Dark DNA, Part III


Well, it’s about time for another post. So, here goes…

2'5' RNA-DNA

Yikes! What is the purpose of this post? Well, it focuses on that mysterious RNA “bridge” that hooks the two replicons together as shown in the previous post. This bridge is important because it acts like a binary switch for embryogensis in particular and development in general. Once the switch is activated, the result becomes irreversible and the two replicons become joined together with only a fragment of the bridge remaining to tell the story. Think of it as a corporate merger where all of the personnel required to maintain two companies is reduced to maintain the final merger. RNA has been fired (removed). Now some of you (probably a very few) may have a problem with this model because scientists have been able to “reverse” this process, allowing stem cells to “demerger” so to speak and reform the original two companies which may then merge with other companies to produce different mergers. If you dive into the blog by putting in search terms you will come up with a number of blogs that deal with this paradox. Simply put, merging is irreversible, there is no such thing as demerging. The RNA will never be put back like it was (look up entropy). Instead, what is going on is functionally equivalent to a demerging process but structurally quite different. Think of it this way:

DNA as corporate mergers




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Dark DNA, Part II

If you are just now reading this post I suggest skipping back to the preceding one to get a better understanding of “dark DNA”. This is a very busy picture, I know, but let’s take it one step at a time, ok? Explanatory text is below these pictures.

Phenol fragments On either side of the microfuge tube at the top are two funny looking models of DNA replicons. If you’ve been reading my posts, you know what a replicon is. If not, you may want to dig back deeper into the blog.

Quick summation: A replicon is a piece of DNA where the initiation of DNA synthesis begins in a cell nucleus. There may be only one like in a bacterium or many of them in higher cells like our own.  The number varies not only by species but also by the stage of the organism in embryonic development and perhaps beyond. The maximum number of replicons in cells like ours begins at conception and decreases as cellular differentiation begins to take place.  If you peruse the blog you will see how replicon loss and the onset of differentiation may be occurring in the same sites on the DNA.

The model on the upper left is that of two DNA replicons joined together by an RNA bridge. The model on the upper right is that of two fused replicons where the bridge and any genetic material associated with it has been removed. The double replicon model represents an undifferentiated state whereas the fused model represents a differentiated state.

In the models below them, they are subjected to physical shearing (fragmentation) by vortexing samples in a mixture of aqueous (water-based) buffer together with a very caustic protein denaturant called phenol. The DNA may have been subjected to chemical breakage using chemical or enzymatic means prior to using the phenol. The ensuing double stranded fragments are shown just below these models.

Now pay very close attention here: Note that all the DNA not associated with the original RNA bridge in both models separates out in the aqueous phase. This is the stuff that most molecular biologists use to sequence DNA and put it back together like a giant jigsaw puzzle using overlapping sequences to figure out the correct alignment of sequences.

The bridge elements may have other kinds of molecules still associated with them like proteins and  phosplipids known to be located near origins of replication on replicons. Even in the absence of such contaminants, these structures do not lend themselves to DNA sequencing because they are not simple linear DNA molecules. They have a higher order or tertiary structure.

So there therein lies the problem: Molecular biologists are trying to sequence DNA as if it were a simple thread. They break it up into small  linear sequences which can randomly overlap with each other. They line them up to generate linear maps using  these sequence overlaps. The problem with this approach is it only works if the DNA is actually a single continuous thread. Not only that, the molecular biologist simply throws out that which does not fit his model and cannot be sequenced. If replicons pair together like my models suggest, the differences could be staggering. It’s as if you were trying to explain a two dimensional painting using only one dimension, a straight line.  Orders of magnitude of DNA superstructure could be overlooked as a result.

There will be another post very soon: Dark DNA, Part III.






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“Dark DNA”?


I found this article on Facebook and responded directly to the author about it. Here is my post: “Dark, hard to find GC rich DNA? Could this be due to a technology issue because of the way DNA is purified and chopped up for sequencing?”

What I didn’t ask was whether or not the author thought tertiary DNA structure might be a problem in isolating these sequences. Tertiary DNA structure is higher level structure above the DNA helix and the secondary structure resulting from DNA wrapping around proteins called histones to form a beaded DNA structure (nucleosomes).  Current dogma suggests that tertiary structure is merely the wrapping up of DNA into tighter and tighter coils until it condenses into chromatin fibers and finally chromosomes. Apparently, there are some wrinkles to be worked out here, hence, “dark” DNA.

When DNA is purified for sequencing, it is generally violently vortexed (whirlpooled) in a microfuge (small centrifuge) tube full of caustic phenol and aqueous (water-based) buffer. When done, these two solutions rapidly separate like oil and water with a thin boundary layer between them that can’t quite make it’s mind up which way to go. The lower heavy phenol phase traps denatured (coagulated) proteins (think cooked egg whites) while the upper aqueous phase collects the water-soluble DNA. I have not read the author’s isolation methods so I can’t be sure this is what he did. After all, methodology changes all the time.  

Phenol extraction

In my past experiments, I have found that the intermediate phase is not completely  devoid of DNA. Most DNA scientists would merely consider it to be impure DNA, a mere waste product to be expected from such an extraction and as such, subject to being discarded because it cannot be sequenced in its present form. However, what if they are wrong? What if there is something to be learned from this kind of DNA, this “dark” DNA? My research suggests they are throwing the baby out with the bath water here. Somebody somewhere needs to investigate the DNA found in this intermediate layer because it may contain unknown secrets about how all of the DNA is actually put together at higher levels.

Learn more by skimming through prior posts and checking out the other pages on this blog. You may also contact me directly at fabernathy@sbcglobal.net with specific questions. You can also help by contributing to my Patreon account. Right now, it is starving to death because I’m old school (69 years old) and I can’t keep up with everything you youngsters are doing on the internet! Help an old retiree out, will you?







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How Scientific Culture Discourages New Ideas

How Scientific Culture Discourages New Ideas

Would you like to be part of new and exciting biological research effort that could break DNA research wide open?  You can, with only a minimal effort on your part. You can do this by sharing this with others and/or providing a small donation to the cause shown at this site. When the funding is sufficient to initiate the research, I will bring you up to speed on how that money is being spent, including an online accounting of where every penny goes. Or you can just throw your money into a black hole like a Jerry Lewis telethon and hope it somehow gets used wisely.

P.S. Jerry Lewis raised billions for muscular dystrophy over a decades long career in show business. Lots of hype, tears, talk, talent, and self- aggrandizement, but no ultimate cure. Imagine what might have happened if even a minuscule amount of that money had gone into other more obscure kinds of biological research? Learn how to help by visiting Patreon.



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Spend Your Money Wisely

Well, the plot thickens: Yesterday I shared this outlandish video from Facebook and there were no problems with it coming up. Today, it has magically disappeared. Something mighty peculiar is going on here. The dude in the video was a rapper that wanted you to give him $200,000 to prove the Earth is not round. I am wondering if he ever watched a lunar eclipse? The people who try and mess with your minds are obviously not happy.

If you ever have an inclination to shell out any money for a “worthy” cause, you might want to consider orphan scientific research. There is plenty of it out there, including mine.  How much of it is baloney, I can’t say. However, a lot of the research money being spent today by mainstream science is probably rife with fraud and deception and spends orders of magnitude more money than even the most suspect of orphan research projects. Choose how you spend any of your money on such causes wisely and with proper vetting. Don’t buy into the hype or the branding. Instead, buy into results. Jerry Lewis “carnie barked” for muscular dystrophy most of his adult life, bringing in untold sums of money for his personal crusade. In spite of all of this, the disease still remains unconquered. Now why is that?  Substitute the phrase  “military industrial complex” with “research industrial complex” and you can better visualize the problem here.  Both of these giant systems suffer from the same kinds of internal abuses. No real oversight, cronyism, lack of transparency, coverup, and outright fraud. One system wraps itself in branding and celebrity status, the other in American flags. To be sure, the research industrial complex is no match for the military industrial complex in terms of the sheer scale of these problems, mainly because the Pentagon receives a huge blank check from the government whenever they want it, carving deeply into the meat of every other kind of government program, including scientific research. There is a solution, but I would digress too much in going into it (think Federal Reserve and the IRS).

Do your wallet a favor and quell your impulses regarding your favorite charitable cause. Check them out on the net and don’t take the first thing to load up on your search page as gospel. They spend money to get there. Vetting is easier now than it’s ever been in the history of mankind. Even so, you have to be careful and you may still get taken for a ride, but don’t worry. It won’t be the first time nor is it likely to be the last time. So spread the “risk” and hope you pick a winner just like any other investment because that’s exactly what it is, an investment. One day, one of those orphan projects may just come up with a cure for muscular dystrophy, one that does not require victims of the disease to file for bankruptcy to get it.

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Thank You For the Wonderful Comments

I want to thank all of the people who have taken the time to comment on my blog posts. As you know, I have to be careful and try to divine which comments are real and which ones are used to sponsor something the “commentor” is selling. I also use Akismet to reduce spam as well. I try to err on the side of honest comments. Please do not send duplicate comments using different links because I can usually spot these right away and will delete them along with other obvious duplicates. Some obvious spam does get into my inbox which has nothing to do with the blog post and those get deleted too. As spammers become more and more clever, I’m sure I will get nailed more and more often. Therefore, I would greatly appreciate it if you could write content more specific to the  post on which you are commenting so I can be more certain you are for “real”. If you are hesitant about doing this, you may send me an email at fabernathy@sbcglobal.net. If you don’t mind, I would like to post your e mail and my answers as a blog post, but will not use any of your personal information without your permission.

I’ve had a number of people ask me to provide more data on a variety of topics and I appreciate their interest. However, I can only do this via “dry” research, i.e. library work, because I have no laboratory in which to work. I’m retired and even if I wasn’t, no cookie cutter laboratory would touch this.  From what I’ve been seeing, it appears the research that I did is not a fertile area for follow up studies. You must understand that I am probably something of a pariah in the scientifc community right now because of the work that I did at Ohio State University. Other work that I have done down the road was far more conventional and, therefore, much more easily accepted. Any straight thinking scientists or “newbies” are going to steer clear of too much controversy for the sake of their own careers and paychecks. I can’t say that I blame them. Right now, scientists are more akin to starving artists, only a few of them make it to the top. The rest simply struggle for their professional existence, usually by kowtowing to the ones on the top.

Quite the dilemma isn’t it? I can publish all the beautiful slides of the discoveries I found at Ohio State from over 20 years ago and you will have no more knowledge about them than if you studied this blog in excruciating detail and followed up on the references I provided. The simple fact is this: Nobody, including myself, even knows what these beautiful mysterious beaded circles are. We need to examine them and learn their composition much like a detective sorting out suspects. The first suspect that comes to mind is chromatin, which contains proteins and DNA, among other things. It is the stuff that makes up our chromosomes and determines not only our genetic makeup but how it is used to create who we physically are over time. This research will not happen in the near future because of fiscal constraints and heavy investments of time, money, and careers into prevailing dogma. So the only answer available is to fund this research via the internet using something like Patreon. I admit I know almost nothing about how to do this, so I simply set up a page at Patreon and explained my position.  I imagine most of the readers here could do a much better job of it and I am always welcome to constructive advice.

Again, thanks for your support

Frank W. Abernathy, Ph.D.

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Would You Like to Help With This Research?

I have decided to set up a Patreon account to help fund this research at a university yet to be named.  Here is the first goal I wrote down at the Patreon site:

This money will be used like a grant. You can learn more about my goals by visiting https://evolution4.wordpress.com. Basically, I want to restart my research from 20 years ago that I did at Ohio State University. Up to now, I have only performed “dry” research, i.e., literature searches while working on other projects in other laboratories. I have since retired. I would like to use the money to hire a graduate assistant at a university, preferably local so I can physically interact there. Short list candidates would be in or near the Dayton, Ohio area like University of Dayton or Wright State University. U.D. is flush with cash but WSU could use these funds and might be willing to provide the laboratory space if I purchase the needed supplies and support one of their graduate students on this project. Here is a synopsis of the proposed research:

How are chromosomes such as our own put together? The conventional dogma states that inside every one of our chromosomes is a single linear strand of DNA all coiled up like a rubber band. I believe this to be patently false and you will understand why if you visit the blog. What are the implications of this being wrong? What difference could it make? I cannot underestimate the differences it would make if this is proven wrong. It’s like saying what difference does it make if the liver is really on the other side of the body cavity? Surgery is surgery. I strongly suggest you go to the blog and check it out thoroughly enough so you can ask me questions about it before you commit to anything financially. Please also vet me as a researcher as well. You can do this easily enough by typing my full name into Google or Duckduckgo and see what pops up. You can also find me on ResearchGate, an online community of scientists.

Learn more about possible research activities by clicking on the menu tab above this post called Future Research.



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