Parsimony Revisited

Leonard Finkleman writes…

Last year I wrote an essay about cladistics and parsimony. It made some rounds and then the deadline for the following month’s essay came up and I turned my thoughts to other things. I suppose this hit-and-run mentality is what we call “blogging.”

This year I took a midterm exam for this first time in more than a decade. While I did well (as one would hope that a full-time professor might), confronting the errors I made on the exam has forced me to revisit my thoughts on parsimony. Today I have to admit: I committed a small error on the exam that’s since revealed a greater error in my approach to cladistics. So, you know, mea culpa.

(That’s right! Philosophers do admit mistakes. The admissions are just expressed in languages they don’t speak.)

Here’s what you’re now getting into: first I’m going to talk about significant figures in scientific measurement and draw out their broader meaning in scientific research; then I’m going to turn back to cladistic parsimony and argue, against the ghost of my 2016 self, for an a priori reason to favor that approach in paleontology.

This is admittedly a dry post, so here's a feathered tyrannosaur (Gorgosaurus libratus) to reward your patience. Art by John Conway.

"Sig figs"

Some day will be my last and on that day I’ll be able to tell you the convention for significant figures in science writing. I’ll be able to do that because I forgot it on my midterm and took some knocks for the forgetting. In that sense my error was a productive one: I won’t make it again. I can’t imagine wanting to talk about this on my last day, but at least the option is there.

What is the convention? Scientists aim for precision as well as accuracy in their measurements, but different fields have different standards of precision. A geologist studying rock strata laid down over thousands of years can hardly be expected to resolve measurements to the same timescale as a particle physicist studying nearly-instantaneous subatomic reactions. Hoping to standardize reporting of numbers in scientific publications, Eisenhart (1968) recommended the following: state a measurement’s potential error to two significant digits and state the measurement itself to the resulting number of digits given for the potential error.

In enrolling for paleontology classes, my goal was not only to learn what paleontologists do, but why they do it. So I did some digging into why this should be the convention.

Alas! Like a bad field season, my digging didn’t turn much up. Eisenhart didn’t justify his recommendation. His paper is a master class in the “it’s right because it is said to be right (by me, who would never use the word ‘I’ in print)” school of science writing.

For my own part, however, I see two goals accomplished through maintenance of Eisenhart’s convention. First, it relativizes scientific measures to the appropriate degree of uncertainty in the discipline. If a discipline’s measurements are uncertain within a calculated range, then that range of uncertainty then determines the discipline’s most precise measurements (i.e., the ones that ought to be reported). The second goal accomplished is to ensure that the expression of a measurement’s uncertainty is never trivial. All scientific results are uncertain to some degree and reporting of those results should reflect that.

Bear in mind that “error” and “uncertainty” are terms of art in scientific practice. They aren’t assessments of truth function or attitudes towards other beliefs. They are, in fact, measurements. When Renne, et al. (2013) measured the age of the Cretaceous-Paleogene event at 66.043 ± 0.043 Ma, the uncertainty—± 0.043 million years—measures not anything about the given value of 66.043, but instead about the range of values that the natural world would yield. Very roughly, scientific error and uncertainty measure just how much our perceptions (i.e., statistical samples) represent the fullness of reality (i.e., populations).

This is (perhaps) another reason why Eisenhart might have thought that significant figures should be determined by uncertainty measures rather than by reported values. A realist assumes that reality determines perception and not the other way around, after all.

You're really sticking it out! As a token of my thanks, here are some woolly Pachyrhinosaurus. Art by Mark Witton.

What I got wrong in my (relative) youth

In my parsimony post, I wrote:

…we would recognize paleontology as a distinct and matured discipline (rather than as a handmaiden to other life sciences) if we could find some kinds of information uniquely valued in paleontological research. Qualitative similarity and temporal placement seem to be two such kinds of information. Inability to account for these kinds of information also happens to be the greatest weakness with cladistic parsimony.

In other words: phylogenetic reconstruction of extinct taxa depends on features that are difficult to quantify (although some cladists have given it the old college try), and so using cladistic parsimony to reconstruct evolutionary relations puts paleontologists at a unique disadvantage. Put yourselves in a position to succeed, people!

I maintain that there are philosophical problems in defining the populations from which fossil samples are drawn. But this is not to say that phylogenetic reconstruction of extinct taxa is purely a matter of perception. Rather, it's a matter of which element of reality we're trying to describe. It might be the relations between features of the fossils themselves (as I've hinted elsewhere) or it might be the evolutionary histories of the once-living animals that left those fossils behind. I'm leaning towards the former view because extinct populations are unobservable in principle rather than in practice, but in either case our phylogenetic reconstructions attempt to capture something real.

In scientific practice measurement of reality (rather than of perception) is expressed in terms of error and uncertainty. If paleontology is to be recognized as a mature and distinctive science, then, its research outcomes must include uncertainty measures. Those uncertainty measures relativize the degree of precision possible in paleontological measurements. All well and good so far.

Cladistic parsimony is one among several analytical methods in phylogenetic reconstruction. The purpose of these methods is to quantify and to measure relatedness between taxa. But among those paleontologists who don't share my esoteric views regarding the metaphysics of fossils, the reality to be captured in phylogenetic reconstruction is not relatedness per se. Relatedness is only a proxy for evolutionary history.

What parsimony measures do that other measures don't is attempt to quantify macroevolution itself. It does this by counting the number of evolutionary changes required to generate an hypothesized evolutionary history. In so doing, the uncertainty of the analysis—its relation to (unobserved) real evolutionary history—can be quantified. Without that measure, hypotheses about evolutionary history would lack an appropriate quantified context.

My original argument was that paleontological hypotheses about evolutionary history would always be imprecise relative to hypotheses generated by other life sciences. That's still true: molecular biologists, for example, can work with much higher-resolution data about changes in the genome. But this is only a problem if paleontologists are held to the same standards of precision as (say) molecular biologists. I now recognize this assumption as false. Maintaining the significant figure convention ensures that measurements in a scientific discipline are held to a standard of precision appropriate to that discipline. The defense against unfair critiques of imprecision (which was my original concern) is built into reporting practices.

Halcyon days of yore!

I still think that there are problems with the integration of paleontological and neontological data. Nothing that I've studied so far has allayed those suspicions, and if anything I'm now more convinced of that. But the harsh lesson about significant figures (delivered with the deduction of a full point of credit!) has at least tempered my views in this one respect: maybe paleontology can be more amenable to parsimony analysis than I originally thought.

Works Cited

1. Eisenhart, C. (1968). Expression of the Uncertainties of Final Results: Clear statements of the uncertainties of reported values are needed for their critical evaluation. Science, 160(3833), 1201-1204.

2. Renne, P. R., Deino, A. L., Hilgen, F. J., Kuiper, K. F., Mark, D. F., Mitchell, W. S. 3rd, Morgan, L.E., & Smit, J. (2013). Time scales of critical events around the Cretaceous-Paleogene boundary. Science, 339(6120), 684-687.

The Wilderness Before Time

Derek Turner writes …

Once I asked a class on environmental ethics how they would define “wilderness.” One student half-jokingly said that “wilderness is any place you can go, where other animals might eat you.” Anyone familiar with Werner Herzog’s film, Grizzly Man, will know that there is something right about this.

Timothy Treadwell, in Alaska's Katmai National Park. This does not end well.

My student’s comment contains an insight: wilderness is where we go to be reminded that nature doesn’t care about us, and that nature always has the last word.

What if the spiritual pull that draws us to dinosaurs is not that different from what draws us to Denali? Or to Alaska's Katmai National Park, which provided the setting for Grizzly Man?

Like Timothy Treadwell, the subject of Herzog’s film, some of the characters in Jurassic Park also get up close and personal with animals that can, and sometimes do eat them.

"Wilderness is any place you can go, where other animals might eat you." 

Is there a connection between wilderness and paleontology?

Consider the following argument:                                                                             

P1. Wild landscapes—places where humans have no permanent presence, and where human activities have relatively little impact—are especially valuable.

P2. Pre-human landscapes were wild.

C.  Therefore, pre-human landscapes were especially valuable.

Let’s call this the WBT (“wilderness before time”) argument.

(I discuss some other possible connections between paleontology and environmental thinking in earlier posts, here and here.)

Is the WBT argument a good one? It is valid, meaning that the conclusion follows logically from the premises. But are the premises true?

The Prehistoric Wild

P2 looks to be in pretty good shape. The pre-human world was wild if anything is. Some have argued that no place on Earth today is truly wild, because human activities—especially the burning of fossil fuels—have altered every square inch of the planet.[1] However, the pre-human wild was the real deal, completely unaffected by anything that humans would ever do in the future. Because we cannot intervene in the past, we can do nothing to “tame” or “civilize” the pre-human wilderness.

Troubles with The Wilderness Concept

P1 is more questionable. Many environmental thinkers in North America, at least since John Muir, have held that wild places have special (possibly intrinsic) value. There have been many efforts to get clear about the value(s) of wilderness, and the literature on this issue in environmental ethics is vast.[2] Speaking autobiographically, though, reading William Cronon’s classic essay, “The Trouble With Wilderness,” has made it very tough for me to get behind P1.[3] 

Perhaps the most serious problem (though by no means the only one) concerns the often violent history of mistreatment and displacement of Native American and First Nations communities. In North America, many of our cherished “wild” places are landscapes that people had lived in and loved and modified and been modified by for a very long time before disease-bearing Euro-American settlers showed up. In some cases, newcomers forced Native people out and subsequently declared those places “wild,” as if they had always been empty, or as if the people living there were less than human. The idea that such areas are untrammeled by humans is a mythical smokescreen that hides a history of injustice. It’s hard to see how to treat wilderness as an anchoring environmental value without confronting this history.

Gratuitous wilderness shot, from a backpacking trip in the Sierra Nevadas, at Thousand Island Lake in the Ansel Adams Wilderness.. Does the human presence mar the scene? 

Another problem with P1 is its negative anthropocentrism. The idea that something has value in virtue of the fact that humans have not interacted with it implies that human interaction with something diminishes the value of that thing. Hence the injunction to "leave no trace" in the wilderness. But that’s just as arbitrary and unmotivated as positive anthropocentrism, the view that membership in a particular biological species confers special moral status. One could just as well define “wilderness” as any place that’s unoccupied and untrammeled by some other nonhuman species—any place untrammeled by squirrels, for example.                                                                                                    

There is much, much more to be said here, but these are two main reasons why I hesitate to defend P1. When it comes to fundamental environmental values, it might be more helpful to talk about biological diversity, or ecological health, or sense of place, or the value of individual living things and biological relationships.

Nevertheless, wilderness can exert a profound pull, even upon those of us who are more than a little skeptical. We go—at least, those who are lucky enough to be able to afford the cost of transportation and the expensive backpacking gear—in order to be humbled and perhaps tested. We go to be reminded that nature, like the gods of the ancient Epicureans, is utterly indifferent to human life and well-being.

So the WBT argument is valid, and P2 is true, but P1 is problematic. I’m therefore not sure we should buy it. But let’s think about what the argument might mean for paleontology.

Paleontology and the wild, Pre-Human Past     

It’s no coincidence that paleontology started to capture the American imagination in the late nineteenth and early twentieth centuries, at precisely the moment in American cultural history when people like John Muir and Theodore Roosevelt begin to lament the “closing” and the “taming” of the North American wilderness. The wilderness preservation movement was born of nostalgia: The distinctive American character was forged in the process of developing and cultivating the wild frontier—or so went the story told by Frederick Jackson Turner and others—and we need to preserve remaining wild places so that people can continue to have those formative experiences. At the same time that the federal government was establishing national parks—Yellowstone in 1872, Yosemite in 1890, followed by many others—wealthy philanthropists were establishing museums in New Haven (1866), New York (1869), Chicago (1893), and Pittsburgh (1896), institutions whose mission was to give people a window on a prehistoric wilderness that really was untrammeled, and where lots of animals would have been happy to eat you or crush you underfoot.

The WBT argument suggests that paleontology might have, in addition to various epistemic goals, the non-epistemic one of putting us in touch with pre-human wilderness.

The scientific effort to reconstruct the deep past is, perhaps in part, a kind of cognitive backpacking trip—a way of visiting a landscape, one displaced from us in time rather than in space, and one whose value depends on the fact that humans do not belong there. The joys of paleontological reconstruction may derive in part from the promise of access to wilderness. This points to another way in which the scientific study of the deep past is suffused with the values of the broader culture (See Joyce’s great discussion that issue here.) Perhaps we feel impelled to reconstruct prehistoric landscapes because they have value qua wilderness.

The familiar epistemic goals of historical natural science blend with nostalgia for wild places that are increasingly hard to find.

In an earlier post, I suggested that dinosaurs might be overrated, in the sense that their high cultural profile is out of proportion to their scientific importance. Why, for example, is it more important to figure out the colors of the dinosaurs than to figure out why the ammonoids had such high speciation and extinction rates?[4] The WBT argument, together with my student’s observation, goes some way toward accounting for this. Perhaps we want to do our cognitive backpacking across prehistoric landscapes where some of the animals could eat us. 

[1] One person who made this point relatively early was Bill McKibben, The End of Nature, Random House, 1989.

[2] See especially the papers collected in The Great New Wilderness Debate, edited by J. Baird Callicott and Michael Nelson, University of Georgia Press, 1998, as well as The Wilderness Debate Rages On, edited by J. Baird Callicott and Michael Nelson, University of Georgia Press, 2008.

[3] William Cronon (1995) “The Trouble with Wilderness, Or Getting Back to the Wrong Nature,” in Uncommon Ground: Rethinking the Human Place in Nature. New York, W.W. Norton, pp. 69-90.

[4] M.M. Yacobucci (2016), “Towards a model for speciation in ammonoids,” in Species and Speciation in the Fossil Record, edited by W.D. Allmon and M.M. Yacobucci. Chicago: University of Chicago Press, pp. 238-277.