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Tuesday, April 30, 2019

The endosymbiosis theory has been debunked for mitochondria

Ajith Harish and Charles Kurland at the Uppsala and Lund Universities in Sweden have in the article “Mitochondria are not captive bacteria” shown that the probability that mitochondria originated from proteobacteria is 44 orders of magnitude lower than the probability they were created locally. That increases considerably the probability that the Organelle Escape Theory describes the real origin of cellular structures. For more, see here.

Monday, April 29, 2019

Novelties and evolvability


Margulis did not only posit endosymbiosis as a source of organelles. REF? She posited that all novelties in eukaryotes are caused by endosymbiosis. In her opinion, bacteria are involved in an intelligent network covering the whole planet. In addition to working to the best for eukaryotes in a teleological manner it also supports our planet and maintains it in best possible ways. This theory was worked out in cooperation with James Lovelock. It is the "Gaia theory".  The intelligence in her model is thereby Gaia herself.

This way to regard bacteria can be seen as a solution to a serious problem in her scenario for cellular evolution. The problem is the origin of bacteria. According to the endosymbiosis theory their fusion starts evolution in a colossal tempo in eukaryotes. But the bacteria hardly evolve at all. That could be explained by the combination being so powerful. But there is another major problem. With Darwinian evolution even the bacteria must have evolved from single molecules. If Gaya created bacteria, then the problem is solved. Margulis criticized Darwinism especially because it is based on random mutations, which as she said:
 “Neo-Darwinism, which insists on (the slow accrual of mutations), is in a complete funk.”

I have illustrated Margulis´ way of thinking in the figure below: 




and my way in this figure: 



Organisms are illustrated by circles where complexity is the size of the circles. Evolvability is illustrated by the thickness of the arrows that show the direction of evolution. My theories do not rely on any intelligence. Instead they rely on evolvability, which is present in eukaryotes today, and which has been present almost from the beginning. There are a range of mechanisms that are typically present in eukaryotes and which are parts of the evolvability apparatus. They are: sex, diploidy, introns and protection against too high selection pressure. These mechanisms give organisms access to ingenious variants (e.g. through new combinations) and avoids stagnations at suboptimal solutions.

Tuesday, April 23, 2019

Evolution of energy production adapted for RNA world in a "pre-RNA world"


Most of the metabolic processes are today driven by enzymes, i.e. proteins. This was known long before the genetic systems, with transcriptions and translation were discovered. Today we know that genetics is necessary for protein synthesis, but in the first half of the twentieth century a common thinking about molecular biology was that proteins could somehow self-replicate. Most scientists today agree that that is not taking place and has never taken place. But there are still some strange hypotheses claiming that such processes in early life periods existed, or that proteins could somehow spontaneously appear in specific sequences.

William Martin and Michael J. Russell have postulated generation of energy in the form GTP or ATP, and they have formulated this suggestion:
"Thermodynamic considerations related to formyl pterin synthesis suggest that the ability to harness a naturally pre-existing proton gradient at the vent–ocean interface via an ATPase is older than the ability to generate a proton gradient with chemistry that is specified by genes."

They have suggested that specific peptide chains survive better than others, and that enzymes were formed from these. This suggestion is most probably not possible at all, and it is totally unnecessary, because life got its energy for formation and handling of RNA molecules in much simpler ways. They suggest that large parts of the metabolic apparatus was already present, based on these, when the first RNA molecules appeared. A lot of enzymes are suggested, forming the reverse Krebs cycle and the Wood-Ljungdahl pathway. But the most improbable and quite teleological suggestion is that the highly complex membranous ATPase was present before RNA. This complex changes an RNA molecule from a high energetic to a low energetic variant or vice versa. The high energetic variant was on the young earth readily present as pyrophosphate and other phosphate chains. RNA molecules were built from these.

Sunday, April 23, 2017

Organellogenesis


With the traditional theory all organelles were created locally, by a process called "organellogenesis". The endosymbiosis process introduced an alternative way that organelles could be 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 processes have been performed once, maybe with the exception of chloroplast genesis, which may have been performed twice. And they were completed more than a billion years ago. The internal incidents of organogenesis may have been slow, iterative processes, but the endosymbiosis events  (incident/event? incidence) 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 were 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 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 (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

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. 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.