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Adaptive Complexity

How to be an Iconoclast in Biology

Every scientist wants to be an iconoclast, but most end up doing rather conventional work. Understandably, because it takes a special sort of nerve to risk your career and reputation on an idea or approach that could be very, very wrong - so wrong that it would be tough to recover from.

You can blog and still get tenure

Yes, it's possible, according to John Hawks (who writes an excellent blog):

Gender and Science in the News: Should We Have Grant Quotas For Women?

OK, I'm about to dive into an issue I probably shouldn't be talking about on a blog, at least if I have any hope of convincing a hiring committee to consider me, but I'm going to dumbly rush ahead.

John Tierney at the NY Times has been looking into the issue of whether Congress is considering "Title IX'ing" science, by requiring some sort of gender quota in funding decisions by federal science agencies. Tierney argues that in this day and age, it is less a matter of discrimination and more a matter of which subjects women choose to pursue:

"The members of Congress and women’s groups who have pushed for science to be “Title Nined” say there is evidence that women face discrimination in certain sciences, but the quality of that evidence is disputed. Critics say there is far better research showing that on average, women’s interest in some fields isn’t the same as men’s."

E. coli As Biology's Decoder Ring

Molecular Biology

A review of Microcosm: E. coli and The New Science of Life

Carl Zimmer, Pantheon, New York, 2008

If you had to pick one organism with which to tell the story of the modern science of biology, you couldn't do better than to pick the tiny gut bacterium E. coli. In his latest book Microcosm, Carl Zimmer, uses E. coli as a decoder ring to open up the dense and diverse world of biological research, taking us on a panoramic tour of some of the most important conceptual advances and outstanding scientific questions in this important realm of science. Biology, in contrast to a science like physics, is a science of particulars. In physics, if you understand one electron, you understand them all, but in biology every organism is unique. In biology it is more challenging to find universals, to pick an object of study that let's you ask big questions with the hope of finding general answers. With E. coli we can come quite close: this tiny bacterium is the hydrogen atom of biology, a model simple enough to be experimentally tractable, but representative of general principles that apply to all life. As the pioneering molecular biologist Jacques Monod put it, "What is true for E. coli is true for the elephant," and also true for us. In Microcosm, we follow E. coli through a survey of some of the deep foundations and controversies of biology.

Let's do some Reading on the Plausibility of Life

I just got my hands on a recent book by two influential biologists, Marc Kirschner, chair of Harvard's recently created Systems Biology Department, and John Gerhart, a professor at UC Berkeley.

Positive Feedback Loops that Drive Cell Decisions

Dividing is one of the trickiest things a cell has to do. The cell needs to faithfully copy its entire genome, with very few mistakes, and it needs to then divvy up those two genome copies equally among the two new cells that are created during division. Going through this process is a bit like going down a double black diamond ski run: once you set things in motion, there's no stopping until you get to the end.

In the case of cell division, there are two critical points of no return: at the decision to start replicating DNA, and when it's time to equally split up the chromosomes. A cell that's going to copy its genetic material had better be ready, with all the necessary supplies in hand, because once the copying process initiates, it's a bad idea to stop: a cell can't really do much with a half-replicated genome, and it's in danger of permanently ruining its genome. And it doesn't do you any good to successfully finish that copying process, only to misallocate what you've copied among the two daughter cells. Without the right chromosomes in each cell, there is only a slim chance of survival.

So how do cells make these critical decisions?

There's a Whole Doubt Industry Aimed At Science

"Can scientists and journalists learn to beat the doubt industry before our most serious problems beat us all?" This is the question asked in an interesting piece at a news? site I've never heard of - "Miller-McCune: Turning Research Into Solutions." I'm not sure about the research and solutions thing, but they do have some interesting comments about the "Doubt Industy."

"Doubt Industry" means organized interests with a strong motivation to get the public to question science: the link between smoking and cancer, the scientific status of evolution, the health hazards of beryllium (apparently a problem for workers in the atomic industry). Whenever scientific results cause problems for someone, especially someone with a strong financial incentive to not believe the science, the time-tested strategy is to question the certainty of the science. A well-known internal memo from one cigarette company in the 1960's famously claimed(PDF):

The Problem is Too Much Biological Complexity

We like to talk about the amazingly complex machinery of the cell: flagella that resemble finely tuned outboard motors, or complex information processing circuits that help a cell process information about its environment. Biologists work hard at understanding how these systems work. They will take a wiring diagram like the following, and ask why is it set up this way?

How Bacteria Recognize Kin

A report in this week's issue of Science describes a set of genes that enable members of the bacterial species Proteus mirabilis to tell the difference between kin and strangers. The bacteria engage in a social behavior (common to teenagers and bacteria) called swarming: they like to get together in groups. If you spread these bacteria on a petri dish, they are able to move together to form a colony.

The catch is this: like humans, bacteria of the same species can be divided up into smaller populations of more closely related individuals.

Anti-evolution 'Academic Freedom' Bills: What is Academic Freedom Anyway?

Science & Society

You may have heard the news that Louisiana's governor recently signed an "Academic Freedom" bill, the first such bill to pass in a recent string of efforts to allow public school teachers to push non-scientific alternatives to evolution. (I previously wrote about Missouri's failed version.) All of these bills claim to promote academic freedom for public school teachers to teach the Intelligent Design movement's so-called evidence against evolution. But the concept of academic freedom in a high school curriculum makes no sense.

In the New Scientist story linked to above, Josh Rosenau of the National Center for Science Education points out that "if you look at the American Association of University Professors' definition of academic freedom, it refers to the ability to do research and publish." The whole point of academic freedom is, like tenure, to protect independent scholars and scientists from having their work suppressed, manipulated, or managed by administrators or other people outside the research community who might want to pressure scholars to alter their conclusions or not research unfavorable topics.

George Will: Why Are We kicking Talent Out of the US?

Continuing my science policy blogging streak (we'll get back to real science here soon, I promise!), it's worth noting Washington Post columnist George Will's recent piece about our "perverse national policy of expelling talented people."

If you've spent any time recently around America's science PhD programs, you'll have heard about the problem: we bring talented people in from all over the world, train them to do great science, and then make it impossible for them to get a job here, even when US companies and universities want to hire them. As George Will writes, this creates yet one more incentive for US companies to send their operations outside of the US:

But one reason Microsoft opened a software development center in Vancouver [Canada] is that Canadian immigration laws allow Microsoft to recruit skilled people it could not retain under U.S. immigration restrictions.

Updating how the US Government Gets Its Advice

Over the last few years, we've seen some bitter political arguments over the role of US Government scientists, political appointees, and the manipulation of technical reports. I'm not going to wade into that fight here, except for one point: occasionally we hear the argument that government scientists are employees of the executive branch, and that they are therefore legitimately subject to the efforts of the President and his appointees to get everybody on board with the President's agenda.

For many positions in the federal government, that argument is correct. If you work for the executive branch, ultimately the President is your boss. But in many cases, especially ones that concern some government scientists, there is a limit to what the President and his political appointees can do, because the role of those scientists has been established by law. Congress has sensibly written several laws to ensure that the government can get sound, unbiased technical advice, free from political manipulation.

Do we know nothing about the origins of the first living systems?

Over at the Panda's Thumb, Nick Matzke weighs in on how scientists should respond to Creationist criticisms that we know nothing about abiogenesis - the origins of the first living systems from non-living systems.

Matzke correctly says that the typical response is two-fold: scientists will say that a) sure, we don't know much about it, but we're working on it, and b) it has nothing to do with the main field of evolutionary biology. Matzke says that

It is high time all of these statements be discarded or highly modified. They are basically lazy, all-too-easy responses relying on hair-splitting technicalities or nearly philosophical assertions of the “even if the creationists were empirically correct on this point, which they aren’t but I’m too busy to back it up right now, it wouldn’t matter” variety. And the worst part is that these sorts of statements mis-describe the actual state of the science among the people who work in the field. It is simply not true that we, the scientific community, know almost nothing about the OOL (what an individual who spent a career working on fossils or fruit flies or speciation might know personally is a different question).

I agree with much of what Matzke has to say, but disagree with him that it's wrong for scientists to say that origins of life/abiogenesis research is a substantially different field from mainstream evolutionary biology.

Harvard Prof on Virtue vs. Money in Science

I've been traveling, often with three whining kids in the back seat of a cramped car - not the best environment for blogging. On part of this trip, we toured this not so well known, but spectacular site:

I'll be impressed if any readers recognize the place - give it your best shot in the comments, if you think you know where it is.

The real subject for today is virtue and scientists: is the ideal scientist a disinterested, virtuous seeker of knowledge? Do academic scientists embody this ideal, and are corporate scientists sell-outs?

Harvard historian Steven Shapin shares his ideas in an interview with the Boston Globe.

The interview is a brief plug for Shapin's upcoming book. Shapin says the wrong way to think about science in academia is with

the presumption is that this is about the unequal distribution of virtue, about threats to the autonomy, integrity, value, and authenticity of science, represented by commercializing interests.

ScienceDebate2008 and 14 Questions on Science Policy for US Presidential Candidates

Science & Society

ScienceDebate2008 has come up with 14 questions they would like to see answered by the US presidential candidates. This group has been pushing for a science policy-focused debate among presidential candidates. That debate is looking more and more unlikely, but in an effort to keep some of the election focus on science, this group is now urging the candidates to answer a set of questions on science policy (abbreviated below - go read the questions in full at the ScienceDebate2008 site):

1. What policies will you support to ensure that America remains the world leader in innovation?

2. What is your position on the following measures that have been proposed to address global climate change—a cap-and-trade system, a carbon tax, increased fuel-economy standards, or research?

3. What policies would you support to meet demand for energy while ensuring an economically and environmentally sustainable future?

4. What role do you think the federal government should play in preparing K-12 students for the science and technology driven 21st Century?

5. What is your view of how science and technology can best be used to ensure national security and where should we put our focus?

6. In an era of constant and rapid international travel, what steps should the United States take to protect our population from global pandemics or deliberate biological attacks?

Getting Your DNA Sequenced: Should Regulators Crack Down on Genetic Testing Companies?

Genetics

California and New York regulators have been in the news lately (such as here and here), with their attempts to crack down on the nascent direct-to-consumer genetic testing industry. These states argue that companies like 23andMe, Navigenics, and several others, are offering unproven and unlicensed clinical tests directly to consumers. Are the services offered by these companies clinical tests, subject to the normal regulations of other clinical tests? Should the government be able to stop you from getting your DNA sequenced?

The answer to the second question is a flat-out no. The government has no legitimate reason to prevent you from getting genotyped. The technology used by these personal genetics companies is very good - in the future, this technology will be cheaper and cover more variants in your genome, but what is available right now is very good. And there are reasonable non-clinical reasons to get yourself sequenced, out of sheer curiosity, or for genealogy purposes, for example. More importantly, this sequence data is a permanent resource for you. Although we may not have very good clinical tests for complex genetic diseases right now, we'll have them in the future, and any DNA sequencing you get done now will be suitable for these future analyses. Once you have your raw DNA data in hand, it's there if you need it in the future.

So, as things stand now, the genotyping serviced offered by 23andMe, DecodeMe, and Navigenics have enough non-clinical use to justify themselves, and these services should not be blocked by state regulators. But simply offering people DNA sequencing is one thing - making disease risk predictions is another.

Multitasking and Science Don't Mix Well

Multitasking is detrimental to how we learn according to two interesting pieces which discuss recent neurological studies of multitasking, in The Atlantis, and in The Atlantic (yes, those are two different magazines). In one study conducted by the Kaiser Family Foundation, a study participant wrote:

"I multitask every single second I am online,” confessed one study participant. “At this very moment I am watching TV, checking my e-mail every two minutes, reading a newsgroup about who shot JFK, burning some music to a CD, and writing this message."

Does this sound like you? It sure sounds like me sometimes (and it's the same way at work, if you replace the JFK newsgroup and TV with reading a science paper, answering email, and doing a Western blot), and personally I think this fragmented way of working leads to a very superficial way of working.

Presidential Science Advice 2.0

A new report at the Woodrow Wilson International Center for Scholars has some recommendations about science advice for the next president. The rationale for this report is that:

The next President will need a superb Assistant for Science and Technology—not
only to evaluate complex issues and develop sound policies but also
to guide and oversee the federal investment in science and technology,
which totaled some $142 billion in fiscal year (FY) 2008.

Chief among the recommendations is to restore the Director of the Office of Science and Technology Policy (OSTP) to the higher status of "Assistant to the President." The OSTP director position was demoted during the Bush administration, and filling that position was a low priority, resulting in a long delay before the current OSTP Director, Jack Marburger was appointed.

This report is essentially saying that the next president should signal that good science policy is a priority, by giving the President's science advisor cabinet status, and by making the appointment early in the new administration. To back up this recommendation, the report's authors have brought together an armful of statements on Presidential science advice by former key players, including Henry Kissinger, Gerald Ford, Al Gore, and many former Presidential Science Advisors, such as George Keyworth, Ronald Regan's first science advisor:

So you want to get a job in biology

What does it take to get a job in science, and what role do universities play? There has been some discussion of these issues in the blogging community lately (here, here, and my thoughts are here). Being on the inside, it doesn't seem that complicated to me, but to someone considering a career in science, choosing a college, or just starting college, it can seem very confusing. On occasion I supervise undergraduate summer students, and from their questions, it's clear students aren't so sure about what job opportunities there are in science, and what educational pathways are involved in getting those jobs.

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