Would love to hear others’ thoughts on this one!

It’s written to EPA administrator Stephen Johnson, from my colleague Baruch Fischhoff, the Carnegie Mellon risk expert and professor who’s chair of the Homeland Security Advisory Committee for the EPA’s Scientific Advisory Board.

Fischhoff wrote:

[S]everal Committee Members, myself included, were distressed at the lack of systematic, scientific attention to communicating with the public.  … It is not unique to this anthrax project, but reflects a general problem in our national emergency planning … As we saw in 2001, a b. anthracis (“anthrax”) attack has enormous potential for achieving our enemies’ goals, even when causing relatively few casualties … Much of that damage came from our own inability to communicate credibly, causing needless concern and distrust that persists to this day.

With its rigorous methodologies and an impressive body of academic literature supporting it, risk communication represents the bounty of wisdom that can be found in the applied social sciences, from fields including psychology, communications, decision analysis, rhetoric, sociology, political science, law, ethics, linguistics and anthropology.

But the scientific aspects of risk communication are often entirely overlooked or dismissed by technical experts and authorities in both emergency preparation and response. Instead, they assume that  their knowledge of technical details, their intuition about what to say to the public, or their charisma (this being the politicians) will give people enough information to respond to emergencies.

Call it ignorance, arrogance or denial, but that attitude is a big mistake, and it has real consequences.

Look back at Hurricane Katrina for some horrific examples. Not only did authorities fail to get the frail and the poor out of New Orleans, it utterly failed to persuade tens of thousands of them who could evacuate the city to do so.

And recall the disaster that one risk expert called the “Duct Tape Risk Communication” emergency preparation strategy, proposed by the White House in 2003, which immediately was turned into a lampoon to skewer the U.S. government, rather than inspiring citizens to take useful action.

People need to trust their leaders and technical experts to tell them the truth in emergencies, in ways that actually answer their questions — questions which will be different for business leaders than for schoolteachers — and address their fears. Without that trust, the public isn’t going to follow instructions.

As Fischhoff said in his letter to EPA, the only way to prepare for emergencies is to have an inventory of scientifically sound risk communications on hand — pre-scripted press releases, print and electronic explanatory materials, guides to self-testing, FAQs and the like — ready to be adapted to specific circumstances. And,

Communications research planning is not expensive.  However, it requires a skill set that is not represented in the anthrax [Techical Assistance Document] task force.  Nor is it present in most other parts of our national response effort [including the Emergency Consequence Assessment Tool and the WaterSentinel Program (PDF)].  As a result, much of what passes for risk communication advice has no scientific foundation.

Thankfully, compared to some of the other problems facing the Obama administration, this is an easy one to fix. And given the nature of some of those problems, they may want to fix this one now.

They’d read my paper on risk and synthetic biology and thought my characterization of their report on synthetic biology, “Genome Synthesis and Design Futures: Implications for the U.S. Economy,” was unfair.

The larger issue that our disagreement is based on — that is, how to pay proper fealty to scientific uncertainty — is at the core of my discontent with how technology innovations are assessed for risk and benefit.

So I told them I would write about our disagreement here. This way, they have an opportunity to respond, and maybe we can get a discussion going on the subject.

Here is what I wrote:

Of the most concern in the context of risk and governance are the reports that uncritically support synthetic biology, as they encourage development and commercial release with little or no acknowledgment of the degree of scientific uncertainty that surrounds the endeavor. A 174-page report on synthetic biology published by Bio-Economic Research Associates in 2007 and funded by the Department of Energy (which itself has invested heavily in synthetic biology research), contained but a single, three-quarter-page discussion of the limitations of the engineering paradigm as applied to living systems. Giving such short shrift to a topic that is still under deep consideration in the broader scientific community lends an air of certainty to a highly uncertain endeavor. Such under-representation has real significance from the perspective of investment and economic risk, as well as from that of health and the environment.

[Italics added by me; they aren't in the paper.]

Aldrich and Newcomb said it was “flatly unfair” to say their report doesn’t touch those issues, and objected to the implication that they were “apologists” for the paradigm of synthetic biology.

They mention the report’s final chapter, “Scenarios for the Future,” about how the synthetic biology future might play out. One of the “major uncertainties” (a key scenario element) is posed as, “How quickly will biological engineering advance?” And they note that in one of these scenarios, “technical challenges impede applications” outside the lab.

But this is precisely my issue. The idea that “technical challenges” are the only issues synthetic biology faces today is flat wrong. The engineering paradigm that synthetic bio is based on — that genetic components are like electronic circuits, with independent, clearly defined functions — simply does not apply to living systems.

Geneticists have known for years that genes and other biological components — the same components bio-engineers are using to snap together their synthetic creations — do not operate independently, like electronic circuits. They have long observed that in addition to whatever their primary function might seem to be, these components appear to operate in some kind of a network, that they interact and overlap with each other in ways that are not yet understood at all.

(The ENCODE study was most recent public acknowledgment of this fact.)

Yet the field of synthetic biology is pretending as though this gaping chasm of knowledge — a chasm that pretty much negates its entire raison d’etre — has no impact whatever upon the viability of its work. I’ve never known a synthetic biologist to proactively address the issue. If confronted with it directly, the most I’ve heard is the equivalent of, “Yes, it’s complicated. But we’ll figure it out.”

At the same time, investors are sinking hundreds of millions of dollars into developing products based on a fundamentally flawed scientific premise masquerading as a technology with predictable, “engineered” outcomes.

OK, back to Aldrich and Newcomb. In fact, I do not think they are apologists for synthetic biology. As far as I know they have no direct investments or interests in any synthetic biology companies. And they explicitly state at the beginning of the report that they did not intend to address issues of safety, unintended consequences, or ethical, legal and social questions.

Still, there is an inside the tent, it’s-a-done-deal orientation to the report that is discomfiting under such highly uncertain circumstances.

With its sections on “Enabling Technology,” “Economic Dimensions of the Biological Engineering Revolution,” and discussions of “Applications of Genome Synthesis and Design” that specifically target the energy, chemical and vaccine industries — and whether it means to or not — the report presents a de facto case that synthetic biology is already a viable investment.

And while it concurs that there may be some technical speed bumps, it simply does not acknowledge the deep, fundamental scientific uncertainties about the very premise on which synthetic biology is based.

From my perspective, this lack of acknowledgment is misleading to investors and anyone else who is trying to understand what a synthetic biology future might mean.

So, all of that to say:  Respectfully, I stand by my story.

But as I started out saying, I do think that the much bigger, critical issue here is about uncertainty itself, and that concern goes beyond any individual report or technology, particularly as private investment is driving science-based innovations to market much more quickly than ever before.

As a society, we have got to find a way to talk more honestly about and have a strategy to anticipate the impact of uncertainty on innovation. That’s the only way regulators will be able to safely bring new technologies like synthetic biology to market without endangering either investors or the public’s health and welfare.

This is the driving force behind much of the work and thinking that I’m doing now, and I’ll be posting more about it as time goes on.

On Tuesday, the New York Times published package of articles that explored new genetic research and new ideas of what a gene is.

Much of the package was based on the findings of the ENCODE study, which was sponsored by the National Human Genome Research Institute.

The upshot of ENCODE, which was published about a year and a half ago, in June 2007, was pretty straightforward: the human genome is not a “tidy collection of independent genes,” after all, with each sequence of DNA linked to a single protein, which in turn is linked to a single function, like the production of an enzyme.

Instead, genes appear to operate in a complex network, and interact and overlap with one another and with other components in ways will challenge scientists ”to rethink some long-held views about what genes are and what they do.”

The lead story in the package notes this perspective, writing that scientists “no longer conceive of a typical gene as a single chunk of DNA encoding a single protein,” and quoting one of them as saying, simply, “It cannot work that way.”

YES! I was so excited that this issue was finally going to get some attention. Not only was one of the central themes of my book, Intervention, but I too wrote a column about ENCODE for the New York Times — called “A Challenge to Gene Theory: A Tougher Look at Biotech” — right after the results were published, in July 2007.

In it, I asked what (to me) is the most obvious and important question, but it was addressed nowhere in the NYT package:

If so much of what we know about genes is wrong, how does this change the decisions made about the safety of the thousands of biotech products already on the market, from pharmaceuticals to living transgenic organisms, that were based on these very faulty — in fact, almost completely backwards — scientific assumptions?

Fact is, all of the proposed benefit of genetic engineering (including its “no-risk” profile) comes from this assumption: that DNA will produce the same protein in whatever genome it’s planted, and that’s all it will do — that the host organism will be essentially unchanged except for expressing that one additional trait.

The FDA’s consumer magazine published an article on plant breeding in 2003 that made the same declaration. The benefit of genetic engineering, it said, is that it is “more precise and predictable … a single gene may be added” to a plant to give it a single specific characteristic without transferring the undesirable traits.

All things considered, revisiting the question of risk is an absolutely logical, rational, fair — and, I might add, pretty important — line of inquiry. Thus I remain completely baffled about why even the smartest journalists in the mainstream media are completely ignoring it.

I understand that these products are having no gross effects. People aren’t dropping in the streets with big oozy pustules, whole farm fields are not being laid to waste, and so forth. If they were that obvious, we’d have figured out a connection.

But physiological effects can be invisible, subtle, and even cumulative. And because there is no required tracking or monitoring of biotech drugs or organisms once they’ve been sold, we will have no way of knowing what these effects might be until it’s too late.

Also, it must be stressed, ENCODE’s findings are not new information.

Molecular biologists and geneticists did and do know that the “one gene, one protein” theory hasn’t held water for several decades.

Just for starters, they know that there are some 20,000 protein coding sequences in the human genome, while there are probably hundreds of thousands of proteins (some even say millions). They know they are nowhere near knowing how the mechanisms work that trigger their production.

Epigenetics, which studies changes in the appearance of an organisms or in gene expression that are caused by mechanisms other than changes in the underlying DNA sequence, is just one of many areas of study in molecular biology that demonstrates a long-standing rejection of this simplistic notion of the gene.

For their part, organismal biologists — those who study whole organisms, like fish and insects and mammals, not just their DNA — as well as population geneticists and evolutionary biologists and behavioral geneticists, have never hewed to the “über DNA” perspective. For them, it has never held explanatory power outside the lab, in the real world that they live in and study.

As one molecular biologist I know once said to me, “This perspective changes the nature of the questions we ask.”

Oh, how I wish that were true!

I am happy to report that in April 2002, Oliver Morton, Hybrid Vigor Fellow and the news and features editor for Nature (as well as the author of two books), wrote a terrific monograph for Hybrid Vigor on essentially the same subject, The Living Skies: Cloud Behavior and Its Role in Climate Change.

POST recently published three POSTnotes entitled “Ecological Networks” [PDF], “Smart Metering of Electricity and Gas” [PDF] and “Autism” [PDF]. The first two POSTnotes for 2008 were on “smart” materials and systems, and synthetic biology.

You can subscribe to the POST reports yourself, by sending an email to: mailto:post@parliament.uk.

“Ecological Networks” considers the possible conservation benefits of ecological network implementation in the UK. Ecological networks are intended to maintain environmental processes and to help to conserve biodiversity where remnants of semi-natural habitat have become fragmented and isolated.

“Smart Metering” examines the potential benefits, costs and policy considerations involved with technology that enables accurate measuring of energy usage and the provision of improved information to consumers, suppliers and the market. Smart meters are expected to be installed in all of the U.K.’s 25 million homes over the next ten years.

“Autism” describes autism and autism research, and considers policy approaches to this disorder whose prevalence is greater than previously recognized, thus putting pressure on service providers and highlighting the need for greater awareness. Autism affects how a person communicates, socializes and interprets the world, and can lead to wide ranging difficulties in every day life, including forming relationships and living independently.

From “Smart Materials”: “The most commonly accepted definition is that smart materials and systems can sense and respond to the environment around them in a predictable and useful manner. For example, the ‘photochromic’ materials used in reactive spectacle lenses become darker in response to increased light. Smart materials arise from research in many different areas and there is a large overlap with nanotechnology.

“From “Synthetic Biology”: “In the US, where most of the research takes place, the term ’synthetic biology’ describes research that combines biology with the principles of engineering to design and build standardized, interchangeable biological DNA building-blocks. These have specific functions and can be joined to create engineered biological parts, systems and, potentially, organisms. It may also involve modifying naturally occurring genomes (an organism’s entire hereditary information usually encoded in DNA) to make new systems or by using them in new contexts. There is sometimes confusion about the definition of synthetic biology amongst those outside the research community, reflecting its position as a complex, new and rapidly developing field.”

IPPY winners in 65 categories were selected from a total of 2,690 national entries came from “all 50 U.S. states, eight Canadian provinces, and 17 countries overseas.”

In the Science category, I’m flanked by books published by Harvard University Press and Yale University Press. I’m proud that li’l ol’ Hybrid Vigor Press has found itself in such good company. Very proud indeed.

… During the breeding season, tiny leeches climb aboard the newts, sucking their blood, and possibly transmitting Icthyophonus, a fungus-like pathogen that hides in the newt’s muscle. Newts have other parasites, too. Tom Raffel, a postdoc at the Center for Infectious Disease Dynamics (CIDD) at Pennsylvania State University, has documented more than 20 different parasites in Pennsylvania newts. Two are new to science.

In the past, a scientist might single out a pathogen, map its life cycle, and describe the consequences for its victims. Although pathogens represent more than half of all life on earth, only a small fraction have ever been studied. So, a new approach to infectious disease is taking root both around the world and here on the shores of Beaver Pond. Raffel doesn’t study newts, or leeches, or Icthyophonus. He studies the Beaver Pond community and the myriad interactions within. Just a few miles away at CIDD, researchers are looking at human pathogens, too – measles, influenza, and Escherichia coli among others – and trying to understand the communities of these pathogens within cities and within hosts, piecing together the way these interactions evolve over time.

Despite advances in vaccine strategies and drug treatments, many scientists worry that not enough is being done to suppress, let alone anticipate, the next pandemic. Scientists at CIDD are taking principles of population biology, community ecology, and evolution and wedding them to epidemiology, immunology, and genomics. This approach could help optimize vaccination strategies, design eradication programs, halt incipient pandemics, and it could identify potential zoonoses before they’ve infected humans. In the three short years that CIDD has been around, it’s become a hotbed of interdisciplinary collaboration with 12 faculty members from departments around the Penn State campus.

Daniel Falush, an evolutionary geneticist at Oxford University, describes one effect CIDD has had in the United Kingdom: “There was a great sucking sound because these famous British scientists were disappearing to Penn State.” Actually, Ottar Bjørnstad, a Norwegian mathematical ecologist, was the first to make the move to State College in 2001. At that time, Peter Hudson was at the University of Stirling in Scotland but was displeased with their new president, who he says wasn’t supportive of biology. When Penn State invited him for a visit, he loved the atmosphere, and it didn’t hurt that his friend Bjørnstad had already scoped out the local pubs. …

[snip]

The piece quotes Hudson as saying, “Our vision really is to have a systems approach to disease,” says Hudson. “Issues that go from intracellular interactions between viruses and cells right the way through to pandemics, something we call the protein-to-pandemic link.”

I daresay that reality will probably turn out to be a bit less linear than that, but at least their linear thinking is horizontal!

The column is basically my entire book, Intervention, crammed into 1300 words. As a result I had to leave out some important stuff, so I decided to post some of it here.

One of the things I would have liked to dig into a bit was the USDA’s statement about the amount of scientific input the agency uses to develop its regulations.

As evidence, the person I spoke with mentioned that in 2002, the agency had commissioned a peer-reviewed National Academies study on the subject, called Environmental Effects of Transgenic Plants.

It was a curious example to choose. Because I read that report when I was writing Intervention, and it sure sounded to me like the USDA got handed its head on a plate.

National Academies reports are invariably written in a combination of academic and public-relations soft-shoe so as not to be offensive, particularly if they’re critical.

In that context, the headline on the official news release for Environmental Effects was positively blaring: “Regulation of Transgenic Plants Should Be Reinforced,” it said. “Field Monitoring for Environmental Effects Is Needed.” No equivocation at all.

The report dinged USDA’s Animal and Plant Health Inspection Service (APHIS) on many serious issues.

In addition to the problems about disclosure and transparency that I noted in today’s column, the report also said that APHIS didn’t evaluate environmental effects with enough rigor before approving them for commercial use, and that it needed to open up its risk assessment process to experts other than its own.

In fact, the authors said, if USDA wasn’t up to the job they should just give it to the Environmental Protection Agency and be done with it.

The committee also recommended that APHIS stop its policy of “deregulation for life,” which is its policy toward transgenic plants today. (That’s not how they put it, by the way.)

Today, once your transgenic and/or pharma plant is approved by USDA, it is no longer regulated. You need never come back for post-market testing, and you aren’t required to monitor the crop to see if your original risk assessment is holding up in the field.

If you’d like, you can read the Executive Summary for yourself.

Five years later, it appears as though the agency has not done much to address the National Academy’s recommendations.

On February 14th, for example, the USDA got a Valentine’s Day spanking by a San Francisco judge who found the agency in violation of the law for its “cavalier” attitude toward the environmental effects of a transgenic alfalfa crop. (Subscription required for the NYT link.)

As for the obviously riskier pharma crops: despite protests from its own research personnel, USDA permitted Ventria to plant several acres of biopharma rice virtually next door to a USDA rice quarantine nursery in North Carolina.

The purpose of a quarantine center is fairly obvious. In this case, its job was to keep harmful genes out of the domestic rice supply.

One of the scientists who protested the Ventria siting is chair of a national rice germplasm committee. The other is a research leader in the USDA’s own Plant Science Research Unit.* Their statements were submitted to a USDA docket in 2005 when the department invited public comments on its preliminary approval for Ventria’s rice.

According to the Union of Concerned Scientists, it obtained USDA records through FOIA that “document the agency’s apparent failure to adequately monitor and inspect pharmaceutical rice fields in North Carolina—even after a hurricane blew through the area, potentially contaminating a nearby rice breeding facility.”

(For the record, USDA disagrees with UCS’s reading of the documents; UCS refutes the refutation.)

* (Or at least they were; I don’t know where they are today.)

In the piece, Scott asked me some questions — about how some journalists have overlooked the risk story, and about why I had to publish the book through Hybrid Vigor, rather than through a traditional publishing house — that I hadn’t talked about before.