Organellogenesis

With the traditional theory all organelles were created locally, by a process called "organellogenesis". The endosymbiosis process introduced an alternative way by which organelles could have been created. For two of the organelles, mitochondria and chloroplasts, the process of endosymbiosis has been used as an explanation for similarities of these to free living bacteria. All these endosymbiosis processes are assumed to have been performed only once, maybe with the exception of chloroplast genesis, which by several theories have been performed twice. And all these processes are assumed to have been completed more than a billion years ago. 

The internal incidents of organogenesis may have been slow, iterative processes, but the endosymbiosis events must have been completed in very short time. That includes not only the establishment of a dependency relation between the intruding bacterium and its host, but also the transfer of genes to the nucleus. That is documented by the introns that are assumed to have been inserted in the genes. They are found on the same places in organisms that are only distantly related.

But organellogenesis takes place also today. REF (small things ) describes an incidence?? of endosymbiosis that has taken place within the last ??? years. In light of the posited PÅSTÅTTE improbability of endosymbiosis (REF Lane) this is a sensation. If this is an endosymbiosis following the evolution trends of the ancient cases, then we should expect to see massive transfer of genes to the nucleus. But that is not reported (??). 

And this is not the only case of organellogenesis reported. In REF NAVN reports the discovery of 18? cases of endosymbiosis, where an organelle has been exchanged (?) with a new bacterium. (SJEKK) Also here there is no finding of massive transfer of genes to the nucleus. This is as far from the evolutionary endosymbiosis at it is possible to come. But such cases have been used as proof for endosymbiosis. It is evident that these organelles have not been created locally independently of the bacteria that surround them. In fact their genomes are in all cases related to local bacteria. But that is not equivalent to origin by endosymbiosis. 

With OET((REF)) new organelle variants with relation to surrounding bacteria may occur in two ways: either by bacteria becoming organelles or by organelles becoming bacteria. In this case a much simpler explanation is that these organelles have originated in their ancient hosts, have evolved to become partly stationary and partly commuting, and the commuting variant would be classified as bacteria. 

It is evident that the commuting organelles that surround the host are related to the stationary variant of the organelle, as they have a common source of genes. In these cases the stationary variant is very autonomous. They are really just temporarily stationary. Either they are equipped from their host with genes to become commuting or they are really competing with variants that are commuting. The best way to regard them is probably as a part of a common community. By chance some variants become stationary for a period before they are outcompeted by others in the community. We could use the term organellogenesis for all these cases, but it is really part of a continuous process, where some commuting organelles become dependent of their host due to loss of some gene. I would not call this endosymbiosis, as the relation between host and guest is present all the time.

The big difference is that mitochondria and chloroplasts are B organelles ((REF. quora OET)) (eubacteria when autonomous), which are basically electron acceptors (or the opposite), while the modern organelles are A organelles (archaebacteria when autonomous). The latter are basically hydrogen consumers. The B organelles are naturally stationary when the final electron acceptor/donor is a neutral molecule. The A organelles however always thrive well outside their host, and are used as stationary mainly as a complement to a B organelle hydrogenosome. 

For an alternative explanation of the origin of e.g. mitochondria, refer to the evolution of metabolism in OET or to OET generally.  

Is it possible that all existent bacteria once were commuting organelles?

TO BE ADDED:
FROM WORD: If we define all "organisms" that are dependent upon eukaryotes by frequently visiting them as commuting organelles, then there today exists quite a few. They are all related to archaebacteria or eubacteria, and it has therefore been assumed that they originate from such organisms. But the fact can be the opposite, that the bacteria were all commuting organelles. 

OM commuting organelles i dag EGET?  

TEXT FROM QUORA, OET:

As explained in the previous posts, the organelles that became bacteria were for a period commuting, before their host became extinct. For some of them the period of commuting could have been quite lengthy, and it seems that some are commuting even today. There are reports that methanogen organelles (in the reports denoted "methanogen endosymbionts", but I prefer the name "methanosomes") coevolve with archaebacteria in the environments, explained as substitution of the organelle with environmental organisms. In “Multiple Acquisition of Methanogenic Archaeal Symbionts by Anaerobic Ciliates” it is concluded that substitution has taken place repeatedly, i.e. repeated endosymbiosis, which is far from the conclusion that endosymbiosis is an extremely seldom event. Nick Lane argues that “it’s probably relatively easy to come up with something like a bacterium and we will see bacteria almost everywhere”. But complex life may in his mind be found only on Earth. In his mind, the acquisition of mitochondria is the event that created complex life, life that could potentially become intelligent and make themselves known to the universe through radio signals. Lane sees the negative results from the SETI project as evidence endosymbiosis is a very improbable event. I agree with him that a creation of mitochondria from a bacterium is improbable, so improbable that it never happened. But organisms that are usually called bacteria are entering organelles all the time to cooperate with its host. The “Methanogenic Achaea” mentioned above is one example. With the Organelle Escape Theory it is the “A organelle”. It is a “commuting organelle” by the OET terminology. They are not only entering their host. They are also exiting. Such exiting is the source of all bacteria. I see them as bacteria when their host or hosts are all extinct.

There are also examples of present commuting based upon the B organelle. One example is the Legionellea pneumophila. They thrive in amoeba and normally reproduce inside them. They are aerobic, i.e. they could potentially have given aerobic metabolism to an anaerobic host. So what is it that makes endosymbiosis so improbable, according to Lane?

In the OET view of cellular evolution Legionellas are example of commuting organelles that evolved in parallel with the stationary variant, that became the mitochondrion. It is the easiness of crossing the membrane for small neutral molecules that has made the commuting variant obsolete and just appearing spuriously as Legionellas.

SJEKK
With OET the coevolution of organelle with environmental organisms would instead be explained by update of the environmental organisms from the host, as all the bacteria were once commuting organelles, but today only a few have hosts that could supply new variants. It is with OET, regarding the organisms as commuting organelles, much easier to explain the observations in the article.

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. That means the endosymbiosis theory is wrong. 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. This is described in the Eukaryote Expansion Theory. 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 oxic 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 gotten 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.

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