Tuesday, April 7, 2009

The emergence of complexity

Carl Zimmer has a nice piece on the development of limbs in the Science section of today's New York Times. He has the space to go into much more detail than Lewis Wolpert was able to on The Forum the other day, and what he describes illustrates the basic principles we've discussed, if not in so many words. He talks about the essential role of the signaling that goes on between cells to tell them what to do next, of contingency, the fact that what a cell does next depends on what it has just done, of cooperation at many levels, of modularity and chance. A pretty simple description of how complexity arises.

Monday, April 6, 2009

Every scientist since yesterday.....

One objective of science is to unlock Nature's 'secrets', and there is a natural hunger to be among those who see most deeply what others have not seen before. That's why our culture properly respects our Newtons and Darwins (and why there are priority squabbles). But (and as priority squabbles show), we have to lobby and promote our ideas to get them both recognized and accepted.

When we do that, especially if there has been financial investment in our ideas, we naturally tend to be defensive about them. We can easily back ourselves into a conceptual corner in doing so. Being wrong is not what our ethos is all about. Defending dated ideas is not good for science, but it is largely the way science actually works, until a better idea forces earlier ones off the stage. This was a central point in Thomas Kuhn's analysis of scientific 'revolutions' (like the Darwinian one of which we're the beneficiaries).

But being wrong and having only imperfect knowledge is part of the game. As put in a cogent quote in a very fine recent biography of Ernst Haeckel by Robert Richards (The Tragic Sense of Life, 2009, U Chicago Press), 'every scientist since yesterday' has been wrong. If there's a lesson here for all of us, it would--or at least should--be to be more humble in promoting our favorite ideas. They are all wrong, in one way or another.

Unfortunately, imperfection is the gap that opponents of science itself often use as a wedge to dislodge an understanding of the world from its empirical foundations. In this case, I've been barraged with a listserv of messages from a group of people (mainly scientists of various kinds) who support a theological interpretation of life by hammering away at the imperfections, and excessive claims, of evolutionary biologists. They use various arguments, but mainly the false syllogism that because evolutionary biologists don't know everything, they must be wrong about evolution....and therefore some God-based explanation must be right.

In genetics and evolution there are many unknowns, and we tend to minimize them (except those that help us in a grant application), and overstate or oversimplify our own particular worldviews. We are doubtlessly wrong in many ways, but it is not true that every scientist since yesterday was completely wrong, and there can be little doubt that we understand Nature much better today than we did yesterday.

Life is a tough subject to study, and we should be more careful about what we don't know and the range of plausible explanations for our phenomena. But it is also true that what we don't know is not evidence for some specific alternative theory, religious or otherwise. Scientific theories may always be underdetermined--more than one explanation being consistent with the available facts, but there is nonetheless likely to be some truth out there, and it must be compatible with those same facts. We should do our best not to shun or exclude alternative ideas, while at the same time defending the nature of science as an imperfect attempt to understand Nature that needs to have a coherent operating framework.

It is, in fact, remarkable that blobs of protoplasm, called 'humans', could have evolved to have even the level of ability to understand Nature that we have. Since every scientist since yesterday has been wrong in one way or another, the Aristotelian kind of argument that we evolved to have a correct intuitive understanding of Nature does not account for our species' abilities. Indeed, we evolved by doing what we needed to do, so it is likely that we would have cognition at least consistent with the relevant subset of the nature of Nature. Beyond that is the remarkable fact that, fallible though we are, the evolution of general problem-solving ability has led us to go so deeply beyond the specifics of our past survival challenges.

Saturday, April 4, 2009

Credible research

Marion Nestle, Professor of Nutrition and Food Studies at NYU, was on campus last week to speak, sponsored by the Penn State Rock Ethics Institute. Nestle is the author of a number of popular books about the politics of food, and an outspoken critic of the influence of the food industry on how and what we eat, and thus, on the health of the American population. She's particularly concerned with obesity in children and the role of advertizing in promoting the consumption of excess calories even in children as young as two. She believes that any money researchers take from the food industry is tainted money. Her point is that it's impossible for a scientist to do unbiased research, however well-intentioned, if the money comes from a funder that stands to gain from the findings. Indeed, it has been found that results are significantly more likely to favor the funder when research is paid for by industry.

The same can and has been said about the pharmaceutical industry and drug research, of course, and, though we don't know the particulars, it has to be equally true of chemistry or rehab or finance or fashion design. But, as we hope our posts about lobbying last week make clear, the problem of potentially tainted research doesn't start and stop with the involvement of money from industry. Research done with public money can be just as indebted to vested interests, its credibility equally as questionable. It can be somewhat different because researchers tend not to feel indebted to the actual source of the money -- the taxpayer -- but research done on the public dollar can be just as likely to confirm the idea or approach the funding agency supports.

Even when money isn't the motivation, there are many reasons that research might not be free from bias -- the rush to publish, the desire to be promoted or get a pay raise, commitment to given results, prior assumptions, unwillingness to be shown wrong. Many prominent journals won't publish negative results and of course journals and the media like to tout if not exaggerate positive findings. There is pressure to make positive findings -- and quickly -- to use to get one's next grant (and salary). This is one reason it is commonly said that one applies for funds to do what's already been done. This makes science very conservative and incremental when careers literally depend on the march of funding, no matter what their source.

Besides the pressure to conform and play it safe, a serious problem is that such bias doesn't necessarily make the science wrong, but it does make it more difficult to know how or where it's most accurate and worthy. And it can stifle innovative, truly creative thinking. Some of the most important results are likely to be negative results, because they can tell us what isn't true or important, and guide us to what is. But that isn't necessarily what sponsors, especially corporate sponsors, want, and it isn't what journals are likely to publish.

So, while it's essential, as Marion Nestle and others consistently point out, to eliminate the taint of vested interest from research, it's impossible to rid research of all possible sources of bias. And the reality is, at least for our current time, that it's only the fringe of those most secure in their jobs etc., who can speak out about the issues (as Nestle said, she has tenure and doesn't need money to do her work, so she can say anything she wants to) -- and they do not have the leverage to change the biases built into our bottom-line, market- and career-driven system.

Friday, April 3, 2009

How does a cell know what to become?

This week on The Forum, a BBC World Service radio program, Lewis Wolpert, a distinguished Emeritus Professor of Cell and Developmental Biology at University College London, and two non-scientists were interviewed. Prof. Wolpert was asked to explain development, and how cells 'know' what kind of cell they will be. The interviewer, Bridget Kendall, is quite well-versed in scientific issues, but when she asked Wolpert to tell her how a cell knows what it will become, while he got some of it right, and certainly knows enough to answer the question, in the end his answer was quite unsatisfying and confused the interviewer as well as her other guests.

Cells talk to each other, Wolpert said. It's to do with signaling. And nobody is in charge.

So far, so good. Cells have to be prepared to receive a signal, and in normal development they have been primed, usually by earlier signals, to respond appropriately.

But then Kendall asked how cells arrange themselves in a certain pattern. How does a cell know it should be in the right or the left hand? A basic and fascinating question, the likes of which has hooked many a developmental biologist.

There is no fundamental difference between the right and left hand, he said.

This didn't help at all. Kendall pressed him.

Cells get instructions from other cells about what to do, he said.

Now one of the other guests was confused. Understandably. He wanted to know how chaos ends in order if no one is in charge. "There has to be a blueprint somewhere so that a human doesn't end up a frog."

"That's the cleverness of cells," Wolpert said. "There is no blueprint whatsoever." He was adamant about this. It's due to genes that a human cell becomes a human and not a frog, he went on to explain. Bringing us frustratingly back to Kendall's first question of how cells develop.

And, indeed, the listener could be forgiven for not being able to quite tell the difference between genes, which tell a cell whether it's to be a human or a frog, which Wolpert allows are important, though boring, and a blueprint, which is an outside document that tells a builder whether to construct a skyscraper or a factory and which Wolpert categorically denied as a useful metaphor for development.

But, are genes a blueprint for an organism? Certainly not literally -- unlike a blueprint, an organism has no designer, for starters. And, much more is inherited along with genes (by which is usually meant classical protein-coding segments of DNA, which make up only 5% of the genome, after all, and by no means all of the kinds of functional elements in genomes), so genes alone don't tell a cell what to become.

Is the whole genome the blueprint, then? Still no, since the fertilized egg contains more than DNA, and environmental factors have a significant influence over how a cell develops -- ambient temperature determines the sex of a developing turtle egg, for example. But the genes in a human cell can't instruct the cell to become a frog, so in some metaphorical sense, they are a blueprint but, unlike a blueprint, the DNA does not come into an awaiting cell and tell it what to do: an organism is already a complete cell, with its DNA and its other materials that interpret the DNA.

How does a cell know what to become?

Wolpert was right that it depends on signaling, but it would have helped if he had gone on to say that signaling happens in order, and what a cell does next is contingent on what it has just done. Step by step, cells all over thee embryo are single-mindedly, so to speak, responding independently to different signals, each one oblivious to what's happening even several cells away. Signal upon signal, response after response, cell division upon cell division, all these steps combined lead to differentiated, semi-autonomous cells all working together to make an organism. Preparing to respond to signals, and then responding, is what cells do.

It's fairly simple -- unless you're concerned with how one cell becomes part of the thyroid gland and another becomes part of the retina of an eye, and you want to know the specific genetic and timing details. Otherwise, it's enough to know that genes code for proteins that become signals, cell-surface receptors to read those signals, and then to respond. Cells know nothing about the bigger picture, and there is no master painter, but step-by-step, because of contingency and cooperation among cells, the bigger picture emerges. These generalizations are, in fact, rather universal and reflect basic properties of the nature of life -- what we might call parts of a broader theory of life.

Thursday, April 2, 2009

When natural selection works as advertized

We and others have written quite a bit about the nature of natural selection and how it is detected (or how hard it is to detect) by various means. Darwin based his ideas of the origin of species on the extrapolation over long evolutionary time periods, of the kinds of effects seen in agricultural breeding. He assumed that eventually, such gradual changes would be adaptive, because nature (like breeders) chose only subsets of individuals for successful reproduction, and because adaptive differentiation would lead to speciation.

It is routine to assume that a trait of interest is the result of adaptive natural selection, and then suggest (guess at) what the selective force might have been. This is a highly problematic enterprise and, we think, scenarios are often asserted with very little to support them....which we think is a mistake and can be dangerous when applied to humans. That's because searches for and studies of selection in humans can easily lead to group generalizations about inherent value, including many forms of racism. So spending research money on such searches should only be done when the evidence is actually strong enough, and the likely societal penalty low enough, to justify it.

But there are instances when classical ideas of natural selection seem to work more or less as advertized, and do have great importance. Our posting today is triggered by a story in the news as a meeting convenes on the risk of global epidemics of multiple drug resistant tuberculosis.

The evolution of antibiotic resistance may not always be simple at the pathogen's gene level, but it does seem to be clearly a genetic adaptation phenomenon due to intense selection imposed by widespread, or excessive, use of too-few antibiotics. The problem can be exacerbated by population crowding, poverty leading to large numbers of unvaccinated people (for some diseases), with rapid global travel, and so on.

Many other initiatives, such as genetically personalized medicine, are clearly less urgent than preventing or containing global epidemics. The latter are clear genetic, evolutionary problems that warrant substantial scientific investment even in tight economic times. There, too, investment in social aspects of group dynamics could be actually effective, unlike much of social science research, whose payoff is modest and indirect at best.

If the genomics industry is too politically powerful or too large to fail (like, for example, AIG and General Motors), then at least funds should be shifted to problems that really are genetic and that ought to be susceptible to molecular technologies -- even if the challenge to do that is great.

So, while we think excessive genetic determinism and selectionism are misplaced relative to what we actually know about genes and about evolution, control of infectious diseases (and similar issues in relation to agricultural pest and disease control) are a totally appropriate application of biological theory and modern biotechnology.

Wednesday, April 1, 2009

Reasons to support, or to oppose initiatives in science

It should be clear by now that we won't hold our tongues when it comes to editorializing about how money is spent in science. We hope to be constructive rather than destructive critics where we express opposition, as we have in regard to major lobbying for biobanks to bring about the miracle of 'personalized medicine'.

There are at least three basic criteria on which it is fair as well as realistic to judge proposed science projects:

1. Scientific merit: is the proposal justified by the known facts?
2. Social politics: is the project well-justified in terms of promised benefits to society, or primarily just good for the science establishment?
3. Social priorities: when resources are limited, and science is supported by the public, is the proposal justified relative to other things that might be done (or the funds used for something other than research)?

The World Bank, no bastion of liberal politics, is estimating that 200,000 to 400,000 people will die (in Africa alone) as a result of the loss of foreign aid (nutrition, vaccinations, health care, &c) due to the economic crisis the West is visiting upon them (Nicholas Kristoff has an op/ed piece about this in today's New York Times). If this is so, it seems immoral and even socially inexcusable to be gearing up for manned trips to Mars, spending money on 'astrobiology', or spending fortunes on large DNA-based 'personalized medicine' campaigns that will mainly feed the research and pharmaceutical industries -- at least for the foreseeable future, even if they are ultimately as successful as promised. And, even if successful, as long as health care funding remains as inequitable as it is today in the US, it would be mainly the rich who will benefit from having their medicine personalized.

So, we object to this kind of spending on ethical grounds. Even if we believed in the scientific merit of biobanks or voyages to Mars (will cages be brought to Mars, to return Martians to Earth in?), they are not justified in the face of widespread disease and other human problems that could be ameliorated with the same funds.

As to priority, these kinds of projects can hardly be claimed to be the most important problems we should be studying, or the best approaches to studying them. It would be easy to name many more justifiable projects -- starting with more stress on truly genetic diseases, more intense efforts in regard to potential antibiotic resistant infectious diseases, nutritional programs for the poor at home and elsewhere, research on neglected tropical diseases and so on. But these problems don't have constituents with lobbyists and vested interests.

It's inevitable that people will disagree on how their tax money should be spent, and various aspects of self-interest will always be a factor. But, when huge amounts of money are locked up in projects based on demonstrably questionable science, at the expense of issues with more likely payoff and better scientific underpinnings, it's especially frustrating.

And, if history is any guide, the most likely thing is that the Martians will carry some disease that'll wipe us out .... or else they'll die of our diseases as soon as they land, a real waste of money. And they probably won't even speak English (which would anger at least a substantial fraction of theAmerican public that pays for the expedition).

Mermaid tales

Strange Brew

From Strange Brew, Mar 31, 2009. Thank you, Jennifer!