Calvin Cycle 2.0

An article recently came out about a a team which used a series of enzymes in a test tube to do something similar to what plants do in carbon fixation. However, the process is not entirely the same in that it uses different enzymes from a variety of sources, including animals and bacteria, to complete the reaction chain. This chimera test tube of enzymes is apparently 25% more efficient than its natural competitor, RuBisCo. Engineering a system more efficient than this shouldn’t come as too much of a surprise because it is actually one of the least efficient enzymes in nature, as I have written previously (see also):

It is indisputable that CO2 concentrations in the atmosphere are increasing, and the burning of fossil fuels causes some or most of it.  However, CO2 is a natural part of the life cycle. Plants fixate CO2 from the atmosphere in order to grow. RuBisCo is the enzyme which fixes gaseous carbon into simple sugars in plants. This is arguably the single most important enzyme in existence. In addition to plants themselves, all animals and fungi, and most bacteria, are dependent on this enzyme working. It creates the food for those organisms. It also happens to be one of the least efficient enzymes. That is, it doesn’t work very well at doing its job, surprisingly. For one thing, it is very slow. RuBisCo is also capable of catalyzing oxygenation of its substrate rather than fixing a carbon dioxide molecule and it does so at fairly high rates. When oxygenation occurs, the energy is completely wasted because the byproduct isn’t useful for the plant. Moreover, energy has to be expended to reverse the process to make the substrate available for carbon fixation again. Some plants have even evolved special CO2 concentrating mechanisms to try to combat this problem. Increasing the carbon dioxide concentration of the air via burning fossil fuels should make plants better able to use this enzyme because increased concentration of the CO2 substrate increases the enzyme’s efficiency. For example, by increasing the likelihood that CO2 will be fixed rather than oxygen molecules. In other words, the expected result of increased carbon concentrations should be bigger plants, faster growing plants, and/or larger numbers of plants. Both agricultural and wild plants could be expected to benefit from this.

Intelligently designing a better system than RuBisCo, then, is seemingly one of the lowest bars in advanced genetics to cross. Not that that makes it easy in an absolute sense, only that it is easier than, say, designing human geniuses. Getting all these enzymes lined up physically and working well together in a chloroplast is no small barrier.

The obvious purpose of this work and research is to combat climate change. Personally, I am very skeptical that climate change as caused by released CO2 is actually something to worry about. I am inclined to think CO2 hysteria is more an expression of crypto-theology. So, the motivations for this work are suspect. That said, I could still see it being useful. Imagine the kinds of crops we could get if we made them 25% more efficient? What if we could use it to generate a very cheap source of organic fuels and/or starting chemical reagents. Even ignoring overblown warnings about an apocalypse, there is still potential use in this technology. I see no reason not to switch from fossil fuels to better sources if they are in fact better and cheaper.

However, there are other environmental considerations than climate change to at least think about. The first thing that comes to mind is what would be the consequences of introducing vastly more efficient plants into the wild, whether deliberate or inadvertent? Such a plant would presumably be at least a little more evolutionarily fit than its wild counterparts and potentially vastly more fit. If so, it could potentially disrupt entire ecosystems on a massive scale in a relatively short time. Out-competed plants would die out and all the life dependent on those plants would follow shortly thereafter, if they couldn’t adapt to the new composition of their environment. The quest to stop climate change could have unintended consequences far outstripping the largely imagined climate apocalypse. However, even in this case I have little doubt life as a whole would adapt and move on even if the disruption is quite severe. I am reminded of this rather charming documentary (called Cane toads: the conquest if the link goes bad) about the introduction of Cane Toads to Australia and all the havoc that caused. Unintended consequences are real, friends, and leftists are masters at generating them.

All this of course is assuming that this new system would actually work as well as they hope it might (and that the plants it was introduced in were otherwise capable of fierce ecological competition in addition to the new fixation system). This is possible. Evolution is subject to path dependence. Once the initial system of carbon fixation evolved, it would be stuck with the basic mechanism and could only adapt from that in minute steps. It would be very difficult to transfer to a completely different system naturally via small steps. In other words, it might be possible to tweak RuBisCo towards more efficiency, but nearly impossible to substitute a whole different enzyme which was much better overall. A newly evolved system, even if potentially better after additional evolution, would likely start off as less efficient as the already long extent and well adapted one and thus would have a hard time sticking around long enough to become a proper better alternative. Therefore, it is quite possible that better systems than RuBisCo are possible yet still unevolved. Some things are quite difficult to evolve.

On the other hand, it is also quite possible that there are good biological reasons for this inefficiency that we don’t know about. If so, other considerations may prevent the newly developed system from working well and/or resulting in a net loss in fitness due to side effects. In which case it won’t work and there is nothing to worry about. Either way, great care should be taken before committing to the introduction of a vastly different system of doing things, and that applies to biology as much as to government.

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Power, Sex, Suicide: Or why do genders exist in the first place?

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There has been a lot of crap happening the last few weeks, so I thought a not particularly political post might be a nice respite for some. Please bear with the large digressions in this post. It may not seem like it, but it is all related in a meandering sort of way. I promise. I will get to the point eventually and hopefully you will learn some interesting things along the way. Anyway, I wanted to expand on the evolutionary origins of two sexes (as opposed to none or more than 2). I did not cover it in Smart and Sexy because it wasn’t directly relevant enough to be included. The focus in the book was the intellectual differences between human genders, not why gender exists in the first place. It would have been too much of a digression to include that. I think it is an interesting question nonetheless and wanted to address it at some point. Especially since a growing group of lunatics keep wanting to expand the number of genders to the limit of infinity.

On to the first “non sequitur,” or so it deceptively seems. There was recently an askreddit thread which asked about atmospheric oxygen concentrations during the carboniferous period and reminded me of the topic of this post. Specifically, the oxygen concentration was an astounding 35% compared to today’s 21% and the person wanted to know why it was so high and why it dropped so much afterward. If we went back in time to that era, we would suffer from oxygen poisoning. I imagine that wildfires then must have been quite a hellish sight. Literally. This high oxygen concentration probably also explains why insects grew to be so large during this time, such as seagull sized dragon flies. Most insects depend upon passive diffusion to get oxygen to their cells and that is more effective at higher partial pressures of oxygen. Our lower concentration of oxygen today probably isn’t enough to enable such large insects, which is why they evolved to be smaller. Anyway, I had actually read some books which tried to answer this question and I relayed that info in the following comment:

Like most of the other ideas here this is a hypothesis. Life has made various evolutionary innovations over history and one idea is that woody bark/stems first evolved some time immediately proceeding the carboniferous. Woody stems are stronger and more resilient because there are protein cross links between cellulose strands. Cellulose being a long strand of linked sugars. Woody stems are very difficult to digest, which is why pretty much nothing eats it. When it first evolved, literally nothing ate it because it was so new and no organism had the tools to break it down. So, during the carboniferous trees and plants with woody stems proliferated because they had few or no natural predators, and probably also because they could grow taller than their competitors thanks to the strong stems and thus had better access to sunlight.  They did still die of old age however, and that woody material would just sit there without decaying. Eventually it would be buried and millions of years later we would dig it out of the ground as coal or oil. Most of the coal and oil deposits date from this period which is why it is called the carboniferous period.

Well, the process plants use to grow is that they take CO2 out of the atmosphere to build cellulose and other structural molecules and release oxygen. So what was happening in the carboniferous was that this was a very one way process. The carbon was being fixated and nothing was breaking down the large organic molecules to re-release it.

That all changed when fungi, think mushrooms and molds, eventually evolved the enzymatic equipment to break down woody stems. Some time at the end of the carboniferous presumably. With this second innovation, the woody part of plants didn’t just sit around waiting to be buried, it was broken down and the fixated CO2 was released back into the atmosphere. Obviously this added a new variable to the equation and the oxygen level in the atmosphere struck a new and lower balance.

I suggest “Oxygen: The molecule that made the world (Oxford Landmark Science)” and “Power, Sex, Suicide: Mitochondria and the Meaning of Life” by Nick Lane if you are really interested in this subject.

Some of the other comments did touch on this same idea but some people argued that the carbon dioxide concentration wasn’t high enough to account for all the oxygen. That honestly doesn’t make sense to me. The only process I know of which can oxygenate an atmosphere is photosynthesis, and photosynthesis absolutely requires carbon dioxide molecules to run to completion and release oxygen. One carbon atom is fixated for every one molecule of oxygen released (elemental oxygen is a diatomic molecule [except ozone which is triatomic oxygen but that doesn’t matter for this discussion]). Yes, CO2 was much lower in concentration than oxygen but that was because it was being used up. Venus and Mars both have much more carbon dioxide, for example, and presumably so would Earth if there were no photosynthesis.  Wildfires and volcanism were probably the main things getting CO2 back into the atmosphere which explains why it was never completely used up. In fact, carbon dioxide concentrations at the time were three times higher than pre-industrial levels, and double today’s level, but that was still only about 1-1.2% of the atmosphere. My guess is that Earth’s core was hotter, and that there was far more volcanism then than today. That would have made for a very high rate of carbon dioxide release which fueled the one way carbon fixation trip going on in the plant world. The point is, the idea that “there wasn’t enough carbon dioxide” is a red herring. oxygen release simply can’t happen without carbon dioxide, period, and the reason it was so low and not 96% of the atmosphere like on Mars is because of the stupid high rates of fixation.

As a side note, life seemed to get along just fine with atmospheric carbon dioxide levels double that of today during the carboniferous… Plants grew so abundantly in fact that this time period produced great deal of our oil reserves; perhaps even most of it. We also had monster sized insects. I don’t know why climate skeptics never mention this. It goes a long way in demonstrating a bit higher carbon dioxide concentration isn’t going to end the world.

At the end of my comment I mention two of my favorite lay-person science books. Both by Nick Lane, the first is Oxygen and the second is Power, Sex, Suicide. (You can consider the majority of this post to be an indirect summary of these books). The first one I read was the later, which also came out after Oxygen. Both books are great, but I have to note that there is a great deal of overlap between the two. For those of you familiar with mitochondria you can probably guess why. If not, the short answer is that mitochondria take oxygen and use it to to break down organic molecules into water and carbon dioxide. The energy released via this reaction is captured and used to fuel life itself. So, a book on the history of oxygen is by necessity going to overlap a lot with a book on mitochondria. My impression overall is that the material in Oxygen was reworked, improved, and added to new material to create Power, Sex, Suicide. Thus, if you read the later you will have most of the information you could have gotten in the former (though not all). If you had to pick only one to read, Power, Sex, Suicide is the best choice.

The title of the book was absolutely inspired. If you read the title your first thought is that it is about some game of thrones-esque political intrigue. Chimps throwing shit at each other is of course one of the most attention grabbing topics for humans available so anytime you see it on amazon, your gaze is instantly drawn there. The provocative title is what made me take a closer look. However, what makes it even better is that it is in no way deceitful. It is a book about mitochondria which are the power stations of the eukaryotic cell. All large multi-cellular life depends on this power generation. This is the most widely known fact about mitochondria and I will leave it to the reader to learn more about it.

Skipping sex for a second to briefly mention suicide, it turns out that mitochondria are important for signaling apoptosis, or programmed cell death. I.E., suicide. Two of the main reasons for this to happen is for fine tuning body structure and reducing the risk of cancer. In the first case, an example would be when hands grow in the embryo they are initially webbed then cells between the fingers intentionally die off so the fingers are separate. In the later, when a cell becomes damaged and malfunctioning (and thus more likely to eventually become cancerous) this can usually be detected and trigger the cell to commit suicide before developing into full-blown cancer. Obviously this doesn’t always work, but it definitely helps to cull damaged cells. Aging may be tied to this phenomenon because over the course of a lifetime the population of stem cells slowly depletes as they become damaged and are culled to prevent cancerous growths. Stem cells are the most likely to turn cancerous because they are the only cells which continue to rapidly divide, which means bad mutations are more likely to occur and regular or rapid cell division doesn’t need to be turned on via new mutations before the cell line becomes cancerous. Of course, having a lower population of stem cells reduces your body’s ability to keep all your tissues in a youthful state. Thus it is possible that aging, at least in part, is a result of evolved mechanisms for reducing the risk of cancer. Those suicidal mechanisms require mitochondria.

And now on to Sex. What does mitochondria have to do with Sex? Well, as it turns out, they have everything to do with sex. But to understand that, you first need to know the history of how mitochondria came to be. When life first came to exist on Earth, the planet did not have an atmosphere with much oxygen. There were plenty of reduced molecules floating around the oceans and being released via volcanic vents which could be oxidized for energy. (The term “oxidized” was originally coined when scientists thought only oxygen participated in this type of reaction, which was a long time ago. The definition has since been expanded to include reactions which don’t involve molecular oxygen but the name stuck. Path dependence. Obviously the first life wasn’t using molecular oxygen to derive energy when there wasn’t any molecular oxygen available.)

Eventually photosynthesis evolved in the ancestors of modern day cyanobacteria and chloroplasts. Light was a readily available source of energy which did not require any preexisting source of reduced molecules. Carbon dioxide at the time was probably at Venus or Mars percentages so that was absurdly abundant too. The cyanobacteria thus did extremely well, spread everywhere including places with no other source of energy, and proceeded to oxygenate the atmosphere at a massive scale. At first, however, preexisting reduced molecules present in the oceans would have quickly reacted with the released oxygen and thus the build up of the gas would have been delayed. Perhaps for millions of years. Evidence for this comes in the form of banded iron formations. Reduced iron is far more soluble in water than oxidized iron, so oxygen would be released, it would react with the iron, then the new molecule (rust basically) would sink to the bottom of the sea floor forming these bands.

Eventually, however, these reduced reactants would have ran out and oxygen would have started building up in the atmosphere. Believe it or not, oxygen is actually a very poisonous gas. And yes, that includes to you as well. We can live in it only because of evolved mechanisms that deal, incompletely, with its extreme reactivity. (This is not an endorsement for antioxidant products, personally I think that stuff is useless. Or worse than useless if it keeps cells functional long enough to avoid triggering apoptosis and thus allowing them to become cancerous). All of this poisonous oxygen in the atmosphere created a selection pressure for mechanisms that could mitigate the problem. In short, eventually this led to not only the ability to mitigate the presence of oxygen free radicals, but to actively harness oxygen as an electron acceptor in the production of usable energy. Some bacteria, including the ancestors of mitochondria, developed this ability. Though it isn’t entirely clear how it happened, one of these oxygen loving bacteria was engulfed by an archaeal cell (site with more detail). Probably with the intention of using it as food. Either that or the oxygen loving bacteria became parasitic on archaeal hosts. At some point this predatory or parasitic relationship goofed up and both cells started working symbiotically. The larger cell could provide shelter and sources of food, while the newly formed mitochondria could use oxygen to efficiently convert that food into energy and possibly transfer oxygen defense mechanisms to the host cell if it started out oxygen intolerant. This was the origin of all subsequent multicellular eukaryotic life, including you. A descendant of this lineage similarly engulfed a cyanobacteria and that become the universal ancestor of plants.

Some time later, the early eukaryotes developed sexual reproduction where genetic material is shared between two individual members of the species in order to reproduce as opposed to earlier binary fission. Reasons why are debated, but my preferred explanation is that sexual reproduction increases the probability of novel genetic combinations which may have increased evolutionary fitness especially with respect to, but not limited to, evading predators and parasites (including infections). Keep in mind that the origin of sexual reproduction is not the origin of the sexes. You don’t necessarily have to have two genders to sexually reproduce. (This is a general biological fact and should in no way be misconstrued as an endorsement of any sort of mental illness related to gender in humans. It doesn’t matter how worms do it, we are human and we only have two genders).

The advent of sexual reproduction, however, created a problem not dissimilar in type to the penis fencing worms in the previous link. That is, evolutionary self interest creating bad incentives for competition during reproduction. In the case of worms they are trying to reproduce without incurring the metabolic costs of growing eggs. Between mitochondria competition needs a bit more explanation, though. Mitochondria within eukaryotic cells have never completely lost their genome even today. Each eukaryotic cell thus has two methods of transmitting genetic information to descendants. One is through the mitochondria and one is through the nucleus. Even though mitochondria only increase in number via binary fission, random mutations can occur during that process thus allowing separate mitochondrial lines to evolve independently of one another. Since mitochondria have their own genome, reproduce, and are variable they are subject to natural selection. If in sexual reproduction two mitochondrial lines are placed together within the same cell, you create a situation of direct competition between both lineages for the domination of that cell and thus the opportunity to be passed on down the line. Competing mitochondria could and would evolve ways of eliminating rivals. Ways which would only have minimum concern for the overall well being of the host cell. What does it matter how the host cell does if that other mitochondria wipes you out?  Even at the cellular level, diversity + proximity = war. An evolutionary war between mitochondrial lineages going on within the cell is obviously not a desirable situation for the organism as a whole. Eliminating the potential for mitochondrial war would be a great advantage to any eukaryotic organism which managed to accomplish it. Basically, the nuclear genome would need to step in and tell everyone to play nice… Na, its much easier to build a big wall.

Which, 2500 or so words in, FINALLY gets us back to the title of this post. I do apologize, but I feel the explanation is incomplete without the requisite background information. Having two sexes is a direct response to this issue of battling mitochondrial lineages and is what gives us our most universal definition of two sexes. Having distinctive male and females genders is “the wall” so to speak keeping different mitochondrial lineages from directly competing with each other. Specifically, the female sex is that which donates mitochondria to offspring and the male is that which does not donate mitochondria to offspring. That’s it. This is the commonality, the only commonality, between all males and all females in all species which have distinct genders. It also explains why more than two genders is in no way necessary. Two individuals is enough to gain the benefits of sexual reproduction and two sexes is enough of a wall to prevent intracellular competition via natural selection in mitochondria.

As I have already pointed out, there are examples of sexually reproducing species which do not utilize two different genders. In the case of fungi, I am not sure how they deal with the issue of mitochondrial war (or if anyone else does) but I am sure they have some mechanism for it even if unknown. Maybe creating billions of spores renders it a moot issue because there is more than enough opportunity for both lineages. In the case of the penis fencing worms, you can see the problem of not distinguishing genders quite saliently. Two individuals attempt to forcefully inject (rape?) each other with sperm while not getting injected themselves. You have got to love the sadistic creativity of nature for creating a species in which each individual acts as both the rapist and the rape victim at the same time. You’ve got to rape before you get raped. This method of reproduction can and does cause injury to the rape “victim” which could lead to infection and other issues. Not exactly ideal from a fitness perspective.

And this is why sexually reproducing organisms have evolved a binary gender dynamic many, many times independently. Evolving a male and female sex is one of the best examples of convergent evolution because it has happened so many different times.  Most people are already familiar with sex determination in mammals which is determined via an XY system. Two X chromosomes gear the human form to passing on mitochondria (i.e., female) as well as other things, while an X and a Y chromosome gears the human form to not pass on mitochondria (i.e., male) again among other things. But the mammalian XY system isn’t the only way this mitochondrial division of labor can be accomplished. Fruit flies, for example, have an independently evolved and completely unrelated XY sex determination system. Hymenoptera insects (ants, bees, and wasps) have a haplodiploidy sex determination system in which the male only has one set of chromosomes (haploid) while the female has two sets of chromosomes (diploidy). A number of lizards and other reptiles use a temperature determination system. Some fish determine sex via social hierarchy. (Again this is not an endorsement of mental illness in humans, despite wikipedia believing it is.) Even plants can’t wait to give up hermaphrodism and divide into two sexes and that has happened independently a ton of different times. Last in my list, though I won’t claim it is exhaustive, is the ZW sex determination system present in some birds, turtles, crustaceans and so on. Mirroring the XY system, ZZ is male and ZW is female. Like with mammals and fruit flies, when these species are not closely related chances are these systems are also independently evolved. It has recently been called into question that the bird ZW is actually independent of the mammalian XY because of discoveries with the playtpus sex determination system. I tangentially discussed this in an April fools article I wrote on hybridization theory a while ago and I will let you read it to come up with your own conclusions. Keep in mind, a joke works better if you mix in some facts to make it more believable…

Regardless, you can see that using two and only two sexes has evolved again and again and again and again and again in completely unrelated species with incredible levels of divergence. Even in the sex changing fish they opted to have two sexes rather than just stay hermaphroditic. The fish are never both male and female at the same time. Having two and only two sexes, regardless of how that is accomplished, seems to be some sort of evolutionary equivalent of an energy minimum. Dealing with mitochondrial war doesn’t strictly require two sexes and other arrangements can work (in species that aren’t human), but clearly the two sex binary is one of the easiest and most effective ways for nuclear genomes to prevent intracellular war between mitochondrial lineages. Judging by the widespread level of convergence, cellular civil war must be a very common and extremely grave problem for biology to deal with. The existential urgency of preventing the internal war probably accounts for why an astoundingly large and diverse list of species have all converged on the two and only two sex binary. They keep falling back to that arrangement via remarkably different yet equally effective systems. And so that is why we have two sexes and not zero or a million. And it is why we will always have two and only two sexes.


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