The title is not a tease but is an exercise in abstraction. I spend most of my free mind time thinking about one or the other of these two subjects. Can I find any overlap in the research going on in these two? That was the challenge. I hope you don’t mind if I spend most of my time on sex. I will reach out to physics near the end.

How can we come up with an abstract definition of sex? The Internet has a significant amount of abstract sex, meaning that most of the traffic in text, images, and audio does not lead to real sex. Wikipedia has statistics on the amount of sexual information on the Internet. A more entertaining presentation features a young lady whose body gets marked up with similar stats, viewed some 16 million times.
Click or skip this dramatic reading
If one was able to make a copy of the bits flowing through a fiber optic cable of a Tier 1 Internet backbone provider, the bits about sexuality look no different from those of stock prices. Layers and layers of protocols such as TCP/IP, IPv6, HTTP, jpg, flash, wmv, and mp3 must be understood before the bits look like human sexuality.

Sex on the planet is mostly non-human. A good book on the diversity of animal sexuality is “Dr. Tatiana's Sex Advice to All Creation: The Definitive Guide to the Evolutionary Biology of Sex” by Olivia Judson Anything you might consider kinky is done on a regular basis by some kind of insect or animal.

That fine book focuses on the multicellular. Even amoebas do it sometimes. Why? Error correction according to one idea cited in the article:
Asexuality is a losing game in the long run, because mistakes accumulate in the genome and get passed down to offspring, eventually killing them. This theory is called Muller's Ratchet, and is traditionally used to explain why sex evolved.
When the genomes are mixed up during the splitting and recombining of DNA during sex, offspring can shed these mistakes. Some asexual animals, like the bdelloid rotifer (a small multicellular animal), have developed other means to recombine their genomes and avoid the squeeze of Muller's Ratchet.
Viruses play the game too via recombination. In my brief stint in grad school, I devised a method to use the Polymerase Chain Reaction (PCR) to detect recombination using restriction enzymes to tell if genetic information had been traded in the polio virus. I was told years later that my proposal was a pain in the ass to do at the bench, but it did work.

Physics is not a story of humans, animals, insects, amoebas, or viruses. Physics is the story of numbers. How could life be viewed as a number? Assign 1 for life, 0 for death. [Survival of the fittest]* is about traits that allow one member of a species to be alive (1) and not dead (0). The survival of the fittest is a story of avoiding zero. Are you fit? I sure am not, being a diabetic with ⅔ of my aeortic heart valves in place, and celliac disease to keep me away from twinkies. I do have a daughter, so I am not a total loser in evolution’s eyes. I sure don’t feel fit.

[* A heck of a lot of the comments below are debates about the exact relationship between various terms relationship to evolution. The point of this blog is to connect biology to physics, a rather difficult stretch. In the initial post I chose the phase "natural selection". I think "survival of the fittest" may be a better match for the intent which is to map alive to the number 1, and dead to 0. There are two other places where I used "natural selection", and it looks like "survival of the fittest" will work in those contexts too.]

Sexual selection is the other huge engine of evolution theory. In puritan America, the subject is suppressed due to the accurate choice of words in the label. One live creature plus the efforts of another live creature lead to the creation of a third being. One plus one makes one.

Cooperative creation, that is sexual selection. Cooperative creation is interesting. The child is not a clone of either successful parent. Instead new creatures are a combination of their parents.

Sexual gene transfers can be either horizontal or vertical. We are familiar with the vertical form that lends itself to family trees. Our great, great, great, …[repeat 10k more times], great grandparents came from Africa.

Horizontal cooperative creation is when genetic information travels across species lines. Viruses are adept at this task. The repeated Alu elements in the human genome are thought to have been an old retrotransposon. Most of the million Alu sequences are shared by our fellow primates, but about 7000 are unique to humans.

Evolution should be taught early and often (you are like your parents, but not quite, explaining the hair and eye color of my daughter). Instead, some want to skip the subject entirely (a big fat zero). If it is taught, the focus is on [survival of the fittest], the battle between zero and one. This is what big business has always done. It is rare to bring up sexual selection. That is too bad, so many wacky things happen due to vertical sexual selection, the peacock’s tail being the most famous of many possible examples. Horizontal sexual selection is never discussed as it is freak show material.

That is what I thought until January 26, 2010 when I read the following article by kdawson on slashdot
LucidBeast tips a mind-bending report at New Scientist on the latest paradigm-breaking work of Carl Woese, one of whose earlier discoveries was the third branch of life on Earth, the Archaea. Woese and physicist Nigel Goldenfeld argue that, even in its sophisticated modern form, Darwin's theory of evolution by natural selection applies only to a recent phase of life on Earth. Woese and Goldenfeld believe that horizontal evolution led to the rise of the genetic code itself.
"At the root of this idea is overwhelming recent evidence for horizontal gene transfer — in which organisms acquire genetic material 'horizontally' from other organisms around them, rather than vertically from their parents or ancestors. The donor organisms may not even be the same species. This mechanism is already known to play a huge role in the evolution of microbial genomes, but its consequences have hardly been explored. According to Woese and Goldenfeld, they are profound, and horizontal gene transfer alters the evolutionary process itself."
[Point of clarification due to Sascha's comment below: the modern theory of evolution is a scientific theory. Should Woese's work withstand further study, it would augment the scientific theory. It is common practice for science reporters to reference a challenge to a long dead great man as a means of generating interest. Please keep this caveat in mind.]
Such big claims required tracking down the relevant article. That was a summary piece which provided vital details. 
Carl Woese was active in the days when the genetic code was cracked. This was not a trivial job, requiring creativity at the biochemical lab bench. A few were straight forward. For the codon GGG, make an mRNA with CCCCCCCCCC... and see what one tRNA binds. Sorry if I am skipping the details of the central dogma of molecular biology,DNA makes RNA makes protein (image by Daniel_Horspool). I want to focus on the genetic code. There are twenty amino acids in proteins along with four DNA bases. A stop codon is also needed. Two bases could code for sixteen amino acids. The simplest code to span the possible amino acids would be three bases, making 34=64 codons. Go ahead, make a genetic code if you like, there is much freedom to choose, about 1083 possible genetic codes. That is smaller than the landscape of vacua for strings at 10500, but still a stupidly big number.

It turns out that life on this planet happens to use just one genetic code.There are a few variants that have been found particularly with the stop codon I believe, but people studying a new organism do not have to break the genetic code every time. There are three branches to life. The Eukaryotes are like you and me, with a nucleus and organelles. The prokaryotes are the single cell sorts that live in our guts, fast biochemical whiz kids that pack everything into one bag. The archaea were seen in harsh environments like the vents in the oceans. Their RNA is distinct from the other two, the key clue to Woese’s discovery about the third branch of life.

The particular genetic code in play is excellent at minimizing the damage from errors in translating DNA into protein. If the third codon is translated wrong - either a mistake gets made creating the mRNA, or the wrong tRNA grabs hold of the mRNA, that usually results in zero change for the resulting protein. If a mistake is made in the second codon, that will usually result in a different amino acid being used. The gods who intelligently designed the code (NOT) made sure that the different amino acids in that situation were not that different chemically: this one is hydrophilic as is that one.

What Woese and Goldenfeld did was see if vertical genetic transfer could generate this most excellent code that all organisms used. What they found in their simulations was that the most excellent code was not created. Instead the trial runs got a pretty good genetic code and kept that for historical reasons. A second problem was that some lines branched off on their own tangent and never every got in agreement with the rest of the crowd of life. Oops, that is not what we see.

They then modelled the evolution of the genetic code with horizontal gene transfer. Those simulations showed that everyone converged to the same most excellent genetic code, just as is seen in the wild. Says Goldenfeld:
"[Horizontal gene transfer] would have acted as an innovation-sharing-protocol greatly enhancing the ability of organisms to share genetic innovations that were beneficial"
I read this article, and I could almost feel my view of evolution bend in my mind. Horizontal gene transfer went from freak show feature to the pole position. It is next to beyond impossible to do anything useful biochemically. It is trivially easy to be stupid. If any creature anywhere figures something out, it is a huge advantage to be able to grab that innovation. That remains true today, even in politics. Trivially stupid is easy, doing something useful is rare.

Vertical gene transfer comes second. Think of the craziest things you have done in your life. There probably was a link to sex, not survival. Sex is a creative process. It creates a new life like no other before in detail.

Survival of the fittest ends up last. It puts handcuffs on sex. Creatures need to eat and avoid being eaten before they can get it on.

In Woese and Goldenfeld’s view, there were different phases of evolution. The earliest mode was dominated by horizontal gene transfer. At some later time, life jumped to the natural selection track.

Not that I will publish anything on this subject, but I think there has always been a tension between horizontal gene transfer, vertical gene transfer, and [survival of the fittest], a trifecta. Some biologists are trying to quantify how much horizontal gene transfer there is (I have seen numbers like 10-30%). It looks to me that all three are dependent on each other. Too much sharing and no one can develop their own niche. Biology is all about obtuse niches. How much time is spent looking for food versus a mate varies.

What changed for me that day was the definition of sex. Sex is about creative cooperation amongst the successful. Sex can happen outside the lines of species. Doing anything useful is stupendously difficult. Sharing genes means sharing success.

In physics, the vacuum has much power over the minds of theorists. The Higgs false vacuum cleaner could provide the mass to 3 gauge bosons. Through the magic of Yukawa couplings, maybe all the fermions too. In murder mysteries, the butler did it. In physics mysteries, the vacuum did it, or is at least one of the prime suspects. I don’t believe the vacuum is the leading candidate for the stable, uniform velocity start of the Universe, the failed Newtonian gravity description of large gravitational systems, or the odd acceleration of galaxies going on now. Note: I avoided the usual labels for these since I focus on the problem, not the most popular yet unproven hypothesis, those being inflation, dark matter, and dark energy respectively.

I think it is all about unity in spacetime. I want to join tensors notation to group symmetry generators at the hip. Tensors allow potentials to add and subtract. The symmetry generators allow multiplication and division. Quaternions do both at once.

That covers the group symmetries seen in the standard model without being the standard model that assumes tensor products between the symmetries, not co-habitating subgroups.

Fermions might involve quaternion triple products. The multiplication table for quaternion triple products is dense.

It might be rich enough to mine all the results we already have. It was this particular figure that convinced me there is no way I can “do this alone”.

My work circles around creative uses of unity, downplaying zero, as I think should be the focus of evolution theory.


Snarky Puzzle. Think about the animation of (1,0,0,0). Compare and contrast that with animations of (0.9, 0, 0, 0) and (1.1, 0, 0, 0). Reflect on the standard model symmetries in curved spacetime.

Google+ hangout: 11:00-11:45pm Eastern time, Tuesday-Friday.
This could be an efficient way to exchange a few ideas. If you have a question or two, hangout.

Next Monday/Tuesday: Snarky Puzzle Answers 4