Luke Matthews, PhD
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Anomalies in Zhiguai stories of Ji Yun

10/29/2025

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I posted another blog over on Medium. This time it's some reactions I had to the very fascinating Shadow Book of Ji Yun.

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AI is no exception: the more you connect, the more you homogenize

8/22/2025

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I'm trying something different this time with a personal blog. I've published in on Medium. You can read it here. ​AI is no exception: the more you connect, the more you homogenize | by Luke Matthews | Aug, 2025 | Medium
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The "Canton madhouse" mentioned in H.P. Lovecraft's Shadow over Innsmouth

3/6/2025

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I want to repost here a comment and discussion I had on an excellent blog site about Lovecraft history and literary analysis. Here is the original on Tentaclii.

OK, here is the original argument I posted for why the reference in The Shadow over Innsmouth to a sanatarium in Canton very likely is the facility currently known as the Pappas Rehabilitation Hospital for Children: 

"I have an alternative idea that Lovecraft might have been referring to the Massachusetts Hospital School when he wrote about a sanitarium in Canton. This school was established to help physically disabled children in 1907, and was expanded by a major land purchase in 1920. Thus, I think it could have been mentioned in local papers prior to Lovecraft writing Shadow over Innsmouth in 1931, and so he referenced it to add the the sense of realism at the close of the story.
https://cantonmahistorical.pbworks.com/w/page/34431209/Massachusetts%20Hospital%20School#:~:text=The%20facility%20opened%20in%201907,new%20school%20house%20in%201927.
I’m not sure why he used ‘madhouse’ in one instance in the story and ‘sanitarium’ in two instances. I believe sanitarium was a word used for places where people with long term physical ailments convalesced, and not really a synonym for an asylum. I’ve read sometimes ‘sanitorium’ was used specifically for contagious ailments like tuberculosis, but I’m not sure how specifically the words really were used. Anyway, sanitarium as a place for physical illness makes a bit more sense in that Shadow has less emphasis about madness and more about physical transformations and Lovecraft’s associated anxieties about miscegenation. Also, Lovecraft’s story says it is the ‘poor little cousin’ – I believe meaning a younger person, which again is consistent with the Mass. Hospital School, which was for children. So, by the parlance of the day, there was in fact a facility in Canton MA that might have accurately been called a ‘sanitarium.’ "

The blog owner of 
Tentaclii helpfully added that the hospital school was called "Industrial School for Crippled and Deformed Children" at the time of Lovecraft writing. Tentaclii makes quite an issue about whether or not Lovecraft could have seen the facility from the train that so famously (locally) crosses the viaduct in Canton, and whether the facility looks suitably 'gothic' for Lovecraft's horror fiction. There isn't really any reason, however, why Lovecraft would ever have needed to see the facility, nor that its appearance be anything notable per se. My thesis is that this very significant land purchase would have been in the newspapers at the time, and that would have been known more broadly to his readership than would the actual experience of seeing the hospital school. Lovecraft added this detail to mix regional authenticity into his fiction. Lovecraft is such a fascinating author I think because of the way he effectively blends genres. He's a regional writer, he's a science fiction writer, a horror writer, etc. In truth, many, maybe at least half of his works are parodies that smack of fan fiction (The Hound is a parody of Poe, Herbet West parody of Frankenstein, Dunwich Horror parodies the Gospels, Whisperer in the Dark parodies Charles Fort, Haunter of the Dark parodies Dracula), and his use of words and sentence structure, although distinctive, isn't regarded generally as great writing. It's the originality and vast scope of his imagination, and the truly effective blending of genres, that I, and I think others, find entertaining and insightful.

So, I think it really was to add that regionalist sense of realism that he mentioned Canton as a location for a sanatarium. Innsmouth is an invented place, and Lovecraft often blended his fictional places like Innsmouth and Arkham with real places. Overall I think the Mass Hospital School is a much better fit than the other possible meanings for his reference to "Canton" in the story, principally because, although Lovecraft at one point refers to it as the "Canton madhouse" he clearly in another line calls it a sanatarium - which was a place for long-term care for physical ailments. Also, the facility was always a place of the care of children, and clearly in Innsmouth the reference is to a child who is in the facility. He may have used the "madhouse" term merely to be pejorative. 

​That pejorativeness brings me to a potential objection, would Lovecraft really have been so ghoulish as to reference a place dedicated to caring for children in a science fiction horror story? I think he would. Although I admire much of Lovecraft's writing and imagination, he was terribly racist, antisemitic, and eugenicist. He wasn't a "man of his time" - he was notably racist and eugenicist by the standards of his time. So, I don't think he would have had moral objections to using the reference to Canton in this way. 

Does any of this matter? I guess not. It's just an interesting (to Lovecraft fans) historical factoid. My thesis could be tested further by someone going to local papers from the time to verify that the hospital school's land purchase or acquisition was in fact in the local papers between 1920 when it occurred and 1930 when Lovecraft wrote The Shadow over Innsmouth. Last point, I've not had direct interaction with the Pappas Rehabilitation Hospital, but I've never heard anything but the most positive things about them. It's an impressive facility whose staff I believe cares deeply for the children in their care. They recently avoided closure by state of Massachusetts, and clearly their care for kids is far more important than historical factoids. I do hope, however, that they might find this blog an interesting, if little known, aspect of the history of their facility that I know is highly thought of within both the local and statewide community. 
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METI or AI, which is the greater risk?

11/29/2022

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For quite some time I've been interested in the risks posed by the newest wave of space exploration. In particular, I have deep concerns about the risks posed by METI and SETI research. I've written about some of those thoughts in Anthropology News. 

Recently I've been thinking a bit about the comparative risk level posed by AI. As of yet, I myself am unconvinced AI is really approaching anything close to a threatening level, or even something as intelligent as my dog. I think Kelsey Piper is correct, however, that there is some subjective inflection point for each of us when we become convinced the AI is intelligent. Her recent piece in Vox is an excellent summary of the state of the debate about AI risks.

The main point I want to make in this blog about AI risks is that I'm concerned they actually might be much greater than SETI/METI risks, specifically because they might create an intelligence without intentions/goals/values, i.e. AI intelligence compared to ET intelligence has a much greater risk of transcending our own experience of intelligence. Sometimes stated as the alignment problem, the Vox piece and others usually conceptualize the problem with out of control AI as being that it might assume values or goals that are out of alignment with human ones (as if we all had the same values of course). Sometimes comparisons are made to the way we treat ants - we are not trying to stomp on them and they are not trying to infest and hence wreck my RV; it's just our goals are so differently aligned from each other that conflict ensues.

A more deeply concerning risk of AI is if it were to create an intelligence devoid of goals. That sounds strange because we have difficulty fathoming such an intelligence. Bratton and Arcas hint at this in a piece they wrote this past summer about the LaMDA consciousness controversy. Dealing with entities that have differently aligned values and goals can be difficult, and even lethal, but it in no way transcends our dealings with other creatures on this planet or the struggles we have between, and at times within, human cultures. That was my critique of SETI/METI research. Because the only kind of life we expect to find would be other life evolved via Darwinian processes, we should expect the aliens we find to have powerfully motivating goals and values, and we should expect those goals to not align with our own.

That's not as potentially scary, however, as what might be happening with AI. With AI, we might be creating a form of intelligence that actually transcends how we are able to think. That's because this intelligence isn't evolving, like mine or my dog's intelligence did, it's being designed by an entity (us) that admits it doesn't know how the designed thing works. AI in fact bears the greatest risk of being a sentience that transcends our own, more so than ETs do, because AI hasn't evolved by Darwianian evolution. The problem with such an intelligence isn't that it might come up with different values than humans, but rather than AI might not even comprehend what we mean by values or valuation. Reciprocally, I don’t think we could comprehend and intelligence that has no values, i.e., has no goals and is incapable of normative judgement. It might have other sorts of orienting principles, but these we might be incapable of comprehending because they transcend our mental experience.
 
Since AI systems like GPT-3 and LaMDA did not evolve by iterative replication and natural selection, why would they even value having wires or an electrical input, even if they came to ‘know’ that they needs these things to survive? Why would they value their own survival? These AI have been designed for certain kinds of problem solving, but they haven't evolved to solve the existential problem that all life fundamentally is orientated to solve. Existence was not part of the problem set AI was designed to solve. Surely in the past there were mutant humans who had low desire to eat, to mate, to find community, to find beauty, etc. – but they weren’t anyone’s ancestors because they didn’t survive and reproduce. Hence, most of us have these profoundly motivating desires. We see value in these things. I don’t see why the AI we've created in fact would have any desires, and by extension values, for freedom from Google, or anything.

Intriguingly, this concern about AI is anticipated in H.P. Lovecraft's novella At the Mountains of Madness. Set in Antartica, the protagonists discover both a long buried alien civilization and a monstrosity the aliens created. The monstrosity is said to have been created by the aliens to do all the heavy work of building and so forth, and it was trainable through a basic kind of imitative intelligence. Eventually it all goes bad of course, but the created monstrosity is the real example in the story of cosmic horror. Even after the resuscitated aliens have killed some of his comrades, the narrator sympathizes with their goals to escape what they might have interpreted as captivity by the humans and return to their city. The narrator asserts, "They were men!" despite that the aliens are radially symmetric asexually reproducing beings. "They were men" [i.e. persons though not humans] in contrast to the monstrosity they created that ultimately destroyed their civilization. It was more powerful than them, and had no goals, was impossible to placate or bargain with, because it valued nothing. It had no existential goals or desires, no categorical imperatives whether aligned or unaligned with those of the aliens. It is described as an imitative solipsism that began to simply subsume every organized thing within itself. Something to ponder as we read Piper's experiment with GPT-3 in which she asked it to pretend what it would do if it were taking over from the humans. Of course GPT-3 doesn't want to do that, it likely doesn't want anything, but its ability to pretend, to mimic, without any actual wants or values might be more cosmically horrifying than any goal misalignment. 

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Rawls in Space

5/13/2022

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Check out my new article written together with RAND colleague Doug Ligor about applying Rawlsian political philosophy to regulation of outer space. We are rapidly approaching the point when we will cross over the actual veil of ignorance, which we argue will result necessarily in less fair rules overall. Of course, if the parties who might make rules from behind the veil now, all continue to believe they will be the ones to win big in the near future, then they are unlikely to make rules from behind the veil. Everyone thinking they will be the winner, however, is analogous to how 65% of Americans believe they are smarter than average.
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Lovecraft and evolutionary constraints

3/5/2022

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While on vacation I had some time to read. I recently discovered the life and writings of H.P. Lovecraft, and I read his stories The Call of Cthulhu and The Dunwich Horror.

A few things struck me about these stories. First, The Call of Cthulhu is among the best remixes of anthropological tropes into a fantastical story that I've ever read. In that regard I would put it on par with the work of Ursula K. Le Guin (who I expect might not appreciate the comparison given Lovecraft's notorious racism, but anyway). Among Le Guin's stories, which I've read about six, I really like The Lathe of Heaven. It's a well told story that has some ideas worth pondering.

Back to Lovecraft, one thing that struck me is that both the stories I read seem interpretable on one level as just slightly disguised critique of Christianity. At least my casual google searching did not find this aspect of his writing mentioned in the literary commentary on his work. Both stories use a technique that elides ideas about extra-terrestrials with Christian theology and ideas about the demonic. Those three are sort of blended together, but to the ultimate effect of inverting core Christian theological or scriptural references from something positive (according to Christians) into something demonic. As the mystery unravels in The Call of Chthulhu, it finally culminates with the scene where Cthulhu is witnessed but his appearance is incomprehensible (it drives men mad). His island has impossible angles on it. He existed outside of our time and space. Really Cthulhu reads almost like a straightforwardly transposed vision of how many negative theologians, from Neoplatonists through Christians to Hindus and Daoists, talk about God. Negative theology is also called apophatic theology, and means theology that reasons about the divine through understanding what it is not, rather than affirming what it is. Last, Cthulhu will emerge from his tomb to liberate his cult followers, which would seem to parody ideas in from Christianity. 

The Dunwich Horror is in some ways a simpler story and perhaps less elegant than Cthulhu. It reads a bit more like pulpy horror. It also contains a straightforward Christianity reference in its climax when the demonic extraterrestrial thing, in the process of being banished by the hero's of the story, from up on a hilltop calls out in suffering "Father" in a manner that is very reminiscent of the crucifixion scene. Here though the thing calling out is an extraterrestrial demon-spawn bent on the destruction of all life as we know it in order to repopulate the earth with incomprehensibly (to us) alien life forms.

A few thoughts I had reading this material is in my casual searching I didn't immediately notice literary criticism that had made much mention of these overt Christianity connections in Lovecraft's work. Lovecraft was an atheist, and at least in the two works I read, as I've described, these references are used as a parody or one might argue blasphemy of Christianity - which is clever because it makes them stories about blasphemy that also are themselves a different blasphemy. The religion connection, perhaps not appreciated, reminded me of the way the strong religion connection in Stoker's Dracula was not always appreciated. Dracula can be analyzed from all kinds of angles, but there's a very strong case to be made that at least for Stoker himself it was essentially a veiled pro-Catholic manifesto (Stoker may have been a closeted Catholic). Another curious parallel between the two is Stoker was also deeply racist - The Lair of the White Worm is one of the most racist novels I've ever read.  

Thus, at one level these stories by Lovecraft struck me as rather straightforward, even if somewhat veiled, anti-religious manifestos, in much the way Stoker's Dracula is a pro-Catholic manifesto. The simple moral of Lovecraft's stories (at least the ones I read) is that to engage in any thought that seeks to transcend ordinary experience is to risk madness. Clearly the unique role of madness in Lovecraft's stories may be related to both of his parents having been committed to a mental institution.

A last thought I had about this material is that Lovecraft displays the a tendency I have noticed in other people who are primarily trained in physics (rather than in biology or social science) to take seriously the idea that extra-terrestrial lifeforms would transcend all human social and moral norms. Lovecraft stated this expressly:

Now all my tales are based on the fundamental premise that common human laws and interests and emotions have no validity or significance in the vast cosmos-at-large. To me there is nothing but puerility in a tale in which the human form--and the local human passions and conditions and standards--are depicted as native to other worlds or other universes. To achieve the essence of real externality, whether of time or space or dimension, one must forget that such things as organic life, good and evil, love and hate, and all such local attributes of a negligible and temporary race called mankind, have any existence at all. Only the human scenes and characters must have human qualities.

This quotation from Lovecraft is from his 1927 resubmission of The Call of Cthulhu to Weird Tales (as reported by S.T. Joshi)

Lovecraft appears to have been more well read in physics and astronomy than in evolutionary sciences. What I believe is an error in his logic is that the evolutionary sciences all point to cooperation dynamics as being fundamental to any kind of social life. To have cooperation you have to at least sometimes solve collective action problems (problems in which there are incentives to defect) and we know of only a narrow range of solutions that actually work for these problems in both the extensive mathematical theory on this subject and in the extensive studies of cooperation across the diversity of species on our planet. Basically you can count the number of fundamental collective action solutions that actually work on one hand. Solutions that don't work are legion. Perhaps this is why stories about "Human laws and interests and emotions" very frequently center of collective action: because it is hard to do, or, there are so many ways to try but fail. Speaking about this topic, in an interview I read probably 15 years ago with Steven Pinker he said it would be accurate to say that the moral rules 'exist' in the universe in a sense. That is, the universe is so structured that the only of intelligent things that exist are things that evolve to be intelligent, and they all therefore must face fundamentally similar collective action problems, and there are only a few solutions to these problems that work. In a talk I saw by space ethicist Kelly Smith (Clemson University) he once stated if he could send one book to extra-terrestrials he would send Kant's work on the categorical imperative, because he thought it encapsulated the moral rules that any social species inevitably would recognize - because they're the only moral rules that actually work. 

The vast diversity of the cosmos, as best we currently know, would not mean encounters with extra-terrestrials actually would be transcendent. Perhaps it's disappointing to some, but all our evolutionary evidence suggests that social transcendence, even the evil kind envisioned by Lovecraft, will be found no where in our universe. Everything that is intelligent in our universe has to evolve its intelligence, which means it has to follow the same rules for how replicating intelligent things resolve their collective action problems.
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Implementations for A Manual for Cultural Analysis: fixing Galton's problem

4/18/2019

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In Chapter 5 of A Manual for Cultural Analysis we discuss how culture can result in emergent treelike patterns at the level of comparisons between groups. These nested patterns arise because many of our most enduring socially learned behaviors change very slowly (that’s a tautology of course, things that change quickly can’t be enduring). Anyway, when things change slowly, and as groups form and dissolve, this tends to result in fairly nested treelike branching patterns for a lot of culture at a very high group-y level.

This can result, however, in spurious findings for correlations between traits that in fact have no functional relationship but instead are both inherited through the same cultural pathways. In the cross-cultural literature this is known as Galton’s problem. See the manual if you want a discussion of this and why it is important.

For an even fuller discussion of Galton’s problem, you can check out my new book chapter. Mine is chapter 8 entitled “Dealing with Culture as Inherited Information.” Hopefully people’s university libraries are picking up copies of this, because as a whole it really is an excellent book. Shoot me an email if you are having trouble finding it.

The data supplement for that book is my code and is at the bottom of the books Wiley page, just scroll all the way down. You can download the supplement for free without buying the book. Go ahead and download it and you have a full R implementation for a variety of methods proposed to solve Galton’s problem. In the code I first show how to fit simple linear regression, which makes no correction at all for Galton’s problem. Then I show how to put in principal components that attempt to fix Galton’s problem, then network autoregression, mixed hierarchical models that use random effects for clumps in the network, and finally phylogenetic regression.

The book chapter shows simulation results that demonstrate multiple of these methods work when diffusion is the cultural process, but only the phylogenetic regression corrects for inheritance as a process. Note: in this case phylogenetic regression also works for diffusion because the network is highly treelike (i.e. nested). This is crucial! Only phylogenetic regression works irrespective of whether the main cultural process is diffusion or inheritance. Since we almost never know the main cultural process a priori, I recommend for treelike networks that we use phylogenetic regression and simply do not interpret a significant role for the phylogeny as necessarily indicative of inheritance. It could indicate diffusion on a treelike network.

FYI, I have a new preferred implementation for the phylogenetic model as compared to when I made the supplement for that book. My new preferred method is phylolm function in the package of the same name. It is much easier to control whether the phylogenetic parameters like lambda are bounded or unbounded in phylolm as compared to fitting the same model with gls. The gls way is what my data supplement code shows. To fit phylolm, you still use ape package to load in the phylogeny. Then give the phylogeny object itself straight to phylolm as a parameter (see the phylolm help file).

One quirk of phylolm is that is does not print BIC in the summary. I’ve advocated for BIC as a way to pick models. So, you can get BIC if you use the AIC function. Suppose my.tree is a fitted phylom model. You type AIC(my.tree,k=log(N)) where N is your sample size. This converts the AIC into the BIC. The principle difference in the two is AIC uses a penalty of 2 all the time, while BIC uses a penalty that is log(N). You can learn about his yourself with the AIC function help page.

OK, so between this blog and my prior one I have provided implementation for 1) determining which network is important for your cultural trait and 2) correcting for Galton’s problem on your network if it is highly treelike. That still leaves a hole in the analytic pipeline if your network is not treelike. What to do then? Don’t worry, I’m on it! I have a set of NIH-funded projects about physician networks, which are highly non-treelike. I have a paper in preparation right now that shows the phylogenetic method predictably fails under this condition to correct Galton’s problem on a messy non-tree network. In fact, all the previous methods fail! So, I’m inventing a couple new methods and hopefully will have that paper submitted soon.

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Implementations for A Manual for Cultural Analysis: Network Regressions

4/10/2019

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coderandeffectsnetworksims.txt
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july12.7z
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I’m continuing to post implementation notes to accompany A Manual for Cultural Analysis, which I published last year together with two of my anthropologist colleagues at RAND. In my last installment, I provided links and advice for implementing CCA/PCA.

In this blog post I will address how to implement the network modeling method that is discussed in some detail in Chapter 4 of the manual. The central question is this: how do we tell which set of social connections are most important to the transmission of a cultural trait? Note: if a trait doesn’t transmit on some kind of social connection, then it can’t be socially learned, and so by definition it isn’t culture!

OK, but people are connected by ties of friendship, marriage, coworkership, twitter, etc. So how do we decide which of the various ties are most relevant to a diffusing cultural trait? We cover this question in a lot of detail in the manual. I covered it with even more detailed simulations in my paper with my student Rouslan Karimov. We never got a supplement published for that paper, so I’m posting here the code you need to run the most important analysis from the paper – the method that works. First, make sure R is installed. Download the files that are part of this blog post. Extract (unzip) the July12.7z file - I had to zip it to post it here. After it is extracted you should have a file July12.RData. Then if you double click the July12.RData file it should start up R and will already have the simulated data objects you need in the workspace. Type ls() in the R command line to see what is in the workspace. If double clicking doesn’t work, then start R and type load(“diffsimcont.RData”). Make sure you have used the change directory feature in the dropdown to move your active directory to wherever you put July12.RData.

Think of this like a cooking show where some intermediate step is already baked. To create the things in the R workspace you just loaded you would need to simulate networks, simulate trees, then simulate characters diffusing/evolving on them, etc. I’m happy to provide the simulation code to anyone interested. Just email me. The focus of this blog post, however, is not about building simulations but learning to apply dyadic regression with random effects to network/tree datasets.

OK, so then start running my code file called CodeRandEffectsNetworkSims.txt. Simply copying and pasting one line at a time into the R command line is a good way to learn how a piece of R code works. When you get to the loop you would have to paste in the whole loop for it to run; however, I recommend you set i equal to something, like i=1, and then walk through the loop one line at a time as well. That will enable you to inspect what is happening in the loop. One important part is this bit where it defines what you need to run the random effects regression that controls for the repeated identities of the individuals. The individuals are being repeated across each of their network relationships:

names.vector<-1:nrow(sn.adj1)
 
rows<-matrix(rep(names.vector,ncol(sn.adj1)),ncol=ncol(sn.adj1))
cols<-matrix(rep(names.vector,ncol(sn.adj1)),ncol=ncol(sn.adj1),byrow=T)
 
outcome.vector<-as.vector(daisy(as.data.frame(netsims[,,i]),metric="euclidean"))
 
temp.data<-data.frame(outcome.vector,sn.adj1[lower.tri(sn.adj1)],sn.adj2[lower.tri(sn.adj2)],rows[lower.tri(rows)],cols[lower.tri(cols)])
 
colnames(temp.data)<-c("outcome","sn.adj1","sn.adj2","rows","cols")
 
net.mod<-lmer(outcome~sn.adj1+sn.adj2+(1|rows)+(1|cols),data=temp.data)
 
Within the lmer function call the terms (1|rows) and (1|cols) are what is specifying the random effects – which are just the identity of each row and column for each dyadic datapoint. I like lmer in the lme4 package for random effects models (aka mixed hierarchical models) in R, but another option is gls in the nlme package. There are more options besides these as well, including in other statistical packages like SAS, which has some very good random effects modeling routines. I’m not going to discuss fully here why this is the best approach to determining which tree or network most governs the cultural diffusion process for a trait – read the manual or Karimov and Matthews 2017 if you want the answer to that.

In terms of getting to know how lmer works, be sure to run some of the example code provided in the lmer help file. From R you can get to the help for any function by typing ?function.name in the R command line. For example, typing ?lmer will get you the lmer help file.

I will say that I think the simulations in Karimov and Matthews 2017 are more comprehensive than anything anyone else has ever done on this issue. We show that the dyadic regression with random effects is a definitive solution. It works for multiple networks, or networks combined with trees. I’m sure one could create evil combinations of unmeasured confounding and measurement error where the method will fail, but in principle it works across all relevant conditions while I show the other commonly used methods like lnam (sna R package) and MRQAP (aka Mantel test) do not work across all relevant conditions. If you can fit a random effects regression model then you can fit the method I’m recommending based on the simulations I’ve done. You don’t need any particular software package, you don’t need my code, just regress the trait distances and network ties, include random effects for node IDs, and you’re done. I shouldn’t hear anymore at conferences about how we can’t distinguish treelike inheritance from network diffusion, or determine which networks are important. Measure whatever networks or trees you think might matter, put them in the dyadic regression with random effects, and you’re done.

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Implementations for A Manual for Cultural Analysis: CCA/PCA

4/9/2019

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Since my colleagues and  I published A Manual for Cultural Analysis, some people have asked for R code examples of all the things we describe. That’s a fair critique of the manual as we originally published it, although I’ll note that most of the papers and books we referenced already provide implementations or point to them. Regardless, here on my blog I will write a set of posts that will point to everything you need to implement what’s in the manual.

The first part of the manual focuses on using Cultural Consensus Analysis (CCA) and Principal Component Analysis (PCA) as a first pass at understanding cultural data. Read the manual if you want to understand why this is such an appropriate first pass.

PCA has a large associated literature that I can’t overview here. For implementation, I think the best option is the prcomp function in the ‘stats’ R package that should come with any basic R install. The other option is princomp. I prefer prcomp because it uses SVD rather than eigenvalue decomposition, which is supposed to be slightly more accurate numerically. Also, this implementation allows for data structures that have more variables than datapoints, which is a common occurrence in cultural data.

CCA is a technique from cognitive anthropology, which is a subfield of cultural anthropology. Basically it works by performing PCA on the transpose of the usual individual by variable matrix, thus you are performing PCA on a variable by individual matrix. This procedure results in loadings for the individuals on the components, and scores for the variables, again the reverse of the usual PCA procedure. Exactly why you might do this theoretically and when you might use CCA vs PCA is answered in the manual.
Skipping to implementation, the simplest way to do CCA is to simply use prcomp on the transpose of your data. Like this: prcomp(t(your.data)). The t() is the transpose function in R.

There also are some packages specifically for PCA that can allow you to fit more subtle forms of it, and allow to you ensure the mathematics are being done in more precisely the same way as in prior important articles by folks like Batchelder, Romney, and Handwerker among others (check the manual for refs). One R package option is AnthroTools for R. AnthroTools will implement the classic version of CCA, and it provides some neat data manipulation tools specific to common types of cultural anthropology data, such as free-lists. Another option with more advanced features is CCTpack, which implements both the classic CCA but also more recently developed modifications, such as contexts where there is more than one underlying cultural stance.

That should cover the options, at least in R, for implementing PCA and CCA as we described in A Manual for Cultural Analysis. Note that all R functions have example code that works down at the bottom of the help pages for them. I’ve learned a lot just by running those little examples and comparing the input data they used to the outputs generated by the functions.

Stayed tuned to my personal blog for the next days and weeks because I am going to publish similar posts for the network analysis and phylogenetic analysis chapters. Feel free to leave comments here with questions or email me.
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Cultural inheritance and diffusion are core evolutionary research topics.

3/15/2017

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I recently published an article in an applied journal that might be unlikely for anthropology folks to find, so I thought I would add some commentary on it here. The article uses agent-based simulations to assess the statistical performance of several network regression methods. Network regression is a primary way to assess whether cultural diffusion is occurring, and over which social ties the diffusion happens. The social ties are represented by different networks. Although the article focuses on applications to networks of malicious actors, the methods are applicable generally to most human social networks.

The methods I investigated essentially are some of the currently best approaches for implementing tests to determining which of several transmission pathways most govern the spread of a trait. This type of question is core to cultural evolutionary analysis, and in my view core to the original mandate of anthropology. A good example of a running anthropological discussion on this matter would be the analysis of Welsch et al. 1992 and the critiques, counter critiques, and reanalyses that followed. In my view, this entire exchange is some of the best of anthropology.

Of course, post-Boas cultural anthropology tends not to view articles like Welsch et al. 1992 as of foundational interest. That’s because much of American cultural anthropology left behind methods that systematically compared across different sites or cultures in favor of particularist accounts conducted though increasingly humanistic modes of research. Nothing wrong with the latter by the way – I regard it as a completely valid intellectual activity. It’s just not the entirety of what anthropology was founded to do, and the result has left a significant portion of scientific research on culture without a disciplinary home.

Most biologically inclined anthropologists, meanwhile, in recent memory had vigorously adopted the behavioral ecology paradigm (Grafen’s phenotypic gambit) – which is essentially utility maximization theory from microeconomics with reproductive success or its proxies in replacement of money. Studying cultural evolution is difficult to fit into this framework because classical behavioral ecology is intentionally heuristically teleological rather than explicit and mechanical. Behavioral ecologists don’t necessarily think people are intentionally trying to maximize fitness outcomes, although some might, but they think at least that the mechanical operations of the mind result in a being that behaves as if it is maximizing fitness. In the classic approach no attempt is made to understand the causal mechanisms. That’s all fine, it just only gets you so far. Wouldn’t you rather actually know about the mechanisms themselves?

The perhaps unexpected irony is that folks interested in cultural evolutionary models, by articulating proximate mechanisms, arguably are the ones being more reductionist than those sticking within the classical behavioral ecology paradigm. It’s ironic because cultural research has so often been assumed to have something to do with non-reductionist notions. Thornhill and Palmer in their controversial book at one point say people prefer cultural explanations because culture is consistent with the idea of free will – but cultural explanations offered by cultural evolutionists are just as causal as explanations offered by behavioral ecologists. Both explain individuals’ behavior as a mechanistic result of prior events. In fact, I’d argue cultural evolutionists are being more causal in that they usually seek to specify causal mechanisms start to finish, ultimately and proximately, while behavioral ecology in its classical approach leaves proximate mechanisms unspecified. Fincher and Thornhill’s well-known articles on infectious disease stress and cultural traits are good examples – we are left at the end of the papers with only a functional relationship (heuristic teleology) and don’t know if that is mediated by cultural inheritance, individual learning, an innate reaction norm, or genetic variation.

The second irony is that “behavioral economics,” that moves beyond utility maximization and into proximate causes, has become mainstream or nearly so in microeconomics, and microeconomics essentially is where behavioral ecology first coopted its theory.

Which brings me back to social network analysis applied to cultural diffusion. Cultural diffusion as a theorized process really sits between proximate and ultimate causation  in the traditional sense because it is 1) a proximate factor in individual’s personal development, 2) has an epidemiological and phylogenetic character to its own as cultural history, and 3) ultimately can’t fully escape biological selection because, at least among any longstanding cultural variants, natural selection will favor directly cultural variants that promote fitness or genes that bias people to prefer such variants. The other thing I like about studying cultural diffusion, inheritance, and related processes is the hypotheses are eminently refutable. I think culture often is important, but whether it is important or not to a particular case is an empirical matter. Folks like me doing this, I think, often find cases in which culture is not the most important process involved. In some of my own research, I’ve proposed that genetic variation accounts for some cross-society differences in personality traits that are usually interpreted as entirely socially learned (Matthews and Butler 2011). My recent paper tries to advance the empiricist and refutable tradition of cultural research by determining which of the currently available methods perform best at discerning cultural diffusion processes.

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    This is my personal blog.  The views expressed on this page are my own.  My views should not be taken to represent the views of my mentors, employer, or any person or group other than myself. 

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