Blogbeat: Frankenfuels and Oakland Docks Protest
stuff of local interest to check out on the net

By Thomas Lord
Monday June 21, 2010 - 05:17:00 PM

This week’s items:Local blogs about a successful effort to delay the unloading of an Israeli ship at the Oakland docks;BP’s money at work – genetic engineering for alternative fuels in Berkeley. Israeli Ship Unloading Delayed by Picket Line 

Israel’s raid on a flotilla bound for Gaza, and the deaths that occurred during that raid, were prominent in the news recently. The raid provoked a local response which received only brief mention in the press but of which the blogosphere has more information. 

On June 20than “ad hoc coalition of dozens of community and labor organizations” converged at the Port of Oakland with the goal of blocking, for 24 hours, the unloading of an Israeli ship. Dockworkers approached but did not cross the picket line. Management insisted that the line should be crossed. An arbitrator was brought in and the union argued that crossing the line posed a threat to the health and safety of workers. The arbitrator agreed and the ship was prevented from unloading for 24 hours. 

Participants in the event blogged about it and provide more video than you might have seen on the news.Obviously their accounts are not from a neutral perspective but they make interesting reading: 

“For veteran Bay Area activists, today's victory echoed a historic milestone in 1984, when ILWU workers in San Francisco refused to unload a ship called the Nedlloyd Kimberley, because its cargo came from South Africa. Just 10 years later, Nelson Mandela was elected president, and apartheid - in its South African form - was dead.” wrote Henry Norr on the Mondoweiss blog (subtitled “The War of Ideas in the Middle East”). 

Of course, not everyone agrees that the action promoted a just cause.As one sample, Christopher Logan writes on the Loganswarning blog – a blog apparently dedicated to sounding alarms about Islamofascism.He offers more footage of the event and concludes “Those that are in support of the Palestinian movement, are actually aiding the worldwide jihad.”  

My own bias about the conflict between Israel and Palestine?I only wish I was so wise as to have one.Neither side seems to me to occupy a higher moral ground in the most controversial actions.And there’s an awful lot of wrestling around in the blood soaked mud. If I have a bias, it is a long standing hope for cooler heads to prevail on both sides. 

Meanwhile, you’ve got to admire the cool heads of the dockworkers union and the arbitrator and management in response to this protest. 

Genetic Engineer, Baby, Genetic Engineer 

There’s good news(!), sorta, from the BP-funded genetic engineering research at the Joint Biosciences Engineering Institute (JBEI).Here is a link to a blog post from Lawrence Berkeley National Laboratory about a recent advance in the science of making alternative, carbon-neutral fuels. After the link I’ll explain it a bit as best I understand it – and share some of my personal misgivings. 

The lede of the article:“Researchers with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) have identified a trio of bacterial enzymes that can catalyze key steps in the conversion of plant sugars into hydrocarbon compounds for the production of green transportation fuels.” 

Well, what the heck are they talking about? 

Let’s suppose that we start with plant matter.Not corn, necessarily.Not even necessarily any plant that will displace food crops. Ideally one that can be harvested without too badly damaging soil. We want to break this down and basically convert it into fuel (e.g., suitable for running a car). 

That’s a sweet deal, if we can get it. The greenhouse gases that fuel emits are greenhouse gases that the plants drew in while growing. In other words, there is a theoretical 0 amount of increase in problematic gasses.On top of that, there’s no need for drilling and the kinds of problems it creates.On top of that, it points the way to a fuel supply we can produce domestically – no need to rely on fuel imports. That’s why BP funds research in these areas. 

To efficiently and effectively convert biomass to fuel on the massive scales needed to displace oil-based fuels is a tricky problem. Scientists look for help from microorganisms which will essentially eat the plants and (pardon me, but) poop the fuel. This is a bit like the way that yeast makes beer or wine – the microorganisms eat up the plant stuff and “poop” out alcohol and other byproducts. The difference is that to sustain anything even vaguely close to our current oil-based lifestyle, the process has to be made far more efficient, to happen on a far larger scale, and to produce chemicals quite a bit more complicated than the alcohol you find in a nice bottle of this or that. 

Harry Beller, “an environmental microbiologist who direct the Biofuels Pathways department of the JBEI’s Fuels Synthesis Division” led a study involving a particular bacterium (“micrococcus luteus”, if you care) whose metabolic processes seemed to do a key step in that conversion from plant matter to fuel. 

This is where it gets tricky: 

As we know, here in the sourdough capital of the universe, if you need a colony of yeast well, you can get a starter going just from what drifts through the air. So youmight think the answer is just mix up a plant mash with micrococcus luteus and wait. It won’t do.It’s not that simple.That’s not efficient.You’ll wind up getting either no usable fuel or else fuel that gives less energy than you spent in making it. 

To the rescue, if that’s what it is, come the synthetic biologists. What is a “synthetic biologist”?It is someone who works on the technology of inserting genes from one critter into another critter to create yet a third kind of critter. 

In the case at hand the scientists carefully studies the genes and metabolism of micrococcus luteus and identified three particular genes that were critical to the process of fuel production. 

In the next step, these genes are isolated and injected into strains of e. coli – yes, there’s unfortunately still more of a “poop” angle here. 

Injected with those genes, the new “franken”-e. Coli begin acting more like micrococcus luteus.They become little specialized critters, man-made, perhaps pointing the way to how to make critters that can very, very efficiently make fuel from plant waste. 

This is all kind of awesome, if you ask me.I dabbled around the periphery of synthetic biology for several years and while much of the biology and chemistry is lost on me, every bit that is not lost on me suggested that this is, indeed, a highly promising area of research. Perhaps, one day, a great deal of oil production will be replaced by large vats of fermenting-on-steroids (so to speak). It’s worth looking into, at any rate. 

What alarms me, though, are the safety and environmental concerns. After all, these bright folks are busy creating entirely novel life forms that nature would almost certainly never come close to producing. In this case, they are tinkering with E. Coli – a bacterium that plays a very important role in the human gut. Ought I to be worried that one day I’ll wake up and (sorry, again with the poop) be excreting fuel? 

It’s not that simple, of course. The particular E. Coli strains that they work with are selected in part because of their weakness: they are darned easy to kill (and tricky to keep alive).Spritz them with some fairly banal antibiotics and a splash of bleach and they’re goners, for sure. Well, probably. 

Inside sources have characterized the situation to me by saying that the only widely agreed upon safety protocols in the US date from the 1970s and that more recent efforts to advance the protocols consistently become mired in politics. Insiders at the Joint Biosciences Engineering Institute have shared gallows humor with me about the prospect of waking up one morning to find the San Francisco Bay covered with a sheen of fuel produced by escaped lab creations. It is not known how easily these synthetic variations on E. Coli could colonize the gut of an infant but it is a risk for which nobody seems to have a good answer. 

In recent years I visited the lab where (most likely) much of this current work took place.I was given a brief tour. I was shown the freezers where the modified E. Coli are kept. I had access to lab benches where they were being worked upon. My potential for personal exposure was uncomfortably high, for my standards. Additionally, at several points, if I were a malevolent actor – I could have trivially and without detection ensured the release of modified E. Coli through (trivial) sabotage.And in the event of an earthquake or fire, I could not see how release into the wild of these franken-critters could be at all unlikely. 

I expressed some of my concerns to some of the grad students there, later, over some beers. “So, you swish out the petri dishes and then literally just flush them down the drain?”Yes, came the reply.But, hey, you should see the kinds of chemicals they used to flush down the drain at MIT and into the Charles River a few years back. Cold comfort, that. 

They say to never look a gift horse in the mouth.That always struck me as odd: carefully studying the gift horse before bringing it inside the gates might have saved Troy. In any event, BP is funded some very promising research in alternative fuels, right here in Berkeley. It’s just the conduct of that research – the wisdom of bringing inside these gates, conducted this particular way – that gives me some concern. 

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