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

Sunday, March 12, 2017

Origin of sex

With the traditional theories, as eukaryotes are held to descend from asexual bacteria, sex has to be invented in some way or another after these organisms had got a nucleus. Nobody has presented a believable theory for how sex could have originated from non-sex. There are however theories on maintenance of sex. These theories explain why sex has not been lost. The reason there is a need for such theories is that loss of sex seems to have some benefits, and there are species that practice sex only very occasionally.

With the Organelle Escape Theory there is no need for any invention of sex. If eukaryotes were the original, then cell fusion was in place very early, and it is quite natural that there would be different variants that would be maintained. Reduction of the number of sexes would however be natural, and the most probable end situation is reduction to two sexes.

Thursday, March 9, 2017

Is Kahneman’s book "Thinking, Fast and Slow" relevant for evolution theories?

Yes it is. Daniel Kahneman defines fast thinking as the kind of thinking that is most efficient when you are under an attack, in a traffic situation etc. Fast thinking focuses on only a part of the problem in order to find a good enough solution fast. In other situations one should rather prefer slow thinking in order to be sure the right solution is selected. But he showed that it is easy to be fooled to think too fast also in situations when there is more than enough time available for thinking. Highly relevant variables or processes may be seen as unimportant, but only thorough thinking can determine if that is true. He had seen that the distinction between the two ways of thinking is relevant in his profession, economics. But I will show that there are also lots of examples of too fast thinking in evolution theories. I will here mention just three of them:

  1. The modern synthesis committee made a decision to see adaptation of allele frequencies in a population as controlled entirely by selection. That may have been a correct decision, but they also posited that evolution, i.e. speciation and creation of new features, was a direct result of such allele frequency changes. But that is a simplification that makes the conclusion incorrect. New features may only be created through the right series of mutations. 
  2. Margulis had to fight for a decade before her theory was accepted, and then one should expect that the thinking was thorough enough. But as I have shown, those that evaluated the theory and found that it was (nearly) proven did not evaluate all the other possibilities that could explain their observations. 
  3. Nick Lane presented "proofs" for a theory that increase of membrane area is needed to support more genes. I have shown that there are many missing links in his arguments. 

Sunday, March 5, 2017

Introns explained with the Organelle Escape Theory

I have always been very interested in finding out how things work, and life is the most interesting. A part of understanding how things work is to understand WHY it was built that way, how the designer was thinking when he decided that solution. For life there is no designer, instead understanding evolution is of the greatest interest. A part of understanding evolution is to understand how the cells have evolved, especially the relation between eukaryotes and bacteria. Two important discoveries that were both made in 1977:

  1. It was found that there are two distinct types of bacteria
  2. It was also found that most of our DNA is not expressed, specially that there are long sequences called introns in our genes that are spliced out before the genes are used to produce proteins
This was about the same time that Margulis’ endosymbiosis theory was accepted. I was speculating during the 1980es how all these discoveries could work together, and it was especially the finding of introns exclusively in the nucleus of eukaryotes, not in any bacteria and not in any of the eukaryotic organelles, that was an enigma. But I was convinced that this was a crucial fact to use in the search for the solution.

It occurred to me in 1994, while reading an article by Leslie Orgel, that eukaryotes are a better candidate for the original organism than the bacteria. They have much more relics from the RNA world, and they are still using them actively. One example is the spliceosomes, that splice the introns, another is the ribosomes, that are used to translate mRNA to proteins. They are used also in bacteria, so I figured that the eukaryotes could somehow have filtered out what was most essential and given this to the bacteria. There is one natural process that removes introns. That is the splicing process that takes place in the eukaryotic cytosol. If the first organelles were produced in their host, than they would naturally use mRNA from the cytosol. A DNA chromosome could easily be produced by reverse transcription from mRNA and a linking process. If bacteria are based on organelles, then they would naturally have no introns. We can say that the organelles worked as a filter that removed all spliceosomal introns, also for their descendants, the bacteria.

There are two conflicting theories for intron evolution, introns-early and introns-late. The former is the most logical. The latter is more or less a construction to match with bacteria-early. It assumes that spliceosomal introns can be created. But there is no known way that could happen. Introns type II can be inserted, but they are of another kind. With OET the most logical solution can be chosen.

I was convinced that the Organelle Escape Theory was the right explanation already in 1994, and I have become more and more convinced since then. One example of an article that supports the theory that eukaryotes are older than the bacteria is one by Anthony Poole, Daniel Jeffares, and David Penny: Early evolution: the new kids on the block. Other observations that support my theory are the findings of organelles like hydrogenosomes and mitosomes. They are in conflict with the endosymbiosis theory.

With my theory eukaryotes would have very long time for evolution of the eukaryotic complexity. Introns serve as delimiters that define genetic building block. They have helped this evolution. 

Thursday, March 2, 2017

Are mitochondria needed for eukaryotes?

There has been a lot of articles the later years that conclude that eukaryotes need mitochondria to produce enough energy. The need for energy has been related to the number of genes. It is especially Nick Lane that has claimed that genes depend on membrane area. I have earlier shown that there is no such dependence for eukaryotes. It is true that under oxic conditions membranes are essential for energy production. But it also holds when there are other electron acceptors, e.g. iron ions present. Membranes are also useful when hydrogen can be used as an energy source, for reducing carbon dioxide. But when no such external electron acceptor or electron donor is available, then there is no need for membrane area for metabolism. Metabolism is then dependent of available volume for the enzymes, not membrane area. And there is no limitation to the size of cells, so under anaerobic conditions, provided there are metabolites available, eukaryote cells can be large if that is practical of other reasons.

It is correct that the mitochondrion is a key to producing much energy from each molecule of consumed glucose. But the membraneous structures that produce energy in mitochondria are voluminous, so there is not much difference between the energy yield per volume in anaerobic and aerobic organisms. In fact, the membranous processes have limitations, even in human muscle cells. They are optimized for aerobic respiration, but when we are lifting heavy weights, then our muscle cells will use anaerobic fermentation, producing lactic acid.

Fermentation gives higher effect, due to the full utilization of the cell volume, while respiration gives more energy per volume of fuel. So the difference is more about how much fuel is needed to drive the cells. It should also be added that the aerobic cells need a continuous import of oxygen, which is in itself a limitation factor.

There are in fact a lot of anaerobic eukaryotes even today, although the access to such conditions is limited. Some of these have other organelles or no organelles at all. The hypothesis is that all eukaryotes once had mitochondria. But if they were the key to supporting an eukaryotic cell organization, how could they then be lost?