Tags: evil

thinking

On the Origin of Species by Means of Natural Selection

если отпустить лягушке
лет немалое число
по бокам возникнут ушки
вспухнет мозга вещество

http://aptsvet.livejournal.com/585550.html

The remarkable fact about Darwin's classic is that it covers every topic under the sun except for the title problem: the mechanics of creativity in Nature and, in particular, "the origin of species." There has been progress with the first part of the unaddressed mystery (what drives speciation in the world that has already been populated by species). There has been almost no progress on the origin of the Darwinian Threshold. Why are there species to begin with?

The question has never been convincingly answered or even intelligently asked. It is worse than that. It is unclear where to begin looking for the answer. Actually, it is worse still. It is not clear that the answer might exist, if you discount "it just so happened" as the answer. Yet I'll try to answer this question to the best of my ability. Of course, it will be pure speculation. Maybe someone will offer a better answer. I do not want to sweep it under the carpet.

Only the eukaryotes have species, and the alternative is before our very eyes: the prokaryotes. Bacteria and archae do not have species, the ecotypes freely swap their genes given the opportunity. There is common gene pool from which one can borrow and to which one can contribute. It obviously works, and it works extremely well: they rule this planet; everything else is marginalia. The eukaryotes do not swap with this pool, though. Each species is a genetic universe upon itself. Surely, the eukaryotes are much more complex than the bacteria, but this, in itself, does not explain speciation. There is no reason to believe that the complexity excludes free swapping of one's genes. After all, we do have sex, right? Why can't we have sex with any other species? The "answer" is that the other species had so much diverged from our own that it is no longer possible for us two to have viable progeny. But that's circuitous logic: the species have diverged precisely for the lack of this cross-breeding ability. It is speciation itself (the creation of artificial barriers to breeding) that enforces the species, and this order of things exists only in the Eukarya. Isn't it strange? Maybe it is just the complexity? Here is Woese:

were [cellular] organization simple and modular enough, all of the componentry of a cell could potentially be horizontally displaceable. Suppose that the primitive ancestors of modern cells were of this nature. That would mean that at its beginning, cellular evolution would have been driven in the main by gene transfers. In its subsequent evolution a primitive cell of this type would become ever more complex, idiosyncratically connected, and thereby increasingly refractory to horizontal gene acquisition, especially the more spectacular forms of it. In other words, there would come a stage in the evolution of cellular organization where the organismal genealogical trace (recorded in common histories of the genes of an organism) goes from being completely ephemeral to being increasingly permanent. This point in evolution, this transition, is appropriately call the “Darwinian Threshold.” On the far side of that Threshold “species” as we know them cannot exist. Once it is crossed, however, speciation becomes possible. The Darwinian Threshold truly represents the Origin of Species, in that it represents the origin of speciation as we know it. It could represent a point in cellular evolution where something drastic occurs. I posit the latter. The cell is a complex dynamic system. As its connectedness increases such a system can reach a critical point, where a phase change occurs, where a new, higher level organization of the whole emerges. That, I suggest, is what the Darwinian Threshold represents, a hitherto unrecognized phase change in the organization of the evolving cell. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC124369/

So we are dealing with one of the most momentous transformations, and no one has any idea what this "something drastic" could have been. The latent potential for speciation might have existed well before it occurred, but decoupling from the common genetic pool would be expected to decrease(!) fitness. If the goal of evolution is producing increasingly fit organisms, the speciation should never had occurred in the first place.

The usual take on eukarogenesis is symbiogenesis. The protoeukaryon archae found an ingenious solution to the inherent limitations of all bacteria: as they store energy as a chemical gradient across their membranes, they have to be small. The host had internalized a bacterium and started using many of such endosymbionts to produce a lot of energy by respiration. Because the latter produces radicals that can easily kill the host cell, the operation of mitochondria had to be tightly regulated and controlled, and their genes passed to the host's nucleus. This increased the demands on the fidelity and the amount of replicating DNA. The host had the machinery for this feat, and the mitochondria provided the energy needed by this costly machinery. For the first time ever, vast amounts of DNA could had been copied with high fidelity. The bacteria need to replicate very rapidly, and they keep their genomes as lean as possible, shedding the DNA that is not neeeded, hoping that another bacteria would pick it up. The protoeukaryon did not need to shed anything. It was accumulating the goodies. Its dramatically increased capacity to copy DNA was immediately exploited by viruses and selfish genetic elements that overrun the genome, but the eukaryon was able to tolerate even this abuse, thanks to its unconstrained energy source. It pursued the classical K-strategy: slow replication, high quality vs. r-strategy: rapid replication, low quality. However, having the potential ability to speciate does not explain speciation. There were still the distinct advantages to swapping genes. Then it all stopped. One idea I've heard is that such potentiality is binding: if there is a physical barrier, the differences between subpopulations would grow so great over time that the gene-swapping protocols would become different and the speciation will occur. I think this is wrong. Such speciation has never happened in the Prokarya, despite very formidable barriers, and the molecular machinery of sex is similar for all protists. The breeding barrier was not spontaneous; it was erected. So the question is, to what purpose? This purpose was not selfishness of the individual, as there was no "individual" at that point. So it was for the greater good of all. But how speciation can be this common good?

It was the logical conclusion of the eukaryogenesis itself. Bacteria do not parasitize on bacteria, as they are too small for such invasions (there are rare exceptions). However, the sheer size of the protoeukaryon made such infections possible. Furthermore, as the latter internalized its bacterial food, the bugs were invited to take advantage of their predator. "The Struggle for Life" has finally began, and it began on unfavorable terms for the Eukarya. The bacteria can live on uranium ore, gasoline, and even crystalline penicillin; living off the eukarya was unproblematic. The only consideration for letting the host to stay alive was (and still is) having someone to feed you. Now, imagine the world with bacterial infections, but no speciation. We get the Red Queen problem.

The bacterial virulence is adjusted to its host and other parasitic bacteria living in the host, but new strains appear constantly. Some of these strains will try to take the undue advantage over other bacterial strains possibly killing the host in the process. The very logic of the parasitism and evolution makes this situation inevitable: bacteria can adjust their virulence only through trial and error. If there are no barriers to eukaryote interbreeding, the killer infection will spread accross the entire population and kill everyone. This is the situation in which speciation is rewarded. Erecting artificial barriers helps to curb such pandemics, as the accumulated differences in the cellular machinery make this bacterial spread limited. The interspecies jumps are devastating but relatively rare which improves the chances for all parties involved. Divided, we stand: speciation IS a communal advantage for the eukaryotes.

One can ask, why does not this logic does apply to bacteria and their phages: why wouldn't bacteria speciate? I think that the reason is that the phages are not free living: they are produced by the bacteria themselves. Furthermore, the bacteria can outpace the phages, but the slowly replicating eukaryons cannot outpace their bacterial parasites. Finally, the bacteria use heritable immunity that relies on high variability and imprecise copying. Again, the eukaryons can't quite do that. The K-strategy limits the choices and makes certain outcomes foreordained. I think that speciation was one of such outcomes. The host-parasite dynamics involving r- and K-strategists inevitably leads to it. The eukaryotes have to be divided into species separated by barriers they themselves erect and maintain, as otherwise the first nasty bacterial infection will do them all in before the bacteria readjust their virulence. For the bacteria, this is business as usual, but for the Eukarya it would be the end of the road. They cannot afford not being species.

In short, I suggest that the speciation was a communitarian means of giving everyone a sporting chance through building robust diversity hampering bacterial parasitism. It was one of the first attempts at making this place a better world, and it ended like other such attempts. It assumed the logic of its own, producing the world as we know it, where a species is against a species, and an individual is against an individual.

Why are there species?

thinking

Why do we suffer? (3) What to do about evil?

(1) (2) (3)

In the previous installment I provided a scenario of how evil crept into this world. In retrospect, even knowing how the Fall happened (and we do not know that exactly) provides few clues as to what could have been done to prevent evil, once the chain of events began to unfold. What took me a few paragraphs to outline, in reality happened over hundreds of millions years in minute, gradual steps in trillions of cells. Each event by itself was not evil, but their cumulative effect unleashed evil. The new form of Life could have been different. The situation could have reversed itself many times over, quite on its own, and other solutions than those chosen could have been tested -- and perhaps were tested -- but the combined forces of random change and the internal logic of genome fusion have led a subset of life into the abyss. That abyss was there from the beginning of time, and yet getting into it was neither inevitable nor preordained. It happened not by malice but because sooner or later anything happens. Our misfortune is that it happened here, to us. But even if it would not happen here, still it would happen, it is happening, and it will happen somewhere else. Our good fortune would only mean that the misfortune of the others. In this sense, evil is inevitable and preordained.

The pertinent question is why was not this evil prevented or extricated? The problem is WHAT became evil. A new form of Life separated itself in the most profound way from its parent. Evil and eukaryotic atomization is one and the same thing; blotting out evil means destroying the only form of Life that this planet has ever produced on its own. The eukaryotes cannot be "mended" without ceasing to be what they are. The question boils down to the following, can the omnibenevolence destroy Life for the sake of good?

It can not. If there is any "evidence" that there is a divine spark in us, it is the fact that our morality commands us what our flesh resists with all of its force. We are given a higher ideal than the might of the individual triumphant over other individuals. The morality, instead of reflecting the grim reality of how we behave, tells us how we should behave would the original sin be extricated. It insists on the sanctity of human life regardless of its merit in our eyes. It tells that any human is an end in itself. If the sanctity of life is the highest good that is given to us, it is even more so for the entire Life. It is love that binds omnibenevolence to treat each Life as an end in itself. The extrication of evil by destroying Life is not an option. Changing its character by external means amounts to its destruction and this is also not an option. Either evil destroys itself or it becomes good, also on its own. In both of these cases, the initiative resides in evil.

Why was evil allowed to happen in the first place? Was it known to happen? My answer is that it was known and allowed to happen.

Atoms are not evil, but the right combination of atoms gives Hitler. This possibility is inherent in atoms and the way they interact with each other. Under the conditions prevalent in the Universe, the probability of these atoms combining to make Hitler is fantastically low, whereas the probability to make a star is reasonably high. May be it is possible to change natural law in such a way that stars, planets, and Life are probable but Hitlers are impossible, but we do not know whether such is the case. You cannot square a circle, whether you are omnipotent or not. The potential for evil is inherent in Life, but Life does not have to be evil. Furthermore, it must not be evil because evil Life cannot create a habitable planet for another Life. If the Universe is created for Life, then it is inevitable that evil will emerge, however small is the probability, somewhere, and yet it cannot be destroyed because evil or not, it is still Life.

Eukaryogenesis was an event with astronomically low odds of happening. The eukaryotic fusion happened once in 3.85 Gya. At each moment, there are 10^30 prokaryotes dividing every 10 minutes. Calculate the probability of this event, and you will see that it is on a par with spontaneous levitation. Shall the Universe be designed in such a way that an event occurring with the probability of 10^-48 in a lifetime of a planet is absolutely excluded? If one is not willing to take even such small chances during the creation, how can one expect new Life ever come into existence? However small is the probability of such an event it is bound to happen somewhere; in this sense there is foreknowledge of evil. This foreknowledge does not tell what to do when the nearly impossible potentiality becomes reality.

There is only one course of action left to a loving creator: to make the extrication of evil inherent in evil. Natural history is the testimony to this potential. The Eukarya almost exterminated itself in the Cryogenian, when hyperactive eukaryotic phototrophs reduced greenhouse gases to such a level that the Earth underwent complete glaciation that severely pruned eukaryotic tree. The essentials of this greatest extinction are familiar to us from the biblical parable of the flood (that followed the snowball glaciation): out of countless antediluvian eukaryotic lineages just a few have survived the calamity. The descendants of these few elect imprinted their character onto the extant eukaryotic Life. This life survived, but it has changed, deeply and irrevocably, on its own. In particular, this event opened the door to multicellular life, in which the individuals were merged into a new entity - the organism.

We do not know what was exterminated in this dramatic event; it is possible that something even more sinister than what we observe today was gathering strength in the Neoproterozoic seas. For all of its evil, the Eukarya has never challenged the Prokarya in the mastery of the planet. However, potentially, it could've gotten the upper hand. The Eukarya that existed before the glaciation was more metabolically diverse and blurred the difference between the predators, the phototrophs, and the absorptive feeders. A super efficient individual with a potential for global takeover could have emerged in this rich milieu, but the eukaryotic community itself delivered the world from this ultimate evil.

More importantly, multicellularity is the development pointing away from selfishness, and so is the evolution of germ-soma division. Down the line, the new individuals started to integrate further, forming societies and larger communities, some of them even became eusocial. The latest development is the emergence of individuals capable of conceiving - albeit only in their imagination - of living that dramatically departs from the precepts of eukaryotic selfishness and having visions of existence that transcends the bounds of individuality. For the first time, the evil has recognized itself as evil. One can only guess how will this story end, but it shows that evil always contained the seeds of good that lead to its extrication, and it cannot be otherwise. This good is evolution, and the evolution - on all scales - is how the world is created. Ours is not the best of possible worlds, it is the world which is recovering from its self-inflicted worst. The evil will either self-defeat or self-destroy. We call biological evolution natural law. Of course, it is, but this natural law is just a way in which our form of Life (aka Nature) reflects the moral law that is above it all.

Meanwhile we suffer evil. The only way to stop this suffering is by death, and we were given this comfort. Our mortality, too, was the inheritance of the great flood of 700 Mya. But this is not the greatest gift we received. We are also given the burning desire not to be evil and the realization that we cannot be good in this flesh of ours. The resolution of this internal conflict, just as the resolution of the original conflict that introduced evil, is the next chapter of creation.

Evil exists, but it does not last. Its temporal character does not alleviate our present suffering, but our suffering is the means by which evil defeats itself. Few people understood the true source of our torment better than St Paul

...the law is spiritual; but I am of the flesh, sold into slavery under sin. I do not understand my own actions. For I do not do what I want, but I do the very thing I hate. Now if I do what I do not want, I agree that the law is good. But in fact it is no longer I that do it, but sin that dwells within me. For I know that nothing good dwells within me, that is, in my flesh. I can will what is right, but I cannot do it. For I do not do the good I want, but the evil I do not want is what I do. Now if I do what I do not want, it is no longer I that do it, but sin that dwells within me. So I find it to be a law that when I want to do what is good, evil lies close at hand. For I delight in the law of God in my inmost self, but I see in my members another law at war with the law of my mind, making me captive to the law of sin that dwells in my members. Wretched man that I am! With my mind I am a slave to the law of God, but with my flesh I am a slave to the law of sin. (Romans 7:14)

thinking

Why do we suffer? (2) The coming of evil

(1) (2) (3)

The problem of suffering can be reduced to the problem of primordial evil. How did the evil originate? In evolutionary biology, the question is known as the problem of eukaryogenesis, though it is not exactly the same problem, because it is, in fact, only one aspect of the eukaryogenesis: the decoupling of the protoeukaryon from the common gene pool. In principle, one can imagine an organism with most of the features of the eukaryon that is freely swapping genes with other eukaryotes and prokaryotes, in the same way it is done by the prokaryotes. If this were the outcome of the eukaryogenesis, no evil would arise, because such critters would rely on each other and their genes would be available to all. It would be just one vast brotherhood of Life. What fundamentally distinguishes the eukaryotes from the prokaryotes is that the former have much larger genomes allowing significantly higher level of complexity. They also posess the source of energy (mitochondria) that is required to replicate and use these bloated genomes. However, these genomes are only for themselves, there is no sharing. Once in a while, the eukaryotes can add to these genomes by stealing genes from the prokaryotes or incorporating bacterial cells, but they never give back. Their complexity is an end in itself: they need their complex organization and genomes to be complex; however, there is absolutely no need to be complex to make one's living. The prokaryotes give and take freely, and they do not need either the complexity or the colossal genomes. They need only what it takes to do their job of changing the environment around them and keep going. Their cumulative operation of maintaining this world in a habitable condition is extremely complex, and their composite genome is mind bogglingly huge, but it is a shared, collective property. The eukaryotes do not share. They only exchange genes with someone they recognize as an almost exact clone of themselves. They want only "their" genes to be replicated. We call this practice sex, and we call these habitual non-sharers species. To understand the origin of evil one needs to answer why the eukaryotes are not sharing. This is the root of our trouble. We do not know when this non-sharing had began. Furthermore, we do not know why, when, and exactly how sex evolved. However, non-sharing is probably older than sex. Sex was the solution to non-sharing rather than the other way round.

The eukaryogenesis started with endosymbiosis of the prokaryotes: one bacterium began living inside the other. There are people saying that complexity is a greater good, as it increases fitness. Eukaryogenesis allowed combining complex traits making the integrated organism more fit. However, it is not obvious that putting two or more specialized, free-living bacteria in a consortium would not achieve just as much or more. There should be a derived benefit that exceeds the merit of mutualistic symbiosis other than complexity of organization as such, and it is not clear what this benefit was. Bacterial consortia are fairly common, as they allow to expand the metabolic range of the partners, but the arrangement of a bacterium inside a bacterium is extremely uncommon; in fact, there is only one known example, for a bacterium-in-a-bacterium living inside mealybug eggs.
http://www.sciencenews.org/20010728/fob4.asp
There are isolated examples of methanogenic Achaea consorting with sulfate-reducing bacteria,
http://www.nature.com/nature/journal/v407/n6804/abs/407623a0.html;jsessionid=10647E0505FCC43BF3569C84A4B1B48C
but the arrangement is not that of a host and a guest, the bacteria form a rind around the archaeobacterium and can dissociate from it . The fusion event that lead to the integration of prokaryotic genomes was the rarity of rarities, and it happened only once as far as we know. My view is that it was not any specific benefit that lead to the evolution of complexity and individuality, but the resolution of the conflict between the host and the guest. In a normal situation, the conflict can be resolved by the partners going their separate ways. The real conflict begins when one of the partners grows so dependent on its partner that it does not let it go. The partnership dissolves into a master-slave relationship. This is what happened.

The Achaea host and the protomitochondrion (a proteobacterium guest) were once good and honest prokaryotes living in an anoxic environment, and they were swapping genes with other prokaryotes as the prokaryotes do. The Archaean host had tough life, and many of its features (e.g. having histone-like proteins to stabilize its DNA) are the testimony to high acidity and temperature of its hellish quarters. It also had pleiomorphic wall that allowed it to associate with the globules of sulfur that it was reducing, and managing such aggregates was assisted by a rudimentary cytoskeletal system that became handy in manipulation of the future guest. Perhaps this host formed consortia with various bacteria, but these consortia were free partnerships. The first step towards evil happened when the Archaean host internalized a free living eubacterium. We do not know whether it happened by endocytosis (ingestion) or gradual engulfment of the externally attached partner, but this step changed the situation radically. Living inside someone is not the same thing as living outside on your own. No harm was done yet, the partnership was not exploitative, but it opened the gates to hell. The host erected a physical barrier for the guest. The intent could've been different from preventing the guest from dissolving their partnership. It could've been protecting the guest from the hostile environment to which the archaeon was exposed; it was in guest's interests too, as it allowed expanding its range. The normal way of protection in a bacterial community is communal, it is a mat building. The host gracefully offered the protection by its own membrane. The road to evil began with the best intentions.

This endosymbiosis was mutualistic. The Archaean provided metabolites and the bacterium produced energy (ATP) by respiration (which may have not been oxygenic at the outset). Hydrogen (in hydrogenosome hypothesis), nitrate or sulfate (in synthrophy hypothesis) have been the sources of the energy. Alternatively, it was metabolite exchange (e.g., the removal of the waste from the bacterium helping the host to survive in more aerobic environments). The important thing is that while this endosymbiosis was mutualistic and beneficial, it was devil's bargain. Food comes and goes and free consortia can dissociate when things are not going well. The protomitochondrion needed food and the host needed energy which its partner produced, and they became dependent on each other. When the food supply dwindled and the guest wanted to get out, the bacteria started their usual defensive reaction in stress situations, which is producing free radicals that were harmful for the host. Either the host was to release these bacteria and face privation in the future, or it was killed in order to get out. Furthermore, the host needed to manage the internalized bacteria for replication. Each time it divided, it needed to retain the bacteria and it needed to control their division both during this replication and the normal operation, because the deficit or overabundance of the bacteria would harm or kill the host. Having the internalized bacteria was paying off, but it was brushing with danger. The resolution of this conflict was in regulating the endosymbionts, and the means presented themselves, as the bacteria were still freely sharing their plasmids. The host exploited this willingness, which was only natural, because the plasmids were injected right into its interior. It also had the energy reserves, thanks to the beneficial part of the symbiosis, to expand its genome and incorporate these shed and shared genes. What it was not able to do was going back on the gene transfer, because its guest needed its biomolecules to be made. For the first time ever, the reduction of the genome for the sake of accelerated reproduction became not an option. The prokaryotes do share, but this is not by their virtue, it is by necessity. Sharing makes the reduction of the genome possible without paying the penalty of losing these genes forever, and the reduction is required to accelerate replication. The chimera was not able to benefit from the reduction, as it needed to maintain the genes for its endosymbiont. For the first time, genomic reduction stopped to be beneficial. Such is the peculiarity of the systemic gene transfer process that unfolded in the protoeukaryon.

The gene transfer from the guest to the host progressed further and further and resulted in dramatic genome reduction of the guest and the concomitant increase in the genome complexity of the host. This was destined to occur because the bacteria voluntarily reduce their genomes to facilitate division, and the host relied on this built-in mechanism. The host was making the building blocks needed by the bacterium and the guest was losing its genes to take the advantage of what looked like once-in-a-lifetime opportunity of replicating for a bargain. It also needed to shed these genes because it was deprived of the increasing portion of the energy that it generated, which was needed for its replication, as it still replicated on its own. In the end, the guest shed most of the genes that are not involved in the basic task of respiration and making proteins involved in the respiration. The reason for incompleteness of the transfer is that local expression and assembly of the enzymes is required to avoid overproduction of radicals in redox reactions taking place in the mitosomes.
http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2447392&blobtype=pdf
There could be other reasons (e.g., differences in genetic codes and high hydrophobicity of the residual proteins that made their import from the cytosol problematic - there are different explanations; see above and
http://www.ncbi.nlm.nih.gov/pubmed/15770678)

When this transfer was complete, nothing per se prevented the host to resume sharing again, but by this time it had stopped reducing a large fraction of its genome for a long time, while constantly perfecting the machinery of managing the increasing genome size and regulating its guest. But the prokaryotes around freely shared, and so acquiring new genes and doing repairs were not a problem. The new machinery and the acquired mitosomes allowed the chimera to incorporate the growing number of prokaryote genes with impunity, further increasing the complexity and allowing the incorporation of more genes. No incentive to share back presented itself, as the tempo of replication was controlled by the ability to grow the sufficient number of mitosomes, cytoskeleton, etc. rather than the speed of genome duplication. The sharer who initially needed to stop sharing for the sake of regulating its guest in the process of incorporating its whole genome became the habitual thief that takes but does not give, simply because it can get away with it. The evil set in. Observe that on its own logic, the chimera did the right thing. It did not do what it didn't need to do.

Eventually, the genome increased so much that no cellular machinery was able to maintain all this complexity and keep pace with replication of the prokaryotes. The chimera took that choice. Slower replication was matched by a new survival strategy: predation. Before, the competition was eliminated by filling a niche through efficient replication. Now it was done by eating the competitors. The evil grew.

The final step down the road was the invention of sex. Cloning and the incorporation of prokaryote genes worked quite well up to a point, but eventually it became insufficient, because some of the genes that the eukaryote relied upon, the ones that were of its own making, never made it back to the gene pool. Not sharing had its penalty. Worse, when the machinery broke down due to these defective genes, the guest starved and began its old game of free radical warfare, which was built into its irreducible redox signaling pathways. The penalty for the defective genes was certain death, but there was no way to repair by stealing new genes from the pool. The only solution was to find a clone and take its genes. This can be done in many different ways (and sex is very different across the eukaryotic kingdom), but the practice of equivalent sharing of the genome was adopted in the end. The particular form sex took could've been random and it has little bearing on our subject. Sex with a clone was the necessity stemming from non-sharing. By that time the eukaryons, as they stole and incorporated different bacterial genomes and never shared them started to look different. Some were more like fungi, others more like algae, and the others more like amoebas. Finding the needle in the haystacks of their expanded genomes for repairs was next to impossible. The only way out was finding a healthy clone (as close as possible to oneself) and using it in its entirety. Any form of replication that would allow this replication would do, and sex was one such way. The specialized eukaryons exchanging genes only with their kin became species. By that time evil became firmly entrenched.

The path to evil came in little steps, each one of which did not look sinister by itself. It was an elegant and simple solution of the problems created at the previous step, every single step down the road. Complexity was not the objective, non-sharing was not the objective, survival benefit was not the objective, speciation was not the objective, fitness was not the objective. These were a means to an end. The good of harmonizing the symbiosis to make it more mutualistic is what started the descent into the abyss. The process immediately acquired the logic of its own that brought it to its final hideous form.

It was as easy as picking an apple from a tree.

How did the evil come into the world?
thinking

Why do we suffer? (1) The root of the problem

(1) (2) (3)

This question has driven many a believer into apostasy. It caused insufferable agony, doubt, and heresy throughout the ages. It causes me agony and doubt. It is sacrilegious and perhaps immoral to turn the tragedy of one's existence into an intellectual pursuit and ponder it as an abstract question. It isn't an abstract question. One earns the answer with one's life. I am aware of that, but I cannot pass on this question, it is too important to me. I cannot answer it either, but I can reduce it to another question and convey my thoughts about this other question. To the best of my knowledge, the answer has not been sought along the lines suggested here.

It is readily admitted by people of vastly different views that a lot of our suffering (wars, injustice, oppression, genocide) is self-inflicted and results from the imperfection of human nature and accruing of bad choices. Could it be that all of our suffering is self-inflicted? What about the disease, the tsunamis and the earthquakes, the aging and death?

For the believers, the problem begins as theodicy, and most of the theodicies, with the exception of Leibnitz's optimism, conclude that evil is nonexistent, that it is a privation of good left for the greater appreciation of this good. Other popular answers posit that the suffering results from free will or that it is a trial of moral strength. The problem with the latter two answers is that only a small fraction of suffering of this world can be explained this way. The problem with the optimism is that no future goal is sufficiently good in itself to justify our suffering here and now. If this is the best way to create the Universe, perhaps it would be preferable not to create it at all.

These answers ring hollow to me. I may be in the minority believing that evil does exist and that all of our suffering is self-inflicted. It is simpler to see this point from specific examples.

We consider the disease as something external to us, furthermore, something from which only disadvantage ensues. Both of these viewpoints are incorrect. First, we are all beneficiaries of the disease, and in a few posts I have provided the examples of this benefit. The Russians exist as polity mainly because of the circuitous course that the plague took in the 14th century. The Jewry exists mainly due to the sudden eruption of pestilence between the Assyrians besieging Jerusalem in the time of king Hezekiah. The Americas are peopled by the Europeans because we are the beneficiaries of genetic homogeneity of the Amerindians that made them unusually susceptible to newly introduced diseases, resulting in the asymmetry of Columbian exchange. Infectious disease consistently benefitted one group of people over the other; it is an instrument of domination and intraspecies competition.

One can counter this assertion with pointing out that this instrument is not controlled by us. This is not quite true. It is controlled by us. It is only by inertia of thought that the viruses are considered as third parties in infection. In reality, the viruses are produced and mutated by our bodies and their virulence is tuned by the interaction with our acquired immune system. The view that the viruses are biological weapons used by the eukaryotes as a means of intraspecies competition does not contradict anything that we know about the viruses. The bacterial infections are no different despite the fact that the infectuous agents are alive. The bacteria are not interested in inflicting suffering and death upon us, they are interested in beneficial parasitism and mutualistic co-existence. It is our own immune system that breeds highly virulent strains by challenging these bacteria, and this immune system is not as much protecting us as constantly induces host-guest disequilibrium, seeking to give the advantage to an individual possessing greater immunity. The immune system, in other words, is also a tool of intraspecies competition, and it needs disease to be a useful tool. Its usefulness is so great that even the risk of autoimmune disease and self-destruction does not outweigh the benefit of having such a weapon. The disease is not the external scourge, it is co-opted and perpetrated; it is the assault weapon wielded to establish the domination of one's lineage.

The genetic diseases also exist for the benefit of the individual. To have an edge over other individuals, the organism has to sample a subspace of genetic variation, as otherwise there could be no new traits conferring selective advantage. It is possible to reduce the rate of mutations dramatically, but that would lower the rate of beneficial mutations. The individual opts for the risk of deleterious mutations in order for its lineage to gain from the beneficial ones and thereby outcompete the others. The same mechanism that perpetrates virulent infectious disease also underlies genetic disorders. Cancer may seem the exception from this rule, but it is not. First, the animals having only the innate immune system do not suffer from cancer as much as those with the acquired immunity, and it is seldom lethal for lower animals. Secondly, the cancer is the consequence of our multicellularity, which is beneficial for the organism as a whole, but is hell for our cells that are constantly induced to die. Cancer is the rebellion of the subjugated; the cancerous cells are doing to other cells of our body what we ourselves do to other members of our species. Senescence and death also result from the advantages conferred to the lineage of the individual; as I've wrote about it before, there is little point in being repetitive. All of this suffering is the direct consequence of us being autonomous individuals competing for the domination of our lineage for the expense of the others. The same nature that causes social evils, causes biological ones.

What about natural disasters? Should the plate tectonics be stopped and our planet converted into the desolation of Mars and Venus for the sake of H. sapience sapienti? The proverbial tsunamis are the case in point demonstrating where the suffering truly comes from. The tsunami is the norm in the Pacific, and the creation and subduction of crust is essential for maintaining Life on this planet. The tsunamis are not rare and the inhabitants of the islands know this well. They know that one day it will come, and they still choose their way of living over safety, because it gives them short-term advantage. Until recently, the Indonesians had good sense not living en masse in the coastal regions. However, the population exploded, and the population pressure and the scarcity of resources drove people into living in highly unsafe places, despite their knowledge of the unavoidable penalty. The population exploded due to the advantages of modern medicine combined with high fertility rates. Now, who should be cursed for the loss of life that resulted from these developments? Was it inflicted by the blind forces of nature or did it result from the upset population dynamics? Was it cruel deity or people themselves who are responsible for the attrition? Throw efficient medicine into the established pattern of biological warfare that controls the population and you are destined to obtain exactly this result. If one constantly seeks advantage over one's neighbor, on however temporary and shaky basis, one would chose to live on the fault in California and one would build a city in the path of a hurricane in Lousiana. The suffering is self-inflicted.

This examination can go on and on, and in one or several steps it becomes transparent where the pain and suffering come from. It comes from ourselves. What seems external is internal. We suffer because eukaryotic Life is atomized into individuals which are at war with each other and stop at nothing. If we do not do it consciously, we do it unconsciously. If our minds do not do it, our bodies do. The original sin is stamped upon us so strongly that no moral revelation can cast it out. It is not individuality per se that tortures us; that is not the problem. It is the autonomy of the individual that does it, the fact that it has almost no stake in the existence of other individuals, but a large stake in their nonexistence. The problem, in short, is decoupling of the eukaryotic individual from the common genetic pool. All of our suffering results from this one misstep. It is the primordial evil, and it manifests itself in a myriad ways. Evil exists. It is not the privation of any good, it is right there at the stem of the tree of Life. We suffer because it exists, and we will suffer until it exists. The problem of evil is in answering (1) how this primordial evil came into existence and (2) why it has not been blotted out. I will try to provide a scenario for (1) and a few guesses for (2), which is a harder problem. The short answers are that it was a specific way to resolve the conflict of interest in a symbiotic relationship, that the evil was weakened and nearly eradicated on its own about 600 Mya, and that blotting it out means destroying the only terrestrial form of Life that ever existed.

Retracing the argument, I agree with St. Augustine and the others that deny the existence of evil as a cosmic principle. The evil is not a principle, it is a specific and palpable thing that happened on Earth about 1.5-2 Gya and that is still going on. It exists, and rather than denying this fact, one should face it and come to terms with it. I suggest that there is a cosmic principle, of good. Life does not harm and destroy another Life, no matter what form it takes. One can call it the cosmic sanctity of Life. We are familiar with this principle, with the lower case l's, as it is the basis of morality which distinguishes us from animals. We and our evil exist because this principle is followed.

Why do we suffer?