Creating Life in the Lab

The J. Craig Venter Institute recently announced their successful synthesis of a complete bacteria genome to an unsurpassed level of accuracy. Researchers were able to replace the genome of the host cell with the synthesized one. Several web sites and commentators have dispelled any aura of the miraculous by pointing out what exactly Venter’s group did and what they did not do. For just a sampling (bolded emphasis is mine):

“What Venter and his team did was to determine the sequence of the DNA in one of the world’s simplest bacteria, use the sequence information to synthesize a copy of that DNA from subunits sold by a biological supply company, then put the synthetic copy of DNA into a living bacterial cell from which the natural DNA had been removed.”{1}

From the original research article on the Venter group’s discovery: “We refer to such a cell controlled by a genome assembled from chemically synthesized pieces of DNA as a ‘synthetic cell,’ even though the cytoplasm of the recipient cell is not synthetic.”{2}

“The idea that this is ‘playing God’ is just daft. What he has done in genetic terms would be analogous to taking an Apple Mac programme and making it work on a PC—and then saying you have created a computer. It’s not trivial, but it is utterly absurd the claims that are being made about it.”{3}

“To clarify the facts, ‘the team put chemically synthesized pieces of the M. mycoides DNA into yeast which assembled the bacteria’s genome. Then, the M. mycoides genome was transplanted into Mycoplasma capricolum and “booted up” to create a new synthetic version of M. mycoides’…For this ‘proof of principle’ instance, they tried to ‘synthesize’ a bacterium as close to the original genome as they could, with the major ‘new’ genetic material being watermark protein messages (e.g. spelling “CRAIGVENTER”). They didn’t use the original DNA as a template, but just as a ‘standard’ for comparison. Since this was a test of concept, the goal was to generate something that already exists.”{4}

Neat Trick or Cause for Concern?

I think one of the most laudable feats of this group that should please many biochemists is that they were able to perfect the DNA synthesizing technology to the point that they reconstructed an entire bacterial genome—a much longer sequence than what is typically done in the laboratory setting—and they were able to do it with such accuracy that the cell’s translational machinery read it. Exciting for biochemists, but advancements in laboratory technique and technology are hardly the stuff of headlines. As a chemist, I think it’s a neat trick; as a bioethicist, I am concerned. My concern is not about the technology itself, but about the underlying presuppositions that seem to go unquestioned, even unnoticed.

The media response has been that of excitement and fear. At the heart of the fear surrounding genetic engineering is power. Why would anyone care about bacteria{5} unless he or she thought it implied something about human beings? Unless they are in the field, most people do not pay particular attention to the musing of a scientist about his research project on some esoteric species identifiable only by its Latin name. We do not care, that is, until that little bacterium has the potential to bring great harm or great good (or both) to human beings.

The fear or excitement (depending on your view of technology and scientists) is spread by two fundamental assumptions:

1) Since every organism, including human beings, is made up of genes, if scientists can manipulate one gene, then they can manipulate any gene, including human genes, and;

2) by manipulating genes scientists are manipulating life itself and the very essence of an organism’s identity. This philosophical assumption, known as reductionism, is what we often assume without thinking about it.

These philosophical assumptions are grounded in a worldview of materialism (a.k.a. naturalism; I will use the term materialism throughout this article). The materialistic worldview says that matter and energy are all there is, there is no supernatural and there is nothing beyond what is in the natural world. If that is the case, then by definition, human beings are defined by their physical parts. There is nothing nonphysical which we can call our identity. That also means that the difference between something being alive versus not being alive must be defined by physical parameters. Since all organisms have a genome, scientists assume that there is some combination of nucleotides (the individual molecules of the genome) or a certain minimal number of nucleotides that makes something alive.

The Venter Group’s Reductionist Project

The Venter group, from the beginning of their project, was quite up front with the goals of their research. When asked about the implications of their project, Craig Venter responded in an interview posted in SciWatch in 1997:

What is life? I don’t think there are that 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….{6}

This is the same sentiment held by James Watson, Nobel Laureate and co–founder of the structure of DNA. In his book, DNA, he states:

Our discovery had put an end to a debate as old as the human species: Does life have some magical, mystical essence, or is it, like any chemical reaction carried out in a science class, the product of normal physical and chemical processes? Is there something divine at the heart of a cell that brings it to life? The double helix answered that question with a definitive No.{7}

According to scientists who hold to materialistic presuppositions, life is chemistry. Who we are boils down to our chemistry, which puts those that can manipulate our chemistry in a position of power.

Given these beliefs, it is no wonder that people automatically jumped from the genome of a bacterium to the implications for people. But one thing science has shown us is that the leap from bacteria to man is not simple or straightforward. Man’s genome is not much larger than many other, simpler organisms, yet scientists have found that human DNA is much more complex. As it turns out, it is more than an issue of connecting nucleotides together like a chain of beads in the right order.

Reductionism and the Human Genome Today: What Is New

Dr. Richard Sternberg of the Biologic Institute conducts research based on several findings that seem to indicate that the blueprint for an organism’s overall body plan is not found by reading the genome on a nucleotide-by-nucleotide basis. There seems to be a more complex interaction between the genome and other cellular functions and between different parts of the genome in different ways that was once thought. His research seeks to identify those interactions and how they translate into an organism’s blueprint.{8}

What scientists are finding is that the genome is not read as a letter–by–letter array (one–dimensional), as was once thought, but that there are spatial and translational (three–dimensional) factors that help determine how our genome is interpreted. No longer is it a simple issue of what letters code for what. Now it is what letters, located where, and interacting how, code for what. This flies in the face of reductionism because now we cannot assume that the chemistry codes for life. Apparently there is more to it than that.

Reductionism and the Human Genome Yesterday: What Is Not New

Even before scientists discovered that there are layers of complexity to the genome, many researchers found that their experiments did not work as expected from a reductionist perspective because the step from bacteria to man is not a direct correlation. By looking back to the beginning of genetic engineering technology, we find that many people held reductionist presuppositions that fueled fear and concern. We also find that reductionism failed to account for the setbacks in going from simple organisms to man. Many people reacted to the discovery of recombinant DNA (rDNA) in the 1970’s and 1980’s with fear, concern, and anticipation.

RDNA involves building DNA strands and inserting them into organisms using something called vectors. Today this technology is frequently used in the lab, and it was used by the Venter group for their procedure. In the 1970’s and 80’s much of the ethical debate centered on the implications of using rDNA in human beings, even though the procedure was only being used in bacteria. We call the use of rDNA technology in humans, human genetic engineering. Ironically, after all of the hype surrounding this new technology, 30 years of using rDNA has not resulted in success in human genetic engineering.

Reductionists would say that because every organism is composed of genes and life must be defined by its physical parts, if we can engineer and replace DNA in simple organisms, we can do the same in humans. However, in reality we still cannot replace portions of human DNA with synthesized DNA because there is a level of complexity in mammalian cells, and human cells in particular, that scientists still do not understand.

Conclusion: The Meaning of Life Is Not Found under a Microscope

The further down you go, even to the level of atoms, subatomic particles and quarks, you will never find the essence of life; at most you can understand structure. Those are two very different things that are confused when you have a commitment to a materialistic perspective. From a materialistic perspective, the essence is in the structure. Man is the sum of his parts. Contrast this to a theistic perspective. Man is made from similar elements as other organisms, connecting him with part of creation, but he is also beyond creation because of his relationship with or access to God. In a Christian theistic view, in particular, the essence of man is not in his parts but in how those parts combined with his spiritual component make him more than a creature. He is something, someone, made in the image of God. Part of that image is our creativity and ability to communicate original ideas, as well as our self–awareness, including our place in time and our mortality. These are all attributes that describe God. Yet these traits don’t seem to be shared by animals, even animals that are genetically similar to human beings.

In a Science article from 1999, several ethicists considered the implications of Venter’s group’s goal to create a minimal genome. Prophetically, the authors caution against reductionist implications: “…a reductionist understanding of life, especially human life, is not satisfying to those who believe that dimensions of the human experience cannot be explained by an exclusively physiological analysis… There is a serious danger that the identification and synthesis of minimal genomes will be presented by scientists, depicted in the press [ref removed], or perceived by the public as proving that life is reducible to or nothing more than DNA…{9}

Now, eleven years later, one of the authors of that same article responded to the Venter group’s recent announcement by saying:

Venter and his colleagues have shown that the material world can be manipulated to produce what we recognize as life… Their achievement undermines a fundamental belief about the nature of life that is likely to prove as momentous to our view of ourselves and our place in the Universe as the discoveries of Galileo, Copernicus, Darwin, and Einstein.{10}

The author perpetuates the very assumption that the original ethics article cautions against! We should be careful to not assume so much. There is no reason to believe that the ultimate nature of life is locked away in our genes, and many reasons to believe that it is not. The Venter group did not create life; they studied and mimicked the structure of Someone else’s creation.

Notes

1. Jonathan Wells, “Has Craig Venter Produced Artificial Life?” posted on May 24, 2010 on Discover Institute blog, Evolution News & Views, www.evolutionnews.org/2010/05/has_craig_venter_produced_arti035081.html.
2. Original research article published in Science Express online: www.sciencemag.org/cgi/content/abstract/science.1190719
3. Steve Jones, geneticist, quoted by Jonathan Sarfati in “Was life really created in a test tube? And does it disprove biblical creation?” May 25, 2010, creation.com/synthetic-life-by-venter
4. Science Integrity, “Notes on ‘Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome’,” (link to cited article found here), scienceintegrity.net/SynthesizedGenome.aspx
5. The particular bacteria, M. mycoides, was selected because it has one of the simplest known genomes.
6. Quoted in Science vol 286, December 1999, p. 2087. Original quote from Anonymous, Sci Watch (September/October), 3 (1997).
7. Watson, James D., DNA: The Secret of Life, Random House, Inc. New York, 2003.
8. Richard Sternberg, “Current Research,” www.richardsternberg.org/research.php. See also: www.biologicinstitute.org.
9. Science, vol. 286, December 1999, pg. 2087, emphasis added.
10. “Sizing up the ‘synthetic cell’,” online version of commentary in Nature, www.nature.com/news/2010/100520/full/news.2010.255.html.

© 2010 Probe Ministries




Human Genome Project

What’s All the Fuss About the Human Genome Project?

In February of 2001, virtually every media outlet, whether TV news, newspapers, radio, Internet news services, or news magazines, was all worked up about the announcement of the completion of the Human Genome Project. In this article we will explore this monumental achievement and what it means for the future of medicine and our understanding of ourselves.

To appreciate this important accomplishment, we need to review a little basic genetics. It may actually astonish most adults just how much genetics the National Institutes of Health assumes we know about our genetic heritage. The educational video from the HGP includes a three-minute review of basic genetic processes like DNA packaging, transcription of DNA into message RNA, and the translation of message RNA into protein. It’s no exaggeration to say that when I played this short piece during a lecture for high school students and their parents, mom and dad were left in the dust.

Honestly, I did that intentionally; because we are only in the beginning stages of a genetic revolution that will transform the way we diagnose and treat disease and how we may even alter our genetic structure. These new technologies bring with them numerous ethical and moral dilemmas we have only begun to address and for which there may not be simple answers. If we don’t take the time to familiarize ourselves with genetic research and its implications, we risk responding out of fear and ignorance and potentially throwing away crucial medical advances.

I have contended for a long time that we can no longer afford to remain ignorant of genetic technologies. They simply harbor far too great a power for both tremendous good and tremendous evil. We must work hard to take every thought captive to Christ and see what there is of benefit and what avenues of research and application we need to avoid to preserve human freedom and dignity.

Well let’s talk about our genome, the sum total of all our genes. In most of the 100 trillion cells of our body are 46 chromosomes. These chromosomes are tightly coiled and packed strings of a remarkable molecule called DNA (Deoxyribonucleic Acid). DNA is a polymer, a repetitive sequence of four molecules, which I will only refer to by their one-letter abbreviations, A, G, C, and T. The human genome sequence is simply the sequence of these four molecules in DNA from all our chromosomes. If you laid out the DNA from all our chromosomes in each of our cells end to end, it would stretch six feet long.

A gene is a segment of DNA that contains the precise coding sequence for a protein. And proteins do all the real work in our cells. By looking at our completed sequence, it is predicted that our genome consists of 30,000 to 45,000 genes in each of our cells. So, now that we have the sequence, what does it mean? We’ll begin answering that question in the next section.

What Does the Human Genome Project Hope to Accomplish?

The National Institutes of Health in cooperation with several international research organizations began the HGP in 1990 in the U.S. There were four primary objectives among the many goals of the HGP{1}.

The first and primary goal of the HGP was to map and sequence the entire human genome. There is a critical and significant difference between a map and the sequence. There are over three billion letters, or base pairs, in the human genome, spread out over 23 pairs of chromosomes. Trying to locate a sequence of say 1,000 letters, the code for a large protein, is a one in a million task. Therefore, researchers needed a refined roadmap to the genome. The map entails particular sequences that can be used like signs on a road map. If the trait a scientist is studying always seems to be present with this marker, the gene involved is probably nearby. In 1995, a detailed map was published with over 15,000 markers, one for every 200,000 base pairs. This will aid greatly in associating genes with particular diseases. And now with the sequence nearly complete, with over 99% accuracy, determining the precise effect of this gene on disease will be even easier.

A second critical goal was to map and sequence the genomes of several important model organisms: specifically, the bacterium E. coli, yeast, the roundworm, fruit fly, and mouse. This information is helpful, because each of these organisms have been used for laboratory studies for decades. Being able to coordinate knowledge of their genomes with cellular and biological processes will certainly inform our study of the human genome and its various functions.

The third important objective of the HGP was to systemize and distribute the information it gathered. Any sequence over 2,000 base pairs is released within 24 hours. The sequence and map data is contained in publicly accessible databases on the Internet. The HGP has also been creating software and other tools for large-scale DNA analysis.

The fourth and final primary goal of the HGP was to study the ethical, legal, and social implications of genetic research. A full 5% of all funds appropriated for the HGP have been earmarked for these kinds of considerations. There are many concerns revolving around the use of genetic sequence data. Not the least of which are worries about ownership, patenting, access to personal sequence data by insurance companies, potential for job discrimination based on personal sequence data, and the prospects for genetic screening, therapy, and engineering. In the next section we’ll begin investigating how the HGP thinks this information can be used.

What are the Long Term Hopes for the HGP?

The completion of the sequence was announced jointly in February 2001 in the journals Nature{2} and Science{3}. Both Science and Nature have made these landmark issues available, without subscription, on their websites.

The importance of recognizing the sequence of a particular gene has three important ramifications.{4} The first is diagnosis. Over the last few years, single genes have been found leading to deafness and epilepsy. Numerous genes, however, will influence most diseases in complex ways. Recently, genetic influences have been found in many forms of hypertension, diabetes, obesity, heart disease, and arteriosclerosis{5}. Genetic analysis of cancer tumors may someday help determine the most effective drug therapy with the fewest side effects. Genetic diagnosis has the potential to more precisely prescribe treatments for many medical conditions.

Second, diagnosing ailments with more precision with genetics will also lead to more reliable predictions about the course of a disease. Genetic information about an individual’s cholesterol chemistry will aid in predicting the course of potential heart disease. Obtaining a genetic fingerprint of a cancerous tumor will provide information concerning its degree of malignancy. Third, more precise genetic information will also lead to the development of better strategies for prevention of disease.

Many more ailments in newborns can eventually be screened more specifically to avoid disorders later in life. Currently, babies in the U.S. and other countries are routinely screened for PKU, a metabolic disorder that prevents the breakdown of a specific amino acid found in proteins. This condition becomes toxic to the nervous system, but can be prevented and managed with appropriate diet. Without dietary changes, affected babies face extreme mental retardation. Hopefully, the number of conditions this type of screening applies to can be expanded.

Screening can also be done for adults, to see if they may be carriers of potential genetic conditions. Certain Jewish and Canadian populations regularly obtain voluntary screening for Tay-Sachs disease, a known child-killer. This information has been used to help make decisions about future marriage partners.

Perhaps the greatest benefit will come from what is called gene-based therapy. Understanding the molecular workings of genes and the proteins they encode will lead to more precise drug treatments. The more precise the drug treatment, the fewer and milder will be the side effects.

Actual gene therapy, replacing a defective gene with its normal counterpart, is still very experimental. There are still many hurdles to overcome involving how to deliver the gene to the proper cells, controlling where that gene is inserted into a chromosome, and how it is activated.

Not surprisingly, some have seen the human genome sequence as a vindication of Darwin. We’ll examine that contention next.

Did the Human Genome Sequence Vindicate Darwin?

Amid the controversy and exultation over the release of the near complete human genome sequence has been a not so quiet triumphal howling from evolutionary biologists. The similarity of many genes across boundaries of species, the seemingly messy patchwork nature of the genome, and the presence of numerous apparently useless repetitive and copied sequences all have been laid out for us as clear validations of evolution. Really!

If Darwin were alive today, he would be astounded and humbled by what we now understand about the human genome and the genomes of other organisms.

Let’s take a closer look at the claims of one bioethicist, Arthur Caplan{6}, who thought the major news story was missed. So let’s just pick a few of the more glaring statements to help us understand that little in his comments should be trusted.

First, Caplan says, “Eric Lander of the Whitehead Institute in Cambridge, Mass., said that if you look at our genome it is clear that evolution must make new genes from old parts.”

While it may be true that we can see some examples of shared sequences between genes, it is by no means true that we see wholesale evidence of gene duplication throughout the genome. According to one group of researchers,{7} less than 4,000 genes share even 30% of their sequences with other genes.

Over 25,000 genes, as much as 62% of the human genes mapped by the Human Genome Project, were unique, i.e., not likely the result of copying.

Second, Caplan says, “The core recipe of humanity carries clumps of genes that show we are descended from bacteria. There is no other way to explain the jerry-rigged nature of the genes that control key aspects of our development.”

Not everyone agrees. The complexity of the genome does not mean, necessarily, that it has been jerry-rigged by evolution. There is still so much we do not know. Caplan is speaking more out of ignorance and assumption than data. Listen to this comment from Gene Meyers, one of the principal geneticists from Celera Genomics, from a story in the San Francisco Chronicle:

‘What really astounds me is the architecture of life,’ he said. ‘The system is extremely complex. It’s like it was designed.’

My ears perked up. ‘Designed? Doesn’t that imply a designer, an intelligence, something more than the fortuitous bumping together of chemicals in the primordial slime?’

Myers thought before he replied. ‘There’s a huge intelligence there. I don’t see that as being unscientific. Others may, but not me.’{8}

Jerry-rigged? Hardly! Confusing at the moment? Certainly! But more likely to reveal hidden levels of complexity, rather than messy jerry-rigging.

It will take more than bluster to convince me that our genome is solely the result of evolution. The earmarks of design are clear, that is, if you have eyes to see.

What are the Challenges of the Human Genome Project?

In closing, I would like to address what are many people’s concerns about the potential for abuse of this information. While there is great potential for numerous positive uses of the human genome, many fear unintended consequences for human freedom and dignity.

Some are justifiably worried about the rush to patent human genes. The public consortium, through the National Institutes of Health, has made all its information freely available and intends to patent nothing. However, there are several patent requests pending on human genes from the time before the HGP was completed.

It is important to realize that these patents are not necessarily for the genes themselves. What the patent does protect is the holder’s right to priority to any products derived from using the sequence in research. With the full sequence fully published, this difficult question becomes even more muddled. No one is anxious for the courts to try its hand at settling the issue. Somehow companies will need some level of protection to provide new therapies based on genetic information without hindering the public confidence and health.

Another concern is the availability of information about individual genetic conditions. There are legitimate worries about employers using genetic information to discriminate over whom they will hire or when current employees will be laid off or forced into retirement. Upwards of 80-90% of Americans believe their genetic information should be private and obtained or accessed only with their permission. The same fears arise as to the legality of insurance companies using private genetic information to assess coverage and rates. A recent bill (June 29,2000) before Congress to address these very concerns was amended to the Health and Human Services appropriations bill, but was removed in committee. The bill will be reintroduced this session.{9} I would be very surprised if some level of privacy protection is not firmly in place by 2002.

Moreover, many are apprehensive about the general speed of discovery and the very real possibilities of genetic engineering creating a new class, the genetically enhanced. Certainly, there is cause for vigilance and a watchful eye. I have said many times that we can no longer afford to be ignorant of genetic technologies. And while I agree that the pace of progress could afford to slow down a little, let’s be careful not to throw the baby out with the bathwater.

After a series of lectures on genetic engineering and human cloning at a Christian high school, one student wrote me to say:

I am a senior, in an AP Biology class, and I find genetics absolutely fascinating. It’s both fascinating and scary at the same time. . . . [You have inspired me] to not be afraid of the world and science in particular, but to take on its challenge and trust God.

Amen to that!

Notes

1. “Genetics: The Future of Medicine,” NIH, Publication No. 00-4873, 2.
2. Nature, 409 (15 February, 2001), www.nature.com.
3. Science, 291 (16 February, 2001), www.sciencemag.org.
4. Genetics: The Future of Medicine, 9-11.
5. Kevin Davies, “After the genome: DNA and human disease,” Cell, 104 (Feb. 23, 2001), 465-467.
6. www.probe.org/did-the-human-genome-project-prove-that-darwin-was-right/.
7. Wen-Siung Li, Zhenglong Gu, Haidong Waing, and Anton Nekrutenko, “Evolutionary analyses of the human genome,” Nature, 409 (15 Feb 2001):847-849.
8. Tom Abate, “Human Genome Map Has Scientists Talking About the Divine – Surprisingly low number of genes raises big questions,” Monday, February 19, 2001, San Francisco Chronicle.
9. James M. Jeffords and Tom Daschle, “Political issues in the genomic era,” Science, 291 (16 February, 2001), 1249-1251.

© 2001 Probe Ministries International