Seth’s blog

In this interviewer Craig Venter says that sequencing the human genome has had “close to zero” medical benefits so far. I thought this comment was even more interesting:

The human genome project was . . .  supposed to be the biggest thing in the history of biological sciences. Billions in government funding for a single project — we had never seen anything like that before in biology. And then a single person comes along and beats scientists who have been working on it for years.

The government-funded people used inferior methods, said Venter:

Initially, Francis Collins and the other people on the Human Genome Project claimed that my methods would never work. When they started to realize that they were wrong, they began personal attacks against me.

The government-funded research was high in quantity (”billions”) but low in quality.

A similar story emerged from the Netflix Prize competition. Netflix had in-house researchers who had tried to do the same thing as the competitors for the prize: predict ratings.  The algorithm they’d developed took two weeks to run. According to my friend David Purdy, one of the competitors for the prize managed to compute the same thing in an hour, the same sort of speed-up that Venter is talking about. The in-house research was high in quantity (it had been going on for years) but low in quality.

From my point of view, a similar story comes from my self-experimentation. Working alone, with no funding, I found several ways to improve my sleep — avoiding breakfast, standing a lot, standing on one foot, eating pork fat, etc. In contrast, professional sleep researchers have found nothing that has helped me improve my sleep. There are hundreds of sleep researchers and they’ve received hundreds of millions of dollars in funding.

Why such big differences in outcome? I think it has to do with the price of failure. When the government-funded genome researchers used inferior methods, nothing happened. They’d already gotten the grant. In contrast, Venter’s group got nothing until they succeeded. In the case of the Netflix in-house researchers, use of inferior methods cost them nothing; they still got paid. Whereas the prize competitors didn’t get paid unless they won. Use of inferior methods would cause them to lose. In the case of the sleep researchers, lack of practical results cost them nothing. They could still have a successful career. Whereas to me, without practical results I had nothing.

Thanks to Paul Sas.

A successor to Medical Hypotheses, called Hypotheses in the Life Sciences, will be edited by William Bains and published by Buckingham University Press (BUP).

ROBERTS Does BUP hope to eventually make money from the successor journal? Or do they merely hope the subsidy required will decrease with time?

WILLIAM BAINS BUP is a small operation, and does not have the resources to subsidize Hypotheses in the Life Sciences beyond its start-up stage, so we hope to make enough money to break even fairly soon. Ultimately the aim is to be profitable. I for one am determined to put scientific quality first, and I have emphasized to BUP that I only want the journal to grow (and hence generate more revenue) when the quality of submissions allows it.

ROBERTS What led BUP to decide to publish the new journal?

BAINS I think a combination of similarity in philosophy and being in the right place at the right time. They thought it was an exciting project which would both raise their profile (in a good way) and make them money. Buckingham University is the UK’s only private university, and as such takes a heterodox, even iconoclastic view towards what the academic establishment says is writ in stone. The Chancellor has a robust approach to academic and individual freedom. So a journal trying to do something rather new, enabling those with good ideas but little power to be heard, fitted with their approach.  For me, an added advantage is that I deal directly with the man at the top. There are no intermediate layers of management to take decisions about the journal, and we discuss everything from philosophy to web page design. This is the sort of immediacy you do not get with a big publisher.

Part 1 (Bruce Charlton). Bioscience Hypotheses, a similar journal founded by Bains.

The second episode of BBC’s The Story of Science is about chemistry. It shows unusual sophistication by emphasizing that early chemists built on the alchemists. The alchemists invented techniques and equipment later used by “real” chemists such as Joseph Priestly — the ones who reached conclusions we still believe. Not everyone understands that some “pseudoscience”, such as alchemy, is valuable.

A few years after I became an assistant professor, I realized the key thing a scientist needs is an excuse. Not a prediction. Not a theory. Not a concept. Not a hunch. Not a method. Just an excuse — an excuse to do something, which in my case meant an excuse to do a rat experiment. If you do something, you are likely to learn something, even if your reason for action was silly. The alchemists wanted gold so they did something. Fine. Gold was their excuse. Their activities produced useful knowledge, even though those activities were motivated by beliefs we now think silly. I’d like to think none of my self-experimentation was based on silly ideas but, silly or not, it often paid off in unexpected ways. At one point I tested the idea that standing more would cause weight loss. Even as I was doing it I thought the premise highly unlikely. Yet this led me to discover that standing a lot improved my sleep.

Richard Feynman, in his famous “cargo-cult science” speech, failed to understand that “real” science can build on “pseudoscience”:

Another example is how to treat criminals. We obviously have made no progress–lots of theory, but no progress–in decreasing the amount of crime by the method that we use to handle criminals. Yet these things are said to be scientific. We study them. And I think ordinary people with commonsense ideas are intimidated by this pseudoscience.

Absence of obvious progress (such as no decrease in crime) doesn’t mean something is worthless. Bizarre ideas or unsupported ideas (”lots of theory but no progress”) doesn’t mean something is worthless. What’s worthless, in terms of science, is not paying attention to reality. Not caring about how the world actually is. The cargo cults Feynman mentioned weren’t worthless. They tested their beliefs. They found out the planes didn’t land. Fine. It wasn’t pseudoscience, it was just early science, where the reasons for doing stuff now appear ridiculous. Of course the alchemists had beliefs we now think ridiculous. How could they not have?

Science is fundamentally on the side of the weak, since it offers hope of improvement. The powerful not only can afford to ignore reality they would like to, because it might be inconvenient. So they do so as much as possible. When I’ve heard “the debate is over” (= it’s now time to ignore reality) it’s always turned out that the person saying this (e.g., Al Gore, mainstream journalists) was powerful or credulous.

It’s not bad that some people ignore reality. We need people like that. I think of the body: parts of it (e.g., sensory systems) are very sensitive to reality, parts of it (e.g., bones) are not. We need both. When leaders ignore reality is when trouble begins.

A successor to Medical Hypotheses, titled Hypotheses in the Life Sciences, will soon be published. I asked Bruce Charlton and William Bains, the founder of the new journal, about the economics of the situation.

ROBERTS Did Medical Hypotheses make money for Elsevier? How much did it cost to run per year (leaving aside time contributed by you and the editorial board)? How much of that did Elsevier pay?

BRUCE CHARLTON  Medical Hypotheses did for sure make money for Elsevier - but I was never allowed to see the accounts. (more…)

In Kathryn Schulz’s new book about being wrong (Being Wrong), she makes an interesting mistake:

In the instant of uttering [”I told you so”], I become right squared, maybe even right factorial, logarithmically right — at any rate, really, extremely right.

Schulz doesn’t know that the logarithm of a number 1 or more is much less than the number itself. For example, log 100 = 4.6.

What’s interesting is that logarithmically right is a good way of describing how one’s beliefs should be transformed to be a fair approximation of the truth. When you think you are right, you probably are — but logarithmically. Much less than you think.

When faced with a scientific paper — the sort that press releases are written about, for example — the naive reader takes it at face value. The little-knowledge-is-a-dangerous-thing reader finds many shortcomings and dismisses it (”how did this get through peer review?”). The more likely interpretation, in my experience, is that the paper, in spite of its imperfection, moves us a little bit forward. Much less than appearances, but more than zero.