The environment – Page 97 – a sibilant intake of breath

BioBricks and synthetic biology

The basic impulse behind synthetic biology is one that human beings have been acting on for thousands of years: the desire to make living things serve our needs and desires better. We’ve domesticated animals, seriously altering their genomes and behaviours in the process, and turned wild crops into agricultural staples. Now, people aspire to use living things for all kinds of purposes: from synthesizing drugs and fuels to performing computations.

One of the most important developments of the Industrial Revolution was standardized parts. Originally used in firearms, having devices comprised of interchangeable components made maintenance and repair far simpler. Instead of having to make a custom widget designed to fit a particular machine, any standard widget of the right sort would do. To some extent, BioBricks are trying to do the same thing for engineered biological systems. Each consists of a DNA sequence held in a circular plasmid, with standard headers and footers. They include sites for enzymes, which allow the bricks to be chained together. Individual BioBrick ‘parts’ contain information such as how to code a particular protein. They are assembled into ‘devices’ that perform basic functions, and ‘systems’ that accomplish higher level tasks. MIT maintains a ‘catalog of parts and devices.’ There is even an iPhone application that allows the “review, annotatation, design, and implemention of standard biological parts.” An assembly kit adequate for 50 reactions can be purchased online for US$235.

One application of synthetic biology has been to make Amorphadiene, a chemical precursor to the ant-malarial drug artemisinin (mentioned here before). Producing the drug from the shrub in which it was discovered is expensive and tricky. As a result, annual demand far exceeds available supply. Producing it in engineered organisms could therefore make treatment more widely available. Amyris Biotechnologies, working with a grant from the Bill and Melinda Gates Foundation, has produced the drug using such an organism, and is hoping to have it on the market by 2012. The company’s founder hopes to eventually be able to synthesize any molecule found in a plant inside an easy-to-grow microbe.

Another mooted application would be engineering photosynthetic algae to produce and release oils, which could be collected and used as fuels. Such a process could be far more efficient than one based on growing conventional algae and then processing them for whatever quantity of oils they contain naturally.

Of course, synthetic biology does raise safety and ethical considerations. While I don’t think tinkering with genetic material is fundamentally morally different from cross-breeding plants or animals, there may be more danger of unanticipated consequences. Weighing the reality of that risk against the promise of what engineered organisms could do isn’t a straightforward task, especially in situations where the groups bearing the risk and receiving the benefits are not one and the same. Regulating the industry, and establishing legal precedents on things like liability, will be an important part of future policy- and law-making.

Sarkozy’s incoming carbon tax

While Canada’s best effort at a carbon tax ended in failure, one worth about $25 a tonne seems likely to be adopted in France. The new tax is intended to be revenue neutral, with corresponding handouts to households (both those that pay tax and those that don’t) and corporations. Some expect the most significant impact to be on liquid fuel prices. Sweden has been rather more ambitious in this regard, having imposed a tax of about $100 per tonne on oil, coal, natural gas, liquefied petroleum gas, petrol, and aviation fuel used in domestic travel.

Like most carbon taxes, the French initiative includes significant loopholes – including for heavy industry and non-nuclear forms of electricity generation. Even so, it represents a bit of good news in the lead-up to the UNFCCC negotiations in Copenhagen this December. Hopefully, it will be progressively expanded to other emitting activities, at the same time as the level of the tax is progressively increased. Here, Sweden sets an encouraging example: when they imposed their carbon tax in 1991, it was at about 1/4 of its present level.

[Update: 23 March 2010] French government backs down on carbon tax plan

Environmentalism and ‘breathing underwater’

The Walrus recently published an article entitled: “The Age of Breathing Underwater.” Written by Chris Turner, it relates to a number of previous discussions here, such as the recent one about being unimpressed with humanity, when it comes to behaving sensibly about climate change.

It begins with a lengthy discussion about some of the life in coral reefs: one of the ecosystems most profoundly and immediately threatened by climate change. Indeed, even with some pretty aggressive mitigation, most will probably perish during the lifetimes of those reading this, as the result of both rising temperatures and increasing ocean acidity. The article quotes scientist J. E. N. Veron saying that by 2050 “the only corals left alive will be those in refuges on deep outer slopes of reefs. The rest will be unrecognisable — a bacterial slime, devoid of life.”

The article also discusses environmental activism, science fiction, the prospect of geoengineering, the concept of ‘resilience’ in a threatened world, and what it means to be alive in the Anthropocene – the era in human history characterized by the impacts of human beings on physical and biological systems. It makes the strong point that we can somewhat reduce the eventual impact of climate change by working to diminish other stresses; reefs threatened by warm and acidic water don’t need dynamite fishing and oil drilling to help drive them to extinction. The same is surely true of terrestrial ecosystems. Resilience is also something that can be built into human systems – the ability to stretch and change without breaking. From my perspective, that is one huge limitation of the ‘survivalist’ approach to surviving climate change. Your little armed colony might be able to sustain itself under present conditions, but it isn’t necessarily very flexible, when it comes to adapting to whatever the future will bring.

The ‘underwater’ metaphor is an interesting one. The author points out that the human capacity to remain underwater for extended periods depends fundamentally on the whole enterprise of modern industry. The author points out that we’re not really trying to save reefs anymore: we’re trying to save the ability of human beings to do things like SCUBA dive. That ability can only be maintained if we maintain an industrial society, while transforming its energy basis. The article’s conclusion addresses this, but is somewhat underwhelming. While renewable forms of energy are surely a huge part of the solution, putting solar panels on top of buildings won’t be anywhere near adequate. We need comprehensive plans of the sort David MacKay has cooked up. Making the transition from surviving underwater using a set amount of compressed air (akin to fossil fuels) in a tank to living in a self-sustaining colony (akin to renewables) requires appreciation of scale and logistics. A few houseplants are not going to do it.

In any event, the whole article is worth reading and responding to. My thanks to my friend Ann, for pointing it out to me.

Composting in Ottawa

Ottawa is starting up a citywide composting system, with pick ups every two weeks through the winter:

Starting Monday, and for the next 12 weeks, the city will be delivering 240,000 green bins and small, counter-top kitchen-catchers to households across the city.

The chief environmental advantage cited, reducing landfill usage, is not overly compelling. We have plenty of space for landfills, and they are very tightly regulated. I would be interested in knowing what the other effects of the program will be, if any, on factors like air quality, water quality, and greenhouse gas emissions.

It is interesting to note that the service will no accept ‘biodegradable’ plastics, because the term doesn’t have a standard usage and there is a risk that the compost produced would be contaminated.

Would finding extraterrestrial life matter?

The most plausible explanation for the origin of life on Earth is that physical processes created organic molecules, such as amino acids, and some combination randomly assembled that could make copies of itself. This may have been somewhat akin to the way crystals form as the result of probability and their own chemical characteristics. From there, these ‘replicators’ became more diverse and capable, ultimately branching out into the entirety of life observed on our planet today. Richard Dawkins may have expressed these ideas best, in the opening section of The Selfish Gene:

Was there to be any end to the gradual improvement in the techniques and artifices used by the replicators to ensure their own continuation in the world? There would be plenty of time for their improvement. What weird engines of self-preservation would the millennia bring forth? Four thousand million years on, what was to be the fate of the ancient replicators? They did not die out, for they are the past masters of the survival arts. But do not look for them floating loose in the sea; they gave up that cavalier freedom long ago. Now they swarm in huge colonies, safe inside gigantic lumbering robots, sealed off from the outside world, communicating with it by tortuous indirect routes, manipulating it by remote control. They are in you and me; they created us, body and mind; and their preservation is the ultimate rational for our existence. They have come a long way, those replicators. Now they go by the name of genes, and we are their survival machines.

If this explanation is basically correct, we should expect there to be a lot of life in the universe. There are millions of billions of galaxies out there, comprised of a phenomenal number of stars. We have already observed planets around some, including small rocky planets like the Earth and planets with orbits compatible with liquid water on their surfaces. The Kepler Mission may discover hundreds more. The Drake Equation expresses this idea mathematically, while the Fermi Paradox considers why extraterrestrial civilizations, which we might expect to be common, have not yet been found.

Finding other forms of life would certainly both answer and raise scientific questions (such as how different forms of life can be.) Would actually observing direct evidence of life (probably microbes) elsewhere have any effect on human perspectives or behaviour? It might for religious people who believe life on Earth to have been uniquely created, but that isn’t a terribly interesting consequence to me. Would it have any ethical, political, or moral ramifications for those who already believe that life essentially arose by accident? Would intelligent life have any effect above and beyond that of observing microbes, even if such life was too far away to ever really engage or communicate with? The question may not be such an abstract one. As described well in one chapter of Oliver Morton’s book on photosynthesis, there are several ways through which we might be able to identify unmistakeable signs of life at great distance.

Perversely, life elsewhere might actually somewhat diminish our perception of how important it is to preserve and protect life on Earth. Right now, as far as we know, we are the sole such example in the universe. Finding others might lend even more strength to the psychological pressures that make us favour immediate interests rather than long-term survival. On the other hand, it might help reinforce the point that we are here by accident and that nothing about the nature of the universe is ‘on our side’ when it comes to survival. Such a realization might prompt some serious thinking of what it will mean to endure in a universe that will endure long beyond the comparatively comfortable circumstances in which we emerged as a species.

Fish certified to be sustainable may not be

The Marine Stewardship Council (MSC) was launched in hopes of making it possible for firms and consumers to select sustainably-produced seafood. Unfortunately, recent events have seriously undermined its reputation:

Their plan to certify Peruvian anchovy is dubious.
The MSC-certified Alaskan Pollock fishery is collapsing.
The same goes for the Hoki fishery, off New Zealand.
The MSC is considering certifying Pacific Hake, over the objections of Oceana and the Monterey Bay Aquarium.

Jennifer Jacquet, of the Guilty Planet blog, goes so far as to say that “the MSC certification process has been co-opted by industry.”

Those who have been salving their consciences by buying certifiably ‘sustainable’ fish should now give some thought to whether the only truly sustainable option is to abstain from seafood altogether, as both Jennifer and I have reluctantly done.

Two interesting Mars space travel tidbits

Firstly, a nice demolition of the idea that a one-way mission to Mars makes sense, written by Oliver Morton, whose excellent book I reviewed. The best concise point:

Most importantly, in terms of costs, there’s the ongoing commitment. A set of Mars missions you can cancel is a much more attractive than a set of Mars missions that you cannot cancel without killing people (“Launch the next rocket or the kid gets it”). To fund a single one way to Mars mission is more or less to sign up to funding them for as long as the colony lasts. That is a far larger spending commitment than required for a small number of return trips.

I certainly wouldn’t want to be one of the decision-makers responsible for keeping a Martian colony alive, while billions are watching via high-definition video links. Watching the astronauts slowly (or quickly) die would be awfully depressing, after all, especially if it was because of budget cuts.

Secondly, a Science article on the importance of not contaminating Mars with terrestrial organisms: Biologically Reversible Exploration. In essence, it argues that contamination from terrestrial spacecraft could forever eliminate our chances of studying life that evolved independently on Mars, if any such organisms exist. It argues that future missions, including any manned missions, adopt protocols so as to be ‘biologically reversible.’ As countless examples of terrestrial invasive species demonstrate, the concerns are not unwarranted, when it comes to microorganisms that might be able to survive or thrive in the Martian environment.

The 10:10 campaign

Previously, I complained about how setting climate targets can actually impede action, by drawing attention towards numbers rather than action, and by giving people the false sense that we can delay change. The 10:10 campaign, which is being advanced by The Guardian, seems like a good idea. It aims to have individuals, companies and institutions reduce their greenhouse gas emissions by 10% by the end of 2010. I like the near-term focus. While we ultimately need to begin a deep and long process of transition to carbon neutrality, the cuts we can make today will be the most valuable. That’s because anything we emit now will still be in the atmosphere by the time humanity is (hopefully) reaching carbon neutrality. We need to change the direction of emission change – from rising to falling – all around the world, as well as begin the institutional transformations that will be needed to sustain the fall all the way to the bottom.

Individual actions are not going to save us. That said, we desperately need to move from a mindset where we expect emissions reductions in 2025 from unknown technologies to one where we are constantly striving to drive our emissions to zero.

Biochar to fight climate change

During the last few years, I have read a fair bit about biochar, a substance generated by burning biomass in a low oxygen environment. Because this charcoal is rich in carbon dioxide (CO2), making it could somewhat draw down the amount of CO2 in the atmosphere. There are also claims that it can make soil more fertile, playing a similar role to the ‘terra pretta’ that apparently makes some Amazonian lands more productive than average.

There are certainly people who make exaggerated claims about what biochar production could achieve. While it might be adequate to generate one small ‘wedge’ in net greenhouse gas emission reductions, it does not seem plausible that it can be a major part of the solution. George Monbiot has been especially critical of those who have hailed it as a solution in itself.

While not a miracle cure, biochar may have some promise, and deserves to be looked into as part of the process of building a low- (eventually zero-) carbon global society.

Unimpressed with humanity

I am increasingly of the sense that humanity doesn’t have what it takes to deal with climate change. We are apparently lacking not only in scientific understanding, but also in empathy and skill in managing risk. We are easily overpowered by those who use weak arguments forcefully, and slow to rally to the defence of even the most well-established of scientific facts.

These comments strike me as an especially poignant example of muddled thinking. The basic message is: “Let’s not argue about what causes climate change, because that is contentious and conflict makes me uncomfortable. Instead, let’s agree to disagree about what’s happening, but begin cutting carbon emissions anyhow.” With such thin soup on offer from those who believe we should take action, it’s not too surprising that more and more people apparently see the climate threat as overblown. People put politeness ahead of rigorous thinking and rely far too much on simple heuristic crutches (past warnings about other things have proved exaggerated, technology will save us, etc). None of this suggests that people have the will and understanding necessary to build a zero-carbon global society in time to prevent catastrophic climate change.

Of course, there is extremely strong scientific evidence that greenhouse gas emissions cause the climate to warm, along with additional consequences like charged precipitation patterns and ocean acidity. Arguably, some of these effects are already rather serious, particularly in the Arctic. We are on track to raise atmospheric concentrations of CO2 from about 383 parts per million (ppm) to over 1000 ppm by the end of the century. Decisive action is required, but politicians have correctly sensed that they are better off dithering: using rhetoric to convince the public at large that they are ‘balancing the environment and the economy‘ while privately kowtowing to special interests. These include both the old smoke-belchers (coal-fired electricity worst among them) and up-and-coming lobbies like corn ethanol producers. The politicians see quite clearly that their political futures do not depend on the habitability of the Earth in fifty years time, and they think and vote accordingly.

I certainly wouldn’t feel confident about having or raising children right now. The world continues to walk straight towards the edge of the precipice – ignoring the feedbacks and lag times that delay the impact of our emissions on the state of the climate – while patently failing to grasp the seriousness of our situation. If those alive and blogging now don’t live to see the worst consequences of that inaction, it seems highly likely that their children and grandchildren will start to, and that those consequences will be felt for thousands of years.