Frank Abernathy on the Evolution of the Eukaryotic Cell, the Origin of All Complex Life

Popular science portrays evolution as a free for all in which organisms kill each other off until there is only one left standing. In reality, natural selection creates a delicate balance in which organisms evolve to be in a state of harmony with each other. Organisms that get too greedy simply kill off their prey or hosts, and ultimately end up weeding themselves out of the evolutionary tree.

Symbiosis, when organisms benefit one another, is an important part of evolution, but Dr. Frank Abernathy takes it a step further. He believes that the cell nucleus is actually the result of several different organisms joining together to form a single entity. While his theory hasn’t won the approval of the mainstream biological community, he has compiled some convincing evidence to argue his case.

With a doctorate from Ohio State University, and several scientific publications that have received dozens of citations, he certainly has the academic clout to make controversial hypotheses. Surprisingly, his easily falsifiable theory hasn’t received the funding necessary to test it, a situation that I hope changes soon.

The Interview

Thanks for speaking with me Frank.

I appreciate your interest in my views on this subject, Carter. Thanks for taking the time to interview me.

You’re very welcome.

Okay, I’d like to dive right in and start talking about your most ambitious research, which is about the evolution of the eukaryotic cell. For those who aren’t aware, there are two types of cells. The primitive prokaryotic cell is little more than a jellylike substance containing genetic material, wrapped in a cell membrane. Bacteria follow this model.

The eukaryotic cell, on the other hand, contains a nucleus and several other complex structures inside of it, called organelles. So Frank, before we get into your theories, I’d like you to discuss why the evolution of the eukaryotic cell is so important.

Literally tons of paper have been printed on the subject of the eukaryotic cell. The amount of data and information accumulated on its structure and function have jumped by staggering amounts. This is thanks in large part to a parallel growth in technology that allows cells to be studied virtually, on a nanoscale, in real time.

To understand the structure and function of the eukaryotic cell is to understand ourselves. In the physical sense, that is what we are: a complex community of eukaryotic cells, all working together for the benefit of the whole. That whole being our living bodies.

That’s an interesting way of putting it, thinking about our bodies as a community.

Communal living is the norm, not the exception, in biological ecosystems. Look at termites, ants, bees, coral reefs, wolf packs, wetlands, even the entire ocean. By definition, an ecosystem is a collection of biological organisms all interacting with one another in a delicate balance. This maintains the ecosystem and enables it to flourish. When an ecosystem breaks down because of invasive species or environmental insult, a death spiral begins and extinction soon follows.

Good point. Popular science spends a lot of time talking about how brutal nature is, and it certainly can be. But there is a great deal of cooperation happening as well.

Now, the subject of your dissertation is closely related to something called endosymbiotic theory. This is the theory that some or all of the complex structures that exist inside of the eukaryotic cell came from the combination of two or more prokaryotic cells.

It wasn’t long ago that this was considered a fringe idea, but mainstream biologists have opened up to the idea in at least one instance. The mitochondria, which generate the chemical energy for the modern cell, are now thought to be a separate organism that was absorbed into a larger cell. I’d like you to discuss why this has become mainstream science and why it might have occurred in the first place.

The endosymbiotic theory dates as far back as the late nineteenth century when a French botanist, by the name of Andreas Schimperm noted that chloroplasts within a plant cell divide in a fashion similar to cyanobacteria. Since 1967, the endosymbiotic theory has been aggressively promoted by Dr. Lynn Margulis to include not only mitochondria and chloroplasts, but also organelles of locomotion like cilia and flagella. Dr. Margulis is primarily responsible for the mainstream acceptance of the endosymbiotic theory as it pertains to mitochondria and chloroplasts.

To understand why endosymbiosis has occurred can be best illustrated by human interactions. Humans thrive best when they are cooperating with one another as opposed to destroying one another. Humans are social creatures. Most humans do not live by themselves. They form families, tribes, villages, cities, states, countries, and global networks. These are hierarchical structures of communal interaction. The same thing applies to many businesses. Those which are most successful do not utilize the “jack of all trades” business model. They cooperate and interact with other businesses that specialize in certain functions.

Symbiosis comes in a variety of “business models.” There is predation, which is basically war. One side wins, the other side loses.

There is parasitism or infection in which one side benefits at the other side’s expense. Think fascism, oligarchies, or monopolies. Note, however, that the most successful parasite is the one that does the least damage to its host.

There is commensalism in which the host and its symbiont live together and the symbiont neither harms nor helps the host.

Finally, there is mutualism, where both the host and the symbiont benefit from the relationship. Of all these “business models,” the one with the most synergy is mutualism. Think of where humans would be today without mutualistic activity involving division of labor. There would be no language, no villages, no farms, no art, no medicine, no inventions or technology of any consequence.

Humans did not invent mutualistic synergy. Civilization is merely an extension of the driving force behind humankind’s own origins.

In short, think of the eukaryotic cell as a confederation of semi-autonomous businesses, all working together for the common good. My focus, however, is on the eukaryotic nucleus which contains almost all of the genetic material of the cell. Think of the nucleus more like a federation or corporation. It formed from several business mergers that eliminated duplication of effort (downsizing).

This is a great analogy. Despite all the advertising to the contrary, it’s clear to almost everybody that businesses are primarily self-serving entities. They act in their own self interest. If they didn’t, they wouldn’t last long. And yet we do see businesses forming alliances with one another and creating “symbiotic” or “synergistic” relationships. I suspect that the reasons for this go deeper than superficial analogy, and may actually have similar root causes.

On a related note, I’d like to ask a more broad question about the way you think about evolution. I am drawn towards Geoffrey Miller’s work because of his emphasis on sexual selection, an aspect of evolutionary theory that seems like it could use more attention. He also uses a business analogy, comparing sexual selection to a good advertising campaign.

But if discussions of sexual selection are rare, discussions of symbiosis seem almost nonexistent. It’s often discussed as though it is little more than a footnote in evolutionary theory, an interesting oddity that only distracts from the pillars of evolutionary theory: natural selection and random genetic drift. Your business analogies above demonstrate beautifully why symbiosis doesn’t conflict with the idea of the “selfish gene,” so why is it that discussions of symbiosis seem so rare? Outside the evolution of the eukaryotic cell, do you think that symbiosis plays a more important role in evolution than most scientists are willing to currently accept?

Genetic drift or random mutations are generally considered to be followed by natural selection which sorts out bad mutations from beneficial ones.  Most biologists tend to think of genetic drift in terms of single point mutations or small deletions or additions to the genome. Massive changes in the chromosomes are also known to occur but are almost always 100% lethal. However, in biology, as in horseshoes, almost always is not good enough, especially when dealing with geologic time scales.

Symbiosis in all its forms is nature’s way of experimenting with the gene pool, i.e., natural selection. Those relationships that provide a selective advantage to the gene pool under a given environmental condition are those which are retained and passed along to subsequent generations.  Most scientists would agree that symbiosis is not only very important, but absolutely crucial in the dynamics associated with natural selection. The controversy about symbiosis arises with regard to the inner workings of the cell nucleus, whether prokaryotic or eukaryotic.

For example, prokaryotic nuclei are generally circular in structure and their genes are arranged in linear groups known as operons. These work together to bring about a certain desired result like the breakdown of a particular sugar.

To accomplish this, several genes are responsible for producing enzymes that break the sugar down sequentially. The promoter, or “master switch,” of the operon transcribes all of the genes within the operon into another format, called RNA. This could be in response to the presence of the sugar in the cellular environment, for example.

The RNA is used to generate the proteins themselves. Gene 1 is used to make  enzyme 1 which begins the process of sugar breakdown. Attached to gene 1 is gene 2 which generates enzyme 2 that breaks the sugar down still further, and so on.  It is a very compact, elegant system of genetic control. When the sugar is gone, the operon ceases to transcribe RNA, and the enzymes are eventually broken down and recycled for reuse in other proteins.

The situation in eukaryotes is very different. There are no operons containing linear stretches of genes devoted to the breakdown of particular substances. Instead, the genes are broken up into segments called introns and exons. The introns represent some of the junk or selfish DNA you have referred to before. The exons are fragments of genes that have been disrupted by the introns. How did such a complex system of gene regulation ever come about? Why is it so different from the prokaryotic model?

One possible answer is via endosymbiotic events.  An intron is inserted into a contiguous gene via a virus using an attachment site as the insertion point. The final product is one intron flanked by two exons. In classical biology this expanded piece of DNA would be represented as a linear piece of DNA composed of a central region, the intron, flanked by linear exons.

Possible circular DNA inside a eukaryotic cell

 

In my models, the intron is in fact a circular piece of DNA that  is plugged into an attachment site within the original gene. It may even carry a foreign exon within it that modifies the functionality of the original gene.

Insertion of foreign genes into prokaryotic DNA by viruses occurs all the time in bacteria. An explanation for how this might occur is shown in greater detail at the website: http://eukaryotes.info, figures 27, 28, 29, and 36.

It is well known that retroviruses come and go within our nuclei on a regular basis. In fact, one such insertion may be responsible for the introduction of live birth from egg laying ancestors by reducing the immune response of the mother to the embryo.  Numerous examples of endosymbiosis abound within the literature. What some biologists call infection, could be the beginning of endosymbiosis. In fact, amoebae can become infected with bacteria and if left to fend for themselves, most will die. However,  a few may survive and in fact become dependent on the bacteria for survival.

This seriously changes the way that I think about DNA. You are saying that our genetic code is full of DNA from viruses that have infected it, and that this is accepted mainstream science. That alone is very interesting to me.

But what you’re saying is that these infections, called introns, are not linear. They are circular, like the DNA that we find in viruses and bacteria. You are also saying that many of these infections could have proven beneficial, similar to the random mutation that can occasionally prove beneficial. If this is true, it means symbiosis played a very important part in the evolution of the eukaryotic cell, the cell found in all multicellular lifeforms.

You mentioned something that surprised me, which is that most scientists agree just how crucial symbiosis is to the process of natural selection, even if they don’t agree with your theory regarding symbiosis in the creation of the cell nucleus. I’d just like to point out how different this is from the popularization of evolution.

When the word evolution is brought up, most people think of “survival of the fittest,” but you’re saying that one of the most important events in evolutionary history was the result of species with completely different genetic backgrounds working together. How and why would this occur?

I believe I have already answered this question for you. However, I will give you another example. Why is inbreeding illegal in this country?  The answer is that continued generation of closely related humans brings out hidden mutations that can have disastrous consequences.

Generally speaking, the most successful organisms are those with the most diverse genomes.  In short, mutts trump blue bloods. This is the very reason sex was “invented.”  So diversity within the eukaryotic nucleus generates its own synergy with regard to evolutionary fitness.

Good point. And this is another analogy that carries over quite well from a business perspective. “Diversity” of thought is definitely being promoted as beneficial for businesses that want to survive in today’s competitive market.

I’m glad that you brought up the evolution of sex. What sex allows us to do is combine adaptations together that would otherwise have gone their separate ways. This is absolutely vital for the emergence of complex life. It strikes me that your theory bears a strong resemblance to sex, since you are talking about adaptations from different sources being combined together in one place: the cell nucleus. Is it possible that nuclear endosymbiosis has something to do with the origins of sex as well?

I would take it one step further back. Endosymbiosis and ectosymbiosis may be responsible for the process of mitosis or cellular division. You might want to check out figures 30, 31, and 37 at the website to see how this might have occurred. Once mitosis was established, meiosis or the development of sex cells could have emerged later.

I suppose bold claims like that are part of the reason why many in the scientific community see you as a threat. Still, I think that it is this kind of spirit that is vital to innovation in the scientific community. Intellectual rebellion is incredibly important, as long as it is tempered with a need to test theories against reality.

There are two very important elements that make up good science. A scientific theory needs to be supported by empirical evidence, and it needs to be falsifiable. A theory that can’t be proven wrong is effectively useless as a predictive tool. So, what evidence have you accumulated to support this theory, and what kind of new evidence could potentially falsify the theory? Does it make any predictions which haven’t already been tested?

Most of my evidence has been accumulated from the works of other investigators: another example of synergy.  All reputable scientists do this. I have listed some recent references of other works on my blog at http://evolution4.wordpress.com. A far more extensive list of references can be found at my website at http://eukaryotes.info or in my dissertation which can be downloaded from my blog.

In terms of my own research, a lot more work remains to be done. I have provided evidence to suggest that the eukaryotic chromosome is not a simple, continuous linear strand of DNA but is comprised of a hierarchical structure of circular elements that reveals how the chromosome evolved from complex endosymbiotic events involving circular DNA such as that found in most bacteria and viruses.

These hierarchical circular elements can be easily visualized under the light microscope, the electron microscope and by scanning electron microscopy. Furthermore, when they are stained with a fluorescent dye, acridine orange, they glow green under UV light. This suggests they are loaded with DNA.

Falsification is very simple and straightforward: Simply regenerate these circular elements from eukaryotic cells and perform in situ hybridizations to determine their composition.  I believe they are composed of chromatin, which is a combination of DNA encased in protein and other biochemicals.  These other biochemicals may include lipids and RNA as well as contractile proteins like actomyosin, all of which can be easily verified with present day technology.

So the elephant in the room is simply this: Why hasn’t this been done? If the funding were available, I would be working on this in a heartbeat. Instead, I continue to search the literature for supporting documentation.  You would be amazed to find the level of indifference, dismissal, or outright hostility that mainstream science has shown in regard to understanding something anyone can see for themselves under the microscope.

If it’s true that scientists are simply refusing to test a falsifiable theory, that’s not encouraging to hear.

No, it is not. Frankly, I have been appalled at the complete lack of interest by the scientific community regarding the concepts I have presented to you. Science is supposed to be about discovery, not covering up what fails to support cherry picked data validated by reams and reams of more cherry picked data.

I sincerely hope that your theory is tested in the laboratory. Preferably before you die, as these things often seem to go.

In any case, let me try to restate your argument. The idea here is that the genetic code of the eukaryotic cell is a hybrid of the genes from several different organisms, including viruses and bacteria. You have discovered circular objects under a microscope which display many of the characteristics of circular DNA, something which is found in bacteria and viruses. If you can verify that this is what those objects are, your theory will have some strong experimental evidence behind it. If not, it means that your theory would need to be scrapped or heavily modified. Is that correct?

Yes.

That seems fairly straightforward to me. You’ve developed a falsifiable theory that can be tested in a laboratory. That’s how science is supposed to work, at least from the perspective of a non-expert such as myself.

In any case, your research about cell death is especially interesting to me. In many organisms, cell death is a highly organized process called apoptosis. This is when the cell seems to literally disassemble itself in a very controlled manner. In contrast, necrosis is when unexpected cell death occurs as a result of injury or something similar. What is it about apoptosis that supports your theory?

Are you familiar with the old “saw,” “ontogeny recapitulates phylogeny?”  This means that the development of the individual from conception to birth seems to emulate the evolutionary transitions that occurred from single cells up to complex multicellular organisms.

In my opinion, apoptosis recapitulates phylogeny in reverse. The cell, or more specifically, the nucleus, is being dissembled back into its more primitive components.  What I did with my research is capture moments in time during this disassembly, and throughout the cell cycle, by interrupting apoptosis. This revealed intermediate structural components containing nuclear DNA.

Why would the cell go to such lengths to sequester and destroy DNA in such an energy-intensive and complicated manner?  Again, the answer is simple: this DNA is genetically dangerous to nearby cells because it is lipid encapsulated and capable of fusing with these cells. It can behave much like a virus, reincorporating back into their nuclei using the same DNA attachment sites that united the original endosymbionts in the first place.

So what you are saying is that when a cell undergoes “planned death,” its genetic code is carefully disassembled and picked apart piece by piece. You argue that this is done in order to prevent the DNA from being spread into the nuclei of other cells. This implies that it is easy for DNA to be spread from one cellular organism to another, which strongly supports your theory. What is the more conventional explanation for the existence of planned cell death? Why do you believe your explanation is more satisfactory?

The conventional explanation for apoptosis is the same as mine: loose DNA is dangerous to other cells because of the possibility of incorporation into the genomes of other cells. There are a variety of mechanisms to explain how such DNA may become inadvertently incorporated. My explanation here is just one of them.

Huh. In other words, mainstream biologists don’t dispute the idea that DNA can easily be spread from one cell to another. Interesting.

Okay. You’ve been talking a lot about linear versus circular DNA. What is the difference, why is it important, and what does it imply about the origins of complex life?

Linear DNA is very susceptible to exonucleases, enzymes which chew DNA up from the ends.  In the case of linear viral DNA which enters a cell, these ends needs to be protected once the viral DNA is released from its capsule, allowing it to safely incorporate into the host DNA.

The most common way to do this is to simply circularize the DNA, eliminating both ends.  Most bacterial DNA is also circular. The question that remains is whether or not the eukaryotic chromosome is either a simple linear structure wrapped up on itself like a tightly wound rubber band, or if it is something more. Mainstream science assumes this to be a foregone conclusion: it is linear and nothing more.  I respectfully disagree with this commonly held assertion.

For a better understanding of the importance of circular DNA and its attachment sites, I suggest going to the blog and reviewing the models I have placed there. Even more models are available at the website and in my dissertation.

I believe complex life has been assembled from a process I call hierarchical endosymbiosis.  This process allows for a rapid buildup of genetic information using only a small number of integration events within a relatively short window of time (Cambrian explosion).

Think of how computers have evolved.  First there were transistors, (simple on/off electronic switches) then, integrated circuits, then complex chips, motherboards, and finally computer networks, including the web itself.  With one simple integration step (plug in) you can change the memory, storage and processing power of a computer by an order of magnitude or more.

In the nucleus, this plugging in phenomenon involves DNA attachment sites. Huge amounts of endosymbiotic DNA can be plugged into a simple nuclear DNA attachment site.

Let me see if I am hearing you correctly. You’re saying that mainstream biologists believe the eukaryotic chromosome is just a series of instructions that are read from beginning to end. But you are claiming that it is more like a network with many potential beginning and end points. You are also claiming that there is a structure to this network, where there are “master” pieces of code calling out to various “subroutines?” Does this sound about right?

Mainstream biologists understand that the eukaryotic chromosome contains master pieces of code calling out to subroutines, but their explanation for how all this DNA fits together physically is severely hobbled by an underlying dogma concerning the superstructure of the DNA itself.

This dogma assumes that each chromosome contains only one continuous uninterrupted strand of DNA. All research must fit this procrustean bed to receive publication in reputable journals and to generate subsequent grant money, both of which are necessary for career maintenance and mortgage payments.

This results in cherry picking or elimination of offending data altogether. Careers can be created or destroyed on this bed of dogma. Mountains of publications, all based on this wobbling house of cards, is used to further validate the dogma. Creationists have accused scientists of worshiping evolution as a religion. Sometimes the truth can be found in the least expected places. When the emperor has no clothes, somebody needs to say so.

You speak poetically when you are morally outraged. I have to say that you have certainly persuaded me into thinking that you have a valid argument worthy of investigation by the mainstream scientific community.

If your theory turns out to be a highly accurate description of the way the eukaryotic cell was created, what does this mean for all of us? Does it turn the current model of evolutionary theory on its head, or would that be overstating your argument?

It is commonly accepted that complex life evolved very rapidly from simpler forms of life during a relatively short period of geologic time (Cambrian explosion). Traditional evolutionary biology tries to explain this in terms of simple “transistor-type” mutations like gene duplications followed by point mutations. If my theories are correct, the implications for science and medicine could be profound because it means a major mechanism for regulating basic chromatin structure has been hiding in plain sight.

Mainstream science is also highly invested in the eukaryotic linear chromosome model. I will let you be the judge of whether my theories turn evolutionary theory on its head or not. However, their recalcitrance in reviewing my work or expanding on it speaks volumes about that very possibility.

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