Evidence That GM Crops and Cloned Cattle are Safe

Two papers in the last week contribute data to the discussion about whether GM crops and cloned cows are safe.  The answer is affirmative.  Sorry, Greenpeace; science trumps ideology, at least in this case.  Fortunately, Toto, this isn't Kansas.

"Insect-Resistant GM Rice in Farmer's Fields: Assessing Productivity and Health Effects in China", by Huang et al in last week's Science, describes a controlled study of a field trial that shows clear evidence for a reduction in use of pesticides, higher crop yields, and improved health of the farmers.  Receipt of GM and non-GM strains for planting was randomized amongst participating farmers, facilitating analysis of the effects of genetic modification.  The results speak for themselves:

This study provides evidence that there are positive impacts of the insect-resistant GM rice on productivity and farmer health.  Insect resistant GM rice yields were 6 to 9% higher than conventional varieties, with an 80% reduction in pesticide usage and a reduction in their adverse health effects.  Such high potential benefits suggest that produces from China's plant biotechnology industry could be an effective way to increase both competitiveness internationally and rural economies domestically.  The benefits are only magnified if the health benefits are added.

There has been considerable discussion about the health and economic impacts of GM food crops, with neither side having much data on their side.  This is particularly important for China, because they want to commercialize both strains studied in the field trial, which makes any uncertainty a threat to success in the market.  Now, however, the evidence indicates GM food crops are both safe and economically superior.

And it isn't just biotech plants that are proving safe.  In a paper in last week's PNAS, Tian et al studied the composition of milk and beef from cloned cattle.  Milk from the cloned cattle was virtually identical to control animals as determined by measuring fat content, lactose content, and protein composition.  The beef cattle were cloned from a bull chosen because of a high fat marbling score; unsurprisingly the clones demonstrated a high fat content as well.

The authors note that while only small number of animals were studied in this pilot project, "most parameters of the composition of the meat and milk from somatic animal clones were not significantly different from those of their genetically matched comparators or industry beef comparators, and that all parameters examined in this study were within the normal range of beef and dairy products approved for human consumption".

Broken Drug Development Model

Sam Jaffe's article in Technology Review, "A Dip in Time", discusses some well known problems with the pharmaceutical industry.  Namely that it costs a ridiculous amount of money to get a drug into testing, which is just the beginning of the financial gamble because it is so hard to predict how new compounds will behave in a large and complex population.  More interesting for me is the suggestion -- within the first sentence, even -- that, "Some [are speculating] that the way new drugs are financed and brought to market will soon be overhauled".

With venture firms basically gambling that one or two in ten investments will pay for the rest, we certainly can't expect innovation from that direction.  Alas.

The article ends with a note that Millennium Pharmaceuticals is using genetic/genomic screening to choose which patients to include in drug trials.  This will certainly help with the trials, but it is rather a backwards strategy to take what you happen to have on hand and see who benefits.  That said, this is what most companies have to work with, and they are looking out for the bottom line first and foremost.  It is clear some significant effort needs to be put in to changing the whole drug discovery and testing infrastructure, so that it is a bit more rational at the front end.

Richard Meagher and Phytoremediation

Richard Meagher, at the University of Georgia, is doing some excellent work using plants to clean up toxic materials in soils, a technology otherwise known as phytoremediation.  Meagher's lab genetically modifies plants and trees so that they express a bacterial gene that helps metabolize complex mercury and arsenic compounds.  His team has achieved impressive results, some of which was described in National Geographic's Strange Days on Planet Earth.

Another biological chassis and power supply

If you want to build new widgets using biology, you need to work with cells amenable to the task.   Tom Knight, at MIT, prefers the innocuous insect commensal bacterium Mesoplasma florum as a prototype biological chassis and power supply for genetic circuits.

After reading my article on garage biology in this month's Wired, David Metzgar, at the Naval Health Research Center, sent me a paper describing another candidate organism, Acinetobacter ADP1.  The paper describes ADP1 as naturally competent for genetic transformation and that it has a "strong natural tendency towards homology-directed recombination."  That is, it likes to harvest DNA from its environment and incorporate it into its genome.  Metzgar writes that, "The close relationship between E. coli and ADP1, combined with the newly available whole genome sequence of ADP1, allows the tremendous amount of existing knowledge related to gene function and metabolism of E. coli to be applied directly to ADP1."  They ported a variety of genes directly from coli to ADP1 without modification.

Since it is common, easily grown, and poses no pathogenic threat to humans, this could be a useful bug.

Technology transfer to middle school students

The upcoming 86th ANNUAL MEETING of the AAAS Pacific Division will be in Ashland, OR, June 12-16, 2005.  There will be a couple of workshops put on by Bio-Rad to help teachers understand how to use various kits within the classroom.  From the looks of it, some fairly sophisticated technology is now being introduced to students as early as middle school.  No genetic modification, but the workshops cover tools everyone uses in the lab to understand the systems they are working on, or systems they are building.

From the Meeting Schedule:

Bio-Rad Corporation of Hercules, CA, is presenting the following five hands-on workshops to give middle school, high school and university instructors the opportunity to try out some of the molecular biology kits they offer to educators. There is no charge for these workshops. However, participants must be registered for the meeting. Be sure to wear your meeting badge to each session. Space is on an “as available ” basis and preregistration is not required. Bio-Rad representatives will provide certificates of attendance for those desiring to utilize these workshops for professional development credits.

Wednesday, June 15

8:30 a.m.Genes in a Bottle. Extract and bottle your own DNA. Introduce your students to molecular biology with their own DNA! In this activity, you will extract and bottle the DNA from your own cheek cells to make a necklace. This real-world laboratory procedure is used to extract DNA from many different organisms for a variety of applications and integrates multiple life science standards in a single lesson. Seeing DNA makes it real. Be the first at your school to wear your DNA!

10:30 a.m. ELISA Immuno Explorer. Biology's magic bullet. Explore immunology with this topical, new hands-on classroom lab.ELISA (enzyme-linked immunosorbent assay) is a powerful antibody-based test used to detect diseases such as HIV/AIDS and SARS, and to trace pathogenic agents in water, food, and the air whether these emerge naturally or through acts of aggression. You will simulate the spreading of a disease, perform ELISA, and learn how this assay is used to identify and track agents of disease , or to detect molecular markers of cancer, pregnancy, and drug use. This kit integrates multiple standards in a single lesson, including antigen-antibody interactions and the role antibodies play in medicine, epidemiology, and biotechnology.

1:30 p.m. PV92 PCR. What pair of genes are you wearing? PCR is central to forensic science and many medical, archaeological, and ecological procedures. You will extract DNA from your own hair samples, then amplify and fingerprint a pair of alleles, an Alu repeat within PV92, a real forensic marker. This activity integrates multiple life science standards in a single lesson and covers a range of core content areas, from DNA replication to evolution to Hardy-Weinberg equilibrium theory.

Thursday, June 16

9:00 a.m. GMO Investigator/Analysis. Have your favorite foods been genetically modified (GM)? Currently, genetically modified organisms (GMOs) in foods do not have to be labeled in the US. Regardless of where you stand in the GM debate, wouldn't it be fun to know if the corn or soy-based foods you eat are GMO foods? This kit uses DNA extraction techniques, PCR, and gel electrophoresis to test common grocery store food products for the presence of GMO foods. This activity integrates and reinforces multiple life science standards in a single lesson.

1:00 p.m. Protein Fingerprinting. Can molecular evidence support evolution? DNA gets a lot of attention but proteins do all the work. Proteins give organisms their form and function and are the raw material for evolution because natural selection acts on phenotypes. Over time, accumulated changes in DNA (genotypes) lead to variation and ultimately, speciation. You will extract muscle proteins from both closely and distantly related species of fish and use protein electrophoresis to generate protein fingerprints to look for variations. This activity integrates multiple life science education standards in a single lesson from physiology to the theory of evolution to exploring the molecular framework of biology. DNA>RNA>Protein>Trait.

Geographical Distribution of Biological Technologies

I just stumbled over William Hoffman's World Stem Cell Policy Map, which shows the geographical distribution of policy about stem cells and major genome sequencing centers.  It is part of a larger project to create Global Maps of Human Technological Development, including Global Biotechnology Clusters and Global Biotech Crops.

With the amount of cutting edge research and development taking place in China, India, Taiwan -- the list goes on -- it is interesting to see things laid out this way.  I have concentrated mostly on how technologies are changing in time, and on constructing analogies to help understand what sorts of technologies we need to do better biology.

But the geographical perspective is instructive.  There are obvious clusters of research, some of which lie in countries that are dramatically more permissive about clinical trials than is the US.  It wouldn't take that much in the way of resources to plunk down a cutting edge center in most of the blank areas of the map.  I hope Mr. Hoffman keeps things updated so we can see how the maps develop.

Stem Cell Therapy in India

The 17 March, 2005, issue of Nature has a story titled, "Indian regulations fail to monitor grown stem-cell use in clinics", by K.S. Jayaraman.  The article explains that guidelines for research will be discussed soon, though stem cell are already being used in clinics.  It is yet another indication of how readily new biological technologies will be adopted as soon as they become available.  Like the clinical use of stem cells in Russia, the article notes there appears to be little central awareness of which studies are being performed where.  The "nation's premier medical institute" is pursuing clinical applications of stem cells for treating a variety of conditions without governmental knowledge or approval.  The article notes that, "The quality of cells being used in therapy is of major concern, as is the failure of clinicians to understand basic stem-cell biology."

If these treatments do show promise, I wonder how quickly US and European regulators will move to get clinical trials underway, or if they will insist that treatments on this side of the world be derived from a more basic understanding of mechanisms.  That will definitely slow things down.

"Stem-Cell Craze Spreads in Russia"

A tidbit from the AP today about quasi-legal stem cell treatments in Russia (via Wired News), "Stem-Cell Craze Spreads in Russia".  Evidently, treatments putatively consisting of adult and/or embryonic stem cells are being used as treatments for everything from cosmetic adjustments to MS.  The treatments are totally unregulated and at best skirt the edge of what is legal in Russia.  It is unclear where the cells are coming from, or whether those performing the injections have the skills and equipment to isolate stem cells in the first place.  No studies are being performed to follow the patients, or to find out if the treatments are causing harm.

This demonstrates the lengths people are willing to go in order to take advantage of new, unproven technologies.  It also suggests the extent of body modification we can expect when real treatments are demonstrated using stem cells, particularly those that have been genetically modified or coaxed to differentiate into particular tissue types.  Feather goatees will be passe.

The Thousand Dollar Genome

I have once again been hearing noises about the "thousand dollar genome" (TDG).  That is, a human genome read de novo for a USD 1000 or less.  Here (REVOLUTIONARY GENOME SEQUENCING TECHNOLOGIES -- THE $1000 GENOME), for example, is a request for proposals from the National Human Genome Research Institute to develop technology that would enable the TDG.

Based on my early efforts to quantify how the productivity and cost of sequencing were changing, Steward Brand asked me back in 2002 when we would get the TGD. 

Thousand_dollar_genome_3Here is the plot I generated in response (click on the figure thumbnail for a full-sized version).

The cost hasn't changed dramatically recently, and at the current pace we we won't get the TDG until sometime after 2020.  With 3 billion (3x109) bases in the human genome, we need to hit USD .3x10-6 per base (which is .3 microbucks, 300 nanobucks, 300 nanodollars per base -- nanoeconomics anyone?) to reach the Thousand Dollar Genome.  However, the numbers on the plot are primarily based on instruments that use slab gel electrophoresis and capillary electrophoresis.  Thus as new technologies emerge we could very well get to the TDG much more rapidly.