Today’s New Reason To Believe

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Scientists One Step Closer to Artificial Life and the Best Case for ID

Today much of the world is celebrating the 200th anniversary of Charles Darwin’s birth. Darwin’s theory of biological evolution has had a far-reaching impact on nearly every area of biology. It has also had profound philosophical and theological implications that fuel the creation/evolution controversy.

When Charles Darwin advanced his theory in On the Origin of Species in 1859, there was much about biology that he and his contemporaries didn’t understand. Darwin was aware of some of the gaps in his knowledge. But there remained much information that he didn’t realize was missing.

Over the last 150 years, scientific advance has yielded important understanding about life’s characteristics. Many of these discoveries, which provide the framework for modern biology, go beyond Darwin’s wildest dreams. Modern-day comprehension makes it possible for scientists to readily manipulate and modify life-forms in the laboratory.

One advance that would have probably surprised Darwin is the capability of scientists to not just manipulate life, but create artificial life in the laboratory. Very few scientists in Darwin’s time would have thought this possible. In fact most scientists even as recently as a couple of decades ago would have viewed this as an unreasonable goal.

As I have discussed for the last few weeks, Craig Venter, one of the pioneers in the field of genomics, recently founded a company called Synthetic Genomics (see here, here, and here for my articles). This group is striving to create artificial, nonnatural microbes for potential commercial and biomedical utility.

The newfound ability to make novel life-forms has been made possible, in part, by advances in the burgeoning new science of genomics These new insights, along with decades of research into biochemistry and molecular biology, have provided scientists with enough of an understanding of life’s most basic system–the cell–so that they can now potentially generate synthetic life-forms.

Nobody in Darwin’s day could realistically foresee such developments. In the mid 1800s, very little understanding existed of what distinguished life from nonlife. (In many respects, we still don’t have full understanding today.) For example, Darwin’s view of the cell comprised a different picture than modern scientists’. Darwin held to the protoplasmic theory–the idea that the cell consisted only of a wall surrounding a nucleus and a homogeneous, jelly-like protoplasm. Biologists and chemists of that time easily envisioned chemical routes on the early Earth capable of yielding the single ingredient believed to form the cell’s protoplasm.

By the end of the 19th century with the rise of biochemistry, however, the protoplasmic view of the cell was waning. Researchers recognized that the cell’s protoplasm was a complex, heterogeneous system. The cell’s marked complexity became apparent with the discovery of enzymes in the protoplasm capable of catalyzing a large collection of chemical reactions.

Over the last century, advances in biochemistry have continued to affirm the complexity of life at a molecular level. The most recent studies from genomics indicate that even the simplest bacterium requires close to 2,000 different proteins in the “protoplasm” for it to exist as a living entity. It’s not just that the cell’s chemical systems are complex: these systems display a remarkable degree of order and organization undergirded by an elegant, sophisticated logic. (For more details see my book The Cell’s Design.

Studies in genomics have also identified the essential genes required for an organism to exist as a life-form. Below a minimum number, about 380 genes, life doesn’t appear to be possible. This insight forms the basis for Venter’s plan to create artificial life in the lab.

The very real prospect of scientists creating life in the lab raises all sorts of concerns. Some conservative Christians think that the manufacture of novel life-forms by human hands eliminates the need for a divine Creator–thus, substantiating the evolutionary origin-of-life paradigm. Many Christians and skeptics alike believe that if scientists can create life in the lab, such a breakthrough will show that there is nothing special about life and that its origin could have easily taken place on the early Earth without God’s necessary involvement. Ironically, instead of supporting an evolutionary origin of life, Venter’s efforts demonstrate that life’s beginnings and transformation cannot happen apart from the work of an intelligent agent.

Minimum Requirements for Life

For example, Venter’s team must identify the minimal gene set required for life’s existence to re-engineer an artificial life-form from the top down. As they continue to hone in on life’s essential genes and biochemical systems, what’s most striking is the remarkable complexity of life even in its minimal form. And this basic complexity is the first clue that life requires a Creator.

Minimal life seems to be irreducibly complex. Based on Venter’s work, there appears to be a lower bound of several hundred genes, below which life cannot be pushed and still be recognized as “life.” As I argued in The Cell’s Design irreducible complexity is a hallmark characteristic of humanly constructed systems. By analogy, the irreducibly complex nature of life even in its bare essence implies that it, too, is the product of an intelligent agent.

In Darwin’s Black Box, biochemist Michael Behe makes the powerful case that irreducibly complex systems cannot emerge through an undirected, stepwise process. This obstacle makes it difficult to envision how natural evolutionary processes could have produced even life in its minimal state.

Hugh Ross and I reached the same conclusion in our book Origins of Life by considering the probability of the essential gene set coming into existence simultaneously. According to this analysis, it is super-astronomically improbable for the essential gene set to emerge simultaneously through natural means alone. If left up to an evolutionary process, not enough resources or time exist throughout the universe’s history to generate life even in its simplest form.

If not for the quest for artificial life, the immense complexity of life in its bare essential form would not be so rigorously demonstrated.

Using Existing Parts

As remarkable as it will be when Venter’s team succeeds in creating artificial life, it’s important not to view their accomplishment as more than it is. Headlines describing their work give the impression that these researchers are generating life solely from building-block materials. In reality, they are not building life from “scratch.” Instead, they are merely remodeling an existing life-form to generate a novel creature, known as Mycoplasma laboratorium.

Picture a microbe as similar to an automobile. In essence, Venter’s group is functioning like a curious auto mechanic disabling the parts of a car engine one at a time to indentify the core components of the engine that must be present for it to run at all. (This corresponds to the work Venter’s team has done to determine the minimum gene set.) Once the mechanic has identified the minimal parts list, he buys the essential engine parts from a “parts store” and assembles them into a minimal engine. (This step corresponds to the synthesis of the M. genitalium genome that I discussed in my three previous articles.) He then removes the motor from a perfectly working car and inserts the minimal engine into the vehicle to see if it still runs. (This step corresponds to the introduction of the synthetic genome into a cell that has had its genome removed.) If all these steps work, then the auto mechanic has not only confirmed that he has properly identified the essential engine parts, but has generated a novel automobile.

Need for Intelligent Intervention

The amount of intellectual effort expended by Venter’s team up to this point is astounding given the conceptually simple steps required to reengineer a life-form from the top down.

As I have discussed for the last few weeks, these researchers didn’t just rush into the lab and start throwing nucleotides into test tubes and running chemical and enzymatic reactions to achieve the total synthesis of the entire M. genitalium genome. Instead, they devised a synthesis strategy with painstaking effort.

Venter’s team carefully segmented the sequence of the entire M. genitalium genome into fragments (called cassettes) about 5,000-7,000 nucleotides (bp) in size. They carefully delineated the boundaries between cassettes so that these demarcations would reside between genes. They also designed the cassettes so that the sequences between two adjacent pieces of DNA overlapped by about 80 bp. This planning allowed them to piece together the M. genitalium genome in a manageable and orderly fashion.

They executed the synthesis and assembly in stages that included:

using automated DNA synthesizers that utilize chemical and physical processes to synthesize and purify, respectively, about 10,000 short pieces of the genome approximately 50 bp in length;

use of enzymes to biochemically combine the chemically made fragments into 101 larger fragments (about 5,000 to 7,000 bp each) that corresponded to the cassettes they mapped out at the drawing board stage;

use of enzymes and the bacterium Escherichia coli to combine the 101 larger fragments into four fragments about 140,000 bp each;

use of yeast to combine the four fragments into the entire genome.

Each stage of this process demanded exact planning and execution.

The technology to chemically synthesize oligonucleotides has been in place for several decades. Today, the chemical production of oligonucleotides is virtually an automated turnkey process. Still, it represents a remarkable technical accomplishment resulting from the dedicated efforts over the course of the last half century of some of the best scientists in the world (including Nobel laureates). Without these achievements, Venter’s team would have no hope of achieving their goal.

To assemble the chemically synthesized DNA pieces into increasingly larger DNA fragments, the Synthetic Genomics team needed to formulate a strategy that includes carefully selecting the appropriate enzymes based on their catalytic properties. It required designing the oligonucleotides–prior to the chemical synthesis step–so that they are compatible with the enzymes, and devising a reaction scheme that will yield the desired recombination product.

Choosing the yeast Saccharomyces cerevisiae to complete the assembly of the M. genitalium genome was also well-thought-out. This organism can take up extremely large pieces of foreign DNA when combined with a genome that is compatible with yeast. Instead of using enzymes in a test tube to complete the genome assembly, the scientists used the yeast’s biochemical machinery inside the cell to assemble the final pieces of the genome before they cloned it.

Given the effort that went into the synthesis of the total M. genitalium genome, it’s hard to envision how unintelligent, undirected processes could have generated life from a prebiotic soup. Though not their intention, Venter’s team unwittingly provided empirical evidence that life’s components, and consequently, life itself must stem from the work of an Intelligent Designer.

The goal of Darwin’s theory was to explain what was considered to be the mystery of mysteries in his time, the origin of species. Darwin proposed that the basis of species occurred through natural selection. Who would have thought that on the 150th anniversary of On the Origin of Species scientists would stand on the cusp of originating new species, not by undirected processes but by intelligently designed and expertly executed methods and procedures?

If Charles Darwin knew then what we know now would he have proposed his theory of biological evolution? It’s hard to say. But knowing what Darwin didn’t has been enough to cause a large number of scientists around the world, representing a range of scientific disciplines, to question the theory. And the attempts to create artificial life provide one more reason to view evolution with incredulity.

Fazale ‘Fuz’ Rana, Ph.D.

Scientists One Step Closer to Artificial Life and the Best Case for ID

About a year ago my family and I (along with some good friends) rode mules down to the bottom of the Grand Canyon. That night we ate dinner at the Phantom Ranch and the next day rode back out of the canyon. In just two short days, I developed a real admiration for the animals we rode. The ability of those mules to maneuver on rugged and narrow trails overlooking sheer drops was impressive.

Since the time of the Neolithic revolution humans have relied on domesticated animals to meet our needs. These creatures provide us with an ongoing source of food and serve as beasts of burden, transporting humans and materials from place to place and plowing fields.

In the last few decades, life scientists have come to rely on their own beasts of burden in their research endeavors. Creatures like Rhesus monkeys, mice, fruit flies, nematodes, yeast, bacteria like E. coli, and a whole host of others have all played critical roles in the development of modern biology. Without these model laboratory organisms, biologists could never have performed the necessary experiments to understand how living systems work. In fact, E. coli and the yeast Saccharomyces cerevisiae are playing a central role in scientists’ quest to create artificial life in the lab.

As I pointed out a few weeks ago, Craig Venter, one of the pioneers in the field of genomics, recently founded a company called Synthetic Genomics. This group is devoted to creating artificial, nonnatural microbes that have commercial utility, particularly for the production of ethanol, hydrogen, and other forms of renewable energy.

Scientists like Venter who pursue the creation of artificial and synthetic life claim that these novel life-forms will benefit humanity. Still, the very real prospect of scientists creating life in the lab also raises theological concerns. Should human beings “play God?” Additionally, many people believe that if scientists can create life in the lab, it would prove that there is nothing special about life itself.

Venter’s team has recently achieved another milestone in the quest to create an artificial life-form in the lab. Researchers at Synthetic Genomics improved upon the method of synthesizing and cloning (in yeast) the entire genome of a wild-type M. genitalium. Ironically, instead of supporting an evolutionary origin of life, this research empirically demonstrates that life’s origin and transformation cannot happen apart from the work of a mind.

Last week, I gave a description of the strategy the team is taking to synthesize and assemble the entire genome of M. genitalium and explained the first stages of its production. This week, I would like to continue describing the effort needed to synthesize and assemble an organism’s whole genome.

Synthesis of a Genome

The Synthetic Genomics scientists didn’t just rush into the lab and start throwing nucleotides into test tubes and running chemical and enzymatic reactions. Instead, they carefully devised a synthesis strategy. They decided to build the genome by first synthesizing small pieces of DNA and then assembling these pieces into increasingly large sections using chemical, biochemical, and in vivo methods until the entire genome was cobbled together.

The Strategy

Before they began any lab work, the research group started at the drawing board. They carefully parsed the sequence of the entire M. genitalium genome into fragments (called cassettes) each about 5,000 to 7,000 nucleotides (bp) in size. They delineated the boundaries between cassettes so that these demarcations would reside between genes. They also carefully designed the cassettes so that the sequences between two adjacent pieces of DNA overlapped by about 80 bp. This planning allowed them to piece together the M. genitalium genome in a manageable and orderly fashion.

Once the cassette map was developed they executed the synthesis and assembly in stages that included:

using automated DNA synthesizers that utilize chemical and physical processes to synthesize and purify, respectively, about 10,000 short pieces of the genome approximately 50 bp in length;

use of enzymes biochemically combine the chemically made fragments into 101 larger fragments (about 5,000 to 7,000 bp each) that corresponded to the cassettes they mapped out at the drawing board stage;

use of enzymes and the bacterium Escherichia coli to combine the 101 larger fragments into four fragments about 140,000 bp each;

use of yeast to combine the four fragments into the entire genome.

Each stage of this process demanded careful planning and execution.

Biochemical Recombination

Once the chemical synthesis and purification of the 50 bp oligonucleotides has been completed, they need to be linked together to ultimately form the 5,000 to 7,000 bp cassettes diagramed onto the M. genitalium genome map. Chemists don’t have enough control over the reactions that generate the oligonucleotides to efficiently and accurately perform this crucial step. The difficulty can be side-stepped by using enzymes to carry out the recombination process.

Once again, biochemists can’t just toss the DNA fragments into a test tube with a mixture of enzymes and get the desired recombinations. Instead they have to painstakingly formulate a strategy that includes selecting the appropriate enzymes based on their catalytic properties, designing the oligonucleotides–prior to the chemical synthesis step–so that they are compatible with the enzymes, and devising a reaction scheme that will yield the desired recombination product.

Venter’s group had previously worked out the procedure used to recombine the 50 bp oligonucleotides into fragments about 5,000 to 7,000 bp by putting together the entire genome (5,386 bp) of a bacterial virus. The process entails:

Treating the oligonucleotides with the enzyme T4 polynucleotide kinase. This enzyme modifies the ends of the oligonucleotides so that they can take part in the next stage of the reaction.

Treating the end-modified oligonucleotides with Taq ligase. This enzyme combines smaller oligonucleotide fragments into larger ones, preparing them for the next stage of the recombination. The oligonucleotides from each of the DNA strands must pair up with each other in the appropriate way. For this to happen, it was critical that Venter’s team carefully design the sequences of the 50 bp oligonucleotides made by chemical synthesis.

Performing a polymerase cycling assembly of the paired and ligated oligonucleotides. Again, the success of this step depends on the careful design of the sequences of the 50 bp oligonucleotides made by chemical synthesis. This cleverly designed procedure uses enzymes called DNA polymerases to assemble small paired DNA fragments into larger ones. The paired oligonucleotides do not fully overlap with one another. Due to their partial overlap, single stranded regions exist. The DNA polymerases fill in those gaps, eliminating the overlap and in the process joining the fragments together, extending their size. The polymerase cycling assembly has to be repeated between 35 to 70 times to build fragments between 5,000 and 7,000 bp.

Performing a polymerase chain reaction amplification of the fully assembled DNA pieces, 5,000 and 7,000 bp. This step not only generates numerous copies of the fully assembled DNA pieces, it also eliminates any partially assembled DNA if the design of this step is done in such a way to allow only the fully assembled DNA pieces to be amplified.

Once the 101 5,000-7,000 bp cassettes were put together, they were further combined in three stages to form four pieces of DNA about 144,000 bp each. These large fragments each equaled one fourth of the M. genitalium genome.

In stage one, the researchers assembled neighboring cassettes in groups of four (1-4, 5-9, 10-13, etc.) along with a segment of DNA from the bacterium E. coli to form pieces of the M. genitalium genome about 24,000 bp each. This stage of the assembly yielded 25 24,000 bp fragments.

The specific steps for this stage included:

Treatment of the 5,000-7,000 bp oligonucleotides with an enzyme called a 3’ exonuclease. This enzyme removes pieces of DNA that are part of the paired oligonucleotides from each of the DNA strands to expose overlapping sequences.

The oligonucleotides were then allowed to incubate for a period of time under exacting conditions to allow the neighboring cassettes to assemble.

Treatment of the assembled oligonucleotides with a polymerase and ligase to fill in the missing nucleotides (removed as a result of the exonuclease treatment) and link the assembled cassettes together.

Assembled cassettes were also joined to a piece of DNA from the bacterium E. coli. Each piece of bacterial DNA served as a marker specific to each of the 24,000 bp cassettes. Because of the unique DNA sequences, the bacterial segments allowed researchers to import the assembled DNA into E. coli so that it could be cloned and amplified for the next stage.

After cloning and amplifying the partially assembled genome, the pieces of bacterial DNA were released. The 24,000 bp fragments were ready to be moved on to the next stage of construction.

During stage two, the scientists joined three adjacent 24,000 bp pieces of DNA to form 72,000 bp fragments utilizing the same enzymatic protocol as used in the first stage of the assembly. Stage three involved combining two adjacent 72,000 bp pieces to form 144,000 bp fragments.

At this point in the building process, the researchers discovered that enzymes and E. coli proved useless since the microbe can’t handle larger DNA fragments. To finish the genome assembly the researchers turned to yeast.

Recombination in Yeast

Venter’s team wisely chose the yeast Saccharomyces cerevisiae to complete the construction of the M. genitalium genome because it can take up extremely large pieces of a foreign genome when combined with DNA that is compatible with yeast. Instead of using enzymes in a test tube to complete the genome assembly, they used the yeast’s biochemical machinery inside the cell to put together the final pieces of the genome before they cloned it. Venter and his coworkers found it unnecessary to bring together the genome in a stepwise fashion (first joining together two quarter genomes followed by two half genomes). Instead they could induce the yeast to take up all four pieces of the genome simultaneously to achieve the assembly. The capacity of S. cerevisiae to take up several pieces of DNA and unite them all at once has intrigued the team with the possibility that added efficiencies could be built into their approach to total genome synthesis and assembly.

Recently Venter’s group showed that stages two through four could be eliminated. Instead of relying on enzymatic recombination together with cloning in E. coli to successively produce 72,000 bp and 144,000 bp pieces of DNA, they could use yeast to recombine the twenty-five 24,000 bp DNA fragments generated at stage one of the process.

The complete chemical synthesis and assembly of the entire M. genitalium genome accomplished by the people at Synthetic Genomics represents a tremendous scientific achievement. The editors at Science voted this work as one of the top ten scientific breakthroughs of 2008 because it will pave the way to better understanding of the minimum requirements for life and because it introduces a key technology in the creation of novel, nonnatural life-forms for commercial and biomedical use. It also has important implications for the creation/evolution controversy. I’ll discuss these implications next week.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Scientists One Step Closer to Artificial Life and the Best Case for ID

Sometimes the solutions to problems emerge from unexpected places. The Human Genome Project holds potential for understanding and treating human disease. Surprisingly, it also may play a role in addressing concerns about climate change and the need for renewable, clean-burning energy.

Even though the Human Genome Project offers the real possibility of transforming health care and medicine, its greatest impact may not be the advances it spurs in medicine and the understanding of human biology. Rather, history is likely to view its greatest achievement as spawning the scientific discipline called genomics.

Genomics, which cross-sects genetics, molecular biology, biochemistry and computer science, focuses on sequencing and characterizing the entire DNA content (called the genome) of organisms. Scientists hope that this endeavor will allow them to gain new insight into the biology and comparative relationships among life (both living and even extinct). Some scientists also think that genomics may be the gateway to creating artificial life in the lab.

As I pointed out last week, Craig Venter, one of the pioneers in the field of genomics, recently founded a company called Synthetic Genomics. This group is devoted to creating artificial, nonnatural microbes that have commercial utility, particularly for the production of ethanol, hydrogen, and other forms of renewable energy—thus, the link between the Human Genome Project and the climate and energy crises.

Scientists like Venter who pursue the creation of artificial and synthetic life claim that these novel life-forms will benefit humanity. Still, the very real prospect of scientists creating life in the lab raises all sorts of theological questions. Should human beings “play God”? Additionally, many people believe that if scientists can create life in the lab, then there is nothing special about life itself because its origin could have easily taken place on the early Earth without God’s involvement.

Venter’s team has recently achieved another milestone in the quest to create an artificial life-form. Researchers at Synthetic Genomics improved upon the method to synthesize and clone (in yeast) the entire genome of a wild-type M. genitalium. Ironically, instead of providing support for an evolutionary origin of life, this research provides an empirical demonstration that life’s origin and transformation cannot happen apart from the work of a mind.

Last week, I provided an overview of the strategy Venter’s team is taking to generate artificial life from the top down and gave a brief report on their progress to date. This week, I would like to begin the process of detailing the most recent work performed by his team. Along the way, I will describe the effort and ingenuity needed to synthesize a genome starting with the four nucleotides that comprise DNA (the molecule that makes up an organism’s genome). Next week I will continue discussing the effort needed to synthesize and assemble an organism’s whole genome. In two weeks, I will look at the implications of this work for the creation/evolution controversy.

Synthesis of a Genome

To achieve the total synthesis of the entire M. genitalium genome, Venter’s team didn’t just rush into the lab and start throwing nucleotides into test tubes and running chemical and enzymatic reactions. Instead, they carefully devised a synthesis strategy. They decided to build the genome by first synthesizing small pieces of DNA and then assembling these DNA pieces into increasingly large sections using chemical, biochemical, and in vivo methods until the entire genome was cobbled together.

The Strategy

Before they began any lab work, the scientists started at the drawing board, carefully parsing the sequence of the entire M. genitalium genome into fragments (called cassettes), about 5,000 to 7,000 nucleotides (bp) in size. They delineated the boundaries between cassettes so that these demarcations would reside between genes. They also carefully designed the cassettes so that the sequences between two adjacent pieces of DNA overlapped by about 80 bp. This planning allowed them to piece together the M. genitalium genome in a manageable and orderly fashion.

Once the cassette map was developed they executed the synthesis and assembly in stages that included:

using automated DNA synthesizers that utilize chemical and physical processes to synthesize and purify, respectively, about 10,000 short pieces of the genome approximately 50 bp in length;

use of enzymes to biochemically combine the chemically made fragments into 101 larger fragments (about 5,000 to 7,000 bp each) that corresponded to the cassettes they mapped out at the drawing board stage;

use of enzymes and the bacterium Escherichia coli to combine the 101 larger fragments into four fragments about 140,000 bp each;

use of yeast to combine the four fragments into the entire genome.

Each stage of this process demanded careful planning and execution.

Chemical Synthesis and Purification

The capacity to affect the chemical synthesis of DNA has been a long time in the making. This process refer to the nonbiological, chemical production of small segments of DNA, called oligonucleotides.

With state-of-the art methods, chemical synthesis can reliably generate oligonucleotides up to about 200 bp in size using automated procedures. The first experiments towards this end began in the 1950s and advanced through several key milestones, thanks to the efforts of some of the most prominent chemists of the last half century.

DNA consists of chain-like molecules known as polynucleotides. Two polynucleotide chains align in an antiparallel fashion to form a DNA molecule. The paired polynucleotide chains twist around each other to form the well-known double helix. The cell’s machinery forms the individual polynucleotide chains by linking together four different subunit molecules called nucleotides. The four nucleotides used to build DNA chains are adenosine, guanosine, cytidine and thymidine, denoted as A, G, C and T, respectively.

The individual nucleotides have several different chemical groups that can react with each other to form bonds between two nucleotides. Yet in DNA, the nucleotides must be linked together in a specific way to form the polynucleotide strands. Enzymes that constitute the part of the cell’s machinery that makes DNA have a high degree of specificity, ensuring that the linkages form in the correct manner. In a test tube without enzymes present, the nucleotides will react with each other to form a variety of linkages. This results in a polynucleotide with a mish-mashed structure and no biological use.

To get around this problem, chemists have devised a strategy that relies on the use of chemical groups to block these reactive sites. Each group has been specifically chosen and designed to uniquely fit the individual chemistry of each reactive site. The blocking groups can be selectively removed by chemists at the appropriate times during the synthetic sequence to make specific chemical groups available to react. When the total synthesis of the oligonucleotides has been achieved the remaining blocking groups are then removed.

If these reactions are conducted in solution, a purification step has to be included after each nucleotide addition to the growing oligonucleotide chain. To get around this cumbersome step, chemists have devised an approach using a solid support. The oligonucleotide chain is anchored to the solid support during the reaction sequence. The first nucleotide is attached to a solid material that has been packed into a column. Chemicals can be poured into the column to initiate reactions with the next nucleotide in the chain. When the reaction is complete, the column is washed. Unreacted materials and undesired side products are removed from the column, while the oligonucleotide remains attached. This not only eliminates a costly purification step, it also increases the accuracy of the synthesis.

The specific steps for the chemical synthesis of oligonucleotides include:

1. Attaching the first nucleotide to a solid support after deblocking the appropriate group.
2. Removing the appropriate protecting group from the attached nucleotide in the first position to allow it to react with the next nucleotide in the oligonucleotide sequence that has had the appropriate blocking group removed from it.
3. Allowing the nucleotides to react under carefully controlled conditions.
4. Adding a chemical cap to any unreacted oligonucleotides. (This step is necessary because a small percentage of the nucleotides don’t react with the attached oligonucleotide chains.)
5. Stabilizing the linkage between the two nucleotides with an oxidizing agent
6. Washing away unreacted nucleotides.
7. Repeating steps 2 through 6 until the entire oligonucleotide has been made.
8. Cleaving the oligonucleotide from the solid support.
9. Removing all the blocking groups.
10. Purifying the oligonucleotide. This step is absolutely critical to ensure the accuracy of the biochemical recombination steps during the whole genome assembly process.

Because the technology to chemically synthesize oligonucleotides has been in place for several decades, it’s easy for scientists to take it for granted. Today, the chemical production of oligonucleotides is virtually an automated turnkey process. Yet, it’s important not to overlook the remarkable technical accomplishment this capability represents. If it wasn’t for the dedicated efforts over the course of the last half century of some of the best scientists in the world (including Nobel Laureates), to develop and improve methods to chemically make DNA, Venter’s team would have no hope of affecting the complete synthesis of the M. genitalium genome.

Next week I’ll continue to describe the steps needed to synthesize and assemble the entire M. genitalium genome by focusing on the biochemical and in vivo assembly of the chemically-synthesized pieces of DNA into the whole genome.

Thanks for hanging in there. The reward comes in discovering a significantly bolstered case for intelligent design.