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.

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