Archive for the 'Biology' Category

Norman Borlaug: green revolutionary

…when journalist Gregg Easterbrook sought a publisher for a popular biography, “they said he was boring,” the self-described “environmental optimist” says. “If he’d killed someone instead of saving hundreds of millions of lives, then they’d have been interested.”

Borlaug is almost unknown, at least in big media, though he contributed more than any other researcher to the “green revolution”. Borlaug’s recent biography The Man Who Fed the World is a must-read.

Paradoxically, 1968 also saw the genesis of an environmentalist dogma that was pessimistic about humanity’s capacity to feed itself. In that year–when the global population growth rate peaked, at 2 percent per year–Paul Ehrlich published The Population Bomb, intoning, “The battle to feed all of humanity is over. … Hundreds of millions of people will starve to death in spite of any crash programs.” The madding crowd of “stinking hot” Delhi was odious to Ehrlich: “My wife and daughter and I … entered a crowded slum area. … People, people, people, people. … [We] were, frankly, frightened.” It was a “fantasy,” he said, that India would ever feed itself. Yet Borlaug’s program delivered such stunning results that India issued a 1968 stamp commemorating the “wheat revolution,” and by 1974 it was self-sufficient in all cereals.

Nonetheless, a neo-Malthusian fear of overpopulation became endemic to environmentalist thinking. Science philosopher and Arts and Letters Daily founder Denis Dutton says, “Well-fed Greens flaunt their concern for the planet but are indifferent, even hostile, to the world’s poor with whom they share it. Some Greens I knew acted for all the world as though they relished the idea of a coming worldwide famine, much as fundamentalists ghoulishly looked forward to Armageddon.” Dutton, who served in the Peace Corps, personally saw the Green Revolution benefit India. “For the catastrophist, India becoming a food exporter was disturbing,” he says. “This wasn’t supposed to happen. They blame Borlaug for spoiling the fun.”

Not all Borlaug’s critics were catastrophists: some opposed the intensity of his agriculture, especially its use of inorganic fertilizer. Borlaug acknowledges the need for care, but he says the “natural” alternative, cow manure, “would require us to increase the world’s cattle population from around 1.5 billion to some 10 billion.” As he dryly observed in a 2003 TV interview, “Producing food for 6.2 billion people … is not simple.” He added, “[Organic approaches] can only feed four billion–I don’t see two billion volunteers to disappear.”

Raised on a farm, Borlaug thinks many of his detractors would benefit from a week or two in the fields. He cites Ghanaian farmers who use no-till agriculture (that is, plant waste is left to improve the humus and reduce erosion) and control weeds with herbicides. Their lives are improved by the reduction in weeding. “Less backache, you see,” he once said. “You know, it’s amazing how often campaigners in rich countries think poor people don’t get backache.”

Why didn’t Africa benefit from Borlaug’s advanced wheat? In short, no irrigation, soils, politics, roads.

Many thought the work that earned Borlaug his Nobel brought an end to stem rust, but it is back, in the form of a variant called Ug99, which emerged in Uganda and spread to Kenya and Ethiopia. “If it continues unchecked,” says Borlaug, “the consequences will be ruinous.”

…The reasons for failure in Africa are complex. “Irrigation is first,” explains Michael Lipton of the University of Sussex’s Poverty Research Unit. “In sub-Saharan Africa, 4 percent of cropland is irrigated. In South and East Asia it’s nearer 40 percent.”

Then there’s soil. “Africa’s soils … [are] equivalent–and were once adjacent–to the Cerrado’s acid soils,” Borlaug says. The Cerrado, an area that extends across central Brazil, historically had some of the least productive soil in the world. But improved crop varieties of the sort that Borlaug created–along with liming, fertilizer, and low- or no-till methods–have led to the single largest increase in arable-land usage in the last 50 years.

Politics, both regional and global, were and are another hindrance. “If the Green Revolution in India was proposed to the World Bank today, it would be turned down,” says Rob Paarlberg, an agricultural-policy expert at Wellesley College. By the 1980s, he says, “public investment in roads, research, irrigation, fertilizers, and seeds was politically unacceptable to the Washington consensus on the right–and on the left, among environmentalists opposed to chemical fertilizers, road building, and irrigation projects.” Thus, real per capita levels of official development assistance for the agricultural sector in the poorest countries fell by nearly 50 percent between 1982 and 1995.

Finally, Borlaug says, “Africa needs roads. Roads bring know-how and fertilizer to farmers and ideas and business for commerce.” Africa, Borlaug argues, also needs concerted international help. Meanwhile, Ug99 has reached Yemen: from there, Borlaug warns, “it can reach Iraq, Iran, India, and Pakistan”–even the breadbaskets of Europe and America. A scramble is on to find resistant varieties, ensure that their yields will encourage farmers to adopt them, and produce sufficient tonnages of seed.

Last year, ABC, CBS, and NBC cameras were absent when Borlaug was presented with the Congressional Gold Medal…

<more>

Craig Venter publishes his diploid genome

Edge 221 is a fun issue, beginning with the translation from German of a Jordan Mejias’ report on the meeting at Brockman’s farm:

Was Evolution only an interlude? At the invitation of John Brockman, science luminaries such as J. Craig Venter, Freeman Dyson, Seth Lloyd, Robert Shapiro and others discussed the question: What is Life?

EASTOVER FARM, August 30th

It sounds like seaman’s yarn what the scientist with the look of a sea dog has in store for us. The suntanned adventurer with the close-clipped grey beard vaunts the ocean as a sea of bacteria and viruses, unimaginable in their varieties. And in their lifestyle, as we might call it. But what do organisms live off? Like man, not off air or love alone. There can be no life without nutrients, it is said. Not true, says the sea dog. Sometimes a source of energy is enough, for instance, when energy is abundantly provided by sunlight. Could that teach us anything about our very special form of life?

J. Craig Venter, the ingenious decoder of the genome, who takes time off to sail around the world on expeditions, balances his flip-flops on his naked feet as he tells us about such astounding phenomena of life. Us, that means a few hand-picked journalists and half a dozen stars of science, invited by John Brockman, the Guru of the all encompassing “Third Culture”, to his farm in Connecticut.

Relaxed, always open for a witty remark, but nevertheless with the indispensable seriousness, the scientific luminaries go to work under Brockman’s direction. He, the master of the easy, direct question that unfailingly draws out the most complicated answers, the hottest speculations and debates, has for today transferred his virtual salon, always accessible on the Internet under the name Edge, to a very real and idyllic summer’s day. This time the subject matter is nothing other than life itself. <more>

Edge offers links to several media reports on the new Venter Institute paper in Plos Biology. Here’s a brief report from ScienceNow:

For the first time, researchers have published the DNA sequence from both sets of chromosomes in a single person. That person is none other than pioneering genome researcher J. Craig Venter. The new sequence suggests that there is substantially more variation between humans than previously recognized and pushes personalized medicine a step closer.

In 2001, Celera Genomics, a company then headed by Venter, and, separately, the International Human Genome Project consortium each published a genetic blueprint for a human. To save time and money, both teams combined samples from several individuals and created composite genomes that contained only half of a human’s DNA. Humans have a diploid genome with 23 pairs of chromosomes–with one of each pair contributed by the father and the other by the mother—and the researchers hoped that these partial “haploid” genomes wouldn’t sacrifice much detail. Wrong, says a massive 31-page paper published in the October 2007 PLoS Biology by Venter, his colleagues at the J. Craig Venter Institute in Rockville, Maryland, and collaborators from three universities.

According to the study, haploid genomes underestimate the amount of genetic variation between individuals by a factor of 5. “We all had very naïve assumptions because we didn’t have that much data to go on,” says Venter.

Venter and co-workers compared his two haploid genomes to assess the differences between the DNA he inherited from his mother and that from his father. They looked for everything from easy-to-find differences in single bases to much more obscure variations in chunks of DNA sequence that had been inserted or deleted from chromosomes. All told, the analysis found more than 4 million variants between Venter’s maternal and paternal chromosomes. This suggests that humans differ by 0.5%, not 0.1% as suggested by earlier estimates. (Some researchers, however, note that recent studies of insertions and deletions have emphasized the same point.)

“This is a great study,” says Harvard University geneticist George Church, an early proponent of the Human Genome Project. “We need to have diploid genomes to sort out our full inheritance. If I walk in to a doctor, it isn’t going to do either of us any good if he just gets my dad’s genome.”

Technorati Tags: ,

End of “the Darwinian interlude”?

John Brockman just published the email exchange between Freeman Dyson and Richard Dawkins regarding Dyson’s essay “Our Biotech Future”. This is in Edge 221 with no direct link — just scroll down to The Reality Club.

As part of this year’s Edge Event at Eastover Farm in Bethlehem, CT, I invited three of the participants—Freeman Dyson, George Church, and Craig Venter—to come up a day early, which gave me an opportunity to talk to Dyson about his abovementioned essay in New York Review of Books entitled “Our Biotech Future”.

I also sent the link to the essay to Richard Dawkins, and asked if he would would comment on what Dyson termed the end of “the Darwinian interlude”.

Early the next morning, prior to the all-day discussion (which also included as participants Robert Shapiro, Dimitar Sasselov, and Seth Lloyd) Dawkins emailed his thoughts which I read to the group during the discussion following Dyson’s talk. [NOTE: Dawkins asked me to make it clear that his email below “was written hastily as a letter to you, and was not designed for publication, or indeed to be read out at a meeting of biologists at your farm!”].

Now Dyson has responded and the exchange is below.

Technorati Tags:

Craig Venter: The Bill Gates of Artificial Life?

There he goes again, says a group of scientists and activists alarmed by the latest rebel moves of J. Craig Venter.

I think that Duncan and ETC may be getting a bit more breathless than the facts merit. As best I can tell Venter is investing his own money towards the laudable goal of harnessing synthetic biology. See the end of Duncan’s post for some perspective.

Since butting heads with the scientific establishment during the sequencing of the human genome–and coming out rich and famous in the process–Venter has had the moxie and smarts to know just when it’s time to blend science with commerce.

This time he’s trying to cash in with a patent for artificial life–specifically, a designer microbe that Venter and his pals at the Venter Institute have been trying to assemble from scratch. In 1999, Venter and Nobel laureate Hamilton Smith used a simple bacterium called Mycoplasma genitalium to roughly figure out the minimal number of genes it would take for an organism to live. Since then they have been trying to synthesize this “minimal genome” inside a cell that could be augmented by additional genes to do things like produce hydrogen or gobble up carbon dioxide.

Three years ago, when I last visited Venter’s institute, located in Rockville, Maryland, he told me he and his colleagues were making great progress on finishing this artificial bug. But so far there has been no announcement of success. “This is not easy to do, to build a living organism from scratch,” he said at the time.

Whatever success or failure the team has had, Venter the businessman quietly filed an application last October that seeks to own the critter his lab wants to create. The U.S. Patent Office published the application (#20070122826) on May 31.



June 18, 2007: Addendum to Readers

After publishing this blog, a spokesperson for the Venter Institute e-mailed me to say that Craig Venter speaks often about the societal implications of synthetic biology. In 1998, the Institute of Genomic Research, founded by Venter, issued an ethical report on the topic authored by a team led by bioethicist Arthur Caplan of the University of Pennsylvania. In 2005, the policy group at the Venter Institute, along with MIT and the Center for Strategic and International Studies, were given a grant from the Sloan Foundation to review societal issues and laboratory practices surrounding synthetic genomics. (Check out the press release issued in 2005.) Their final report from this review will be issued in July. The Venter Institute spokesperson said that the ETC was invited to attend meetings and present comments, but apparently it did neither.

Venter seems determined to forge ahead with his work and with his patent–which is his prerogative as a scientist. It is also the prerogative of critics to continue to challenge Venter and others as they push science to the edge of what society may or may not tolerate at the moment. In between is the great mass of society that will undoubtedly pay scant attention to either side, although the outcome of this discussion may have far-reaching implications–if Venter is able to create a truly synthetic organism.

I plan to closely follow this issue and read the Sloan-funded report next month. Let’s pick up this discussion again then.

Technorati Tags:

LS9: biofuels from microbes

Here’s another Vinod Khosla biofuels venture — this one betting on synthetic biology. In this case, to design bacteria that can cost-effectively convert sunlight + land to hydrocarbons.

…LS9, of San Carlos, CA, is using the relatively new field of synthetic biology to engineer bacteria that can make hydrocarbons for gasoline, diesel, and jet fuel. Hydrocarbon fuels are better suited than ethanol to existing delivery infrastructure and engines, and their manufacture would require less energy. To make biological production of hydrocarbons a reality, the company is bringing together leaders in synthetic biology and industrial biotechnology.

LS9 is at a very early stage: the company was formed in 2005, but its existence was announced only this winter. It plans to engineer microbes to incorporate gene pathways that other microbes, plants, and even animals use to store energy…

The company has $5 million in funding from Khosla Ventures, of Menlo Park, CA, and Flagship Ventures, of Cambridge, MA. Its acting CEO, Douglas Cameron, is former director of biotechnology research at Cargill and chief scientific officer at Khosla Ventures. Flagship CEO Noubar Afeyan cautions that no one can tell the extent to which any biofuel will displace fossil fuels. “That is a subject of great debate and great prognostication,” he says. “The opportunity is so large that I don’t have to believe in much more than a few percentage points of market penetration for it to be worth our investment.”

…LS9 is counting on the fact that ethanol is not really the best biofuel. Del Cardayre notes that ethanol can’t be delivered through existing pipelines. It also contains 30 percent less energy than gasoline, and it must be mixed with gasoline before being burned in conventional engines. LS9’s fuels would have none of these disadvantages. What’s more, LS9’s fuels might be produced more efficiently than ethanol. For example, at the end of ethanol fermentation, the mixture has to be distilled to separate ethanol from water. LS9’s products would just float to the top of a fermentation tank to be skimmed off. Overall, the LS9 process consumes about 65 percent less energy than today’s ethanol production, the company says.

As I read that LS9 is projecting they can produce some sort of biofuel [of what energy content?], for 1/3 the energy input of which kind of ethanol. Not much we can get our teeth into, but I wish them success.

Life 2.0: synthetic biology

…I’m a geneticist, I write code… “scientist” in “Red Planet”

Lee Silver wrote a fairly useful Newsweek piece on developments in synthetic biology [“SynBio”]. I expected very little from Newsweek, but Dr. Silver did a pretty good job [he is a professor of molecular biology at Princeton].

I’ve been following [better said, attempting to follow…] the pioneering efforts of Prof. Drew Endy of MIT. Endy is the prime mover behind the BioBricks Foundation and openwetware. The aim of the BioBrick™ program is an open source [!!] catalog of standard biological parts that bio-engineers can design into innovative new life [i.e., Life 2.0]. Unlike evolved natural life, BioBrick™ parts come with a “user manual”, have well-defined interconnects and transform behavior. Think of the biologic equivalents of NAND gates or inverters but typically with proteins as inputs/outputs in place of logic levels.

For more background, see this 8 Jan, 2007 post which goes into some detail on Endy and synthetic biology. From an interview with Dr. Endy on Futures in Biotech 8:

…in 10 years we’ll have the technology to construct human genomes - from scratch. …So what the genetic engineer of the future wants is a laptop computer hooked up to a database of standard bio-parts. On that computer I want to run software that allows me to mix and match the parts to define a big piece of DNA that will be the program for the bio-system I want to build. The design I develop with my program gets shipped to a DNA synthesis company which ships the finished DNA back to me by overnight express. Think of chip design/chip fab — but for living systems.

Also in the Newsweek issue is this essay by computer scientist, scifi author Rudy Rucker Our Synthetic Futures: What might happen if we repurpose biology to our own ends? [speculation, not science].

Technorati Tags: ,

DNA sequencing is fast getting faster

Co-discoverer of DNA James Watson was recently presented with a draft of his personal genome! Here’s an update on the rapid innovations in DNA sequencing over the last ten years.

The goal of $1000 per unique human genome sequencing is not far away — I’ll speculate about ten years, perhaps sooner. The $10 million Archon X Prize for Genomics could be awarded in 2009. In brief, the prize is for achieving a repeatable cost of $10,000 per genome:

to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 per genome.

The human genome is comprised of about 3.2 billion base pairs [three gigabases]. The first draft genome sequence cost about US$ 3 billion [1991 dollars, the total of a 13 year research program]. But the cost per gigabase was dropping sharply during the course of the project:

It took 4 years for the international Human Genome Project to produce the first billion base pairs of sequence and less than 4 months to produce the second billion base pairs. In the month of January 2003, the DOE team sequenced 1.5 billion bases.

Craig Venter’s Celera Genomics shotgun sequencing effort cost about $300 million, undertaken in 1998, near what turned out to be the end of the first draft genome sequencing. Venter’s technology was an early breakthrough in fast sequencing. For an update on the impact and pace of innovation in genomics, there are two excellent TED Talks, both available in both audio and video:

Juan Enriquez on genomics and our future

Craig Venter on DNA and the sea

Today 454 Life Sciences is one of the latest innovators slashing sequencing cost and time. I first encountered “454″ in the Futures in Biotech segment on “Ancient DNA -The Neanderthal Genome“, a fascinating interview with Dr. Svente Paabo, Director of the Department of Genetics at the Max Planck Institute for Evolutionary Anthropology and Dr. Thomas Jarvie, Technical Application Manager at 454 Life Sciences. Here is a synopsis of the Neanderthal project, with links to published papers.

So sequencing is fast getting faster, and faster is generally proportionally cheaper. This week there are two MIT Technology Review articles on fast sequencing. Co-discoverer of DNA James Watson was recently presented by 454 with a draft of his personal genome — a truly remarkable milestone:

On February 6, 2007, executives from 454 Life Sciences showed 78-year-old James Watson a first draft of his own genome. There was something downright poetic about this. Watson, of course, had won a Nobel Prize 45 years earlier for his role in discovering the double-helical structure of DNA; he was also a prime mover behind the Human Genome Project, which by its completion in 2003 had spent nearly $3 billion over 13 years extracting the blueprint that those helices encode. Now 454 had moved a step beyond that megaproject, which pooled many people’s DNA to determine the genetic sequence of what amounts to a model human. The company and its so-called next-generation sequencing machine had single- handedly read the genetic code of an individual–one whose work had done so much to make the achievement possible.

…The vast majority of labs that do sequencing today use a machine made by Applied Biosystems that spits out about two million bases a day.

The latest sequencer from 454 can read 300 million a day.

“Project Jim” so far has cost $200,000 and is not completely finished. But a year ago a personal genome sequence was in the 3$ million range, so we are close to reaching another order of magnitude reduction — as Craig Venter achieved in 1998. If sequencing cost behaves roughly like Moore’s law, we should see cost/time reductions of about 1000 per decade.

Low-cost sequencing will generate a revolution in drug development and drug delivery. E.g., unless the patient is one of the roughly 20% of breast cancer victims having a particular variant of the human genome, there is no point in administering Genentech Inc.’s drug Herceptin. If your personal genome places you in that 20% group then your quality of life is likely to be far higher. Similarly for several other anti-cancer drugs already approved, and for dozens currently in trials. More from Technology Review [part 2] on the impact of single-molecule sequencing:

…The traditional sequencing method looks at DNA from many different cells. But if one of those cells is, say, a tumor cell, its sequence can differ slightly from those of the healthy cells. In such cases, the computers select the sequence that’s most commonly found and discard the others. Next-­generation sequencers like the ones marketed by 454 instead clone and sequence single molecules of DNA, allowing “ultradeep” probing that can unearth rare variants. (Traditional sequencers can also analyze single molecules, but it’s prohibitively expensive.) The implications of single-molecule sequencing are enormous for medicine. While it is not practical to use conventional sequencing to sniff out the DNA differences between healthy and diseased cells, the new machines can perform such experiments easily.

Matthew Meyerson, a clinical pathologist at the Dana- Farber Cancer Institute in Boston, has published a study showing how the 454 machine can help uncover mutations linked to lung cancer. Lung-cancer drugs now available target the gene that Meyerson is sequencing, and he hopes that physicians will ultimately gain a better handle on who will respond to which drugs by learning whether the patient has a particular mutation. “I imagine in a few years all cancer patients will have their tumors characterized by single-molecule sequencing if the technology continues to decrease in cost,” he says.

In a variation on this theme, Michael Kozal, an AIDS clinician at Yale, has joined with 454 to do ultradeep sequencing of HIV to determine the presence of minor populations of drug-resistant virus. Early tests of the technique in patients detected about twice as much resistant HIV as Sanger sequencing did. This information, too, could help physicians individualize treatment regimens, which would increase cost-effectiveness. “It’s practical to do in our system,” says 454 chief scientist Michael Egholm, who is collaborating with Kozal. “Before, it simply wasn’t affordable.”

What do we do when we get there?

…It is realistic to expect that within the next ten years, rapid low-cost sequencing of the human genome will become a reality. “Nearly 70% of expensive medical decisions are made literally on the spot. Rapid sequencing could provide essential information about individual genomes that could immediately affect bedside care,” says [Jonathan] Rothberg [founder and the chairman of 454].

“Sequence-directed choice of care will be especially critical for heterogeneous diseases like cancer. For insurance purposes, sequencing should decrease overall patient-related costs, including days in the hospitals or number of procedures. In this case, the cost of diagnostic sequencing could be substantial, perhaps several thousands of dollars, and still provide financial benefit for the insurers.”

Undoubtedly, genetic information could provide for great benefits to patients. At the same time, issues of fairness in the use of this information loom. “Consequences of the abuse of the genetic information are important to consider,” says Dr. Peterson. The U.S. DOE and the NIH devote 3–5% of their annual Human Genome Project budgets toward studying the ethical, legal, and social issues surrounding availability of genetic information.
For you researchers, the three teams who have registered to compete for the Achron X Prize for Genomics are VisiGen Biotechnologies, 454 Life Sciences, and the Foundation for Applied Molecular Evolution.

Technorati Tags:

Extending health span, Futures in Biotech

Via Glenn Reynolds, here’s a useful interview of two leading researchers in human aging:

Participants: Lenny GUARENTE, PH.D.: Novartis professor of biology at M.I.T. and author of “Ageless Quest: One Scientist’s Search for Genes That Prolong Youth.”; Robert N. BUTLER, M.D.: Founding director of the National Institute on Aging, a founder of the Alzheimer’s Disease Association and winner of a Pulitzer Prize in 1976 for “Why Survive? Being Old in America.” He heads the International Longevity Center.; SARA DAVIDSON: Author, most recently, of “Leap! What Will We Do With the Rest of Our Lives?”

For a much more in depth discussion with Dr. Guarente, I recommend Futures in Biotech 2: Dr. Leonard P. Guarente on Aging.

If you would like to hear top scientists in molecular biology explain their latest research, Futures in Biotech is a remarkable resource.

Technorati Tags: ,

INSTEDD: pre-TED2006 outline of Larry Brilliant’s proposal

Bruno Giussani posted an email outline of Larry Brilliant’s INSTEDD proposal [International Networked System for Total Early Disease Detection]:

UPDATE 19 April 06 - Here is something Larry Brilliant wrote a few weeks before TED2006 describing his vision for what he later called INSTEDD, for International Networked System for Total Early Disease Detection (this text was sent a few days ago by TED curator Chris Anderson to a few thousand people in the TED mailing list). I’m reproducing it here because it’s a powerful vision, and because it offers a few more details that are not in the texts above:

I’ve been in conversations with WHO, CDC, Johns Hopkins and the other universities from the Pandefense “consortium” about using the prize - and the TED community - to build a virtual earth, with

multiple webcrawlers
infobots
comparative historical databases
hi-res coordinated satellite photography
IM and text messaging
several other IP based systems

for the earliest possible detection of new outbreaks of bird flu, novel diseases like SARS and ebola, as well as new emerging biological threats, whether bio-terror or bio-error - and extending to famine, flood, natural disasters, chemical and industrial spills, forced migration and other catastrophes where time is of the essence in responding.

The world would not today be playing catch up with new pandemics if we had such a system in place 30 years ago; governments would not be able to hide cases of bird flu or genocide, they would not be able to delay reporting cases of polio and the world would have an entirely different view of emerging new communicable diseases if such a system were operative.

I don’t know if you know that SARS was first discovered by a group in Canada following up on reports from a webcrawler about cases of fever, even though the first cases were in China. The system they used, GPHIN (Global Public Health Intelligence Network) is a courageous Canadian government-owned system which crawls newspapers, websites, and public documents in only half a dozen languages. I would like to use the resources of the TED community to produce a “GPHIN on steroids” that would crawl 150 languages, be fully open source, transparent, and a trusted system, openly available to anyone especially at country and local level in the concerned countries, and at universities…

Latest news, Google, the Omidyar Foundation and VC firm Kleiner Perkins have pledged support, and many individuals around the world have done the same (there is room for more).

Technorati Tags: ,

Venter’s expedition finds DNA coding for six million new proteins

A year ago I wrote about Craig Venter’s Sorcerer II Expedition. For more background there are four other posts on Venter’s work here.

Three papers based on the work of the ocean sampling expedition have just been published in the journal PLoS Biology. According to MIT Technology Review, the new papers reveal

six million new proteins, doubling the number of known protein sequences. “Everywhere we sampled, we found new proteins,” says Venter.

Researchers focused largely on analyzing new protein-coding sequences, rather than on identifying specific microorganisms, because the variety of DNA made it difficult to assemble into single genomes. (DNA sequences generated from a drop of seawater contain fragments from the genomes of many different microorganisms. Scientists liken this to trying to put together a puzzle from a box containing a few pieces from a thousand different puzzles.)

This new collection of proteins should shed light on how proteins evolved, and perhaps even hint at the genetics of our earliest ancestral organisms. “With a diverse collection of proteins, you can build a phylogenetic tree and try to infer function and how it evolved,” says Shibu Yooseph, a scientist at the J. Craig Venter Institute, in Rockville, MD, and the lead author of one of the PLoS Biology papers. “For every family we’ve looked at, both the number and diversity of new proteins was really unexpected.”






Bad Behavior has blocked 2451 access attempts in the last 7 days.