Are our chromosomes dumber than we are, or is it just the opposite?

Before science became mainstream, natural phenomena were explained in terms of things like witchcraft, magic, and miracles. The same thing applied to biology. Animals had “instincts”. The eating instinct, the breathing instinct, the “fill in the blank” instinct. At one time, cells were considered to be little more than bags of protoplasm with the occasional amorphous inclusion body, like the nucleus. Then came along the tools necessary to unlock the secrets of the cell like never before. Slowly but inexorably, protoplasm gave way to a vast complex of intricate organelles and sophisticated macromolecules displaying ever increasing hierarchical levels of complexity and interactions. The cell wasn’t just a bag of enzymes floating around in a sea of saline anymore. There were enzyme complexes that worked together like an assembly line to go through the myriad steps to convert substrate A into product G. There were cables and molecular motors pulling things from point A to point B. There was organization on nanoscale levels. The cell was starting to look more and more like some kind of factory…or perhaps even a city.  Suddenly, all of the inventions, machines, and factories man has generated begin to look like just mere extensions of what had already come before. Before man, before animals, perhaps even before the very first animal cell. On the surface, human civilization does appear to be an extension of what came before in a biological sense. However, humans can also be their own worst enemies. Some of them can be jealous and petty to the point of being obstructionist and “destructionist”.  If they didn’t create it, think of it, or discover it…watch out!  These same kind of people also tend to be charismatic, self-promoting, narcissistic, close-minded, uncompromising, and even ruthless. The quintessential qualities of true “leadership”.  Look at the Taliban as an example. They destroyed ancient buddhas created by a civilization not of their own making. Examples of civilizations ground into the dustbin of history by other civilizations abound.

Are practitioners of the scientific method somehow above the fray that plagues other forms of human endeavors? A nice thought, perhaps, but unrealistic. Scientists are afflicted with the same kinds of human frailties as everyone else. They may be trained to “overcome” them to a certain degree, but such training has its limits, especially when confronted with some of the human qualities mentioned earlier. So as with other forms of human endeavors, the steady flow of scientific knowledge has come in halting steps. “Potholes” have been created to stop or divert this flow into a direction more in agreement with current dogma and self-interest. Gasp! Scientists can have self-interests beyond the acquisition of pure knowledge?  You bet they can!  Publish or perish is one of them. Scientists need to eat and have shelter just like everyone else. In order to get published, one must take the road most traveled. Scientists must follow in the footsteps of those before them, lest the ladder be pulled up before they can reach the end. This tactic rarely leads to discovery. Instead, it is used to “validate”, perpetuate, and further entrench the current dogma of the “masters” who are the gatekeepers for deciding whom may climb the ladder of success. The longer this road is traveled, the deeper the entrenchment becomes until a point is reached where discovery must be filtered, massaged, and manipulated in order to protect the dogma. If it cannot, then, it must be ignored and swept into the dustbin of history, hopefully, never to raise its ugly head ever again. Sounds very much like religion, does it not? The creationists may have a point when they accuse scientists of practicing religion by “believing” in evolution.

So what has all of this got to do with our chromosomes? After all, that is really what this blog is all about. Well, frankly speaking, chromosome structure as stated in the literature hasn’t “evolved” much beyond where it was in the 19th century. It is still considered to be little more than a string of beads (genes) dispersed along a simple rope of chromatin, much like pearls in a necklace. These beads have now been resolved down to the level of DNA and are considered to be super wound coils of protein coated linear DNA. When wound further, they form the physical structure of a metaphase chromosome. In other words, a fully unraveled chromosome minus its protein coat is considered to be nothing more than a single continuous strand of uninterrupted DNA. Simple. Easy to understand, and probably dead wrong. When you observe how cells and their nuclei fall apart under conditions of stress, the results are nothing less than astonishing. All manner of underlying complex substructures begin to unfold, right before your very eyes. Some of them even pulsate and move, guided by some unknown power. Yet none of this is even considered or questioned in terms of how it fits into current theories about chromosome structure. Considering we are now well within the 21st century, this is quite the pothole. Perhaps, more like a gigantic sinkhole or even a black hole. The cardinal sin of scientific inquiry is when you force the data to fit the theory, instead of forcing the theory to fit the data. Chromosomes are anything but simple coiled ropes of DNA. They are factories within factories, working together in much the same manner as the rest of the cell. It’s time to give them the credit for which they are long overdue. You can start by clicking on this link  that takes you to photomicrographs where you will see images that are both beautiful and breathtaking in their complexity.

 

 

 

 

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Creationism versus Evolution

Burn!

You may have heard about the recent debate that Mr. Nye. and Mr. Ham had regarding the age of the earth and other worldly matters.  Mr. Ham’s arguments seem to be based on the premise that one cannot use pre-existing artifacts to extrapolate back into time and draw any conclusions about how they were actually “created”. However, that is not the subject of this particular post because what I am actually doing here is the old  “bait and switch” routine.

Scientists have repeatedly used the old argument that creationists cling to their ideas with a religious fervor that is not based on anything other than dogmatic belief. Creationists have turned the tables and accused scientists of doing the same thing. Could there be any truth to this? Well, the short answer is… yes. They can be as adamantly dogmatic about certain topics as even the most zealous creationist. They can go so far as to cherry pick data to conform with these dogmatic beliefs in order to get papers published (the old publish or perish routine). The more papers are published that conform to the dogma, the stronger  and less assailable it seems to become. Scientists can actually become brain-washed to the point that even the slightest challenge to the dogma can result in a vicious Pavlovian response. I know, because I have been “bitten” by them.

This blog runs contrary to the monolithic, dogmatic belief that eukaryotic chromosomes are simple, continuous strands of DNA wrapped up in a protein package. I have evidence in this blog that suggests otherwise. If such evidence is only slightly challenging to the scientific dogma, then, it needs to be addressed for what it is and everyone should move on. However, when a professor at a major university tells you to your face that “they will kill you for this”, that is quite telling, don’t you think?

stake

 

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Nature is Art

When it comes to nature and art, nothing beats water in either liquid or solid form. Take a look at these amazingly beautiful high speed images of water droplets and you will begin to see why water is so essential in the creation of living cells. Take a look at snowflakes too. They look amazingly like diatoms. Now, take a look at some of the pictures in this blog of cellular subcomponents.

Circle    Circles    degrading cell

                               (click images to enlarge)

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Are complex layers of chromosomal superstructure being virtually ignored by the scientific community?

Image

Conventional science tells us that chromosomes are arranged in a linear fashion with the genes spread over them like beads on a string. Simple, easy to understand. But is that really the case? What if there is more to it than that? What if chromosomal superstructure is incredibly complex? And scientists are studying them as if they exist in only two dimensions instead of three? In terms of complexity, one could consider multiple layers of dimensions. Or not. Is this important to know? Only if you want to get a better handle on how they really work.

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Junk DNA, not so junky anymore.

Un-Junking Junk DNA is hot off the presses.  “Islands” of protein coding DNA are separated by “oceans” (large swaths of “junk” DNA) that appear to be important in determining just how the mRNA in these islands is alternatively spliced together to make a variety of different proteins. Conventional definitions of DNA superstructure require these islands of DNA to be separated by vast stretches of junk DNA. If so, how do they physically interact? Could it be that DNA structure is being over simplified?  Perhaps, the linear DNA model should be modified like the time-space model. It can curve onto itself and even make “worm holes” that allow interactions between the junk DNA and the protein-coding DNA that generate potential mRNA splicing pathways. In other words, the DNA is more circular than linear. Check out these two models in which circular DNA elements involving both protein-coding and “junk” DNA can be used to generate mRNAs using alternative splicing.

Intron lariat model

Linear intron model

All models

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Where did we come from?

Where did human beings come from? Did we come from ape-like ancestors? If so, how? Where did apes come from? Or for that matter, mammals, birds, reptiles, amphibians, fish and everything else that is composed of more than one kind of cell? Where did single celled organisms like amoeba, paramecium, and euglena come from? What about bacteria and viruses?

These kinds of  “simple” questions are nothing short of profound. Yet people are driven to the point of obsession in trying to find the answers. I am one of them. To understand how all living things are connected to one another requires an understanding of their genetic lineage. We need to understand the DNA and how it has been put together over eons of time. To do this, we need to first understand that there is much more to DNA structure than its primary code of four simple bases (A, T, G, and C). This genetic code can be used to construct countless numbers of different kinds of primary protein transcripts, but doing so requires a vast amount of temporal regulation. Otherwise, all we have are simple one-celled organisms loaded with a chaotic mix of proteins, many of which would interfere with one another. Can this kind of temporal regulation be accomplished in the absence of any DNA structure above the level of the primary DNA strand? If so, how did such a complex system ever evolve  above the level of  that seen in bacterial in the short time span allotted to it in the Cambrian explosion?

That is the whole point of this blog, to provide an explanation for how higher levels of DNA structure evolved that allowed for the rapid expansion of the myriad kinds of multicellular life forms that came about during this relatively short period of biological time. I will provide links for various topics that have been posted in this blog relative to this discussion. Or you may want to simply scroll through the blog to follow the various postings as they were “laid down” over time.

Pride goeth before a fall

How are whole animals cloned from adult cells?

Pericentriolar recycling endosomes

Can the physical structure of the human chromosome be compared to a simple piece of rope?

How is an animal built from a single cell?

Hierarchical endosymbiosis in real time

What lit the fuse for the Cambrian explosion?

Creationism versus evolution (scraping the rust off of evolutionary theory)

The evolution of mitosis

Could our DNA have evolved from simple viruses?

Are textbook depictions of our chromosomes accurate?

Are cancers new species?

Cellular differentiation and endosymbiosis revisited

Could multicellularity in animals have been the result of endosymbiotic “fungi”?

Hierarchical endosymbiosis (the “wheel and hub” motif)

Prison escape by cellular inmates?

Does apoptosis recapitulate phylogeny in reverse?

Dinosaurs and cellular differentiation

This photograph is inconsistent with a eukaryotic chromosome that contains only simple, linear DNA

Why are pluripotent stem cells falling short of expectations?

Introduction

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Help fund this research

Money for basic research is being killed off by Congress and special interests. We need to understand how chromosomes are put together if we are ever going to fully understand how they operate. Please scan this blog to learn more about this. Follow this link to understand how your donation will be used and how to donate.

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