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The Bonobo Genome and Rewinding the Tape of Life

The views expressed are those of the author and are not necessarily those of Scientific American.

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When I wrote for The Scientist, I covered the debuts of several genome sequences – fruit fly, rat, pufferfish, and the plague bacterium, to name a few. An illustration in my human genetics textbook resembles the intro to The Brady Bunch, a checkerboard of nine new genomes with each edition, now with more than 1,000 to choose from. In just the past few weeks, several salad ingredients have had their genomes unveiled.

But the genome sequence to intrigue me the most, except for our own, is that of the bonobo, aka Pan paniscus.

A bonobo looks like a sleeker, smaller-headed, longer-legged chimpanzee (Pan troglodytes). Discovered as a skull specimen in the Tervuren museum in Belgium in 1929, rather than in its home in the Democratic Republic of Congo, south of the Congo River, the bonobo was once considered a pygmy chimp. But as anthropologists catalogued distinctions, the animal got its own species name, in 1954.

Bonobos have had roles in recent fiction. These include Robin Cook’s 1998 Chromosome 6, in which the unfortunate primates provide spare parts for wealthy humans; the supporting role Koba in last summer’s Rise of the Planet of the Apes; and in Sara Gruen’s wonderful Ape House.

Chimps and bonobos have stark behavioral differences, especially in the sexual arena. Bonobo authority Frans de Waal dubbed them the “make love, not war” primates, calling them “a belated gift to the feminist movement” in the March 1995 Scientific American. And they are sensitive souls, he wrote. During World War II the bonobos in a zoo in Germany dropped dead from fear at the sounds of falling bombs; the chimps were oblivious. Bonobo females dominate their peaceful societies and move among them, while males remain attached to their mothers for life. Male chimps are aggressive, battling for dominance and forming roving gangs.

Ape Genomes

We three – chimps, bonobos, and people — are intimately related. We share 98.7% of our genome sequence with these other two ape species.

Kay Prüfer and Janet Kelso of the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany and their colleagues, including Svante Pääbo, sequenced the genome of a female bonobo named Ulindi, from the Leipzig zoo. And the genome held quite a surprise.

Partial sequencing had revealed that we parted ways from chimps and bonobos about 5-7 million years ago; they parted from each other about 2 million years ago. Many researchers expected the bonobo genome to be a subset of the chimp genome, with perhaps a few DNA base changes after their split.

But it isn’t so straightforward. “We’ve discovered that on average the genomes of bonobos and chimpanzees are equally distant from human, but for particular regions of the genome, composing a total of 3% of the human genome, this relationship is unequal: for some regions of the genome humans are closer to bonobos than they are to chimpanzees, while in other regions humans are closer to chimpanzees,” Drs. Prüfer and Janet Kelso told me in an e-mail. Chimps and bonobos could have retained different subsets of gene variants at the time of their separation, but since all the variants descend from the ancestor common to all three of us, we can indeed share DNA sequences with one Pan but not the other.

Geography may explain the curious evolutionary journeys of chimps, bonobos, and us. Many anthropologists think that the Congo River divided the ancestral population that diverged, giving rise, eventually, to the two Pan species.

A Dave Matthews Analogy

I had a hard time envisioning how we could share some sequences with only chimps yet others with only bonobos. Then I thought about more familiar terrain, based on an event near my house last weekend, when I was reading the bonobo genome paper.

Imagine three carloads of kids leaving a Dave Matthews concert in Saratoga Springs, New York. All three cars drive downstate to New York City on the Thruway. Once they reach the city, one car veers off towards Brooklyn (humans). The other two enter Queens, reaching the end of their journeys in two different neighborhoods. One car stays put (bonobos), say in Forest Hills, but the other drives around a bunch of other neighborhoods (chimps)

All three cars would have gravel and other crap from the Thruway embedded in the grooves of their tires as well as from the secondary roads, markers of where they’ve been. But once the three dispersed, a few of the markers would have changed, the chimps’ more so than the bonobos because, presumably, they would have faced different environmental conditions as they spread out in Queens.

And so the Brooklynites – the humans – could have some road residue in common with both Queens cars – the chimps and bonobos — or either. But 98% of the road rocks are shared from the original split, the Dave Matthews show.

Three Lessons

The sequencing of the bonobo genome made me think of three things.

1. Evolution makes sense. The idea of a Supreme Being creating information-dense genomes, enticing us to make comparisons and consult mutation rates to trace how species are related, seems like too much work. Why would She have bothered?

The bonobo paper also brings up the oft-missed point that we branched from a shared chimp/bonobo ancestor – we didn’t descend from apes, we ARE apes. A 2009 Nova television series, Becoming Human, made this mistake repeatedly, even in the title teaser: “Six million years ago, what set our ancestors on the path from ape to human?” This prompted my friend and colleague Michael Dougherty, PhD, Director of Education at the American Society of Human Genetics, to write a heads-up guest editorial in The American Biology Teacher in February 2011.

2. Sex. To bonobos, according to de Waal, sex is “part and parcel of social relations.” And the animals do it all ways (except mother-son pairings) and they do it often, albeit quickly (average act 13 seconds) and sporadically. The happy, erect and ready bonobos have face-to-face sex, once thought to be uniquely human. Females are always interested, particularly in rubbing their privates together (“genito-genital” or “GG” rubbing). Males enjoy “penis-fencing,” when they hang from branches and rub their members, according to de Waal. Scrotal rubbing is also popular. Sex often precedes a meal, the opposite of human dating rituals.

Unlike the macho chimp males who compete to assure their rank on the dominance hierarchy and obtain their sex with aggression, bonobos have apparently discovered the joys of the act, and for both genders. They use sex “to resolve conflict, show affection or excitement, and to reduce stress. Bonobos remain playful throughout their lives, show high emotional sensitivity to other individuals, and there is no evidence for lethal aggression between them,” the researchers told me. The bonobos have sex in its eclectic guises just to have fun. And among them, females rule.

So how did the bonobos sequester a group of gene variants that led to a tranquil, XX-centric, sex-loving society? Is it that compared to chimps and us, bonobos didn’t travel far from their moist forests, preserving a moment in evolution under certain conditions when males were kinder to females? And do some of the gene variants that separate bonobo from chimp perhaps explain humans with sexual predilections outside the mainstream, such as Jerry Sandusky?

I can’t wait to find out the answers, and neither can the researchers. “Linking genetic features to these traits would be immensely interesting. The sequence provided by our study is the first step in providing the data needed to make these links,” they said.

3. Rewinding the evolutionary tape of life. Becoming human capped many millions of years of genetic change, as we branched from other species, losing some characteristics, gaining others. It might have happened any of a near infinite number of ways, given the information content of even the simplest of genomes.

Paleontologist and science writer Stephen Jay Gould called this idea of what might have been “rewinding the tape of life” (a tape was a device that recorded sound). I wrote his Obit, also in The Scientist, in June 2001.

Dr. Gould summed up the wonder of our evolutionary history better than anyone in the Academy of Achievement in 1991, and the sequencing of the bonobo genome brings it back to me:

“We want to know why we’re here. To a large extent it is a grand-scale accident that we’re here. Evolution has oddly contingent pathways, and we never run the same way twice. If you could go back 500 million years and run the tape of life again, you wouldn’t get human beings, and you probably wouldn’t get anything conscious.”

Images: Max Planck Institute for Evolutionary Anthropology

Ricki Lewis About the Author: Ricki Lewis received her PhD in genetics from Indiana University. Her ninth book, The Forever Fix: Gene Therapy and the Boy Who Saved It, narrative nonfiction, was just published by St. Martin’s Press. Most of her other books are college life science textbooks, including "Human Genetics: Concepts and Applications," (10th edition, 2012) from McGraw-Hill Higher Education. Routledge Press published "Human Genetics: The Basics" in 2010. Ricki has published thousands of magazine articles, from Discover to Playgirl, but mostly in The Scientist. She is a genetic counselor at CareNet Medical Group in Schenectady, NY and teaches "Genethics" online for the Alden March Bioethics Institute of Albany Medical College. Ricki is a hospice volunteer and a frequent public speaker (Macmillan Speaker’s Bureau). Ricki’s blog Genetic Linkage is at and she tweets at @rickilewis. Follow on Twitter @rickilewis.

The views expressed are those of the author and are not necessarily those of Scientific American.

Comments 20 Comments

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  1. 1. StevenTorrey 2:10 pm 06/14/2012

    Ricki Lewis: “The idea of a Supreme Being creating information-dense genomes, enticing us to make comparisons and consult mutation rates to trace how species are related, seems like too much work. Why would She have bothered?” Was that intellectual gas really needed.

    There is more than enough evidence–yes evidence–for the miraculous in science. For example, while Neanderthal is contemporaneous to Homo-sapiens, Homo-sapiens is not a descendant of Neanderthal. Neanderthal and Homo-sapiens share taxonomic commonalities but the differences are of sufficient import to count as the miraculous. Specifically, the Homo-sapiens larynx. To dismiss this miraculous is to dismiss an important part of science.

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  2. 2. gametheoryman 4:41 pm 06/14/2012

    I’d bet geography has more to do than allow the genetics of a population split by the Congo River diverge enough to create two species. I also expect significant environmental differences on the two sides of the River.

    If valuable resources are in various places in different parts of a year or if the environment is just as easy for strangers to overtake an area as for others to defend it, frequent friction between bands would lead to wariness towards strangers and possibly violence. Think Sioux Indians or Poland.

    If defense is significantly easier than offense in one location that offers good natural resources year round, most interactions will be within a band, and cooperativeness wins out. Think Hopi Indians or Samoans.

    Anyone know about the environmental conditions on both sides of the River?

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  3. 3. rickilewis 6:22 pm 06/14/2012

    Steven, my statement is my opinion, as an atheist and a geneticist. You can disagree, that’s fine. There is no room for miracles in science as I learned it — but I will agree that certain aspects of the natural world are so wondrous as to seem like miracles.

    Gametheoryman, interesting points. But geographical/environmental differences would usually not impact genomes in noticeable ways (via natural selection) unless a great deal of time has passed — but not always, and that gets back to Stephen Jay Gould. Thank you!

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  4. 4. stargene 2:20 am 06/15/2012

    Dr. Lewis: Your comment in point #1 is similar to
    something I posted elsewhere on the evidence supporting

    Assuming that a God desires to be known for his (her) great works, which would necessarily include the great suite of life forms just created a la the Old Testament,

    And assuming that this God is transcendentally and infinitely intelligent and creative..

    Surely, an infinite God, all powerful and constrained
    by no restrictions whatsoever, could have found many
    ways to create all the life forms of today and
    the past in such a way that their separate DNA
    genomes would each carry a unique, distinct signature which would call out loudly and unmistakably that
    EACH of these forms was manufactured as an absolutely original and non-derivative creation… each ‘from scratch’ as it were, each completely distinct and never to be conflated with any other as its ‘ancestor’ or
    its ‘descendent’.

    Thus, on the most fundamental levels of biology, such
    a God, wishing to be divinely clear and unambiguous
    to all of its sentient creations, and never deceive
    them, could have easily created genomes for all life forms which display no commonality in their DNA whatsoever. One could in fact go so far as to say
    that such a Being would have had no trouble in
    creating completely different DNA and RNA bases and proteins, one set for each different species.
    (Even mortal organic chemists will confirm that a
    vast array of genetic bases is possible.)

    This would in itself state inarguably, in the stuff
    of nature itself, that no species could ever possibly mutate into another species, however gradually or transitionally. Because each species would be in
    effect an alien species when compared to any other species, on the most fundamental levels of genetic
    and protein makeup. To expect any two such mutually alien species to be connected via evolutionary
    processes would be like expecting ordinary bio-
    chemical processes to be able to transform copper
    into a box of twinkies and back again.

    And yet we do not see anything remotely resembling
    such an unmistakable Godly signature. The dilemma
    for fundamentalists at least, of any religion, is
    that to claim that their god deliberately designed
    life in such a way as to be misdiagnosed and confused
    as essentially evolutionary (as a ‘test’ for the
    faithful) is also to define their god as one who
    favors massive deceit, manufacturing an effective
    infinity of false testimony. All people and all
    cultures have a name for such a being.

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  5. 5. rickilewis 6:55 am 06/15/2012

    Stargene that is a very eloquent and reasoned explanation. But you lost me at the last line — “all people” — denies that atheists exist. We do. In fact, a researcher at Columbia University is writing a book right now about how atheists are ignored.

    So at the risk of sounding defensive, all I really meant by that tiny part of my blog was that to me, the evidence embedded in the sequences of genomes is so logical, and so extensive, that it makes more sense to me that life would have unfolded from the chemical properties of nucleic acids — a molecule with a sequence — than just deposited here fully formed. The evolution of the first cell-like structures from interacting polymers long ago — in the oceans, on clay, whatever or perhaps both — is something I and others can follow, in laboratory experiments (since we don’t have time machines), step by step. I personally find this type of thinking more satisfying than claiming that some sort of being, in a few days, put everything here. Or even that that being created the polymers or cells. It just doesn’t answer all my questions. This is personal, the way I think. We do not all require belief in such a being. I am a hospice volunteer and often marvel at how helpful religion is to people at the end of life. I envy their belief and go along with whatever will help them. But I have a difficult time discussing matters of evolution from a science perspective when my own viewpoint — that of a non-believer — is dismissed not only as not being valid, but of not even existing. Unfortunately it happens all the time. That is why atheists and agnostics tend to be rather quiet. It is sad. But thanks for your post. It is perhaps the most reasoned explanation I’ve ever read.

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  6. 6. Bill_Crofut 6:30 pm 06/15/2012

    Dr. Lewis,

    Re: “It might have happened any of a near infinite number of ways, given the information content of even the simplest of genomes.”

    What is the evolutionary explanation for the origin of information?

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  7. 7. stargene 6:52 pm 06/15/2012

    Hi Dr. Lewis
    Apparently I wasn’t clear in that last line. Having
    been born into a family of very far left-wing thinking,
    and since my parents ranged from atheist (my mother)
    to agnostic (my father), I and my brothers spent rather
    a lot of time trying futilely to espouse those points
    of view to our friends in the neighborhood. So I too
    am familiar with not only being ignored, but on occasion
    being ostracized. As I grew up, I found myself more
    of an agnostic, though my atheism still flares up from
    time to time. :-)

    In my last thought I meant that all people (I hope)
    would find that any being who perpetrated such
    obfuscation and misinformation, manufacturing vast amounts of false evidence, would be no more than
    a liar and perjurer; that any ethical court of
    law would necessarily arrive at such a judgement.
    My position is that atheists, agnostics and religious
    people having any independence of mind would arrive
    at the same conclusion.

    So, to clarify, with apologies, I would never
    exclude atheists and agnostics from the human
    endeavor. Great human good has come about from
    their courage, care, ideas and work.

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  8. 8. rickilewis 8:40 pm 06/15/2012

    Bill, this is a listing of Dr. James Ferris’s experiments with clay, where he combines certain small molecules to generate polymers that are nucleic-acid-like. He’s been doing this for decades. The origin-of-life simulation experiments date from Dr. Stanley Miller in the early 1960s, in which he combined methane, ammonia, water and hydrogen in a closed system, added a spark, and chemical reactions occurred that formed simple amino acids. There are many variations on these themes — I vividly recall repeating the Miller experiment in college. This is all off the top of my head, but there is an entire field based around how chemistry might have become biology. Other variations involve how simple membranes might have enclosed the amino acids and nucleic acids, forming primitive cell-like structures. Of course we can’t ever know for sure how it happened, but it is fun to think about.

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  9. 9. rickilewis 8:45 pm 06/15/2012

    Stargene, thank you for the explanation. I read your post over about 8 times, it is so well done. I just love the twinkies and copper comparison. And I do now see that we are not far apart at all in our thinking — I just need to think about it more. I never tried to get into the hypothetical Being’s head, but what you say makes perfect sense — the creator would have created very distinct species. I’ve passed this discussion on to my local humanist society, and you’ve got us all mulling it over. Thanks!

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  10. 10. elucify 7:54 am 06/16/2012

    “a tape was a device that recorded sound”

    Alas, I am old.

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  11. 11. elucify 8:36 am 06/16/2012

    How sad that the commentary on this fascinating post about ape genomes and the signatures of our histories should be hijacked by one comment on the specious “issue” of miracles. Against that view, there are better arguments than “why would God try to deceive us.” God may be merely have been lazy, using what was at hand to create the next new thing, or maybe spent a few days playing Cat’s Cradle with DNA, moving from one form to the next.

    More interesting to me is, why is the idea of “miracles” (and angels and other sorts of related nonsense) so plausible to so many people? A comment complaining that you didn’t give sufficient credit to leprechauns magically creating bonobos from bananas would have received very little serious attention. It seems to me that memes like miracles, final causes, “creation” and so on are a major reason so many Americans remain willfully and pugnaciously ignorant on fundamental scientific concepts like evolution. You can’t talk people out of believing in bonobo-creating leprechauns by questioning the leprechauns’ motives. The problem goes a bit beyond that.

    About the question of bonono vs. chimp evolution, and their different temperaments: Robert Sapolsky has had a very interesting and illuminating career with baboons in the Serengeti. Apparently baboon social interactions are so ferocious that they make chimpanzees look like Unitarians. Yet, in one troop Sapolsky observed, when a tuberculosis outbreak killed off many of the more aggressive babboons, the new social organization that followed was much more pacific, and persistently so. (See

    This raises interesting questions about the relative interplay of genetics, selection, environment, and culture in social organization and speciation. The whole story about the bonobos certainly includes genetic and geographic factors, but as you point out, also probably involves contingency and feedback at several different levels.

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  12. 12. Bill_Crofut 11:40 am 06/16/2012

    Dr. Lewis (COMMENT 8),

    Regarding the origin-of-life experiments, Miller/Urey is arguably the best known. However, an anoxic atmosphere was assumed:

    “Assuming that terrestrial life did evolve on the earth, what was the planet like when the process began? One thing is certain: the atmosphere contained little or no free oxygen and hence was not strongly oxidizing as it is today. The organic matter that must accumulate as the raw material from which life could evolve is not stable in an oxidizing atmosphere. One tends to forget that oxygen is a dangerously corrosive and poisonous gas, from which human beings and other organisms are protected by elaborate chemical and physical mechanisms.”

    [Prof. Richard E. Dickerson. 1978. Chemical Evolution and the Origin of Life. SCIENTIFIC AMERICAN, September, p. 70]

    Yet, a pair of geologists would seem to have refuted the notion:

    “Geological evidence often presented in favor of an early anoxic atmosphere is both contentious and ambiguous. The features that should be present in the geological record had there been such an atmosphere seem to be missing….Ever since the work of Oparin…
    and the success of the experiments conducted by Miller…the dogma has arisen that Earth’s early atmosphere was anoxic, probably highly reducing…Conjecture and speculation, based on a knowledge of the chemistry of living matter, gave to them the composition of their starting materials, and it would have been surprising if they had not achieved the results they did.”

    [Harry Clemmey and Nick Badham. 1982. Oxygen in the Precambrian Atmosphere: An Evaluation of the geological Evidence. GEOLOGY, March, p. 141]

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  13. 13. rickilewis 1:56 pm 06/16/2012

    Elucify, I agree completely and couldn’t state it all better. But I think believing in miracles can give people hope. I run into this with my new book about gene therapy. I am often asked, at the start of an interview, about the “miracle” of gene therapy. I’ve thought about this a great deal, and I answer that it was science that gave a boy sight through gene therapy, not a miracle. I realize that might turn some people off, but I just can’t use the “m” word to describe scientific research.

    Thank you also Bill. There have been many variations on the Miller/Urey theme. I cover a few in my intro bio textbook, which is itself a fossil by now. The simulation experiments that attempt to bridge chemistry and biology are wonderful, but we can’t ever really know — although I wouldn’t put it past Craig Venter to figure out how to create life ex vivo. He’s almost there.

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  14. 14. johndecoville 7:02 pm 06/16/2012

    Congrats Ricki for your article. And Stargene, your post on Creationism really impressed me. Maybe I will compose an “Elevator Speech” version of this to run on my Creationist acquaintances. Or not! I am ever amazed by the miracle of closed minds with “don’t go there, don’t touch that” responses to a whole palette of subjects.

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  15. 15. subterra 10:08 pm 06/16/2012

    Dr. Lewis,
    Fascinating article, tho I have one question: “We didn’t descend from apes, we ARE apes.” Are all the hominid species (all unfortunately extinct except ours) taxonomically considered a subset of apes? Where’s the division, if there is one? Just wondering…

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  16. 16. rickilewis 11:32 pm 06/16/2012

    Thanks John and Subterra.

    From wikipedia (I know we’re not supposed to let our students use it, but it is pretty accurate for genetics, at least):

    Hominidae consists of orangutans, gorillas, chimpanzees, bonobos and humans.[1][2] Alternatively, the hominidae family are collectively described as the great apes.[3][4][5][6]

    Genetically we are so close to our hairier brethren that some investigators have suggested that chimps and bonobos be classified as Homo and not Pan, although this conflicts with the australopithecines. Those australos are the guys who truly fascinate me. Imagine a time when there were at least 4 types of hominids.

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  17. 17. Percival 3:01 am 06/17/2012

    Steven Torrey et. al. arguing miracles vs. evolution; consider that life forms do indeed share similarities in form (and function in their environment) mediated by specific inheritable physical structures that allow them to interact with their common environment. Any deity would have little choice but to use common building blocks to form life capable of functioning on Earth. Humans fingers and fish fins, eyes of all sorts, various body plans, and so on are all the macroscopic manifestations of interacting genes that code for those structures, and such genes are in all life. Such “miraculous” inheritable similarities and differences could be hallmarks of either creation or evolution.

    Dr. Lewis, this apatheist finds all that less interesting what I infer from your blog- the possibility that genes may not only code for structures, but also for behaviors. This flies in the face of conventional wisdom that behaviors are cultural, transmitted by social reinforcement among beings with the same genes. In this American election year, I find myself involved in many discussions about same-sex marriage. When the “unnaturality” of same-sex behavior is brought up I like to point to Pan paniscus as a counterexample.

    It seems to me that we humans exhibit a strangely polarizing mixture of paniscus’ promiscuity and troglodytes’ aggression; mention of the former brings out the latter in some, but not all of us, suggesting a bi-valued inheritable predisposition to consider same-sex behaviors as acceptable or unacceptable. It’s almost as if some humans are more like paniscus, and the rest like troglodytes. Perhaps the common ancestor of humans and both kinds of chimp had the same conflict in its makeup, and we got stuck with it while the Pans express one over the other.

    If such behaviors are inherited they will show up in the small differences among primate DNA. Is anyone looking?

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  18. 18. rickilewis 10:26 pm 06/17/2012

    Genes encode proteins, and it is what those proteins do that determine phenotypes, including some aspects of behaviors, the shape of a nose, a blood type, a susceptibility to cancer in the face of a particular environmental insult. A gene that encodes an enzyme that controls testosterone synthesis at a specific, key point in prenatal development, for example, could influence aggression. I do think that most behaviors are learned, not inherited — but this isn’t my area of expertise. A teacher might have more insight into this question than I do. In general I do not like the idea of genetic determinism. There is much that we can do to mold who we are, especially how we behave.

    I agree with your idea, Percival, of us and chimps and bonobos taking different traits from that original, long ago pool of possibilities. Well stated!

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  19. 19. Mr. Peabody 3:34 pm 06/20/2012

    Elucify has an interesting point regarding Baboon behavior, both the stability (or lack thereof) of that behavior, and as compared to chimp. I think it’s fascinating that the four African apes (including us) span such a wide range of mating behavior. It’s particularly interesting that the baboons, who, like humans represent tree dwellers that moved onto the plains, are so extremely different from us.

    It suggests that the behavioral differences may not be so much dictated by environment but might represent a kind of Nash equilibrium. If so, it’d be interesting to speculate on what it would take to upset such an equilibrium and move a population to another point. Is the behavior really fixed, or does the species have the capacity for multiple patterns depending on circumstances? Or to put it another way, if humans, bonobos, chipms, and gorillas all had a common ancestor, does their behavioral radiation tell us anything at all about the common ancestor’s behavior, or could the common ancestor have behaved like any one of them, or entirely differently?

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  20. 20. MmeLapin 7:50 pm 06/21/2012

    Great article, thank you!
    So only us, unicorns made it to Manhattan? :)

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