Friday, June 28, 2013

Twitter, Twitter, little star!

Well, this week's thriller on the news wires, as in the BBC report we saw, is that a star called Gliese 667C has at least three (count 'em) planets orbiting it within the proverbial Goldilocks  'habitable zone' in which life can occur.

What the sky might look like from Gliese 667C; BBC
 Habitable zone?
This is the region where temperatures ought to allow for the possibility of liquid water,although no-one can say for sure what conditions are really like on these planets...
The planets would need an atmosphere to sustain liquid water on their surfaces, but at a distance of more than 200 trillion km, there are no means currently to determine what the precise conditions are like or whether life would have any chance of establishing itself.
Nonetheless, Dr Tuomi believes M-dwarf stars are good candidates to go hunting for potentially habitable worlds.
The fact that these three planets could have liquid water "...single-handedly demonstrates that low-mass stars can be hosts of several potentially habitable planets," explained one of the investigators, helpfully. We've seen this many times before, cosmologists using 'life' to mean 'life as we know it', the marketing criterion by which to get discoveries of orbiting rocks into the mainline news.

Whether these planets have any atmosphere is a trivial detail that current research can't answer.  In part, this is because the planet is a mere 22 light years away (about 200 trillion kilometers!).  The star is about a third the size of our sun, and the planets about 3 times the size of the earth.  These planets, the story hopefully enthuses, have annual orbits of 28, 39, and 62 days.  Because the pseudo-sun is smaller and cooler (it's what is known as an M-dwarf star), planets can be closer to it than the earth is to our sun and life still may have evolved there, and they can orbit fast without being singed beyond recognition.

Now, finally!  We have planets that might plausibly (and hence the news writers and scientists would like us to assume, must) have life.  And just imagine what it's like!
Twitter, twitter, little star!
Life  on Gliese 667C  would be quite a whirlwind.  Let's take 40 days as the typical orbit.  Days and nights, and years, would (literally) race around like cars in the Indy 500.  A message as long as this would take a week to write.  For poor students, a 15 earth-week (say, 100 days) semester would take 3 Gliese 667C years!  Students would reach retirement age shortly after graduating.  And don't get too fond of your pets.  With a 10-year lifespan, kitty would only last 400 days--about one earth year!

Indeed, circling this little star so quickly would have taught everyone long ago to communicate fast.  We hypothesize that Twitter was invented on Gliese 667C, and somehow transmitted to earth.  With the world, so to speak, passing by with such dizzying speed, one would not wish to dawdle over every correspondence.  A long-time earth friend you've known for 5-10 years would be the equivalent of a Gliese 667C friend you met only a couple of hundred days ago.  We'd all have to wolf down our food to prevent noticeably aging during a single meal.  And nights would not last long enough for even a single 90-minute dream cycle!

The implications of life in the fast-orbit are dizzying.  It seems almost impossible to imagine.  And contemplating life on Gliese 667C raises further very serious and perhaps even more profound questions, that lead us (ever the skeptics!) to doubt claims or hints that life really does exist on Gliese 667C.  Here are some of the problems. 

Is life in the fast-spin possible?
  • Life heavily depends on the annual cycle of seasons.  For example, mating takes place in the cold season when many creatures are hibernating or pupating, so that young are born in the spring when their prey are hatching.  Because embryos take time to develop, if the year is too short, they will be born at the wrong time relative to their food sources.
  • Similarly, many plants shed their leaves to refresh their growth after an off-season.  Deciduous plants require fertilization from insects who are active (and hence whose larvae have matured) when the leaves are new and the plants are in flower.   It's true that on earth bees and plants and other animals have different gestational times from fertilization to maturity, but winters need to be long enough for that to happen, and that takes months rather than just a few days.  The short days and weaker amount of light from this lesser star would also play havoc with chloroplasts' needs for enough light to achieve enough photosynthesis in the brief daytimes, so trees might not be able to grow big enough nor produce enough nutrient energy to support their leaves, limbs, roots, flowers, and seeds.  Bad news for the squirrels, bees, bugs, and even woodpeckers.  Apples won't have maturing time to become, well, actual apples.  They'll just be tiny runts.
  • At the same time, the lesser energy may yield far fewer thunderstorms and hence  fires to clear the vegetation for forest health.  And this in turn may also not provide enough tropical rainforest to absorb enough CO2 or release enough oxygen as needed for other life on the planets.  And the growing seasons might be so short that only bonzai trees could survive, providing no sustenance or low- (or high-) hanging fruit for insects or mammals.
  • We don't know whether these exoplanets have atmospheres or not, but if there's life then of course they must.  But whether the 'air' would be dense enough for bird or even insect flight, or pollen dispersal, is highly problematic.  There must of course be sufficient oxygen for breathing as well as to provide a shield against dangerous cancer-causing UV radiation from Gliese 667C.
  • Sea life depends, at least for animals, on buoyancy, which requires that the salt content of the exoplanetary seas be suitable for algae, crustaceans, fish and sea mammals.  Likewise, the evolution of land life from sea life requires sufficiently strong  (but not too much!) gravity for support by bony structures, so the expansion onto land would allow mobility for searching for prey or escaping predators.
  • Even the climate makes a difference.  Spring runoff and the like provide fresh water when more animals are active.  Tectonic (geologic) activity is needed to shape the land and sea and its interface and even to provide some minerals and building materials for life.  But would it be fast enough, or too fast?
We have just outlined a few of the requirements for life on these new planets, and you would be able to imagine others along similar lines.  For example--do you think it's just trivial?--if the land, atmosphere, climate and so on were not appropriate for tree life, there would be no paper for books and hence no advanced civilization to evolve.

Of course, we're just spoofing here.  When cosmologists and the media (including sci-fi writers and Hollywood) talk about 'life' elsewhere, they almost always mean 'intelligent' life and even human-like life.  Talking about 'habitable zones' reflects this.  Yes, carbon, oxygen, water and the like are vital to life here, and could be important elsewhere.  But it is only a paucity of imagination, and a penchant for self-promotion, that leads to reports like this being treated as more than just the discovery of a few rocks in space.

Life need not be as we know it, or perhaps we have so provincial an understanding that the word itself really means our kind of molecular activity.  What other forms of self-perpetuating activity might exist, in or out of 'habitable zones', who can say?

Gliese 667C is a very close star to us, as these things go.  For starters, there are 56 stars known to be less than 17 light years from the earth (e.g., Wikipedia 'List of nearest stars').  These are, of course, stellar systems as dead as doornails as far as we can tell.  We get no radio rock music emanating from them.  So we must go farther afield to find our nearest neighbors. 

But even as close as 22 light years, which is much closer than most other stars even in our own galaxy (which is about 100,000 light years across) not to mention other galaxies, even if there were human life on Gliese 667C, and even if they were, unbelievably, in the same fleeting fragment of their existence to use electromagnetic (i.e., radio) means of distant communication, and even if they had some sort of 'language', and even if they were curious about what aliens might exist out beyond Gliese 667C, just to set up communications would take lifetimes (44 years just to exchange one message, and how many cycles to learn to read each others'?

Let's think about this.  There will be no Rosetta stone signaling from space--signals with translation into an earth language.  Decoding ancient (simple) cuneiform tablets, like the famous Mycenean  Linear B from the ancient Mediterranean world (see below) took a lifetime and more of scholarly work to understand and translate.

Linear B: Wikipedia
So, suppose, for example, we detected some dot-dash code-like electromagnetic emanations from Gliese 667C.  To establish recognized communication, first to show the 'signal' wasn't some sort of astrophysical artifact, much less to translate and actually converse, would it take, say, 100 messages, 50 each way?  Well, 100 messages means 2200 years, longer than it's been since the classical Greek era! And of course even the NSA (who may already have secretly recorded the emanations!) couldn't decode things that fast!

Actual travel even at high but imaginable speeds (assuming light is the fastest way to go and approaching it would require ginormous amounts of fuel energy), a one-way trip to Gliese 667C would take longer than hominids have existed.  So even contemplating contact, even with a nearby star, even having human-like intelligence (if that's not just a self-flattering term!), verges on putting us in a mind, much less a time, warp.

Is there life out there?  We've written about this before here on MT.  Given that there are on the order of billions of galaxies, each with billions of stars and hence likely multiple billions of rocks orbiting around, it would seem implausible that there is not a variety of forms of 'life' all over the place.  But while it is entrancing to muse about, it is to a great extent not even a scientific question to ask.  It is musing, it's philosophy or even religion perhaps, but it's not science. 

ET; The Guardian
We already have Hollywood to deal with this sort of thing, better than reality can. Rather than hawk the public to pay for it via 'research' grants, let the movie makers -- the dream-weavers -- bear the cost.  In a world of competing needs, it is not proper for scientists or media to hint, obliquely or otherwise, that discoveries such as this, interesting as it certainly is, is more than confirming in a specific instance what we've already long known: there are lots of orbiting rocks in the universe.

Thursday, June 27, 2013

My dogs' evolutionary history. Part 3: Inside scoop and why

Recall that we ordered DNA testing kits for our mutts. First we made predictions, then we revealed the results. Today I want to tell a bit more of the story...
Remember that time a doctor used a vibrator on my hips because I had a cyst on my knee? I was all into it "for science." It was an opportunistic science sting operation. There was totally gum on my shoe. There was all kinds of pseudoscience that day.

Anyway, I was all psyched up for that sort of Dateline-style, hidden camera intrigue when I called up Mars Veterinary, the people who do the analysis for Wisdom Panel doggie DNA kits, last Friday afternoon. I was all psyched up because, as Kevin said, I needed, "to make sure they're not defrauding people."

Me? I do? Little old me?

That sounds about right. I mean, just because I can see all the educational potential here doesn't mean I should be endorsing it without understanding it better. And while I'm understanding it better shouldn't I make sure they're not entirely full of s--t?

But I already know they're not full of s--t because they gave us results for both Elroy and Murphy that made sense. They didn't report crazy results and there are lots of ways they could have... there are 200 breeds on that list, most of which do not look like our dogs or like they've wafted their DNA anywhere near our dogs.

So, they can't be completely fraudulent. Whew. Okay then, less of a burden on me for this interview. But wait. Could it be maybe a little more nuanced, this hypothetical fleecing? After all, they're the ones who saw my blog and reached out to me to have an interview--isn't that a little big brothery? And, after all, their website doesn't tell us what their methods are, not really, not for those of us who have ever operated a PCR machine or run a gel. And they don't tell us what these markers are in our dogs' reports that led them to make the reports. I'm used to having too much information, even, because of 23andMe.

Anyway, there were all kinds of reasons to be professional when I called up the veterinary geneticist. But after she answered my first question so well, I pretty much lost all professionalism and drooled all over her, albeit through the phone.

Here's what I learned. Please bear with me... I didn't take direct quotes because (a) that's hard to do without a hands-free headset (or fancy recording software I don't have because I never needed), and (b) I got a wee bit excited and flailed my arms most of the conversation. 

All questions and answers are my paraphrasing.

Question: Are you using a chip or what? How are you genotyping?
Answer: A chip like 23andMe's isn't cost effective. Yes, there's a chip but it's not specific to the test. They use a sequenom platform. It's PCR markers combined into panels.  They run those PCRs for 321 markers, broken up into several panels, optimized so that they don't interfere with each other clearly and don't have to change primers. They use nested PCR for segmenting around the mutation and then to get the exact SNP they throw the DNA in a mass spec to find the particular A, T, C or G mutation. Each has a different weight, so each can be identified. 

Question: Do you get both alleles from that?
Answer: Yes. They don’t sequence in both directions but they sequence both chromosomes.

Question:  Are those 321 markers for visible or perceptible phenotypes? 
Answer: No. None are visible phenotype. They're ancestry markers/SNPs.

Question:  Have you found any dogs that have none, not one, of those breed markers?
Answer: No. And we don't expect to. But it's not completely out of the question given the spectral nature of variation over space and time. 

Question: How did you validate your mixed breeds family tree methods? Do you have mixed dogs with known parents and grandparents and type them all in the family?
Answer: The pure breed tests validate so well already. And also, yes, they do validate with mixed dogs with known heritage but not many. The methods are built out of Ostrander's research with 85 breeds, 5 dogs from each and 96 microsatellites. She licensed the patent exclusively to WisdomPanel. 

Question: How do your mixed breed reports compare to how people guess based on external cues? Aren't people already good at guessing their mutts ancestries?
Answer: Actually they're not. Ancestry DNA testing is much better. People aren't that good at guessing mutt ancestry based on phenotype, as far as the few studies suggest. (There's one by Victoria Voith that I want to check out and there's one by Levy on pitbulls specifically.)

We chatted for much longer than that and she shared all kinds of interesting information about genetics for dogs' visible traits and also lots about their reproduction which I'm keen to learn about. But that right there's all the relevant information regarding our doggie DNA testing experience that I got during the 30 minute phone call. She was completely open with me about everything which is why I'm kicking myself that I forgot to ask why they require the dog's weight when you submit its cheek swabs. I have a hunch, however, that it's got something to do with validating their mixed breed body size estimates given how many people use WisdomPanel on shelter puppies that will be better adopted if their projected size is known. 

So the question remains... If you don't have a puppy or don't care what it will grow up to look like or be like, why do Wisdom Panel? 

The promotional video on the homepage sums up why many people might do it: 

I wasn’t sure what my dog was made up of...Pretty sure she wasn’t just a [breed name]...I wanted to know so I could tell people when they ask me 'what kind is she?'

This is fascinating.

Why do we care where our dogs come from or what kind they are? Same reason we care the same things about humans and ourselves. And it all boils down to the fundamentals of the field of anthropology... and it's complicated.

And finally, why have I titled all three of these posts "my dogs' evolutionary history"? 
Because evolutionary history is a synonym for family history and for ancestry. And vice versa, all around. And, clearly, I'm trying to make a point about that.

When you type "evolution" into the Wisdom Panel website search, this is what you get:

But that's not going to stop me from using this to teach evolution. I've decided that Wisdom Panel will be a good alternative for students who aren't interested in doing 23andMe in my anthropology courses, so I'm going for it.

Dogs, humans, what's the difference?  A lot and not.

Wednesday, June 26, 2013

Can you throw with half a brain?

Homo erectus had half the brains that we have. This guy's got even less. (source)
This being at least my third post about the evolution of throwing here on the MT ("A prehistory of throwing things" and "Hurling words and turds, an evolutionary link"), I think I should give a little background about my interest. Even before I started graduate school my doctoral advisor got me (a lifelong athlete) interested in it, we teamed up with a biomechanist, did some modeling, wrote about what throwing might have been like for extinct hominins like Lucy and the Nariokotome Boy ("Throwing and bipedalism: A new look at an old idea" will email the pdf, just ask), and I was awarded an NSF graduate fellowship for the proposal to come out of that project.

So obviously I earnestly thought I was going to study hominin throwing for my dissertation, but when I started to try to pull a comparative experimental study together and realized that everything I wanted to do would require that I go somewhere(s) else and work with someone(s) else, it didn't make much sense. I needed a biomechanics lab and I needed lots of practice in one too. And, I couldn't even begin to figure out where to find chimps or other primates that I could work with, let alone that I could get to visit me in that biomechanics lab. Or I'd have to learn ways to study kinematics of animals without much control. And I'd have to go somewhere else to do most dissections too. And let's not forget how much smaller the fossil hominin sample was 12 years ago. It wasn't feasible for my dissertation.

It was okay though because while I was doing what eventually became my dissertation research on Proconsul feet in Kenya I met Neil Roach who was just starting his studies at Harvard and was working on the evolution throwing! If it wasn't going to be me, at least someone was going to figure this out for us, and that someone had the resources to do so. And that someone's research made the cover of Nature this week.

The paper's called "Elastic energy storage in the shoulder and the evolution of high-speed throwing in Homo." [link to paper]

Here's a promotional video that Harvard posted:

In the paper, the authors ask, Why can we throw like we do and why can't chimpanzees? and they look to the musculoskeletal differences between us to find out.

In this paper, it's all about the whip-like motion of the human body during a throw and the slingshot-like energy storage in tendons, ligaments and muscles that makes it work. They elegantly describe this process and write about three key differences between humans and chimpanzees that they say are critical to why we throw like pros:

(1) our flexible torsos that allow more rotation at the waist
Human (a) and Chimpanzee (b)
(Source: Figure 3 from Bramble and Lieberman, 2004)

(2) our lower amount of humeral torsion in our throwing arms
from Roach et al., 2012: "Fig. 1 Humeral torsion (in blue) is determined by measuring the angle
between the orientation of the humeral head and the distal condyle
of the humerus. In the clinical literature, the same angle is referred to
as humeral retroversion (in yellow) and is measured in the opposite

(3) the lateral, not cranial, orientation of our shoulder joints

From the study's website: "This image shows differences in the position of the shoulder between chimpanzees (left) and humans (right). These differences can be seen in both the muscular anatomy and in the bony anatomy of the scapula (shoulder blade). (Image credit: Brian Roach/Neil Roach)" 
Then the meat of the paper is devoted to their experimental analyses of a group of skilled human throwers that appear to support the importance of these traits in throwing, particularly for storing elastic energy for fast throws. I say "appear to" because I wasn't given any of the supplemental materials and what's in the main text (which is all I have) doesn't quite pull the analyses and those traits together for me, but that could just be my very rusty biomechanics training rearing its rusty head. Or it could be my incredibly high and probably impossible expectations about what we can take to the fossil record with only a study of human throwers upon which to rest our assumptions of functional anatomy.

For example, humeral torsion is often asymmetrical in humans, being lower in the dominant arm, adding support for the assumption that humeral torsion changes depending on activity during an individual's lifetime. Is it fair to compare that trait to chimpanzees when it's not necessarily an in-born difference? Yes. But that makes explaining selection on that trait a little bit more difficult. I think it's fair to consider it, at least its asymmetry, a marker that an individual may have been habitually throwing during its life. So in that regard, it's worth looking for in the fossil record.

But then there's another snafu: How important could it be in reality and across space and time when there is so much overlap in the quite acceptable (but relatively small compared to reality) sample here?

from the study (with my blue box added to highlight overlap): "d, Humans and chimpanzees show comparable degrees of torsion5, although throwing athletes show reduced dominant-arm torsion2 consistent with low torsion in Australopithecus and Homo erectus5. Chimpanzees are a combined sample as they do not show arm dominance, whereas human values are split between dominant and non-dominant arms as they show arm dominance. In d, the black and grey boxes and whiskers show torsion-angle quartiles, and the red dot shows the torsion angle mean."

There's good reason to believe that low torsion is different. But there's also reason to wonder if it's necessarily due to throwing or to, say, using the dominant arm to do any number of things, one of which is throwing.

There's also good reason to curse the early hominin fossil record for providing us with only five individuals to include in this figure!

And there's also good reason to curse australopiths for not clearly fitting in the human or chimpanzee box.

And there's also good reason to curse chimpanzees for not being different enough from us so that our evolutionary histories are easier to reconstruct.

That these three traits listed above do exist in Homo erectus means Homo erectus could have thrown like us. (How else would they have experienced such a shift in foraging strategy?) And that these traits don't exist in australopiths (although the flexible waist issue is still up in the air) means that australopiths couldn't have thrown like us, not with the force that we can put behind a projectile.

And if that caused you to pause and recall that chimpanzees are stronger than us, and to wonder why such a powerful animal is such a weak thrower... then you're right here with me, in my head.

This paper provides a strong explanation: it's all the elastic energy storage and the coordinated movements of the body to maximize it and to maximize its transfer to the projectile.

But that may be only part of it.

And because it's probably like most things about living organisms are (and like most things in the universe are), human throwing is probably more complicated... even more complicated than a complicated sequence of elastic energy storage and use.

There's a large body of literature that explains human throwing with another major difference we see between chimpanzees and humans: Our big brains.

That coordinated fine motor control of the body, head to toe, during a forceful throw is brainy. Is it brainier than what a chimpanzee's working with? It's not yet known, but it's not a bad assumption.

That fine-tuned timing of release that's crucial for accuracy, particularly with forceful throws is also brainy. Is it brainier than what a chimpanzee's working with? This is also, I believe, not yet known, but it's not a bad assumption either.

This isn't to say chimpanzees are klutzes. Far from it. It's to say that evolutionarily new and/or simply more motorneuronal matter in the brain and throughout the body is probably required to throw like a human, and to do all the things we do with our dexterous and powerful fingers, hands, and arms, and to do new-fangled, fast, sequential coordinated movements with our bodies. And it's probably a big part of why chimpanzees cannot or do not. (But trust also that it's highly likely that they have neurologically based abilities that we do not!)

Unfortunately, in this department, all we really have is brain size for early hominins and that's just not going to cut it for parsing apart these details we need to reconstruct throwing in extinct hominins even if we knew exactly what our brains were doing to aid in throwing. But comparative work with living species will continue to be enlightening about the brainy differences among us, even if they don't enable us to nail down behavioral details about fossil hominins.

Even still, I think there's a lot we can still hope to figure out about australopith throwing. We have a biped without a modern body. It would be really useful to better understand how well australopiths could throw under these circumstances. There’s a lot of variation on the baseball field but none that comes close to that between us and the australopiths. If we knew about their throwing ability and style, we could better know how they foraged for food, thwarted predators, and socialized with one another since action-at-a-distance is key for all. It's also important to know because there's only a bit (as one would predict), but there's evidence for tool use among them  (for example). What if having all the built-in throwing skill of a chimp is good enough as long as you’re built to be upright, you’ve been practicing, and you’re hungry?

As our 2003 research suggested...the long australopith arm would have given them a larger release window for slow, lobbing throws, something their puny brains could work with and still hit a target. But as arms got shorter with the genus Homo, particularly the forearms, the release window shrank, particularly as throwing velocity increases, and that’s when their larger brain would help with accuracy, especially for fast, flinging throws.

But that's only if the brain matters.

But it probably does.

And if brains do matter, then Homo erectus, with its half to three quarters of ours, was either throwing like a pro without all our fancy gear (suggesting we’re over-equipped) since it was pretty good at hunting  ...or that Homo erectus overcame its lackluster equipment somehow and still survived and reproduced just fine. Fine enough so that they could, over time, leave much brainier descendants. 

And then there's of course the running issue. Aside from humeral torsion, all the skeletal traits for human throwing are also for running. And doesn't every little step you take in a run feel like a little throw?

And then, to add to that, throwing anatomy appears to be important for making and using tools of all kinds, not just projectiles. If that's not intuitive, think of the similarities between throwing a ball and swinging a bat. If we want to reconstruct hominin evolution as a sequence of origins of traits and selection "for" this or that trait...this then that then this then that then tadaaa: modern  humans... we'll have to parse apart adaptations for throwing and for running and for tool making and use. But if that makes you wince, like I'm doing, that's because maybe that's the wrong question, the wrong tack. The more we understand about things like throwing, the more obvious it becomes that things are complicated (even moreso than this) and things are interrelated and they always were and in varying ways back through time.

While we're figuring out whether Homo erectus could throw like us with only half the brains that we have (at least as far as we're limited by cranial capacity and reconstructions of spinal cord diameter), and while we're figuring out more about what the australopiths could do, let's also figure out why chimpanzees are so much stronger than us. Is it because of this hypothesis about trading off muscular strength for speed? If someone has solved this mystery and I just missed out, please leave a comment! I feel like I could ramble on and on and on, but I'm going to leave it right here for today.

Note: References are linked within.

And here's one I just found while writing that I haven't read yet: "The uniquely human capacity to throw evolved from a non-throwing primate: an evolutionary dissociation between action and perception."

Tuesday, June 25, 2013

Dogs, crows and garbage: phenogenetic drift

Scavenger hunts
Monday's the day trash gets picked up in our neighborhood. When I was out running early this Monday morning, I passed a scene I see not infrequently -- a group of crows congregated around a plastic trash bag, its contents spilling into the street and the birds tugging at anything in it that looked appetizing.  As I ran by, two of the birds flew but one brazen bird stayed right where he was, guessing that I was no threat to him.

Crows are very smart, and not just because they've figured out how easily plastic garbage bags are breached.  I've also seen them congregated around trash barrels with the lids knocked off.  I've never seen them actually take the lids off, but it must be they do.  When I was a child it was dogs who got into the trash.  This was before leash laws, when it really was a dog's life.  Dogs we keep as pets now have only ancestral memory to recollect the halcyon days of wandering the streets untethered on trash day.  Now it's a crow's life.

But sometimes it's bears, too.  A mother bear and her three cubs were making the rounds of our neighborhood a few weeks ago, knocking down bird feeders and compost bins, and this isn't an unusual occurrence.  The wilding of America?

This morning's sighting reminded me of a piece in the February 21 New York Review of Books by Russell Baker in which he reviews a book by Jim Sterba, Nature Wars: The Incredible Story of How Wildlife Comebacks Turned Backyards into Battlegrounds. I have not read the book, though now that I'm remembering this, I just might have to. Unhappily for the author, Baker's is one of those pieces that makes you think can skip the book, even as he gives it a fine review.

In any case, Baker describes seeing a pair of foxes mating in his garden situated, he says, just two blocks from the county courthouse in the bustling center of town. The encroachment into human-populated areas of animals who were once sighted only at a distance is becoming increasingly more common.
Sterba ... argues persuasively that events like this foxes-in-the-garden sighting are evidence that humans are losing some kind of property rights struggle with creatures of the wild. He cites an extensive history of resolute and sometimes blatantly hostile real-estate invasion by beavers, Canada geese, wild turkeys, and white-tailed deer, all of which were once assumed to be picturesque and even lovable denizens of the dark and safely remote forest. In-town appearances by coyotes and bears are now commonplace in communities across the country, and trespassers in my own garden, aside from the foxes, have included groundhogs, possums, skunks, feral cats, and one blue heron that ate all the koi with which we thought to beautify the fish pond.
Lucky heron.  As Baker points out, in the last fifty years these animals have discovered that life can be a lot easier closer to town, and food a lot more abundant.
The woods have no garbage cans and dumpsters filled with discarded food, no lovingly tended tomato plants, no ready-to-pluck dahlias and nasturtiums, no tasty, newly planted shrubs. 
Best of all from the animal viewpoint, humans are no longer the same dangerous predators who once pushed the beaver close to extinction and reduced the entire North American white-tailed deer population to a trifling 500,000 scarcely a century ago [there are now 25-40 million]. Sterba believes that this human withdrawal from combative relations with woodland animals is one of the major causes of their proliferation: man as killer has undergone a softening change.
Indeed, the crow standing in the middle of the road waiting for me to run by its food source is evidence of exactly that.

It doesn't matter who does it
But here's the thing -- whoever's doing the scavenging, there's still garbage spread all over the street.  And this is an apt metaphor for an important way that evolution works.  Yes, gene function is often conserved, so that the same gene (Pax6) is involved in photoreception in the eye of fruit flies and frogs and humans, and the human form of the gene can be transplanted into even distantly related species and the eye will still be made.  But it's also true that often a trait is conserved but the genetic scaffolding is very different.  Natural selection might preserve the phenotype, the trait, but it can't see the genotype, leaving it free to vary.

Ken and his then post-doc, Malia Fullerton, published a paper in Theoretical Population Biology in 2000 describing just this, though others have described it as well (reviewed by Brian Hall in his 2003 book, Keywords And Concepts In Evolutionary Developmental Biology.) The effect is called 'phenogenetic drift' to indicate that the trait's genetic basis can change. This is not the same as genetic drift, which is when genetic variation that has no effect on a trait, or at least on reproductive success ('fitness'), changes over the generations, and it's not the same as phenotypic drift, when traits vary over generations but that variation doesn't affect fitness.  This happens, therefore, regardless of whether there is selection, even strong selection, or not.  A prerequisite, or partial one at least, is that many genes contribute to the trait, so that different combinations of variants in these genes can lead to similar traits.

Hall uses the example of proteins that make up the lens of the eye. They can be unrelated among taxa, as long as they let light pass through. Kazu Kawasaki, a very skilled research scientist in our lab, has written a number of papers describing the evolution of mineralization in vertebrates. One of his early papers is on the changing genetic basis of vertebrate teeth. He has found a gene family, that he calls SCPP genes, that varies widely among species, and yet contributes to the formation of mineralized tissues -- teeth and bone -- in all of them.

As Hall concludes his section on this subject, "Phenogenetic relationships are less determinative for more complex traits."  There are many genetic pathways to being tall, or to developing heart disease, or to being a fast runner  And that's before we even throw environmental factors into the mix.  Genetic determinism, which we've blogged about often, is simply too easy to assume, often incorrectly so.  When you look out the window on trash day and see garbage strewn all over the street, don't leap to judgment about who did.  It's only when you find the bear scat or a crow feather that you'll know.  But even then, do allow for the possibility that the neighbor's dog got loose.

Monday, June 24, 2013

Descent from the Alps.....

We are still catching our breath from 10 days in Switzerland and France.  All pleasure this trip: we had a great time visiting family, who showed us their beautiful new neighborhood (i.e., the Alps), taking us hiking and watching BASE jumpers (we post a breathtaking video below from a 2012 National Geographic piece on the sport) and paragliders in the valley of Lautenbrunnen.  We hiked, ate (drank beer and Alsatian wine) and enjoyed great conversation in a fine bed and breakfast by a very small lake in the very small town of Sewen in Alsace, France as well.  No internet service there, we really were on vacation. The other guests spoke Dutch, French (some of them), and German and English (some of them), so it was a rather interesting table.

We want to thank Holly and Dan heartily for filling in here on MT while we were away.  Holly's writing a good little book this summer, as you all know, so we thought she might post once or maybe twice, but yikes, yeoperson's duty!  Fortunately, she says that what she wrote for MT will overlap with the grand little book, so all is good.

And Dan is off soon with his family for 6 months of field work on malarial transmission in Thailand, which means that anything he could write for MT while we were away was indeed a distraction from his final preparations for that.  So we especially appreciate his post on the intensity of the problem of malaria in low-tranmission areas.  We hope he'll be checking in here from time to time with thoughts on what he's finding while he's in the field.

Meanwhile, a few photos from pretty near the top of the world.  When one stands and regards this splendor, it takes one's mind away from the details of genome mapping, association studies, determining disease causation and all that.  It makes one realize the majesty of natural processes, and our rather humble place in all of it.  Now that we're back home, we'll have to make a come-down from the Alps, to lower our attention to those more mundane topics....hopefully a descent, but not from the sublime to the ridiculous...

Eiger, Mönch and Jungfrau

Halfway up to Stockhorn

View from Stockhorn

Paths not taken

Thursday, June 20, 2013

Evolution's got a P.R. problem

People aren't just anti-evolution, evolution-averse, or pro-"teaching the controversy" because they're clinging to supernatural explanations that help them identify with a tribe. Culture is mighty powerful but it's a lot more complex than stubborn beliefs in the supernatural as deciphered from, and reinforced by, an ancient text.
Evolution's got a public relations problem that spans beyond fundamental Creationism. It's not exactly looked upon favorably by many non-fundamental yet kind, open-minded, and educated folks either! Here I've jotted down a few thoughts about why...

1. Who cares about evolution? Sheesh, what's the big deal?
Evolution doesn't appear to matter to so many people. And getting frothy over evolution can certainly spark interest but it can also, in gut reaction, intensify the apathy. We love to go on and on about how "human" it is to wonder where we came from or to wonder how the world works. Well, it's not exactly a species-wide phenomenon, at least acting on that wonder isn't. With these folks, we can just keep doing what it is that we do and hope that they will come around to see why evolution matters and hope that until then they don't influence others to be as tuned out or turned off.   People are less likely to voice apathy about knowledge that they're accustomed to like biology, history, chemistry, geology, physics, literature, English, composition, mathematics. I think this attitude about evolution will go away once biology becomes a synonym for evolution in K-12 classrooms and beyond. 

2. Mystery is mystical by default. 
It's still acceptable to fill-in ignorance about biology with the supernatural. This is not as much the m.o. with chemistry or physics, but we tend to do it there too (like with quantum mechanics). I couldn't explain how the Internet works but I assume it's not magic and I don't know anyone who thinks it is either. Yet, missing pieces of understanding in biology are not, as default, just missing pieces of understanding. We jump automatically to magical thinking rather than assume that we just don't know and that maybe someone already does! Unfortunately, gaps in our biological knowledge don't always spark us to take more classes, to read, or to watch videos to see that many of those mysteries aren't mysteries to anyone who's studied them. Gaps in our knowledge don't always spark us to undertake controlled observation or to devise experiments at home. For some reason, instead... and I think it's the Bible and other powerful cultural influences, and also the way that the history of science unfolded ... biology's mysteries are comfortably cloaked in magic. If biological mystery is mystical, then it's easier to uphold allegiance to Creationism, or to maintain intellectual empathy with fundamentalists who ask that we simply "teach the controversy." 
3. It takes quite a bit of study, observation and life experience to understand evolution. 
Evolution is a complex, multi-disciplinary matter that few people can master in one semester of study. You need anatomy, physiology, genetics, behavior, comparative anatomy, zoology, ecology, geology, history, math, philosophy, etc. But you need only dabble a few toes in those areas to begin to form the picture. Because the e-word is so often left out of K-12 classrooms, students don't realize that they're learning it all along, in all its bits and pieces as they advance year to year. When they finally do get to a classroom that uses the e-word, they think it's a whole new subject matter and that's actually quite an obstacle. Plus, that evolution takes a while to understand in any sort of useful way means we have an under-informed population full of people who, at best, had one year of solid evolutionary exposure in high year of learning our one natural explanation for all of biology. That's evidently not enough to bring everyone far enough along to overcome #1 and #2. 
4. Evolution's not even well-understood by those who claim to. 
It's not. There's a lot we don't know about evolutionary history, about how it unfolded, and that means there's a lot that we are earnestly trying to figure out. And it's clear that public patience for science is lacking and that's rooted in a lack of appreciation for how science is done, how knowledge is formed, and how the truth changes. On the one hand there are those who know full well that feeble, foibly humans are devising this knowledge and on the other hand are those who've got far too much respect for "KNOWLEDGE." (The latter is revealed on the petrified faces of my students when I announce they're "creating knowledge" by doing a laboratory assignment.) Both perspectives are working against science every time something pops up in the press as being "debated" or "overturned." Every piece ends with "more research is needed." No wonder patience is running thin. The skeptics think science is fraught with fraud because it's done by people. The others flirt with thinking (or do literally think) that knowledge comes from on high, or from Revealed Natural Truths, and not possibly from mere humans. And then there are those who study evolution who are not earnestly trying to  understand it better. They're using a half-baked tool that they call "evolution" to do their work or to advocate for evolution education. And often when their views get in the popular press they're parroted or presented uncritically by writers with an equally non-nuanced understanding of evolution, who are equally oblivious to it. 

5. Evolution is being pushed by so many unhuggable atheist intellectuals. 
This has to do with what many public intellectuals like to call "tribalism" and in-group, out-group identity. Aligning yourself with professors or intellectuals is social and political suicide for many. Aligning yourself with the godless can be even worse. Of course there are lots of folks who retain their beliefs and accept evolution, but there are fewer of them (at least in the limelight) than us who eschew or reject the supernatural.  We need more huggable atheists. We need more huggable intellectuals. We need fewer anti-intellectuals. We need fewer anti-atheists. Lack of belief in the supernatural needs to be seen as a legitimate way to be a friend, a parent, a child, a relative, a neighbor, a community member, a leader, a teacher, a human.  

6. People don't want to be animals.

With education, people come to accept reality. And they accept what they cannot change. Right?

7. Evolution seems to support racism, sexism, (and atheism, intellectualism, evolutionism, vegetarianism,) and every other -ism that's wrong with humanity.  
But it doesn't. There's too much to unpack here in this small space, but this is a huge problem contributing to the aversion to evolution out there. Evolution isn't just subversive because it goes against established religious dogma. It's subversive because it, as completely misunderstood and misapplied, supports racism and sexism and murder and warfare and rape and infanticide, etc etc etc... Understood well, or even just a little bit well, evolution cannot be used in those ways and then, as a result, avoided by those who are afraid to align with such an unsavory worldview. Evolution is just generation to generation change in lineages that have shared ancestors in the past. Evolution describes how everything depends on what came before. That is all. Evolution requires no differential value placed on one species over another (human exceptionalism). Evolution requires no differential value placed on one skin color over another (racism).  Evolution requires no differential value placed on one sex over another (sexism). Those are human inventions. Culture is powerful.  

8. Evolution tells me I'm going to die when I die. 
This is the human condition. Belief in the supernatural or not, acceptance of evolution or not, this is what we're all dealing with. We often lament how, "evolution reduces the meaning of life to survival and reproduction." Well, if it does, is that so bad?
Evolution's got a lot more than fundamental religious beliefs working against it.  As an educator, I can't help but think that, first and foremost, a clear understanding of what evolution is (and isn't) is key to addressing all of these issues contributing to evolution's P.R. problem.  Yesterday's post was my attempt to help provide that clear understanding: 

Wednesday, June 19, 2013

Evolution is the only natural explanation. And it's all we need.

With the ongoing adoptions, state by state, of the Next Generation Science Standards (, and with the familiar cries of resistance against a national level emphasis on both evolution and climate change...
...I thought it might be a good time to point out to everyone, new or old, big or small, nonbeliever or believer, something that's often overlooked:

Evolution is our only natural explanation for nature, life, biology, you, me, peaches, lobsters, trees. 

All other explanations are supernatural. 

All. Others. Are. Supernatural.
It's the same for explaining televisions and toasters...we have only one natural explanation: physics. 

All other explanations for toasters are supernatural.

Toasters are as supernatural as tarantulas. 

So today...just so everyone's up to snuff with our only natural explanation for all of biology, here's a brief guide. 

The Earth is old. The universe is older

This is what we poetically refer to as deep time

And over all these vast stretches of all this deep time, and across our vast continents, and underwater within our vast oceans, there's been a lot of reproduction. 

Our planet, under a UV lamp, glows like a cue ball. 
And now you know why. (source)
So because of all this reproduction all over the place, stacked up in deep time, there's been lots of lineages and, over time, changes have occurred along those lineages because offspring are rarely identical to parents or siblings. 
That’s not just because kids are a unique combination of only some of each parent's information, but kids are also different from mom and dad (or whatever spawned them) because each individual also has new information (mutations) that their parents don’t.

I do. You do. We all do. 

We're all built of brand new combinations of old parental molecules (i.e. old mutations) mixed with absolutely brand new molecules (i.e. brand new mutations). 

As in brand new to the Earth. And maybe even brand new to the universe.

So here we are then. There's been change over deep time in numerous (to be ridiculously conservative) lineages. Everything alive on Earth right now is not only unique but is the end of a unique lineage that began 4 billion years ago. 

You. Me. Babe the bacon. Frank the bean. Each of us is the end of 4 billion years of what Sagan called an "unbroken thread."

The processes of change that occur across these unbroken threads, these processes that change living and nonliving matter, unfold before our eyes during our lifetimes. Just as they've been doing so throughout Earth's history. This is what's known as uniformitarianism. It's an unfortunate term that appears to mean that things have been uniform over time but it actually means that change has been constantly occurring through time.
(link to quote source video)
Change, or evolution, has always been happening and it will always happen into the future.

That's just another way of defining time: perpetual change. 

So, one of the few rules of our universe is time goes on and that means constant change occurs and because of that constant change there is always variation.

The landscape at the beach is different moment to moment. Each member of a sea turtle lineage is different generation to generation.

There's been so much deep time and so much change during it that what we see on the planet right now is only a tiny fraction of the life and the variation that lived before today. 

Most everything in my and your lineage is long dead by today. 

Further, most lineages that have existed have ended before today, just like my neutered and spayed dogs' will certainly end with them, and like mine will end if I don't "have it all."

But humans have named it all!

We have names for just about everything alive now and that makes "humans," "apes," "monkeys," "dogs," "lobsters," "sea turtles" seem separate, disconnected from one another, naturally. Especially since most species are designated by their inability to reproduce with others--talk about separate!

But, for example, if you go far enough back in my lineage there'd be an ancestor you'd probably call an "ape" rather than a "human." 
Australopithecus afarensis reconstruction from 3.4 million year old fossil bones found in Ethiopia (source)
Or you might get creative and call her an "ape-human" but that's just our limited vocabulary based on animals we know are alive right now. Then if you go further back in my lineage, you'd arrive at a point where something would remind you more of a squirrel than a human or an ape. The same thing's happening. You're relating my ancestors, 65 million years ago, to what you're familiar with on Earth today. And that's fine, but today's just a snapshot of all Earth's history and those aren't actually squirrels like the ones in our dumpsters and freezers today. 

Every single one of those ancestors in my, and your, lineage is unique. None would look exactly like anything alive now. Just like I don't and you don't. Many of my ancestors would seem like mixes of different things alive now. Many would have traits that aren't in existence on Earth right now!! If you keep going further back in my lineage, you'd see what looks like today's reptiles, and further there'd be fishes. 

Maybe that's because there are limited ways to be alive during 4 billion years on planet Earth...
hippocampus and Hippocampus (source)
Anyway, at no point does a mother seahorse give birth to a kid reptile. At no point does an ape give birth to a human. At no point does a human give birth to a little green man species, except that a scientist, accustomed to divvying up the spectrum of variation in the world into boxes, says so.

See how it's so completely obvious where red ends and yellow begins? See where everyone, even with the same exact eyeballs, would agree that blue ends and purple begins?
Not. They would not. (source; and fun; and fun too)
Color labels are fraught with some of the same issues as our labels for life. They are discrete words that stand for fuzzy-edged concepts that arbitrarily break up a spectrum and, thus, they interfere with the debate about human origins, about when "human" begins in the fossil record. Same for "ape" beginnings or "chimpanzee" or "dog" or "plesiosaur" or anything. 

Nature is a connected spectrum of variation over space and time that we must arbitrarily cut apart so we can talk about about it and study it the only way we know how.  But that doesn't mean we forget that populations, species, genera (whatever we're labeling), like the rest of nature they belong to, are neither uniform nor discrete. 
Species are not uniform across space and time, are not discrete across time, and aren't necessarily discrete across space either. (source)
Species are not uniform across space and time, are not discrete across time, and aren't necessarily discrete across space either. 
If species were discrete across time, we'd have no reproduction. 

If species were uniform across time and space we'd have no evolution. 

So the way we're tempted to think of species as essential, as discrete and uniform, is not only inaccurate but it is antithetical to what's occurring in nature, antithetical to constant change and common ancestry of each unique individual, which is all antithetical to evolution. 

It's not just the words we use specifically to understand that sometimes inhibit our understanding (!)... we're also working against our limited scope. 

We're here for only a fraction of what's been happening in the universe and will continue to happen into the future. As a result, we don't get to witness much evolution in action. 

We can witness evolution in lineages that reproduce quickly like cane rats better than we can witness it in, say, humans and chimps. It's unfortunate but we don't get to watch evolution in long-lived species as if we're watching a film.

We can, however, reconstruct that film using the biology of living, dead, and sometimes well-preserved extinct creatures. We just have to compare and contrast their traits.
Things that are more similar genetically, anatomically, etc... are more closely related to one another than things that are less similar. That's all there is to it. 

I could probably pick your parents out of a lineup if I'd never even met them. The same sorts of cues, and methods for identifying those cues, are applied beyond our families and our species to establish the fact that dogs are more closely related to wolves than to dogfishes. Humans are more closely related to dogs than to dogfishes. 

And we can reconstruct these family trees--populated by people, dogs, wolves, dogfishes--far beyond our own parents and grandparents, and back into deep time. 
T. Ryan Gregory's 2008 paper "Understanding Evolutionary Trees"
And we can test those reconstructions with help from the fossil record. 

But our reconstruction of the Tree of Life is not a perfect reconstruction because fossils are usually restricted to preserving only bits and pieces of the biologies of organisms--parts like bones and teeth. 

Plus, we don't have fossils of every single thing that ever lived. That would be impossible. Dead bodies have to be recycled into living bodies for there to be living bodies. 

If the fossil record was complete, we probably wouldn't be here to study it.

And even if we are lucky enough to find a fossil that was lucky enough to preserve, that's just that one animal struck dead at one little moment in its lifetime, at one little flash in the entire 14 billion years since the big bang. 
And we often struggle to link relatedness up, and reconstruct change over time in lineages in the fossil record because we rarely get more than two generations in the same deposit.  And when we do, one is usually teeny tiny compared to the adult. 
Pregnant plesiosaur (Source: Robin O'Keefe)
The fossil record is a great source of evidence for evolutionary history and that it's necessarily limited is okay. As discussed above, we actually don't even need fossils to support evolution over a supernatural explanation, because living organisms provide enough evidence.  
We look at chimpanzees and bonobos and see they share more with us and we with them than anything else on Earth. When we line up our molecules, we find the same thing, just as we  predict. These relationships we deduce among living things don't require any fossil evidence to support, but fossils do help to make sure, no doubt about that. And fossils show us all the weird creatures that had to live and die first in order for all of us to be here now.

So, fossils or not, evolution explains all the similarities we have with everything else alive on Earth. That's our common ancestry at play.
And evolution explains all the differences too. That's mutation at play. Mutations are always occurring. They are part of the uniformitarianism that describes the constant state of change, of flux, of all of history. Change over time is also due, at the population level, to differential reproduction. Some individuals have more offspring than others. Therefore, future generations are always comprised of a different biological landscape, both with higher and lower proportions of some variation compared to their parents' generation, and always with some brand new mutations thrown in there as well. far so good. We've got deep time, change over deep time in related lineages from common ancestors, like family history writ large. Some ancestors are preserved as fossils, most are not and many of those that are have not been discovered yet. Most evolutionary history is unobservable because of the inconvenient impossibility of time travel. Similarities among organisms reflect shared heritage. Differences and distance reflect constant change that occurs via mutations and constant change over the generations due to the fact that some individuals have fewer offspring than others, leaving their mutations, their traits, in lower frequencies in the next generation. 

Darwin's term "selection" describes some of this differential reproduction among individuals. Some variation dies, some variation does not reproduce, some variation enhances reproductive output and when it does, that variation shows up in greater proportion in future generations... as long as it continues to enhance the reproduction of those with it...a condition that is usually heavily determined by the environment where all this reproducing is taking place! 
Like mutation, differential reproduction is always occurring. That means that selection is always, on some level, occurring. Some traits, like a new mutation that prevents growth of the ovaries, would prevent that woman from passing that on. Selection can also describe how mutations or variation proliferates in future generations if it causes those individuals to contribute more of their variation, their mutations, to the future gene pool than others.

Selection describes how a baby that could fit through the birth canal and, with those adequate birth canal genes, can grow up to have an adequate birth canal for fitting her own offspring through. It's that simple. And babies with genes for adequate birth canals are much more common in a population than otherwise.  Fitness (a.k.a. reproductive success or reproductive output) is such a fitting term when it's truly about fit!

But saying that "differential reproduction is always occurring," also means that drift, which is differential reproduction due to chance and differential passing of this or that gene into future generations due to chance, is always occurring too.  

And in spite of constant mutation and constant drift... that is perpetual chance change...we've managed wonderfully for 4 billion years.

It's far too common to read descriptions of evolution as if selection is the only or the main process for change and they're not telling the whole story. 

Change is perpetual underneath all of that selection. Selection, as a result, is weaker than we tend to think of it. 

Constant change can be kept in check by selection against it or it can be tolerated and incorporated into a lineage, which is usually the case. If change wasn't tolerated by selection, we'd have stasis in lineages, with clones upon clones upon clones. Instead we have myriad sexually reproducing organisms that do not produce clones. Change clearly works!

All this constant change has got to make us think twice when we describe each and every amazing trait in animals as "adaptive" which is to say they're the result of selection. Perhaps they are, but perhaps adaptive traits are just the tolerated survivors that got through selection's filter. 

In that sense, nearly everything that's not a dead-end can be considered "adaptive" at any given moment. That is, all the underlying processes, quantum, molecular, chemical and physiological that keep an organism running could be considered adaptive at any point of observation. 

Inherited genetic material that's involved in growth, development, metabolism, reproduction, etc... (i.e. all life's processes) is evolving with each and every generation thanks to recombining parents' genes, mutations, genetic drift and selection all working always together. Yet, organisms are continuing to survive and reproduce like pros. 

And we have been for 4 billion  years. 

Everything is because of what came before. 

That's all evolution is.  

And that's all we need.