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

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?

Tuesday, February 28, 2017

Does the number of genes in an organism relate to the cell membrane area?

The question about energy in comparison to information processing has been treated by Nick Lane. It is relevant to compare the two, because in the same way as a computer needs energy for information processing, life also needs a lot of energy for processing data. And in the same way as energy consumption in computers depends on the technology, life uses variable amounts of energy for the various types of information processing. There are two types of such processing that are extensively used in life: DNA transcription to RNA and translation of mRNA to proteins. The latter is much more complicated and power consuming than the former.

But Nick Lane has introduced a strange concept: energy supply per gene. This is strange because a gene does not consume any energy. The energy consumption of a computer is not either dependent on the number of programs installed. It is the use of the programs that consumes energy. It is exactly the same with life. DNA in the cells does not consume energy at all, except when it is copied. And DNA is copied only when the cell is replicated. Energy is used for gene processing mainly when proteins are produced. Lane also states that, as he says:
"What we discovered is that there is an extraordinary energetic penalty for growing larger. If you were to expand a bacterium up to eukaryotic proportions, it would have tens of thousands of times less energy available per gene than an equivalent eukaryote. And cells need lots of energy per gene, because making a protein from a gene is an energy-intensive process. Most of a cell´s energy goes into making proteins."
As we see, Lane agrees with me that it is protein production that is energy intensive. But there is no direct relation between the number of genes and protein production. Genes are read when they are needed, and there could be lots of genes that are not read at all, especially in multicellular organisms. To find out how Lane reasoned when he came up with the concept "energy supply per gene" I will make an analysis of the article by Nick Lane where I fetched the former citation. It was found in New Scientist 23. June 2012: "Life: Inevitable or fluke?", where he also says:
"At first sight, the idea that bacteria have nothing to gain by growing larger would seem to be undermined by the fact that there are some giant bacteria bigger than many complex cells, notably Epulopiscium, which thrives in the gut of surgeon fish. Yet Epulopiscium has up to 200,000 copies of its complete genome. Taking all these multiple genomes into consideration, the energy available for each copy of any gene is almost exactly the same as for normal bacteria, despite the vast total amount of DNA. They are perhaps best seen as consortia of cells that have fused together into one, rather than a giant cells. So why do giant bacteria need so many copies of their genome?"
He here refers to a giant bacterium with a lot of genome copies. The argument is that to serve a large membrane area, more copies of the genome is needed. He then turns this argument around, to say that the more genes there are, the more membrane area is needed:
"So the problem that simple cells face is this. To grow larger and more complex, they have to generate more energy. The only way they can do this is to expand the area of the membrane they use to harvest energy. To maintain control of the membrane potential the area of the membrane expands, though they have to make extra copies of their entire genome - which means they don´t actually gain any energy per gene copy.
Put another way, the more genes that simple cells acquire, the less they can do with them. And a genome full of genes that can´t be used is no advantage. This is a tremendous barrier to growing more complex, because taking a fish or a tree requires thousands more genes than bacteria possess.
So how did eukaryotes get around this problem? By acquiring mitochondria. About 2 billion years ago, one simple cell somehow ended up inside another."
He was thinking of the bacterium that he assumes became the first mitochondrion. He further says:
"As the mitochondrial genome shrank, the amount of energy available per host-gene copy increased and its genome could expand." 
He must have thought that by reducing their genome size, but not the membrane area, the mitochondria would have a lot of membrane area "free" to support the genes in the nucleus. But it is not true that the more genes there are, the more membrane area is needed. Energy is only needed if the genes are expressed by producing proteins. There could have been lots of more genome copies. And in fact, there are a lot more copies before reproduction by cell fission, when the number of copies is halved.

So his argument is based on a dependence that does not exist, but he makes it even worse by transferring the alleged relation to eukaryotes. In eukaryotes even the first relation does not exist. There is no need for extra gene copies to serve more membrane area, because while bacteria express their genes directly after reading them, which gives limitations e.g. due to available volume. Eukaryotes stores a copy for multiple use, as mRNA is transported to where they are needed.

In that respect eukaryotes work more like computers do. Before a program is run it is copied from the disk to faster memory, where it can be run many times. An analogy to bacteria would be to execute the program directly from the disk. Then multiple disks would be needed to have enough processing capacity.

To show that eukaryotes really utilize the freedom of repetive expression of genes, I will refer to CELL BIOLOGY BY THE NUMBERS, which shows by an example that an eukaryote produces 10 times as much protein per mRNA. In addition we must of cause also count the extra limitation in bacteria when transcription rate is limited to the expression rate. But it seems that there is not a large difference in the speed of these two processes, also according to CELL BIOLOGY BY THE NUMBERS.

When Lane says that "the more genes that simple cells acquire, the less they can do with them. And a genome full of genes that can´t be used is no advantage.", then it is true under the following assumption: All genes should have a certain amount of expression to have a right of existence. He argues that "a fish or a tree requires thousands more genes than bacteria possess". This is correct, but here he compares to multicellular organisms that have a lot of genes that are expressed in certain cell types, and also genes that are used only in the development phase. The number of genes used in a certain cell under normal circumstances may even be less than in an average bacterium. What is interesting is however to compare bacteria to single celled eukaryotes.

Based on this NCBI source the average bacterium has 3000 protein coding genes and the average eukaryote has 10 000. If we assume that the ancient organisms had gene numbers comparable to what is in the lower range today, then we find an opposite trend. There are quite a few eukaryotes that have less than 100. On the other hand, very few of the sequenced bacteria have less than 1000 protein coding genes. Below 100 genes we hardly find any bacteria.

One reason there is today in average more genes in eukaryotes than in bacteria is that eukaryotes have a lot of variants of the same enzymes. This is much less common in bacteria, and if we did not count them, then the bacteria might have, also in average, had more genes than eukaryotes. That is because there are a lot metabolic enzymes that are not needed in many of the eukaryotes. They typically live in symbiotic relation with bacteria. We can just look at the vitamins that humans depend upon, but which are produced by intestinal bacteria. And when we are calculating the need for energy, then we should not count enzyme variants, because they are typically used under different conditions or, for multicellular organisms, in different cell types.

There is one more missing link in his argumentation. He argues that membrane area is needed because there is need for more energy. But that is true only for organisms that use membraneous electron transport chains in their energy metabolism. At anoxic conditions there is no need for such metabolic paths. All enzymatic reactions take place at substrate level, and energy supply is only dependent upon volume, not membrane area.

Lane also speculates how the first cells could have managed:
"The enzymes that powered the first life cannot have been as efficient, and the first cells must have needed a lot more energy to grow and divide - probably thousands or millions of times as much energy as modern cells."
Based on his conclusion about cell organization it is strange that he then assumes that life originated as bacteria. It would be much more according to his argumentation to conclude that life must have originated as eukaryotes.

While there is no relation between gene number and membrane area, the genome size may limit the reproduction time for cells. And even though there is no significant difference between gene number in bacteria and eukaryotes, the eukaryote size is normally very much larger. That is due to the non-expressed sequences, introns and spacers. But this is no limitation for eukaryotes. Actually, it is a limitation for bacteria, because they have only one position to start DNA replication. Eukaryotes have a lot of them, so they avoid this limitation.

Thursday, February 23, 2017

How to use the terms bacteria, archaebacteria, eubacteria, eukaryotes, prokaryotes, akaryotes

There are two types of life: eukaryotes and bacteria. And there are two types bacteria: eubacteria and archaebacteria. Eukaryotes are much more complex and contain a nucleus. Bacteria are alternatively denoted "akaryotes" to say that they do not have any nucleus. But also mature red blood cells are devoid of nuclei, and they are not bacteria. "Prokaryotes" has also been used as a name for bacteria, but that insinuates that they are older than eukaryotes, which we cannot know for sure. We do not need any of these confusing terms, but Woese created some confusion when he defined archaebacteria, eubacteria and eukaryotes as domains, and called them for short: "Archaea", "Bacteria" and "Eukarya". It is especially the name Bacteria that is confusing, because that is the same as what has traditionally been called eubacteria. It is not enough to use the capital letter to differentiate between Bacteria and bacteria. The latter is also sometimes used in the beginning of a sentence. In my meaning we do not need these confusing terms, and I will therefore only use the terms eukaryotes and bacteria, the latter consisting of eubacteria and archaebacteria.

OET, The Organelle Escape Theory

The Organelle Escape Theory is published here for the first time internationally. It was first published in Norwegian in Universitetsavisa. It is one of four possible sequences for the origins of eukaryotes, organelles and bacteria, as mentioned in my earlier blog post. There are many observations that have been used in support of the endosymbiosis theory. Most of them are based on similarities between organelles and bacteria. But there is no easy way to see direction from similarities, so based on similarities my theory is in fact supported equally with Margulis’ theory. The endosymbiosis theory has been interpreted to mean the occurrence of several events that were very improbable and occurred just once in history. But endosymbiosis is observed even today. That is in line with my theory, as it is fundamental in the theory that bacteria are commuting organelles that became more and more autonomous until they could survive without a host. In a few cases the process is not completed, however. E.g. some types of Rickettsia are still commuting organelles. But, as stated above, the theory is based upon missing evidence for the endosymbiosis theory as the only possibility.

Lynn Margulis and her endosymbiosis theory may not have been the scenario that nature followed

Lynn Margulis has been associated with endosymbiosis. She was not the first one to propose the idea. It was proposed several times in the period 1883 to 1927, involving Andreas Schimper, Konstantin Mereschkowsky and Ivan Wallin. None of them could prove the theory, and it was mostly rejected. It got new interest during the 1960s, however, as it was shown that these organelles contain DNA.  Hans Ris was the first to re-evaluate the idea,  but also Lynn Margulis became very interested in the theory. In 1967 she published an article in the Journal of Theoretical Biology. Concurrently there was also an article in Nature by Jostein Goksøyr. It was however Margulis who became associated with the theory, and after a decade of aggressive fight it was accepted as more or less proven. Her victory was partly due to her stubbornness, but genetic research eventually came her to assistance.

The ruling theory at her time was that organelles were produced locally, and eukaryotes were generally held to be the product of bacteria. She pointed out that there are a lot of similarities between organelles and bacteria, and when DNA analysis became available in the 1970s, then it was shown that they are genetically related. The support for the theory increased, and there were several attempts to prove it. In 1982 Michael W. Gray and W. Ford Doolittle evaluated earlier attempts to prove the theory in the article:

"Has the Endosymbiont Hypothesis Been Proven?"

Here they showed that earlier attempt were not full proofs. Instead they made a new analysis based on two different kinds of chloroplasts (plastids). One of the central conclusions in this 42 page article is:

Taken at face value, this means that cyanobacteria and red algal plastids diverged from each other more recently than either did from Euglena (or Lemna) plastids and thus either that cyanobacteria evolved from plastids or (more reasonably) that the most recent common ancestor of Porphyridium and Euglena (Lemna) plastids was not itself a plastid, but an oxygen-evolving photosynthetic procaryote.  (my emphasis)

It is interesting to see that they mentioned the possibility that "cyanobacteria evolved from plastids". It does not seem that they gave this much weight, however. It is other reasons why they concluded that the endosymbiotic origin of at least one of the organelles was just nearly assured.

There are four possible sequences of the origin of eukaryotes, bacteria and organelles. Two of them have the bacteria as the original. In one of them bacteria became eukaryotes and these created organelles. That was the old theory. The other possibility is that bacteria were imported and became organelles. I illustrate them in this way:

 B->E->O Traditional theory

B->(O and E) Endosymbiotic theory

But eukaryotes could also be the original. In that case there is also two possibilities: They could have been reduced to bacteria, which subsequently created organelles. That is the theory proposed by Patrick Forterre and supported by Anthony M. Poole and David Penny, the thermoreduction theory. Another possibility is the one that Michael W. Gray and W. Ford Doolittle only mentioned as a theoretical possibility: that the eukaryote created both organelles and bacteria. The two possibilities are illustrated here:

E->B->O Thermoreduction theory

E->(O and B) Organelle Escape Theory, OET

I have called the latter Organelle Escape Theory because some of the organelles that were created got a commuting role, and among them there were many that became autonomous bacteria. OET, the "Organelle Escape Theory", which describes this scenario. It explains not only the origin of organelles, but also the origin of bacteria. The possibility mentioned above, that cyanobacteria evolved from plastids is a direct consequence of OET. When they say that this possibility is less reasonable, it is not based on any reasoning at all. I think it is very reasonabe. The conclusion of Michael W. Gray and W. Ford Doolittle should therefore have been that either the endosymbiosis theory or the Organelle Escape Theory is nearly assured. But if OET is chosen, then we do not have to say "nearly".

Monday, February 6, 2017


Neo-Darwinists believe that selection is a creative force that drives evolution. But there is a severe problem with this view. If there is some change that makes the organism better, then it will be maintained by selection. If there is a new improvement that can take place in one step, then that improvement will again be maintained by selection, and so on, until there is no more improvements possible. Evolution under hard selection pressure tends to stagnate at a suboptimal state. After a period at this state only deleterious changes are possible. There may be neutral mutations, but none of them lead to any improvement as the next stage, else they would have been tested already. What is needed for progressive evolution to proceed is a control system that can allow further improvement. By controlling selection this system can allow further trial-and-error. The key to progressive evolution is therefore the smartness of this control system. I have called it "the contra-Darwinistic system". Contra-Darwinism is not in conflict with Darwin’s theories, but I have called in contra-Darwinism because it is in conflict with the neo-darwinistic view that selection is a progressive force. By seeing selection as a maintenance force that has to be controlled to allow evolution, it is much easier to understand how biological systems can be improved to become very ingenious systems. And it is also possible to understand the creation of novelties in life. Contra-Darwinistic systems are present in various variants in different forms of life. Those that are most efficient are found in the organisms that have evolved in the most ingenious ways.

Evolution and intelligence

Intelligence is a result of evolution. That is a fact that nobody can deny. But was there some form of intelligence present already before the origin of life?  A lot of people prefer to answer this question with a "yes". There are a lot of different view on the question, but most of them belong to one of the groups "creationism", "Intelligent Design", "The Third Way" and neo-Darwinism.

All the various forms of creationism depend on a theistic force to drive evolution. Intelligent Design depends on a super intelligence that could predict everything so well that it could construct an initial form of life that would evolve according to readymade recipes stored in the cells of every organism. Lynn Margulis had another variant. She posited that bacteria forms an intelligent network. This network controls the evolution of all higher forms of life, i.e. eukaryotes, but also the conditions on the Earth surface. That follows from the Gaia theory that she launched together with James Lovelock. There is a group of scientists that have organized under the concept "The third way". Most dominating in the group are James A. Shapiro and Denis Noble. They have inherited a lot of Lynn Margulis’s thinking, probably also her bacterial intelligence theory.

Darwin did not refer to any intelligence, but he probably believed that life contains something that is not existing in non-life, and must have a theistic origin. He said that: "There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”

Neo-Darwinists do not believe in intelligent control of evolution. I do not know what they think about the origin, as that is not a part of their theory. But instead of intelligent control, they posit that selection in some enigmatic way controls evolution.

If there is something in nature that is reminiscent of an intelligence or could be seen as an enigmatic control system, then it is the "contra-Darwinistic system". It is present in nearly all forms of life, and the better variants of the system is found in organisms that evolve better, i.e. have the most innovative evolution.

Tuesday, January 31, 2017

Why was the modern synthesis committee so successful?

I think they found that if you want to spread a message to most people, then it must be simple. We see it also in Donald Trump’s strategy. Trump once said that: "The day I realized it can be smart to be shallow was, for me, a deep experience". By using very shallow argument based on just selection in combination with observation of changes based on sexual recombination the committee managed to have their arguments accepted by the general public. When they could not find factual arguments, e.g. when a paleontologist like Stephen J. Gould raised too difficult questions, then they used unfactual ones, as Maynard Smith in 1984 said about population geneticists: "...the attitude of population geneticists to any paleontologist rash enough to offer a contribution to evolutionary theory has been to tell him to go away and find another fossil, and not to bother the grownups." Such arguments are much like Trump’s arguments when he attacks other politicians.

There is no connection between allele frequencies in a population and new features in life. The former can take place without any mutations. It is adaptation, while the latter is the result of mutations. Adaptationists however try to imply that there are such a connection, by saying that microevolution results in macroevolution. That may seem quite logical. And it is logical if one with microevolution means small steps of evolution, but they imply that the adaptation that takes place without a single mutation is the same as microevolution. They used the changes of allele frequency that took place under the industrial revolution as a proof of microevolution.

But that is wrong. Those changes were pure adaptation. They could have happened without any mutation at all. It is about time we start telling people what a big lie that has been told by the modern synthesis committee. We should instead tell the correct story, i.e. how mutations can result in new features. But that story is much more difficult to understand. And as long as there are scientists like Richard Dawkins who tell the simple solution, people prefer to listen to them. Instead of listening to the true story they prefer stories that are completely wrong.

Tuesday, January 17, 2017


According to Wikipedia, at least for the moment, "symbiogenesis" is the same as "endosymbiotic theory". But that is not in accordance with Lynn Margulis´ use of the terms. She was the most prominent of users of both these terms, but when Wikipedia defines it in this way, by giving the common explanation of the term endosymbiosis to both there terms, then the real meaning of the word symbiogenesis will for many people remain unknown.

Symbiogenesis is in general a transfer of genetic information from one organism to another, e.g. a bacterium to a eukaryote. Endosymbiosis is the inclusion of a bacterium inside a eukaryotic cell.


Richard Dawkins opposes to the idea that randomness is an important part of evolution. He has eventually, after many years of critique from Larry Moran and others, accepted that there are neutral mutations, but he does not accept that they are of any use for evolution, just for genetic research. He sees evolution as predictable, which is a kind of teleology. Thereby his standpoint could be compared to those of his enemies, Intelligent Design followers like Michael Behe, creationists and Lynn Margulis. For Margulis the creation of novelty was about Lamackism, partly epigenetics and partly symbiogenesis. She held that the bacteria which according to her are the source of novelty in eukaryotes are intelligent. They together constitute a big intelligent network. This intelligence is partly used to create novelties, partly to control the status of the Earth surface. She cooperated with James Lovelock on this theory.

According to the blog "THE EVOLUTION LIST" Dawkins is not the only adaptationist that holds teleology as part of his philosophy:

One of the bedrock assumptions underlying both modern physics and modern biology is non-teleology: the assumption that natural processes do not include any teleological input. I personally think that this is wrong, and base my objection to this idea on Ernst Mayr's monumental book, Toward a New Philosophy of Biology, published in 1988. Mayr argued very persuasively that teleological explanations are entirely appropriate in biology insofar as they refer to the development and maintenance of living organisms. According to Mayr, both of these processes (and indeed all biological processes) are directed by programs (i.e. genomes, etc.) that pre-exist the entities and processes that they specify and regulate. In the jargon of the current debate, genomes and other developmental programs are "designs" for the assembly and operation of living organisms.

In this case the author, who is apparently himself a teleologist, holds that Ernst Mayr was one. There is an introduction to this post here.

What is "phenotype"?

Marleen raised the question whether or not introns belong to the phenotype. Her question in a comment on Sandwalk about a paper by E.V. Koonin goes like this:

"Isn’t it true that adaptions regard only the phenotype? Can we consider introns and their evolution as traits that are yes or no under selection?"

Wikipedia says about "phenotype: "A phenotype is the composite of an organism’s observable characteristics or traits...."
Further on it says:
"A phenotype results from the expression of an organism’s genetic code, its genotype,.."

Based on these definitions all components of the phenotype must be observable. Introns are not genotype, because they are not expressed. If we search for "extended phenotype", then we find Dawkins’ definition of behavior as phenotype. But if no microstructures are phenotype, then we would have to use a special terminology for microbiology.

I would see introns as phenotype.

Sunday, January 15, 2017

Richard Dawkins is creating confusion and misconceptions

The misconception that evolution is the same as adaptation was created by the "Modern Synthesis" committee. They posited that the mechanisms that control allele frequencies in a population are the same as the frequencies driving evolution of life, including speciation and creation of new features. Their theories were based almost exclusively on natural selection. Dawkins is presenting a theory in his books that is based only on selection, as he says that mutation rate should ideally be zero. Denis Noble is at odds with this theory, but his theory is no better. See my previous post for more information about the confusion that terminology is creating.

Tuesday, January 10, 2017

Evolution vs adaptation

The word "evolution" was in use long before Darwin. Even though he did not use it in his book, he is associated with the word when we talk about biology. The reason may be that he indirectly defined it in the last paragraph of his book, that ends with "evolved":

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.

"Adaptation" has been used as a contrast to evolution to denote the changes of organisms that scientists before Darwin, such as Lamarck, described. But these are changes exclusively within a species. They used the observations of such changing as a proof of species constancy, e.g. that dogs can change into highly different races, but still the species is the same.

But from around 1940 there was created some confusion of this terminology. Persons behind "the modern synthesis" used "evolution" to denote changes of allele frequencies in a population. These processes do not involve any novelty, i.e. no speciation and no creation of features. They are therefore adaptations, and no evolution. Some of these persons may have allowed mutations, but then just as a way to fill up the reservoir of alleles. Richard Dawkins, who is basing his writing on adaptation, said in the Homage to Darwin debate with Lynn Margulis that for eukaryotes the ideal mutation rate is zero.

The confusive terminology is therefore still in use, and due to the popularity of his books, this may give rise to misconceptions that should be avoided. You may find some background information in this site.


This is a new blog intended for discussing various misconceptions in evolution theories. I started the blog because I saw so many claims that I found not in accordance with common sense. We can know for sure that there are misconceptions, because several theories contradict each other. If you have found this page by Googling or otherwise, then you are probably interested in evolution, and you probably also want to identify common misconceptions. You have probably already visited other blogs with the same theme, but if not, I will present a list of the blogs that I have found most interesting:
Of these, the one that I find most useful is Sandwalk. Larry Moran is doing a wonderful job with Sandwalk. If you by chance have not yet discovered what a treasure this is, then you should try it out. Larry has been active with this blog since 2006, and I hope he will be active for many years to come. Beware of this one:
The author believes that evolution is controlled by some teleological program, that is in mystical ways constructed by selection.