Sunday, September 28, 2014

The Bones of the Matter

(Picture from here.)

I've been getting over an injury I got doing judo about a month ago. So, of course, I started thinking about bones.

The skeleton is one of our most obvious anatomical features. I know we can see and feel skin and eyes and hair. But the skeleton is one of our clearest examples of an anatomical system. The bones articulate. They move together. Muscles attach to them.

Where did they come from?

Well, we're vertebrates. That meas we have a dorsal notochord. There's an erroneous concept that vertebrates are animals with backbones. But that's a little tough since chondrichthyes (cartilaginous fish) don't have a "bone" in their skeleton, excepting teeth. The structural members are all cartilage, not bone. A more precise definition is that vertebrates are animals that have a vertebral column, which may or may not be composed of bone. The column is composed of different elements, called vertebrae, and house the spinal cord. And that sharks have, too.

The two great branches of fish in the vertebrates are the chondrichthyes and the osteichthyes. And that's where mammalian heritage of bone begins. We are descended from the osteichthyes and the hard, calcium rich substance has been with us since.

Fish evolved cartilage before they evolved bone. The cartilaginous fish evolved into two groups: Agnathostomata (fish without jaws) and the Gnathostomata (fish with jaws.)  Agnathostomata include such pleasant fish as lampreys and hagfish.

The Gnathostomata are no stranger to bone. Placoderms showed up over four hundred million years. Some species have bone; some do not. The bones serve as armor, teeth or other purposes. They do not server as structural members. That came later.

The critical feature of bone is the mineralization of the softer tissue. At some point, we developed the ability to impregnate that nice soft tissue with rock. More importantly, we impregnated particular tissue with rock. Structural tissue. Cartilage, though, is crucial. The processing of cartilage is a necessary precursor to bone growth-- mice grown without crucial genes involving cartilage development lack bone. (See here.)

So, how did mineralization get going.

Well, about 1.5 billion years ago a tremendous amount of Calcium Carbonate (CaCO3) were washed into the oceans from volcanic and other sorts of tectonic activity. So many organisms took advantage of this new found chemical trove. A lot of weird animals in the Cambrian showed up a bit more than .5 billion years ago. Animals that wore their skeletons on the outside.

A skeleton, inside or outside, soft or hard, gives muscles something to pull against. The structural skeleton can be made out of enclosed water, cartilage, other muscle or bone. The important thing is to give a rigidity to the structure so that organized movement can occur-- at least more than squishy oozing along.

We had, back then, no shortage of skeletons on the outside. This should not come as any sort of surprise. Lots of animals had hard outer bits. Clams, for example, Growing hard bits on the outside was relatively common. So it doesn't seem all that hard to put hinges between the hard bits and get crustaceans and trilobites.

Vertebrates belong to the phylum Chordata, animals with notochords. We have notochords, too. Inside our vertebral column. We like to call it a spinal cord. What's different about chordates is they put their notochord on the dorsal (back) side instead of the belly side. Very early on, we wrapped that notochord with vertebrae and we were off. The skeleton evolved from the vertebrae. Consequently, our skeleton evolved from the inside out while the other animals with hard parts evolved their skeleton from the skin inward.

All of the animals at that time with moving hard parts refined them. We end up with shrimp, crabs and the afore mentioned trilobites. Back in vertebrate company, we evolved fishes, fishes with jaws and jawed fish with bony armor. But no mineralization of the structural members.

One big shift in the vertebrate world was to shift from our friend calcium carbonate, so beloved by our exoskeletal brothers, to calcium phosphate. (CaPO4). This was in the form of calcium hydroxyapatite. (Ca5(PO4)3(OH))

Why change strategies when calcium carbonate had been around for a long, long time?

One idea was that the original use of calcium phosphate wasn't as bone at all. Instead, it was a storage mechanism of phosphorus-- often a biochemical limiting factor. Anyone who has used phosphate based fertilizer knows its utility. ATP/ADP (adenosine tri-phosphate and adenosine di-phosphate) are the way the cell stores and release energy. That P in the abbreviation is for phosphorous. But as nice as this is, why did vertebrates evolve it and not invertebrates? After all, it would have been good for both. It could be that the change to phosphorous was for a wholly different reason and the storage advantage was a happy accident.

Another idea derives from vertebrate activity. From the fossil record and from observation of vertebrate animals in the wild, it looks like we're active creatures. We don't sit around. We run. We hunt. We don't sit and wait for our food to come for us. We go and get it. One of the side effects of this activity is a change in pH-- the acid or base values of the tissue. Calcium carbonate is much more soluble material than calcium phosphate. Consequently, fish that tried to swim hard could find their hard bits not so hard.

The first structures resembling bone we find in the fossil record are teeth or teeth like structures. They are with us to this day. Sharks have teeth. Lampreys have teeth. Teeth are a bit different from normal bone. Both bone and teeth are calcium phosphorous structures but teeth are much harder than bone. But bones can heal. Teeth can't. However, the biochemical structures are close enough that one wonders if the biochemical pathway that brought forth teeth was torqued a bit to bring forth bone.

There are also teeth like structures in the skin to form shields. Remember placoderms? One of the arguments in paleontology is which came first? Teeth or shields? Genetically, they appear to derive from the same source.

Early skeletons were cartilaginous but were not based on collagen, the primary structural protein in connective tissue. Later, when collagen evolved, it was used in the skeleton such as those involving sharks and such. It fell to the ancestors of the bony fishes to invent ossification.

There are two mechanism of ossification: intramembranous ossification, where the bone is laid down directly into connective tissue, and endochondral ossification, where cartilage serves as a template for the bone. Intramembranous ossification happens in bone repair and in the early construction of certain head structures. Endochondral ossification is how the skeleton gets formed.

It didn't happen all at once. Apparently, endochondral ossification started with surrounding connective tissue-- biochemically similar mechanisms for embedding bone in the skin. Eventually, the process of cartilage replacement occurred. How this occurred. There is fossil evidence that early sharks had the ability to deposit bone in tissue though it was not used structurally.

There is also current evidence (see here.) that some sharks can mineralize cartilage in a similar way to how bony fish do it. That said, is this development that occurred since sharks diverged from the rest of the fish? After all, the biochemical means by which mineralization occurs is very old in the vertebrate family tree-- recall our constant friend, the placoderm. And the mechanism for laying down a supportive skeleton is represented in both the boney and cartilaginous fish. We often look at what we call primitive animals and forget that they've been around just as long as we have with just as nasty and powerful selective pressures on them. Sharks diverged from our line 400 million years ago. But they haven't been sitting around since then. They've been evolving, too.

Once structural mineralization occurred, though, the advantage it gave was tremendous. It enables fish to swim fast. In fact, the cartilaginous fish have to derive structures analogous to bone in order to get that upper speed.

Marlins, for example, have a bony skeleton stiffened not only by having just a few vertebrae but also by strapping those vertebrae together with bony strips and ropes of connective tissue. Mako sharks are similarly fast but don't have any such things. How do mako sharks swim fast? They increase their internal pressure against a skin which does not stretch. In this way they mimic what the marlin does. Essentially, they create a fluid skeleton to make up for any deficiencies in their skeleton.

Not to mention that a mineralized skeleton set the stage for invading the land. There are a lot of reasons even an average sized vertebrate dwarfs the largest land invertebrates that ever lived. Skeletal scaling is one of them.

Which brings me back to my ankle. I wish its intramembranous ossification process would get its act in gear.

Sunday, September 21, 2014

Consideration of Works Past: Farnham's Freehold

(Picture from here.)

I've been avoiding writing this post for a bit now. Heck, I've been avoiding reading Farnham's Freehold for a while now. There is a whole lot of controversy on that book. While race showed up regularly in his work, FF was the only book where he attempted to actually confront it.

There was a controversy about Podkayne of Mars. It is nothing compared to the controversy around Farnham's Freehold.

Spoiler alert: it's a bad book and not worth re-reading.

But not for the reasons one might think. Or, at least, not solely for those reasons.

Here's the plot, FF's main protagonist is Hugh Farnham, a self-made millionaire. He's one of Heinlein's Perfect Men: He's older, handsome, able to shoot a gun and appreciate a Picasso, incredibly wise-- so wise that everyone defers to his wisdom even when they completely disagree with him. So intelligent that other people appear stupid around him-- wait a minute. Other people are stupid around him. Farnham has a reasonable IQ and everyone else is a Delta Moron. Did I pick up Idiocracy by mistake? Nope. Heinlein's name is on the front page and it's a book, not a movie. Hm.

Anyway, Farnham has built the worlds greatest fallout shelter in his basement and, because Farnham is always right, a nuclear holocaust occurs. They all go to the shelter: Hugh, his worthless son, Duke, his whiny useless wife, Grace, his somewhat useful daughter, Karen, Karen's hot friend, Barbara, and Hugh's black servant, Joe. All of them act out all sorts of Generation of Vipers shtick to show how smart Hugh is and how callow everyone (but Barbara and Joe) is. Everyone goes to sleep except Hugh and Barbara. And they have sex. After all, what should a twenty-something beauty do during the apocalypse than have sex with her grandfather?

The big one hits and blows them forward in time a thousand years. They don't know this originally. They just know that they're in exactly the same spot as they were but everything is beautiful and rustic.

They eke out the pioneer life with Hugh as boss. Karen is also pregnant-- predating nuclear holocaust because, well, reasons. Hugh will not consort with Barbara because he is an Honorable Man and still married to whiny, bitchy Grace. So it looks like it's going to be a Karen/Joe and Barbara/Duke future Eden. (Except that Karen tells Barbara that if Hugh would have her, she'd pick him. Incest be damned.) But Karen dies in childbirth.

Then, they are discovered by the true rulers of earth: Black People.

Turns out that Africa wasn't harmed by the nuclear exchange and ended up colonizing the USA and Europe. All white people are slaves. Our merry band of misfit toys would be slaughtered for just being there (it's a park, sort of) but for Joe. Since Joe is black, they must be his slaves and therefore they won't be hurt but Joe is held responsible.

Long story short: Hugh makes himself indispensable to the Lord Owner. (Surprise!) Grace ends up Lord Owner's consort-- which she likes. She finagles her son (Duke) to be with her but that requires Duke to be castrated. She's comfortable with that. Since he's getting good drugs, Duke is, too. It is discovered that not only have the Black Lords enslaved white people, they are eating them. White people are the main meat staple of the culture. For thousands of years. I'm guessing cows, pigs, chickens, kangaroos, armadillos, dogs, cats, possums and rats were in short supply.

Got to say this about human beings. We're as hard to kill (and as uplifting) as a cockroach.

Lord Owner sends Hugh back to his own time with a device to make it accurate so he can commercialize it. Hugh, of course, dumps the device. They find a mine shaft and stock it in the time they have left and then sweat out the apocalypse with the idea they will be able to change the future. Or it's a parallel world. Something. Afterwards, they make themselves into good frontiersman libertarians. The end.

Okay. That took longer than it should have.

Here's what I think Heinlein was trying to do. And I'm being charitable here. So don't shoot me. I think Heinlein was less malicious than he was inept.

First, I think deep in the abscesses of Heinlein's mind he was thinking that he really wanted to treat any black characters as he would treat any other character. He probably thought the sameness was a virtue. I'm sure he thought he was combating racism. Hugh had to be white-- he was espousing all of Heinlein's pet ideas. He was, in effect, Heinlein himself: he had to be white.

He wanted to put his white characters in a position of oppression-- a role reversal. That's obvious enough. Black/White role reversal to combat racism has a long history from Watermelon Man (Godfry Cambridge) to White Man's Burden (Travolta/Belafonte) to John Howard Griffin's Black Like Me. (The book, not the movie made from the book.) One cannot fault Heinlein for attempting something difficult in a noble cause. One can fault him for doing it badly.

But he had a problem: Hugh has to be right. This is the salient point of the entire novel. Hugh is always right. But he's white so if the oppressors are black, Hugh is not going to get much traction. Hence, Joe was born. Joe could have been a partner. A colleague. A friend-- but the structure of the novel prohibits that. Hugh can have no peer. Joe could have been family but Heinlein wasn't that progressive. So Joe is a servant.

Later in the novel Joe ends up throwing in with the black aristocracy. There's a rather good scene where Hugh upbraids him for doing so. Joe responds that until Hugh has tried to hitchhike in Mississippi, he has no understanding of the situation. It is likely the sole place in the book where somebody stands up to Hugh and isn't immediately forced to admit the error of his ways.

And that example is one of a few things where I think the book was on point. Joe owed Hugh (or Heinlein) nothing. Shoes on the other foot: fine. We can't all be saints and it's clear in the context of the book that Joe is trying to get them as good a deal as he can get within the limits of the culture he's in and without sacrificing his own neck.

You can make the argument that the blacks were merely white men with black skins. I can see that. The book takes place thousands of years in the future so I would not expect future blacks to resemble current African American culture. You could make the argument that Joe, being a representative of current African American culture should actually resemble said culture. But Joe is on camera so seldom compared to the white folks he scarcely gets the chance. You could make the argument that Joe, being second only to Hugh in importance of the frontier family's survival and probably the second most important character in the book should have a lot more camera time.

Yeah, you could.

Which brings me to the real problem with the book. Yes to a lot of the criticism of it. Yes it handled race badly. But the core issue of the book is that it is inept. It's clumsy. It stumbles. It's broken. It should have been pulled by the editors as a bad book. Not a controversial book.

Like the whole cannibalism thing. Okay, Heinlein was probably thinking that slavery consumes people's soul. So it's a metaphor for what slavery does to the human spirit.

Come on, Bob. This book was published in 1964. I surmise it was written in 1963. King's I Have A Dream speech, Bob. The Medger Evers murder, Bob. The Birmingham Campaign, Bob. The Birmingham Church Bombing, Bob. Hell, I was an eleven year old kid in Thousand Oaks, California, and I heard about these things. Do you think that maybe, just maybe, a book where a black aristocracy is literally eating white human flesh could be, oh, misinterpreted? 

Like Barbara, and every other woman that shows up in the book (with the exception of his wife) wanting to sleep with Hugh. Including his own daughter. I mean, Heinlein's view of women in this book is little more than sex kitten/breeders but even in that context that's a bit much.

(It would be an interesting thought experiment to rewrite the book from Grace's point of view. Hugh is every bit the despicable villain Grace thinks he is. He connives what he does and makes good sounding excuses afterwards. He built the fallout shelter because of a sick, paranoid fantasy. The fact the nuclear annihilation actually occurs is a coincidence. She is sick and distraught at what she has to do to save herself and her son, viewing the role Lord Owner's consort as consent to rape. Pretty much what every slave woman submitting to master probably thought. That it would have been better to die in the nuclear fire than to have to live here under these circumstances, under these rules. To have Karen think about having sex with Hugh to appease him. Barbara having to view her coming child as a brutal compromise for survival. But I digress.)

Like vast numbers of pages taken up describing interminable hands of bridge. Pages. People agonizing over decisions they made. In bridge.

The book was published in 1964 sandwiched between Podkayne of Mars and The Moon is a Harsh Mistress. I commented on Podkayne here. Podkayne has its problems. Harsh Mistress is, in my opinion, Heinlein's best adult book. It's flawed but he manages to pull everything he's ever tried to do together in one book. I think it works though it is a product of its time. One of these days I'll put up a post justifying my opinion.

Harsh Mistress is followed by I Will Fear No Evil, which I had considered the worst Heinlein book I had ever read until I reread Farnham's Freehold. Clearly, it was the beginning of the end.

What I was hoping to find was a book where a writer whose work I respect had come out swinging at a subject few in SF were considering in 1964. A swing and a miss is still a swing. What I found was a boring slog through the mud. The game was rained out long before it ever had a chance to start.