Sunday, May 7, 2017

The Organelle Escape Theory

I am working with an article that describes the Organelle Escape Theory. For the moment, what is finished is how fast thinking is not suited for evolution theories, how introns impose difficulties for the endosymbiosis theory and how these difficulties inspired to finding new explanations, how origin of life with eukaryotes is much more logical than old bactria, a brief scenario for the theory, and how sex originated with the theory. I have also shown that what is claimed to be a proof for endosymbiosis, is not more than a proof for endosymbiosis OR the  Organelle Escape Theory. The article, when it is finished, will appear here. It will be based on a comparison to theories about our solar system. 

Tuesday, April 18, 2017

Evolution of the eukaryote with OET and the endosymbiosis hypothesis

I will here describe briefly most of the evolution of eukaryotes, from the simplest cellular life form to sexually reproducing cellular units with a lot of different organelles. Evolution of introns is described elsewhere. Also the special evolution that gave rise to bacteria as separate forms of life is described in separate posts (Ref. to be added). How the evolution of eukaryotes resulted in anaerobic and aerobic forms is also treated separately. The separation of the eukaryote into two main compartments, the nucleus and the cytosol, is however treated here.

With OET all the eukaryotic features, such as organelles and sex, were created successively from the start of life in the simplest form. This simplest form was not a bacterium, as the endosymbiosis hypothesis holds. Neither archaebacteria, nor eubacteria existed at the time. The first cells originated in the RNA world, and they were quite similar to the nucleus of modern cells. In the RNA world, catalysis was controlled by ribozymes, not enzymes built from proteins. Genetics were primary also built on RNA, but DNA came into use for long term storage, much as we see it today. With the invention of translation, which was, and also today mostly is, built on RNA structures, separation into two compartments was a benefit. Special channels in the outer membrane were created. Bubbles were "blown" from these, and eventually all the bubbles united into the cytosol. With this separation the control system was well protected, and it was possible to use simple single membranous organelles. They were used to import and export metabolites from the environment. Later, also double membrane organelles were created. Viruses were created as a way to transport genetic material to other organisms, and commuting organelles were created to transport whole systems between organisms. As these could be autonomous, they could however also be used by just commuting to the environments. They became the bacteria, as described elsewhere.

With the endosymbiosis hypothesis the simplest eukaryote cell was not the nucleus, but a bacterium. Very often an archeabacterium is used as the source for the eukaryote in the various forms of endosymbiosis theories. The various forms of the hypothesis, described respectively by Lynn Margulis, Tom Cavalier-Smith and Martin & Müller propose different states of evolution of the host that received the bacterium that became the mitochondrion. But common to all of them is that evolution had a boost following this event. Features like sex and a series of organelles were invented after this event, mainly in the toxic world. In OET all these basic concepts were invented in the anoxic world, long before any bacteria existed.

The separation of the eukaryote into a nucleus and the cytosol has not been given any good explanation in the endosymbiosis hypotheses. Margulis saw the nucleus as just another organelle, and assumed that it was also the result of some endosymbiosis event. Martin & Müller may have a better explanation, but they are all quite speculative.

Why are there anaerobic eukaryotes?

Margulis described eukaryotes as aerobic organisms thriving under toxic conditions. And bacteria, that are mostly anaerobic, were by her given the honor of creating an advanced aerobic form, the eukaryote. But there are also anaerobic eukaryotes. These are with the endosymbiosis hypothesis posited to have been reverse evolved by loosing all the features that were needed for aerobic respiration, and instead new features for use under anoxic conditions were constructed. The results of this evolution were organelles like the hydrogenosomes and the mitosomes.

With OET these organelles were created at an early stage of evolution. The mitochondrion and the chloroplast represents the terminal stage of evolution, not any start of reverse evolution. OET holds that anaerobic eukaryotes are ancient, not recent forms. And that is also consistent with the phylogenetic studies that have been performed, if they are interpreted correctly.

With the endosymbiosis hypothesis we could wonder why there are anaerobic eukaryotes at all. But people, when they have been used to the endosymbiosis hypothesis, are also used to events that are almost impossible. The prevailing conditions any place where there is light is the oxic condition. And light is needed for energy generation. The anaerobic eukaryotes are therefore found only where there is no access for oxygen and where thee is a constant supply of metabolites. Typical places are in the ground and in the stomach of cows and termites. They must be older than the animals, so they must have thrived in the ground.  With OET they have remained where oxygen has not got access. With the endosymbiosis hypothesis they must have had a lot of problems moving from oxic conditions to anoxic while their metabolism has been reduced and then reinvented in another direction, a direction that was based on cooperation with certain methanogen archaebacteria. And in these habitats they would have to compete with bacteria, that were well established.

Sunday, March 26, 2017

Why are bacteria seen as very ancient?

Before 1859 all the smallest organisms were seen as novel. They were seen as spontaneously generated under the right conditions. These organisms cannot be seen by the bare eye, so it was the invention of microscopes that made us aware of them. The first organisms that were identified through the microscope were multicellular, but better microscopes also identified single celled organisms. And eventually also bacteria, that are much smaller and simpler than eukaryotes were observed. When Luis Pasteur in an experiment in 1859 showed that their existence could be demonstrated by fermentation, he also showed that they are not spontaneously generated. This year Darwin had ready for publishing a theory based on common descent, i.e. that all life originate from one cell. His book hypothesized evolution by gradual changes. The result of evolution can be observed in present species. And for eukaryotes it shows that there has been a lot of evolution.

Bacteria are special in comparison to all other forms of life, especially because they evolve differently. It is evident from the forms of life that we see today that eukaryotes have evolved by constantly creating new and ingenious features. There are eukaryotes that have not participated in the latest evolution trend, multicellularity. Even though single celled eukaryotes or "protists" are much simpler than the visible, multicellular forms of life, they are very diverse and despite of their simplicity, they are still enormously more complex than bacteria.

Bacteria have not by far evolved as ingeniously as eukaryotes. Their evolution is more like adaptation to the current conditions. The bacteria that we find today represent the stage of evolution when they first occurred. No trace of any earlier stage of evolution exists, it appears as if they emerged in the way Lynn Margulis express it: "They had to emerge ALL AT ONCE, No stepwise manner is possible, all systems are INTERDEPENDENT and IRREDUCIBLE." (Can anybody tell me from which book or article this citation originate?)

When we trace evolution backward in history, then we often compare genetics of one special feature, but we can also compare the set of features that exists in a clade. The organism that originated the clade may have had the set of features that is common to the clade and maybe a few more. The same philosophy may also be used for all protists. The set of common features contains almost all the features that are present in bacteria. I may therefore seem that we could rather use the bacterial features as the origin for all eukaryotes. There are a lot of features that exist in all eukaryotes that are not found in any bacteria, so an evolution from bacteria to eukaryotes would be a great enigma from which there exists no traces. And there are two groups of bacteria, archaebacteria and eubacteria, that have so different features that they would represent a branch by themselves, branches as separate from each other as they are to the eukaryote. But there is no trunk for the branches to attach to.

Carl Woese posited spontaneous emergence of the two bacteria types, as Margulis did, but he also included eukaryotes in the process. And he used another mechanism. Instead of basing it on an intelligence, as Margulis did, he assumed that both bacteria and eukaryotes occurred through a "crystallization" process. When uses that expression it is because it should be similar to the process whereby a fluid crystallizes when it is cooled.

The evolution from protists to all multicellular eukaryotes can be traced quite well through analysis of genes found in existent organisms. Evolution before the simplest eukaryotes can however not be traced at all. If bacteria represent one stage of this evolution, then there is not much help to get in finding how the evolution happened.

How can anybody suggest that something as complex as the two types of bacteria and the eukaryotes could emerge through a crystallization process? Is the action of an intelligence the only other possibility? Margulis does not call it "design", as the Intelligent Design followers do or the action of some God, as the creationists do. Her bacteria creating intelligence is rather non-specific. But she also posits that bacterial networks represent an intelligence that controls the conditions on Earth (the Gaia theory). But that intelligence could not have created itself?

Luckily, there are other possibilities. With the Organelle Escape Theory there is no need for any intelligence or enigmatic crystallization to create bacteria. They are created by eukaryotes through the same process that creates organelles in eukaryotes. Organelles and bacteria share so many features that bacteria have been posited as sources of some of them. Margulis held bacteria as the origin of all of them, but the most accepted theory limits this to organelles that cannot regenerate in the host.

With OET all organelles were originally created in the eukaryote itself or its ancestors. Some organelles reproduce so well that they do not need any regeneration process, so this process is not in use any more.  It is among these that we find most of the escaped organelles. Of cause regeneration could have been active also for commuting organelles as a safety mechanism, but with safe reproduction resident as well as commuting organelles had no use for their regeneration mechanism.

With OET there is no unconnected branches. The eukaryote branch works as branch for all bacteria through their escape. As bacteria in this model has a history as dependent organelles becoming more and more autonomous, the different features occurred at different times in the history of evolution. Some of these organelles started commuting to their environments and eventually became autonomous enough that they survived as autonomous organisms even when their host became extinct. They became the bacteria. Eubacteria and archaebacteria differ so much due to the time they established their first autonomy. The translation feature has been used as a measure in comparisons between bacteria and eukaryotes. As the archaebacteria got their translation apparatus much later than eubacteria, their apparatus is more similar to the eukaryotic system.

Friday, March 24, 2017

What is the right level of complexity for evolving systems

(prerelease) In some cases, e.g. in physics, scientists have found solutions that explain observations extremely much better than traditional ones. ....Example geocentric. .. Later, Newton showed that the orbits could be described by the same forces and equations for motion that are valid on the Earth surface. In evolution, there was at Aristotle’s time a lot of different for origin of life and evolution. They thought that there were multiple origins and conversions of life forms, so origin and evolution was quite intervened (??). Darwin simplified the thinking by postulating just one origin. He also disregarded some of the evolution theories, most notably those with saltational effect, such as origins of new species by conversions (metamorphoses) during the night. And he also disregarded teleological effects. Instead he added one mechanism that Aristotle had disregarded, the effect of selection. After Darwin, especially during the last past of the twentieth century, a further reduction became quite popular. In this reduction the source of novelties was also disregarded. The reduced theory works well in the short run on isolated populations, and it is almost impossible to prove experimentally that it does not work in the long run. Therefore the notion(?) has been widespread that this simplified evolution (or rather adaptation) system works also in the long run. Occam described a method to judge how complex an explanation needs to be. It is known as Occam’s razor. According to this principle we should choose the simplest possible explanation, but it should not be so simple that it does not explain everything in the system(??). The simplest possible system that explains evolution is probably Darwin’s system of evolution based on inheritance, variation and selection. The problem, as also Darwin noted, is to describe how variation occurs. Life consists of cellular systems, some that contain a nucleus and organelles, and some that are similar to organelles. The latter are the bacteria. An early evolution stage was the one that created this configuration. Originally life most probably consisted of just single membrane systems. These may have been most similar to the complex variant, eukaryotes, or they could have been similar to bacteria. A theory based on bacteria as the most primitive, some process to convert these to eukaryotes and import of bacteria to become some of the organelles is a dominant theory. That is the endosymbiont theory. There are variants of the theory, e.g. based on how much of the evolution from bacteria to eukaryotes took place before and how much after the endosymbiosis event. And there are variants based on which organelles are involved and at what state of evolution of these the endosymbiosis took place.
Endosymbiosis Woese progenote OET
Spontaneous Spontaneous/ Gradual/INVENTION
Many events enigmatic/ Many events
Once, spontaneous, enigmatic complex Many events
Complex, enigmatic Complex, enigmatic
Many events Many events
Gradual, reverse Gradual, reverse