Tuesday, April 16, 2013

On Truth and the Limits of Knowing

The Australian comedian Tim Minchin has a routine that consists of an 8 minute beat poem called Storm about a girl he met at a dinner party. Minchin, who has made a name for himself as a vocal Skeptic (I capitalize because there’s something of a cult of skepticism that has arisen in recent years, and because calling them a cult will piss them off) was deeply offended by Storm’s new age-y beliefs, which – to paraphrase – stemmed from a belief that life was a mystery that we cannot fathom. Yes, we can, says Minchin, and goes off on a diatribe about how what we discover about life through the application of the scientific method is just as beautiful and elegant and lyrical is anything that can be imagined through superstition. Or something like that – you can watch the routine here,

I was thinking about Storm the other day, because I began to wonder if I was inadvertently playing the role of hippie in a discussion about the limits of scientific understanding. I tried to discuss this with my wife - who had dragged me into the whole thing by enlisting me to review course materials on phylogenetic systematics to be supplied to students and teachers - and after several minutes of my trying to explain myself, she snapped. “If I actually though you cared about this, I would never have asked you to do it.” So that was the end of that. Or so she thinks. Ha! Because when I get annoyed about something, I go and blog about it - so now the whole world knows what I think. That’ll show her!

Anyway, the job in hand, as I said, involved course materials for high school students and teachers about phylogenetic trees. Or, as the writers put it, The Tree of Life. Note how I capitalized again, because this is The Tree of Life we’re talking about, like the One Ring to Rule Them All, or the Word of God. Hey kids, when you do phylogenetic systematics, you’re not just figuring out how things are related to each other. You’re helping to build the One True Tree of Life, the Tree that links you to wombats, priapulid worms, and the fungus that grows on your skin when you have poor hygiene. How Sick is that!

As you can tell, I’m a bit jaundiced about the Tree of Life.

Let’s be clear: the idea is a very important one. All living things on this planet are linked to each other by varying degrees of common ancestry in a pattern that is dictated by the process of evolution. By mapping the pattern of shared characters between different organisms, you can reconstruct that shared ancestry and hence the processes that generated the pattern. And you can visualize the pattern as a series of nodes and branches that looks kinda like a tree, which is a powerful metaphor to use when talking to people about evolution, because trees are a living, naturally generated structure, and because we also use them – in genealogy – to talk about our own immediate ancestry.

Metaphors are dangerous things, because when stretched they can take on a life of their own. “Genes” are a good example of this. When I say “gene” in this context, I don’t mean what a molecular biologist would mean – a stretch of nucleic acid, corresponding to a unit of inheritance, whose molecular sequence codes for a functional polypeptide chain or RNA. I mean it in the selfish, “Dawkins” sense, which is a phenotypic difference between two organisms that has a heritable basis, and which affects the fitness of the organism.  I have a bigger tail than you, females dig guys with big tails, I make more babies than you, and my babies have bigger tails too. Voila, natural selection in action. Or, to put it simply, I have the “big tail gene.”

Of course, there’s probably no such thing as “a” big tail gene. More likely there are lots of  different genes, whose combined affect is to give me a bigger tail. But when you’re trying to explain something complicated, like kin selection and the evolution of altruism, to a lay audience, simplicity is vital. Hence “The Selfish Gene,” Richard Dawkins’ 1976 masterpiece, one of the all-time greatest pieces of scientific writing and the book that made me want to be a zoologist. I try to remember that when I see the author today, a wild-eyed fundamentalist ranting away about God on the TV and calling otherscientists “Quislings.” What on earth happened to the guy that wrote that book? It’s hard to believe they’re one and the same.

Like most people, my education in science followed a well-trodden path. Each year you were taught something new. Then, at the beginning of the next year, you were taught that what you learnt in the previous year was not exactly true, because at some level you weren’t ready for the truth.  A vicar friend of mine (yes, I am a scientist who has friends who are vicars. I am a Quisling!) referred to this, in the context of bible study, as “milk and meat” – you start out on milk, but as you get older and wiser you’re ready for some scriptural “meat.” Why is it that everything evangelical Christians say comes out sounding inadvertently sexual? But the fact that science and bible study have such commonalities suggests that that maybe the Templeton Foundation is on to something (“Quisling!”)

Unfortunately we live in a time when it’s all too easy to call someone a liar for telling you less than the complete truth. This is the narrow path we have to tread when we develop pedagogic materials for science. Hence my concern over phylogenetic trees versus The Tree of Life. A phylogenetic tree is just a hypothesis about evolutionary relationships, based on available evidence. It cannot “be” the evolutionary history of the group of organisms in question; most of them are missing due to the incompleteness of the fossil record. It’s also essentially subjective, because you pick the characters that you analyze, and – if you’re looking at anything more than a handful of them – you run them through phylogenetic analysis software that makes a bunch of assumptions about how evolution works.

This is not to say that phylogenetics is in any way bad science. But neither is it infallible. Any tree can change with the emergence of new evidence. Sometimes it’s a newly discovered organism, recent or fossil. Sometimes it’s the inclusion of a known organism that had previously been excluded from the analysis. Sometimes its because of a new character set, a new analytical technique, a change in the assumptions underlying the software algorithms that are being used to reconstruct the phylogeny. Some relationships are more stable than others, being robustly supported by multiple lines of evidence, but nothing is completely certain.

When I put this to one of my colleagues, she expressed concern that if we didn’t give people the sense that there is real information in the trees, they might not care about this at all. I understand this perspective, but it’s a dangerous one. As scientists, we are comfortable with uncertainty. In fact, for many of us, uncertainty is what drew us into science in the first place. By our nature, we question everything, repeatedly, and this questioning drives our understanding forward. Unfortunately, most people outside of science want certainty. They expect us to be able to provide them with answers – if I eat this, will I shorten my life expectancy: yes or no? And they don’t like it when the answer is “maybe.”

But this does not mean we should give them certainty where none exists. To use an example provided by the same colleague, it is true that we are probably not going to change our minds next year and decide that gorillas are more closely related to us than chimps. But neither can we say with certainty that we won’t, if evidence emerges to support the alternate relationship. Twenty years ago, you wouldn't have found many scientists who thought whales and hippos were closely related, but now it's a widely accepted hypothesis. This may be frustrating to the lay reader, but it’s also science. We go where the evidence takes us, which is why we differ from creationists.

From uncertainty it’s a relatively short step to the unknowable, and this is where a lot of my colleagues get really uncomfortable, because we’re talking about the limits of science. Tim Minchin may think “Storm” is a dumbass for believing that there are aspects of the human body that are a mystery, but where paleontology is concerned there are all sorts of mysteries. We are stuck in what my graduate advisor used to call “evolution's epistemological gap” – we can see the end result of evolution, in terms of the diversity of species, and we can analyze and manipulate the processes that may have generated that diversity at a micro-evolutionary level, but our lifespans aren’t long enough for us to directly observe one leading to the other. We have a lot of powerful supporting evidence, but the most critical component – the fossil record – is hopelessly patchy.

In some cases, we can fill in the gaps with new fossil discoveries, and these often change the evolutionary narrative significantly. When I was a kid, I was told that we “knew” that our distant ancestors were fish with lungs that developed 5-toed limbs from their fins. They were able to survive out of water because of their lungs and the fins helped drag them back to the water, and so evolved into limbs. Very neat and also (probably) not true. We now know that things were more complicated than that; between 400 and 360 million years ago there were a bunch of different animals that were not quite fish and not quite land animal, that developed feet with far more than five toes, and that had gills, not lungs. The first feet may have had more to do with moving in an aquatic environment than the terrestrial one. And we will continue to find fossils that fill out the gaps in this story, in sometimes surprising ways.

Or maybe we won’t. As I said, the fossil record is patchy. The circumstances under which an animal is preserved are very specific and very rare. The likelihood that erosion exposes that animal at a time and place where someone can discover it is equally rare. And fossilization does not capture all of the evidence about the organism. I may have an exquisitely preserved oreodont skeleton, but I can’t tell you what color fur it had, what sounds it made, what it smelt like, or how it digested its food. And given the circumstances under which these animals are usually found, which do not allow for the sort of exceptional preservation seen in other fossil deposits, I may never be able to tell you. I don’t know about you, but I find that really exciting.

The “Tree of Life” is a bit like the Rudolph Zallinger murals that we have on the walls of the Peabody Museum. At first sight, the Age of Reptiles and the Age of Mammals look like panoramic views of the evolutionary history of these groups. But they are not. We now know – because of new evidence - that many of the animals pictured looked nothing like their reconstructions and would not have done the things that they are shown doing. Many of the species pictured together are actually separated by millions of years, and sometimes tens of millions of years. Even when they are contemporaries, the animals shown represent only a tiny fraction of the ones that would have been present in the environments pictured, let alone all those that have ever lived.

Does this mean the murals are useless? Not at all. Even now, they remain a powerful tool for teaching about evolution. As I’ve discussedelsewhere in this blog, The Age of Mammals is one of the best summaries of the effects of global climate change that one could ask for, while the Age of Reptiles shows us how our ideas about dinosaurs have changed as a result of the work of paleontologists, while still being an awe-inspiring work of art in its own right.

The Tree of Life is the same thing. It is a powerful metaphor for the interconnectedness of life, a good way to visualize our current understanding of how different organisms are related to each other, and a starting point for developing hypotheses of how evolution might have generated this pattern. But the idea that its neat pattern of nodes and bifurcations completely encapsulates the infinitely complex, intricate, and painstakingly slow process by which populations of millions of individuals change over time to give rise to new species is no more correct than saying that Zallinger’s mammal mural is a photographic record of what life actually looked like in the Oligocene.

When I first mentioned my concerns to my wife, she said (in a tone of barely suppressed outrage) “Are you telling me that you don’t believe in the Tree of Life?” (No, I’m not kidding – she really did say that). And yes, at some abstract level, I do. It’s even possible to believe that one day we might be able to build a complete Tree of Life – that we will describe every species of life on Earth (in a way that accounts for individual and population-level variability); that we will find all the fossils that we need to reconstruct the complete evolutionary history of every group that has ever lived; that we will develop unambiguous character sets that are devoid of homoplasy and immune to the effects of convergence; that we will build algorithms for phylogenetic reconstructionthat accurately reflect the true process of evolution. And that, having done so, we will stand back and admire our handiwork; a complete, entirely inclusive, 100% stable, and totally true Tree of Life. But to believe this will happen requires, dare I say it, quite a measure of faith.

I think I’ll stop there.

Monday, March 25, 2013

Nazi Cow

























Sunday, April 29, 2012

On Cake



Thursday, April 26, 2012


I stole this shamelessly from Spineless Wonders, a blog by my colleague Jess Utrup. You can read her post about it here.

Going to the Moon

Last week my friend Beth Merritt (we'll come back to her in a minute) shot a photo from her office window of the Space Shuttle Discovery, piggybacked on a NASA 747, flying over downtown Washington DC on its way to its new home at the Smithsonian's National Air and Space Museum (left). It was a poignant moment - the end, at least for now, of America's manned space program. For the time being, U.S. astronauts are going to ride into Earth orbit (which is as far as anyone has been for the last 40 years) on a mix of Russian and commercial spacecraft.

Fear drove America into space and on to the Moon - fear of a "missile gap" between Russia and the USA (which John F. Kennedy had used to get elected in 1961), fear about being left behind in a technological competition with the Soviet Union, fear of a loss of leadership and prestige. When Kennedy committed the nation to landing a man on the Moon by 1969, it unleashed a frenzy of technological creativity, riding on a tidal wave of dollars. At its peak, there were more than 400,000 people working on the Apollo program, which required the support of over 20,000 industrial firms and universities. The total cost was over $24 billion; the estimated costs of in 21st Century dollars vary from $109 billion to $170 billion. It has been described as the largest commitment of resources ever made by any nation in peacetime, but war - in this case a Cold War - and the fear of war was what really lay behind it.

Apollo seized the public's attention. In 1968, televised pictures from Apollo 8, the first manned spacecraft to orbit the Moon, formed the basis of the most widely watched television broadcast up to that time. The following year, an estimated one-fifth of the population of the world watched the live transmission of the first Apollo moonwalk. The definining image of Apollo may have be the view of Earth as a fragile, small blue planet floating in space, as captured in photographs taken during the lunar missions. It was the first time our species had viewed its planet from such a distance. The 24 astronauts who traveled to the Moon are the only humans to have observed Earth from beyond low Earth orbit and in 40 years, no-one has traveled farther from Earth.

Apollo required the organization of tremendous public resources within a vast, centralized bureaucracy under government direction; a rich irony for a program intended to showcase the superiority of the capitalistic, free-market system as represented by the US. But the economic payoffs of space exploration to the commercial sector have been huge: LEDs, infrared ear thermometers, artificial limbs, aircraft de-icers, temperfoam mattresses, babyfood, and cordless vacuum cleaners are all built on technologies first developed by NASA (NASA even has a journal, Spinoff, devoted to publicizing its technological innovations).

But despite all this, without the fear it's been next to impossible for NASA to sustain a manned space program. The current U.S. Administration has abandoned the idea of a return to the Moon in favor of a so-called "Flexible Path" strategy that might involved the Moon, might involve Mars, might have Americans orbiting Mars (but not landing on it) by the 2030s, and which depends on a heavy light rocket that might built sometime after 2015. It's not exactly visionary, but it does reflect the reality of trying to support a large scale, Federally-funded science and technology program in these financially-straightened times.
By now, you may be wondering what all of this has to do with natural history museums. Well, last month saw the publication of a "call to arms" by the systematic biology community to undertake the taxonomic equivalent of putting a person on the Moon; describing every one of the estimated 10 million species of organism on the planet and completing the project in less than 50 years. The project is called "Mapping the Biosphere," and you can read a press report here; for those of you with on-line journal access, the paper itself (from Systematic Biology) can be downloaded here. Mapping the Biosphere comes with a price tag of $1 billion a year for the next 50 years (presumably adjusted for inflation), although the authors do note that others (e.g. Carbayo & Marques, 2011: TREE 26, 154-155) have come up with a cost that is over five times as high.

I'll admit to being a bit jaundiced about these sorts of efforts. UK readers with long memories may remember a similar effort in the early 1990s that proposed to reinvigorate the taxonomic community in Britain. As I recall, we were exhorted to abandon research on vertebrates and instead throw all of our efforts into sequencing nematodes and tardigrades. This would generate a host of phylogenetic trees that could then be used as the basis for evolutionary studies (the so-called Phylogenetic Comparative Method or PCM). The people issuing this battle cry were, not surprisingly, people using PCM who didn't have access to the trees they needed. For all of their considerable intellect they were not systematists, and it showed. No flood of funds was released, although the Natural Environment Research Council (NERC) did create a five-year program that funded some postdocs, students, and training courses. The UK is still trying to get out of first gear as far as taxonomy and systematics is concerned - for the latest effort, see here.

So what about this new vision for a 50-year effort? As it turns out, there's a lot to like about it. First of all, it's written by people who actually work in systematic biology, although a quick scan of the names suggests that it's more chiefs than indians. But after all, that's why we pay them the big bucks, right? And there are a lot of people in there that I know/like/respect. Next, the scope is probably about right, both in time and money. This really will need to be a major effort, employing thousands of people. The authors suggest that improvements and innovations in technology will mean that the rate of species description may accelerate, although it seems likely the rate-limiting step will be field collection.

Another thing that I appreciated was the high profile given to museums and collections. You may think that this would be an obvious part of any wide-ranging attempt at large-scale species discovery, but there have been times in the past when this has not been the case. But in the words of the Systematic Biology paper "No outcome of an intensive campaign to inventory species will be more important than the growth and development of collections... if the existing ratio of museum specimens to known species is about right... we can anticipate museum collections about six times the size of those at present." I particularly enjoyed this statement, because it blows a substantial raspberry in the face of the UK museum community, where a mania for sustainability has been translated into some quarters into a call to severely limit collecting. Sustainability is a critical issue, but using it as a fig-leaf for the fact that you don't have enough resources to do your job properly is a bit wet.

Not that the issue of sustainability has been overlooked. As the paper's authors go on to say, "International planning and cooperation is essential in order to avoid unwanted redundancy in effort... it is an appropriate time to modernize existing physical plants to assure optimal conditions for the long-term conservation of specimens.... and to re-examine the efficiency of storage systems themselves that have changed little in more than a century." The paper also proposes reviewing and changing work practices in our collections, something that we're already looking at for collections digitization (subject of a future PoH post). The authors even talk about speeding up the process of accessioning - possibly the first time the word "accessioning" has ever appeared in Systematic Biology - and maybe going as far as creating regional centers for specimen processing to assist resource-starved museums.

There's also a well-deserved wrist-slap for the funding agencies; "Given the importance of collections to the documentation and understanding of biological diversity, it is unconscionable that so little funding is made available for the maintenance, growth and improvement of natural history collections." With NSF looking to halve funding for the Collections in Support of Biological Research program by making it a biennial competition (of which more in the next post) this is a timely rebuke. Funds are still available for collections support, and the Advancing Digitization of Biological Collections program is giving a much-needed boost to collections accessibility. But it's still nowhere near enough money for a program of the size envisioned in this paper.

Which is where we get off the positivity express and take a cold shower of reality. Fifty years is a very long time - the Apollo program managed just over ten years before it all came to a grinding halt. Administrations come and go, priorities change, new opportunities emerge, new crises require a response. Sustaining a focused scientific effort over that period will be an enormous challenge - maybe a bigger challenge than getting the funding in the first place. Not that funding isn't a problem as well. $1 billion a year doesn't seem like a lot of money in the context of the U.S. Federal budget. This year, the U.S government proposes to spend $3.796 trillion. A quarter each goes to pensions, defense, and healthcare; not surprising if you consider the fear-based motivation we looked at earlier - everyone's afraid of getting sick, getting old, or being blown up by terrorists. The last quarter gets divided up between everyone else. Science accounts for about 2% of the budget (see here for details) and when you get into the nitty-gritty of where that money goes, $1 billion starts to look a lot bigger. It would be 12.5% of NSF's annual budget for 2012 - 30% more than all of the funds that NSF currently provides to its BIO Directorate. And all this so that scientists can name beetles? You can imagine the Fox News headlines already.

Of course no-one's arguing that one agency should support "Mapping the Biosphere," or even one country, but looking at the paper you could be forgiven for thinking so. It has 39 authors from 25 institutions; 34 of those authors and 21 of the institutions are U.S.-based and only 1 author is from a country with an emerging economy (in this case Brazil) despite the fact that most of the world's undescribed biodiversity resides outside the United States and Europe. It seemed to me that this was a major flaw. There is a considerable (and perhaps understandable) resentment in many parts of the world directed towards the mining of biodiversity by "First World" institutions and one would expect that any large-scale program of species description would deal with this front-and-center.

As it was, I had flashbacks to the early nineties taxonomy debates, with their emphasis on "parataxonomists." For those of you who haven't come across this concept before, a parataxonomist is a (usually local) worker who has been given basic training in species identification. They carry out the initial sorting of specimens, but as soon as something interesting emerges, an "expert" (usually not local, and more often than not from a First World institution) swoops in to describe it. The work of the parataxonomist thus saves the more valuable time of the expert. How anyone could look at this arrangement and not think about colonialism beats me (back when I was a student - admittedly some years ago - I actually heard someone describe parataxonomy, without irony, as "barefoot taxonomy"). In the 21st Century these sorts of attitudes just won't do; the only way this massive species description effort will work sustainably is with at least some of the leadership coming from the countries that actually "own" the biodiversity; as many of them are struggling to lift their people out of the trap of poverty this will be a big hurdle to overcome.

Another challenge is how to grab the public's imagination, critical if long-term support is to be established. Consider the Large Hadron Collider, a project that is cited by the paper as having a similar scale and return on investment as a global species discovery effort. The science that underpins the LHC is, frankly, next to impossible for a layperson to understand, but the statistics of the collider itself are staggering. 17 miles long, buried 500 feet underground, with instruments the size of a house. It contains 1,600 superconducting magnets, weighing up to 27 tonnes each, which are cooled to -271 C using liquid helium. Protons travel round it at only 3 meters per second less than the speed of light. Who cares what it does - it's awesome! NASA has rockets and can drive a robot across the surface of another planet hundreds of millions of miles away, beaming back high definition photos to Earth. Natural history collections are Big Science, in their own way, but it's a hard sell. The public may love museums, but they don't think of them as something that comes with a $1 billion a year pricetag.

There's also an issue that "Mapping the Biosphere" is a journey without a clear end. Apollo had an unambiguous goal; Kennedy promised that an American would walk on the Moon by 1969 and that goal was met at 02:56 UTC on July 21 of that year, when Neil Armstrong's left boot hit the surface of the Sea of Tranquility. The ultimate goal of the proposed species documentation effort is a lot less tangible, because there isn't really an end to it. Since we don't know how many species there are, we can't know when we're done. And even if we get to an "end," taxonomists being what they are, many of the species described earlier will already be the subject of fierce debate, or have been consigned to the dustbin of synonomy.

So, I've given you some positives and some negatives and now, if you care about this issue one way or another, go off and take a look at this blog post by Beth Merritt (I told you I'd get back to her in the end). For those of you who don't know her, Beth is the Director of the American Association of Museum's Center for the Future of Museums, and she thinks museums can change the world. Also, because she's super smart and started out in natural history museums, she believes that "natural history museums have the greatest potential, among their brethren in art, history, science, to play global superhero, if only because the need is greatest." Maybe "Mapping the Biosphere," for all its flaws and challenges, is what we should be doing. Or maybe we should be doing something completely different. If so, we'd like to know your thoughts about what that might be.

Beth will be leading a day-long forecasting exercise on June 16, at the annual meeting of the Society for the Preservation of Natural History Collections in New Haven, CT, which will explore some of the pressures on natural history collections and how they will adapt to changes in science society over the next few decades. For my sins, I've agreed to help her with this; we'd love you to attend, but even if you can't you can still participate on-line. Beth's blog post will tell you how, but to return to the very beginning of this post, one of the things we'd like you to think about is what might drive changes in museums. Cold War fears ultimately put Neil Armstrong on the Moon; what drivers might, for example, lift "Mapping the Biosphere" off the ground?

Sunday, March 25, 2012

Ways of Seeing













