Have you got what it takes to form a scientific theory?

Making a scientific theory is actually more difficult than you might think. The first step involves surveying what knowledge is already available. That comes in two subsets: the actual observational data and the interpretation of what everyone thinks that set of data means. I happen to think that set theory is a great start here. A set is a collection of data with something in common, together with the rule that suggests it should be put into one set, as opposed to several. That rule must arise naturally from any theory, so as you form a rule, you are well on your way to forming a theory. The next part is probably the hardest: you have to decide what interpretation that is allegedly established is in fact wrong. It is not that easy to say that the authority is wrong, and your idea is right, but you have to do that, and at the same time know that your version is in accord with all observational data and takes you somewhere else. Why I am going on about this now is I have written two novels that set a problem: how could you prove the Earth goes around the sun if you were an ancient Roman? This is a challenge if you want to test yourself as a theoretician. If you don’t. I like to think there is still an interesting story there.

From September 13 – 20, my novel Athene’s Prophecy will be discounted in the US and UK, and this blog will give some background information to make the reading easier as regards the actual story not regarding this problem. In this, my fictional character, Gaius Claudius Scaevola is on a quest, but he must also survive the imperium of a certain Gaius Julius Caesar, aka Caligulae, who suffered from “fake news”, and a bad subsequent press. First the nickname: no Roman would call him Caligula because even his worst enemies would recognize he had two feet, and his father could easily afford two bootlets. Romans had a number of names, but they tended to be similar. Take Gaius Julius Caesar. There were many of them, including the father, grandfather, great grandfather etc. of the one you recognize. Caligulae was also Gaius Julius Caesar. Gaius is a praenomen, like John. Unfortunately, there were not a lot of such names so there are many called Gaius. Julius is the ancient family name, but it is more like a clan, and eventually there needed to be more, so most of the popular clans had a cognomen. This tended to be anything but grandiose. Thus for Marcus Tullius Cicero, Cicero means chickpea. Scaevola means “lefty”. It is less clear what Caesar means because in Latin the “ar” ending is somewhat unusual. Gaius Plinius Secundus interpreted it as coming from caesaries, which means “hairy”. Ironically, the most famous Julius Caesar was bald. Incidentally, in pronunciation, the latin “C” is the equivalent of the Greek gamma, so it is pronounced as a “G” or “K” – the difference is small and we have now way of knowing. “ae” is pronounced as in “pie”. So Caesar is pronounced something like the German Kaiser.

Caligulae is widely regarded as a tyrant of the worst kind, but during his imperium he was only personally responsible for thirteen executions, and he had three failed coup attempts on his life, the leaders of which contributed to that thirteen. That does not sound excessively tyrannical. However, he did have the bad habit of making outrageous comments (this is prior to a certain President tweeting, but there are strange similarities). He made his horse a senator. That was not mad; it was a clear insult to the senators.

He is accused of making a fatuous invasion of Germany. Actually, the evidence is he got two rebellious legions to build bridges over the Rhine, go over, set up camp, dig lots of earthworks, march around and return. This is actually a text-book account of imposing discipline and carrying out an exercise, following the methods of his brother-in-law Gnaeus Domitius Corbulo, one of the stronger Roman Generals on discipline. He then took these same two legions and ordered them to invade Britain. The men refused to board what are sometimes called decrepit ships. Whatever, Caligulae gave them the choices between “conquering Neptune” and collecting a mass of sea shells, invading Britain, or face decimation. They collected sea shells. The exercise was not madness: it was a total humiliation for the two legions to have to carry these through Rome in the form of a “triumph”. This rather odd behaviour ended legionary rebellion, but it did not stop the coups. The odd behaviour and the fact he despised many senators inevitably led to bad press because it was the senatorial class that wrote histories, but like a certain president, he seemed to go out of his way to encourage the bad press. However, he was not seen as a tyrant by the masses. When he died the masses gave a genuine outpouring of anger at those who killed him. Like the more famous Gaius Julius Caesar, Caligulae had great support from the masses, but not from the senators. I have collected many of his most notorious acts, and one of the most bizarre political incidents I have heard of is quoted in the novel more or less as reported by Philo of Alexandria, with only minor changes for style consistency, and, of course, to report it in English.

As for showing how scientific theory can be developed, in TV shows you find scientists sitting down doing very difficult mathematics, and while that may be needed when theory is applied, all major theories start with relatively simple concepts. If we take quantum mechanics as an example of a reasonably difficult piece of theoretical physics, thus to get to the famous Schrödinger equation, start with the Hamilton-Jacobi equation from classical physics. Now the mathematician Hamilton had already shown you can manipulated that into a wave-like equation, but that went nowhere useful. However, the French physicist de Broglie had argued that there was real wave-like behaviour, and he came up with an equation in which the classical action (momentum times distance in this case) for a wave length was constant, specifically in units of h (Planck’s quantum of action). All that Schrödinger had to do was to manipulate Hamilton’s waves and ensure that the action came in units of h per wavelength. That may seem easy, but everything was present for some time before Schrödinger put that together. Coming up with an original concept is not at all easy.

Anyway, in the novel, Scaevola has to prove the Earth goes around the sun, with what was available then. (No telescopes that helped Galileo.) The novel gives you the material avaiable, including the theory and measurements of Aristarchus. See if you can do it. You, at least, have the advantage you know it does. (And no, you do not have to invent calculus or Newtonian mechanics.)

The above is, of course, merely the background. The main part of the story involves life in Egypt, the aanti-Jewish riots in Egypt, then the religious problems of Judea as Christianty starts.

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Origin of life, and a challenge!

Here is a chance to test yourself as a theoretician. But do not worry if you cannot solve this. Most people will not, and I predict nobody will, but prove me wrong! And as a hint, while nobody actually knows the answer, as I shall show eventually, getting a very reasonable answer is actually relatively simple, although you need a little background knowledge for the first question.

Just before Christmas, I posted with the title Biogenesis: how did life get started?” (http://wp.me/p2IwTC-6e ) but as some may have noticed, I did not get very far along the track indicated by the title. The issue is, of course, somewhat complicated, and it is easier to discuss it in small pieces I also mentioned I was about to give a talk on this early this year. Well, the talk will come on March 4, so it is approaching quickly. Accordingly, I have put out an abstract, and am including two challenges, which readers here may or may not wish to contemplate. Specifically,
1. Why did nature choose ribose for nucleic acids?
2. How did homochirality arise?
Put your guesses or inspired knowledgeable comments at the end of this post. The answers are not that difficult, but they are subtle. In my opinion, they are also excellent examples of how to go about forming a theory. I shall post my answers in due course.

The question of, why ribose, is a little complicated and cannot be answered without some chemical knowledge, so most readers probably won’t be able to answer that. Notwithstanding that, it is a very interesting question because I believe it gives a clue as to how life got underway. RNA is a polymer in which each mer is made up of three entities: one of four nucleobases, ribose and a phosphate ester. The nucleobase is attached to C-1 of ribose (if you opened it up, at the aldehyde end) and the phosphate is at C-5 (the other end, ribose being a five carbon sugar. The nucleobases are, in general, easy to make. If you leave ammonium cyanide lying around, they make themselves, but that is the only thing that appears to be easy about this entity. Sugars can be made in solution by having formaldehyde, which is easily made, react in water with lime, and a number of other solids. That seems easy, except that when you do this, you do not get much, if any, ribose. The reason is, ribose is a high-energy pentose (five carbon sugar) because all the hydroxyl groups are eclipsing each other in the closest orientation (axial, for those who know some chemistry). In the laboratory, double helix nucleobases (duplexes) have been made from xylose and arabinose, and in many ways these have superior properties to ribose, but nature chose ribose, so the question is, why? Not only did it do it for RNA, but the unit adenine – ribose – phosphate turns up very frequently.

Adenine combined with ribose is usually called adenosine, and the adenosine phosphate linkage turns up in the energy transfer chemical ATP (adenosine tripolyphosphate), the reduction oxidation catalysts NAD and FAD, where the AD stands for adenosine diphosphate, and in a number of enzyme cofactors, to give solubility in water. Giving solubility in water is an obvious benefit, but putting a sugar unit on the group would also do that. Giving an electric charge would also be of benefit, because it helps keep the entity in the cell, nevertheless there are also other ways of doing that. You may say, well, it had to choose something, but recall, ribose is hard to make, so why was it selected for so many entities?

The phosphate ester also causes something of a problem. In the laboratory, phosphate esters are usually made with highly reactive phosphorus-based chemicals, but life could not have started that way. Another way to form phosphate esters is to heat a phosphate and an alcohol (including the hydroxyl groups on a sugar) to about 180 oC, when water is driven off. Note that if water is around, as in the undersea thermal vents that are often considered to be the source of life, the superheated water converts phosphate esters to phosphate and alcohol groups. Life did not start at the so-called black smokers, although with sophisticated protection mechanisms, it has evolved to tolerate such environments. Another problem with phosphate is that phosphates are insoluble in neutral or alkaline water, and phosphate esters hydrolyse in acidic water.
However, notwithstanding the difficulty with using phosphate, there is no real choice if you want a linking agent with three functions (two used up to join two groups, one to be ionic to enhance water solubility). Boron is rare, and has unusual chemistry, while elements such as arsenic, besides being much less common, do not give bonds with as much strength.

Homochirality is different matter. (Chirality can be though of like handedness. If you have gloves, your left hand has its glove and the right hand its, even though they are identical in features, such as four fingers and a thumb. The handedness comes from the fact you cannot put those fingers and thumb on a hand where the top differs from the bottom without making the right hand different from the left.) The sugars your body uses are D sugars (think of this as right handed) while all your amino acids are L, or left handed. The problem is, when you synthesis any of these through any conceivable route given the nature of the starting materials, which have no chirality, you get an equal mix of D and L. How did nature select one lot and neglect the others?
Put your guesses below! In the meantime, my ebook, “Planetary formation and biogenesis”, which summarizes what we knew up to about 2012, is going to be discounted on Amazon for a short period following March 6. This is to favour those going to my talk, but you too can take advantage. It has a significant scientific content (including an analysis of over 600 scientific papers) so if your scientific knowledge is slight, it may be too difficult.

Theory and planets: what is right?

In general, I reserve this blog to support my science fiction writing, but since I try to put some real science in my writing, I thought just once I would venture into the slightly more scientific. As mentioned in previous posts, I have a completely different view of how planets, so the question is, why? Surely everyone else cannot be wrong? The answer to that depends on whether everyone goes back to first principles and satisfies themselves, and how many lazily accept what is put in front of them. That does not mean that it is wrong, however. Just because people are lazy merely makes them irrelevant. After all, what is wrong with the standard theory?

My answer to that is, in the standard theory, computations start with a uniform distribution of planetesimals formed in the disk of gas from which the star forms. From then on, gravity requires the planetesimals to collide, and it is assumed that from these collisions, planets form. I believe there are two things wrong with that picture. The first is, there is no known mechanism to get to planetesimals. The second is that while gravity may be the mechanism by which planets complete their growth, it is not the mechanism by which it starts. The reader may immediately protest and say that even if we have no idea how planetesimals form, something had to start small and accrete, otherwise there would be no planets. That is true, but just because something had to start small does not mean there is a uniform distribution throughout the accretion disk.

My theory is that it is chemistry that causes everything to start, and different chemistries occur at different temperatures. This leads to the different planets having different properties and somewhat different compositions.

The questions then are: am I right? does it matter? To the first, if I am wrong it should be possible to falsify it. So far, nobody has, so my theory is still alive. Whether it matters depends on whether you believe in science or fairy stories. If you believe that any story will do as long as you like it, well, that is certainly not science, at least in the sense that I signed up to in my youth.

So, if I am correct, what is the probability of finding suitable planets for life? Accretion disks last between 1 to even as much as 30 My. The longer the disk lasts, the longer planets pick up material, which means the bigger they are. For me, an important observation was the detection of a planet of about six times Jupiter’s mass that was about three times further from its star (with the name LkCa 15) than Jupiter. The star is approximately 2 My old. Now, the further from the star, the less dense the material, and this star is slightly smaller than our sun. The original computations required about 15 My or more to get Jupiter around our star, so they cannot be quite correct, although that is irrelevant to this question. No matter what the mechanism of accretion, Jupiter had to start accreting faster than this planet because the density of starting material must be seriously greater, which means that we can only get our solar system if the disk was cleared out very much sooner than 2 My. People ask, is there anything special regarding our solar system? I believe this very rapid cleanout of the disk will eliminate the great bulk of the planetary systems. Does it matter if they get bigger? Unfortunately, yes, because the bigger the planets get, the bigger the gravitational interactions between them, so the more likely they are to interact. If they do, orbits become chaotic, and planets can be eliminated from the system as other orbits become highly elliptical.

If anyone is interested in this theory, Planetary Formation and Biogenesis (http://www.amazon.com/dp/B007T0QE6I )

will be available for 99 cents  as a special promo on Amazon.com (and 99p on Amazon.co.uk) on Friday 13, and it will gradually increase in price over the next few days. Similarly priced on Friday 13 is my novel Red Gold, (http://www.amazon.com/dp/B009U0458Y  ) which is about fraud during the settlement of Mars, and as noted in my previous post, is one of the very few examples of a novel in which a genuine theory got started.