– I’d like it better if my comments on other blogs were pending immoderation.
– A clumsy ballerina walks into a barre…
– Who decided that Pachelbel’s canon was Christmas music? And on that topic, you can (pretty much) sing the Green Day song Basket Case over it.
– Along similar lines, Jabberwocky can be sung to Greensleeves. And Home on the Range/Joy to the World works as well. But the winner is Purple Cow/It Came Upon a Midnight Clear. Next time you have an ‘It’s a Small World’ ear worm, just try that Purple Cow thing – guaranteed to make you long for Disney tunes lickity-split.
Favorite old jokes:
– Two cannibals are eating a clown, when one turns to the other and asks: “Does this taste funny to you?”
– What do cannibals serve at cocktail parties? Donner party mix.
– A spy is sent to rendezvous with a contact named O’Reilly at an Irish pub. In order to get the information, he is to give O’Reilly the password: “The moon shines bright upon the heather.”
When he gets to the pub, it is crowded – hey, its the Irish. Since no likely candidate presents himself, the spy decides to act – he goes up to the bartender and asks, “Say, has O’Reilly been by this evening?”
“O’Reilly?” responds the bartender, “Why, this town if full of O’Reillys – there’s O’Reilly the butcher, and over there’s O’Reilly the baker, O’Reilly the bricklayer – in fact, I myself am an OReilly.”
The spy decided to risk it. Glancing furtively left and right, he says to the bartender, “The moon shines bright upon the heather.”
“Oh, so it’s O’Reilly the spy you be lookin’ for!”
Merry Christmas (for 6 more days! Hurray!) and a Happy New Year!
Back in the age of reason, by which of course I mean the Middle Ages, where the great thinkers were too busy using their minds to waste time crowing over how reasonable they were, it was recognized that people are the only earthly creatures created for their own sake. The rest of the material universe was created, at least as far as we could tell, for the sake of something else. That something else was us.
This bit of philosophizing would, I suppose, strike the desiccated post-post-modern mind as rank hubris. It is in fact common sense, both in the abstract sense of what a sensible person would believe and in the more concrete sense of how we all commonly sense things.
We know, somehow, that we are in charge, sort of, at least on a day to day basis. Caretakers. Sure, stuff happens, and its not like we’re in control of the weather or can boss the whales around – but it’s our job to sort of see to things, keep tabs, and maybe step in, once in a great while, to nudge things back on course. In this sense, we are different from the other animals – if we behaved like any other animal, we’d throw the last panda on the barbeque without a second (or first) thought.
Even crazy people get this. When they complain about how people are destroying the planet* they tacitly admit that we have a duty not to destroy it – a duty shared by no other creature. And we should save it (whatever that means) for what or whom? Is death by red giant in a billion years really better than death by – what, exactly? – right now? Why? Who cares?
Lurking necessarily here is the belief that people are different – better, even – than animals. We are different in that we can in fact be held responsible for what we do to the world. We are different, ultimately, because the world was created for us. We are to live in it, learn from it, love it, care for it, and use it.
The real hubris is believing that we have the power to destroy the planet. Ratcheting down the hyperbole a notch or 10, what people seem to mean by ‘destroy the planet’ is something like ‘disrupt some of the ecosystems so much that life becomes difficult and unpleasant for people’. Sure, the language used includes concern for species going extinct slightly before their time, but that just betrays a lack of understanding of Darwin – species go extinct, get used to it – and an assumed point of view where it is natural and good to care about other species – why would that be, exactly? I suppose if we really put our minds to it, we could even kill off all people and other large land animals with a huge nuclear war. However, even in that unlikely event, earth would keep on keeping on. In a few million years, a visitor from another planet wouldn’t even know anything in particular had happened without a Geiger counter. If the recovery from whatever wiped out the dinosaurs is any indication, in a few million years all the niches will be filled and fascinating new animals and plants and fungi and such will be all over the place, and just as inhuman as Darwin can make them.
Which, one would presume, would be fine with that particular brand of anti-human nature lovers. So, like, why don’t they just shut up already? If what they want is a world free from the pollutant of human beings, and what we are now doing is destroying the planet in the sense of making it unlivable for humans, all that’s required for their particular Nirvana is patience. And if you lack patience, you could always kill yourself, which both helps the process along and improves the mental environment for those of us left behind.
Further, to even want to save the planet from us betrays a certain lack of perspective. Mammalian species typically only last a few million years, tops, so the earth stands a really good chance to be rid of us in short order, naturalistically speaking, no matter what we do. Unless, of course, we’re not just animals.
But, alas! We are not in fact destroying the planet, even in the limited sense a less unhinged view demands. Baring a space princess event, if anything it could be argued that we rather seem to be making it better – a fact certain to infuriate a number of people.
How are we making it better? If, in fact, the world has been created for us (how or by whom doesn’t really matter for the argument), then the more people able to live well on the planet, the better. Right now, there are about 6 billion people living pretty good lives on this planet. They’re not starving, they have a place to sleep at night and clothes on their backs. All they need are family and friends to be pretty happy, as far a human happiness goes. And – here’s the kicker – we’re pretty much aware that, on the whole, life is better and more interesting the more interesting creatures live in the world. We like forests and rivers and lakes and mountains, and so, for the most part, we have begun to take care of them – for our sake. Who else’s sake could we possibly be doing it for?
Recently, Google published an amazing map showing the world’s forests. It shows places where the forests have, on net, been cut down, increased and stayed the same. While most of the essays I saw used this map for the usual panic mongering (one notable exception was an essay that pointed out that, if trends continue, pretty soon deforestation in Brazil will stop entirely) what I saw was more mixed and interesting. For example, zooming in on Vermont shows a state almost completely forested. Yet, a couple hundred years ago, Vermont was heavily farmed. What happened was simple: once land in Ohio and the rest of the Midwest – much better land and climate for farming – became available, Vermont farms started shutting down. Today, Vermont is one of the world’s major producers of quaint, and the land has gone back to forest (except for a few quaint farms).
So, sometimes forests come back. Darwin** wrote about the primeval mixed chestnut forests of the American southeast, how they had been largely cut down by the native American mound builder cultures, yet, by the time curious English naturalists got a look at them 400 years later, it was all but impossible to tell they were not old growth. America shows vast areas that are now forests that had been cut down at some point. Even here in California, where we stopped cutting down redwoods (more or less) once we were down to 5% or so of the original forests, there are vast areas once clear cut that, in a few hundred years, are going to look very much like primordial forests.
What the map showed me was that it’s not a one way street. In Europe and America, it appears forests are on the whole spreading. When I see the areas in Canada and Siberia where heavy logging is now taking place, I wonder about how those areas looked 100 years ago and how they will look 100 years hence. In 100 years, there very well might be more Brazilian rain forests than there are today – that would certainly fit the pattern.***
And this pattern – people wanting to restore nature for their own pleasure – is everywhere. Out here in California, a number of efforts are underway to restore the Bay and Delta wetlands. Turns out we like wildlife and natural beauty. Chesapeake Bay is being quickly, in environmental time-frames, being restored. Sure, the argument says we care about nature – but we can only care about it means something to *us*.
Of course, there are many environmentally bad things going on. Getting the rare earth metals and other materials for wind farms and electric car batteries, for example, have created this. (The irony, not to mention hypocrisy, involved in creating huge toxic sites and poisoning third world peasants so that rich westerners can feel better about our extravagant use of energy is bracing.) But it is simply wrong to think that, in general, people are careless of the environment. We all like to live someplace pretty, tidy and safe – that desire, barring other considerations, extends to the world around us.
So, no, “we” are not “destroying the planet”. We couldn’t, even if we wanted to. Instead, people all over the world are working out how to make the earth a more pleasant place to live – for people. Which includes, happily, making it a more hospitable place for life in general.
* The people destroying the planet are not them, personally, of course – they chose paper, drive a Prius and recycle, activities which in some mysterious way save the planet. The problems of logging to make the bags, safely creating and disposing of the batteries in the Prius, or the rapidly diminishing returns on recycling are just better or more easily ignored problems than the problems of, say, frakking, which merely helps supply the cheap energy needed to keep the internet up and running and all their gadgets and gizmos (including that Prius) humming at prices hundreds of millions of people can afford to pay. But let’s not over think this – that would require some initial thinking.
** I think it was Darwin in Origin of Species. One of those early guys. I haven’t even finished my coffee.
*** Isn’t anybody working on regrowing the north shore Mediterranean pine forests? The ones cut down to make triremes? That would be cool.
We made 5 of 9 5:30 a.m. Masses this year, including the big Christmas Eve finale today.
Then we had breakfast in the gym. There was a band:
In real life, they are in better focus. To answer the burning question in the minds of all musicians who have ever performed in public: yes, they were pretty much in tune, and, no, the ratio of time spent tuning to time spent performing wasn’t 30:1. How you tune 6-8 instruments with what looks like about 20 strings each so as to 1) get into the in-tune ballpark; and 2) stay that way for more than about 3 minutes in a drafty gym is yet another Christmas miracle beyond human ken.
There was food, including chicken soup:
The little brown stuff in the nearly empty bowl on the left is roasted garlic to sprinkle on the soup.
And desserts which, like the band, are in reality quite in focus:
Here’s what it looks like all put together as an artsy still-life:
This bowl of soup was 50% chicken chunks – luck of the draw, I suppose. The brown noodles are semi-regulars at simbang gabi breakfasts. The desserts consisted of 3 different gelatinous goodies. The purple stuff is quite elastic – the guess is that it’s some sort of taro root thing. One little degenerate square-oid is the right amount, pictured here. The cream and caramel colored ones were quite yummy. In fact, the breakfast as a whole was quite delicious.
Filipinos are happy fun people. The priest mentioned in today’s homily about joy how Filipinos just love to be happy, and said his favorite picture from the late typhoon disaster was of a young mom carrying a baby daughter against a backdrop of destruction – smiling and flashing a victory sign.
Wow. But not surprising.
A happy, holy and blessed Christmas to all of you and yours!
We’ve made 4 out of 8 of the 5:30 a.m. novena Masses so far. Filipinos are such warm people. Tomorrow, for the last day, they hold the post-Mass breakfast in the gym, with live bands and dancing. Seems a good way to wrap up Advent. We’ll be going, finishing up having attended 5 out of 9 – our typical batting average over the last few years.
More musing on evolution, following this and this. Sometimes, it seems people get confused by genes as the units of selection versus genes as the gene sequencing machines process them. So here goes:
Let’s call the first idea philosophical genes. When one says that a race horse has inherited great speed and fragile ankles from its parents, one is not concerned primarily with the molecules that effect this inheritance. It could be (and seems to be) that inheriting a trait as complicated as running speed involves a constellation of molecules in the horse’s DNA. Be that as it may, for evolution by means of natural selection to work logically, there must be a mechanism or mechanisms by which a) traits that can be selected are generated; and b) such traits can be passed on.
This logical requirement is prior to whatever mechanisms embody it – we wouldn’t even go looking for physical genes if we didn’t require them philosophically to make sense of natural selection.
I’ve gotten my history of Darwin’s theory after its initial promulgation a bit piecemeal, but if my understanding is correct, this requirement of a mechanism for the production and inheritance of traits was seen as a weak spot, since inheritance itself is tricky: offspring do not always appear to be some 50/50 blend of parental traits, or any other simple formulation. Traits can skip generations, then reappear. Actual inheritance as expressed in traits that can be selected appears too messy to hang an entire revolutionary theory on.
Mendel fixed all that. (Eventually – the entertaining Catholic Encyclopedia article from 1917, less than 2 decades after Mendel’s work was finally brought to light, says: “T.H. Morgan does not hesitate to say that Mendel’s laws give the final coup de grace to the doctrine of Natural Selection, and others consider that his views, if finally proved to be correct, will at least demand a profound modification in the theories associated with the name of Darwin.” See the rabbit holes here? Now I want to find out what T.H. Morgan says – and who the heck is this T.H. Morgan, anyway?) Or sort of fixed all that – Mendel’s theories are tidy for very carefully selects pairs of mutually exclusive traits, which are far from all or even most traits that attract our attention. But at least a simple framework within which to investigate had been established.
Within that framework, we can start to see, however dimly, how the mechanical workings of organic chemistry result in, say, slime mold or birds or Yankees fans. But we’d hardly bother if we didn’t have the logical need, under Darwin, to look into it.
Dawkins concerns himself almost exclusively with philosophical genes. How it is, exactly, that perturbations in strands of DNA produce Darwin’s finches isn’t nearly as interesting to him as the existence of the finches in the first place. The evolutionary biologist needs for there to be a mechanism, but doesn’t necessarily need to know how it works.
In my chicken scratchings here, I likewise focus on the logical fall-out from embracing a gene-centric view of the origin of species. I tend to think it’s the correct way, scientifically and philosophically, to view it. From a gene-centric point of view, predictions can be made that are a bit counter-intuitive – which are the best kind. Key among these is the dizzying perspective of the gene’s eye view, how behaviors and traits that make no sense from the individual organism’s survival can nonetheless make perfect sense.
(An hour* to kill, so let’s muddy the water on, as Dr. Xavier says, Eeeevolution!)
So, we last left the topic of evolution by means of natural selection as described by Dawkins in his Summa The Selfish Gene and in his follow up The Extended Phenotype with a couple of bald assertions:
1. The key intellectual assertion underlying Darwin’s Origin of Species is the claim that tiny pressures can, if consistently applied over long enough time, result in substantial, material change. I’ll add here the critical lemma: these changes may appear as if they could only arise by conscious design, but that is an illusion.
2. A key idea implicit in The Selfish Gene is that selection pressure doesn’t need to be applied to every individual in every generation to have an effect, allowing for the possibility that traits might be selected for that promote survival in the face of comparatively rare yet sufficiently recurring ‘pressures’.
To expand: Darwin was famously influenced by the geological uniformitarianism of Lyell and Hutton. (BTW: People who come up with 10 dollar words like uniformitarianism should be taken out and shot. How about calling it the Same Laws Assumption? Two fewer syllables, clear, easy words. That, I suppose, would be too pedestrian for big-time science guys. But I digress…). Tiny, generally imperceptible geologic events can result, over time, in the Alps or the Grand Canyon. And so, the seemingly tiny yet controversial step: same thing applies to living creatures.
Update: Still totally swamped at work (and, since our company serves companies that finance equipment used by business, this may be a very positive leading indicator of economic activity – this is not an offer to sell, nor a solicitation of offers to buy, and so on and so forth…). Having to be content to fire off short posts that don’t involve reading more books or doing any research. Will get back to that kind of stuff soon, assuming our customers deign to allow me to take time off at Christmas.
When I read the Selfish Gene and the Extended Phenotype, Dawkins’s conclusions seemed obvious and bit tame to me. Dawkins gives this big wind-up to the second book, about how it represents his original contributions to the field, and my reaction was: didn’t everybody get, from the first book, that genes would necessarily, in their expression as physical traits and behaviors, interact with the other genes? That my genes would necessarily interact with the genes of every other creature in my environment – in fact, that the sum of those interactions is what a biological environment IS? (Mechanistically speaking, of course.)
I guess not. Further, I thought Dawkins stopped a little short – I thought there were things he should have said, as obvious conclusions based on his premises, that he did not say. (NOTE: not saying that the observable evidence supports these conclusions – although I would be personally surprised if they didn’t – but only that the logic explained in the Selfish Gene requires them.) For example:
– After a couple billion years of evolution, one would expect a given genome to be carrying around lots of genes that have proved advantageous in the past, but may not at the moment be expressed. (Using the term gene philosophically to mean that by which phenotypes are expressed and traits passed on, not the mechanical meaning used in gene sequencing as of a particular set of molecules)
Given the above, this set of formerly useful but not currently expressed genes is subject to the same selection pressures as any other gene – does it cost more to carry it about than it is worth? The cost can be very low, that much should be obvious, so many genes will hang around because it’s cheap, survival wise, to keep them. But what about the benefits? Are there any? Couple ways to look at this:
– Hybrid vigor is an adaptation. In the careful balancing act of gene expression, where certain genes are switched on or off in certain sequences to produce proteins that produce, ultimately, physical traits and behaviors (a process that we’re only now beginning to understand), could it be that rolling the dice and allowing for greater variation when the environment has been disrupted is a winning strategy?
Note when hybridization generally happens: when the environment has been seriously disrupted by the introduction of another breeding group with which an existing breeding group has long been separated. On a chemical level, this means that there may be variations within each population in the mechanisms that control gene expression, so that, upon hybridization, much more variation occurs, as the controls behave differently in heir new ‘blended’ environment or perhaps are merely less efficient in suppressing variation.
So, when hybridization occurs, one would expect more variation in phenotypes: bigger, stronger, smarter – and, perhaps, smaller, weaker, and stupider. Here’s the key step: the environment has been disrupted – that’s how the hybridization was able to happen in the first place – meaning that niches are opening, closing, being established. Some of these variations might well survive better in the new niches than either of the original phenotypes from which the hybrid variations were created. The bald fact that hybridization has taken place means that the environment has changed, and all bets are off as far as how well adapted the old forms will be to this new environment.
The final piece: this process – the disruption of an environment by the introduction of a breeding group different from the closely related breeding group already there – has been going on constantly for over a billion years. Winners and losers have been selected in hybrid environments hundreds of billions of times. Using Darwin’s fundamental insight – that small pressures consistently applied can create real changes – it would be shocking if hybrid vigor were not an adaptation.
Circling back: therefore, we should expect that, among the ‘useless’ genes (in the philosophic sense), there would exist those which have proven useful to survival in hybrid situations. Let’s take people, for example: many human hybrids are bigger, stronger, and more physically attractive than the average person from either group. Given how humans tend to behave, these sure look like traits that would better help individuals survive in the new, likely to be socially chaotic, environment.
– Second – this is what triggered this brain dump – what about situations where the environment has been disrupted in some other way? Where, for a given species, traits that had helped them survive in the past are no longer relevant, and traits that are desperately needed are only partially present? In this case, little fish got washed into caves a few thousand years ago – and promptly went blind (no eyes), lost all skin coloring, and got real good at finding stuff in the dark.
The question never asked in the article: how often does it happen that fish will end up in caves and not be able to get out? Because, if it’s a common enough occurrence, we would expect that, just as with hybridization, genes would be preserved which had proved useful in such situations in the past. These genes function by producing proteins. Therefore, the presence of proteins that affect the phenotype of individuals is not a new idea in concept, although the researchers here seemed surprised to find it working as it is claimed it is working.
The article focuses on a particular protein, which acts to ‘keep in check’ a species’ genetic mutations.*
Cavefish underwent a process called “standing genetic variation,” according to study researcher Suan Lindquist, who has extensive experience in the subject. During less stressful times, certain species’ pool of genetic mutations are kept in check by a protein called HPS90. Dramatic circumstances, however, can deplete the protein and leave the organism open to all of its genetic possibilities. In the case of the cave fish, as Lingquist and fellow researchers proved in this study, stress triggered the right genetic expression — or at least triggered the right genetic expression in enough fish, Laboratory Equipment reported.
Be this as it may, this scenario fits perfectly under my more general claim – that organisms carry around genes that are only comparatively rarely useful, but are very useful once in a while. Those once in a whiles include hybridization – and fish getting washed into caves they can’t get out of. In other words, life has evolved to evolve; organisms carry around within themselves the genetic materials that allowed their ancestors to survive in very different environments, on the Aristotelian principle that anything that has happened is possible – that if your ancestors got washed into a cave and survived, you, too, have a non-zero chance of getting washed into a cave.
Fish have been around a couple hundred million years; rivers and caves for considerably longer. So, we can expect that, over time, billions upon billions of fish have gotten washed into millions of caves – and that some small percentage survived. Some of the offspring of those species managed to get washed *out* of the caves, where, presumably, some survived – and passed on the genetic capabilities found useful for survival in caves. So, today, hundreds of millions of years and billions and billions of fish into this process, we have some fish which, when washed into caves, are genetically predisposed to survive and reproduce. This survival involves gaining the necessary and shedding the expensive but unnecessary – they lose eyes and skin color, and their already superb ability to navigate blind becomes, perhaps, enhanced. (Fish in general aren’t exclusively dependent on sight – water is often murky and darkness falls every night.)
This is nothing more than evolution by means of natural selection at work across a longer time-frame than an individual lifespan. It can work across many lifespans, so that traits that are useful about every thousand years, for example, will be preserved if they don’t cost too much. That’s where I wish Dawkins had taken it.
* ?! This sort of wild speculation makes me feel I ought to just don the Sacred Lab Coat of Science! and proclaim my untethered amateur speculations THE TRVTH! They’re as good a theory as any, and have as much empirical support as most. How, even in concept, could one validate the theory being expressed here? And there’s no evidence they even tried – they played around with some proteins in a lab, maybe dissected a few fish – and make a global claim about evolution? Science is hard, after all, in the sense of difficult and harsh. Further, I can’t let the claim that ‘psychological stress’ activated this process pass – we’re now studying the psychology of fish? Pull-ease!)
“Young larvae (triungulins) of the blister beetle have a remarkable system of finding a bee host, Habropoda pallida(Anthophoridae). The beetle larvae aggregate together on the vegetation and mimic the appearance of a female bee. Male bees confuse the larvae aggregate for a female and attempt to mate. This results in the larval aggregation attaching to the underside of the male. When the male finally finds a female and mates, the beetle larvae transfer themselves to the female and get transported back to the nest where they feed on the pollen collected by the female for her offspring.”
If the beetle larvae’s behavior can be explained by natural selection without appeal to the intelligence of the insects, the alligator’s behavior can likewise be explained. Yet, in the link above, the hunting behavior of the alligators immediately triggered a ‘Wow, they must be smarter than we thought! They use tools!’ response in the human observers who, as professional biologists, should know a lot better.
Insects don’t look like us and don’t behave like us. They do all sorts of creepy insect things. Alligators, for all their inhuman weirdness, behave a lot like us, in that they patiently hunt food in a manner reminiscent of how humans hunt food. Their food even looks like food.
So, they’re smart, but insects are not. Any other reasons to suppose this?
This is cool, unless you happen to be a nesting bird:
Dr Dinets and his colleagues spent a year observing alligators in Louisiana at two rookeries used by great egrets, snowy egrets, white ibis and spoonbills. Their findings are published in the journal Ethology, Ecology and Evolution.
They observed alligators collected twigs and balanced them across their snouts as they floated in the water.
This behaviour was only seen during the birds’ breeding season – between March and June.
The scientists claim the sticks were then used as lures to bring birds within striking distance of the alligators’ jaws.
Dr Dinets also reported similar behaviour witnessed by mugger crocodiles at the Madras Crocodile Bank near Chennai in India.
He said if birds got close enough the crocodiles would lunge for them.
All very cool. But then:
It is thought to be the first time reptiles have been found to use tools – something that was thought to be restricted to apes and intelligent birds such as crows.
The findings suggest that crocodiles and alligators are far more intelligent than has been previously thought.
No, it doesn’t suggest that at all, any more than their being brownish-green and lying very still suggests they’re smart. Over the course of the last 100 million years, some alligators happened to have a few twigs on their snouts as they floated motionless waiting for prey. Those twiggy alligators, as a whole, had a higher success rate staying fed over time, and therefore left more offspring than those who reflexively shook off the twigs – just like the well camouflaged and really patient ones did.
That they would then seek out twigs to put on their snouts by instinct when birds are nesting nearby is just vanilla evolution, the same sort of process by which wasps hunt particular caterpillars or bears fatten up for winter – doing so ‘works’ in the sense of promotes more offspring over the long run. This requires no more intelligence in the alligator than is possessed by the twigs.
But very cool. Not as cool as fire ants eating Burmese pythons, but cool.