Sex And Unified Field Theory R&D
By Doug Sweetser | July 19th 2011 12:21 AM | 62 comments | Print | E-mail | Track Comments

Trying to be a semi-pro amateur physicist (yes I accept special relativity is right!). I _had_ my own effort to unify gravity with other forces in...

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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.
$\\(1,0,0,0)=\frac{A^*}{|A|} \frac{B}{|B|} \lhd U(1) \lhd SU(2) \lhd SU(3) \quad eq.~1\\ if A = B$
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.

Doug

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. http://gplus.to/sweetser
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

Darwin's theory of evolution by natural selection applies only to a recent phase of life on Earth ... different phases of evolution. The earliest mode was dominated by horizontal gene transfer. At some later time, life jumped to the natural selection track.
Could you not commit this silly mistake of every time there being some little improvement to the details of biological evolution calling out that Darwin got it all wrong and there is no natural selection? That other media and even the involved scientists do it does not excuse you. Darwin is correct and it is all natural selection. Yes, even with horizontal gene transfer or epigenetics or whatever is fashionable tomorrow, it is natural selection of the outcome (not perhaps two bacteria shaking hands and exchanging some piece of code that seems particularly useful after discussing the future of their environment).
unproven hypothesis, those being inflation, dark matter, and dark energy
Dark energy is not an unproven hypothesis (like dark matter still is), it is plainly a term in the Einstein equations that has been established to be non-zero by observation. Even if you are right and it is fundamentally made out of the sweat of horizontally gene swapping quaternions, it will still be dark energy.
hat other media and even the involved scientists do it does not excuse you. Darwin is correct and it is all natural selection. Yes, even with horizontal gene transfer or epigenetics or whatever is fashionable tomorrow, it is natural selection of the outcome
A good point (and a good article, Doug) - in his example it is still natural selection.

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).
I am one of those who think evolution shouldn't be taught in high school and this shows it - two very smart men (and then me) don't fully understand natural selection, mutation, migration, and genetic drift so expecting a teacher to understand it well enough to have students not misunderstand evolution is difficult.    We teach anatomy in high school but not brain surgery, we teach Newton but not Schrodinger and we could easily teach genetics and not evolution.    Evolution is so complex it really does take a biologist to get it and telling students to simply have faith in experts is not going to be satisfactory to the kinds of skeptical, inquisitive minds we are supposed to be creating in schools.  It's better to mention it and give an overview and then save it for college.  Not everything can be taught in lower grades - if we drill it into young minds and tell them not to question it, we just create robots taught to believe in authority.
I sure am not for faith-based science education. I still get chills with "The game of life", the computer game where shapes change in time. I bet there are even better apps now available. They can question the game (depending on how the game is implemented).

Only the college educated elite would get to learn evolution. No one with a high school education would know why they got over a cold. What happens is there are cells that are always on the lookout for foreigners. When one of them does recognize a foreigner, that cell gets excited and divides. The new cell is usually just like the first one, but it is actually designed to make mistakes often. Why?, well the mistake could result in a better foreigner detector. If the new cell is better, it gets even more excited than the first cell about dividing. Do this a few times, and you have a super-foreigner killer that wipes out the invaders in about a week. With no one left to slaughter, the super-foreigner killer goes into sentry mode, waiting for a return. That is a practical example of evolution.
Explaining to kids why they get a cold is basic biology.    The non-college-educated non-elite either accept evolution or they don't right now.  If so, they did not accept it because they were taught it well in high school, they accept it simply because they accept it.    The non-college-educated non-elite do not actually understand adaptive radiation even if they claim to accept evolution, nor do 99.9% of college students and, I would argue, 50% of biologists.   The most common refrain from biologists here about other biologists (on other sites, naturally) is they they 'know just enough biology to be wrong'.

Your example is, however, a fine brief overview of evolution, and I am not saying it should not be addressed.   Teachers should simply try not to teach it, because they will be wrong.  An example like yours is fine, and then teachers can move on.

Evolution is not basic so  your belief that a kid not smart enough to get into college should be taught it poorly at an even younger age is confusing.   Evo/devo types who want it taught in high school are engaging in vanity, not good science education, especially once they see how little biology teachers actually know about evolution.
I completely disagree with your point about evolution not belonging into school. There is only one problem: It should not be taught by biologists! Evolution is not a biological theory (that is just one area where it can be applied and it happens to be the one where it was discovered). Evolution is basic, much more basic than biology, and it should be taught along with basic physics by a physicist or mathematician. If the biologists stop confusing basic evolution with all those details that are perfectly beside the point (what the genes actually look like, sexes, ...), then evolution will be understood by kids.
I have to give you credit for being bold.  As long as you are okay having uncertainty taught to 8th graders by psychologists, it makes perfect sense.
Sorry, I do not get this at all (what about psychologists all of a sudden? They are the worst!). I think this discussion simply disappears once kids explore evolution via simple computer games as Doug already referred to and as R. Dawkins for example did it in the vision impaired watchmaker. And yes, of course if dumbasses design the games ("and now be god and turn the knob that lets the legs grow"), they would perfectly backfire, which is why mediocre biologists should not be involved (Sorry to all serious biologists - I had particularly bad bio teachers maybe, you can blame it on them.).
Mathematician is to teaching evolution as psychologist is to teaching uncertainty
There is a key difference. The mathematician is probably capable of understanding evolution.

If you hope to foster minds that challenge authority, a good anatomy assignment would be to compare the skeleton of a rat and a bat, versus a human and an angel. Young kids would want to know where the fingers of the rat were on the bat (the fingers make up the wings). We don't have any angel skeletons, only artist images. Where would the big wings connect? Just added it to the back? Doesn't make the same amount of sense as the rat and the bat having a great, great,... and morphing to different shapes.

Morphing shapes is part of popular culture. I had to do a little googling before I recalled the title, but Michael Jackson's video "Black or White"  is surrounded on all sides on YouTube with ads (I did enjoy watching it again). Any of the movies backed by Marvel comics have one shape morph to another. Computers morph with ease. Evolution does something like that, but not for any one person, but for their line of great grandparents.
Evolution does something like that, but not for any one person, but for their line of great grandparents.
No, that's part of the misconception.  Evolution does something like that for populations.  Evolution does nothing for the individual.
Mundus vult decipi
There are levels of understanding. A high school student should be able to understand evolution at about the level Charles Darwin himself understood it. It gets more complex, but that complexity can build off of this solid foundation of understanding in college.

I think all physics up to quantum mechanics and the standard model should at least be introduced along with the basics of calculus. I don't think the basic ideas are that difficult really- mathematically you only need the idea of a function being the solution of a PDE. But it isn't just about understanding the science. It is about giving the students an accurate impression of the field as it is today so they can decide whether this interests them and if it is something they are suited for.

You're missing the point.  What a student should or should not be able to understand is certainly debatable.  However, the primary problem is whether the majority of teachers understand it well enough to not misrepresent it.  If you can't assure the latter, you can't achieve the former.
Mundus vult decipi
I believe he made two points. His first point was that evolution is too difficult for students to grasp. That's false. Then he said this is especially true when the teachers are poorly qualified. Then these teachers should be fired. If they can't be, then the laws should be changed. Teachers should be evaluated and tested periodically. If a teacher can't explain the basics of evolution, then that teacher is too stupid to be in the classroom.

OK, I get that you're ranting, but that's not any kind of solution.  If you truly believe that high school science is taught by qualified high school science teachers, then I don't know what to say.

Also to suggest that teachers should be fired, is hopelessly idealistic when it is nearly impossible to even get them tested.  When you include parental pressures that will also determine what is considered acceptable curriculum (especially pertaining to subjects like evolution), you're dreaming.

In addition, the first point is also correct, because evolution is far too difficult for most students to grasp.  Again, we're talking about ALL students and not a subset that might be interested in science.

You're confusing "ought" with "is".
Mundus vult decipi
It should be possible to construct courses that are basically fool proof regarding evolution. I doubt many teachers are really too stupid to teach the basics correctly. Most of them are guilty of lazily describing evolution as "survival of the fittest." I think that the terrible situation in mathematics is much more difficult to correct than this. Consider the example of Darwin's finches. Is this sort of speciation really that difficult to grasp? It's dead easy compared to teaching mathematics.

My drum is evidence based education. I read recently about an effort for mathematics whose numbers looked great. Their thing was to chop math into really small bits. Small bits are easy to master. Get a half dozen small skills mastered, and the students are able to weave new stories together. That work did have the before/after data. Too bad I don't recall what the math education program was called.
It's a good approach, but it is difficult to teach students anything when all they really want is to be taught useful tricks the can memorize. You can only get so far in mathematics through memorization before everything falls apart. So changing the students attitude about mathematics is necessary and that is nearly impossible. If I taught, I would try to mix physics into the math curriculum. Formulas about such things as the entropy of a black hole are simple and exotic enough to engage some students. Word problems shouldn't be avoided either, but they could be so much better than they are.

I added the following comment after the quote:
[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.]
I did not include the words "natural selection" as I had used a much narrower definition in the blog, the difference between being dead or alive, so that I could compare it with horizontal and vertical gene transfer. Without gene transfer, natural selection narrowly defined as survival of the fittest does not matter. I also avoided using Darwin's name since people think the great old guy had to get everything right at the start. We do like to personify scientific theories.

We will remain in disagreement on the status of dark matter. I do have a proposal for gravity that is different from general relativity. General relativity could be wrong in the scientific sense, meaning it is really, really, really great and still useful, but there is another body of work that is slightly better. That small space is where I hope my work may end up. I don't think my proposal is cosmological constant friendly. My technical speculation about the relativistic rocket effect was discussed in a different blog. That speculation is just that, speculation, far weaker than dark [energy]. What does stand either way is the observation on acceleration. We have disagreed on this issue before, so at least we are both consistent.
You seem not to have understood my comment, neither part of it. Our disagreement is not about dark matter, but dark energy. You again and again, in best crackpot manner, confuse them just because of the name, and you refuse to learn. On the first part: natural selection, that is all, ah f' it, I give up.
At work, I am in a rush. The correction has been made. And yes, my mind is sloppy with labels after months of 6 hours of sleep. That is an observation more than an excuse. My mind will stay sloppy with labels, darn it.

If GR is wrong, then everything rooted in GR is wrong. That is WAY bigger than dark e n e r g y, it is a threat to the huge canon on black holes. Not a paper on black hole physics, every theoretical paper that uses the Schwarzschild or Kerr or the Friedmann-Walker metric. All that cosmology work with the Wheeler-DeWitt metric, gone. Defend the honor of the little tree known as dark energy (got it right that time). There has been a 90 year draught in theoretical physics in getting GR to play nice-nice with the rest of physics. This is a large scale napalm attack warning. That is a crackpot threat. The match is in the hands of the folks at the Europhysics conference, and what they have to say about the Higgs boson. I hope there is a Higgs, then I can get my rest, be less sloppy (for example, I need to correct all the Goldenfeld references in the post, tossed in an extra i).

Natural selection is a mechanism in evolution. Sexual selection is another mechanism. Lots of choices in regards to sex appear silly on the surface. If you mean that sexual selection lives in the house of natural selection, I don't think that is the proper relation between the two words. It is all evolution.
Doug, it is time to do something about your lack of sleep and blogging til dawn may not be the indicated medicine. Your "GR is wrong" BS should be far below you. The SS metric is not something of mysterious black holes. It describes the physics around our dear Sun for example, similar holds for FRWL in cosmology, so please get some well undeserved rest. Science cannot be sloppy with labels - if you do not know what you are talking about, only confusion and no progress at all can be expected. Even if you may some day find an improvement to GR, this does not make GR "wrong", neither did GR prove Newtonian physics "wrong" by clarifying its domain of applicability and improving on it - only crackpots (the annoying kind I thought you do not belong to) talk that way.
General relativity could be wrong in the scientific sense, meaning it is really, really, really great and still useful, but there is another body of work that is slightly better.
Sounds like we are on the same page to my ear. That was 3 really's. When push comes to shove, people do say Newton's theory for gravity is wrong: instantaneous effects being its most obvious flaw. The most obvious, unfixable flaw in GR is the lack of integration with QM. Standard line of logic.
" 'GR is wrong' BS should be far below you."

But isn't it possible that dark energy doesn't exist? That Einstein's equations are just wrong? I think this is what John Moffat believes. He thinks that dark energy is an ad hoc hypothesis analogous to the hypothesis, based on Newtonian gravity, that a small planet was perturbing the motion of Mercury. There was no planet. Instead, Newton'sgravity equation was wrong.

It isn't an absurd idea considering all the trouble the equations are causing.

But isn't it possible that dark energy doesn't exist?
You ask the equivalent of "But isn't it possible that the friction term in the equation of the simple harmonic oscillator (SHO) does not exist?" Answer: No, it is not possible, since it is right there in the equation when I write it down. You may disagree about the nature of the friction term (air resistance, the spring coil's metal heats up, energy conservation violated by quaternions eating breakfast), but you cannot because silly people may call the term "dark term" claim that it does not exist. Even in a system where there is no friction, the term in the equation still exists, it just happens to be zero.
Dark matter may conceivably not exist in the way it is proposed (extra particles), but dark energy is a term in the GR equation that is quite similar to friction or say a driving force in the SHO equation, and when we put cosmological measurements into the theory of GR (which is correct in as far as it is confirmed by observation), the term turns out non-zero. If Doug finds a better theory, it will still have to agree with and reproduce (!) GR wherever GR is confirmed by observation, and thus his theory is bound to have the equivalent of the dark energy term, no matter it turns out to be quaternions farting after having eaten to many hyperspace octahedrons in reversed infinite dimensional fractal time.
The confusion hangs probably on the religious concept about energy being some sort of substance that is somehow fundamentally conserved. It isn't.
"If Doug finds a better theory, it will still have to agree with and reproduce (!) GR wherever GR is confirmed by observation, and thus his theory is bound to have the equivalent of the dark energy term,no matter it turns out to be quaternions farting..."

Doug believes that quaternions, like beautiful women, don't fart.

Of course, Einstein's equations with a cosmological constant agree with observation and therefore dark energy exists in that sense.

"..reproduce.."

That is true and ideally it would make accelerated expanion inevitable. This sort of thing has been accomplished before in physics. In GR the cosmological constant is just tacked on to agree with observation. It isn't logically neccesary.

"it woud still be equivalent..."

But, to me, this is like saying, in the Newtonian case, that the equivalent of a planet would still be out there perturbing the motion of mercury. The postulate did agree with observations of mercury, but there wasn't a planet there. This dark energy could simply not be there, but Einstein's equations, without a cosmological constant, can't account for the accelerating expansion of the universe without adding it. That is a difficulty for GR IF this energy isn't there. (Another example, In a rotating frame Newtonion Dynamics adds rotational energy that isn't really there)
It could be possible that this case is fundamentally different because we can't ever observe the energy directly without using some theory to interpret it as energy. It could be a mere choice between alternate models that are equally consistent. But I still feel that this energy is either really there or it isn't.

At the very least, dismissal of dark energy isn't quite a crackpot idea. It's slightly better than that.

Natural selection is a mechanism in evolution. Sexual selection is another mechanism.
I think you're confusing concepts here.  Sexual selection, genetic drift, mutations, etc. are all inputs into natural selection.  However, it is only the selection process that determines whether an organism passes into the next generation.
Mundus vult decipi
You're going to annoy a lot of biologists, likely the way many of the comments probably would.   Natural selection is one of the basic mechanisms of evolution, along with mutation, migration, and genetic drift.  Variation, differential reproduction, and heredity lead to evolution by natural selection.

This all confirms my belief that evolution is too complex for high school teaching.  Really smart people cannot get a solid grasp of this so no way over-worked teachers talking to disinterested students will.
Natural selection is one of the basic mechanisms of evolution, along with mutation, migration, and genetic drift.
I beg to differ, since the mechanisms you've outlined are the means by which change is introduced, but until it is selected, it doesn't go into the next generation.   Without a selection mechanism, they are merely present and don't affect the population in any material way.  In other words, the selection process may be weak where many variations can survive, or it may be narrow in which case large scale survival is difficult.

In short, none of the mechanisms you've mentioned assure survival ... that's what selection does.
Mundus vult decipi
Biologist make a distinction between natural selection, the survival stuff, 0 and 1 in this blog, and sexual selection, how mates are chosen, so that one and one make a new one. When you compare choices made to survive versus those that are made to get laid, there is little overlap. Little does not mean none, as food and sex are linked for some creatures. The dead don't pass along anything to the next generation. Neither do virgins.

What is fun about horizontal gene transfer is it allows a huge expansion on what one defines as the population of genes available for future generations.
Physics is also hard to teach. Students often don't change their minds after a semester of lectures. I am a fan of David Prichard (and others) of evidence based teaching. Measure what students understand before the class, measure what they understand after. If no one can design a program to teach evolution in a way that can be measured by before/after tests, I will support Hank's position. I do have more faith - and it is faith, not a reading of technical papers on evolution education - that the basic ideas of evolution can be taught.
There are so many conceptual blocks for most people to overcome when learning basic physics. It is probably much more difficult than evolution in that way. Most of our brains are basically Aristotelian.

Natural selection is one of the basic mechanisms of evolution, along with mutation, migration, and genetic drift.
This is perfectly wrong just like the above "natural selection is one mechanism and sexual stuff is another one". You can take out sexual stuff and still have evolution. You can take out genetic drift and there would still be evolution. You could even take out certain forms of "mutation" (e.g. if sexual shuffling is already established), and you still would have evolution. But one thing basically equals evolution (given a certain, low entropy background to start with): Natural selection. Take natural selection away, regardless how much mutation and genetic drift is still there, and you have religion left.
You can take out sexual stuff and still have evolution.
What planet do you come from? On this here planet, most creatures don't have an asexual option. My dad did have sex with my mom at least four times, maybe more, and I have come to terms with it. Many creatures that do have the asexual option also can mate with others. Amoeba, yeast, and some worms come to mind.

evolution = natural selection
Basically equals? Equals or not equals. That's what I learned about equals. I am guessing your natural selection fetish is based on being right (that would be your view), but an underlying reason would be it involves entropy and probability, which sounds more like physics, a real science.

That bastion of never wrong information, wikipedia says in part:
Natural selection acts on the phenotype, or the observable characteristics of an organism, but the genetic (heritable) basis of any phenotype which gives a reproductive advantage will become more common in a population (see allele frequency). Over time, this process can result in adaptations that specialize populations for particularecological niches and may eventually result in the emergence of new species. In other words, natural selection is an important process (though not the only process) by which evolution takes place within a population of organisms.
Please, go delete the "(though not the only process)". Until then, I will stick with:
evolution > natural selection

Lest we forget the content of this very blog (quite common in comments), it was about the dominant means of evolution of the genetic code. The code one uses for phenylalanine is not "an observable characteristic of an organism" since GGC will do as well as CCG. The study proposed the mechanism for all life having optimized the same genetic code: horizontal gene transfer. The genetic code is a specific, concrete example of a fundamental biological system that is not a niche. That is why this article bent my vision of evolution. Otherwise, I would be on your side.
You can take out sexual stuff and still have evolution. ... What planet do you come from?
From the planet where life started by natural selection without sexual recombination having been evolved yet (by natural selection) for many many many years. How the hell can sexual stuff be vital for evolution if it is itself evolved??? The division into two (rather than three for example) sexes is something that evolution came up with Doug, it is something that was naturally selected!
Woese and Goldenfeld claim specifically that horizontal genetic transfer started out first. The reason is that one cannot select for better traits when hardly anything works. When hardly anything works, it is more important to develop means of sharing inovation. I am using sex here in the more general form - not odd mating dances - but as combining creatures that figured out how to do stuff.

The math behind natural selection leads to non-optimized genetic codes that are not shared by all organisms. How do you address their observation? Honest, before that paper I sure would have voted for natural selection as the way to construct the most important asset in the biosphere, the genetic code. It sure would not be sex which does the odd stuff. The paper reintroduced me to the ideas of vertical and horizontal gene transfers. I interpret your vote against sexual selection as one against vertical gene transfer, which I agree with. I think horizontal gene transfers may be as low tech as eating genetic material and incorporating a small fraction in one's own genome. That would be doable early on, no fancy dancing.
Woese and Goldenfeld claim specifically that horizontal genetic transfer started out first.
Evolution doesn't start after god throws a bunch of genes onto the earth and then blowing the life force into them. The RNA molecules came from molecular evolution (NATURAL SELECTION) before there was any hint of horizontal, vertical or diagonal circular DNA transfer, except if you want to go down to the level of what "gene" generally means, in which case the transfer goes of course all kinds of ways, we did not need Woese do misrepresent his findings about DNA in that case.
Except for one clearly marked joke in the blog, I have only talked science, no deities, no magic. Software on a computer somewhere did a few billion rounds of evolution (full disclosure, I have read only the summary article, not the technical journal). One round of modeling used trusty natural selection. That did not match what we see today. It did match the sorts of things natural selection does so well - it works, but it is not super-optimal. Certainly there could be many problems with the details of how the model was run. They ran the code with horizontal gene transfer probably about the same number of times, and all the computer creatures had the same most excellent code. Early life cooperated more than it competed.

The claim of Woese and Greenfeld was backed up by their computer experiments. I go with the data as I always do out on the ultra conservative fringe. The paper apparently made no impression on you, so it goes. If you reject their findings, natural selection wins, simple as that. I am confident they did not talk about god or a life force.
One round of modeling used trusty natural selection ... They ran the code with horizontal gene transfer probably about the same number of times ...
Both times it was natural selection, once without horizontal transfer (HT), once with HT, and HT reproduced what we see today, because HT was naturally selected in the real world. HT enables fast adaption in certain environments, so it is naturally selected, it emerges by natural selection just like sex emerged. Such naturally selected mechanisms speed up the evolution of complex systems and co-evolution of the environment - all this is well known and no computer simulation that shows acceleration of evolution by adding some mechanism X can possibly argue against X being evolved by natural selection or proof X being more fundamental, earlier, or a replacement of natural selection.
The claim of Woese and Greenfeld was backed up by their computer experiments.
The claim of Darwin being wrong and natural selection not being fundamental is there to promote the work in the media and none of it is supported by their computer program. Wake up.
You can make some computer program, call some parameter that goes to zero "natural selection" or "dark energy", and then claim to have a computer simulation that disproves natural selection and dark energy, and yes you will get media coverage and lots of ID people and crackpots will befriend you. Do not expect that serious people will not criticize you for such silliness.
Sorry, my friend, on this one you are out of your element.   100% of biologists will accept what I wrote and 0% will accept your substitute.
Yeah, I can see where I probably over-stated my definition.  You're right and I was wrong.
Mundus vult decipi
Actually, that was to Sascha when he disputed
Natural selection is one of the basic mechanisms of evolution, along with mutation, migration, and genetic drift. Variation, differential reproduction, and heredity lead to evolution by natural selection.
He is 100% wrong when he replied "This is perfectly wrong just like the above "natural selection is one mechanism and sexual stuff is another one".

He just doesn't see that, to biologists, he is the kind of crank he ridicules (when they do it about physics) when he persists in trying to recover an argument that is completely flawed, against all evidence and outside the science that 100% of biologists accept.
I think part of the point is that the description isn't completely accurate if part of the definition of evolution is to include components that evolved.  In other words, to claim that sexual selection is fundamental to evolution, is misleading since evolution had to already operate for sexual selection to have occurred.

In short, evolution started before biology therefore anything that depends on a biological condition cannot be fundamental to evolution.

Basically one must begin with some initial condition (molecule, chemical reaction, etc.).  If that condition is "beneficial" or becomes prevalent, then it has been "selected" for the next round.  In other words, some filtering process ensures that this condition tends to displace other conditions that are competing for the same resources/space/environment.  That filtering process is natural selection.  Genetic drift simply allows for some random event, while migration allows for an environmental change, while mutation allows a base "coding" change.  However, each of these will be subject to selection to determine their ability to "compete" in the next round (generation).

Once again, the point being that if evolution occurs at the molecular level, then natural selection is a fundamental process why which that occurs (long before sexual selection even exists).

This is similar to a discussion I had with Josh Witten some time ago, where the question came up about why cells should divide at all.  Why not simply keep all the resources for yourself, so that each "organism" effectively just fends for itself.  Why develop a mechanism to divide yourself and essentially introduce competitors?

The idea was that any organism that developed the means to replicate itself would have gained such an advantage over its competitors, that natural selection would fairly guarantee that all future organisms would have to be capable of replicating to even have a chance.  This would be an illustration of evolution having existed long before there was DNA/RNA, genetic drift, sexual selection, HGT, etc.
Mundus vult decipi
Biological evolution gets started with abiologic evolution that comes up with the macro molecules like RNA. If biologists are 100% of the opinion that life started with god making complete RNA/DNA reproduction systems and then dropping them on the freshly made earth (I strongly doubt that 100% of biologists believe that, but here you go), it will just prove my point: Do not let biologists teach evolution.
You may talk about genetic drift and mutation in more general terms (genes not being molecules but genetic information), but if you do, you are basically talking about algorithmic evolution (math) and against people who claim that something naturally and late selected like DNA transfer is vital to evolution.
Hank claims 0% of you biologists out there agree with me! Anybody with a biology degree reading this and not feeling like God made DNA? One is enough to prove 0% wrong.
Please refrain from that dog spelled backwards word. I read it as a put down to biologist, they haven't figured it out, so they need the dog.

The start of life on this planet is a HARD problem that biologist have not solved. The leading candidate is an RNA world, but there are other possibilities (I recall one that uses clay). The start of the big bang is a HARD problem that physicist have not solved. This paper makes a specific contribution to the scientific debate. There will always be people who use the dog to solve unanswered problems in science.
I use the doggy because your dangerous argumentation feeds the doggy. Just look at
The start of life on this planet is a HARD problem that biologist have not solved.
What are you trying to do? Get ID proponents to read your blog? Life naturally emerges via natural selection inside a large enough background stage (eternal chaotic inflation provides here both, the big bang and all that is needed for the start of life). All else is details that emerge from natural selection. How long do you want to ride around on missing links because there is always some more detail missing whenever you fill in one (that is the usual progress of science!). Darwin wrong, natural selection not as important as sex between Adam and Eve, start of life a HARD problem, ... that is all doggy shit and you started it.
I have no fear of people who promote Intelligent Design (ID). Such folks are free to read my blog. As we both agree, Intelligent Design is not a scientific theory. Here was the line that "started it" as you say:
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.
Most readers would agree that this is an explicit joke made at the expense of folks who have faith in intelligent design. It would disappoint, but in no way shock me, if this quote was misquoted, deleting the one word in parentheses. People who promote intelligent design have been caught many times distorting the record of the scientific process as applied to biology.

A part of my ultra-conservative fringe outlook is to not overclaim. We have the Miller-Urey experiment that shows we can make organic molecules in the early Earth. We have data that says RNA can do enzymatic reactions. I recall a study or two that thought about the first "bags" for cells. There are many missing links, some of which we may never answer. To me, that makes the science honest. The missing elements are worthy of thought and further experimentation.

As a skeptic, it is my practice to point out flaws in an intelligent design proposal. I do the same thing for people who have proved special relativity is wrong. I rarely win them over to my side, but that is not my goal. I have met my responsibility.

Looks like I have to read the paper now, a good thing :-)
Sascha, you are priceless!
Luve ya work.
And Doug, an excellent discussion!
K. Vetsigian, C. Woese, N. Goldenfeld:"Collective evolution and the genetic code." PNAS 103(28), 10696–10701 (2006)

does not once mention "natural selection" and nowhere indirectly identifies "Darwinian" with "natural selection" [although there is one tiny bit against survival of the fittest that could be misconstrued, but it is against the centering of selection on individual systems rather than collectives like gene pools, it is not directed against natural selection as such.].

In reticulate evolution, there is no unique notion of genealogical descent: genetic content can be distributed collectively ... we must necessarily invoke an evolutionary dynamic distinct from that identified originally by Darwin.
Vertical or Darwinian evolution does not lead to a reduction in the distance between codes.
In summary: A not helpful definition of "Darwinian" as signifying descriptions only having vertical gene transfer and too focused on individual small systems. The later has been long since improved by turning the focus on gene pools for example. So the news here is the importance of horizontal transfer (HT) as necessary in order to get to one globally shared and optimally error robust genetic code. Nowhere in the text is there implied that HT is not a naturally selected mechanism itself or that the runs with HT switched on have natural selection switched off.

Woese started as a physicist by the way, Goldenfeld being a physicist apparently, so if this text is showing anything more above HT being necessary for the globally optimized code, than maybe that physicists rather than Biologists should teach evolution, as I was saying all along.

Thanks for the paper reference which can be found on line here. Of course you are correct that the phrase "natural selection" is not in the text of the PNAS paper. Let's look at the abstract:

A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early communal life generically lead to refinement and selection of innovation-sharing protocols, such as the genetic code. Our proposal is illustrated by using a simplified computer model and placed within the context of a sequence of transitions that early life may have made, before the emergence of vertical descent.

In an earlier post, you have equated evolution with natural selection. The abstract sounds like a broadside attack. If you wish to read them specifically slapping natural selection around, that would be in a different paper, "How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis", Carl R. Woese and Nigel Goldenfeld, Microbiol Mol Biol Rev. 2009 March; 73(1): 14–21.

As for evolution, it had been developed from a phenomenological description centering around what was generally termed natural selection into the modern evolutionary synthesis through its union with Mendelian genetics. The modern evolutionary synthesis should have been the 20th century's evolutionary bastion, the forefront of research into the evolutionary process. No such luck!
The basic understanding of evolution, considered as a process, did not advance at all under its tutelage. The presumed fundamental explanation of the evolutionary process, “natural selection,” went unchanged and unchallenged from one end of the 20th century to the other. Was this because there was nothing more to understand about the nature of the evolutionary process? Hardly! Instead, the focus was not the study of the evolutionary process so much as the care and tending of the modern synthesis. Safeguarding an old concept, protecting “truths too fragile to bear translation” is scientific anathema. (The quote here is Alfred North Whitehead's, and it continues thus: “A science which hesitates to forget its founders is lost” [32].) What makes the treatment of evolution by biologists of the last century insufferable scientifically is not the modern synthesis per se. Rather, it is the fact that molecular biology accepted the synthesis as a complete theory unquestioningly—thereby giving the impression that evolution was essentially a solved scientific problem with its roots lying only within the molecular paradigm.

The concluding few paragraphs are also quite a strong message against the standard version of evolution. This paper probably triggered the New Scientist article.

Let's list a few ways selection works. There is artificial selection. That is when dog breeders pick short dogs with long hair to mate with other short dogs with long hair. The dogs evolve due to the fancies of dog breeders. We have many an odd animal out there because of this selection.

There is no religious element to selection.

You'll be happy to see the following quote about ecological selection

Ecological selection (or environmental selection or survival selection or individual selection or asexual selection) refers to natural selection minus sexual selection, i.e. strictly ecological processes that operate on a species' inherited traits without reference to mating or secondary sex characteristics. [citation needed].

I would lik eto see the citation :-) Their equation is:

$\rm{ecological \;selection} \;+ \;sexual \;selection = natural \;selection = evolution \quad eq. ~1$

I had not heard of ecological selection in my studies. As I remember it, what is being called ecological selection was natural selection. My training was:

$\rm{natural \;selection} \;+ \;[vertical]\;sexual \;selection = evolution \quad eq. ~2$

In my discussions with you from now on, I will adopt equation 1. I do hope a Darwin evolution nerd comments on which equation they think holds sway.

So does horizontal gene transfer fall into equation 1 natural selection? I don't think so. Selection is about competition for food, water, and mates. Horizontal gene transfer is about sharing and cooperation. Selection leads to niches. Horizontal gene transfer leads to universal consensus. Both can and do work at the same time in Nature.

It is obvious that Woese and Goldenfeld were physicists. Physicists have made significant contributions to biology. When they do, they overvalue their efforts, downplaying all the work of ordinary biologists. As for biologist contributing to physics, it can never happen culturally, there is too much contempt. My expectation is if and only if I am barking near the right tree with the GEM Lagrangian, it will be discovered independently by a real physicist. Fortunately, as a biologist, I take a long view and don't give a shit. I never explicated to be a standard model blasphemer as equation 1 in this blog suggests. I am having fun believing in my technical mirages.

"As for evolution, it had been developed from a phenomenological description centering around what was generally termed natural selection" I interpret as a criticism of other's wrong aplication of the term (as if something else is as general that is not so general, see "generally"). It is not as far as I see a criticism of natural selection. But I am not going to start reading texts with you - if they were doing whatever, that does not make it correct. If you want to use equation 1, there is only one thing I have to answer: You do not understand evolution. General remark: Reading the paper should idealy come before writing an article about it, just saying.
The problem with both equations is that they are only applicable within the context of existing life.  It would do nothing to address any evolutionary process that occurred in origin of life scenarios.  I think the point here is that invariably there must be a replication process (i.e. such as vertical or horizontal gene transfer in biology), and then a limiting factor (i.e. available resources) which allows one particular process to gain dominance or preference over another.  It is this combination of replication and selection (filtering) that produces evolution.

Replication in the absence of filtering simply produces a lot of variety, but it can't actually be said to be evolving (since all forms are equally likely to exist).  Once selection occurs, then we can establish "fitness" (or suitability) as one particular process is more likely to succeed than another.

Obviously in biology, we have to consider the replication of the information from an organism in the process of some form of gene transfer, but strictly speaking, I would think that any definition of evolution must also consider the selection of processes that produced the genes in the first place.
Mundus vult decipi
"Rather, it is the fact that molecular biology accepted the synthesis as a complete theory unquestioningly—thereby giving the impression that evolution was essentially a solved scientific problem with its roots lying only within the molecular paradigm."
That's the problem exactly! Well almost exactly. Other related disciplines made the same mistake.

Which equation holds sway?
Neither.
Natural selection + time = evolution.
Let's not get too far from accepted definitions, because that's been another problem.
Evolution is change over time.
This is why I checked out.  When the definition of evolution itself is thrown out, like it has been here, along with the long-known mechanisms that go into it, there isn't much value in the discussion.
I think you have to be careful in using a term like evolution that is typically considered within a specific context (i.e. biology) and yet find it is being used in all other cases.  Without getting into the issue of the universe, etc.  It is problematic when considering the discussion around "origin of life" issues.  The whole point here is that we expect that the processes leading up to life were not simply random.  They were in fact, "selected" because they worked better than other methods and so such processes "evolved".

Therefore if we are going to use evolution to discuss the gradual development of processes leading to life, then we can't very well use the definitions of life's characteristics to get there.  You may not agree with the distinction, but you can't use "sex" as a mechanism of evolution, and then use evolution to explain how sex evolved.
Mundus vult decipi
I believe the definition of evolution that you're using is simply too constrained, and being used is circular and self-referential.  Consider these statements which would hardly be considered an abuse of the term, and yet would fail according to the definitions made here.
Instead,  let’s make the plausible assumption that an enormous number of random polymers are synthesized, which are then subject to selection and evolution.

Bartel and Szostak’s results have been repeated and extended by other researchers, and they demonstrate a fundamental principle of evolution at the molecular level.

In other words, species of molecules appeared out of this random mixture in an evolutionary process that closely reflects the natural selection that Darwin outlined for populations of higher animals.
http://www.science20.com/stars_planets_life/calculating_odds_life_could_begin_chance
There would obviously be nothing in these definitions that refers to genes, sexual selection, etc.
Mundus vult decipi
I like your equation :-) People can fight bitterly over what goes where. One could claim that natural selection only makes sense integrated over time. Hank's makes a solid point that definition fights are not worth watching. What is your view on the core claim of the paper, that because the genetic code is both universal and optimal, that indicates a different type of "process" was going on, with nothing spiritual implied?
Without proper definitions how can anything be meaningful?
...tension between horizontal gene transfer, vertical gene transfer, and natural selection, a trifecta.
This is an example (in my view) of confusing terms where horizontal and vertical gene transfer are established processes that represent different ways in which replication occurs, whereas natural selection is a completely separate element that fulfills the role of filtering such changes when competition arises.

While you may dispute my definitions here, but what possible meaning can there be to vertical or horizontal gene transfer without natural selection?  Without knowing if some mechanism is "better" or not, then your claim of a hierarchy is meaningless.  How can a genetic code be "universal and optimal" without a filtering mechanism that ensures that only successful processes are passed on?  Therefore the genetic code exists because it (and the processes that replicate it) were selected for.
Mundus vult decipi
Evolution is change over time.
Steve, I'm going to quibble over this statement to differentiate simple change from evolution.  To use a simple example, if I boil water, I can't claim that liquid water is "evolving" to steam.  It is simply changing, since there is no filtering that would allow it to do anything else.  It is the filtering (i.e. selection) that allows evolution since it makes "choices" regarding the changes that are successful enough to be replicated into the future.  The primary point is that evolution requires that some changes not be allowed to perpetuate.  If all changes are allowed, then the system is certainly changing, but it can't be said to be evolving.
Mundus vult decipi
I added the following comment to the blog:
[* A heck of a lot of the comments below are debates about the exact relationship between various terms 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.]