Let me make this as simple as possible

Folks, I understand not everybody’s into chromosomes or how they’re put together. I get that. In fact, a lot of people are not that much into science…period! I get that as well. Science can be tough to understand, even for the best of scientists. So let me make this as simple as possible. Below is a diagram of what most biologists believe is the structure of chromosomes such as our own:

Classic Model of Linear Chromosome

It’s pretty basic stuff. A single chromosomal DNA strand is pushed together as loops which are, themselves, wound up into supercoils until it looks like a chromosome under the microscope. We won’t go into all the reasons for these assumptions here. You can read more about this in the blog.

Ok, enough of that. Now we come to another model (my model) which is about as different from the linear DNA model as you can get:

Circular Model of Chromosome.jpg

Don’t freak, just skip to the part where you see circles. Can you tell the difference in the two models? The classic model is a simple, glorified piece of string. My model is a complex set of circular chromatin structures, paired together to form a vast array. Ok, nuff said. Which model best explains the evidence shown below:

 

slide 6

slide 7

DNA 35 mm slides_Page_004 copy

Do these things look like strings to you or do they look like circles? Take all the time you need. All done? Good! I am going to go out on a limb and venture to guess that you think they look like circles rather than strings. So far, so good, unless you happen to be an extremely dogmatic DNA scientist who’s full of themselves or one that’s afraid of losing their job for stating the obvious. Don’t believe me? Go ahead, pull any biology book off the shelf and see what they have to say about chromosome structure, or for that matter, just do a Google search. They all say the same insipid, brain dead thing. Chromosomes contain a single linear strand of DNA. They base all of this on telomere theories which were constructed to explain how “linear” chromosomes replicate. They looked high and low for enzymes that could do the job they were looking for. They were so busy cherry picking data to fit their theory that they overlooked or ignored my research which is obvious to any two year old that understands basic shapes. This is a classic example of the emperor having no clothes on and all of his minions being too damn afraid to tell him so. Well, I’m telling him so, and I’ve been doing it for about 25 years now!

If you would like to help push chromosome research out of the 19th century and into the 21st century where it belongs (too late for the 20th), please contact me. I may be 69 and retired but I still have all my mental faculties and I realize how important it is to understand chromosome structure. It could even be a matter of life or death for some people! I can be reached at fabernathy@sbcglobal.net. Otherwise, I’ll just practice my piano, instead. I have played on cruise ships for free and gotten accolades from passengers and staff, but apparently I’m too damn old to work on one. Talk about ageism! Guess I’ll just stick to skiing, doing pushups, riding my bike, and aggravating my grandkids, instead; oh, and aggravating scientists too!

 

Posted in cancer, cell cycle, cellular differentiation, endosymbionts, evolution, Fallacies in science, mitosis, Stem Cells, virus | Leave a comment

Entitled Science

There was once a time when biological science was about unbridled exploration and discovery. Things got discovered, things got done. Nowadays, it seems to be more and more about tweaking or squeaking timidly by while scurrying about within the acceptable boundaries of established dogma. Stray too far and the mousetrap slams shut. I know discoveries are still being made along with advances, but that’s like running an eight cylinder car with only four of them working some of the time. It’s even worse than that: The damn car can barely get out of the garage; and when it does, everybody applauds. Biological science has become sclerotic, and that’s putting it mildly.

If you have been following my blog, you know I discovered something really amazing. I don’t know whether I was the first person to find these beautiful beaded circles or not but that shouldn’t be the point. I’m the first one with enough courage to actually talk about them. Everybody else just sweeps them under the rug or buries them so far into their publications it would take Indiana Jones to uncover anything. Ask any typical biological scientist about the circles I found and you would get any number of comments or reactions: I will list a few of them here:

  • Deer in headlights
  • “Those are really interesting” (yawn)
  •  “So you got circles, so what?”
  •  Deafening silence
  •  Complacency
  •  Defensive and reactionary
  •  Combative and territorial
  •  Smug, surly, self-assured arrogance
  •  Dismissive
  •  Petty jealousy
  • Tunnel vision, highly focused with filters on high beam, (see dismissive)

Remember, these people are biological scientists; which means they are supposed to be excited about scientific exploration and discovery, not afraid of it or angry because they, themselves, didn’t discover it first. The most damning indictment of biological science in all of this stems from the fact that I discovered these structures almost 23 years ago! In the interim, I have contacted many different scientists all over the world about my results, all to no avail. I have seen nothing in the literature that indicates anybody anywhere is following up on my research. (So much for the myth of peer review). Perhaps I should list these scientists here, in case you would like to contact them about their tepid “responses”.  It’s possible that Donald Trump is not terribly impressed with these kinds of attitudes and decided to do something about it. Who knows?

If you would like to get involved, please start by reading the two posts just under this one. It’s not as hard as you might think. However, if you’re still naive enough to think conventional scientists are going to do anything about it, think again. Remember, some of them have known about this for about 23 years now! Sometimes, you just have to take matters into your own hands.

Best regards,

Frank

Posted in cancer, cell cycle, cellular differentiation, endosymbionts, evolution, Fallacies in science, Life versus inorganic minerals, mitosis, Stem Cells, virus | Leave a comment

Questions?

I would like for this blog to become more interactive by inviting questions from people on particular topics. Remember, any questions you may have are probably on many other people’s minds as well. You may do so through the comments section or through e mail at fabernathy@sbcglobal.net. If there is an interest, I may try my hand at live streaming or some kind of chat. I’m sure there must be questions about a lot of things I have discussed and I am a teacher as well as a blogger. In addition, I would appreciate any information you might provide that might be relevant to the point of the blog as well. Together, we can all learn from each other.

Best regards,

Frank

Posted in cancer, cell cycle, cellular differentiation, endosymbionts, evolution, Fallacies in science, Life versus inorganic minerals, mitosis, Stem Cells, virus | Leave a comment

Would you like to help?

I have been getting lots of favorable comments on my blogs recently and I will go out on a limb by assuming the majority of them are “real”. Please understand I am an old school baby boomer who has a lot of trouble trying to keep up with everything the kids are doing online these days. Back in my day, I used a manual typewriter and lots of whiteout. In school, I actually had to go to the library to find most things out. As everyone knows, what is real and what is fake is becoming increasingly more difficult to discern. It certainly tries your intellect and forces you to do more research. Of course, nobody has enough time in the day to research everything posted on the web and that includes me. Having said all of that, let me explain the reason for this posting.

I sense that people like what I post as long as it’s not too arcane. However, the reason for all the postings is to draw people’s attention to the research I have done over the years, particularly at Ohio State University.  Assuming I accomplish this, I try to help them understand that my laboratory research came to a screeching halt about 25 years ago. Beyond that point, all “my” research was “dry” as opposed to “wet”, i.e., bench work was impossible so I did paper research instead, while I worked for a living. Actually, scientists should always do both, but in my case, I had no other choice. I have gone to great lengths to explain the fallacies behind “big” science and why coloring outside the lines of dogma is strongly discouraged and even censured.  It is much worse than mere prima donna ego bruising. Corporations discourage any research that fails to promote their products or machinations. In my case, I believe it is a prima donna territorial thing rather than corporate intrigue. In either case, the bottom line is still the same: censorship.

I have watched Neil deGrasse Tyson videos on Facebook where he croons eloquently about the virtues of science, the scientific method, and peer review. He sounds very much like a politician or salesman discussing the virtues of a particular political viewpoint. It all sounds nice, neat, sanitized,  and so right. In reality, it’s all rigged. People are mad about Trump cutting science funding, leaving the climate agreement, cutting social programs, etc etc.  Maybe he knows bad deals when he sees them. I didn’t vote for Trump or Hillary, but right now, he’s all we’ve got. So, I want to make one final statement here: Is there anybody out there in the blogosphere who would like to see me continue doing my research? If so, please send me an e mail at fabernathy@sbcglobal.net. Don’t just post a comment. If I see enough interest, I will post another blog about possible ways to go about doing just that, and yes, it will involve money, but not nearly as much as you might think. Otherwise, thanks for all your comments, real or otherwise.

Frank Abernathy, Ph.D.

Posted in cancer, cell cycle, evolution, Fallacies in science, Introduction, mitosis, Stem Cells, virus | Tagged , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , | Leave a comment

The plot thickens…

(Click here for the latest posts)

I have discussed “Thing one and Thing Two” in previous posts. However, I think it is befitting to talk about them some more, in light of how nuclear envelopes are put together. Nuclear envelopes are double membranes that encompass all of the chromatin within the nucleus. If you’ve been keeping up with my posts, you should know that chromatin is where all the chromosomal DNA is located. However, nuclear envelopes are not just spherical membranes or simple bags of DNA. They form tubular invaginations that form a complex network within the nucleus. If these tubules were released from a dying cell, would they look like this?

72

If so, how exactly is the chromatin arranged within them? Obviously, some of the tubules have empty spots where the contents have been completely destroyed. Others contain material that lights up just like DNA. Green color is intact DNA, orange indicates necrosis and/or apoptosis. These apoptotic bodies appear to be moving in a linear fashion along the long axis of these tubules until some of them exit to the outer tips. Apoptosis is programmed cell death involving the orderly sequestration and destruction of chromatin fragments. The question here is this: Are these apoptotic bodies randomly produced or do they tell us something about chromatin organization within the nucleus? Are they remnants of endosymbionts? (see last post under this one).

pic3pic13

This linear arrangement of discrete bodies can be seen in other forms as well (see above). Sometimes they are generated from circular structures (lower right). Do they have any connection to nuclear tubules within the nucleus? Nuclear bodies like cajal bodies exist as little DNA manufacturing plants within the nucleus and may provide a clue as to what constitutes an apoptotic body, i.e., something that must be sequestered and destroyed when it no longer serves a useful purpose such as during cell death. Note how these bodies all line up in a linear fashion, much like you see in mitotic chromosomes. This linearity may be a clue as to why geneticists still assume that the DNA itself is linear within chromosomes. However, the photomicrographs below fly in the face of such assertions.

In my last post, I mentioned an elephant. It referred to how bacterial chromosomes could be integrated into eukaryotic DNA when the nuclear envelope only allows very small molecules to pass through it via nuclear pores. That is indeed quite an elephant! However, these nuclear pores are not always present throughout the cell cycle. During the onset of mitosis, the nuclear envelope begins to disintegrate as the chromatin begins to condense into chromosomes. Nuclear tubules may be opened up at that point just like what you see in the first photomicrograph in this post where apoptotic bodies have migrated to what appear to be exit points. Such “exit” points may also be used as “entry” points as well for large chunks of foreign DNA to enter nearby cells, hence the need for apoptosis to avoid genetic corruption leading to cellular dysfunction and possibly cancer. In multicellular organisms like plants and animals, cancer must be avoided at all costs because it screws up the viability of the entire organism. Thus, foreign DNA must be kept out at all costs. However, in more primitive unicellular organisms, foreign DNA may have provided an evolutionary advantage over similar competitors by providing them with new kinds of “nuclear bodies” that enhanced metabolic function or allowed them to digest previously unavailable sources of food, etc. In these cases, the foreign DNA may have been welcomed to travel into nuclear channels where they attached themselves to an adjacent nuclear body, thus increasing the length of the parent chromosome. In fact, such nuclear upgrades may have allowed the development of specialized cells that function together as a multicellular organism. When a complete multicellular organism is formed, apoptosis comes into effect to prevent further entry of either outside DNA or nuclear body DNA released from adjacent dying cells.

Ok, so what is going on with all those circles of “DNA”? How do they fit into the picture of nuclear bodies? Well, sorry. You’ll just have to wait for the next post! Or you could start from scratch and read this blog from top to bottom.

 

 

Posted in cancer, cell cycle, endosymbionts, evolution, mitosis | 4 Comments

Sex isn’t the only way to get your DNA

There are three references that I added today. They, as well as others, can be found under the page tab called Additional References.

In this post, I would like to focus on the one about horizontal gene transfer. As stated in the reference, this is different from sexual transfer (also known as vertical gene transfer) because it does not involve parents.

Here is an excerpt from the article. If you wish, just skip on down to the next paragraph which explains it in simple english:

“Prokaryotes can exchange DNA with eukaryotes, although the mechanisms behind this process are not well understood. Suspected mechanisms include conjugation and endocytosis, such as when a eukaryotic cell engulfs a prokaryotic cell and gathers it into a special membrane-bound vesicle for degradation. It is thought that in rare instances in endocytosis, genes escape from prokaryotes during degradation and are subsequently incorporated into the eukaryote’s genome.” 

For those readers not of a biological scientific bent, let me explain this in plain english: Prokaryotes are bacteria, eukaryotes are cells like we have. Enough said about that for now. Note how this excerpt says the process of horizontal gene transfer in eukaryotes is not well understood. It goes on to suggest that it is possible gene donor cells like bacteria may be ingested via endocytosis and instead of being digested and “eaten”, somehow DNA from these cells manages to escape the process and enter the nucleus where it can hook up with the eukaryotic DNA. It provides no specifics on how all of this is done.

Now pay very close attention to what I am about to say here: For DNA to get out of a digested bacteria and somehow escape into a nucleus is virtually impossible. Its best chance of doing this is in the form of a plasmid which is a small circle of DNA that is little more than a naked DNA virus. However, cellular restriction enzymes will usually turn circular DNA into linear  DNA which will be completely degraded by other enzymes.  Horizontal gene transfer can be done via genetic engineering by flooding the cell with DNA and swamping out the cellular digestive enzymes, but this is artificial brute force imposed by humans, not the rule in nature. Viruses are really just plasmids with a protective coating that allows them to invade the nucleus without getting destroyed in the process.

So, the question still remains. How can some hapless bacterium or small eukaryote like a yeast or protist (think amoeba or algae) be ingested by a large eukaryotic cell and digested just enough to release fragments of its DNA such that they can be incorporated into the host DNA?  It can’t be done under natural conditions because the DNA needs to be protected in some way. This can happen if the bacterium or other cell simply invades the nucleus intact, just like a virus. Once there, it needs to find a mechanism to attach it’s DNA to the nuclear DNA if it is going to be replicated as part of the cellular DNA. Otherwise, it will simply be diluted out during the next cell division (see abortive transduction). How this could happen is the crux of this entire blog. Suffice it to say here that there is a DNA attachment site somewhere on the donor DNA that plugs into the host DNA, just like a virus. During subsequent cell replications, this donor DNA may get pared down to the bare essentials or completely removed based upon whatever desirable traits it provides to the host. Such is the basis for natural selection based upon environmental pressures.

Endosymbiotic memory

Ok, please don’t freak, I’ll explain, as I always try to do. I hesitate to go into great length about the term endosymbiosis because it has been explained in great length throughout this blog, so I’ll be brief here. Any cell that incorporates into another larger cell and survives the process becomes an endosymbiont. If it causes a disease in the process, it is a parasite. If it provides some benefit to the host, the relationship is called mutalism. When I say endosymbiotic “memory”, what I mean is that even though the original cell donor may have been pared down over time to the point that it can no longer function as as an independent cell, it still “remembers” where it came from. During the course of host cell death, this memory may be invoked much like a virus that emerges from dying bacteria or eukaryotic cells (see temperate phage). In other words, the donor DNA tries to “escape” from the dying host cell and become independent once again. In the case of temperate viruses, it works because they still have the means to form a new virus particle. In the case of a degenerate endosymbiont, this results in a separation of the donor DNA from the host DNA, much like a virus, but it does not have the capacity to form a new donor cell because it no longer contains all of it’s original DNA. Such DNA may have the potential to escape from a dying cell and enter a new host cell at some random attachment site. By doing so, it can corrupt the genetic machinery of the new host cell and even impose its “will” upon it by forcing it to replicate in order to replicate the degenerate endosymbiont. In the human body, as well as in others, this could lead to uncontrolled cellular replication or cancer. Our cells use a remarkable process called apoptosis to sequester DNA during cell death so that it can be safely degraded.

Notice the elephant in this post? I never talked about how a bacterium could penetrate the nuclear envelope using nuclear pores that are far too small for this to occur. Maybe I’ll do that in the next post.

Posted in cancer, cell cycle, endosymbionts, evolution, mitosis, virus | 3 Comments

Does apoptosis recapitulate phylogeny in reverse? (revisited)

This is an old post from May, 2011. I didn’t include any images before, so I thought I would try to do a better job this time.

You can blow a house to smithereens using explosives or you can carefully deconstruct it to avoid collateral damage. Necrosis is the former, apoptosis the latter.  The intricate apoptotic  pathways used to safely deconstruct cells are widely documented. You can learn more about them by visiting these images. The question that remains is why such a highly sophisticated, energy expending process ever came into being in the first place. Shown below is an example of cellular necrosis with blebbing occurring. 1 = denuded cell nucleus, 2, 3, display advancing nuclear swelling with blebs, vesicles and filaments. This process is more chaotic than apoptosis and involves random degradation of nuclear elements.

pic2

So you can now compare and contrast necrosis and apoptosis. They seem to be opposites of one another, chaos versus order. However, things are not always as simple as they sometimes seem. For example, just what is going on here?

2

At first glance, this looks some some form of apoptosis. There are definite discrete particles here that are being released in the form of beaded circles with different sizes. One of them (far upper left) even has a centralized bead associated with it. Now, if were to show this to any typical scientist studying apoptosis they would ask you one simple question: “What in the hell is this?”  They would ask you that because they would have no clue what it is themselves. Therefore, what you are looking at here is something quite distinct from apoptosis as scientists define it. You could say this is an aborted kind of apoptosis because these structures were forced out of the dying nucleus using hydrochloric acid. So a number of questions should begin to stir in the minds of the readers. How did these things form, and what form were they prior to acid treatment?

In the literature, you will find images that show a roughly similar rosetting  effect within the confines of a defined membranous structure; but nothing comes close to the display of beaded circular and irregular “strings of pearls” seen in the photomicrographs shown in this blog. In addition, these beaded circles come in a range of sizes that may include several orders of magnitude. Furthermore, the beads seem to be interconnected by something beyond the resolution of light microscopy. So what exactly is going on here? I believe these images are showing a hierarchical deconstruction of the DNA superstructure based upon how it was originally constructed throughout the course of evolution.  Envision a house made up of bricks “A” which are composed of bricks “B” which are made from bricks “C”.  In this scenario, the house can be deconstructed in three ways: 1) Reduction to bricks A, 2) reduction of bricks A to bricks B, and 3) reduction of bricks B to bricks C. The result is three levels of bricks in various stages of deconstruction. Why is apoptosis so carefully regulated to insure these “bricks” get completely destroyed? Is it because they may be more than just simple, random chunks of DNA cut off from the chromatin? I think we can all agree that apoptosis is far too sophisticated a process to be so mundanely trivialized. An alternative explanation is that these “bricks” are genetically dangerous because they are capable of self-replication. In other words, at one point in time they belonged to an independent organism. Without careful deconstruction prior to release, they are genetic “bombs” looking for cells in which to reinsert themselves, causing massive mutations and cancer.

Posted in cancer, endosymbionts, evolution, virus, What are they? | 7 Comments