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.

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Workplace Narcissism

I know this appears to have almost nothing to do with chromosomes or scientific research but everything in life is connected. Dysfunctional personalities are the bain of everybody’s existence, including scientists.  I’ve seen several posts about this subject. One in particular simply says to steer clear of them. This is great advice unless you happen to be employed by one or work with one. I’m sure the next piece of advice would be to quit your job and find another one. If you do that, you’ll be doing a lot of job hopping, and that doesn’t look good on a resume. Sadly, the best answer is to learn how to cope with them; which of course requires the ability to know one when you see one. The second step is to outsmart them by using their narcissim against them. (They’re not half as smart as they think they are). There is a number of approaches here, but one of my favorites is to make their lives more unpleasant to be around you than for you to be around them. Do not reward their narcissism with a desired reaction. Instead, treat them like they are mental and do so in a very condescending way. Of course, this doesn’t work with a boss or one of their mouthy pets. In this case, you need to be subtle and passive aggressive. Punish them in a way that they can’t really put their finger on it. You know, be as stupid as you can get away with. If and when they back off, your level of intelligence can suddenly rise to a newer and more productive level as a means of rewarding their behavior. If they backslide, you can always get stupid again.
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The Human Population Time Bomb

I have talked about human population in other venues, but when I saw David Attenborough’s video on Facebook, I had to share the link here. Let me say this about such an incredibly important topic: Many people have been brainwashed into thinking they must have as many babies as possible, even to the point of suffering and deprivation. Apparently, the Catholic Church is one of them but Islam is right up there with it. The Mormons and Evangelicals are also included, as well as others I will never know. I have had first hand experience with an individual who was otherwise a brilliant doctor, but was completely brainwashed when it came to having children. My best guess is that she was a catholic. In my humble opinion, and it is only my opinion, child bearing should be a privilege, not a right, and certainly not an entitlement worthy of demanding other people’s money through taxes, charities, and guilt. It seems most of the people having children are those who can least afford them and they seem to be from the shallow end of the gene pool. Most thoughtful intelligent people prefer to wait until they can take care of themselves first before they make any attempts at raising children who will not turn into society’s worse nightmares; in other words, planned parenthood involving love, nurturing, non-indoctrinating education including critical thinking, and healthy forms of socialization. Most of them will only attempt to raise two or three children so can can provide what the kids need at an optimum level.

I would hazard to say that most of the world’s problems is the result of overpopulation, and it will only get worse. Pyschopathic maniacs stir this pot to their advantage. In fact, the encouraged breeding of children by cults and religions is for manufacturing brainwashed human fodder to do the bidding of their masters. Let me attempt to break this down in a mathematical way: Assume people reproduce just like cells do, exponentially, which in the case of cells, means a population doubling with every generation. In fact, this is not far from the case right now. Our world population is doubling in a very exponential way, much like a population of cells. So here we go: Assume Generation 0 (G0) is only one cell or the initial population. Here is the way exponential (geometric) growth compares to arithmetic or linear growth:

tables

By now, you should be getting some idea of the power of exponential growth compared to how most people think about things, which is in terms of linear or arithmetic growth. This is why a person can be perfectly healthy one day and eaten up with cancer in just a few months. World population is now well over seven billion people. If it continues to grow exponentially, here’s what will happen in just three human generations or sixty years.

(G0) 7 billion, (G1)14 billion, (G2)28 billion, (G3) 56 billion.

In another 60 years, the population , if unchecked, would reach 448 billion, just under half a trillion! This kind of growth will never end unless something is there to stop it. With it comes catastrophic environmental ruin, war, disease, famine, and death. The four horsemen of the apocalypse. We cannot afford the luxury of living as if we have infinite resources because we live on a planet with FINITE resources. We are in very real danger of killing the very base of the food chain where oxygen is generated, our seas. They are heating up and becoming acidified with carbon dioxide and polluted with all kinds of industrial and radioactive wastes. This will all end, one way or the other. If we curb our excesses now, we may have a chance at survival as a species. If not, we will be facing a major extinction event from which we may not survive. If so, earth will finally begin to heal from our hubris and folly. It always heals and life moves on. If you ever shared anything in your life, now is the time to do it. So, without further ado, here is David Attenborough:

Humans are a Plague on Earth

 

 

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Regarding Comments

????????

I have been getting quite a lot of comments lately. Some of them are repeats. They are almost always positive in nature but somewhat generic in content, meaning they could apply to other blogs as well. So, I am in a quandary as to what they actually mean and the motivations behind them.

I get the feeling that when some people surf the net, they use a cut and paste comment to certify their stamp of approval. If so, I certainly appreciate it.  However, I would appreciate it even more if you asked me some questions. I know you must have some and I am a teacher as well as a scientist. This means there are no wrong questions. If you are reticent to do so in a public forum, you may contact me at fabernathy@sbcglobal.net. Please be advised that I may share the discussion on the blog but will not reveal your information unless you give me permission to do so. Is that a fair deal?

P.S. I will be the first to tell you that I don’t have all the answers, but then again, who does? We can and must learn from each other.

Best regards,

Frank

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

Thing One and Thing Two

 

So let’s summarize most of the March and April posts I’ve done here. What are “Thing 1” and “Thing 2” here? Do you know? Does anybody else know? Are they being discussed in any reputable scientific journals, blogs, or any other forum beside this one? If they are and you know about it, please share this information with me.

Here’s a second picture. Now, what exactly are these “things”? Call em “Thing 3’s”, if you wish. They look all the world like a string of yeast cells and most scientists would agree with that. The only problem is that they were not there, initially. Now here is where the plot thickens a bit. Most scientists would say they that they were there to begin with and I just didn’t see them beforehand; in other words, poor technique and observation on my part. However, the simplest hypothesis is not always the best hypothesis. Scientists who engage in long term tissue culture generally will not use antibiotics for their main cultures because doing so only covers up bad technique which will eventually result in gross contamination of their entire cultures with antibiotic resistant bacteria and/or fungi. I avoided antibiotics whenever possible for that very reason. Let me reiterate: Anybody who has ever used tissue culture in their laboratories knows what eventually happens even when antibiotics are being used: They don’t get subtle, scattered contamination as seems to have occurred with Things 3 in the above photo. When the tissue culture flask is removed from the incubator, what they have is fungi trying to unscrew the cap to get out. The thing is totally loaded up with either fungi, bacteria or both; nothing subtle about it. Put a sample under the microscope and you wouldn’t be able to see the forests for the trees.

Let’s wrap this up with one more picture out of the many that are on this blog: There is so much going on here that I won’t even attempt to label everything. There are little circles of whatever flying away from a bigger circle of whatever encompassing an intricate network of “whatevers”. I could go on and on with this but I think you get the point: There is a hell of a lot going on here that nobody seems to be talking about but me. Again, if they are, I would appreciate it if somebody would let me know.

So here is my summation in a nutshell: The problem here is not scientific discovery per se, but censorship and dismissal of “inconvenient” scientific discovery. You know, kind of like climate change denial and drug studies that dispute drug side effects and effectiveness. This seems to be a deep and abiding problem that is exacerbated by the way scientists are rewarded or punished for their efforts. In fact, it has crossed the line into the realms of extortion, fraud, and reckless criminality. Instead of addressing the problem, our government continues to cut into the red meat of scientific funding, rewarding only those efforts that are little more than corporate commercials for drugs, oil companies, or whatever.  You know this is true. Real scientists are starved for money while the government can’t throw enough red meat at the military industrial complex and other unsustainable freeloading corporations who destroy the landscape for nefarious reasons that only make sense to the criminally insane.

I, for one, would like to understand what is going on with all of the structures shown here and on the rest of this blog. I think it is critically important to understand what they are, where they come from, and what function they have in a living cell. How are we ever going to cure diseases if we refuse to understand how cells are actually put together? I am hoping someone out there is willing to help me to do this or knows someone who might. After all, even the elite are but mere mortals. Old Rockefeller just kept butting his head up against a stone wall, thinking that if he just had enough heart transplants he could live forever. He was wrong. Quantity is no substitute for quality, and money is no substitute for the truth.

Posted in endosymbionts, evolution, Fallacies in science, What are they? | Leave a comment

Cellular Upgrades Via Endosymbionts

The fourth post below this one compared cellular evolution to corporate mergers. However, the devil’s always in the details, isn’t it?  So let’s try to get to the semi nitty gritty here. You can also think of cellular evolution as a computer upgrade where chips (endosymbionts) are plugged into  a computer motherboard or mainframe (cell nucleus).  How advanced the upgrade is depends upon how sophisicated or complex the chip is. In other words, the chip itself may have been upgraded prior to insertion into the motherboard. Computers are basically nothing more than transistors, simple on/off switches. How smart they become depends upon how many of these things get installed. It’s the same thing with cells. The more complex the endosymbiont that gets installed, the better the upgrade. So the next question should be straight forward: What is the mechanism of installation? Well, we might want to revisit earlier posts to assist in explaining how this might occur: Hiding in Plain Site.  In lieu of this, however, let me provide a stand alone explanation: In the computer world, a bit is simply a transistor. It takes eight of these to produce a byte which is the smallest piece of information that a computer can use to generate text. In the case of cells, a bit is a single DNA nucleotide like A, T, G, and C. I won’t bother you with chemical details here. It takes three of these nucleotides to generate the smallest piece of information that a cell can use to determine how to translate the DNA code into usable “text”.  Let’s just let it go at that before we fall into a molecular biological black rabbit hole from which there will be little chance of escape.

Ok, so now what? Well, before we can plug anything in we need to generate a port, and not all ports are created equal and for good reason. Plug the wrong thing in and you can put a hex on the whole dang thing (exploited from Will Smith, Independence Day.) Put another way, you could potentially corrupt the whole computer. In the case of cells, you could potentially cause cancer. So what kind of “ports” do we find on nuclear DNA?  Again, let’s avoid as many pitfalls as possible lest we fall into that rabbit hole. As you probably know, DNA is double stranded. It manages to do this because those magical letters, A, T, G, and C are capable of pairing up with each other, but only in one way: A only pairs with T, and G only pairs with C. So if one DNA strand has the following sequence: AGGTA it will only pair up with a strand having the sequence TCCAT. So this is kind of like dovetail joints in woodworking. The more of them you have, the stronger the bonding of the two strands. However, these joints are flexible and reversible. In other words, they can “breathe”. Therefore, the more of them there are, the less likely they are to come apart because not all of them breathe at the same time. Under normal conditions, these kinds of “ports” require roughly 100 base pairs in order to provide a semi stable connection between nuclear DNA and endosymbiotic DNA. Because of the size of chromosomes during cell division, these connections are quite delicate and easily disrupted by physical movement. Therefore, reinforcements are required beyond simple base pairing. One form of reinforcement is proteins like histones which bind up the DNA and protect it from physical disruptions. However, during DNA replication and RNA production (don’t ask), a portion of the DNA must be uncovered for these processes to occur. Under these conditions it must be easy for DNA to separate into single strands and come back together again once the process is over. However, if connections between endosymbiotic and nuclear DNA only rely on base pairing, there is a great risk that the endosymbiotic DNA will separate and become lost. This can be avoided by coupling the two DNA compartments together using covalent chemical bonds (again, don’t ask) which are much stronger than base pairing bonds. Now the DNA has become branched. The branch that is created is the very crux of this blog. This is where switching can occur, much like on a railroad track. Take a simple circular virus, for example. It base pairs with a port on the nuclear DNA, but instead of fusing with it, it forms a four strand switch that is linked together by covalent bonds. Whew! This is getting heavy. Time for a picture! This switch is binary, just like a transistor. The circle can either fuse with the main DNA or it can be released and lost based upon which covalent bonds are disrupted on the switch. Here, have a pic.

Fig 40crop

Ok, don’t freak out, I’ll explain, ok? The two rectangular shapes labeled 1 (see A) are  complementary “circles” of double stranded DNA. The coiling has been removed for clarity. The rungs in these ladders represent base pairing between the two strands. Remember what I just said about based pairing?  As the rungs open in Fig. B, some of them begin to base pair with the strands beneath, forming a four stranded structure (Fig. C). This is the “railroad”switch I was talking about. When it is in one position, the strands fuse together as in Fig D and E.  Note that if the  structure in Fig. D occurs, information has been lost within the switch which makes this irreversible. However, no information has been lost in the structure in Fig. E. It can either fuse the two circles together or it can reverse the process and release both of them.

This picture is also the crux of this blog because it explains how this kind of a switch can be used to add complicated endosymbiotic DNA to the cell nucleus using a simple port. However, such a port is also a two-edged sword. If the wrong DNA gets incorporated into it; this could corrupt the cell machinery, eventually leading to cancer. Apoptosis is one way to prevent this from happening.

Next Post. Thing 1 and Thing 2.

Posted in cellular differentiation, endosymbionts, evolution, Introduction, virus | Leave a comment

Non-english comments

I really appreciate all the comments and compliments I have received on this blog and look forward to more. However, I have to say something about comments in languages other than english. In this day and age, it has to be fairly straight forward to translate from your language into english using a translator such as the one I have provided on this blog. I am unable to translate non-english comments on the blog, so if you would like me to read them and possibly post them, please translate them into english first. Otherwise, they will simply get deleted. The same thing goes for duplicate comments, whenever I can catch them.

Best regards,

Frank

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