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 particularly liked Bob’s phrasing of the “collective margin call” on the banks. It indicates that part of what’s happened is a failure in coordination: banks have cash on hand as long as only a few percent of their patrons want to withdraw their cash. This echoes a theme of a post I wrote about the credit crunch back in June. Here’s an excerpt from that post:

Clearly, a great crime has been committed. An entire nation has been robbed. World markets are shaken. But who’s responsible? Nobody. And everybody. The insidious nature of this crime is that we all collaborated to commit it and without a master plan. Can such collective action crimes be avoided? Or is the commons forever doomed to be the scene of tragedy?

Bob’s comments on risk management are also strongly reminiscent of Denise’s work on risk management in the biotech industry. Bob writes:

Risk management failures created the current financial crisis, and risk management failures have also created the personal information disclosure crisis, and the malware crisis, and a bunch of other problems which are not yet crises. We do risk management poorly in all disciplines. We do it poorly for a bunch of reasons: executives don’t understand their own businesses well enough to understand their risks; risk managers don’t know how to talk to executives about risk; incentives favor creating long-term risks in order to accrue short-term profits; the list goes on and on.

Denise’s main assertion in her book, “Intervention: Confronting the Real Risks of Genetic Engineering and Life on a Biotech Planet,” is that the biotech industry is similarly awash in poorly managed risk. Genetic engineering is another impending crisis that, once it reaches crisis levels, people will be dumbfounded to explain.

As an avalanche of new laws and regulations hit Wall Street over the next few years, I fear that we’ll lose sight of the most important learning to take away from this disaster. Again, Bob Blakley explains:

A final thought.  The financial crisis exists because of a failure of risk management. There will be a temptation to fix the problem using compliance mandates. Compliance mandates, however, don’t fix risk management problems. All they do is prevent specific risk management failures from happening over and over again. Organizations whose risk management is weak will find new ways to fail – and these new ways will circumvent compliance regulations. The right way to fix a risk management problem is to do a better job of risk management.

But Intervention delivers a much broader message, about how the human propensity for hamartia isn’t miraculously expunged by mathematics, statistics, or the scientific method.

In proving her point about assessing the risks of genetic engineering, Denise calls into question the seemingly unassailable position of science in our culture. The book suggests we desperately need “a new kind of science” (to borrow Steven Wolfram’s phrase) — one that accounts for the nature of the beings (i.e., us) who are wielding its increasingly powerful tools. Try as we might, whatever model we create to try and describe reality, our scientific models inescapably say much more about human beings than they do about some objective reality. In the book, Denise exposes our lapses in rationality due to cognitive, social, and technological realities. Such lapses are everywhere in the areas I cover (technology, social trust, and privacy).

So while reading the book, I decided present my views on these issues in a blog post. Admittedly, going into some depth on Denise’s book on the Hybrid Vigor blog (which is Denise’s creation) seems almost self-congratulatory. But I think the larger themes in Intervention are relevant to most of the really difficult problems we’re trying to solve globally today, and understanding these issues will help focus our discussion at Hybrid Vigor.

Softening the Hard Sciences: The Triple Threat to Rationality

1. The Limits of Human Cognition

On the cognitive level, scientists may subconsciously fall in love with logical fallacies they create, without realizing that any theory they concoct is inseparable from their cultural conditioning. Models and theories are as much expressions of a person’s worldview as an expression of scientific truths. On this point, Denise quotes Paul Thurman, a Columbia professor of statistics and data analysis, who puts it rhetorically: “If I’ve built a model based on certain assumptions, that’s what I believe.” (p. 63)

Any assumptions built into the model are virtually undetectable to its creator and patrons; the model becomes a Matrix: “a prison that you cannot taste or see or touch. A prison for your mind.” Mike Walter, whose blog I follow from time to time, calls this brand of irrationality the “Wizard of Oz Syndrome.” The problem here is more than simple self-delusion; it’s the cognitive disability in human beings to view their work and their environment with true objectivity.

In theory, science is based on empiricism, so logical fallacies are supposed to be weeded out by peer reviews. To believe that model of the scientific method only illustrates my point. In practice, reliance on empiricism is the crux of the problem, because in most cases not enough data exist to form an effective model. To do good science, you need good data.

But as Denise puts it, “How do you know what to measure … when you’re looking for the risks in something completely new?” (p. 76)

2. The Effects of Sociality on Scientists

On the social level, we have learned that logical fallacies elicit cultish behavior. Once a fallacy attracts believers, it becomes a shibboleth to distinguish the intellectual elites from the ignorant masses — or “innumerates,” as the math nerds call us. Denise skillfully refutes their case against the innumerates with several examples, including the Long Term Capital Management debacle.

The problem with innumerates isn’t only that we lack perspective about numbers. … What’s more, [we are told,] we tend to personalize things — to be misled by our own experiences rather than being objective and rational and informed by the facts, an error in judgment that apparently no mathematician or scientist ever makes. … [But] to conclude that “innumerate” people cannot understand risk because they don’t understand sophisticated mathematical concepts is inaccurate at best and it certainly isn’t an objective truth. Thurman’s Nobel-winning economists doomed Long Term Capital Management by building their models on faulty assumptions, which they then relied on to make decisions.

Denise’s argument here reminds me of a hilarious episode of Zefrank on the role of consciousness. It’s good comic relief if you want to go check it out before continuing with the rest of this post!

Once a group of like-minded people isolate themselves from independent thinkers, groupthink sets in, and group members can be made to believe almost anything.

3. The Psychological Effects of Technology on Scientists

The introduction of technology into a social setting has demonstrable psychological effects on human beings, including scientists. An intervening technology may change people’s perception of a problem so they come to rely on the technology (a structural solution) and accept its authority. The result is blind deference to the intervening technology. Denise again allows Paul Thurman to make the point:

Many researchers simply believe the numbers that come out of the computer…. They say, ‘I have a model; that’s the right thing to believe. If there’s anything out of pattern, then I must have done something wrong.’ They rarely think that the model itself could be wrong. People don’t do the simple sniff tests anymore … they immediately cut to a quantitative explanation…. They infer a scientific precision that isn’t there…. But obviously even Nobel winners can build erroneous models. (p. 63)

The Absurdity of Certainty

Epistemology is the term philosophers use to describe the ways of knowing. Rather than try to define it, I’ll offer a small thought experiment. Answer these questions in your mind:

• How good-looking are you?
• How intelligent are you?
• How do you smell?
• How sure are you about your answers and how do you know?

Whatever your answers, the only certainty about this exercise is that you’ll be wrong. But something in the human psyche allows us to guess and make up answers — and then to believe in what we just made up as if it were factual.

There’s a game called “blind man’s bluff” that illustrates this point rather well. Blind man’s bluff is a kind of reverse-poker, in which players can see everyone else’s hand, but not their own. Players then make bets on their hands, not knowing what cards they themselves hold. It’s a riot to play. (Note: if you watch the video in the link above, in my opinion the game is more fun if you force people to place bets and not allow anyone to fold.) If you haven’t ever played blind man’s bluff, you should stop reading this blog post, get a few friends together immediately, and play a round. Go ahead! I’ll wait.

When you understand blind-man’s bluff, you’ll begin to understand that we humans are much more socially aware than we are self-aware. In fact, without others to play the game with us, we have no way of knowing the cards we hold.

As social creatures, our need to belong makes us just conscious enough of “self” to sense aloneness. We’re not adapted to survive completely on our own, so we bond with others. One of the primary ways we bond is by concocting stories about ourselves and others. Good stories are ones that help people coordinate behaviors and improve cohesion within a social unit. So naturally, we are also willing to believe others’ stories.

Our ability to believe is a virtue, not a flaw. The human propensity to invent stories and believe others plays a key role in the survival of our species. But it also means that our survival instinct favors social cohesion over intellectual acumen. In my opinion, if scientists understood the relationship between belief and social instinct, there would be little tension between religion and science.

I was glad to find that Denise avoids the pitfalls she writes about in the book. She doesn’t fight science with science. Instead, she simply asks for greater caution, in light of human frailty that leads to irrationality — the scientific community not excluded. And so I’m rating this book a “must-read” for the rational being.

So far much of the conversation has been focused on deliberative processes for assessing risk, and we are just starting to wade into deeper waters with talk of the precautionary principle and whether or not Hillary could manage to re-start the Office of Technology Assessment without wrecking it with politics.

You don’t have to be a WELL member to read the conversation, but if you aren’t a member and want to start prodding me with some questions, just send an email to <inkwell@well.com> to have them added to the thread.

The host of the conversation is the redoubtable Jon Lebkowsky, a Texan who I’ve known for many years from the technology world who now writes a regular column for Worldchanging.com.

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.

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.

I will be interviewed — although more likely there will be questions flying in both directions — by Joel Garreau, author of Radical Evolution, staff writer for the Washington Post, and fellow Big Thinker.

Dave Rejeski, who runs Wilson Center’s Foresight and Governance program and isdirector of the Center’s Project on Emerging Nanotechnologies, will introduce me. And Baruch Fischhoff of Carnegie Mellon, with whom I’ve been working on various risk projects for the past few years, is expected to chime in by teleconference.

To cut to the chase: Worldchanging reviewed Intervention last month. And all I can say, still, 2+ weeks later, is wow.

We normally don’t cover problems here on Worldchanging. Indeed, our manifesto says “We don’t generally offer links to resources which are about problems and not solutions, unless the resource is so insightful that its very existence is a step towards a solution.” This book does offer some solutions (about which, more later), but mostly it offers a fervent, well-reasoned call to action. When such an “alarm bell” book offers such clear thinking (I learned more about biotechnology from this book than any other I’ve read), it becomes a step towards solutions. And when the person ringing the alarm bell is no luddite, but one of our brightest technology writers, the alarm demands our attention.

What terrific acknowledgment, from such a terrific source. Quick anecdote about how Alex Steffan heard about the book: In early February I was checking out how Intervention looked on Amazon, as I am occasionally wont to do, and noticed that the Worldchanging book was then (as it is now) offered as a “Better Together” deal with Intervention.

I wrote Steffan a note and he said, “It looks interesting — send it to me.” And the rest, as they say …

RU was a co-founder and editor-in-chief of the legendary, visionary and often delightfully mad cyber/counterculture magazine Mondo 2000, and when he heard that I’d published Intervention, he invited me onto the eclectic podcast show that he hosts, called Neofiles, to talk about it. The resulting Show #65: Fear of a Transgenic Planet is the first of a two-part interview.

Even though I’ve known RU for a looong time (I’ve decided to declare a moratorium on explicit shout-outs of how long I’ve known someone or done something), I was a little nervous about going on Neofiles, which bills itself as exploring “the experimental edge of human endeavors.” This tends to include lots of nanotech, life-enhancement, we-made-it-to-be-good-thus-it-is-good, nouvelle Ray Kurzweil kind of stuff. As he warned me before I showed up, “most of our guests would tend to be very pro-biotech.”

But as it turned out, I was nervous for no reason. He totally got the message of the book. Intervention is not anti-biotech. It’s very pro-science — science in the context of reality, that is, of how technologies work and operate in the real world, not just in the controlled conditions of the lab or as viewed through the rose-colored lens of traditional risk assessments.

Update: Here’s Part 2 of the RU interview … enjoy!