The complex evolution of personality

So, apparently even sea anemones have personalities.  The idea that non-human animals can be measurably, say, bolder or shyer than others of their species may or may not be a surprising idea to you, perhaps depending on how many cats, dogs, horses, laboratory mice you have known.  But, scientists who study animal behavior are currently focusing on animal personality in a big way.  The BBC Radio 4 program Discovery discussed this the other day, and to us, the discussion raised some unintended points.

Hermit crab; Wikipedia

Presenter Adam Hart interviewed behavioral scientists studying personality in animals as diverse as songbirds and sea anemones. All agreed that variation is the norm.  Daniel Nettle, at the University of Newcastle, described five different dimensions to human personality: extroversion, neuroticism, agreeableness, conscientiousness, openness to experience.  They aren't all found in non-human animals, he said, though some seem to be, and all seem to be present in chimps.

Personality variation in the great tit, a small songbird, has been studied by many people (e.g., here and here).  For example, Samantha Patrick from the University of Gloucestershire described catching birds in the wild and releasing them into a room furnished with artificial trees, which they hadn't seen before.  Each bird's behavior upon first seeing the room is recorded, and its 'exploration score' calculated, to determine where the bird sits on a boldness/shyness range.  Fast explorers are more aggressive, and more willing to take risks than slow explorers.  And, when birds are artificially selected for parental aggression or calm, heritability of such personality traits is consistently around 50% -- that is, 50% of the behavior seems to have a genetic source.  But behavioral plasticity has been found to be common in great tits as well.

Great tit; Wikipedia, photo by Lviatour

But it's not just vertebrates that are being studied.  Mark Briffa at Plymouth University studies boldness and shyness in hermit crabs. He disturbs them by lifting them out of the water and turning them upside-down, leaves them thus for five seconds, and then replaces them in the water, and measures the time it takes for them to return to normal.  He then gives them a boldness rating.

Hart asked Briffa whether boldness in hermit crabs is at all equivalent to human extroversion.  That is, whether understanding hermit crab behavior give us any insights into human behavior.  Briffa's answer was that humans share an ancient neurobiology with other animals, including hermit crabs, and looking at that will help "simplify the problem" of human behavior.  Maybe.

So, there are conscientious crabs, those that spend a lot of time investigating empty snail shells as they make the decision about which one to move into next.  And there are bold hermit crabs, who seem to choose with little consideration.  There are evolutionary trade-offs to each of these behaviors, Briffa said.  The conscientious crabs get better shells, but waste a lot of time looking, while the bold crabs get iffier shells but saved time.  Time for what, exactly, it wasn't clear.  Can't be making more hermit crabs, because personality traits are not linked with fitness, and Briffa was not the only interviewee who said this about the animal they study.  That is, there's no individual reproductive advantage to being bold or shy, conscientious or not.  If there were, of course, there'd be a lot less variation in personality because it would have been selected out of the population in favor of the personality trait that led to more offspring.

How did these traits evolve?
This means that these traits aren't here because they were favored by natural selection, at least not in the present if these studies are any indication.  They could be here just by chance for reasons of ecology or population structure of some kind in the species' pasts.  Or, it might mean that there's a lot more plasticity in personality than is being reported, or identified by current methods, and that in some way plasticity is genetically enabled.  And indeed this would be expected, given that adaptability is so widespread that we've called it a fundamental principle of life.  A brain that can sense its circumstances, evaluate them, and plan responses may be what has evolved, but different brains, even if they were developed from the same genotype, might make different decisions.

However Hart, and interviewees, asserted that natural selection has favored a variety of personality types. But if no personality type has more offspring, gradually out reproducing the others, this can't be. It's only possible if group selection, natural selection that can see, and thus choose traits that benefit a group, is at work.

So, great tits can be shy or bold.  If an entire flock is bold, they are often on the move and able to locate new food sources, but they ignore each other, and that's bad for the cohesion of the group.  Shy birds stay together, but they don't move to new food sources, and that's bad for the health of the group.  A mix of bold and shy birds is ideal; the bold birds ensure that the flock moves to new food sources, and the shy birds follow.  Group selection would have favored a flock that includes a mix of personality traits, for the benefit of the flock rather than only a single personality trait, with its serious flaws.

But, this is a controversial issue.  Even Darwin, who himself addressed behavior including that in humans and our closer relatives, was rather mixed on this point.  The kind of mixed-flock just described could be a case of complex balanced polymorphism if the traits are genetically determined.  Too many bolds, bad for the group, too many shy, bad for the group.  The bold/shy genotypes' fitness is a function of the population in which they occur.  That would be standard genetic theory.

Group selection is coming back into fashion, being seen these days by all sorts of theoretical modelers and empirical investigators.  It has a checkered history.  The issue is that individuals shed their genes or not, and a genotype that engenders a particular behavior that is good for the group is fine -- so long as it's even better for the individuals with the genotype.  The reason this is contentious is that those strong Darwinians who are unhappy with any sort of resistance to pure individual selection argue that a genotype that favors the group cannot proliferate if that is at the relative expense of the individual with the genotype.  Otherwise, the group may do fine, but the genotype cannot become more relatively common over time.  At least not within the group.

The issues are quite mixed, and anthropomorphizing evolutionary modelers often say that an altruistic group-favoring gene variant will either be outcompeted, or that in effect it enables 'cheaters', without the good-guy genotype, to succeed at the good-guys' expense.  So the altruism-conferring variant loses out in the end.  If a group grows at the relative expense of other groups of the same species, the good-guy variants might overall increase in frequency (since the group without good guys disappears), but eventually, from a strongly deterministic Darwinian view of natural selection, the good-guy gene will get driven out.

How much does the work described above help explain behavior and the evolution of behavior in humans, where sociocultural factors clearly play a larger part in behavior than in non-humans?  The assumption, presumably, is that what's being explored here is the genetic aspect of behavior.  But, if personality is only 50% heritable in great tits, who don't share the extent of cultural influence on behavior that humans have, then it's hard to accept that we're getting at something that can be explained primarily by hard-wiring in humans.  At the very least, chance is playing a role comparable in strength to selection in determining group and individual success.  Of course, anthropomorphizing is difficult to avoid and it's difficult to tell when it's justified or not; indeed, cultural evolution has been described even in great tits, with the spread of learned behavior across a wide area.

Darwin wrote quite a lot about behavior, including altruism, aesthetics, personality and so on in Descent of Man, where he tried to show continuity between humans and other species.  His specific agenda, and even explicitly stated, was to displace religious creationism as an explanation for animal (and plant) diversity.  So he wanted humans to have traits that other animals have.  Several chapters deal with his ideas of these sorts of behavioral and communal sharing, including explanations of altruism.  He stressed behavioral continuity also in his Expression of the Emotions in Man and Animals.

Darwin was hand-waving much of the time when he did this.  And while he talked of selection, his main point was continuity and descent from common ancestry.  This is very different from observing what other species do, assessing when or how or if a trait is actually genetic in a way simple enough for selection to screen it at the gene level, and determining if, in fact, variants of the trait affect fitness.  Short term observations and risk of things like anthropomorphizing, and the likelihood that behavioral patterns for individuals may vary during their lives or in different circumstances, make the area difficult to study definitively in evolutionary terms.

But one thing is definitively clear:  animals do behave in variable ways, and that's fascinating enough.

You know porn when you see it, don't you?

The other day we wrote a post reacting to a NYTimes article that said that we really don’t know what ‘life’ actually is, that life is only a ‘concept’ we have, not something we can rigorously define.  But one thing about life, whatever life is, is that reproduction is essential.  Successful reproduction proliferates viable genetic variation via both chance and natural selection.  Sex is the way that happens for many species, like us.  That makes sex very interesting to scientists (for purely abstract theoretical reasons, naturally), and to the general public who are the participants in the reproductive circus.

There are various theories about how sex is or how it should be done successfully, not so much in regard to positions, but as to who does it with whom.  As humans, we each have a vested interest in this, and this is at least in part why homosexuality as well as heterosexuality attract attention.  Many studies are done to see how sex works, that is, how the intense and selective competition takes place and all of that.  Because we’re all in this competitive arena together, we naturally are curious to keep an eye on what our fellow competitors are up to.  So, besides the titter, that makes sexual behavior newsworthy.

Of course, the intense scrutiny of behavioral evolutionists centers on the strategies by which males purportedly want to inseminate as many females as possible, to spread their genes, but females want to ‘catch’ their man since they have to care for the few children they can bear, and want a steady breadwinner to help out.  Since this is so fundamental to success, and has been that way so intensely for so long, sexual patterns are often said to have been inscribed deeply in our genes ages ago, to ensure that the genes’ bearers don’t just bear all, so to speak, indiscriminately, but bear fruit in the process. 

Impersonal sex

Thus, for completely scientific and detached intellectual reasons, the news media are curious about sexual behavior.  So a recent newsworthy description grabbed our attention (as scientists). 

The story relates to one aspect of contemporary sexual activity or, one might call it, ‘performing’.  Attractive young people having sex with many different partners, sometimes different from day to day.  The pairings are arranged at the last minute, more or less as a planned business matter.  The performers often don’t know the person they’re doing the very most intimate acts with, or afterwards wonder who s/he was.  They cannot be sure that they were protected from disease or pregnancy, partly because they may be under the influence at the time they’re engaged in their romp with these strangers.  You may see a record of their activity on posted videos showing the various sexual positions, devices, and activities that are involved.  Those activities may include serial sex or group sex—you name it! 

Of course, we must be talking about the porn industry, because there the evolutionary rules are apparently suspended for some reason.  Perhaps society seems to frown on the activity because its random impersonality leads to licentiousness that might upset the evolutionary apple cart.  Fortunately (you breath a sigh of relief!), at least this is a somewhat underground aberrant activity on the fringe of society.

Wrong!  What we describe is today’s ‘hookup’ culture.  This is what many college students (and hence educated and privileged and should-know-better, not just desperate deviant addicts) are doing.  They write and boast about it in their college newspapers.  Campuses are ringed with bars where the ‘auditions’ for partners take place.  The sex that results is no less real, varied, graphic, and impersonal than porn.

Hookup, or porn?
Source: http://www.thedailybeast.com/witw/articles/2013/11/15/does-hookup-culture-hurt-women.html

But there’s a difference

Actually, there is a difference between hookup culture and porn.  Porn performers work openly in daytime, with formal contracts, under at least partly regulated conditions.  They are clear in advance about what will be performed, and there is at least some protection related to medical health and contraception.  Their activities take place under controlled conditions, with witnesses.  No waking up afterwards and wondering what went down, with whom (or how many).  It’s completely voluntary, partners not chosen in a stupor.  And they are paid in money, not just beer and vodka.

If you think of it in this way, porn could be seen as a more savory kind of activity than hookup culture.  College students do often voice regrets about their hookup experiences with its drug or alcohol connections, its anonymity, its nocturnal furtiveness (porn is daytime work).  But they still do it regularly, even if they sometimes report feeling ‘used’.  One main difference is that porn is at least always planned for posting on the net, but hookup adventures less often so.

We aren't defending the porn industry which has both its advocates and its critics.  But we write because of a recent news frenzy that concerned a student at a prominent university whose porn activities were outed by a classmate.  This hit the headlines, and the performer (a women’s studies major) became an overnight media interview sensation (interviewed on Piers Morgan/CNN for instance).   She is unapologetic about the fact that she does this to help pay her way through college (here's one of countless stories).  By contrast, hookup culture, if anything, may reduce the performers' chances of getting through college successfully.

If hookup culture is so widespread--and even if we avoid asking why this doesn’t give pause to the evolutionary theorists (one can always find after-the-fact explanations of why this doesn’t really violate the assumed genetic mandates, even though it obviously seems to)--we can ask whether the porn industry is any sleazier, rarer, or more deviant than what’s happening right now in the local bars in your town. 

Why is a college student, doing what she does in what seems a responsible way compared to what her friends are doing in their seemingly less responsible way, considered a sort of shocking misbehavior sensation?  Why is she being scorned or even threatened, as she says, by frat boys and other classmates--who may be watching or up to similar acts?  Why isn't the question not about the porn industry and its exploitation, but rather about the turn of our society in recent years towards amateur porn under the name ‘hookup’?  (See this link from which we got our figure.)

There are a lot of things one can think about the meaning of this state of affairs, knowing that it is transitory and that sexual behavior varies greatly among countries and over time within country (and here we don’t even need to consider the current rise of acceptance for homosexual and transgender/transsexual aspects).  There’s a big nature-nurture difference of opinion about this**, but our own view is that evolution has indisputably given us the drives for sex, either because of its immediate pleasure and/or for whatever other cognitive reasons.  But when it comes to it, like so much in human affairs, culture rules.

One might almost wish that bars would impose similar standards as at least some of the porn industry apparently does, but that the hookup culture apparently doesn’t.

----------------------------

**We will be screening any comments on this post to avoid it being mired in that divisive often polemical area.

Why can we count?

Remember in 4th grade when your teacher tried valiantly to teach your whole class to play the recorder?  Learning the fingering was hard enough, but then you had to learn note values and how to count them, and halves of them, and quarters of them, and rests, and how to keep the beat and so forth.  This is one of the most frustrating aspects of learning music for just about any beginner.  But, by the time students actually enjoy playing their instruments, the whole issue of counting notes, and time between notes and all of that, has become second nature.  They've internalized something that the rest of us never really did.

Recorder; Wikipedia

Our son-in-law Niocla Barbieri, an Italian professional double bass player who plays baroque and classical music, put it this way when I asked him about the experience of keeping time in an ensemble, including about the rubato, an expressive stretching of the beat.  I quote him at length because it's such a beautiful and evocative description.

Staying together in synch is not usually a conscious thing and I would say that the more the ensemble we play with is good, or close, or “harmonious”, the less you have to think about that and the less it stays conscious… Or the less you have to want it, I would say, because it happens by “itself”… I wouldn’t say it is something automatic, either, because it is very far from any idea of being something stuck or rigid, but the feeling is more something towards a fluid idea of a continuous chain of perceiving and reacting, detecting and responding, more like a very relaxed dialogue… 

Sometimes, from the top of a bridge you overlook down into the water of the river and you see the flowing of it, the general flowing, you perceive a whole fluid movement of a big mass… But some other times you watch better and you can notice several small currents and streams that seem to have independent “will” from the main one… They seem to slow down and then accelerate and then move sideways, as if a part of the water is going to move away from the rest… That’s just an impression, because all the big mass is still traveling as one... 

This is the flowing of the time, in orchestra and this is the rubato, I would say… Of course in a good group, where nice things happens without effort and with a sort of natural relax (“sprezzatura", we used to call it in the Italian baroque era), like the one of the flowing of a river...

A new paper just published in the Journal of the Royal Society ("Optimal feedback correction in string quartet synchronization, Wing et al.) takes a look at how professional musicians correct lapses in synchronicity. Sensorimotor synchronization happens in many organisms (fireflies that synchronize their pulsing, e.g.), so synchronization is of long-standing interest for a variety of reasons.  Musicians do sometimes have lapses -- indeed, sometimes it's intentional -- but they also are adept at getting back in synch.  How?  What have they internalized?

Wing et al. analyzed two different professional string quartets playing the fourth movement of Haydn's  quartet Op. 74 no. 1.



The question was how the members of each quartet responded to expressive, unrehearsed variations in timing.  Generally, members of a string quartet follow the lead of the first violinist, although with more or less strict adherence to this rule, depending on interpersonal dynamics and the philosophy of the group and so on.  So, correcting timing may be a matter of getting back in synch with the first violinist, or it may be more fluid than that.  In any case, the authors propose a feedback mechanism to correct timing that gets off, a linear phase correction.

Time series analysis of successive tone onset asynchronies [that is, musicians who aren't in time with each other at the start of a tone] was used to estimate correction gains for all pairs of players. On average, both quartets exhibited near-optimal gain. However, individual gains revealed contrasting patterns of adjustment between some pairs of players. In one quartet, the first violinist exhibited less adjustment to the others compared with their adjustment to her. In the second quartet, the levels of correction by the first violinist matched those exhibited by the others. These correction patterns may be seen as reflecting contrasting strategies of first-violin-led autocracy versus democracy. The time series approach we propose affords a sensitive method for investigating subtle contrasts in music ensemble synchronization.

If musicians always played the music in front of them exactly as scored, it could be dull.  And, they aren't automatons -- they hear a piece in their own particular way and want to express what it means to them and they have plenty of freedom to do this, within limits.  We, the audience, give them that freedom, and also adjust whatever internal metronomes we listen to music with (even those of us who failed 4th grade music have developed a sense of timing) to go with the flow of the music we're listening to -- within limits.  This is the rubato.  But there are limits, and apparently they are internalized.

According to Wing et al., musicians use linear phase correction to regain synchronicity with either other musicians or with the tick of a metronome.  That is, they know when their count is off, because it has been set previously, by the relationship between note values and time between notes, and they are able to tell when they're off, and adjust to get back into the beat.  Musicians learn their skill by spending tens of thousands of hours counting notes; that they can internalize it quickly, and correct it when it's off is no surprise.

It is often said that musicians are good mathematicians and vice versa.  The earliest formal musical theory was by the Pythagorean school of mathematics, in ancient Greece.  They figured out the mathematics of basic harmonies.  But many musicians didn't take, or hardly squeaked by, in mathematics.  So are they doing implicit time-series math in their heads implicitly?  How?

And try this on for size:

This is an excerpt of an ensemble playing John Adams' "Shaker Loops", with its fiendishly minimalist, relentlessly repetitive and syncopated measures (with endless slight deviations) that goes on for around 25 minutes.  We heard an ensemble play this a few years ago at Ithaca College, and the violist who was a friend told us the stress and horrors of trying to stay in synch.  But they did, beautifully, and in that instance (unlike the YouTube) they had no conductor!

In this general vein, what explains this curious phenomenon that I've observed numerous times, after decades of knitting?  Just last night I was casting on stitches to make a scarf.  The pattern called for 85 stitches.  There are too many distractions for me to be able to count stitches as I cast on, so I just take time out to count them a few times as I go along.  Remarkably -- at least I think so -- last night when I stopped to count I had cast on exactly 85 stitches.  But I've had this happen when the pattern called for 285 stitches too.  No phase correcting there, do I have an internal counter that turns itself on as I start to cast on, and then alerts me when I've met the target number?  If so, it seems like a rather frivolous way to spend brain cells though, even if useful.

Casting on; Wikipedia

I remember once being at my daughter's youth orchestra rehearsal when one of the violin teachers told me to watch the conductor when he stopped to talk to the players.  "He'll pick up the beat right where he left off," she told me, and indeed he did.  After years of conducting, he had developed an internal metronome that kept on ticking even when he wasn't waving his baton.

And then there's the internal alarm clock that always goes off 2 minutes before the alarm we'd set.  I don't remember the last time I've heard an alarm -- except when I couldn't figure out how to turn the bloody thing off on my phone.

So, this mathematical explanation for musicians correcting themselves when they get off the beat.  It might well be a good description of what happens, but it's not an explanation of what they are doing or feeling. To us, the deeper question is why we're able to do all this counting and time keeping anyway.

It's said that infants can count.  Or at least have numerical awareness.  As do non-human primates, and even dogs. Crows can count, parrots can count to six, and even have a concept of zero, according to at least one source.  Apparently even frogs can count.



So the ability to count must have evolved long before humans. But why?  Or better put, what kind of ability is it really?  It's easy to imagine adaptive scenarios (the duck had to be able to count her ducklings, to shepherd any stragglers away from predators, the wolf had to know its pack was intact, and so forth), but like most such stories, impossible to test them.

But maybe it's not an adaptation at all, really.  Maybe it's just one of the many ways we take in information about our surroundings, a by-product of there being more than one of any of us, or of any food, or of anything else in our environment.  Maybe recognizing that there are two lions over the crest of the hill is exactly the same as noting their color or even just that they are there.  It's just another observation; when we turn it into a number, that's when it becomes higher math.

Many pre-agricultural cultural groups are reported only to have numbers one, two, and many in their language, which may be consistent with the idea that formal 'math' and counting are recent cultural add-ons.  It is interesting that math and music were seen by evolution's co-discoverer Alfred Wallace as attributes that could not have evolved because, after all (he argued), our primitive ancestors didn't need them and so could not have been selected for them.   He used this as a reason to invoke the existence of God and human exceptionalism.

We wouldn't go that far, and instead are grateful for music, which, if it is but an evolutionary spandrel, is one of the more beautiful things we do with our ability to count.

lolhumans

"This pelican looks like a urinal. 
Go home, evolution, you are drunk." 
(wtfevolution.tumblr) 

Urinalification is so lol.

But it's calling evolution drunk that really got you, isn't it?

Steven Pinker (as of the late 90s) might say that personifying evolution's funny because it juxtaposes or mixes up what are normally separate rules or domains of our intuition. Personification's funny the way slapstick comedy's funny: Without any warning (but with a well-placed banana peel) a guy goes from being a dad to being a bag of molecules.When we give nonhumans human potential, Pinker says that we’re marrying “our intuitive psychology to our intuitive biology.” [1]

Personification is the same sort of thinking that enables us to discover, to know, to understand how the world works. It’s story, analogy, metaphor, unseen imaginative b.s. that we misfire like crazy. And even though we've overcome much of our reliance on it, we tend to preserve the spirit of it anyway. 

The powers of life, death and destruction aren't the only things worthy of personification. We'll give agency to a triangle or square. Just shapes. Being two-dimensional and moving around is all it takes. We are constantly up to this and as Dawkins said, 

“The reason we personify things like cars and computers is that just as monkeys live in an arboreal world, and moles live in an underground world, and water striders live in a surface-tension dominated flatland, we live in a social world. We swim through a sea of people. … We are evolved to second guess the behavior of others by becoming brilliant intuitive psychologists. Treating people as machines may be scientifically and philosophically accurate, but it’s a cumbersome waste of time if you want to guess what this person is going to do next. The economically useful way to model a person is to treat him as a purposeful goal seeking agent with pleasures and pains, desires and intentions, guilt and blameworthiness. Personification and the imputing of intentional purpose is such a brilliantly successful way to model humans, it’s hardly surprising the same modeling software often seizes control when we’re trying to think about entities for which it’s not appropriate, …”[2]

Although many other animals have desires and pleasures and pains and generally have experiences—at least they do as long as we assume we do—we should extend Dawkins’ reflection to our personification of nonhuman animals. There's very good reason we do this as scientists. It's not a terrible null hypothesis that if you observe an animal behaving like a human could, then it might be thinking like a human could. This is the argument by analogy or as I call it doing demonstrates knowing. How else could you reverse engineer cognition? You're a human, you think like one, you know how humans think from a scientific perspective better than you know how any other animal thinks. This makes sense. It's a good default. But that's all it is. And scientists get that. They taught me all this after all. (Reading a lot of Shettleworth, Povinelli, and Tomasello lately.) But the rest of us who don't work on animal behavior and who have very little experience with real animals at all are taking this perspective literally without caution. For example, maybe we should perk our ears but cock our heads skeptically when the website for Dognition (a service rooted in good science that sells cognitive testing for your furry friends) says, “Learning who your dog is as a ‘person’ will help you make the most of the time you spend together.”

Sometimes anthropomorphism smells like money and sometimes it makes us angry for no good reason. For example. Ed Yong wrote a piece "Male frog extracts and fertilises eggs from dead female" about an Amazonian frog that bleeps to death and still procreates. (No survival necessary--take that, Darwin!) Yong didn't personify the frogs but that didn't stop a reader. 

And thanks to the delightful woman who accused me of misogyny for my piece on the necrophiliac frogs. They. Are. Frogs.
— Ed Yong(@edyong209) March 1, 2013

I have a hunch that our habit of anthropomorphizing (combined with some empathic and also narcissistic tendencies) makes it much harder for us to understand reality, to understand scientific explanations for the universe, and to stumble onto new ones.

I wonder a lot about how our language encourages these mistaken habits. I've written before about how I don't use "force" to describe processes and mechanisms of evolutionary change. It's one of my f-words of evolution.

I've got similar concerns about our language that describes animal behavior. Take for example this fascinating paragraph written by the primatologist Toshisada Nishida about the chimpanzees he studied at Mahale, Tanzania:

“In an effort to maximize their reproductive output, males and females may cooperate when it is to their mutual advantage. However they may also control, manipulate, betray and even attack each other when they have conflicting interests. Chimpanzees maintain a promiscuous mating system, for which females develop a huge swelling of sexual skin and males large scrota. These morphological features make sperm competition the characteristic features of chimpanzee sexual activity. Males are expected to mate with as many females as possible, while female are expected to be more choosey because reproductive output over their lifetime is more limited. A powerful constraint on female chimpanzees is the need to consider males’ tendencies toward infanticide.”[3]

I added those italics to emphasize the language that could be interpreted to give chimpanzees more cognitive ability and more agency than the author intended or has evidence for. That paragraph, re-written to avoid any overstatement of chimpanzee cognition and any hint of calculated intention by chimps or by Mother Nature, could look like this:

In a system where higher reproductive output means more of whatever traits lead to it in future generations, males and females may behave cooperatively because it has been perpetuated by higher reproductive output in the past and will continue to do so until something changes. However, depending on the circumstance, they may also control, manipulate, betray and even attack each other if cooperation is supplanted by another behavior that is and has been perpetuated due to its increase of reproductive output, instead, in that sort of circumstance in the chimpanzee’s life. Chimpanzees maintain a promiscuous mating system and, because higher reproductive output of females with huge sex swellings and males with large scrota, females have huge sex swellings and males have large scrota. These morphological features exist, as hypothesized, because sperm competition has been occurring over chimpanzee evolutionary history. Males that mate with as many females as possible have, and have had, higher reproductive output, while females mate less frequently and have much more limited procreative potential over their lifetimes, so they appear to be choosier than males about their copulatory partners because doing so (assuming they are actually choosier than males) has and does increase reproductive output. A powerful influence on female chimpanzee mating behavior is males’ tendencies toward infanticide because females who have babies that are killed have lower reproductive outputs.

There. I managed to suck all the fun out of chimp sex. Not only that, but if you made it far enough you must be wondering how I could be so circumspect about female mate choice. That’s something for another day, but let’s just say that we should be circumspect about male choosiness too since they can’t decide which females (or males, or other circumstances) will give them erections.

Oh, hello! Now you’re awake! Why did my translation of Nishida’s paragraph fail to engage you? Here’s a try: Because it wasn’t a narrative and there were no interesting actors with calculating minds raging with intentions. There was nobody to figure out, to empathize with, to love, to fear, to root for. You just don’t tell stories without those kinds of characters.

But listen up close: that’s the true story of most of Earth’s evolutionary history. Agency evolved (maybe), but evolution itself did nothing purposefully, or even whimsically, to cause it.

Left to our naïve devices, how we talk and write about animal behavior affects how we think about their truths, their essences. The animals we put on the big screen are now just CGI manipulated reality--no cartoon drawings necessary for a pig like Babe to politely request sheep to scram, or for the pups in Space Buddies to bark interstellar commands. If only they had our mouths and throats these creatures could tell us about all the complex thoughts and feelings they experience! My mom has named this the Disney Syndrome. Some might blame the fertile “lolcats” and other such memes. We don’t just anthropomorphize animals, though, we personify oak trees, grandfather clocks, and toenail fungus.

Let's not pile all the blame our limited language, our love of agent-driven narrative, our teachers, scientists and Disney. Because how removed we are from “nature” probably affects our perceptions of animals too. Urban and suburban Americans might be the worst about this. In a piece about Joe Henrich's work, Watters writes,

“While studying children from the U.S., researchers have suggested a developmental timeline for what is called “folkbiological reasoning.” These studies posit that it is not until children are around 7 years old that they stop projecting human qualities onto animals and begin to understand that humans are one animal among many. Compared to Yucatec Maya communities in Mexico, however, Western urban children appear to be developmentally delayed in this regard. Children who grow up constantly interacting with the natural world are much less likely to anthropomorphize other living things into late childhood. Given that people living in WEIRD societies don’t routinely encounter or interact with animals other than humans or pets, it’s not surprising that they end up with a rather cartoonish understanding of the natural world.”

Nobody's saying to give it up completely. It's adorable.It's funny. It's lovely, actually. But if we coddle it like crazy in our children and if we don't check it once in a while in ourselves, this cultural phenomenon is going to continue to contribute handily to the scientific challenges that we face with increasing urgency.

Before submitting a scientific manuscript about animal behavior, evolution, climate, or any process that tempts us to infuse agency, make sure it's not drunk.

---

[1] From Pinker's lecture "How the mind works" published in the Annals of the New York Academy of Sciences

[2] Richard Dawkins's TED talk at about 21:00 - http://www.ted.com/talks/richard_dawkins_on_our_queer_universe.html

[3] Nishida, T. (2012) Chimpanzees of the Lakeshore (Cambridge University Press), p. 201

Oh, what a tangled web we weave

Walter Scott is responsible for the famous line:  Oh, what a tangled web we weave, when first we practice to deceive.

It sounds profound, but is it wise words, or just bollocks?

Here, at least is the latest in the 'evolution was just like this' department.   A study on reasoning  that is part of an issue on the subject in the Journal of Behavioral and Brain Sciences, concludes that reasoning evolved to be deceiving rather than to tell the truth.  At least, the authors of this new just-so story don't claim it's genetic: deceptive rhetoric evolved socially. 

As the NYTimes reports, it has long been assumed that reasoning evolved to enable us to search for and determine Truth.  But,

[n]ow some researchers are suggesting that reason evolved for a completely different purpose: to win arguments. Rationality, by this yardstick (and irrationality too, but we’ll get to that) is nothing more or less than a servant of the hard-wired compulsion to triumph in the debating arena. According to this view, bias, lack of logic and other supposed flaws that pollute the stream of reason are instead social adaptations that enable one group to persuade (and defeat) another. Certitude works, however sharply it may depart from the truth.

The idea, labeled the argumentative theory of reasoning, is the brainchild of French cognitive social scientists, and it has stirred excited discussion (and appalled dissent) among philosophers, political scientists, educators and psychologists, some of whom say it offers profound insight into the way people think and behave. 

Now whether this is true in all societies, a uniform cultural evolution or a parallel one (similar in, say Pacific Islanders and African Ashanti or San, but of independent social-evolutionary origin) is a valid question.  In fact, much as we hate to take sides with the genetic-evolutionary view (!), there have been numerous arguments that human language is basically an extension of eons-old display tactics that were designed to intimidate or deceive, as in mating competition.  Such things are not new to humans, or even primates, so if it is biological it predates our species and the explanation is more general.

However, let's ignore whether it's cultural or biological.  The same people who fervidly see competition-everywhere, the arch-darwinian view of life,  will love the idea that she dissembles to deceive.  If you're looking for a rival under every bed, you'll certainly go along with the idea that we use language (reasoning, persuasion, rhetoric) to distract, derail, or deceive potential competitors:  you really do, as the article says, want to win rather than to inform others.

This certainly is one way language is used (at least in cultures in nation-states, where we have daily evidence).  But is it 'the' truth?  Is it part of culture, or only of some cultures....or did cultures evolve reasoning 'for' deception per se?

It is easy to see a polar opposite to the latest assault of selectionism.  If you deceive, you can cause others to come to loss or grief.  Why should they not have a long memory, that they'll use to even the score later?  Why isn't truth good for the group, and deception a way to make everyone vulnerable?  Our ancestors--including primates--lived in very small local groups.  They might be very vulnerable to internal misinformation.  Why is telling the truth institutionalized in many if not most cultural norms--what children are taught, for example, even if we're not perfect at it?  Is that because if everyone is convinced you're truth-telling, it's easier for you to mislead?  Or is it because truth-telling really is what's important, and you mutually have to rely on it for your survival?

Further, what is truth and how do you know what people's motives are (whether they are even aware of them or not)?  Since 'truth' is what we think we perceive, and since we always have imperfect data, imperfect perception, and imperfect intelligence, why should we assume that 'reasoning' is false rather than flawed?  After all, even 'experts' in most fields related to behavior (to wit: economists, pundits) are grossly wrong presumably because of ignorance or bias rather than intentional deception.  One might suggest that the journal article's authors' interpretation of the intent in reasoning is more a reflection of their ideologies and biases, than it is of the underlying truth (or are we just saying that to make you believe us??).

Anyway, why should our ability to reason have evolved for only one purpose?  Did our hands evolve just to let us hunt?  Like most traits, reason is multi-purpose, and can be as useful for cooperation as well as competition -- and many other things. It's how we express how we assess our environment, our circumstances.  Often it is verbal expression, imperfectly representing our internal thoughts.  We can reason our way to figuring out from these footprints what kind of prey we're likely to find if we hang out long enough at the waterhole, or that that plant is poisonous, or to formulating a mathematical proof just as we can clap with our hands, help another across a creek, and caress a child's cheek. And, it's not just that the functions other than winning arguments are exaptations (purposes beyond the one the trait first evolved 'for') of the ability to reason, because ants and bees can reason. Or is deceptive reasoning limited, by social constraints, to certain but not all topics of conversation?

The choice of a single overriding purpose for our ability to reason says more about the those doing the choosing than it does about the trait.

The evolution of complexity without natural selection

There is a very interesting report in Nature this week (see the BBC story, if you can't access Nature) about the evolution of complex life and the role of natural selection in that.  The BBC writes

A comparison of proteins across 36 modern species suggests that protein flaws called "dehydrons" may have made proteins less stable in water.

This would have made them more adhesive and more likely to end up working together, building up complex function.

The Nature study adds weight to the idea that natural selection is not the only means by which complexity rises.

These flaws are a particular aspect of proteins that make them less likely to do their assumed original or 'proper' job as well as the normal form of the protein would. This molecular deficit makes proteins stickier and more likely to adhere to each other.  The authors suggest that this can enable more complex molecular interactions, and hence more complex living forms.

The analysis showed that organisms with smaller populations - such as humans - had accumulated more of these defects than simpler organisms with vastly higher population numbers.

One of the authors, Michael Lynch, has been trying to persuade biologists that classical Darwinian natural selection is not the only way that complex traits can be enabled.  The other author, Ariel Fernandez, is an expert on the particular biochemical aspects of these modified proteins.  If a population is small enough, traits that are not quite as 'good' (in terms of their darwinian fitness) as some other version of the trait in the population can nonetheless proliferate and even displace the 'better' one.  This works when the supposed deficit is small relative to the best-available, and the population is small.  The consequent advance in frequency of the less robust forms can lead to new traits--such as the aggregation of similarly deficient proteins to lead to more complex structures and hence new or more complex traits.

This is not an argument that classical kinds of natural selection don't or can't occur, but it is an argument that nature is not always relentlessly perfecting and purifying what exists.  So it is a challenge to the kind of universal selectionism that we often see and hear stated as 'the' theory of evolution.  Of course, if something advances, an ardent Darwinian can say that, however indirectly, this variant was in a sense the best after all, or that the new complex trait would not evolve without being favored by selection.  So a Darwinist would argue that it is wrong to refer to these as 'flaws' in molecules, just as, from an evolutionary point of view, humans' poor night vision, worse than that of, say, owls, is not a 'flaw': in our evolutionary history, it was the best available.

We won't delve into that argument, which involves definitions of terms, ideas very hard to test scientifically, short-term ideas assumed to apply steadily in the long term, as well as stubbornly held ideological views about evolution.

But we will point out that the idea of Lynch and Fernandez relates to a major interest of ours, here on MT here and in the book after which we named this blog: it relates to what we have called cooperation in the nature and evolution of life.  Evolutionary success has involved at least as much successful interaction among cooperating units--in this case 'defective' proteins--as it has involved relentless all-seeing selective competition.  Selection and cooperation exist, perhaps at all levels of life.  The major question for biologists who want to understand life rather than just assert an ideology about it, is to understand how these two factors, along with many aspects of chance, explain how life works and how it got that way.

Eugenics and other genetic risks, continued

Again, we return to a topic we said months ago we'd follow up on, but never did.  Holly touched on it here recently in her post about genetics and intelligence -- and, in fact, here's a quick followup on that subject; in particular, scroll down a bit in that link and read the sidebar on what happens to the brains of London cabbies -- and we wrote about it yesterday.  But, as the issues won't go away, and yet another paper is out this week in PNAS by the same characters using the same set of data, we think a topic we began to write about months ago is worth another look.  Especially given our focus this week on randomness and probability, and once again on genetic determinism and eugenics. 

Back in October, we, and many others, blogged about the paper by Fowler et al. that reported that genes largely determine political ideology.  The data set Fowler et al. mined for that paper, have mined before, and mine again for their PNAS paper this week, is the 2,600 subjects included in the National Longitudinal Study of Adolescent Health, a study of 20,000 adolescents in grades 7-12 in 1994, and followed up in 2001-2002 when students were 17-24 years old, and a subset more recently followed up with biomarkers, including DNA.  The study was designed to look at the effects of social context on health behaviors like seat belt use, drug use, sexual activity, nutrition and so on.  

The small subset who donated DNA were genotyped for 7 candidate polymorphisms. 

The initially targeted candidates are the dopamine transporter (DAT1), the dopamine D4 receptor (DRD4), the serotonin transporter (5HTT), monoamine oxidase A (MAOA), monoamine oxidase B (MAOB), the dopamine D2 receptor (DRD2), and the dopamine D5 receptor (DRD5).

Why these particular genes were   chosen is not something we could easily find but presumably it has to do with previous reports of their association with particular behaviors.

A cursory literature review shows that using these genetic data, researchers have, to date, found 'the warrior gene', that is, an association with DAT1 or DRD2 and gang behavior and serious delinquency, a link with low grades and DAT1, a dopaminergic gene, and that "students with a single, DRD4 variant had significantly lower grades in English and math, but only marginally lower grades in history and science", the genetic basis of victimization, the genetic basis of our place in a social network, that is, popularity, an association with genes and smoking behavior, as well as the links with political behavior and ideology reported by Professor Fowler et al.  And, the new study by Fowler et al. reports that people who share the same DRD2 allele associated with alcoholism tend to be friends.  

Ok, let's just take the DRD4 gene.  This gene that has been associated with numerous behaviors previously, including attention deficit disorder (the association is with a 48 basepair VNTR, or variable number of tandem repeats, in exon 3), novelty-seeking (that exon 3 VNTR again), externalizing behavior in toddlers (exon 3 VNTR), temperament in children with the exon 3 repeat allele if they are given poor quality parenting (or 'differential susceptibility to child rearing'), aggression at age 4 (long repeat), attachment disorganization in infants (48 bp repeat), to cite just a few of the studies reporting an association of behavior with this long repeat in this dopamine receptor gene.  And there are plenty more.

The idea, as proposed by Hamer et al. in 1996 in the precedent-setting Novelty Seeking study, was that the number of repeats in the gene affects the structure of the receptor, thus how dopamine binds to it, and so the efficiency of neurotransmission.

But now there's this, a 2010 genomewide association study by Verweij et al.:

Variation in personality traits is 30–60% attributed to genetic influences. Attempts to unravel these genetic influences at the molecular level have, so far, been inconclusive. We performed the first genome-wide association study of Cloninger's temperament scales in a sample of 5117 individuals, in order to identify common genetic variants underlying variation in personality. Participants’ scores on Harm Avoidance, Novelty Seeking, Reward Dependence, and Persistence were tested for association with 1,252,387 genetic markers. We also performed gene-based association tests and biological pathway analyses. No genetic variants that significantly contribute to personality variation were identified, while our sample provides over 90% power to detect variants that explain only 1% of the trait variance. This indicates that individual common genetic variants of this size or greater do not contribute to personality trait variation, which has important implications regarding the genetic architecture of personality and the evolutionary mechanisms by which heritable variation is maintained.

No association with DRD4 and Novelty Seeking.  And no association with DRD4 and Novelty Seeking was found in 2 samples in New Zealand, and while some studies in birds have shown an association with a DRD4 variant and exploratory behavior, it isn't consistently reported.  A study of one of these repeat polymorphism has shown that the effect of the variation depends on your socioeconomic status: negative for low SES, positive for high SES.  Context determines what the genotype determines.

Now, all the usual caveats that we mention over and over again apply here -- the definition of the trait may vary enough between studies that they are comparing apples and oranges, and the association may in fact be real in some populations and not in others.  But GWAS should find genes with large effects, and the Verweij et al. study did not.

What if that's because the trait is due not just to a single gene but to gene-and-environment interaction? Would a GWAS still pick it up?  This would depend in part on the size of the study sample and the amount of environmental variation among those sampled.  GWAS detects net results, basically, especially if the environmental factors are not known or measured.  Large effects found in a GWAS may be because there was some tractably invariant environment among the sampled people, that may not be present in another sample, and the same allele may not have its purported effect in those data.

The association of this gene with political ideology could be real.  Or it could be a chance positive result due to multiple testing or other statistical aspects of the sample.  Or it could be real....but only ephemeral, changing rapidly with societal context.  The notion that we can predict these kinds of things very meaningfully is one we should be very circumspect about.  Even after extensive (and expensive), very technically sophisticated studies (unlike many of the behavior one-gene studies mentioned here), we can't make good predictions of very clearly genetically-affected traits like how tall you are or whether you'll have diabetes (and if so, what its particular characteristics, severity, response to treatment, etc. will be).

Every trait you can name probably has at least some heritability; that is, genetic variation contributes to variation in the trait.  Heritability is usually substantial.  But so are chance and the various aspects of lifestyle and environment.  High heritability means that genes are relative important in the population, but does not mean that an individual genotype predicts that person's trait reliably.  GWAS experience, which is now extensive, shows that high penetrating power of single (or even a few) genetic variants is not common.  Often, the trait definition is crude (like 'intelligence' or 'IQ', or 'asthma' or 'autism' or even obesity), but the definitions are changeable and cultural, the measures sometimes arbitrary, and people can have the same value for different reasons.  People with high intelligence measures can have better ability to memorize, or to learn quickly from one exposure to a fact or challenge, or to integrate repetitive exposure, or to do mental work by visualization or by other means, and so on.  

Change the environment or the measuring criterion and you can change the result.  Different approaches to modifying the achieved trait, like therapy for a disease, can apply differently to different people with similar measurement value.  People with similar glucose levels have different ways in which the 'same' trait is manifest during their respective lives.  This should be obvious, since diabetes and IQ have both increased substantially in recent decades, but the underlying genetic variation hasn't.


This is in rough terms why things can be genetically affected in real and substantial ways but, we would say, not genetically determined.  Again, the problem lies in overstating the latter and putting it into policy.  This is where the idea of 'eugenics', that is, of using ideas about inherited worth to make policy to 'improve' the human species and its genome, become heavily sociopolitical rather than scientific.  Historically this has led to discrimination against individuals and against whole groups.  One might be tempted to say that it's 'right wing' to believe in genetic determination of traits like ability or behavior, or the inherent value of one race vs another.  But this would be vague at best and misleading at worst.


To caricature affiliations, we can say that it's not just rapid right-wing behavior genetics that we should be wary of.  The rabid left has left its own trail.  While the Nazis were gassing people who were inherently 'inferior', the Soviets were starving people because, under the influence of one Trofem Lysenko, they believed life was improvable by experience alone rather than by inheritance (a view generally attributed originally to Lamarck in 1813).  In both cases, categorical beliefs about the role of inheritance led to disaster on a major scale.


That is why, despite the fact that of course genetic variation contributes to all biological variation, we should be very careful about making pronouncements that could be used for societal policy.  Today that policy might be favorable to you....but what about tomorrow?  Even if nothing untoward is being done with genetic data these days, prevention is the better part of valor.

Of course, if you want to make strong statements about the genetic determinants and evolution of ostrich knees, feel free, because only a few 'experts' in the world will care one way or the other.

Beat Takeshi Kitano at Fondation Cartier, Paris

Our daughter suggested we go to the special exhibit of Beat Takeshi Kitano's art at the Fondation Cartier pour l'art contemporain while we were in Paris. She had been planning to go for months herself, and we were happy to go with her. We enjoyed it a lot, but had no idea he'd be so pertinent to MT.

Beat Takeshi is a very well-known Japanese actor, artist, television personality, filmmaker and much more. He's outrageous, funny, slapstick, pointed, whimsical, quirky and poignant, and the exhibit was all that.

His T Rex piece really hit home (we're hoping the video, including this piece from the exhibit, that we're trying to embed will work, but if not it's here). He'd built an 8 foot tall dinosaur, and surrounded it by illustrations with possible explanations for why the dinosaurs went extinct, including that:

• They couldn't stop smoking
• Their front limbs were so short that they couldn't reach to wipe their behinds
• And they couldn't reach to hit their opponents back in a fist fight
• They got metabolic syndrome (from drinking soda and eating junk food)
• They always came out scissors when they played Paper Scissors Rock (their digits are scissors-like)
  

And so on. It struck us not only as funny and whimsical, but as a commentary, whether intended or not, on the often hopeless search for causation in science. Indeed, they couldn't wipe their behinds and might well have gotten metabolic syndrome, but again, correlation is not causation.

Another piece that was pertinent was the large watch Beat Takeshi had disassembled-- he'd placed the pieces inside a shaking dome and labeled it something like, "The probability of life on Earth is less than the probability that vibration will reassemble this watch."

This is the famous argument by William Paley that a watch is so well-organized that it implies the existence of a watchmaker. The Watchmaker is God, according to Paley. Richard Dawkins made the argument, known as the argument-from-design, famous in modern popular-science culture. Creationists love to argue (smugly) that the hundreds of individual pieces of a watch could simply never be assembled by random chance -- which they erroneously (and by now knowingly) say is the evolutionists' view of natural selection.

Of course, this is a straw man argument by creationists because no legitimate evolutionary biologist means this when saying that selection screens genetic variation that arises 'by chance'; what we mean is mutation happens 'by chance relative to functions it might have', and that natural selection provides the organizing force. How that works is a separate question, but Beat Takeshi's exhibit of a vibrating table with dissassembled watch parts makes the point: in decades of vibrating, the parts are still separate -- they've not (yet) formed themselves into a watch!

Evolutionary theory would actually go several layers better. As Jonathan Swift famously wrote:

"So nat'ralists observe, a flea
Hath smaller fleas that on him prey,
And these have smaller fleas that bite 'em,
And so proceed ad infinitum."

The relevance here is that the parts of the watch themselves would have needed a 'blind partsmaker'. Screws, watch-faces, housing, crystal glass, springs, gears, arrowed hands, and the like themselves do not exist in Nature. They have to have evolved. For an organism, one might say that we have parts (stomachs, fingers, eyes) and they have their own evolutionary history.

The wonder of evolution is that this nesting of 'origins' proceeds ad infinitum. At least, all the way back to the origin of life; the same thing is true even of the molecules acting in a cell. And in a sense it is that ever-nested nature of all aspects of life that makes evolutionary theory (and, we believe, the principles of organization we've written about here and in the MT book) so fascinating and powerful an explanation.

And if that's the story of life, Beat Takashi has put some life into the story.

Really something to crow about!

We used to think that we were Man the Toolmaker, because that was what made us uniquely human. Then, we lost our special place to other clever primates, who also could use tools. Marvelous, stunningly surprising, if humbling.

Step by step we are returned to the ordinary. But crows? Could they, too, put the kabosh on our egos? Of course, it's been known that they're clever (after all, Rossini wrote an opera, The Thieving Magpie, about that!). But you have to see this story and video from the Beeb. Here a crow uses a sequence of tools to get his treat. Apparently, according to the story, they do it even without prior exposure to the layout, and on the first time.

Maybe we have to even farther down the evolutionary Chain of Being before we get to the bottom of our uniqueness. But birds and humans have been separated for hundreds of millions of years, so this means that it's not an evolutionary shared trait (too many dumb-bell species on the way up both branches?). It evolved independently. That's even worse, as it makes IQ even more ordinary.

Oh, well, we're still the only species that can throw a baseball (at least, guys can....)

Penetrating the fog of 'penetrance'

In genetics there is a hoary old concept called 'penetrance'. It's not a definition of sexual success, so those of you who come to this post (no pun intended) with prurient interest should seek satisfaction elsewhere.

Penetrance is the probability that an individual has a specified trait given that s/he has a specified genotype. Usually, we think of the latter in terms of an allele, like the proverbial dominant A or recessive a in classical Mendelian terms in which genetics is taught.

Penetrance can range from zero -- the trait is never found in a person with genotype G -- to 1.0 (100% of the time the trait is present in persons with genotype G). If 'G' refers to an allele, that allele is called dominant if its presence is always associated with the trait, or recessive if the trait is present only in the absence of the other allele (in gg genotypes).

The key concept, that links simple Mendelian inheritance with general aspects of penetrance is that penetrance is almost always a relative term. The effect of an allele is always dependent on the other alleles in the individual's genome, as well as to aspects of the environment, and also to chance.

Sometimes things seem simple enough that we need not worry too much about these details. Very strong effects that are (almost) always manifest are examples. But when things are relativistic in this way, genetic inherency usually must take a back seat to a more comprehensive understanding.

The first step, and usually a difficult one, is to specify just what genotype you are referring to and, often even more challenging, just what phenotype (trait or aspects of a trait) you are referring to. To use the Einstein phrase that applies to relativity in physics, you have to be clear about your frame of reference.

This is much, much more easily said than done. Is 'heart disease' a useful frame of reference relative to alleles at some gene like, say, ApoE (associated with lipid transport in the blood)? We work with a colleagues, including Joan Richtsmeier here in our own department, who are concerned with craniofacial malformations. There are many such traits, including abnormal closure of cranial sutures (where bones meet in the skull). And, cancer is a single word that covers a multitude of syns (syndromes).

These are examples in which no two cases are identical. When that's so, how can we tell what the penetrance is of a mutation in a particular gene? Probabilistic statements require multiple observations, but also that each observation be properly classified (since probabilities refer to distinct classes of outcomes).

Since a given mutation affects only a single part of a single gene, it can be identified specifically (if, for the moment, we discount the mutations that take place within the person's body each time any of his/her cells divide). But traits can be variable and hard to define precisely, and the rest of the genome will vary in each person, even in inbred mice (because they undergo mutations). The amount of variation depends on the situation, but is very difficult to quantify precisely (recent work on genetic mutations in cancer begins to show this in detail, though we've known it in principle for a long time).

Most of the additional variation, not to mention purely chance aspects of development, homeostasis, and every cell's behavior, is unknown and much of it perhaps not even documentable in principle. Thus, in trying to characterize complex traits, we face real challenges just of definition, and much more so of understanding.

The same is true of evolution. An allele that has zero penetrance cannot be seen by natural selection. An allele with 100% penetrance is always 'visible' to selection in principle. But even there it has no necessary evolutionary implications unless it also affects fitness, that is, reproductive success. And that is another layer of causation with complex definitional issues, that we have written much about.

One bottom line is that just knowing a complete DNA sequence from some representative cell of an individual does not explain phenotypes, phenotypic effects, or evolution.

Smart dogs & dumb people

There was a story in the NY Times Week in Review section on Sunday about intelligence in dogs. They are increasingly being used in service to people with an ever widening range of conditions, such as epilepsy, phobias, panic disorder, autism, and so on. And, it's thought that they can detect some cancers before our technological methods can -- perhaps this has to do with their exquisitely sensitive odor detection. Several reports over the last few years have shown that dogs have the ability to learn the meaning of hundreds, if not thousands of words. As the story in the Times says:

By giving dogs language learning and other tests devised for infants and toddlers, Dr. Coren [psychology professor at the University of British Columbia] has come up with an intelligence ranking of 100 breeds, with border collies at No. 1. He says the most intelligent breeds (poodles, retrievers, Labradors and shepherds) can learn as many as 250 words, signs and signals, while the others can learn 165. The average dog is about as intellectually advanced as a 2- to 2-and-a-half-year-old child, he has concluded, with an ability to understand some abstract concepts. For example, the animal can get “the idea of being a dog” by differentiating photographs with dogs in them from photographs without dogs.

But this story makes some of the usual kinds of mistakes that we believe people should be wary of.

When it is said that a dog has the intelligence of a 2 year old child, this is misleading in several ways. It may -- may -- be accurate to say that a dog has the human-like cognitive abilities of a 2 year old human, but that is far from the way the statement is typically made or construed.

Why not say that a adult human has the dog-like cognitive abilities of a newborn pup? We wouldn't last more than a few minutes in the wild. It's hard to imagine anything dogs regularly do (even dumb breeds, not to mention fully-genomed wild dogs not protected by vets and Alpo) that even a super-intelligent human can do nearly as well. And it's arrogance of the worst kind to say that a dog is just hard-wired by its nose. Much of a dog's behavior is highly cognitive.

Dr Clive D. L. Wynne, associate professor of psychology at the University of Florida, a specialist in canine cognition, is reported in the Times story as believing that the brains of dogs and humans shouldn't be compared.

He argues that it is dogs’ deep sensitivity to the humans around them, their obedience under rigorous training, and their desire to please that can explain most of these capabilities. They may be deft at reading human cues — and teachable — but that doesn’t mean they are thinking like people, he says. A dog’s entire world revolves around its primary owner, and it will respond to that person to get what it wants, usually food, treats or affection.

But to say that dogs use their intelligence only to find food and favor, or mates, implies somehow a rudimentary or more hard-wired kind of behavior than that of us noble humans. Why do we go to work in the morning, or to the bar at night? Our species-hubris is extraordinary.

From an evolutionary point of view, of course we're not dogs. We're many millions of years separated from our common ancestor with dogs. But we are related and have very similar genomes and very similar neurobiology (indeed, flies have similar neurobiology in some ways, which is why some grant-seekers may stretch the point but relate their fly work to human psychiatric disorders).

We can invoke Darwin's nostrum that Natura non facit salum -- nature works slowly but doesn't make leaps, to make the obvious point that we and dogs are similar enough that certainly we must share much of our cognitive experience. To what extent that applies to our notion of conscious experience, which is really what people are talking about, we have no current way to know. But we can be sure there are rudiments of it at the very least, since our brains are so similar -- even if not identical.

After all, your mental 'age' and your cognitive experiences, are not the same as ours. For evolutionary reasons they are likely to be vastly more similar than your experience is to your poodle's, but there is almost certainly more continuity than those who would like university research ethics panels (IRB's) to approve the experiments they propose on the grounds that dogs are just animals; those are the same people who argue that fish don't experience pain or fear.

Dogs seem to have remarkable intelligence, even in human-like ways, more than had been expected (though any dog owner might argue that this has always been obvious). If we want to set ourselves as an arbitrary baseline, it is legitimate to ask about the mental age of dogs. But we might learn more if we study rather than dismiss the cognitive mechanisms by which dogs vastly exceed our abilities, and by doing more than just counting the number of smell-receptors dogs have.

From a dog's point of view, we humans are really rather incompetent.