Oh Koko!

We'll be sharing much more, in the coming months, about why Anne and I are a wee bit obsessed with Koko the gorilla. She's one of the stars of a project we've got going--a project that will likely diminish our chances of ever meeting the lovely and extraordinary creature.

It's because we've been stalking Koko that Anne and I were perplexed, but not surprised, by this recent piece in The Atlantic:

Click here for the article.

Our eyebrows arched just reading the headline.

It leads a reader to anticipate a conversation with Koko the gorilla, but instead it is mostly an interview with Koko's main human, Penny Patterson. So, I guess the headline is describing what that interview is about--a conversation about conversing. There's no other way to make sense of it. Yet, it's still problematic because gorillas don't converse. Not even Koko.

The piece begins with an anecdote about Koko describing herself with the "queen" sign. Morin, the article's author, follows it with this quote of explanation from Patterson:

Koko understands that she’s special because of all the attention she's had from professors, and caregivers, and the media.

And this is where, to my mind, any interviewer actually fascinated with Koko's mind asks: This is amazing...how could Koko understand that she receives more human attention than most other gorillas on the planet? And how does she make the connection between this concept, this existence of hers, and that of a queen? When you taught her "queen," what was the definition? 

Unfortunately, this isn't the direction the piece goes. That nugget was a foray into her backstory about her sign language training and her home in California.  And just because the written product of Morin's interview doesn't dive into questions like those italicized up there, it doesn't mean it didn't. But if he did go there, why on earth didn't that gold make it into the piece?

More to the point, why have I never read an interview about Koko that asks penetrating questions about the stories that Koko's humans tell about her mind? Is that nuts and bolts stuff merely uninteresting fodder for readers or is it off-limits to writers who are permitted access? There's an answer at the end of this blog post.

But first, I have more, seemingly infinite, questions... How does Koko's language ability, and let's add Kanzi's too, compare to a highly-trained border collie like Chaser?



Is it categorically different, indicating an actually different kind of cognition?
You might be thinking about this video of Kanzi and saying, yes, yes it's different:



But how is it different? Kanzi is just pairing up two things, which is not really all that different from Chaser getting one toy at a time. It might appear to be more extraordinary than it is because in pairing the two objects for which Kanzi knows the English words, he behaves with them in ways they're meant to be behaved with by people.

That was a sentence worthy of a tinier brain than mine.

What I'm trying to say, poorly, with my human language "abilities," is that grabbing two things, like a soap pumper and a ball, and behaving routinely with one of them (like pumping the soap, which is what one does with a soap pumper) doesn't necessarily require as much human-like comprehension of what Sue's saying as a we might assume--that is, without thinking it through more deeply, or perhaps without trying to think like a dog or like a bonobo, or like a toddler.

Or like a gorilla--a gorilla who's arguably not a gorilla, given she's not socialized like one and given how her humans have admitted that they've intentionally raised her as a human and consider her one:



As they've raised Koko, they've narrated her mind as if it works like ours.This is evident right from the beginning of the interview portion of Morin's article. Patterson is explaining how Koko generalized the sign for "food", saying:

She would perch on this high spot where she could watch people come and go and she would sign “food” to them. It might mean “Give me the treat you’ve got,” or it might mean “I want my toothbrush,” or even just, “Engage with me.” She understood that signs had power. That particular sign got her food, so she wondered, “What else can I do with it?

She did? She wondered? And it was about how to use a sign in different settings to get what she wants? It's not just simply that it's something she could produce and did, in various circumstances? I think describing such processes as "wondering" would be giving humans too much conscious credit most of the time. But it's how we talk about minds. It's how we narrate one another's behaviors, and that of our pets, and that of whatever Koko is.

Often this is lumped into "anthropomorphism" and it's not all bad, but one could argue that it's to be avoided like the plague. If the goal is to understand how an animal thinks, then anthropomorphism risks being more of an obstacle than a helpful metaphor.

Whether the Koko project is scientifically rigorous, I have absolutely no idea. But Patterson's fantasy description of wild gorilla communication rings more of science fiction:

The free-living gorillas might talk about simple things like “Where are we going to get our next meal?” but here [at the research facility] there is so much more to talk about.

Death is one of those things. Here's Patterson's evidence that Koko understands things about death:

The caregiver showed Koko a skeleton and asked, “Is this alive or dead?” Koko signed, “Dead, draped.” “Draped” means “covered up.” 

Again, this is where my dream interviewer asks, What is the connection between "dead" and "draped"? It's even harder to understand the connection between a skeleton and draped. Can you help us understand the logic of her language? 

But we're not given that in this piece.  Morin does follow with "How would Koko know about death?" but it's not demanding a response that gets at the crucial connection between her mind and her signs.

We need to know whether what Patterson says about Koko's mind is true or not and no one seems to be able to  help us learn this. As the piece continues, my desperation for such a person escalates.

Patterson describes how Koko was making a sign that her brother made just before jumping off a rock. It took Koko's people a while to understand what she was trying to say because they hadn't seen her brother do this, but once they saw a film, it was apparent that the sign...

...means “take off” in the sense of “jump off.” Koko wanted us to take off our lab coats.

How does Koko's mind connect "jump off" a rock with "take off" your lab coats? If Morin asked this, he neither published it nor the answer. If Morin asked this question, then he is hoarding the gold all to himself.

The rest of Morin's piece is fascinating, and in parts it's heart-warming, especially if you have a soft spot for gorillas and for people who have those soft spots too. But there's still no conversation with a gorilla, or a conversation about a conversation either.

Read far enough into the article and you'll see what happened to Morin as he prepared to meet Koko:

Patterson cautioned me earlier to refrain from asking Koko questions. I was to let the gorilla take the lead. “She has that royal air about her,” the researcher explained, “and she doesn't entertain questions. Just like you wouldn’t question the queen—Koko is the same way. She’ll disengage.”

So, no conversation is going to be had with an ape, conveniently, because that totally capable ape wouldn't like it if he tried. Hm.

But there would be some lovely and touching moments through the enclosure's fence.

After recounting those, Morin reflects on what I've been discussing:

There was no way to know how much of her behavior was intentional and how much was my own or Patterson’s projection. Allegations of selective interpretation have accompanied ape-language research from the beginning. Still, it was impossible to be there interacting with her, and not feel that I was in the presence of another self-conscious being.

I don't see anything wrong with describing her as self-conscious while also doubting that her mind works like ours.  I live with a one-year old. And even before I had this baby, before I lived with an alien mind, I didn't see anything wrong with this thinking. Morin's final thoughts compare Koko's mind to an alien's, but his piece paints that alien as just another Hollywood humanoid.

When you share the link to Morin's The Atlantic piece on Facebook, the headline in the feed reads: "What gorillas can teach us about being human"

Well, what can they?

I think it's obvious from the article, and from others like it, that Koko is teaching us about our limitations. She's teaching us that we wouldn't care as much about gorillas without her fairytales; that we wouldn't care as much about these truly magnificent animals if they weren't furry humans. And that would be less depressing if we were any good at caring about actual humans.

Have gorillas really inbred themselves into the future?

By Anne Buchanan and Ken Weiss

NOTE:  This is a revision of our original post, because a mistake on our part was pointed out by a commenter, to whom we offer thanks.  Our main point hasn't changed....unless there are still misperceptions on our part.

BBC Earth headline: "Inbreeding Makes Mountain Gorillas Genetically Healthy." We are so tempted to add an exclamation point to that, but we won't.  Anyway, you know it's there, whether we add it or not. Everyone 'knows' that inbreeding is bad; what a juicy story!

And, to summarize, the story is this: Mountain gorillas are an endangered species, surviving now in just two small groups in central Africa, a total population of only about 800 individuals.  Their numbers had fallen to just under 300 in the 1980's, for multiple reasons including poaching and loss of habitat, but Diane Fossey made their conservation her life's work, and the population more than doubled since its lowest point.

                  Location of eastern and western gorillas; Xue et al., Science 2015

But, their small numbers led to extensive inbreeding, which is always worrisome to conservationists because it may reduce a population's ability to adapt to changing environments.  But, the BBC writes:

Now scientists have discovered inbreeding has actually benefitted mountain gorillas by removing many harmful genetic variations. They are also genetically adapted to living in small populations.

And,

Fewer harmful genetic mutations, which stop genes functioning and can cause serious health conditions, were found in the mountain gorilla population than in the western gorilla populations.

Ok, let's step over to the actual paper ("Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding," Xue et al.), in Science last week, to get the story without the go-between.  So, the investigators sequenced the whole genomes of 13 eastern gorillas, including seven mountain gorillas and six eastern lowland gorillas.  They compared these sequences with published sequences of lowland gorillas further west, and found lower genetic diversity in both the mountain and lowland gorillas from the east, which they report as consistent with the smaller population sizes there.  Their analysis, they report, confirms that the eastern lowland and mountain gorillas are two genetically distinct populations.  Genome wide linkage disequilibrium was higher in the eastern gorillas than the western, evidence of different demographic histories of these populations, and suggesting a recent population bottleneck in the eastern gorillas.

Foraging gorilla, Congo; Wikipedia, Pierre Fidenci

In eastern gorillas, chromosomes were found to be homozygous across 34 to 38% of their length, while in western lowland gorillas, they were 13% homozygous, indicating that the eastern gorillas have a recent history of several generations of close inbreeding.  Xue et al. also report that the eastern and western populations diverged perhaps 150,000 years ago, with no mating history in the last 20,000 years or so.  And, overall, it seems that gorilla population sizes have been small for thousands of years, and thus probably have been inbreeding for all of that time.

Again comparing mountain with lowland gorillas, Xue et al found no evidence for natural selection or adaptation favoring functional genes in either group.

Such adaptation might be expected from the fact that mountain gorillas range over high altitudes (1500 to 4000 m), with consequences for diet, morphology, and physiology. However, we found no significant enrichment in any functional category of genes, although there are interesting examples related to nervous system morphology, immunoglobulin quantity, and red blood cell morphology. Mountain gorillas carry a significant excess of variants in genes associated with blood coagulation in humans (fig. S21), perhaps linked to high-altitude living. We also identified variants associated with cardiomyopathy, including in one deceased individual (Kaboko) in whom post mortem analysis revealed evidence of muscular hypertrophy. Cardiovascular disease has been identified as a notable cause of death in captive western lowland gorillas.

With respect to unfavorable effects of inbreeding, the authors report the opposite, saying that inbreeding seems to have purged deleterious mutations from the genome.  They suggest that gorillas have found workarounds for inbreeding effects, as well, such as by "natal dispersal and gene flow between isolated populations."

Xue told the BBC that gorillas have been coping with small populations for thousands of years, and,

"While comparable levels of inbreeding contributed to the extinction of our relatives, the Neanderthals, mountain gorillas may be more resilient. There is no reason why they should not flourish for thousands of years to come."

No reason? 
But, we can think of a number of reasons.  The Ebola virus has been devastating to chimps and gorillas, wiping out 95% of some groups of gorillas in which it has spread.  And, there's always the possibility that other infectious diseases may emerge, or reach these animals, and be equally, or even more devastating.

And, poaching continues to be a problem, and hunting for bushmeat.  Loss of habitat continues to be a problem.  Climate change will surely have consequences for these animals.  As with any other animal, including humans, environmental change and its consequences are unpredictable.  Whether or not any species has the genetic wherewithal to adapt to that change is unpredictable; it's impossible to know what any single gene will do in every possible environment, never mind what every gene, and every genetic interaction will do.  This is, of course, true with respect to predicting our own futures from our genomes as well. 

What is 'inbreeding' and what does it mean?
There are several things about this paper aside from the apparent obliviousness of the research report to the real threat to gorilla 'fitness', namely that they're widely projected to become extinct because of human incursion and predation, in addition to disease. We might also ask, if the western gorillas have so little relative homozygosity, why they aren't plagued with the sorts of defects that the easterners have already purged, and on the verge of collapse -- or long gone?  

The answer is that both populations (not just the eastern) did well enough to be here today.  Both low and high homozygosity are obviously good enough, because neither wiped out either population structure in their past.  So why tell the story as if one way's better? It seems to be the tired old evolutionary trope that we cannot seem to escape: To be different from is to be better than, to evolve away from is because it's a better way.  But, mutation is always happening, genetic drift is always happening, and if a variant works, it works. It isn't necessarily selected because it's better, or more adaptive, than anything that came before. 

This paper is in a sense an exaggeration of, and in a way confusion about inbreeding and its effects.  There are several meanings of 'inbreeding' that are relevant here** . The classical meaning refers to mating with close relatives relative to random-mating. The issue there is the classical one of increased incidence of recessive disorders with inbreeding.  In that context, the probability of an allele being homozygous more than just by chance: if the latter is p^2 when there is random mating, the former is p^2 + Fp(1-p), where p is the frequency of the variant in question, and F is the excess probability of being homozygous due to non-random mating. That may be because of socially constructed preferential kin-mating or just a deviation from random mating. In many, if not historically most, human populations, mating was prescribed as to be between cousins of various types. If variants are harmful but recessive so that their harm is only seen in homozygotes (both copies in a person being defective), then mating between close relatives can increase the frequency of such events, and the loss of the harmful variant from the population, but of course only at the expense of the carriers of those harmful genotypes. One can argue that if something like close-relative mating were so dangerous it would never have evolved to be, in a sense, the ancestral human way as it has.  Or, one can note that the reason for local group endogamy or exogamy (how mates are chosen in any population, human or otherwise) has to do with social structure, resource distribution, and control of internecine and intergroup strife--not because of disease genes.

The authors appear not to have done this kind of calculation, however, and samples would have been too small for it to make sense.  Instead, they looked along the genome to see what fraction was homozygous (that is, variant sites along the region in the sequenced animals).  This reflects a different use of the term 'inbreeding', and we think what this paper is referring to, is the rise in homozygosity due to genetic drift in small populations.   In a small population, rarer alleles (genetic variants) are lost more rapidly from the population, mainly just by chance. Homozygosity at a given site is an inevitable reflector of population size, and in a small population the region of a chromosome that is homozygous (not varying) would be larger than in a large outbred population. That is not an automatic indicator of a history of loss of harmful mutations, recessive or otherwise. In any population harmful variants have a shorter staying time than helpful ones, but their duration depends on many different factors that can't be inferred from the stretches of homozygosity alone.

Do western lowland gorillas, with their lack of a history of 'inbreeding' as presented by this story, show some detectable load of sub-par individuals? If so, that would be relevant news. In fact, both groups have coefficients higher than human cousins relative to each other, as a commentary on this paper notes. But so what?  In fact, and perhaps to the contrary, being too inbred in the small-population sense could, as far as just-so stories go, mean there would not be enough variation in the population to respond to environmental challenges.

What the study does no doubt actually show is that the two gorilla populations have had different demographic histories. That is ecologically interesting and perhaps useful for understanding wildlife conservation issues.  But in itself it says basically nothing about purging harmful variation except that it would be somewhat faster, on average, in one group than the other -- but only slightly so, because if that were not the case the burden of loss could have threatened the very survival of the group in the past so that it never made it to the present, which obviously isn't the case.  'Inbreeding' in headlines may have a juicy sound and catch the lascivious eye, and that's why the news media go for it so readily.

It should also be noted that extensive, detailed, biomedically documented studies in human isolate populations have found each to have particular instances of elevated recessive diseases or other traits due to inbreeding effects, but the overall burden of genetic disease has not been particularly increased, if at all.

***The often and perhaps still confusing issue of inbreeding have been clarified long ago, e.g., by Albert Jacquard in 1975, in J. Theoretical Biology, "Inbreeding: one word, several meanings", by various wrtiting of Warren Ewens back in the 70s, or see Templeton and Read, Conservation Genetics, 1994; they are discussed in any good population genetics text.