Elements of Dynamic Network Analysis: a new series

John Terrell

During the second half of 2018 SCIENCE DIALOGUES will be featuring a series of reports on the steps that have been taken at the Field Museum in Chicago since the early 1970s to develop dynamic 4-dimensional (space-time) approaches to networks analysis in the social and historical sciences. 

The goal of these reports is to prepare the way for writing a book about how networks analysis is currently revolutionizing scientific (and hopefully human) thought about the world we live in and our place in it.

The first posting in this new series on human nature is available here along with a link to the second post  now online at SCIENCE DIALOGUES.


Cover art (a fantasy) for the proposed book on networks thinking.

Challenging our assumptions about the antiquity of trade and social networks in Middle Stone Age Africa

Nature human behavior has just published a research highlight written John Carson about work at the Sibilo School Road Site in Kenya done by Nick Blegen, Harvard University, that has recovered large quantities of obsidian along with Middle Stone Age (MSA) tools . The finds are thought to date back at least 200 kyr.

As Carson summarizes: “Geochemical analyses demonstrated that the majority of obsidian pieces had their provenance at a source site >160 km away, indicating long-distance transport of raw materials during the MSA.” Previously, East African sites evidencing long-distance resource transport have all be less than <50 kyr old.

Evidently known MSA sites of this age are rare in East Africa. If more sites can be found and excavated, the “big story” usually told about the evolution of human social behavior may need updating: far-reaching resource networks and/or intergroup trade in raw materials could have developed earlier than generally believed in the history of our species. If so, then in Carson’s words: “we may gain greater insight into the timeline of social evolution that eventually led to our modern group behaviours.”

Blegen’s report was just published (unfortunately behind a paywall) in the Journal of Human Evolution. Here is the abstract you will find available there for free:


This study presents the earliest evidence of long-distance obsidian transport at the ∼200 ka Sibilo School Road Site (SSRS), an early Middle Stone Age site in the Kapthurin Formation, Kenya. The later Middle Pleistocene of East Africa (130–400 ka) spans significant and interrelated behavioral and biological changes in human evolution including the first appearance of Homo sapiens. Despite the importance of the later Middle Pleistocene, there are relatively few archaeological sites in well-dated contexts (n < 10) that document hominin behavior from this time period. In particular, geochemically informed evidence of long-distance obsidian transport, important for investigating expansion of intergroup interactions in hominin evolution, is rare from the Middle Pleistocene record of Africa. The SSRS offers a unique contribution to this small but growing dataset. Tephrostratigraphic analysis of tuffs encasing the SSRS provides a minimum age of ∼200 ka for the site. Levallois points and methods of core preparation demonstrate characteristic Middle Stone Age lithic technologies present at the SSRS. A significant portion (43%) of the lithic assemblage is obsidian. The SSRS obsidian comes from three different sources located at distances of 25 km, 140 km and 166 km from the site. The majority of obsidian derives from the farthest source, 166 km to the south of the site. The SSRS thus provides important new evidence that long-distance raw material transport, and the expansion of hominin intergroup interactions that this entails, was a significant feature of hominin behavior ∼200 ka, the time of the first appearance of H. sapiens, and ∼150,000 years before similar behaviors were previously documented in the region.

© 2016 Elsevier Ltd. All rights reserved

Neuroscience, psychology, and the noble art of blog boxing

John Edward Terrell

Please note: this commentary, recovered on 3-Febr-2017, was originally published in Science Dialogues on 16-June-2014.

Abstract: According to some, the current debate in psychology about “direct replication” as a way of being vigilant against scientific fraud and sloppiness is devolving into a boxing match fostering snottiness, snark, and downright bullying. However, focusing on the downside of this call to arms may be sidetracking us from attending to a more fundamental question—when is research replication the right thing to do?

ONE OF THE THINGS I LEARNED while struggling to write a book  about friendship, human nature, and evolution is that neuroscience  and neurotic are not all that far apart. Before saying why I got this impression, however, I need to say something first about psychology today.

Late 19th century phrenological chart (source: http://thegraphicsfairy.com/vintage-clip-art-antique-phrenology-head/)

While reading journal articles garnered using Google Scholar I got the impression that different researchers working in different laboratories aided perhaps by different sorts of machinery are not only coming up with seemingly incompatible conclusions about how the human mind works (e.g., is there or isn’t there a lateral bias to creativity up there in the cranium?), but also that the left hand isn’t always aware of what the right hand is doing. Different research fiefdoms seem to be chugging along more or less unawares of how others are tackling the same issues. And I had the suspicion few are trying to replace the out-dated unity of wisdom of Sigmund Freud with anything approaching a holistic model of the mind. Why so, if this is true?

I am willing to admit my ignorance, but am I wrong to think experts in neuroscience nowadays are a lot like the famous blind men and the elephant? Each research team may have a firm grip on a piece of the puzzle, but does anyone really know how that beast called the brain actually works?

But wait a minute. What’s neurotic about the picture I am painting? A recent blog exchange between my friend Jim Coan at the University of Virginia and the anonymous science blogger Neuroskeptic has brought me some enlightenment on what sure seems like neuroticism to me.

According to Coan, there is currently a strong push within the field of neuroscience and psychology in general for something called “direct replication” (Klein et al. 2014)—a push that he finds both charming and naive. His real beef, however, is that some are taking this push to mean what might be called “replication failure” (my phrase, not Jim’s) is not just a worry confined (to succumb to a bit of word play) to the boudoir. Failure to replicate, real or perceived, evidently is giving rise to a rash of social nastiness he labels Negative Psychology that strikes me as being akin (or so it would seem) to the worst excesses of the post-modernist critique. “When we criticize each other using the tropes of Negative Psychology—that is, with moral outrage, hostile humor, and public shaming—we train the public to either disregard science altogether, or . . . to confuse outrage with rigor.”

While Coan points his finger as one case in point at Neuroskeptic anon., the latter in response has pleaded not guilty. In fact, Neuroskeptic anon. says he (or she) and Coan are on pretty much the same page and wavelength, and darnitall Jim would know this if he had bothered to read everything Neuroskeptic anon. has written in her (or his) blog over the years since ca. 2008.

I am not sure I should confess this, but I am not a great fan of blog sites. Until Jim’s entry into the fray (his first, by the way) I had paid scant attention to Neuorskeptic anon.’s corpus of writings on the web. Nor do I want to weigh in now as a qualified referee for minding the rules of the noble art of blog boxing. But I do agree with Coan on one thing.

He begins his own blog piece with this statement: “People on all sides of the recent push for direct replication—a push I find both charming and naive—are angry.” I think I know charm when I see it, and I don’t find much that is charming about what’s happening in the sciences of the psyche. But I do think the word naive is worth taking to heart.

According to some, skepticism is fashionable these days, and not just in psychology. One could argue, for example, that this is also a core tenet of climate-change deniers and the Tea Party in the U.S.A. Furthermore, who anywhere on earth could possibly deny that the replication of research results is the gold standard of scientific excellence?

Well maybe here and now and maybe me.

Perhaps more so than Jim Coan may be prepared to argue judging by his blog on Negative Psychology, I would at least like to cast a stone or two in that general direction. By focusing as he and Neuroskeptic anon. do on snark and snottiness at the core of modern skepticism in its many stripes, I think they may both be getting sidetracked from attending to a more central issue—namely why does anyone think research replication is such a good thing to do?

No doubt about it, failure to replicate research results may certainly be a flag on the field, but as Coan has said, anyone with a respectably nuanced view of why replications may fail knows they may do so for all kinds of reasons. What would be naive is to accept that not failing to replicate is proof of the pudding.

Why is this naive? Because doing the same thing over and over again in precisely the same way may amount to little more than making the same damn mistake over and over again–and thereby arriving at the same (erroneous) resolve over and over again. Said differently, direct replications that are just repetitions of the same-old same-old ought to be taken with a grain of salt and viewed with suspicion.

Now am I suggesting that like the United States in 1933 scientists should go off this gold standard? Maybe.

In 1966 the biologist Richard Levins published a paper on model building in population biology that has become a classic in the practice and philosophy of science (Levins 1966, 1993). I have long felt that Levins was leaning a lot on what Henri Poincaré (1905) and Alfred North Whitehead (1938) had written about such matters, and should have said so. Nonetheless, I am not alone in thinking what Levins wrote was inspirational and wise. And one of his main conclusions has become famous: “truth is the intersection of independent lies’’ (1966:423).

What he meant by this provocative statement has been richly discussed and debated (e.g., Levins 2006; Odenbaugh 2006; Orzack 2005;  Orzack and Sober 1993; Weisberg 2006a, 2006b). One of the pragmatic lessons, however, taken home after reading his paper (as indeed after reading Poincaré and Whitehead) is that for all sorts of reasons there is no such thing as the definitive single approach, experiment, or scientific model capable of capturing reality in all its chameleon-like complexity.

Therefore, as Levins wrote retrospectively in 2006, we need different ways of converging on the truths we are looking for. Consider this:

In the dispute about climate change, a rising temperature in several cities is suggestive. Adding more cities to the list gives a diminishing return. But independent lines of evidence—ocean temperatures, cores from glaciers, decline of coral reefs, spread of species into places that had been too cold for them, accumulation of greenhouse gasses—each may have some separate idiosyncratic explanation or source of error but jointly converge on an unavoidable conclusion. We have to seek lines of evidence as independent as we can in order to support a large scale conclusion. (Levins 2006:753)

Where am I going with this? The strategy Levins is talking about (as did Poincaré and Whitehead before him) is not the one at the heart of the current drive in psychology and other sciences to replicate evidently successful experiments others have done. No, instead the take-home directive is this one: Can we do a different experiment to see if we get the same resolve? And if not, why?

If this strategy were routine, then there would be no doubt about it. To repeat earlier experiments that led to different results if nothing else is a way to become more confident before making headlines with what we have just done that we have given others due and proper benefit of the doubt. But this wouldn’t be something that might be called “knee-jerk direct replication.” This instead would doing something called “just good science.”


Bohannon, J. 2014. Replication effort provokes praise—and “bullying” charges. Science 344:788–789.

Klein, R. A. Klein, K. A. Ratliff, M. Vianello, R. B. Adams Jr., Š. Bahník, et al. 2014.  Investigating variation in replicability: a ‘‘many labs’’ replication project. Social Psychology 45:142–152.

Levins, R. 1966. The strategy of model building in population biology. American Scientist 54:421–431.

Levins, R. 1993. A response to Orzack and Sober: formal analysis and the fluidity of science. Quarterly Review of Biology 68:547–555.

Orzack, S. H. and E. Sober. 1993. A critical assessment of Levins’s The strategy of model building in population biology (1966). 1993. Quarterly Review of Biology 68:533–546.

Odenbaugh, J. 2006. The strategy of ‘‘the strategy of model building
in population biology.’’  Biology and Philosophy 21:607–621.

Orzack, S. H. 2006. Discussion: what, if anything, Is “the strategy of model building in population biology?” A comment on Levins (1966) and Odenbaugh (2005). Philosophy of Science 72: 479–485.

Poincaré, H. 1905[1952]. Science and hypothesis, reprint ed. New York: Dover.

Weisberg, M. 2006a. Forty years of “the strategy”:  Levins on model building and idealization. Biology and Philosophy 21:623–645.

Weisberg, M. 2006b. Richard Levins’ philosophy of science. Biology and Philosophy 21:603–605.

Whitehead, A. N. 1938[1968]. Modes of thought, reprinted ed. New York: Free Press.

© 2014 John Edward Terrell. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. The statements and opinions expressed are those of the author(s) and do not constitute official statements or positions of the Editors and others associated with SCIENCE DIALOGUES.

Do men and women think differently?

Marc Kissel

Please note: this commentary, recovered on 28-Jan-2017, was originally published in Science Dialogues on 3-August-2014.

Years ago I mentioned to a group of female friends that I didn’t think men and women were really that different (well, besides the obvious ones). This caused quite the kerfuffle and led to the conclusion that I was an idiot. Yet, while it seems self-evident that men & women think differently this doesn’t mean that it is true . After all, it wasn’t too long ago were it was “obvious” that race was biology, that the sun circled the earth, and that jorts were a good idea.

A paper published last January caused quite the hubbub when it claimed to find significant differences between male and female brains (Ingalhalikar et al. 2014). Not tested in the paper, however, was whether those differences were cultural (in fact, the differences between sexes increased as the age of the children studied increased, which may suggest that something other than biology was at play).  A new study by Daniela Weber and colleagues (2014) investigates the role cultural factors may play in these apparent differences. They do so by examining cognitive task results from surveys of “nonindustrialized” men & women over 50 living in Europe, merging 13 countries into three regional groups and then comparing within and between these populations. The main results are shown in Figure 1.

Figure 1. Source: Webster et al. 2014.

For episodic memory (how well someone recalls a list of previously read words), women in Northern Europe have a higher average score than men, but the situation is more complex in other regions. Results differed in numeracy & category fluency categories based upon region as well. If you thought male/female difference were hard-wired, this shouldn’t be the case.

What causes these geographic differences? The Nick Wade’s of the world would probably suggest genetic differences are at the heart of the matter, but that does not seem to be the case. Instead access to education, along with other social factors, may be at the root of much of this.

Figure 2. Source: Webster et al. 2014.

This isn’t the clearest of figures. On the Y-axis is the average level of education for women minus that of men. When the number is negative, men on average spend a longer time in school than women do. On the X-Axis, is women’s cognitive performance minus men’s cognitive performance. I added colored lines at ‘0’ for each axis. Points to the right of the red line represent cohorts where women outperform men, while points above the blue line are when women have higher levels of education than men. As can be seen, in almost all cases men have reached higher education levels. It is interesting that, for episodic memory, as the mean years of differences in education years decreases, the difference between the sexes also decreases. Or as they put it: “These findings suggest that if women and men had equal levels of education, we should expect a female advantage in episodic memory, a male advantage in numeracy, and no gender differences in category fluency” (Weber et al. 2014:3).

In other words, reducing differences in access to education should lessen the differences in test scores.  Trying to discover sex-based differences without acknowledging the role cultural plays is always going to cause anthropologists to be wary so it is nice to see this acknowledged. As noted in the paper, there are many confounding variables that cannot be tested here and it is difficult to rule out  decline in mental acumen due to age-related cognitive decline. Further, I wonder about the geographic populations they define. What patterns would emerge if you didn’t group the 13 countries together in the same way as is done in this paper? Also interesting, though not really discussed, is that Northern Europeans (here represented by Denmark & Sweden) did better on all the cognitive assessments.

But it is always nice to see approaches that note that differences may be cultural rather than biological. Oh, and don’t get me  started on the blue = boys and girls =  pink nonsense.


Ingalhalikar, Madhura, et al. “Sex differences in the structural connectome of the human brain.” Proceedings of the National Academy of Sciences 111.2 (2014): 823-828.

Weber, Daniela, et al. “The changing face of cognitive gender differences in Europe.” Proceedings of the National Academy of Sciences (2014): 201319538.

Marc Kissel (Ph.D, University of Wisconsin-Madison) is a native New Yorker transplanted into the wilds of the Midwest. His dissertation examined genetic models that try to explain why humans are so inbred compared to the living apes and asks if these models conform to anthropological reality (spoiler alert: they don’t!). He is interested in human evolution and likes to apply mathematical models, genetic data, and anthropology to questions about our evolutionary history (especially Neandertals). Currently he is a postdoc at Notre Dame studying the evolution of wisdom. You can find him him on Twitter @MarcKissel
© 2014 Marc Kissel. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. The statements and opinions expressed are those of the author(s) and do not constitute official statements or positions of the Editors and others associated with SCIENCE DIALOGUES.

Reconfiguring biological diversity 2. Coming to grips with diversity

John Edward Terrell

This is part 2 of a two part article

Coming to grips with diversity

Perhaps the greatest stumbling block to deciphering how biological diversity is patterned, or structured, in space and time within any given species is that most existing ways of modeling such diversity presuppose that genes are nested in some fashion within demonstrable and persistent primary units that can be labeled as populations, subpopulations, demes, communities, stocks, races, and like. Yet is this how biological reproduction works? Aren’t genes perfectly capable of “escaping,” so to speak, from such allegedly defining and confining “boxes” through the very acts of reproduction, reassortment, growth, and development?

It could be argued that there is irony in the fact that molecular genetics now has made it possible for scientists to map diversity at the genetic level. Yet many are still given to thinking about diversity as if they were compelled by the old limitations of their laboratory techniques to lump this new fine-grained evidence into inclusive nested sets (e.g., Pritchard et al. 2000; Greenbaum et al. 2016; Skoglund et al. 2016).

Perhaps it is not surprising, therefore, that some have concluded that “the observed pattern of global gene identity variation was produced by a combination of serial population fissions, bottlenecks and long-range migrations associated with the peopling of major geographic regions, and subsequent gene flow between local populations” (Hunley et al. 2009).

All three of these identified processes are plausible reasons for biological diversity in time and space. But aren’t all three of these population-level explanations ignoring individual agency and decision-making? Not to mention love, lust, and human compassion?

Moving beyond population modeling

Current population-level modeling based on molecular genetics is arguably an advance over older metapopulation models framing diversity as an ever-changing flux within species among discrete subpopulations inhabiting separate habitat patches linked by migration and extinction (Fig. 2). Certainly few today would accept that diversity within any species can be adequately explained solely or even largely as the product of fluctuating colonization and extinction events.

Figure 2. A simple metapopulation model at two time periods (A and B) attributing spatial diversity to a shifting dynamic of colonization and extinction events.

Similarly, the concept of the fitness landscape (also known as as an adaptive landscape; see Fig. 3) introduced by the geneticist Sewell Wright in 1932 is another long-debated way of modeling the dynamic interplay—or balance—of a number of plausible determinants of genetic variation in space and time. As Wright explained in 1932:

The most general conclusion is that evolution depends on a certain balance among its factors. There must be gene mutation, but an excessive rate gives an array of freaks, not evolution; there must be selection, but too severe a process destroys the field of variability, and thus the basis for further advance; prevalence of local inbreeding within a species has extremely important evolutionary consequences, but too close inbreeding leads merely to extinction. A certain amount of crossbreeding is favorable but not too much. In this dependence on balance the species is like a living organism. At all levels of organization life depends on the maintenance of a certain balance among its factors. (Wright 1932)

Figure 3. “Field of gene combinations occupied by a population within the general field
of possible combinations. Type of history under specified conditions indicated by relation
to initial field (heavy broken contour) and arrow.” Source: Wright 1932, fig. 4.

A “balance of factors” sounds right and reasonable, but are the ones he mentions the only major factors that must be taken into account? Surely adaptation is not the only driving force of evolution?

Agency and social networks

Consider the observation that human beings are notably variable in stature, weight, and other characteristics of their appearance. Clearly the gene mutations supporting such phenotypic variation have not resulted in what Wright would describe as “an array of freaks.” Evidently such diversity is not selected against—to use Wright’s way of framing the discussion. Why? Because much of the burden of human adaptation does not need to be genetically endowed. Instead, as most social scientists would insist, much of what we do supporting our survival and reproduction is accomplished using socially learned skills rather than by genetically inherited biological means.

Recently Greenbaum and his colleagues observed that the research strategies and tools of modern network analysis are increasingly being used to explore genetics questions in genomics, landscape genetics, migration-selection dynamics, and the study of the genetic structure of species more generally speaking (Greenbaum et al. 2016).

Adopting a networks approach to genetics makes it possible to come to grips not only with the ways in which racism—to return to Roseman’s point raised earlier—has shaped human variation in the past few hundred years, but also how our species’ mobility, adaptive skills, technologies, and social behaviors have been configuring human variation throughout the history of our species.

Figures 4 and 5 illustrate the potential value of using of network analysis in the study of genetic diversity. The first figure is a network mapping of localities reported in a genome scan published in 2008. While the patterning is complex, there is an obvious geographic signal in the genetic linkages shown. Figure 5 resolves the relationships among a smaller subset of the localities that had been sampled, specifically those in the Bismarck Archipelago-North Solomons region of the southwest Pacific.

Figure 4. Spring-embedding network mapping of the localities sampled in a genome scan of autosomal markers (687 microsatellites and 203 insertions/deletions) on 952 individuals from 41 Pacific populations). Mapping derived from the mean STRUCTURE assignment probabilities when K = 10 reported by Friedlaender at al. (2008) color-coded by geographic location. Blue-white = Asia; blue = Taiwan; black = Europe; red = Polynesia; pink = Micronesia; yellow = New Britain; purple = New Guinea; dark green = North Solomons; green = New Ireland; light green = New Hanover; pale green = Mussau. Source: adapted from Terrell 2010b, fig. 3.


Figure 5. Nearest-neighbor structuring of interaction among the localities sampled in the Bismarck Archipelago and North Solomons color-coded to show genetic clustering (blue nodes represent locations not represented in the genetic scan). Source: Terrell 2010b, fig. 11.Both network mappings suggest that geography has influenced the structuring of genetic similarities among people living in the sampled localities shown. Yet it also is apparent that the linkages shown may often be closer than geographic distance alone would lead us to expect. Judging by figure 5, the effect of isolation by distance is evidently constrained by social networks (as projected in this figure using nearest-neighbor linkages). Hence while geographic distance may be contributing to the patterning of genetic diversity among people in this part of the world, geography is by no means the whole story.

The network analysis briefly introduced in figures 4 and 5 had two principal aims, one phylogenetic, the other tokogenetic (Terrell 2010b). Do people living today in the Pacific segregate genetically along lines concordant with the reputedly separate (i.e., cladistic) histories of languages spoken there, principally the divide drawn by linguists and others between speakers of Austronesian and non-Austronesian (Papuan) languages (Terrell 2006)? To what extent does the genetic similarity among people living in different residential communities correlate with the nearest-neighbor propinquity of these sampled places?

Neither of these aims presuppose that the research goal is to define genetically discrete human populations (or subpopulations, demes, groups, communities, races, and the like) either a priori or by using, say, individual-based clustering (IBC) methods (e.g., Ball et al. 2010).

These two aims have more in common with those of the emerging field of landscape genetics (Dyer and Nason 2004; Garroway et al. 2008) than with most previous research in population genetics. However, both of these aims focus more directly on the genetic consequences of the behavior of organisms in space and time—in this case, humans—than on the geography, ecology, and environmental history of the locales where the people in question reside.

Both can also be seen as stepping back from Roseman’s observations about the impact of racial politics and social practices on the human genome in the past few centuries to underscore a more general issue in evolutionary biology: How much do the mobility and social behavior of individuals within any given animal species structure the genetic variation of that species?

As Dyer and Nason (2004) have remarked: “The evolution of population genetic structure is a dynamic process influenced by both historical and recurrent evolutionary processes.” Using network theory and visualization techniques to map the genetic structure of a species in space and time is still in its infancy. Reconfiguring how science grapples with the inherent complexity of evolution as an ever unfolding process using network approaches has the promise of making it easier to explore how comparable or dissimilar species are in their strategies for survival and reproduction (Fortuna et al. 2009).

Looking long and hard at what other species do to survive and reproduce may make it easier for us to see just how toxic our own social strategies—and the assumptions supporting them—can be.


I thank Neal Matherne and Tom Clark for their comments on a draft of this commentary.


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© 2017 John Edward Terrell. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. The statements and opinions expressed are those of the author(s) and do not constitute official statements or positions of the Editors and others associated with SCIENCE DIALOGUES.

In the works: Mating, variation, and speciation: An interdisciplinary conversation

Source: https://commons.wikimedia.org/wiki/File:Limenitis_archippus_mating_2.jpg

While using network theory and visualization techniques to map the genetic structure of species in space and time is in its infancy, reconfiguring how science grapples with the inherent complexity of evolution as an ever unfolding process using network approaches has the promise of making it easier to explore how comparable or dissimilar species are in their strategies for survival and reproduction. Looking long and hard at what other species do to survive and reproduce may also make it easier for all of us to see just how toxic our own social strategies—and the assumptions supporting them—can be.

Darwin’s use of “use” and “disuse” (Part 3)

Tom Clark

Please note: this commentary, recovered on 8-Jan-2017, was originally published by the author, Tom Clark, on Science Dialogues on 14-Mar-2015.

DARWIN IS CREDITED with dethroning humans from their special place between animals and angels. As Copernicus had done astronomically, so had Darwin biologically.

Pryor Mountain Wild Horse Range, Montana. http://www.blm.gov/pgdata/etc/medialib/blm/mt/blm_programs/whb.Par.0228.Image.198.149.1.gif

But Darwin achieved continuity of humans with animals as much by humanizing animals as shrinking humans. Resisting “the too-ready ascription of action to instinct” (Beer 2009: 242-255), Darwin imagined that horses “admired a wide prospect,” baboons had “capacious hearts,” earthworms made aesthetic choices, and snails showed “some degree of permanent attachment.” He did not imagine that biology could benefit, as physics had, by abandoning animism, animals being so . . . animistic.

It was the neo-Darwinian assumption that genes and environments were sufficient causes of animals’ behavior that turned natural selection from an animate doing into a physical happening. Attributing behavior to stable causes both inside (molecules) and outside (environment) turned animals into spectators, along for the ride. Their mental lives were made redundant in the British sense of unemployed. (Compare John and Gabriel Terrell’s thoughts about self-generated, stimulus-independent, internally directed thought in their March 3 post Thinking about Thinking 2. Through the Looking Glass.)

Misreading Darwin’s use of use and disuse as simply Lamarckian enabled the neo-Darwinian demotion of both humans and animals, as meaningful roles for ancestors and Gods were, like baby and bathwater, summarily thrown out.

The word purpose is singularly inapplicable to evolutionary change … If an organism is well adapted … this is not due to any purpose of its ancestors or of an outside agency, such as “Nature” or “God” … (Mayr 1961: 1504).

The purposeful activities of ancestors were not final or ultimate causes. They were some among many causes. Yet they were bundled with God’s finality and dismissed. In the last paragraph of Origin of Species (Darwin 1860: 490) between his “entangled bank” metaphor and the poetic “endless forms most beautiful,” Darwin summarized the key elements of his theory. Two have been pushed to the edges of mainstream evolutionary thought, the ultimate activities of “the Creator” and the contingent activities of ancestors—”use and disuse.”

In the margins of an article by Wallace, Darwin wrote “use of moral qualities” (Greene 1981: 102), telegraphing a view of our moral origins that insinuated these dignifying lines of descent:

  • Life is inherently autonomous.
  • Autonomy has evolved (Rosslenbroich 2014).
  • Nervous systems support flexible, adaptive responding.
  • Vertebrates specialized in intention, allowing metabolic support for increasingly larger brains (Wrangham 2009).
  • Birds and mammals made relationships vital heritable resources (Kemp 2006), expanding autonomy by cooperating in relationships of secure dependence and interdependence.
  • Humans extended these achievements with ethics (Boehm 2012) and friendship (Terrell 2015).

The twentieth century dethroning of humanity carried out in Darwin’s name clipped human dignity more than Darwin intended. The following affirmations return to the evolutionary image of ourselves buds of autonomy and responsibility that Darwin was careful to leave on our family tree.

affirmWhen we consider the evolutionary role of animal behavior—or as we also say, ancestors’ activities—scientific theory becomes human nature mythology, the telling of which must be recognized as a moral act (Bock 1994: 8). The moral significance of our origin story hits home with the realization that how we tell this story can leverage or constrain personal and collective action toward sustainability (Clark and Clark 2012), peace and justice (Chorover 1979; Oyama 2000; Novoa and Levine 2010).

The sense we make of ourselves and each other shapes who we become, including our capacities for learning, cooperation and self-regulation. “Knowing” that intelligence is fixed inhibits learning (Blackwell et al. 2007). “Knowing” that personality attributes are inherited impels hasty negative judgments of others, foreclosing opportunities for constructive encounter (Dweck 2000). “Knowing” that free will is illusory engenders cheating (Vohs and Schooler 2008) and aggression (Baumeister et al. 2009). “Knowing” that humans are selfish by nature favors policies that crowd out reciprocity and trust, inducing selfish behavior (Bowles 2008). And “knowing” that metabolism is natural while intention remains a supernatural specter (Mayr 1982) hedges responsibility for our extended metabolism—energy consumption—compromising our ability to regulate our own inventions.

Knowing there is a choice to make and it matters what we choose to do prepares us for wising up to shared responsibilities and cooperating in the good use of resources.

Biologists rightly argue that a clear understanding of our evolutionary past must inform our plans for a sustainable future (Vermeij 2010: 253). Explaining the evolution of sighted animals as a blind process blinkers our understanding of the past, so also our outlook. Envisioning and motivating sustainable living is better served by an origin story that includes the vision and intentions of ancestors.

Evolution is not only what happened to our ancestors while they were busy making other plans. Ancestors did not plan our evolution, but their plans, successful or not, with consequences intended or not, were part of the story.

In the way he used use and disuse, Darwin recognized our ancestors’ part in how we came to be and our part in resolving where we go from here. By affirming our autonomy and interdependence, Darwin’s origin story also demands of us continued use of our moral imaginations.


Baumeister, R. F., E. J. Masicampo, and C. N. DeWall (2009). Prosocial benefits of feeling free: disbelief in free will increases aggression and reduces helpfulness. Personality and Social Psychology Bulletin 35: 260–268.

Beer, G. (2009). Darwin’s Plots (3rd ed.). Cambridge: Cambridge University Press.

Blackwell, L. S., K. H. Trzesniewski, and C. S. Dweck (2007). Implicit theories of intelligence predict achievement across an adolescent transition: a longitudinal study and an intervention. Child Development 78: 246–263.

Bock, K. (1994). Human Nature Mythology. Urbana: University of Illinois Press.

Boehm, C. (2012). Moral Origins. New York: Basic Books.

Bowles, S. (2008). Policies designed for self-interested citizens may undermine ‘the moral sentiments’: evidence from economic experiments. Science 320: 94–112.

Chorover, S. L. (1979). From Genesis to Genocide. Cambridge: MIT Press.

Clark, T. and E. Clark (2012). Participation in evolution and sustainability. Transactions of the Institute of British Geographers 37: 563–577.

Darwin, C. R. (1860). On the Origin of Species (2d ed.). In J. van Wyhe, ed., 2002 The Complete Work of Charles Darwin Online(http://darwin-online.org.uk).

Dweck, C. S. (2000). Self Theories. Philadelphia: Psychology Press.

Greene, J. C. (1981). Science, Ideology, and World View. Berkeley: University of California Press.

Kemp, T. S. (2006). The origin of mammalian endothermy: A paradigm for the evolution of complex biological structure. Zoological Journal of the Linnean Society 147: 473–488.

Mayr E. (1961). Cause and effect in biology. Science 134, 3489: 1501–1506.

Mayr E. (1982). The Growth of Biological Thought. Cambridge: Harvard University Press.

Novoa, A. and A. Levine (2010). From Man to Ape. Chicago: University of Chicago Press.

Oyama, S. (2000). Evolution’s Eye. Durham: Duke University Press.

Rosslenbroich, B. (2014). On the Origin of Autonomy. Cham: Springer.

Terrell, J. E. (2015). A Talent for Friendship. Oxford: Oxford University Press.

Vermeij G. J. (2010). The Evolutionary World. New York: St. Martin’s Press.

Vohs, K. D. and J. W. Schooler (2008). The value of believing in free will: encouraging a belief in determinism increases cheating. Psychological Science 19: 49–54.

Wrangham, R. (2009). Catching Fire. New York: Basic Books.

Tom Clark

As a psychologist, I have been interested in the role of behavior in evolution since my graduate training at the University of South Florida.



© 2015, Thomas L. Clark. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. The statements and opinions expressed in this article are those of the author(s) and do not constitute official statements or positions of the Editors and others associated with SCIENCE DIALOGUES.



Darwin’s use of “use” and “disuse” (Part 2)

Tom Clark

Please note: this commentary, recovered on 8-Jan-2017, was originally published by the author, Tom Clark, on Science Dialogues on 7-Mar-2015.

AT CHICAGO’S CENTENNIAL CELEBRATION of Origin of Species, Julian Huxley (1960: 14) attributed to Darwin this “Lamarckian error”:

… he did believe in the inheritance of certain “acquired characters”—the effects of the conditions of life and of use and disuse.

Though Darwin had been careful to use the terms use and disusedescriptively in Origin of Species, Huxley took them as categorically Lamarckian, a separate alternative to natural selection that did not mingle with it.

Ernst Mayr also presented Darwin’s thinking about use and disuse as singularly Lamarckian, in support of which he quoted from Origin of Species (1859: 134):

There can be little doubt that use in our domestic animals strengthens and enlarges certain parts and disuse diminishes them; and that such modifications are inherited.

Underscoring his Lamarckian take on Darwin, Mayr adds (1982: 691):

Use and disuse, of course, is of importance only if one believes in an inheritance of acquired characters. This Darwin affirms repeatedly … Darwin is quite positive: “Modifications [caused by use and disuse] are inherited.”

Standing alone, the sentence Mayr quotes from Origin of Species looks like a Lamarckian match. With each step back to see it in context, the resemblance fades.

In the next sentence, Darwin (1859: 134) refers to “… the effects of long-continued use and disuse,” not one generation to the next.

In the same paragraph he places use and disuse in the situation of stable selection pressures, offering as examples the “… wingless condition of several birds, which … inhabited several oceanic islands tenanted by no beasts of prey.”

On the next page he explicitly rejects Lamarckian inheritance of mutilations.

On the following page he clarifies “long-continued,” referring to “thousands of successive generations.”

And throughout Origin of Species, Darwin uses “acquired” only in reference to species across many generations in the context of specific selection pressures, not in the Lamarckian sense of individuals transmitting from one generation to the next characteristics acquired during their lifetimes.

In context, the “domestic animals” Darwin drew to our attention were domesticated species, not his neighbor’s individual dogs. Darwin saw species acquiring traits that became heritable when long-continued activities shaped selection pressures.

Jean Gayon repeated Mayr’s Lamarckian misreading of the identical quote from Origin of Species a decade later (1998 [1992]: 150).

Gayon is in the good company of many besides Huxley and Mayr. Science educators bemoan their failure to convince students that natural selection “does not involve effort, trying, or wanting” or “organisms trying to adapt” (Understanding Evolution, 2014). When their students accurately intuit that evolution has produced animals capable of effortful adaptation and these efforts can affect selection processes, this is considered “a significant departure from a scientific understanding of how animals change via natural selection” (Kelemen 2012: 71).

Huxley, Mayr, Gayon and science teachers stumbled over that ordinary and useful habit of thought, categorizing, while overlooking Darwin’s earnest doubts about the categories of his cultural inheritance (Beer 2009: xxx). The terms use and disusegrew into their common biological usage during the Lamarckian half-century that preceded Origin of Species. While Darwin was growing up, they acquired conceptual, social and political significance beyond concrete reference to specific animal activities. For many, the terms were synonymous with Lamarckian inheritance. Lamarckism has been called use-disuse theory.

When Darwin used these terms, he knew the importance of their secondary meanings for his readers. He also recognized the scientific and public relations merits of using these familiar terms for animal behavior in a more descriptive, pared down way.

Scientifically, he advanced more modest claims of animal agency than Lamarckian use of the terms. Darwin’s descriptive use of use and disuse created conceptual space for a developmental view of evolution that was not Lamarckian.

At the same time, Darwin wanted his readers to follow his argument and not give up on it. Pushing against the constraints of traditional terms by using them in nontraditional ways, Darwin’s “generous semantic practice” (Beer 2009: 33) allowed the reader to adjust their own yoke to the terms use and disuse. From his calibrated ambiguity, readers could hear in the text such Lamarckian overtones as their sensibilities favored.

Darwin’s semantic generosity quickened after publication of Origin of Species, as he responded to waves of criticism with a strategic retreat toward inclusiveness. In Variations of Animals and Plants under Domestication (1868), “anything which had been documented and accepted by a fellow scientist was included and assessed” (Vorzimmer 1963: 386). Darwin admitted for discussion a provisional hypothesis of Lamarckian inheritance that he had carefully avoided in Origin of Species. Darlington (1959: 41) complained that during this time “ambiguity … became the mode and standard of Darwin’s expression … which in the end soothed and satisfied the troubled world.”

As he changed successive editions of Origin of Species – to his wife Emma’s delight, adding “the Creator” in the second edition – Darwin remained committed to respectful, empirical inquiry that doubled as good public relations for his theory.

Bufflehead, Morro Bay State Park CA. by Kevin Cole 2008. http://commons.wikimedia.org/wiki/File:Male_Bufflehead_taking_off.jpg

While molecules eclipsed the behavior and development of whole organisms in 20th century evolutionary thought, accounts from Darwin’s vantage point persisted. Nobel physicist Erwin Schrödinger (1944: 113) echoed Darwin most clearly.

You simply cannot possess clever hands without using them for obtaining your aims… You cannot have efficient wings without attempting to fly… Selection would be powerless in ‘producing’ a new organ if selection were not aided all along by the organism’s making appropriate use of it….

Joining Huxley at Chicago’s centennial celebration of Origin of Species, Conrad Waddington (1959: 1636) presented a model of evolution that included animal choices.

Thus the animal by its behavior contributes in a most important way to determining the nature and intensity of the selective pressures which will be exerted on it.

Half a century on, Renée Duckworth (2009: 514) marked Origin’s sesquicentennial by reminding us that:

Changes in either the environment or an organism’s behavior can alter selection pressure. This places behavioral change on an equal footing with environmental change as a potential cause of evolutionary change … but despite the intuitive appeal of this idea, it remains largely unacknowledged in current evolutionary theory.

And Mary Jane West-Eberhard (2008: 902) rendered Darwin in contemporary terminology.

Much of Darwin’s discussion of … “use and disuse” refers not to Lamarckian inheritance but to what we would now call “phenotypic plasticity” [flexibility of the whole organism].


Beer, G. (2009). Darwin’s Plots (3rd ed.). Cambridge: Cambridge University Press.

Darlington, C. D. (1959). Darwin’s Place in History. Oxford: Basil Blackwell.

Darwin C. (1859) On the Origin of Species. In J. van Wyhe, ed. (2002), The Complete Work of Charles Darwin Online (http://darwin-online.org.uk).

Darwin, C. (1868). Variation of Animals and Plants Under Domestication. In J. van Wyhe, ed. (2002), The Complete Work of Charles Darwin Online (http://darwin-online.org.uk).

Duckworth, R. (2009). The role of behavior in evolution: A search for mechanism. Evolutionary Ecology 23: 513–531.

Gayon, J. (1992) [1998]. Darwin’s Struggle for Survival. Cambridge: Cambridge University Press.

Huxley, J. (1960). The emergence of Darwinism. In Evolution After Darwin, vol. I: The Evolution of Life, Sol Tax, ed., pages 1–21. Chicago: University of Chicago Press.

Kelemen, D. (2012). Teleological minds: How natural intuitions about agency and purpose influence learning about evolution. In Evolution Challenges: Integrating Research and Practice in Teaching and Learning about Evolution, Rosengren, K.S., S. K. Brem, E. M. Evans, and G. M. Sinatra, eds., pages 66–92. Oxford: Oxford University Press.

Mayr E. (1982). The Growth of Biological Thought. Cambridge: Harvard University Press.

Schrödinger E. (1944). What is Life? Cambridge: Cambridge University Press.

Understanding Evolution, University of California Museum of Paleontology, 01 January 2014 http://evolution.berkeley.edu/evolibrary/misconceptions_teacherfaq.php

Vorzimmer, P. (1963). Charles Darwin and blending inheritance.  Isis 543: 371–390.

Waddington, C. 1959 Evolutionary systems – animal and human. Nature 183 4676:1634-1638.

West-Eberhard, M. J. (2008) Toward a modern revival of Darwin’s theory of evolutionary novelty. Philosophy of Science 75: 899-908.

Tom Clark

As a psychologist, I have been interested in the role of behavior in evolution since my graduate training at the University of South Florida.



© 2015, Thomas L. Clark. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. The statements and opinions expressed in this article are those of the author(s) and do not constitute official statements or positions of the Editors and others associated with SCIENCE DIALOGUES.


Darwin’s use of “use” and “disuse” (Part 1)

Tom Clark

Please note: this commentary, recovered on 8-Jan-2017, was originally published by the author, Tom Clark, on Science Dialogues on 28-Feb-2015.

LIKE OTHER NATURALISTS OF HIS DAY, Darwin thought that when animals used their bodies in some ways and not others, doing this and not that, these activities affected the evolution of their kind. Insect wings and rodent eyes became larger or smaller, more useful or less, depending on their ancestors’ use or disuse of their wings and eyes.

Unlike his peers, Darwin imagined animal behavior influencing evolution without Lamarckian inheritance of acquired characteristics. His most important discovery, natural selection, allowed him an alternative. Instead of direct transmission, from one generation to the next, of changes brought about by an animal’s activity within its lifetime, Darwin saw that such activity affects both how animals grow into adults—variation—and how natural selection plays out. And by way of long continued selection outcomes, characteristics expressed while growing up—specific variants—can become, somehow, more likely to develop in later generations. Hence, evolution.

Stretching to browse on trees did not cause giraffe ancestors to have offspring with longer necks. Rather, giraffe ancestors’ browsing habits swayed selection so giraffes that grew longer necks tended to have more offspring.

Giraffa_camelopardalis (5)
Photograph of Giraffa camelopardalis by Scott Harrison, Kruger Park 2006. http://commons.wikimedia.org/wiki/File:Giraffa_camelopardalis.JPG#file

Growing up mattered. Darwin observed variation among whole animals through their lifetimes, not variation among genes. Anything that made a growing child “not absolutely similar to the parent” was a source of variation that could make a difference in selection processes and outcomes (Darwin 1857). Darwin’s view was developmental, not Lamarckian.

Darwin understood that separating variation and selection was tidier in theory than in actual lives-in-progress. He took up his discussion of use and disuse in a chapter called “Laws of Variation” with a subheading “Use and disuse, combined with natural selection” (Darwin 1859: 131, italics added). What animals did with whom was a central and natural aspect of selection, as well as a source of variation. Animal behavior comprised and induced variation that was grist for selection and also part of the mill.

So he shows us in Origin of Species (1859: 136–143) that “the wings of some of the insects have been enlarged, and the wings of others have been reduced by natural selection aided by use and disuse.”

The wingless condition of so many Madeira beetles is mainly due to the action of natural selection, but combined probably with disuse.


The eyes of some burrowing rodents are rudimentary in size… probably due to gradual reduction from disuse, but aided perhaps by natural selection . . . natural selection would constantly aid the effects of disuse.


On the whole, I think we may conclude that habit, use, and disuse, have, in some cases, played a considerable part in the modification . . . of various organs; but that the effects of use and disuse have often been largely combined with, and sometimes overmastered by, the natural selection of innate differences.

Animals were protagonists in Darwin’s evolutionary plots. Theirs was an unwitting participation, animal intentions being of evolution, not about evolution. Still, animals’ semi-autonomous activities affected the evolution of their own kind and of others who came to their attention. Darwin saw, for example, that arbitrary “aesthetic” preferences of pollinating insects—going to these flowers more than those—affected selection of the flowers and of the insect’s nose, used to reach that flower’s nectar.

Darwin concerned himself with mechanisms of biological inheritance but had limited evidence to go on. Mendel published his experiments on plant hybridization in 1865 but with just three citations in 35 years, they never came to Darwin’s attention. Though he eventually proposed a Lamarckian mechanism of inheritance in his “provisional” hypothesis of pangenesis, Darwin continued to view the role of animal behavior in evolution as more developmental than Lamarckian. Animal activity naturally “either checked or favored” selection (1868: 234).

His developmental view of evolution endured August Weismann discerning a “barrier” between somatic and germ cells. Weismann’s famous barrier, allowing transmission of only germ cells to the next generation, was the death knell for Lamarckism. Yet Weismann affirmed Darwin’s view that “use and disuse” affected evolution by way of natural selection.

Weismann contrasted “mere disuse” with its consequence that “natural selection ceases to act” (1889: 15–16). By this relaxation of selection, disuse induced evolutionary change. Regarding use,

. . .  the direct influence of increased use during the course of a single life [cannot] produce hereditary effects without the assistance of natural selection (1889: 91).

And with the assistance of natural selection, it can.

. . . the use and disuse of parts can have no direct share in the process. . . . The fact, however, that we deny the transmission of the effects of use and disuse, does not imply that these factors are of no importance. . . . both use and disuse may lead indirectly to variations . . .  [that change selection processes and outcomes] (Weismann 1893: 395–396).

Darwin’s developmental view fell to the margins of evolutionary thought with the rediscovery of Mendel’s experiments that began the 20th century and initiated its turn toward a molecular gaze. In an historic cultural shift dubbed “bath-waterism” (Ewer 1960: 162), evolutionary thought threw out, along with the bath water of Lamarckism, the whole organism as an agent of evolutionary change. Evolutionary science transformed our image of ourselves from protagonists in the story of life to products of natural laws and chance, from the result of ancestors’ doings to the result of chemical happenings.

Our story changed from processes of selection that naturally had the benefit of vision and other senses and capabilities for the past 600 million years to “blind” selection the whole way; from an understanding that manners maketh the man, and action maketh the organism, to an understanding that tiny entities inside us make us who we are; from a story at the scale of organisms and lifetimes to a story about molecules across eons; from a story that includes growing up to a story that moves from one adult generation to the next by incantations of genes, environments and their so-called “interactions” (genes, of course, interact only with intra-cellular environments); from plot without humans to humans without plot; from a story teeming with human agency and meaning to a story of eggs regarding chickens as merely a way to make more eggs; from a story that tells us of life’s expanding autonomy, so what we do matters, to a story that tells us choice is a comforting illusion so we have no say in the course nature takes.

Among the ideas slanting these images of ourselves has been a misreading of Darwin’s use of use and disuse as simply Lamarckian.


Darwin, C. (1857). Letter to Asa Gray, 5 Sept. http://www.darwinproject.ac.uk/entry-2136.

Darwin C. (1859). On the Origin of Species. In J. van Wyhe, ed., (2002), The Complete Work of Charles Darwin Online (http://darwin-online.org.uk).

Darwin, C. (1868). Variation of Animals and Plants under Domestication. In J. van Wyhe, ed., (2002), The Complete Work of Charles Darwin Online (http://darwin-online.org.uk).

Ewer, R. F. 1960 Natural selection and neoteny. Acta Biotheoretica13:161-184.

Weismann, A. (1889). Essays Upon Heredity. Oxford: Clarendon Press.

Weismann, A. (1893). The Germ Plasm. New York: Scribner.

Tom Clark

As a psychologist, I have been interested in the role of behavior in evolution since my graduate training at the University of South Florida.



© 2015, Thomas L. Clark. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. The statements and opinions expressed in this article are those of the author(s) and do not constitute official statements or positions of the Editors and others associated with SCIENCE DIALOGUES.