Oil-Eating Microbes

Most people probably don’t know that there are naturally-occurring microbes that make their living by eating naturally-occurring hydrocarbons (hydrocarbons are organic compounds that consist entirely of hydrogen and carbon, and that are found in crude oil). The existence of such microbes are good news, in the context of a major oil spill like the one that recently contaminated the Gulf Coast.

By David Biello, for Scientific American: How Fast Can Microbes Clean Up the Gulf Oil Spill?

These are boom times for oil-eating microbes in the deep waters of the Gulf of Mexico, thanks to BP’s Deepwater Horizon accident that has added some 600 million liters of hydrocarbons to those waters. And now research published online in Science on August 24 shows that an array of new and unclassified oil-eating bacteria are feasting on the newly rich resource of hydrocarbons.

Interestingly, the story makes little mention of biotechnology — basically none at all, except to note that the scientists currently studying the microbes munching away at the Gulf Coast spill are from the Energy Biosciences Institute. The omission is interesting, given that a bunch of work has been done on genetically engineering microbes to boost their oil-eating powers.

Posted in environment, genes, industrial biotechnology, risk | 4 Comments

Imitating Evolution

Someone (I can’t recall the source) once said that rather than envy the creative power of nature, we ought to emulate it. Genetic algorithms have, for a couple of decades now, allowed scientists and engineers to harness the power of evolutionary processes to evolve (literally) new solutions to hard problems in silico. A new technology developed by George Church at Harvard seems aimed at allowing scientists to do the same thing in vitro.

Here’s the story, by Arielle Fridson, writing for Bloomberg: Harvard Scientists Speed Up Evolution, Aim to Sell Technology to DuPont

Evolution often plays out over millennia. George Church says he can make it happen in days.

He and his team of researchers at Harvard Medical School in Boston invented a table-top machine that can generate multiple changes in the DNA of bacteria all at once, speeding up the evolutionary process. Aiming to sell the technology for use in chemicals, energy, and the drug industry, they’re talking with DuPont Co. and other companies, members of the team said….

This of course is pretty much the exact opposite of the kind of genetic engineering that makes use of careful insertion of genes with known functions. It allows a kind of generate-and-test procedure: generate a bunch of mutations, and see which ones do what you wanted them to do. This allows for enormous creativity, as the literature on genetic algorithms attests. (Back in grad school, I fiddled with G.A.’s and ecological programming a bit, and got to watch novel — and sometimes radically weird — solutions to hard problems literally evolve.) Along with this creativity also comes risk, when the things evolving are potential pathogens. Church is right to worry (as the Bloomberg story notes he does) about the potential for misuse.

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Berkeley Backs Down on Gene Tests for Students

I blogged here a few months ago about UC Berkeley’s plan to do (voluntary) genetic testing on this year’s entire first-year class. (See: Genetic Testing and the College Freshman)

Now the university is backing down. Or rather, the university has been forced to back down by the California Department of Public Health. Here’s the story, by Rob Waters, writing for Bloomberg: UC Berkeley Backs Off Gene-Test Program for Students, Blocked by State

The University of California, Berkeley, won’t tell about 700 students the results of genetic tests performed on their saliva, after the state health department barred the institution from proceeding.

The state Department of Public Health views the tests as providing medical information and must, by law, be processed in certified laboratories, Mark Schlissel, the school’s dean of biological sciences, said today in a conference call. The results now will be analyzed collectively and the project will proceed as a research and educational effort, he said….

Regulatory issues aside, lots of people (mostly ethicists) expressed concern about the idea of testing the entire freshman class. As I noted in my previous blog posting on this topic, there were concerns about whether testing could be truly voluntary, and about whether students would be able to understand, on an individual level, the meaning of their test results.

For the most part, I agree with my colleagues who urged caution. I’m skeptical about such tests doing much good, and I’d rather see such testing done on smaller groups of students in a controlled way than on 1000s all at once. But — just to play devil’s advocate — it’s worth asking just what the risk here is. To put it bluntly, no one has ever died from genetic testing, as far as I know. For that matter, where are the horror stories of people’s lives torn apart by their test results? There is evidence that genetic tests can have interesting implications for family dynamics, in families with hereditary diseases. But aside from that, it’s not clear that anyone’s been hurt by a genetic test like the ones Berkeley was proposing. Compare: when Ralph Nader published Unsafe at Any Speed back in the mid-60s, calling for auto manufacturers to make their cars safer, he was able to point at statistics showing actual deaths — lots of them.

Now, again, I’m not a huge fan of personalized genomics. But if we’re going to debate particular cases, it’s worth putting it on the table: the tests may not be all that useful, but if we’re going to forbid them, we ought to be able to point to some actual dangers.

Posted in ethics, genes, genetic testing, health, risk | 1 Comment

DTC Genetic Tests: Justifying Regulation

Regulation and ethics aren’t the same thing. But when done properly, good regulation is rooted in good ethical reasons. If we want to think in a constructive way about existing or potential regulations, we need to consider the values and principles we think those regulations ought to embody.

Here’s a ‘point of view’ piece I wrote on that topic, for the current issue of Genetic Engineering & Biotechnology News, called “Justifying Regulation of DTC Tests.”

The Food and Drug Administration recently signaled, in no uncertain terms, its intention to regulate the provision of direct-to-consumer (DTC) genetic testing….

But if we really want to understand the “big picture,” the full ethical context within which to situate the question of regulating DTC genetic tests, it’s worth considering the way in which the ethical justification of regulation is rooted in the ethical justification of market behavior more generally.

We generally think that people ought to be free to buy and sell according to their own needs, interests, and preferences. This implies a freedom to conduct exchanges in a relatively self-centered (or profit-seeking) way. But it’s worth considering what the ethical underpinning is for that freedom….

Posted in ethics, genes, genetic testing, regulation | Leave a comment

Meat and Milk from the Offspring of Clones

Over at my Food Ethics Blog, I’ve got a new (short) posting about cloning animals for food: Milk and Meat from the Offspring of Clones.

(Not surprisingly, given that this is 2010, there’s turning out to be a fair bit of overlap between that blog and this one, as the months go by.)

All I’ve got to add here is this: it’s interesting (worrisome, to some) that “cloned foods” (loosely speaking) are entering the food chain by stealth. So, fodder for discussion: is this a good or bad thing for biotech, generally?

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Venter on the Past & Future of Genomics (etc.)

From Der Spiegel: Interview with Craig Venter: ‘We Have Learned Nothing from the Genome’
The whole thing is worth reading, but here are a few snippets I found interesting.

First, here’s Venter being dismissive about fears related to genomic knowledge:

SPIEGEL: The genome project hasn’t just raised hopes — but also worries. Do you understand those concerns?

Venter: Yes. There are two groups of people. People either want to know the information or they prefer to live like an ostrich with their head in the sand, not knowing anything. The fear is based on the ill-founded belief that those who know the DNA sequence also know every aspect of life. This nonsense has been spread by the same geneticists who were afraid of the commercialization of this stuff. From the time of the first few discoveries of gene defects — Huntington’s disease, for example, everybody thought that if you knew your genome, you would know when you would die and what you would die from. That is nonsense.

This bit strikes me as right:

SPIEGEL: And what about the fears about the abuse of gene data through insurers or employers, for example? Do you see that as sheer hysteria?

Venter: Abuse is not a question of whether the data is available. It is an issue of laws. You can’t do anything to change the availability of genetic data. Look at this bottle that you have touched — that’s all I need to obtain your entire genetic information.

SPIEGEL: How much would you be able to learn about us by doing so?

Venter: If anything, we don’t really know how to read the genome and it can’t tell us very much right now. So what’s the ethical debate about?


SPIEGEL: So the Human Genome Project has had very little medical benefits so far?

Venter: Close to zero to put it precisely.

SPIEGEL: Did it at least provide us with some new knowledge?

Venter: It certainly has. Eleven years ago, we didn’t even know how many genes humans have. Many estimated that number at 100,000, and some went as high as 300,000. We made a lot of enemies when we claimed that there appeared to be considerably fewer — probably closer to the neighborhood of 40,000! And then we found out that there are only half as many. I was just in Stockholm for the 200th anniversary of the Karolinska Institute. The first presentation was about the many achievements the decoding of the genome has brought. Then I spoke and said that this century will be remembered for how little, and not how much, happened in this field.

…and on the (current) value of genomics to medicine:

SPIEGEL: Why is it taking so long for the results of genome research to be applied in medicine?

Venter: Because we have, in truth, learned nothing from the genome other than probabilities. How does a 1 or 3 percent increased risk for something translate into the clinic? It is useless information.

So, at least Venter is consistent. His own genome is sequenced, and even published. But he says that knowledge is worth relatively little. His genome is sequenced, in other words, not because doing so is meaningful and valuable, but because it isn’t.

Posted in Craig Venter, ethics, genes, Human Genome Project | Leave a comment

The Death of the UK’s Human Fertilisation and Embryology Agency

Government involvement in biotech takes many forms, and government agencies take a variety of shapes and play a range of roles. Direct regulation — setting standards, prohibiting this and that — is not the only option. So when evaluating the usefulness of a governmental or quasi-governmental body involved in regulating (in the broad sense) some bit of biotechnology, it’s important to look at what kinds of activities, in particular, it was involved in.

Here’s Zoe Williams, writing for The Guardian, about the demise of the UK’s Human Fertilisation and Embryology Agency: After the burning, a raft of IVF horror stories to come

So this function is vital: there will always be biotechnological advance, and there will always be ethical concern. Nobody else synthesises these. [Ethics professor Donna] Dickenson comments: “We don’t have a statutory national ethics commission. Almost every other European country does … the consultative function [of the HFEA] is very important: it’s notorious that biotechnology moves very fast, and outstrips legislation. It’s very hard for the public to keep up because the science is changing all the time.”

It’s difficult to predict what the result would be of the discursive vacuum left by a disbanded agency. Someone will occupy that space: it’s possible that a clear-eyed, neutral party might step in to present evidence in an unsensational way. But it’s more likely to be the Daily Mail, with a raft of IVF horror stories. A small but noticeable amount of the HFEA’s time has gone in correcting misleading stories from the press. It’s interesting to consider whether IVF could ever have become so acceptable a procedure without these interventions….

Posted in embryos, Europe, IVF, regulation | 1 Comment

Europeans & Cloned Food Animals

Check out this blog entry over at my new Food Ethics Blog: Cloned Animals, Food, Ethics.

The short version: attempts by European Parliamentarians to ban food from cloned animals was predictable, and based on what look to be pretty terrible reasons.

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Uncontrollable Risks of Genetic Testing

A lot has been written about the risks & mostly theoretical & associated with genetic testing. Genetic information is highly personal, often difficult to understand, subject to considerable interpretation, and of widely variable predictive power. Two main kinds of worries arise. One pertains to how the individual will react to genetic information about him- or herself. Another pertains to how others & including employers, insurers, etc. & will react to it.

But there’s an interesting twist, here. Part of the risk of genetic data lies in how that data is interpreted, and how it’s interpreted depends in part upon what kinds of studies have been done on the relevant bit of genetics. The fact that you happen to have a certain string of DNA is meaningless until interpreted in light of relevant scientific studies. But here’s the problem. If you get tested today, and get your test results next week, new information released next month may alter the interpretation of those results. That may change the risk you face.

The result is that at least some of the risks posed by a genetic test are entirely outside of the control of the company that sells that test. That’s pretty odd, as product safety goes. Who determines just how safe a chainsaw is? The maker of that chainsaw. Who determines how many safety features are built into a new car? The maker of that car. Who determines the risk of a genetic test? That’s much harder to answer.

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Genetic Testing and the College Freshman

Gone are the days when a college student’s first exposure to genetics came after the first day of school, in a biology class.

U.C. Berkeley is offering (or should I say “offering”) genetic testing to a few thousand freshmen this year.

Here’s the story, by Tamar Lewin, in the New York Times: College Bound, DNA Swab in Hand

Instead of the usual required summer-reading book, this year’s incoming freshmen at the University of California, Berkeley, will get something quite different: a cotton swab on which they can, if they choose, send in a DNA sample.

The university said it would analyze the samples, from inside students’ cheeks, for three genes that help regulate the ability to metabolize alcohol, lactose and folates.


Those genes were chosen not because they indicate serious health risks but because students with certain genetic markers may be able to lead healthier lives by drinking less, avoiding dairy products or eating more leafy green vegetables.

This is bound to raise concerns. Yes, the testing is voluntary. But the risk is that many students won’t read the fine print, and will worry (perhaps irrationally) that failure to comply will be held against them. And, as with all genetic tests, there’s the risk that students will misunderstand the results. Questions are also bound to arise about whether students will understand the future uses to which their DNA samples (or merely their data) will be put.

As economist Tyler Cowen put it, “Don’t be surprised if this is soon canceled.”

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