Is Evolution Real?

I just got “finished” debating someone on Facebook regarding whether evolution is real or not. It was lively as well as civil, an unusual combination for social media. It ended (for me, anyway) when I presented an actual repeatable example of evolution occurring in real time under controlled (artificial) conditions. The other person dismissed the findings by saying nature was incapable of doing the same thing in the wild. Now what did ole Ian Malcolm say about life in Jurassic Park? It finds a way.

Here is a link to the real time evolution example I provided together with the text from the actual debate. It involves mating between a radish and cabbage to generate a brand new species.

Facebook Post (below), non text removed for better reading

Mark Whyatt Adaptations are not evidence of evolution

Frank W. Abernathy I’ll bite: If adaptations are not evidence of evolution, what is?

Mark Whyatt Nothing cos evolution is a lie…or more kindly, a scientific “theory”.

Frank W. Abernathy Do you even understand what evolution is?

Frank W. Abernathy Pardon my presumption, but do you believe all life is immutable?

Mark Whyatt Yes, its a scientific theory that species can change into other species.

Frank W. Abernathy That’s part of it. It also states that in order to do this, the genetic material has to change and provide selective advantages to the offspring.

Frank W. Abernathy The altered offspring either adapt to a new unoccupied niche or overwhelm the original species leading to the former’s extinction unless it can find a protected niche of its own.

Mark Whyatt If you believe in evolution then you belief that humans evolved from fish that decided to crawl out of the sea and then evolved into mammals…I’ll leave that there unless you can show me any scientific evidence of a species ever changing into another species.

Frank W. Abernathy The problem with doing that Mark is generation time. We need to look at organisms with very short generation times so we don’t die of old age watching them change into something else.

Frank W. Abernathy That’s done using viruses, bacteria and other simple organisms.

Frank W. Abernathy Can we start there as an example?

Frank W. Abernathy You see, it is all but impossible for one species to evolve from another in a single generation. It’s done incrementally over time with many missteps in between.

Mark Whyatt https://youtu.be/MUa8lXyIwFE

Frank W. Abernathy You want me to bail on our conversation to watch this video or can you sum it up for me?

Mark Whyatt It’s a theory but that doesn’t stop science and education claiming it as a fact…a theory is based on faith rather than fact, same as creation.

Frank W. Abernathy Some of it is theory and some of it is fact.

Mark Whyatt It’s only 13 mins long Frank

Frank W. Abernathy evolution can occur in less than a day, even hours.

Frank W. Abernathy I’ll watch your video, Mark, but can we find a stopping point. I’m not done yet.

Mark Whyatt The fact is no one as ever observed one species turning into another, ie a bird turning into a fish…that’s the basics behind evolution isn’t it?

Frank W. Abernathy Ever heard of antibiotic resistant bacteria?

Frank W. Abernathy Not really.

Frank W. Abernathy That part is theory based upon extrapolation from known facts.

Frank W. Abernathy Nobody has a time machine.

Frank W. Abernathy You do realize that chimps and humans have 95% genetic compatibility, maybe even more.

Frank W. Abernathy You can line extant species up along an evolutionary tree based upon genetic compatibility.

Mark Whyatt Surely if evolution was a fact and species turned into others they would be hundreds if not thousands of species on the planet just about ready to change at any point in time? …or did they all decide to change species at exactly the same time?

Mark Whyatt When man isn’t looking?

Frank W. Abernathy You’re right, species change all the time. Most of the time these changes have no impact on viability or they kill off the unlucky individual that acquired them.

Frank W. Abernathy These changes can be passed on when a male and female that have them mate.

Frank W. Abernathy Happens all the time in all living organisms.

Frank W. Abernathy This is a fact, not a theory.

Frank W. Abernathy The theory part comes when we delve back in time with only fossils to check and no available genetic material.

Mark Whyatt The fact is no one as ever observed or scientifically proven that one species can change into another, its just a faith based theory like creationism. We can reply to each other all night but you know evolution can’t be scientifically proven.

Frank W. Abernathy Do you believe bacteria are living things?

Frank W. Abernathy Let me provide you with an example of evolution in the lab by man using radishes and cabbage. I could have the two species wrong but the example is still the same.

Frank W. Abernathy A botanist fused together the plant cells of two different species to instantly create a brand new species that could not mate with either of the original parents. That, Mark, is artificial evolution.

Frank W. Abernathy It is also repeatable.

Frank W. Abernathy I learned this in a botany class. You see, I went to college to become a scientist.

Frank W. Abernathy Shall I watch your video now?

Frank W. Abernathy Maybe you would be interested in my blog: Here is the link: https://evolution4.wordpress.com.

Evolution Turned Upside Down

Mark Whyatt Yes lol…and when science can proof one species (not a bacteria or cabbage) can turn naturally (not artificially) into another I may listen to evolutionists

Frank W. Abernathy If man can do it, so can nature.

Frank W. Abernathy We are simply using the tools nature has provided us to understand how they work.

Advertisements
Posted in evolution | Leave a comment

What difference does it make to you how chromosomes are put together?

This is your friendly retired scientific pest making his presence known…..AGAIN!

Sigh!

This particular post is not for jaded scientists per se but rather for you, the average blog surfer who is looking for the latest and greatest on the internet. You see, I was going to accommodate you today with an animated presentation! Never done one before but I know how cool they can be as opposed to static verbose blog posts such as mine. Anyway, I soon realized I could get in over my head really fast by trying something like that so being long in the tooth and all, I have decided to do a little bait and switch. I’m going to appeal to your intellectual side, instead. So here goes…

What difference does it make to you how chromosomes are put together? Excellent question. On the surface, it kind of sounds like counting angels on the head of a pin, doesn’t it? Strictly an academic exercise for those with plenty of time on their hands and lots of professional expertise. Academically speaking, I would say you’re mostly right. However, the problem is that academics have been very slow out of the gate with the angel counting business. You see, most of them think the job’s already been done, a very long time ago… like in the 19th century! Hard to believe? Well, look at any biology textbook or go online and look up chromosome structure for critters such as ourselves. They all say the same thing, over and over and over again. Each of our chromosomes contain a single wound up piece of linear DNA. All research on chromosome structure is subservient to this old-fashioned model, to the virtual exclusion of anything else. I know, because I have a different model, one I proposed over thirty years ago and nobody to my knowledge in the scientific community is screaming it’s praises from the roof tops. When you think about it, that’s actually kind of scary. After all, aren’t scientists supposed to be skeptical and wary of all models?  Sounds more like religion, doesn’t it?  I won’t go into all the sordid details about the resistance I’ve met regarding my counter model. You can read more about that by digging deeper into my older blog posts which go back as far as October, 2010.

So before we get off too far on a tangent let’s get back to the original question at hand: to paraphrase Hillary Clinton: “What difference does it make, anyway?” Well, actually it can make quite a bit of difference… to YOU and/or your loved ones. Why? Because if chromosome research is going in the wrong direction, fueled by the momentum of a monolithic runaway biological research industrial complex, it can only spell disaster.

Really, you say? Please, let me explain. Compared to military spending, biological and medical research receive only a pittance of federal funding. Unlike the out-of-control military… scarce biological and medical research funds can ill afford to be spent chasing sacred cows day after year after decade, accomplishing only a fraction of what it could or should be doing. Unfortunately, it does have one thing in common with military spending: rampant fraud to achieve a desired end, i.e., the acquisition of still more and more taxpayer’s money with precious little to show for it. Cleaning up government waste and fraud may seem beyond the reach of the common citizen such as yourself, but don’t despair. There is such a thing as microfunding of projects, including biological research. I like to think of this like block chain technology, similar to bitcoin. Let the people decide the merits of various projects by voting with their pocketbooks.

In case you think I failed to make my point about the relevance of chromosome structure to your everyday life, let me say this: We cannot fully cure diseases without understanding how chromosomes operate, because all life begins when the chromosomes begin to generate what is needed for life to exist. You can’t get much more basic than that. How can we understand how chromosomes work if we refuse to understand how they are actually put together?

So you have to ask, what makes me so sure the old model is wrong? Well for one thing, long linear strands are quite different from circles: Compare what I found thirty years ago (on the left below) to a conventional model of chromosome structure on the right:

Is This Model Wrong?

Please let me know your thoughts on this funding business. Currently, I’m retired but that could change based on a sea change in attitude from enlightened and engaged citizenry toward what I have said here. With even a modest amount of funding, I could approach a university to financially support a postdoc or graduate student who would be willing to engage in this kind of research with me as their mentor. My email is fabernathy@sbcglobal.net.

Posted in cancer, cellular differentiation, chromosome, circular DNA, endosymbionts, evolution, Fallacies in science, Funding research | Leave a comment

Human circular DNA is commonplace

As of late, I have been somewhat lax in my perusal of the literature.  I guess my retirement is finally getting the best of me. Anyway, I did a little fishing online today and came up with a fine catch. This particular paper published in March of this year acknowledges that circular DNA is common in normal cells as well as in cancer cells and can be derived from gene-rich areas of the chromosomes. Imagine that! Circular DNA is part of normal chromosome structure! I’ve only been saying this for thirty years now. Anyway, here is a link to the paper: Circular DNA elements of chromosomal origin are common in healthy human somatic tissue.  Sooner or later, some astute young scientist is going to have to come to grips with how these circles are actually generated, i.e., the physics behind their circularization prior to exiting the chromosome. For example, how can the ends of supposedly linear megabase sized chunks of DNA somehow magically find each other within the nuclear milieu to become circles of DNA? Scientists could start looking for that answer by perusing some of what has been written in my blog here.

Posted in cancer, chromosome, circular DNA, endosymbionts, evolution | Leave a comment

Anatomy of the Peer Review System

The average scientist belongs to a whipped dog breed.  All one needs to do is read just one of their peer reviewed papers to confirm it.  They start out well enough with an abstract or synopsis of the paper, giving the reader a brief overview of what it is all about. This is a form of professional courtesy, because scientists are a busy lot and don’t have time to wade through a plethora of papers that may have little relationship or content pertinent to what they are looking for, which is usually papers they will be citing as they write papers of their own.  Time is a premium for the professional paper publisher.

Next is a formal introduction to the previous bodies of work (including their own).  Citations are listed here to provide additional impetus to the thesis that will be presented later in the paper.

Beyond this point, the author assumes the reader is ready to dive into the technical details at hand, including cited general methods and those peculiar to the paper at hand. Assumptions are made that anyone wading in this far already knows how to do most of the techniques and procedures being addressed.  Just in case, however, citations are made available to earlier works which when also read, more than likely refer to even earlier works and one and on until the end of the yellow brick road is finally reached.  Likely, these final yellowed ancient papers were written by the dearly departed whose technical machinations and “tricks” are either buried with them or hidden away in a kind of scientific archeological dig.  With any luck, somebody down the line actually wrote standard operating procedures for such matters, allowing science to progress as intended.

The results of the work are presented in dazzling detail, like a magnificent fireworks display, leading to inevitable “oohs” and “ahhhs”.  So the paper proceeds smoothly along like a well oiled machine, leading up to the grand finale: the inevitable foregone conclusions to be derived from the data.

Herein, lies the rub:  There is a section of the paper called the “Discussion”.  It is here that the author proceeds to pick apart his data.  In essence, he may dispute and minimize it to such a degree that the reader begins to wonder why the paper was ever written in the first place! After going to such great lengths to present his findings in the most elegant way possible, why on earth would he do this?

It is the nature of the beast called the peer review system. The whip of conformity has been applied by way of two to three editorial rejections before the author was ever able to get his manuscript accepted. No doubt, the peer review system works much of the time. Papers of dubious quality get rejected out of hand while others are salvaged by addressing the concerns of the reviewers.  However, being human, reviewers are not infallible and may fall easily into a jaded cookie cutter rut.  By doing so, they may cut into the red meat of novel discoveries rather than simply trimming the fat. Worse still, other high profile more prolific authors may be rubbing elbows with editors at the country club and/or taking money from vested interests with an agenda that conflicts with the thesis of the paper presented by the unfortunate author.

I will end on this final note:  When anyone reports novel discoveries in a manuscript or grant proposal, it is not the job of the reviewers to squelch them or dismiss them out of hand as “trivial”.  They are in no position to make such a value judgement until additional evidence is forthcoming, and how can additional evidence be forthcoming if the means for acquiring it have been solidly blocked by the “system”?  To the best of my  knowledge, other than what I’m telling you in this blog, none of my findings have ever been reported in any peer reviewed journals over the last thirty years.

 

Posted in evolution, Fallacies in science, Funding research | Leave a comment

The biggest myth ever told by biologists

Why are human chromosomes depicted as single linear strands of DNA in every textbook and practically every scientific article ever printed?

I know I’m going out on a limb by calling out practically every DNA scientist that lives or ever did live but that’s exactly what I’m doing here. My statement is simple but profound: 

Where is the evidence that every chromosome in our cells is composed of a single linear molecule of DNA? Where is the evidence for this in the cells of any other creature? Where is it? Show me, call me out, enlighten me. I’ll be waiting.

 I know what to expect if any answers are forthcoming: Such chromosomal DNAs are linear because they have telomeres which are used to allow them to replicate. 

Really? Ok. Show me physical evidence of this. You don’t even have to unwrap an entire chromosome for me, just unwrap a few megabases without breaking the entire chromosome in the process. Can’t do that? Ok, how about less than a megabase? Can’t do that either? Hmm…we have a problem here, Houston. 

Sounds kind of like somebody put the cart before the horse. The assumption that such DNA must be linear required coming up with the telomere model to explain how they replicate. This is circular logic at its best because it proves absolutely nothing. 

Where is the physical evidence that proves beyond a shadow of a doubt that chromosomal DNA is completely linear from one end to the other? Short answer: there isn’t any. Ok, so is there any physical evidence to the contrary? You betcha! Evidence is scattered in copious quantities all throughout this blog indicating that our chromosomes are composed of circular elements of DNA arranged in a complex hierarchical array. 

This isn’t some indirect theory; it’s an obvious fact that stares you right in the face.

Scientists have been busy ignoring this for well over 30 years now, happily going about the business of worshipping, protecting, and coddling the linear DNA model like it was some kind of heathen god. You do not question the god, lest you be expelled from the cult. For this, science should be embarrassed if not completely ashamed of itself.

Is This Model Wrong?

Posted in cancer, cell cycle, cellular differentiation, endosymbionts, evolution, Fallacies in science, Funding research, mitosis, Stem Cells, virus, What are they? | Tagged , , , , , , , , , , , , | Leave a comment

Chromonomes?

I have been browsing the web via Google and come across a number of catchy words and phrases such as chromonome (not chromosome), genome assemblies, contigs, scaffolds, micro-synteny, non-random chromosome organization, and chromosome level assemblies. All of this terminology refers to how the DNA appears to be organized within chromosomes. It relates to the field of genomics where short pieces of DNA that have been precisely sequenced (contigs) have been cyber pasted together into longer linear structures (scaffolds). Unfortunately, such a process can generate errors as well as gaps between the contigs.

So the elephant in the room that needs to be addressed is this: If DNA within a chromosome is completely linear, why can’t it be completely sequenced free of any gaps and errors? Why indeed. Are stubborn molecules like proteins getting in the way? If so, why can’t they be removed the same as other molecules during the DNA purification process? The most obvious possibility is that such offending molecules, assuming they exist, must be covalently attached to the DNA in some manner. Such attachments would have to be quite stable and long lasting to generate such persistent errors and gaps within the genome. Perhaps the only way of getting rid of them is by breaking the offending links, which inevitably damages the DNA at that site.

If such is the case, it has to be said that the concept of uninterrupted linear DNA within chromosomes is nothing more than a mere myth, stubbornly sustained throughout the literature with mindless rabid fervor equal in ferocity to that of blind religious zealotry.

Take a moment to think about the statement I just made above.

If you’re a biologist, think about it very hard.

I just called out every major publisher who persists in spreading misconceptions about linear DNA in eukaryotic chromosomes. That’s pretty bold, don’t you think?

Then check out the models on this blog that offer an explanation for why chromosomal DNA is not a simple linear molecule at all.

A butterfly chromonome reveals selection dynamics during extensive and cryptic chromosomal reshuffling, 2018.

P.S. I can think of only three reasons why publishers persist in promoting this linear DNA tripe: 1) they succumb to irrational peer pressure for fear of  financial losses and/or loss of “prestige”, 2) they are too intellectually comfortable in their safe and secure bubble to change anything, 3) they actually believe what they are printing. None of these reasons should be acceptable to any person whose agenda is seeking the truth.

 

 

Posted in cellular differentiation, endosymbionts, evolution, Fallacies in science | Tagged , , , , , , , | Leave a comment

More OSU Research Fraud

If you search for OSU research fraud scandals on the internet, you will find several links. Here are three of them, including one that was published today. I find these both distressing and disturbing, considering that I am an OSU alumnus. In no way do I believe OSU is unique in this regard. Below these links is a letter I wrote to the editors of the Lantern, the OSU campus newspaper.

Lantern article, 2018

New York Times article, 2017

Retraction article, 2012

Hi Summer and Owen:

I was sorry and disappointed to learn about the most recent cancer research fraud scandal uncovered at Ohio State University, almost on the anniversary of the last big one in 2017. These scandals are exposing the seamy underbelly involved with research funding, not only at Ohio State but nationwide and globally. So called “prolific” researchers are rewarded with lavish funding based upon the “publish or perish” mantra. They develop into brand names, cranking out research papers on the backs of hungry graduate students and postdocs who must conform to the rigid status quo that is the source for continued funding. Simply put, “If it ain’t broke, don’t fix it”. However, the toxicity goes even deeper than this: These winning formulas for continued success are usually based upon grants sponsored by a pharmaceutical lobby or some other vested interest. Such funding screams conflict of interest at the highest levels and is a guaranteed recipe for data corruption. Such a witch’s brew of conspiracy taints the entire process of scientific discovery, giving ample ammunition to all the conspiracy theories that now abound on the internet from GMO’s to vaccines.  Even more tragic is the fact that such funding eclipses truly innovative research and honest scientific discoveries that help point us in the right direction in terms of understanding biology in general and diseases in particular.

I know about this on a very personal level because I received a Ph.D. in zoology from Ohio State University 30 years ago in March of 1988. I was so excited about my work that I continued working on it in my spare time for free at OSU while I earned a living, working on unrelated projects in other laboratories. Of course I tried to get manuscripts published and applied for postdocs related to my work, all to no avail. When I discussed my hypotheses with a high profile professor at OSU, his parting comment to me was bone chilling: “They will kill you for this!” I was bucking the establishment which considered itself immutable, inviolate, and above scrutiny. No wonder creationists compare evolution to just another rigid belief system.

If you would like to learn something about my heretical theories that have so offended the sensibilities of the scientific community, you may do so by visiting my blog: https://evolution4.wordpress.com.

Best regards,

Frank W. Abernathy, Ph.D. and OSU alumnus

More on Research Fraud: Killing for Profit

 

Posted in cancer, Fallacies in science, Funding research | Tagged | Leave a comment