Accelerating Future

A proposed name for the new kingdom of synthetic life: Anthropobiota.

(This is hardly original… see Anthropocene, but it seems most likely to catch on.)

The first member of Anthropobiota will likely be Mycoplasma laboratorium, at the J. Craig Venter Institute. The group also “hopes to eventually synthesize bacteria to manufacture hydrogen and biofuels, and also to absorb carbon dioxide and other greenhouse gases”, according to the Wikipedia page. This would lead to additional species for specific purposes. The point of Mycoplasma laboratorium is to implement a “minimal bacterial genome”, a jumping-off point for future synthetic species. All of these species would fall under Anthropobiota, as long as the genetic material is entirely synthetic. If not, that’s just genetic engineering.

Anthropobiota would be located outside the root of the Tree of Life. It would be a complementary Tree, at first much smaller than the original. The Tree of Life contains between 10 million and 1 billion bacteria species, between 10 and 30 million animal species, and some unknown quantity of archaea. So quite a few new species would need to join Anthropobiota for it to rival the current Tree.

I seem to remember an accusation in some phylogenetics journal that a group of Archaea was outside the root of the Tree of Life, but I can’t find it for the life of me. Anyway, there could be two or more separate Trees of Life. Anthropobiota will be a new one. The Tree of Synthetic Life.

Two different species within Anthropobiota need not evolve from other species in the same group. Each one could be created from scratch, by scientists in a lab. Once we develop the technology to reliably and inexpensively synthesize long genomes from nucleic acid precursors, and swap them for native genomes, we’re in business. The flood gates for new species — both benign and malign — will open.

The Lifeboat Foundation A-Prize page is a foresightful effort to to put development of artificial life forms in the open, where it should be. It a reward to whoever creates the first life form that “must execute at least one synthetic nonbiological operation in order to complete its life cycle”.

On the A-Prize page, Dr. Alan H. Goldstein, Professor of Biomaterials at Alfred University, creates four classifications of life: Natural Biological, Genetically-Engineered Biological, Synthetic Biological, and Synthetic Nonbiological (Animat). According to his classification system, Mycoplasma laboratorium would fall into the third category: Synthetic Biological. It will not be eligible to collect the A-Prize, because that would require an organism that integrates an entirely nonbiological, consistent (over generation) element into its biological life cycle.

Anyway, I’m looking forward to the creation of Mycoplasma laboratorium later this year. I hope that creating synthetic life stays expensive for at least a couple more decades.

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The are several categories relating to the Tree of Life which I consider important.

The first category includes all extant creatures. By adolescence, we are familiar with thousands of animals. Scientists estimate there are somewhere between 5 and 100 million species altogether. Most are probably insects and arachnids, including over a million species of both mite and beetle.

The second category includes all species that have ever lived. This number is somewhere between 10 and 100 times greater than the number of extant creatures, therefore somewhere between 50 million and 10 billion. To me, making sense of the first category requires understanding the second. I am fascinated by the second category because most people don’t know too much about it, and it’s like visiting an alien world — there are so many unusual and fascinating creatures in the fossil record.

The third category includes all species that could ever theoretically exist. We can really blow this up to huge proportions, including species based on something besides DNA, including non-carbon-based life forms, if they are physically possible, which seems likely. In this category I include alternate evolutionary paths.

In my view, there is a strong element of randomness to the specifics of evolution. In a parallel universe, Earth may have been inhabited by entirely different intelligences, born from an entirely different Tree of Life. Sauropsids may have become intelligent instead of synapsids, or something even more radical.

I like to draw my “circle of empathy” large — so large, in fact, that I can go so far as to say that any form of self-reflective general intelligence with subjective experience is worthy of value, regardless of the biological context it grew up in. We can go even further and include non-conscious animals, though these may be considered as deriving their value from the appreciation of conscious beings.

When biotechnology advances to the point where can synthesize animal-sized genomes from scratch (we’ve already gotten to the level of bacteria), humans will surely create entirely new animals, both for study and pleasure. Leaving aside issues of regulation, I think that the first category will expand to include many elements of the second and third categories. Eventually, we will recognize that members of the second and third categories have the same inherent value as members of the first, and all will share the matter-energy resources of the local area.

So, as an environmentalist, I care about preserving existing biodiversity, but as a transhumanist environmentalist, I also care about the creation and preservation of de novo biodiversity. These creatures will provide an interesting accompaniment during our journey greening the Galaxy.

This may sound futuristic, but the first synthetic life will be created in a lab this year.

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A challenge in making people care about techno-apocalypse is that most of the proposed technologies which could cause it exist in the future, not the present.

There’s all-out thermonuclear war, sure. If the Bush administration is dumb enough to attack Iran before he leaves office, then we could have serious problems with Russia (the country my family left when the Communists took over), whose minister of defense has cautioned the US not to lay a hand on Iran. If Putin’s successor is as gangster as he is, then Cold War part II (or Hot War part I) can’t be ruled out.

But would this kill everyone? Not too likely. Although burning cities do create black clouds which can initiate widespread crop failure, this effect is temporary. The world is a big place, and you can’t nuke it all.

So, in examining possible sources of human extinction risk, we have to look to the future. In a way this is reassuring, because we have time to prepare, but in another way it’s not, because some of the scenarios are too futuristic for people to take seriously.

I suppose the step after global thermonuclear war is genetically engineered plague. I’ve talked to four separate recombinant geneticists who say they would have a good chance at wiping out 90% of the human population in a decade if they had several million dollars and complete secrecy. (Their claims were more or less in tune even though they don’t know one other, to my knowledge.) Are they exaggerating? I don’t know, I’m not a biologist, but I think I’d rather err on the side of trusting them on this one.

What I do know about is history. The Black Death, which was possibly not the same thing as the bubonic plague, killed as much as half of Europe. Perhaps modern-day hygiene would prevent this from ever happening again, but the Spanish flu happened in conditions of nearly-modern hygiene, still killing 50-100 million, and spreading as far as the Arctic and remote Pacific islands (those are the two regions you need to watch if you care about extinction risk).

Would nuclear war threaten Tristan da Cunha, the most remote archipelago in the world? No. But a sufficiently powerful plague might. Especially a plague that spread to hundreds of millions of people before they started to display symptoms. Would such a thing be possible to genetically engineer? I’ve been talking with scientists about it since I got out of school but they often contradict each other, so I’m still confused.

My intuition tells me that when mankind can engineer something from scratch, it opens a vastly wider design space than nature alone could access. This is why humanity came up with computers, supersonic planes, and rocket ships, and the fastest swallow can’t even break the sound barrier. That’s why the Luddites got angry — because specialized looms could create textiles way faster than they ever could. Perhaps specialized microbes could kill people faster than any conventional weapon, or even nuclear weapons. I’d rather not watch it in action to find out.

I like thinking about the genetically engineered bacteria because it’s a happy medium in its future shock between thermonuclear war (which most accept as a possibility) and AI/robotics (which people have bizzare reactions to). There’s also nanowar, but that is also more futuristic.

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Today’s edition of Newsweek has an article on synthetic life, a topic of significant interest and concern. To use Alan Goldstein’s classification scheme for various types of synthetic life, the kind being discussed here is Type 3, “synthetic biological”, life forms with DNA/RNA programming, utilizing traditional biological building blocks such as proteins, with a genome synthesized from scratch in a laboratory. This is distinct from Type 2, “genetically-engineered biological” life forms, which are based on tweaks to preexisting genomes, and Type 4 life forms, “synthetic nonbiological”, where DNA/RNA and traditional biological building blocks are not used and all functionality is engineered from scratch, like any machine.

The article reports that Craig Venter, famous for leading one of the first teams to sequence the human genome, has founded a new startup, Synthetic Genomics, which plans to make artificial organisms for converting sunlight into biofuel. Also interesting is that, apparently, some religious skeptics don’t even believe that synthetic life can be produced. It’s difficult to determine why. There are already millions of examples of functioning organisms coded by DNA, it seems odd that introducing a new one would somehow be physically forbidden. But creating life in a lab directly challenges religious fantasies that this is something only God can do. Everyone’s favorite bioethicist, Leon Kass, is quoted in the article, saying, “I find it very hard to believe that, starting from scratch, we can somehow come up with a better [biological] system — one that’s going to have much success.” This is the same guy who believes that studying cadavers or eating ice cream in public are immoral.

Despite the odd pronouncements of anti-science dogmatists like Kass, we’ve been creating life and modifying genomes for thousands of years already, through selective breeding. Dogs, for instance. Many of the fruits we eat on a daily basis are modified versions of natural ancestors that were smaller, less nutritious, and more susceptible to the elements. Of course, there is a difference between selective breeding and creating new forms of life de novo. The latter is surely more powerful, but also more dangerous.

Rudy Rucker, a computer science professor made famous by his science fiction books, submitted a commentary on the topic of synthetic biology, also available on the Newsweek site. In the commentary, he dismisses away the dangers, saying, “What’s to stop a particularly virulent SynBio organism from eating everything on earth? My guess is that this could never happen. Every existing plant, animal, fungus and protozoan already aspires to world domination. There’s nothing more ruthless than viruses and bacteria—and they’ve been practicing for a very long time.” He then goes on to talk extensively about some potentially radical benefits of the technology.

People like Rucker make transhumanism look bad, by spending all their time talking about the benefits, while handwaving away the risks. Synthetic biology will indeed be a serious global risk. The huge difference between intelligent engineering and blind natural selection should be obvious to someone as educated as Rucker, but apparently not. If I am knowledgeable about biology and have the tools to create new organisms from scratch, then it would be entirely plausible I could certainly construct something that poses a threat to all extant life.

The intelligent construction of synthetic organisms opens up a vastly wider design space than the one previously exploited by evolution and natural selection. In evolution, every genetic step must be independently adaptive, forcing a path through local maxima. Evolution cannot plan ahead, or intelligently construct adaptations oriented towards solving environmental challenges in the most general possible way. Evolution does not understand the concept of over-designing or fault tolerances - for an organism to be successful, it just has to reproduce a little bit faster than its competition, not ten times faster. When humans design a bridge, we design it to withstand a weight tens of times greater than its average load. Evolution can do no such thing.

One day, some synthetic biologist will become capable of designing a supervirus that can wipe out humanity. Then, ten will, then a hundred, and eventually, thousands. That’s the nature of scientific knowledge - the bleeding edge of today is the used textbooks of tomorrow. Information wants to be free. Because synthetic biology will definitely become a real threat in the future, we have to start taking steps now to ensure that the field has proper regulation and oversight. SynBioSafe, a two-year, $312,000 project set up by the European Commission, is an excellent step in this direction.

Even if we think the chance of any given synthetic biology project in any given year leading to a global disaster is relatively small, over sufficiently long timeframes and for sufficiently many projects, the probability reaches unity. Synthetic biology is much more worrisome than global warming, nuclear war, or peak oil, because these things cannot kill everyone while synthetic biology can.

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Eurekalert:

Why are there so many more species of insects? Because insects have been here longer

J. B. S. Haldane once famously quipped that “God is inordinately fond of beetles.” Results of a study by Mark A. McPeek of Dartmouth College and Jonathan M. Brown of Grinnell College suggest that this fondness was expressed not by making so many, but rather by allowing them to persist for so long. In a study appearing in the April issue of the American Naturalist, McPeek and Brown show that many insect groups like beetles and butterflies have fantastic numbers of species because these groups are so old. In contrast, less diverse groups, like mammals and birds, are evolutionarily younger. This is a surprisingly simple answer to a fundamental biological puzzle. They accumulated data from molecular phylogenies (which date the evolutionary relationships among species using genetic information) and from the fossil record to ask whether groups with more species today had accumulated species at faster rates. Animals as diverse as mollusks, insects, spiders, fish, amphibians, reptiles, birds, and mammals appear to have accumulated new species at surprisingly similar rates over evolutionary time. Groups with more species were simply those that had survived longer. Their analyses thus identify time as a primary determinant of species diversity patterns across animals. Given the unprecedented extinction rates that the Earth’s biota are currently experiencing, these findings are also quite sobering. We are rapidly losing what it has taken nature hundreds of millions of years to construct, and only time can repair it.

The uniform rate of species generation across diverse phyla tells us something interesting both about the process of evolution and the search space that natural selection is navigating. It tells us that multi-niche supremacy is difficult to achieve. If a particular species could adapt effectively to two niches, it would displace competitors in both, creating a biodiversity asymmetry across phyla over time. Evolution is notoriously incrementalist - it cannot create a multi-talented species if it decreases the species’ fitness in its traditional niche even by a small margin.

What is really unusual about this finding is that it shows there is no relationship between species diversification and generation time. Some insects have generation lengths of about a day, whereas certain primates have 20-year generations. This is a 7300:1 difference. This is why laboratory eugenics on insects or bacteria takes months or years while eugenics on mammals takes decades. Why are insects diversifying so slowly, given the numerous chances for natural selection to generate new variants at a greater rate than animals with longer life-cycles?

On the issue of species going extinct, there is a simple solution - save the genetic material. An arbitrary number of organisms can be generated later. A fly or a tree does not feel anguish when it dies. This is a property exclusive to species with more complex nervous systems, such as pigs and cattle. Environmentalists should support economic development even if it means sacrificing some biodiversity, because marginal improvements in the economy translate to accelerated scientific research and the nearing of the day when previously extinct biodiversity can be restored and novel biodiversity artificially generated at a tremendous rate.

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From Eurekalert:

Silver bullet: UGA researchers use laser, nanotechnology to rapidly detect viruses

Athens, Ga. – Waiting a day or more to get lab results back from the doctor’s office soon could become a thing of a past. Using nanotechnology, a team of University of Georgia researchers has developed a diagnostic test that can detect viruses as diverse as influenza, HIV and RSV in 60 seconds or less.

In addition to saving time, the technique – which is detailed in the November issue of the journal Nano Letters – could save lives by rapidly detecting a naturally occurring disease outbreak or bioterrorism attack.

“It saves days to weeks,” said lead author Ralph Tripp, Georgia Research Alliance Eminent Scholar in Vaccine Development at the UGA College of Veterinary Medicine. “You could actually apply it to a person walking off a plane and know if they’re infected.”

The technique, called surface enhanced Raman spectroscopy (SERS), works by measuring the change in frequency of a near-infrared laser as it scatters off viral DNA or RNA. This change in frequency, named the Raman shift for the scientist who discovered it in 1928, is as distinct as a fingerprint.

This phenomenon is well known, but Tripp explained that previous attempts to use Raman spectroscopy to diagnose viruses failed because the signal produced is inherently weak.

But UGA physics professor Yiping Zhao and UGA chemistry professor Richard Dluhy experimented with several different metals and methods and found a way to significantly amplify the signal. Using a method they’ve patented, they place rows of silver nanorods 10,000 times finer than the width of a human hair on the glass slides that hold the sample. And, like someone positioning a TV antenna to get the best reception, they tried several angles until they found that the signal is best amplified when the nanorods are arranged at an 86-degree angle.

“The enhancement factors are extraordinary,” Dluhy said. “And the nice thing about this fabrication methodology is that it’s very easy to implement, it’s very cheap and it’s very reproducible.”

Tripp said the technique is so powerful that it has the potential to detect a single virus particle and can also discern virus subtypes and those with mutations such as gene insertions and deletions. This specificity makes it valuable as a diagnostic tool, but also as a means for epidemiologists to track where viruses originate from and how they change as they move through populations.

The researchers have shown that the technique works with viruses isolated from infected cells grown in a lab, and the next step is to study its use in biological samples such as blood, feces or nasal swabs. Tripp said preliminary results are so promising that the researchers are currently working to create an online encyclopedia of Raman shift values. With that information, a technician could readily reference a Raman shift for a particular virus to identify an unknown virus.

To make their finding commercially viable, they’re developing a business model, seeking venture capital and exploring ways to mass produce the silver nanorods. Next year, they plan on moving their enterprise to the Georgia BioBusiness Center, an UGA incubator for startup bio-science companies.

Presently, viruses are first diagnosed with methods that detect the antibodies a person produces in response to an infection. Tripp explained that these tests are prone to false positives because a person can still have antibodies in their system from a related infection decades ago. The tests are also prone to false negatives because some people don’t produce high levels of antibodies.

Because of these limitations, antibody based tests often must be confirmed with a test known as polymerase chain reaction (PCR), which detects the virus itself by copying it many times. The test can take anywhere from several days to two weeks. Tripp said the latter is clearly too long, especially in light of emerging threats such as H5N1 avian influenza.

“For some respiratory viruses, you’ve either cleared the infection at that point or succumbed to the infection,” Tripp said. “What we’ve developed is the next generation of diagnostic testing.”

Big win! This will be useful to avoid the coming Doomsday Virus.

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There’s so much relevant news from the past week, I can’t just focus on any one thing… so here are five of the most significant things to hit my radar in past week:

In ascending order of importance.

5. On Marginal Revolution: What are some unknown but incredibly important inventors? Why can’t we get rid of the penny? And what is the moral basis of capitalism?

4. Lawrence Berkeley lab and Oxford University researchers developed a particle accelerator that takes electron beams and powers them up to a billion electron volts (1 GeV) in only 3.3 centimeters using a technology called laser wakefield acceleration. If these particle accelerators become popular and start to edge out conventional accelerators, then we’ll both learn a lot more about particle physics, and put ourselves at greater risk for creating a stable strangelet. Doing a risk/benefit calculation is difficult because of uncertainty in the probabilities involved.

3. If all goes well, we may start running our automobiles on ceramic ultracapacitors which take us 500 miles on only $9 worth of electricity using a battery that recharges in 5 minutes. Eric from Digital Crusader did a few basic calculations and found that transferring that amount of energy would require a rate of 1.2 megawatts, much greater than anything seen in current home electronics systems. The inventors of this technology claim that one day it will completely replace the internal combustion engine.

2. The mouse brain has been mapped down to individual cells. It only cost $41 million to do. A 3D atlas of the common lab mouse brain can be found here. If we had computers a couple orders of magnitude more powerful than today, we could start trying to simulate that mouse’s brain in a virtual environment. The success of the mouse brain mapping project is also a testimony to the success of high-level philanthropy. Paul Allen, co-founder of Microsoft, contributed $50 million to the project, more than it even needed. This Merkle paper is relevant as background.

1. Chris Phoenix proposes the creation of cubic micron DNA structures. Specifically, Chris proposed “solid molecular constructions, using DNA as a backbone, plus other arbitrary molecules precisely positioned within the volume. ” He estimates that it would be possible to design one for $10 million to $100 million once the entire process is automated. The idea came out of a thought experiment about what would be possible with today’s technology and only a “moderate amount of engineering”.

The idea would be to build bricks that can independently manufacture other bricks, to produce a rudimentary DNA nanofactory. Less ambitiously, you could design bricks that perform specialized tasks, like breaking down garbage efficiently, and then mass-produce the bricks to perform that function. The power of the approach is that, with current technology, you can precisely specify the DNA structure within a cubic micron volume, making it possible to eventually build any structure that can be designed. Because the density of DNA is about 1.3 nm^3 per base pair, it would take about 500 million base pairs worth of DNA to fill a cubic micron space. At current DNA synthesis prices ($0.10 if it’s your machine) that works out to $50 million/block, but the cost is rapidly falling.

Chris expounds a bit more on the concept here. Meanwhile, CRN argues “yes, it’s coming soon“.

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