"Trying to define the undefinable": are taxonomists too focused on species?

A recent article in the New Yorker includes a good overview of why identifying species can be problematic:  

"You Name It: Carl Linnaeus and the effort to label all of life" by Kathryn Schulz, August 21, 2023 

Extended quote from article:

"What Linnaeus sought to do was organize nature according to its fundamental, intrinsic divisions--to carve it at the joints, in Plato's famous formulation.  But what he actually did, for the most part, was impose artificial categories on the natural world for the convenience of scientists.

This is not a retroactive assessment; Linnaeus himself knew full well the limitations of his classification method.  To achieve a system completely in accordance with nature was, he wrote, "the first and last wish of botanists."  But the more closely you looked at her bounty the more difficult that prospect became--so, in the meantime, "artificial systems are absolutely necessary."

In philosophy, this tension between intrinsic and imposed categories takes the form of a debate between nominalism and realism.  Realists believe that nature is full of real and discrete categories, from 'amphibian" to "zinc," and that the job of the scientist is to discern them accurately.  Nominalists believe that nature lacks clearly defined categories, and that we simply impose those distinctions upon it--creating, as it were, the illusion of joints where none really exist.  

This is not just the position of post-truth relativists.  "I look at the term 'species' as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other": that is Charles Darwin, in the second  chapter of "On the Origin of Species."  That book, of course, trumpeted to the world a very large problem with the entire notion of a species.  According to evolutionary theory, species are constantly changing--emerging, diverging, going extinct.

The very concept of a species is in radical flux, too, with more than twenty competing definitions in circulation.  Choosing a definition is not just a matter of what goes in the dictionary under "species"; which one you use will determine how you divide up nature, such that a group of creatures that would be regarded as a species by one standard might not merit the label by another.  

All this confusion comes, as Darwin wrote, "from trying to define the undefinable."  Yet committed realists continue to promulgate more and more definitions, in the belief that one of them will map perfectly onto some intrinsic and stable feature of nature.  Darwin called that idea "laughable," a word that captures the impossibility but not the gravity of arbitrarily imposing categories on living beings.

Paleo Diet Reading List

Reading about human origins can be fascinating, and informative.  It has been said that nothing in biology makes sense except in light of evolution, and the same could be applied to diet. I originally wanted to understand the physiological biochemistry of digestion, but several textbooks later I had lots of facts but very little understanding.  While strolling at the zoo, I realized I needed textbooks that described the differences between animal digestion -- a comparative physiology textbook, perhaps.  But again, after reading all of the most popular titles, I had only scattered facts and no theory of the differences between human and animal digestion, or even between carnivore, omnivore, and vegetarian modes of sustenance.

Luckily, two Harvard professors have written books on human evolution with particular emphasis on how dietary changes made us human.  In the process, they provide the best, although somewhat contradictory, source of information on comparative dietary physiology.  Daniel Lieberman's The Story of the Human Body (2013) is a more traditional telling of human evolution, but it is written in an attempt to answer the question of how our paleo bodies have adapted (or not) to modern lifestyles.  Richard Wrangham's Catching Fire: How Cooking Made Us Human (2009), is an extended argument concerning the importance of cooking to human evolution, but he does deal extensively with the comparative behavior and anatomy of humans, proto-humans, chimps, and other primates.  Only at the end of his book does he tackle the problem of modern dietary choices for humans, and then only as a parting shot.  John Hawkes, at the University of Wisconsin, is often mentioned as an authority on human evolution, and I would include his Great Courses lecture (2011) in this triumvirate of human evolutionary tales.

The above works often reference modern accounts of extant hunter-gatherer tribes to understand what life might have been like during the Paleolithic era.  The most notable of these books are Lee's account of the !Kung San, and I would also suggest Weston A. Price's classic Nutrition and Physical Degeneration: A Comparison of Primitive and Modern Diet and their Effects.  A modern synthesis and review of the same subject matter can be found in Lindeberg (2009).

It is interesting to compare the literature on human evolution with the diet book literature making use of ideas in human evolution.  The originator of the "Paleo Diet", Loren Cordain has several books specifying his interpretation of the evidence.  While his 2002 book specifies a diet that seems more restrictive than what I've read in Lieberman and Wrangham, I haven't had a chance to read his 2012 book yet.

1. Lieberman D. The Story of the Human Body: Evolution, Health, and Disease. Knopf Doubleday Publishing Group; 2013.
2. Wrangham R. Catching Fire: How Cooking Made Us Human. Profile Books; 2009.
3. Price W. Nutrition and Physical Degeneration: A Comparison of Primitive and Modern Diets and Their Effects (Hardback). Benediction Classics; 2010.
4. Lindeberg S. Food and Western Disease: Health and Nutrition from an Evolutionary Perspective. Wiley; 2009.
5. Lee RB. The !Kung San: Men, Women and Work in a Foraging Society. Cambridge University Press; 1979.
6. Cordain L, Friel J. The Paleo Diet for Athletes: The Ancient Nutritional Formula for Peak Athletic Performance. Rodale; 2012.
7. Cordain L. The Paleo Diet: Lose Weight and Get Healthy by Eating the Food You Were Designed to Eat. J. Wiley; 2002.

Antinutrient Resources

In general, plant secondary metabolites can have positive and negative effects (Weston A. Price). The reason I don't try to categorically avoid them, but treat them with caution, is that these effects are multiplicitious and biological: very hard to predict what they will do, good or bad...

However, unless we know about the problems with antinutrients, we won't know why eating raw flour or dough is dangerous, why green potatoes are toxic, or how many raw red kidney beans it takes to kill a man (not very many).

But on the whole, unless you are allergic, most antinutrients will be digested, and some are actually good for you. For example, this article mentions that inositol hexaphosphate is a break-down product of phytic acid. Most phytic acid is broken down by digestion, and there is evidence that it can have beneficial effects as well as deleterious effects.

This article points out that most sweet potato antinutrients are destroyed by baking, as opposed to boiling. This FAO article on all the major food crops and their antinutrients specifies that " Heating to 90°C for several minutes inactivates trypsin inhibitors", which explains why baked sweet potatoes are nontoxic. (But the article also points out that diseased or moldy sweet potatoes may have toxins that are not completely deactivated by cooking ....moldy vegetables should not be consumed. Apparently, toxins in normal potatoes are also not destroyed by normal cooking methods. Furthermore, sweet potatoes do not have lectins, but normal potatoes do. These compounds can have some antidigestive effects, but most should be destroyed by cooking.

Antinutrients are important, but I think methionine and nutrient density / glycemic index considerations are more important overall. A few potatoes or slices of bread shouldn't hurt most people, but if you have the luxury of chooses less toxic plant products, sweet potatoes and especially squash and pumpkins are some of the best sources of nutrients, with the least amount of antinutrients.

New Theories in Evolution and Ecology

Sometimes it can be hard to see progress in biology the way we hear about physics discovering new particles or proposing Grand Unified Theories that explain the entire universe.  It is tempting to believe biology is just too diverse, variable, and multitudinous to be tractable, and that we should content ourselves with Nature-special documentary anecdotes.

But recent research has uncovered at least three major advances toward predicting evolution, social altruism, and a universal explanation of biodiversity. We may soon be able to predict short-term (9-12 month) evolution of the flu virus, rigorously describe conditions necessary for social altruism, and extrapolate biodiversity estimates using insights from thermodynamics.

The complexity, idiosyncracy, and exceptions-to-the-rule in biology are still important, but so too are these simplifying general explanations.  The stories of new "universal laws" linked below are perhaps best thought of as null-theories; jumping-off places rather than destinations in themselves:


1) Predicting Evolution ... Testable Fitness Values (link to article by Carl Zimmer)

Simple selective pressures yield relatively simple predictions: fitness increases linearly at first, but in the long run, weird mutations may diverge populations along novel and unpredictable trajectories.  The tractable problem, then, is short-term evolution, which can still be incredibly important when it is applied to, say, the next 12 months of evolution in the flu virus.  The breakthrough came with the ability to quantify fitness to predict evolvability.

One of the biggest problems of evolutionary theory has been a lack of predictive power, because fitness could only be defined tautologically, post hoc based on survival and reproduction.  If biologists are able to assign fitness ranking with any skill (link) then we may finally be able to understand evolutionary ecology -- the rise and fall of species in their environment.  Will most threatened and endangered species prove to be genetic weaklings, as suggested by this correlational study?

2) Predicting Social Altruism ... What Makes A Good Theory? 

This is an insightful philosophy paper that deconstructs a long-standing debate about whether altruism is predicted by fundamental evolutionary pressures.  The important step forward here is a robust definition of key terms and a searching analysis of what we should expect from abstract mathematical theories.

3)  Predicting Biodiversity .... Metabolic Scaling Laws to the Rescue! 

The tractable problem is to estimate the number of species in a given area when ecologists can only count species in relatively small plots.  The breakthrough came by realizing that only two additional variables (population density and total number of species) are necessary to "collapse" idiosyncratic species-area curves into a single universal curve.

The discoverer, Dr. John Harte, explains:

"If you look at all the known species-area (S-A) curves in the world, of everyplace where somebody’s gathered species-area data, and you plot them all on one big piece of graph paper- log species vs. log area, you will find that the data points fill the graph almost completely. You get every possible behavior when you just do a plot of log S vs log A. There’s no regularity. I didn’t really think that had to be the case. What I learned from developing the theory of macroecology based on the maximum-information entropy principle, is that the theory makes a very startling testable prediction about the shape of the species-area relationship. It says that if you take any species-area curve and you plot the local slope of the log-log plot, what we call ‘z’, at any scale against a certain scaling variable that the theory identifies, namely, the number of individuals at that scale divided by the number of species at that scale, all species-area curves should collapse onto a single universal curve. And it turns out that they do"

(Quoted here.)