The Sociodynamics of Science

The title is a bit of an exaggeration as to the importance of this post, nevertheless since I was at what was probably my last scientific conference (NZ Institute of Chemistry, at Christchurch) I could not resist looking around at behaviour as well as the science. I also gave two presentations. Speaking to an audience gives the speaker an opportunity to order the presentation so as to give the most force to the surprising parts of it, not that many took advantage of this. Overall, very few, if any (apart from yours truly) seemed to want to provide their audience with something that might be uncomfortable for their preconceived notions.

First, the general part provided great support for Thomas Kuhn’s analysis. I found most of the invited speakers and keynote speakers to illustrate an interesting aspect: why are they speaking? Very few actually wished to educate or convince anyone of anything in particular, and personally, I found the few that did to be by far the most interesting. Most of the presentations from academics could be summarised as, “I have a huge number of research students and here is what they have done.” What then followed was a very large amount of results, but there was seldom an interesting unifying principle. Chemistry tends to be susceptible to this, as a very common student research program is to try to make a variety of related compounds. This may well have been very useful, but if we do not see why this approach was taken, it tends to feel like filling up some compendium of compounds, or, as Rutherford put it rather acidly, “stamp collecting”. These types of talks are characterised by the speaker trying to get in as many compounds as they can, so they keep talking and use up the allocated question time. I suspect that one of the purposes of these presentations is to say, “Look at what we have done. This has given our graduate students a good number of scientific publications, so if you are thinking of being a grad student, why not come here?” I can readily understand that line of thinking, but its relevance for older scientists is questionable. There were a few presentations where the output would be of more general interest, though. I found the odd presentation that showed how to do something new, where it could have quite wide applications, to be of particular interest.

Now to the personal. My first presentation was a summary of my biogenesis approach. It may have had too much information across too wide a field, but the interesting point was that it generated a discussion at the end relating to my concept of how homochirality was generated. My argument is that reproduction depends on it because the geometry prevents the formation of a second strand if the first strand is not either entirely left-handed or right-handed in its pitch. So the issue then was, it was pure chance that D-ribose containing helices predominated, in part because the chance of getting a long-enough homochiral strand is very remote, and when one arises, then it takes up all the resources and predominates. The legitimate question then is, why doesn’t the other handed helix eventually arise? It may be slower to do so, but it is not necessarily impossible. My partial answer to that is the mer units are also used to bind to some other important units for life to give them solubility, and the wrong sort gets used up and does not build up concentration. Maybe that is so, but there is no evidence.

It was my second presentation that would be controversial, and it was interesting to watch the expressions. Part of the problem for me was it was the last such presentation (there were some closing speakers after me, and after morning tea) and there is something about conferences at the end – everyone is busy thinking about how to get to the airport, etc, so they tend to lose concentration. My first slide put up three propositions: the wave functions everyone uses for atomic orbitals are wrong; because of that, the calculation of the chemical bond requires the use of a hitherto unrecognised quantum effect (which is a very specific expression involving only universally recognised quantum numbers) and finally, the commonly held belief that relativistic effects on the inner electrons make a major effect on the valence electron of the heaviest elements is wrong. 

As you might expect, this was greeted initially with yawns and disinterest: this was going to be wrong. At least that seemed to be written over their faces. I then diverted to explain my guidance wave interpretation, which is essentially the de Broglie pilot wave concept, but with two additions: an application of Euler’s complex number theory that everyone seems to have missed, and secondly, I argued that if the wave really causes diffraction in the two-slit-type experiment, it has to travel at the same speed as the particle. These two points lead to serious simplifications in the calculation of properties of chemical bonds. The next step was to put up a lot of evidence for the different wave functions, with about 70 data points spanning a selection of atoms, of which about twenty supported the absence of any significant relativistic effect. (This does not say relativity is wrong, but merely that its effects on valence electrons are too small to be noticed at this level of analysis.) What this was effectively saying was that most of the current calculations only give agreement with observation when liberal use is made of assignable constants, which conveniently can be adjusted so you get the “right” answer.So, question time. One question surprised me: Does my new approach do anything new? I argued that the fact everyone is using the wrong wave functions, there is a quantum effect that nobody has recognised, and everyone is wrong with those relativistic effects could be considered new. Yes, but have you got a prediction? This was someone difficult to satisfy. Well, if you have access to a good physics lab, I suggested, here is where you can show that, assuming my theory is correct, make an adjustment to the delayed choice quantum eraser experiment (and I outlined the simple change) then you will reach the opposite conclusion. If you don’t agree with me, then you should do the experiment to prove I am wrong. The stunned expressions were worth the cost of going to the conference. Not that anyone will do the experiment. That would show interest in finding the truth, and in fairness, it is more a job for a physicist.

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.