Energy, Evolution, and the Origins of Complex Life
L 95: “Bacteria are the smallest unit of function.” There is no division of labor by locale within the bacterium, except for the membrane that encloses the bacterium. During splitting there is a slight sense of the membrane’s equator which shrinks to form two cells. Somehow the two DNA strands tend to end up in one per daughter cell.
L 133: Preserved proteins are slow to evolve and thus slow to arise in the first place, there being so few adjacent-possible alternatives, via which they arose.
L 271: Lane promises that energy explains all.
L 391: Calendar
L 492: “Something changed.” “Whether or not it was specifically the rising tide of oxygen that triggered the Cambrian explosion, there is general agreement that environmental changes did indeed transform selection.” (near the Cambrian Explosion). Yes. I recall hearing that the hox genes arose which allowed DNA to express a body plan. I think that Lane has a concept of ‘constraint’ that I do not grasp. Is lack of the hox gene a ‘constraint’?
L 689: I think that Lane is asking why prokaryotes have stayed simple, even after spawning the eukaryotes. I can only imagine that they are defined somehow by their niches and those niches do not favor complexity. Eukaryotes seized many of the niches for complex organisms. The gap remains mysterious however. Perhaps there are no viable business plans any simpler than the simple eukaryotes deploy. The archezoa are fallen eukaryotes that partly fill the gap and partly break the rule above.
L 720: Kindle software does not grok exponents, except in footnotes. I presume that the 10300 should be 10300.
L 726: Lane goes on to partly discredit my scenario. Another explanation is that the first eukaryote was less probable that he imagines and that there are indeed few other possible paths to effective complexity. The prokaryotes try but effective complexity is too damn hard. Perhaps there is some yet unknown trick that the nucleus has that enables some sort of expressiveness in our DNA. It could be as simple as how DNA information codes proteins, or how introns direct production of proteins. The much later hox genes explain, in part, the Cambridge explosion. There may be an earlier analog.
Yet another possibility is that the only way forward was the synergy of bacteria and archaea. Margulis convinced me that there is amazing chemistry expertise in each. The combined chemistry is incompatible in one vesicle; gene swapping doesn’t do it. The first eukaryote may have stumbled on the only adjacent possible exploitation of that synergy. The first eukaryote and its progeny had first mover advantage.
Lane’s question is very good and needs an answer.
Lane let the cat out of the bag in the introduction about energy and so I will speculate: Mitochondria solve so many energy problems that eukaryotes can afford more experimentation than the prokaryotes. This is curiously similar to the notion that homo habilis learned to cook and thus allowed us to thrive with less bodily alimentary apparatus—smaller teeth, shorter gut.
There are pitfalls here when we try to reason about the evolutionary landscape including that portion never explored by Earth life. That landscape remains deeply unknown. We can sort of think about the ‘adjacent possible’ as conceived by Kauffman.
L 965-1087: Lane’s description of the transformation of energy by mitochondria does not do it for me. I find the theatrics distracting. I suppose that the result is separation of charge, as required below.
I am charmed with the mechanical description of the ATP synthase. It sounds like the torque is formed differently than for flagella. At L 1339 Lane says that the flagella of bacteria use the same mechanism, but those of an archaea differ.
What Lane makes clear is that mitochondria hold energy in the form of ‘charge separation’. Charge separation happens when all the protons move a little farther to the left than all the electrons, on the average. The membrane separates these two regions; on one side there are more electrons and on the other, more protons. Electrical engineers call this a capacitor which stores energy marvelously. The same thing happens with ‘ordinary chemistry’ but there the separation is only on the order of the size of a small molecule. The mitochondria are indeed not doing ordinary chemistry; Mitchell was right.
Several points made in the book are more plausible with the capacitor metaphor. Indeed it is strictly not even a metaphor; it really is a capacitor!
L 1213: It becomes clear that prokaryotes have mostly low energy life styles.
L 1221: “An atmosphere could never be full of fluorine gas, for example, as it would immediately react with everything and disappear.”
Thank you. You can have too much of a good thing.
L 1289: This portrayal of glycerin shows a molecule which is its own reflection. That may be failure to distinguish subgroups OH and H.
L 1370: Lane draws an analogy between a ‘water channel’ and ‘metabolic pathway’. I think that the metabolic pathway has no geometric locality as does a water channel. I presume that the ‘enzymes’ which define the pathway are intermixed. ‘Confinement’ is achieved by specificity with which the enzymes do their thing.
L 1674: See this about pH, proton density, etc. I was confused, and may still be. I bet a lot of other readers are too.
L 1858: “Well, maybe. In an infinite universe, anything is possible; but that doesn’t make it probable.” Actually you must still obey physics in an infinite universe and physics must allow the reaction. All we know is that physics allows at least one way.
L 2029: “What’s different” between bacteria and archaea? I am glad he asked. I could not find this on the web. He gives only a short list.
L 2182: I am beginning to think that Lane is confused. Thought experiment: Two beakers of pure water on the table. Add some HCl to one and NaOH to the other. Now take a 1000 volt battery with two leads. Put the negative lead in the beaker with the HCl, and the positive lead in with the NaOH. Which beaker has more H+’s? I will bet that it the beaker with the HCl. Now do the experiment in a beaker with two compartments and a small hole between them where you can install a membrane such as we are considering. We are careful to make the hydrostatic pressures equal. An H+ near this hole will sense the 1000 volts and not the difference in ‘proton density’. There is more to pushing a proton than proton density.
I think that upstream of the ATP generation, (free energy stream, that is) there is something that creates a good old fashioned battery style potential difference. Not 1000 volts, of course, but a substantial fraction of a volt and that is what drives the ATP synthase.
L 2196: I postulate that LUCA had little or no ‘DNA duplication machinery’. The machinery of bacteria and archaea were invented post split due to increased selective pressure.
L 2196: I need to understand how these “inorganic barriers” came about.
L 2253: “proton gradient” That is not what moves protons; potential gradient does. The proton gradient is typically matched by a gradient of negative ions whose field pushes equally in the opposite direction.
Latching onto the notion of ‘pumping a proton across a membrane’ we must consider preventing negative ions also crossing. The negative ions are typically more complex. Fl− is simple but rare. If you can pump Na+ across and no other ions pass you are charging a capacitor which can do real work in the ATP synthase.
L 2545: Lane wonders (pedagogically?) about the very large gap between the most complex bacteria or archaea today, and our last eukaryotic ancestor. A species needs at least one niche to survive. Perhaps the new eukaryotes displaced its recent ancestors. Biologists seem confident that whole genera have not disappeared. The history book may be missing chapters.
L 2576: Lane raises pedagogical conundrums and sometimes I run ahead to answer them. Sometimes I am right and Lane can be credited with describing the conundrums to enable this. I thus suggest the following answer. The prokaryotes were and are single cell. That is like building a processing plant with one reaction chamber. There is chemistry you can’t do that way even if that chamber can alternate processing modes. When the ingested the bacterium it gained a second chamber. There were immediate problems, but also immediate benefits. But the adjacent possible had suddenly greatly expanded. Many genes moved gradually from the mitochondria to the nucleus which hides the evidence. (We must explain the nucleus.) (I have read other books on this.)
L 2974: I had wondered why some mitochondrial genes stayed behind. I buy Lane’s (and Allen’s) story. In other computer words, it is latency. Expression of genes is part of a control loop that does not tolerate much latency and diffusion to and from the nucleus means too much latency. The control loop has to do with maintaining the insulator in the capacitor.
I like this line of reasoning. Subtle division of labor into multiple reaction chambers and consequent synergy. It is like a developing economy which other authors have likened biology to.
L 3008: Syntrophy is much like synergy—slightly different connotations.
L 3076: “Every conceivable niche is occupied, with each species exquisitely adapted to its own space.” Those and more niches that we would and seen as niches until we found microbes in them.
L 3083: “It is nor easy for one bacterium to get inside another one and to survive there for endless generations, but we know a few examples, so we know that it does happen.” The books includes pictures of other symbionts (Figure 25). It would be good to see the ancestors of these particular cells. The implication is that this is a whole line of symbionts. Their cell division mechanics might provide clues if they are a line.
L 3855: The reason for migration of genes to the nucleus seems clear to me. The high tech genetic duplication machinery of the nucleus means that mitochondrial genes that are accidentally transcribed to the nucleus last longer and remove the pressure to conserve the same genes in the mitochondria. It is the why the nuclear mechanisms evolved in the first place—a better place for genes. Lane suggests several other good reasons.
L 3938: Apoptosis—sounds like an opera plot.
L 3999: “Exactly why the mitochondrial genes of animals evolve much faster than nuclear genes is unknown.”
I thought that there are error correction mechanisms in the copying of nuclear DNA, as well as other clever hacks.