Eating the Elephant Bite by Bite

Eating the Elephant Bite by Bite

New Work Takes Scientists One Step Closer to Creating Life in the Lab

An elephant float takes two scoops of ice cream. And once the elephant is floating in root beer, the only way to consume the beast is one bite at a time.

This is the same approach that Craig Venter and his collaborators at the J. Craig Venter Institute and Synthetic Genomics are using to create artificial life—one bite at a time, or, more appropriately, one step at a time. Recently, Venter and his team reported another milestone in a series of accomplishments that brings them closer to producing an artificial microbe.

The very real prospect of scientists creating life in the lab prompts all sorts of theological concerns. Many people, both theists and atheists, believe that if scientists can create life in the lab then there is nothing special about any life and its origin. In light of this groundbreaking research, they reason that life could have easily arisen on the early Earth without God’s necessary involvement.

Ironically Venter’s research actually demonstrates that life’s beginnings and transformation could not have happened apart from the work of an intelligent Agent. To understand why, it’s necessary to appreciate the strategy Venter’s team is using to create artificial life and examine in some detail their most recent work.

Steps to Creating Artificial Life

To create an artificial life-form, Venter and fellow researchers are using an approach called a top-down strategy. It involves starting with a naturally occurring microbe (Mycoplasma genitalium), stripping it down to its bare genetic and biochemical essence, and then modifying it by adding nonnative genes to the minimal genome to generate a nonnatural form of life. A few months ago I detailed their strategy and issued a status report of their progress.

Venter’s team has already identified what they think is the essential gene set. And as I described in detail, they have developed the methodology to synthesize an entire genome from the four genetic building-block molecules (called nucleotides.) (See here and here for articles discussing this work.)

One of the key hurdles to creating artificial life is the ability to transplant the synthetic genome into a microbe and, thus, transforming it into a nonnatural life-form. In 2007, Venter’s group developed a method to do this and demonstrated its feasibility when they transferred the genome of Mycoplasma mycoides into a closely related Mycoplasma capricolum.

As it turns out, however, this methodology is not very robust and didn’t work when they tried using a synthetic genome or attempted to use it to transplant an M. genitalium genome into M. pnuemoniae.

New Genome Transplantation Methodology

These difficulties motivated the researchers to attempt to improve the genome transplant methodology. To do this they worked, once again, with M. mycoides and M. capricolum. In short, the team isolated the M. mycoides genome after inserting specialized DNA sequences into it and transferred the genome into yeast. They then engineered the genome in yeast, isolated the engineered genome from yeast, and then altered it with a special enzymatic treatment that increased transplantation efficiency. The genome was then transplanted into M. capricolum, transforming this microbe into M. mycoides.

Though conceptually straightforward, this methodology relies on a clever strategy that borders on genius to make it work. It also required a large team of highly skilled molecular biologists to perform detailed laboratory manipulations. It is safe to say that this tactic is intelligently designed and is dependent on intelligent agents to execute it.

For example, before the M. mycoides genome was isolated and transplanted into yeast, Venter’s team introduced a piece of DNA into it. Known as a vector, this DNA piece contained a number of specialized yeast sequences that enabled the yeast cells to recognize and replicate the genome, thus permitting researchers to manipulate the genome inside of yeast. The vector also contained genes that imparted the bacterium with resistance to the antibiotic tetracycline. This defense mechanism helped the scientists to select M. mycoides cells that had successfully incorporated the vector into their genome. They then placed the microbes in growth media that contained the antibiotic. This strategy ensured that only the cells with the vector could grow and that the researchers were working with the desired microbes.

After incorporating the vector into the M. mycoides genome, the molecular biologists isolated it and used it to transfect yeast cells. Because of the specialized DNA sequences, the genome functioned as a plasmid inside the yeast.

Introducing the M. mycoides into yeast was critical for two reasons. First, the final steps for the synthesis of genomes take place inside yeast. This insertion allowed the researchers to develop a more realistic method for genome transplantation. And second, yeast provides an environment for the researchers to modify and engineer the genome. To illustrate this point, they deleted a gene from the M. mycoides genome through a sequence of carefully designed and executed steps.

Once Venter’s team engineered the M. mycoides genome in yeast, they isolated it and attempted to transplant it into M. capricolum cells, but were unsuccessful. They reasoned that perhaps M. capricolum restriction endonucleases were digesting the M. mycoides DNA, frustrating the process.

Restriction endonucleases are enzymes that cut both strands of DNA at specific nucleotide sequences called restriction sites. Specifically, restriction endonucleases protect the cell from foreign DNA, like viruses, by cutting the invaders into fragments.

These vital biomolecules occur in conjunction with DNA methylases, proteins that attach methyl groups to the same DNA sequences that would normally be cleaved by restriction endonucleases. When these sequences are methylated, restriction endonucleases cannot cut them. Restriction sites of the bacterial DNA are methylated to completely protect the bacterial DNA from being chopped up by its own restriction endonucleases. Foreign DNA, however, is not afforded this same protection.

Venter’s team conducted three separate experiments to test the idea that M. capricolum restriction endonucleases interfered with the genome transplantation process. The first experiment involved deleting the genes for restriction endonucleases from the M. capricolum genome, leaving it without protection against foreign DNA. The second and third involved treating the engineered M. mycoides genome isolated from yeast with cell extracts from M. capricolum and purified methylases from M. capricolum, respectively. Both treatments methylated the restriction sites of the engineered M. mycoides genome, protecting it from the M. capricolum restriction endonucleases.

In all three cases, the researchers were able to successfully transplant the engineered M. mycoides genome isolated from yeast into M. capricolum, and in many instances, the newly transplanted genome took over transforming M. capricolum into M. mycoides. They confirmed their success by sequencing the genome isolated from the cells that were transformed from M. capricolum into M. mycoides.

This work sets the stage for Venter’s group to introduce a synthetic genome derived from the minimum gene set of M. genitalium and introduce it into a closely related Mycoplasma species, altering it into an artificial life-form dubbed Mycoplasma laboratorium.

Creation of Artificial Life and the Case for Intelligent Design

Given the conceptual simplicity of the steps to reengineer a life-form from the top down, the amount of intellectual effort that Venter’s team has expended is astounding. (See here for an article that details features of this effort.) Their most recent work on genome transplantation only serves to highlight the necessary ingenuity and expert laboratory manipulations required to create life in the lab.

It’s difficult to envision how unintelligent, undirected processes could have generated life from a prebiotic soup. Venter and his researchers unintentionally provided empirical evidence that life must stem from the work of an intelligent Designer. And that is the elephant in the room for the evolutionary paradigm.