Rambling #4


So, what’s been happening for the last 3 months?  As I’ve mentioned before, my parents are very likely to pass the century mark and increasing disabilities have pretty much required us to go from assisted living to memory care for them, and for the last several months we have talked with them about over a dozen different options for doing that along with visiting each facility (including seeing some multiple times because they couldn’t remember what they were like).  If you wind up in that situation, remember to take lots of videos and photos.  To make a very long story short, my mother found only one of them acceptable, and we had to make arrangements for when an opening would occur, followed by reminding them every time we visited about eventually moving.

In the meantime, several relatives have died or become sick, and my wife is the only one who seems to make time to help.  My brother-in-law died late last year, and my father-in-law was diagnosed with an aggressive form of lung cancer.  Until a year and a half ago, my father-in-law had a huge (between a third and half an acre) backyard garden, and after supplying the family with all the vegetables we’d need for the rest of the year, he gave the rest to his neighbors.  Once or twice a week, he’d have a party for the remaining members of his family (all four of his sons have died).  He cooked meals for everyone who visited, and we figured that if anyone was going to make it past 100, he was it.

He started chemotherapy with my wife trying to take care of him.  On top of everything else she takes care of the grandchildren several days a week.  Occasionally, so do I on weekends.  When we get a break in our schedule we try to work in a vacation, which invariably gets cut short when something happens at home (usually with our parents).  The last time (over a month ago now) we drove along the Gulf Coast and took our youngest granddaughter to Destin for a week.

When we got back, my father-in-law was in the hospital with pneumonia, and he wasn’t having any of it once he could breath again.  A short while later we found out that his cancer had spread and that he wanted to go back on chemo again.

Three weeks ago, everything hit.  As I’m sure I mentioned before, I’m autoimmune central, with rheumatoid arthritis (RA) and the accompanying psoriasis, myelodysplasia (MDS – for myelodysplastic syndrome), and what has tentatively been diagnosed as lupus erythematosus (LE).  The last diagnosis had an unintentionally funny side to it.  The prime symptom was being covered in welts and it often happened in the first two days of a vacation – so I dubbed it the vacation syndrome.  Over a span of a few years, over a dozen specialists, and many biopsies whose number I lost track of, I got the same diagnosis – “Good news.  It’s not cancer.”  The eventual diagnosis finally came as a result of an apparent interaction of the RA and MDS that didn’t make sense.

Recently I was in for my scheduled maintenance.  It was for a bone marrow extraction (or aspiration in medicalese).  It’s not much fun having a heavy-gauge needle driven through your bone to get to the marrow.  At the same time, they found that my hematocrit was plummeting toward 20, which is less than half the hemoglobin a normal person has.  That’s just one of the wonderful things you can expect with MDS.  The only cure is if you can get a bone marrow transplant with a compatible donor, which is what happened for Robin Roberts of ABC’s Good Morning America.  It didn’t work so well for Carl Sagan, who died after his third attempt at a transplant.  I’m not a good risk for a transplant, so that option is out.

That was the same day that my father-in-law, who was back in the hospital for pneumonia again, died.  It wasn’t supposed to happen that way.  I had to spend the next day getting a blood transfusion, and that screwed up our schedule for getting my parents moved.

Since then, my wife arranged a celebration of my father-in-law’s life (among many other things, he was a decorated hero of WW II) before his burial.  We got my parents moved – not a simple matter.  I’ve been to three other doctors for related problems, and I’m off methotrexate for the RA since it’s a myelosuppresant and it counteracts the drugs for the MDS.  I’ve been through 4 chemotherapies for my various diseases and I just started another 8 months of azacitidine for the MDS today.  It’s been a long three months, and we’re both exhausted, and now I have to wasted another day with a second transfusion.  Time for a vacation, but I doubt we’ll get that opportunity for a while.

Anyway, I haven’t been ignoring everyone else.  I’ve been trying to catch up on my mail and the blogs that I follow, and there aren’t enough hours in a day.  I’m not sure anything I’ve written so far makes any sense, but it’s time to plow on.

While my blog has taken back seat to real life, the writing I want to do has been on hold for almost a year and has suffered when I take time out for my blog.  I started a science fiction novel about 20 years ago, and it’s pretty much dead.  There were 13 chapters, and I liked what I wrote on the first chapter, but the second chapter was tedious because I tried to include the science behind what was happening.  I didn’t work.  Later chapters were really uneven, and I quit after the next few and all that remains after that is an outline.

The second book was privately written for my dad.  He was having problems with God of the Gaps and seeing deism as the only alternative at the time, and he couldn’t see a natural explanation for nature.  The book’s scope was pretty simple – Life, the Universe, and Everything.  It began with a quick run through relativity and the history behind Einstein’s equation for gravitation.  It continues with solutions for Alexander Friedmann’s and Georges Lemaître’s equations for the evolution of the universe (the big bang), followed by Alan Guth’s and Alexei Starobinsky’s ideas about an inflationary universe.  There was a brief follow-up for the ideas of modifications to the original inflationary models including a multiverse, how ideas other than the Standard Model affect outcomes, and Stephen Hawking’s idea of how a transformation from a positive-definite dimensional space to a space-time with a Lorentz metric might lead to and affect inflation.

Something that gets a short shrift in discussions of inflationary theory is baryogenesis.  A major problem with inflation is that it predicts an equal quantity of matter and anti-matter, so why wouldn’t they annihilate each other and leave a fermion-free (matter-free) universe?  It’s well-known that there is an asymmetry in the decay of matter and anti-matter, but mechanisms known at the time couldn’t match the extent of the asymmetry.  I suggested several possibilities like asymmetry of bottom and top quark decay and the possibility that Majorana (as opposed to Dirac) neutrinos could play a role.  Bottom quark decay turned out to be a good guess, but the other two possibilities are still in the air.  (By the way, top quarks are particularly tricky to deal with.  Many sources, including Neil deGrasse Tyson, mistakenly state that there is no such that as a solitary isolated quark because QCD guarantees that they will always be associated with other quarks.  When a top quark is formed, it is possible for it to be isolated because its exceptionally brief life may not allow the formation of another quark before it decays.  What-if scenarios abound on this.)

Next, I took up the formation of the first (population 3) galaxies and traced them to the formation of population 1 galaxies.  There were a few things that, in looking back, I got wrong like the formation of closed (galactic) clusters.  Fred Hoyle’s group untangled the mechanics of supernovae in the 1950s. and I used some of the results to trace the development of solar systems for moderate to late-type stars and their planetary systems.  I discussed non-virial [note the extra ‘i’ – it’s not ‘viral’] star and planetary beginnings through chemical accretions and how they affected later virial collapse.  The idea avoids the embarrassment of having to start with electrostatic dust bunnies or dark matter planetary accretions prior to gravitational collapse.  I also suggested some differences between my ideas and the standard concepts of very early atmospheric and surface formation and their impact on how life may have begun.

I traced how complex organic compound were formed before being delivered to earth in meteors and how mechanical shock of the meteor’s entry into our primitive reducing atmosphere (which I think was somewhat different than that currently accepted in the very early Hadean aeon) affected delivery of organic molecules.  I notice that the idea of mechanical shock seems to have caught on.  Concentration on or in a substrate was required for any further substantial reactions to occur, although there are now a few good possibilities that I didn’t have then (How Did LUCA Make a Living?) where LUCA stands for Last Universal Common Ancestor.  I suggested a simple mechanism for amino acid chirality and why only alpha amino acids are used in proteins.  It was a simple chemical selection process.

Ribozymes had already been discovered by the 1990s, and there was an unfounded jump to an RNA world that led to all other requirements for life – except for where the energy to drive the process came from.  I found possibilities for both, but missed the obvious energy source provided by chemiosmosis.  (Note that I wrote this before any of the genome studies had even started, and I was missing a lot of information.)  My layout for abiogenesis was sketchy at best, and there have been some major developments since I wrote that chapter.

My next attempt was to outline the development of life on earth, but the only real difference between what was accepted at the time was my argument that there was an excellent possibility that viruses were a fourth domain of life.  It was a simple idea in which I pointed out that viruses shared the same genetic structure as cellular forms of life and the only known examples at the time were obligate parasites.  The accepted dogma of that time was that based on that, viruses obviously must have descended from mutations within cellular genes that they infected and further mutations allowed them to form protein jackets, protecting them from the hostile environments they would need to cross to infect something else according to the wisdom of that time.  I thought and still think that the idea is pretty far-fetched.

My idea was that the only place anyone had ever looked for viruses and found a way for detecting them was as diseases in cellular life – as obligate parasites.  There are also many obligate parasitic cellular critters, so why don’t we discount those as non-living beings the way we do viruses?  The proof of the pudding would be to find a virus thriving in a non-parasitic setting or to find a virus with a complete (or near-complete) set of genes that would allow independent survival.  I now feel somewhat vindicated with the discovery of the super-sized viruses sometimes found in environment not dependent on cellular life and with comprehensive genetic structure, such as the megavirus, the mimi- and mamaviruses, the pithovirus, the pandoraviruses and many more.  Something that was particularly important to me was that some of these newly discovered viruses have an internal membrane, pointing to the possibility that they were part of the spawn of LUCA, sharing the same chemiosmosis mechanisms (and the same genetics) as other forms of protolife that eventually adopted a cellular structure.  Something shared in all viruses is a lipid coat around the protein viral shell.  Although I feel pretty sure I’m right, few other people agree with my assessment.

There were many details left to be filled in later, but my dad found the contents a little beyond what he could take in, I think he enjoyed the challenge to his deism.  I gave up on finishing the last two chapters – especially the history of life (other than my opinions on viruses) when he didn’t feel he gaining from it.

And that brings me to my current book, which looks at the relation between science and mathematics.  While reading Sears and Zemansky’s University Physics just before starting college, it struck me that Newton’s laws of motion seemed tautological to a large extent, and then seeing the very ideas I had considered earlier written explicitly in the first edition of Resnick and Halliday’s Physics, I knew I had to figure out where definition and physical content parted ways.

I found the answer in my sophomore year, which seems appropriate if you translate the root morphemes as “wise fool”.  It was based on how you define mathematics and science, and it shows the differences and how they fit hand-and-glove with each other.  I figured out later how the language you use affects the way you treat the definitions.  That happened when I was trying to invent combinitorial logic, not realizing that Haskell Curry had already done it.  I came up with a method horribly inferior to his, but it had the advantage that it applied directly to a language and was not restricted to any form of logic.

I had already decided in eighth grade that I was going to write a book on introductory foundations of mathematics, since I didn’t know of any that existed at the time.  With my new definitions of math and science, I had an approach that no one had tried before, and I was encouraged when I found a long article by one of my personal icons and Nobel Prize winner, Eugene Wigner.  I think it was in The Humanist magazine and it was asking the same questions I felt I had already answered.

Starting the book took many years because I didn’t have a word processor and then didn’t have the fonts I thought I needed to write the mathematics.  Neither Maple nor LaTeX has the ability to write what I need.  I finally started writing anyway after deciding to develop a font later to replace the special character combinations I’m using for the missing font entries.  It’s been slow and it doesn’t help the clarity trying to untangle the character combination stand-ins for the missing font characters.

Since so few people seem to read my blogs, I am considering giving it up after the next posting so I can work on my other writing.  There were several topics that seemed appropriate, but I think that since I know at least two of my readers enjoy math, that was going to be my last post.

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One response to “Rambling #4

  1. Pingback: Rambing #4 - Todd DeanTodd Dean

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