Lifeboat Foundation: Safeguarding Humanity
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Category: biotech/medical

According to ScienceDaily:

The British-American biotech company Acambis reports the successful conclusion of Phase I trials of the universal flu vaccine in humans. The universal influenza vaccine has been pioneered by researchers from VIB and Ghent University. This vaccine is intended to provide protection against all ‘A’ strains of the virus that causes human influenza, including pandemic strains. Therefore, this vaccine will not need to be renewed annually.

InfluenzaWhat would make this new vaccine different from the ones already available is that it would target M2e, a conserved region of influenza “A” strains. Since that part doesn’t constantly mutate and about 2/3 of seasonal epidemics and all pandemics are due to type “A” strains, it could be a very efficient weapon against repeats of the “Spanish Flu” (1918−1919) that killed at least 50 million people worldwide. Only the future will tell if phase II and III trials are successful.

You can learn more about the Lifeboat Foundation BioShield program here.

Reposted from Next Big Future which was advancednano.

A 582,970 base pair sequence of DNA has been synthesized.

It’s the first time a genome the size of a bacterium has chemically been synthesized that’s about 20 times longer than [any DNA molecule] synthesized before.

This is a huge increase in capability. It has broad implications for DNA nanotechnology and synthetic biology.

It is particularly relevant for the lifeboat foundation bioshield project

This means that the Venter Institute is on the brink of sythesizing a new bacterial life.

The process to synthesize and assemble the synthetic version of the M. genitalium chromosome

began first by resequencing the native M. genitalium genome to ensure that the team was starting with an error free sequence. After obtaining this correct version of the native genome, the team specially designed fragments of chemically synthesized DNA to build 101 “cassettes” of 5,000 to 7,000 base pairs of genetic code. As a measure to differentiate the synthetic genome versus the native genome, the team created “watermarks” in the synthetic genome. These are short inserted or substituted sequences that encode information not typically found in nature. Other changes the team made to the synthetic genome included disrupting a gene to block infectivity. To obtain the cassettes the JCVI team worked primarily with the DNA synthesis company Blue Heron Technology, as well as DNA 2.0 and GENEART.

From here, the team devised a five stage assembly process where the cassettes were joined together in subassemblies to make larger and larger pieces that would eventually be combined to build the whole synthetic M. genitalium genome. In the first step, sets of four cassettes were joined to create 25 subassemblies, each about 24,000 base pairs (24kb). These 24kb fragments were cloned into the bacterium Escherichia coli to produce sufficient DNA for the next steps, and for DNA sequence validation.

The next step involved combining three 24kb fragments together to create 8 assembled blocks, each about 72,000 base pairs. These 1/8th fragments of the whole genome were again cloned into E. coli for DNA production and DNA sequencing. Step three involved combining two 1/8th fragments together to produce large fragments approximately 144,000 base pairs or 1/4th of the whole genome.

At this stage the team could not obtain half genome clones in E. coli, so the team experimented with yeast and found that it tolerated the large foreign DNA molecules well, and that they were able to assemble the fragments together by homologous recombination. This process was used to assemble the last cassettes, from 1/4 genome fragments to the final genome of more than 580,000 base pairs. The final chromosome was again sequenced in order to validate the complete accurate chemical structure.

The synthetic M. genitalium has a molecular weight of 360,110 kilodaltons (kDa). Printed in 10 point font, the letters of the M. genitalium JCVI-1.0 genome span 147 pages.

Planning for the first Lifeboat Foundation conference has begun. This FREE conference will be held in Second Life to keep costs down and ensure that you won’t have to worry about missing work or school.

While an exact date has not yet been set, we intend to offer you an exciting line up of speakers on a day in the late spring or early summer of 2008.

Several members of Lifeboat’s Scientific Advisory Board (SAB) have already expressed interest in presenting. However, potential speakers need not be Lifeboat Foundation members.

If you’re interested in speaking, want to help, or you just want to learn more, please contact me at [email protected].

I’ve been taking a look at an “international civil society organization” called the ETC Group. The “ETC” group is also known as the “Action Group on Erosion, Technology and Concentration”. To be honest, I can’t figure them out. Here is a summary:

“ETC Group is an international civil society organization based in Canada. We are dedicated to the conservation and sustainable advancement of cultural and ecological diversity and human rights. ETC Group supports socially responsible development of technologies useful to the poor and marginalized and we address international governance issues affecting the international community. We also monitor the ownership and control of technologies and the consolidation of corporate power.”

So they look like a somewhat standard leftist environmentalist technology oversight group. Alright.

Here is their stance on nanotechnology:

“Nanotechnology refers to the manipulation of matter on the scale of the nanometer (one billionth of a meter). Nanoscale science operates in the realm of single atoms and molecules. At present, commercial nanotechnology involves materials science (i.e. researchers have been able to make materials that are stronger and more durable by taking advantage of property changes that occur when substances are reduced to nanoscale dimensions). In the future, as nanoscale molecular self-assembly becomes a commercial reality, nanotech will move into conventional manufacturing. While nanotechnology offers opportunities for society, it also involves profound social and environmental risks, not only because it is an enabling technology to the biotech industry, but also because it involves atomic manipulation and will make possible the fusing of the biological world and the mechanical. There is a critical need to evaluate the social implications of all nanotechnologies; in the meantime, the ETC group believes that a moratorium should be placed on research involving molecular self-assembly and self-replication.”

(Bold by me.)

This is a touchy issue for researchers. At the Lifeboat Foundation we sometimes talk about the Religion of Science, which states that science must progress as quickly as possible and that any attempt to limit it is foolish and immoral. We’ve had people leave our Scientific Advisory Board when they realized that we did not subscribe to this Religion, but in fact question whether any scientist should be allowed to do just anything.

But we do not go as far as the ETC Group, which is proposing a blanket ban on all molecular self-assembly, a very large and potentially incredibly fruitful field.

What prompted me to write on the ETC Group was a news release they sent me today on synthetic biology:

ETC Group
News Release
17 October 2007
www.etcgroup.org

Syns of Omission:
Civil Society Organizations Respond to Report on Synthetic Biology
Governance from the J. Craig Venter Institute and Alfred P. Sloan
Foundation

A report released today on policy options for governance of synthetic
biology is a disappointing effort that fails to address wider
societal concerns about the rapid deployment of a powerful and
controversial new technology. Synthetic biology aims to commercialize
new biological parts, devices and living organisms that are
constructed from synthetic DNA – including dangerous pathogens.
Synthetic biologists are attempting to harness cells as tiny
factories for industrial production of chemicals, including
pharmaceuticals and fuels. ETC Group describes the synthetic biology
approach as “extreme genetic engineering.”

The report, authored by scientists and employees from the J. Craig
Venter Institute, Massachusetts Institute of Technology (MIT) and the
Center for Strategic & International Studies (Washington, D.C.) was
funded by a half-million dollar grant from the U.S.-based Alfred P.
Sloan Foundation and billed as a “project to examine the societal
implications of synthetic genomics.” The study was more than two
years in the making, but the report makes no policy recommendations
and failed to properly consult civil society. While the authors do
acknowledge possible bio-error (i.e., synbio accidents that cause
unintended harm to human health and the environment), the emphasis is
on how to impede bioterrorists “in a post-September 11 world.”

“This report is a partial consideration of governance by a partisan
group of authors,” explains Jim Thomas of ETC Group. “Its authors are
‘Synthusiasts’ – or, unabashed synthetic biology boosters – who are
primarily concerned about holding down costs and regulatory burdens
that could allegedly stymie the rapid development of the new
industry. By focusing narrowly on safety and security in a U.S.-
centric context, the report conveniently overlooks important
questions related to power, control and the economic impacts of
synthetic biology. The authors have ignored the first and most basic
questions: Is synthetic biology socially acceptable or desirable? Who
should decide? Who will control the technology, and what are its
potential impacts?”

The report’s authors include representatives from institutions that
have a vested interest in commercialization of synthetic biology.
According to the J. Craig Venter Institute, one of the three
institutions that led the study, scientists are just weeks or months
away from announcing the creation of the world’s first-ever living
bacterium with entirely synthetic DNA and a novel genome. Scientists
from the Venter Institute have already applied for patents on the
artificial microbe, and Craig Venter predicts that it could be the
first billion or trillion dollar organism. The report fails to
address issues of ownership, monopoly practices or intellectual
property claims arising from synthetic biology.

“The sixty-page report has oodles of input from a small circle of
scientists and policy ‘experts,’ but the 20-month long study fails to
incorporate views of civil society and social movements,” points out
Hope Shand, ETC Group’s Research Director. “An insular process like
the one that produced the Sloan report instills little confidence in
the results.”

The economic and technical barriers to synthetic genomics are
collapsing. Using a laptop computer, published gene sequence
information and mail-order synthetic DNA, it is becoming routine to
construct genes or entire genomes from scratch – including those of
lethal pathogens. The tools for DNA synthesis technologies are
advancing at break-neck pace – they’re becoming cheaper, faster and
widely accessible. The authors acknowledge this reality, and evaluate
several options for addressing it.

One proposal aimed at “legitimate users” of the technology – those
working in industry labs, for example – is to broaden the
responsibilities of Institutional Biosafety Committees, which were
established (in the US) to assess the biosafety and environmental
risks of proposed recombinant DNA experiments.

Edward Hammond, Director of the Sunshine Project, a biotech and
bioweapons watchdog, argues, “Institutional Biosafety Committees are
a documented disaster. IBCs aren’t up to their existing task of
overseeing genetic engineering research, much less ready to absorb
new synthetic biology and security mandates. The authors of this
report are aware of the abject failure of voluntary compliance by
IBCs, including by the Venter Institute’s own IBC. So it is very
difficult to interpret their suggestion that IBCs oversee synthetic
biology as anything but a cynical attempt to avoid effective
governance.”

Options for governing synthetic biology must not be set by the
synthetic biologists themselves – broad societal debate on synbio’s
wider implications must come first. Synthetic microbes should be
treated as dangerous until proven harmless and strong democratic
oversight should be mandatory – not optional. Earlier this year the
ETC Group recommended a ban on environmental release of de novo
synthetic organisms until wide societal debate and strong governance
are in place.

ETC and other civil society organizations have called repeatedly for
an inclusive, wide ranging public dialogue process on societal
implications and oversight options for Synthetic Biology.

The full text of “Synthetic Genomics: Options for Governance” is
available here:
http://www.jcvi.org/

ETC Group’s January 2007 report on synthetic biology, Extreme Genetic
Engineering, is available here:
http://www.etcgroup.org/en/materials/publications.html?pub_id=602

Backgrounder: Open Letter on Synthetic Biology from Civil Society,
May 2006:
http://www.etcgroup.org/en/materials/publications.html?pub_id=11

~~~

Does synthetic biology need more oversight? I believe it does. But I am hesitant to support the ETC Group in full, because some statements on their website have a Luddite flavor. For instance, I think it is infeasible to call for a moratorium on molecular self-assembly.

Another cause the ETC Group seems to be involved in is that of “Terminator” seeds — seeds that grow into plants which are sterile, forcing farmers to return to the seed market. They call this “an immoral application of biotechnology” and I’m inclined to agree.

The ETC Group also seems preoccupied with the phrase “Playing God” to scare up support a little too often for my liking.

I think that new technologies such as MNT and synthetic biology need to be regulated, but I don’t like the extremes I’m seeing: either pure boosterism, or borderline Luddism. The only organizations we can trust are those not attached to any particular extreme. The Lifeboat Foundation seems to be one.

What do you think?

Robert Freitas, Jr., Lifeboat Foundation Fellow and head of the Lifeboat Foundation’s Nanomedicine Division has won the 2007 Foresight Institute Feynman Prize in Communication.

Dr. Pearl Chin, President of the Foresight Nanotech Institute, said Freitas received the award for “pioneering the study and communication of the benefits to be obtained from an advanced nanomedicine that will be made possible by molecular manufacturing [and for having] worked to develop and communicate a path from our current technology base to a future technology base that will enable advanced nanomedicine.”

Prior to his Feynman Prize win Robert shared the Lifeboat Foundation’s 2006 Guardian Award with technology legend Bill Joy. Freitas and Joy shared the Guardian award for their many years of work on mitigating risks posed by advanced technologies.

The European Commission is funding a 2-year, $312,000 study on the safety and ethical aspects of synthetic biology. From the introduction part of the site:

We will pursue our objectives by means of a fact-finding mission, contribution to the European “inaugural” Conference on Synthetic Biology in Zurich (SB 3.0), an open e-forum and an international workshop. The foreseen impact of our project will be no less than to stimulate a European debate on these issues at an early stage. Past experiences, especially in the field of GM-crops, have shown the importance of an early bio-safety and ethics debate. The community recognized this need, but up to now discussions are fragmentary. Our project aims to stimulate a European debate in a proactive way. That way we will contribute to the European synthetic biology community, supplementing genuine biosafety and bioethics aspects.

Looks like a great start on addressing a very important area of concern. For a blog post of mine that goes into a bit more detail on the issue of synthetic biology and its risks, see here.

Five evolutionary stages of pathogen progression from animals to human transmission have been identified A proposed monitoring system of viral chatter has been proposed to provide warning of new diseases before they spread to humans.

In 1999, Wolfe began field work in the jungles of Cameroon to track “viral chatter,” or the regular transmission of diseases from animals to people, usually without further spread among humans. By monitoring the habits and the blood pathologies of bushmeat hunters and their kills, Wolfe and his team have identified at least three previously unknown retroviruses from the same family as HIV, as well as promoted safe practices for handling animals and animal carcasses.

“The Cameroon project demonstrated that it’s possible to collect information on viral transmission under very difficult circumstances from these highly exposed people,” Wolfe said.

With Cameroon as a prototype and a $2.5 million National Institutes of Health Pioneer Award as seed money, Wolfe has gone on to create a network of virus-discovery projects that monitor hunters, butchers, and wildlife trade and zoo workers in some of the world’s most remote viral hotspots. The network of a dozen sites in China, the Democratic Republic of Congo, Malaysia, Laos, Madagascar and Paraguay include source locations for such emerging diseases as SARS, avian flu, Nipah, Ebola and monkeypox.

There are more details of the five stages and a proposed study of the detailed origins of disease.

Wolfe and his colleagues begin by identifying five intermediate stages through which a pathogen exclusively infecting animals must travel before exclusively infecting humans. The research team identifies no inevitable progression of microbes from Stage 1 to Stage 5 and notes that many microbes remain stuck at a specific stage. The journey is arduous, and pathogens rarely climb through all five stages:

Stage 1. Agent only in animals: A microbe that is present in animals but not detected in humans under natural conditions. Examples include most malarial plasmodia.

Stage 2. Primary infection: Animal pathogens that are transmitted from animals to humans as a primary infection but not transmitted among humans. Examples include anthrax, rabies and West Nile virus.

Stage 3. Limited outbreak: Animal pathogens that undergo only a few cycles of secondary transmission among humans so that occasional human outbreaks triggered by a primary infection soon die out. Examples include the Ebola, Marburg and monkeypox viruses.

Stage 4. Long outbreak: A disease that exists in animals and has a natural cycle of infecting humans by primary transmission from the animal host but that also undergoes long sequences of secondary transmission between humans without involvement of animals. Examples include Chagas disease, yellow fever, dengue fever, influenza A, cholera, typhus and West African sleeping sickness.

Stage 5. Exclusive human agent: A pathogen exclusive to humans that involves either an ancestral pathogen present in a common ancestor of chimps and humans or involves a more recent pathogen that evolved into a specialized human pathogen. Examples include HIV, measles, mumps, rubella, smallpox and syphilis.

In addition, the team examines 25 diseases of important historic consequence to humans. Of the 25 diseases, 17 impose the heaviest world burden today: hepatitis B, influenza A, measles, pertussis, rotavirus A, syphilis, tetanus, tuberculosis, AIDS, Chagas disease, cholera, dengue hemorrhagic fever, East and West African sleeping sicknesses, falciparum and vivax malarias, and visceral leishmaniasis.

Eight more imposed heavy burdens in the past but have been reined in or eradicated thanks to modern medicine and public health practices: temperate diphtheria, mumps, plague, rubella, smallpox, typhoid, typhus and tropical yellow fever. Except for AIDS, dengue fever and cholera, most of the 25 have been important for more than two centuries.

The research team considered the varied pathologies of diseases originating in temperate (15) versus tropical (10) regions, as well as differing pathogen and geographic origins. Among the conclusions:

– Most of the temperate diseases, but none of the tropical diseases, are so-called “crowd epidemic diseases,” occurring locally as a brief epidemic and capable of persisting regionally only in large human populations. Most of the diseases originating in temperate climates convey long-lasting immunity.

– Eight of the 15 temperate diseases probably or possibly reached humans from domestic animals, three more from apes or rodents, and the other four came from still unknown sources. Thus the rise of agriculture, starting 11,000 years ago, plays multiple roles in the evolution of animal pathogens into human pathogens.

– Most tropical diseases have originated in wild, non-human primates. These animals are most closely related to humans and thus pose the weakest species barriers to pathogen transfer.

– Animal-derived human pathogens virtually all arose from pathogens of other warm-blooded vertebrates plus, in two cases, birds.

– Nearly all of the 25 major human pathogens originated in the Old Word (Africa, Europe and Asia), facilitating the conquest of the New World. Chagas disease is the only one of the 25 that clearly originated in the New World, while the debate is unresolved for syphilis and tuberculosis.

–Far more temperate diseases arose in the Old World because far more animals that furnish ancestral pathogens were domesticated there. Far fewer tropical diseases arose in the New World because the genetic distance is greater between humans and primates in this part of the globe.

The conclusions of the review illustrate large gaps in the understanding of the origins of even established major infectious diseases. Almost all studies reviewed were based on specimens collected from domestic animals, plus a few wild animal species.

The researchers propose an “origins initiative” aimed at identifying the origins of a dozen of the most important human infectious diseases as well as a global early warning system to monitor pathogens emerging from animals to humans.

This work is relevant to the lifeboat bioshield

darpaachievements.jpg

DARPA (the defense advanced research projects agency) is the R&D arm of he US military for far-reaching future technology. What most people do not realize is how much revolutionary medical technology comes out of this agency’s military R&D programs. For those in need of background, you can read about the Army & DARPA’s future soldier Landwarrior program and its medtech offshoots as well as why DARPA does medical research and development that industry won’t. Fear of these future military technologies runs high with a push towards neural activation as a weapon, direct brain-computer interfaces, and drones. However, the new program has enormous potential for revolutionary medical progess as well.

It has been said technology is neutral, it is the application that is either good or evil. (It is worth a side-track to read a discussion on this concept)

The Areas of Focus for DARPA in 2007 and Forward Are:

  1. Chip-Scale Atomic Clock
  2. Global War on TerrorismUnmanned Air Vehicles
  3. Militarization of Space
  4. Supercomputer Systems
  5. Biological Warfare Defense
  6. Prosthetics
  7. Quantum Information Science
  8. Newton’s Laws for Biology
  9. Low-Cost Titanium
  10. Alternative Energy
  11. High Energy Liquid Laser Area Defense System

the potential for the destructive use of these technologies is obvious, for a a complete review of these projects and the beneficial medical applications of each visit docinthemachine.com

From MIT’s Technology Review:

Researchers at the University of Twente, in the Netherlands, have developed an ultrasensitive sensor that could potentially be used in a handheld device to, within minutes, detect various viruses and measure their concentration. The sensor could be used to quickly screen people at hospitals and emergency clinics to control outbreaks of diseases such as SARS and the bird flu. All it would take is a tiny sample of saliva, blood, or other body fluid.

Currently available methods to detect viruses are also sensitive. But they require laborious preparation of the fluid sample and only give results after several days. Since viral diseases can spread rapidly, researchers are looking for easier, faster ways to directly detect viruses. “You want a tool on which you apply the [fluid] sample on-site and in a few minutes say whether or not the person has the SARS virus,” says Aurel Ymeti, a postdoctoral researcher in biophysical engineering and the sensor’s lead developer.

Looks promising. Hopefully this model can be extended to other nanoscale threats, like prions and genetically engineered viruses.