No I'm not making up words. RuBisCO is the arguably most important enzyme on the planet, its function is the first step in the capturing of carbon dioxide in plants in order to make biological matter, ergo it is where all the work of photosynthesis gets done, and that no exaggeration because it so inefficient and its fidelity so poor that the single greatest efficiency loss in photosynthesis is here! RuBisCo is so painfully slow, garbing only a few carbon dioxide molecules per second that plants have to produce incredible amounts of this enzyme making it the quite possibly the most common protein by mass on the planet! In some plants up to 50% of there protein mass is RuBisCo! Its fidelity is such that it will capture oxygen instead of carbon dioxide undergo a energy losing process called photorespiration in which substrates are broken down and energy must be spent simply to repair the substrates, this happens at least 1/4 of the time! Plants have evolved rather hair-brain ways of trying to improve the efficiency and fidelity of RuBisCo. Take C4 plants for example which capture CO2 by a completely different pathway, only to pump the capture CO2 deeper inside the leaf away from oxygen and then release the CO2 in concentration around RuBisCo, this process is energy wasteful but worth it for the gain in efficiency and fidelity of RuBisCo. The only problem is dear god why not just cut RuBisCo out all together and use the CO2 captured by a faster more efficient pathway! Evolution is not a smart process. I remember my bachelor days when I was making a Best-Fit Algorithmic in MatLab, the algorithm would search through 12 dimensions of scalar and vectored data, picking points at random and asking how well its results fit the data, and then repeating around points that had had good results. Often the program would get stuck around localized mimima, areas where it could not make a better fit or get out of but was still off from the true answer. I relies evolution works like this: it finds answers at random through mutation and those answers may be far from the best possible but the mutations required to find better solutions are so unlikely, so out of range, that it gets stuck optimizing a poor solution rather then finding a better one. This is what I think RuBisCo is, an optimized poor solution that biology is stuck utilizing. This is why C4 plants have their hair-brain work around because to develop a completely alternate pathway would require so many new enzymatic steps that evolutionarily its too unlikely to happen and be competitive off the bat, hence the half-way pathway 'dump it back on RuBisCo' solution. There is significant biotechnological work focused on genetic engineering a more efficient and accurate RuBisCo but so far they have not made significant progress, I don't think they will, I think the enzyme has been optimized as best it can for each plant. The more they increase the rate of reaction the more they reduce the fidelity and increase photorespiration, and vis versa. Why did biology get stuck with this pathetic enzyme? Well if you look at it from the fact when photosythesis evolved 3.5 billion years ago carbon dioxide concentrations in atmosphere were thousands of times greater then today and oxygen concentrations were non-existent, back then RuBisCo was probably the best photosynthetic pathway around and plants got stuck in that pathway to this day despite how inadequate RuBisCo is for today's atmosphere. Any ideas, confusions, disagreement what not? Just Ranting.
Feller U, Anders I, Mae T (2008). "Rubiscolytics: fate of Rubisco after its enzymatic function in a cell is terminated". J. Exp. Bot. 59 (7): 1615–24 "Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39) is present at very high levels in photosynthesizing cells and must therefore be considered as the most abundant protein in the world (Ellis, 1979). Rubisco is the predominant protein in leaves of C3 plants and may contribute up to 50% to the soluble leaf proteins (Spreitzer and Salvucci, 2002) and 20–30% of total leaf nitrogen (Evans and Seemann, 1989; Makino 2003; Kumar et al., 2002). In leaves of C4 plants, Rubisco still contributes ∼30% to the soluble proteins (Sugiyama et al., 1984) and 5–9% of total leaf nitrogen (Sage et al., 1987; Makino et al., 2003)."
So what you are suggesting is that intelligent-designed plant life could be extremely efficient, compared to evolutionary-designed life with tremendous inefficiencies that need to be overcome. Probably the same would be true for animal life. Anyone with sci-fi thoughts for space-aliens or thoughts for future-of-humanity plots?
I was suggesting many things but sure that could be one of them. Animal life has many flaws biochemically and physiologically that I have seen. Do you know how much energy we waste piss out urea instead of metabolizing it all the way to nitrogen? Most animals waste energy farting instead of promoting hydrogen and acetate fermenting gut bacteria whose anaerobic waste products can be absorbed by the body and used for energy aerobically, (unlike methane in farts which is very hard to capture biochemically). And don't get me started on external testicles: the obvious and far better solution has even evolved before (in birds): just makes sperm production viable at core body temperate and keep the balls inside! Only evolution or a drunken deity would move testicles outside the body! But on this topic alternate photosynthetic pathways have evolved before and exist in some prokaryotic algae, but they are very uncommon: http://en.wikipedia.org/wiki/Carbon_fixation#Microorganisms I assume they never caught on because of inefficiencies they have and/or they never were absorbed and form symbionts and became part of eukaryote life. Evolution is very goal orientated and does not care how one gets to the goal (reproduce more) thus for example having an inefficient photosythetic pathway but all the advantages of being a higher organism make up for it and then some: a set of very good solutions make up for another set of poor solutions. Sure it would be nice if those higher organisms had acquired the better pathways: life on earth would be far richer what with it being able to support a larger biosphere if it could absorb energy more efficiently, but fate just was not in the mood.
"...sci-fi...thoughts for future-of-humanity plots? " I wrote a short story in middle school where a researcher modified plant DNA to create a new form of chlorophyll which absorbed all wavelengths of light including green, and appeared black on its surface. He then spliced it into his own genome, and no longer had to eat. He did, however have to start running miles a day to burn off the extra energy which was produced in such amounts that his body couldn't turn it to fat fast enough. Eventually, he became hugely overweight, couldn't run anymore, and burst into flames (hey, it was middle school). Please Register or Log in to view the hidden image!
Interesting idea, but I don't think there is enough surface area on the body absorb enough light provide enough energy to keep a person alive an and active, more so your character could have just lived in the dark. As for the Chlorophyll there are algae that have wider range light absorption, but again they were not the blue-green algae that became symbiotic into eukaryotic plants and thus never came out of the water.
yep, evolution's a kludge. And RuBisCo is the absolutely annoying reason my tomatoes don't produce too well... Also why they grow tomatoes in hothouses...and maybe, just possibly, a small help for the whole global warming thing...but probably not enough to offset the general mayhem. Hadn't thought of it, but making a bacteria to do that with miscellaneous organic waste of all sorts...well, right now we have a problem in that it takes natural gas to make nitrogen for fertilizer...we need to solve that problem before we run out of fossil fuel in large quantities... Maybe if that was also a petrimeat-a meatlike substance, dish-grown... (Before you go "Uck!" look up xanthan gum. You're already eating bacterial products.) Ben Franklin instructed us to fart proudly... ...That would be a very, very interesting metabolism indeed-for some reason I'm visualizing dual hydrogen-oxy respiration, though...rocketgoat? Or maybe some of Terry Prachett's swamp dragons...
If I was to guess, the low CO2 capture efficiency of RuBisCO is connected to its dual utility; also captures O2 for respiration. The sun only shines part of the day with night needing an alternate energy pathway which uses O2 and generates CO2. If the enzyme was more efficient and therefore more selective for CO2, it would be less selective for O2. The 3 to 1 CO2/O2 capture says 2 extra units of CO2 accumulate with only one unit of CO2 being oxidized by O2, to maintain system night energy requirements. The early earth did not have significant O2. Photosynthesis was what generated the O2. The magic ratio of 3 to 1 could have something to do with the primal CO2 to O2 ratio when the RuBisCO prototype evolved. In terms of entropy, photosynthesis is endothermic (absorbs solar energy) and lowers entropy as it builds molecules. The respiration releases energy and increases the entropy back to smaller products. The photosynthesis entropy loss would have set a potential for reversal, analogous to pumping water up hill with the water seeking a lower level.
Well that not quite how it works. Plants respire with oxygen independently of RuBisCO, and RuBisCO undergoes respiration it is ribulose-1,5-bisphosphate that is being oxidize rather then being carboxylated (with CO2). The oxidation products need to recycled and reduced costing energy. The early earth atmosphere had FAR more CO2 then O2, starting out likely with a majority CO2 atmosphere in the first billion years, but lets take this reports word that between 2.75-2.2 billion earth CO2 levels were no more then 100 times today's or at most 3.6% CO2, Oxygen levels at that time went from trace gas to <5% making a ratio of ~1:1 CO2 to Oxygen, I guess there was a point it passed a 3:1 ratio but I don't see the relevance of it.
