the biology laboratory.  Debates over stem cells, embryonic use, abortion, and the creation of human-hybrid species are all affected by merely "cracking the manufacturing code" as Craig Venter appears to have done.

 

As new scientific breakthroughs and advances in technology allow previously unbelievable scenarios (ie creating organisms from scratch) to come into being, a shift in how we construct and view the ethical and moral ramifications is needed.  Ethicists call for a systematic vision of the moral character of the world we hope to be moving toward. What are the most basic principles that would guide public policy and individual choice concerning the use of genetic interventions in a just and humane society in which the powers of genetic intervention are much more developed than they are today?

 

The book: From Chance to Choice: Genetics & Justice attempts to answer the above question.  Written by a compilation of philosophers and medical ethicists, the authors propose two main models for genetic intervention:

 

1. The Public Health Model

 

- this approach stresses the production of benefits and the avoidance of harms for groups

- the appropriate mode of evaluating options is some form of cost-benefit calculation, as in, it assumes that whether a policy or an action is deemd to be right is thought to depend solely on whether it produces the greatest balance of good over bad outcomes

 

2. The Personal Service Model

 

- this approach has as its most fundamental value: individual autonomy

- ie whether a couple at risk for conceiving a child with a genetic disease takes a genetic test and how they use the knowledge thus obtained is their business, not society's

- the authors criticize this approach saying that it honors only the autonomy of those who are in a position to exercise choice concerning genetic interventions, not all those who may be affected by such choices.

 

As a rebuke of the above two approaches, the authors present a third, modern-day approach:

 

Although respect for individual autonomy requires an extensive sphere of protected reproductive freedoms and hence a broad range of personal discretion in decisions to use genetic interventions, both the need to prevent harm to offspring and the demands of justice, especially those regarding equal opportunity, place systematic limits on individuals' freedom to use or not use genetic intervetions...our view steers a course between a public health model in which individuals count only so far as what they do or what is done to them affects the genetic health of "society" and a personal service model in which the choice to use genetic interventions is morally equivalent to the decision to buy goods for private consumption in an ordinary market.

 

The authors ethical theory rests on two institutions: Justice, and the Prevention of Harm.

 

The authors are also quick to point out that their investigation of ethical principles for a just and humane society capable of powerful genetic interventions is not an attempt to advance concrete policy recommendations for our own society at the present time...instead, their aim is to explore the resources and limitations of ethical theory for guiding deliberations about public policy.

 

One of the most striking counter-arguments that the authors put forth is their belief in the risk of reinforcing "gene-mania."  Such a stance flies in the face of someone as outspoken and flashy as Craig Venter. 

 

For the authors, genetic determinism betrays, above all, a failure to understand that genes are always only contributing causes.  Whether a given trait will be present depends not just on the gene or genes in question, but also on the environment, including the envrionment of the organism's body at a particular stage in the organism's development.

 

The authors go so far as to relate genetic determinism as a variety of fetishism: a fetish being an object that people endow - in their imaginations - with supernaturual powers, or at least with powers that the object does not have.

 

- genetic determinism is not merely a tendency to make erroneous causal judgments about genes; it is a cognitive error that fosters the abdication of moral and social responsibility

- genetic determinism thus plays an exculpating role. If academic and econoic 'underachievement', aggression, depression, criminal behavior, and sexual infidelity are all caused by genes, then there is indeed a double exculpation. Individuals are not responsible for their behavior, nor are we respnosible for critically evaluating and perhpas reforming existing institutions and social practices, since these are largely irreleveant to the problems that most concern us.  If there were an all-powerful and all-knowing being who was resolutely committed to shielding the existing social and political order from critical scrutiny, it is unlikely that it could hit upon a better strategy than implanting genetic determinist thinking in peoples' heads.

 

The book goes on to further explore the concepts of:

 

- genes, justice and human nature

- positive and negative genetic interventions

- having the best children we can

- reproductive freedom and the prevention of harm

- genetic intervention and the morality of inclusion

- policy implications

- meanings of genetic causation

- eugenics

 

 

Conclusion

 

Craig Venter has spearheaded research that has used genome transplantation methods to replace Mycoplasma capricolum's genome with that of Mycoplasma mycoides.  It is the first step toward his ultimate goal of creating a tailor-made organism, essentially "out of scratch."  As our genetic knowledge and technological prowess increases, the moral and ethical implications become more and more relevant in scientfic discussion.

 

 

---

 

References

 

Cho M. K. et. al. "Ethical Considerations in Synthesizing a Minimal Genome." Science. 1999. 286(5447): pp. 2087 – 2090

 

Dunning Hotopp J. C. et. al. "Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes." Science. 2007. 317(5845): pp. 1753-1756

 

Gibson D. G. et. al. "Complete Chemical Synthesis, Assembly and Cloning of a Mycoplasma genitalium Genome." Science. 2008. 319(5867): pp. 1215-1220

 

Lartigue C. et al. "Genome Transplantation in Bacteria: Changing One Species to Another". Science. 2007. 317(5838): pp. 632 - 638

 

Nicholas Wade. "Scientists Transplant Genome of Bacteria." NewYorkTimes 29 June 2007. 12 March 2008 <http://www.nytimes.com/2007/06/29/science/29cells.html?partner=rssnyt&emc=rss&oref=slogin>

 

 

Allen Buchanan et al. From Chance to Choice: Genetics & Justice. Cambridge: University Press, 2000.