Saturday, December 19, 2009

Taking a break from Phylogenetics.

     I had to read something a little less painful, so I picked up a new Philip K. Dick novel I purchased from Amazon. The Man Whose Teeth Were All Exactly Alike was written in 1960, right before he wrote the Hugo award winning novel The Man in the High Castle. Here's a scan of the most uncomfortable and odd-looking cover art:

     This is a realist novel, capturing the actual life of a small town in 1960 California. It was never published while Dick was alive; no one would buy it. The first printing was in 1984 and that one is very expensive. I was only able to read this book because of the reprinting, in 2009.
     Just because this book is not science fiction doesn't mean you're going to walk away without something interesting to chew on. On page 136 he writes:

     "It's always that way. The guilty party never pays. It's the innocent. That's the real meaning of Christianity."

     Besides reading that excellent and very strange book I also saw Avatar. The most interesting thing about watching James Cameron's Avatar was the imagery it provoked in my mind. Normally my mind wanders when I watch movies because they are not good enough; I have to supplant the images with those from my own imagination. I had to do no such thing while watching Avatar - the imagery is on par with what one imagines while reading a first rate science fiction novel. Notably, the impressive use of bioluminescence brought to mind the following novel:

     The movie Avatar looked exactly like what I had imagined while reading that book, many years ago. Although the locations were different as Avatar took place in a forested environment and The Hero of Downways took place underground, the imagery is remarkably similar.
     The main idea in Avatar, that is, of transplanting a human into an alien environment by changing the species of the human into that of an alien is not new. Clifford D. Simak wrote about that in City and Timothy Zahn wrote about it in Manta's Gift.
     Most disturbingly, I must now resume my studies of Phylogenetic Systematics. Perhaps I will benefit from it, perhaps not. Either way, I feel it is something I must understand (I don't know why).

Sunday, December 6, 2009

More abstruse words.

     On page 89 in Phylogenetic Systematics is when things start to supercharge in difficulty. Several new words are introduced that the author does not define very well, nor are they words I have ever seen prior to reading this material. Even worse, the words are used often, which means if one is not intimately familiar with them, then all the processing is spent on dealing with the words and being further frustrated by the difficult content.
     So a different type of reading strategy must be used in order to successfully read this book. I am accustomed to reading books within a few days and dashing over to my dictionary whenever an unfamiliar word appears. What I am accustomed to cannot be maintained when reading something of this caliber. I have to take time out and research words before I can continue reading. Here are some more of them:

     1. Plesiomorphous, Plesiomorphy - As with most words in phylogenetics, the authors seem to enjoy putting them together out of Greek roots. This reminds me of when I used to study calculus; the authors enjoyed using Greek letters in the equations. It was not necessary as standard Roman characters would have sufficed. But in phylogenetics it seems to me that it is necessary, perhaps not with Greek, but most certainly with something. In order to cope with these words, one must know that plesio-, plesi- correspond to "near" or "close". And morph- corresponds to "form", "shape", or "structure". In phylogenetics, the meaning refers to traits that are similar within a group, but not unique to that group. As an example, all mammals have a backbone, but so do fish and reptiles. Thus, the backbone is plesiomorphic to mammals, because they were not the first to evolve it, but they all have one. (Most common example I could find.)

     2. Apomorphous, Apomorphy - apo- corresponds to "separate", "away from", "derived from" and refers to traits that are derived from a different group. As an example, the "arms" of birds are used as wings. Thus, having wings is an apomorphy for birds because they did not evolve limbs and they use them for a different purpose. (My example.)

     3. Symplesiomorphous, Symplesiomorphy - sym- corresponds to "together with", "united", or "similar". This simply refers to plesiomorphous traits in different species. I decided to consult wikipedia for an example:

"A famous example is pharyngeal gill breathing in bony and cartilaginous fishes. The former are more closely related to Tetrapoda (terrestrial vertebrates, which evolved out of a clade of bony fishes) that breathe via their skin or lungs, rather than to the sharks, rays, et al.. Their kind of gill respiration is shared by the "fishes" because it was present in their common ancestor and lost in the other living vertebrates."

     4. Synapomorphous, Synapomorphy - This refers to the presence of apomorphous traits in different species. As an example, the opposable thumb in some new world monkeys is synapomorphic. It is a derived condition that they share with each other but not with all other mammals. I suppose that if all mammals had opposable thumbs, then the trait would be apomorphous. (I found that example doing a google search.)

     5. Autapomorphous, Autapomorphy - I can't find a definition that is pleasingly simple. All I can seem to find is that it refers to "uniquely defined traits". My guess is that abstract reasoning would be an autapomorphic trait for humans, even though such reasoning is without structure itself. Or is it? Morphology does not need to be restricted to those structures that are readily visible. The folds of the brain could also be a part of morphology, as well as the new "structures" in the brains of humans; the thinking that we do might have an actual shape in the brain, traceable by synapses.