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

For years, the physical structure of the human chromosome has been considered to be about as interesting as a piece of tightly wound rope.

If this assertion were true, a fully unwound chromosome would basically be a straight piece of “string”.

Why do so many scientists believe that?

That’s an excellent question.

However, I will resist digressing from the point I’m still trying to make here.

If the physical shape of the human chromosome (among other eukaryotic species) is nothing more than a simple uninterrupted string of chromatin, then, how does one explain structures such as these?

(please click on the photo to enlarge it)

Does this look like a simple rope structure to you?

There are circles of chromatin coming out of larger circles of chromatin. There are all kinds of complex, bizarre shapes.

This particular UV photomicrograph is just one example.

There are lots of photographs similar to this on this blog and elsewhere.

Some have even more bizarre structures than the ones shown above.

They are in various stages of decomposition that seem linked to what stage of the cell cycle they came from and how long they were allowed to degrade.

So what goes here?

Is this important?

Should this have any impact on how scientists study human chromosomes?

Let me put it another way.

No more than comparing driving to the grocery store versus flying to the moon.

No more impact than learning that instead of just two dimensions there are actually three.

In other words, if these structures were pre-existing components of the chromosome, this changes everything anyone ever thought about how human chromosomes evolved and operate.

And how chromosomes operate has everything to do with genetic research, including cancer, human development, and all kinds of genetic diseases.

So yes, understanding what these things are is probably incredibly important.

The next big question is simply this: why isn’t anybody working on this?

Well, I would like to continue to work on it myself. However, the ugly fact of the matter is there is no money to fund it. If funding were available, finding a lab to continue this work should be no problem.

That’s why I put up a funding button on this website called simply (help fund this research). You don’t have to be rich to help out here either. Even a few dollars would be helpful. Here is the funding link: http://www.gofundme.com/2bhiqs

Constructive comments and questions are appreciated and welcomed.

You can also contact me by e mail at frank@eukaryotes.info.

How is an animal built from a single cell?

How is something as complex as an animal built from a single cell, i.e., a fertilized egg?

Obviously the fertilized egg must divide and form trillions of copies of itself in order to generate the mass needed for an entire organism; but it has to do more than that…much more.

It has to generate hundreds of different kinds of cells to form all the different tissues and organs within the body. Furthermore, these cells have to be generated at the right place at the right time in order to do their jobs.

How does a single cell know how to do all of that?

It all comes down to genetic programming which is very similar to how a program is run on a computer. There are hierarchies of subroutines, all of which must be activated at exactly the right time in order for the organism to develop properly.

How are these routines and subroutines organized within the cell? More importantly, how did they originate from primitive ancestral cells over eons of time? How do you go from a simple bacteria all the way up to a complex animal?

Obviously, the simple passage of time is not the answer because otherwise, there would only be bacteria on the planet or something even simpler.

The knee jerk answer is that DNA mutations in the bacteria led to the development of more complex cells. That may be the case, but it is so vague an answer as to be virtually meaningless in terms of understanding what really went on here.

This blog attempts to address some of these questions in terms of how DNA became arranged the way it did in complex animals cells. I hope you will find it to be interesting.

Questions are also welcome and appreciated and can be sent to me at frank@eukaryotes.info.

Hierarchical endosymbiosis in real time

This just in. They found an amoeba from contaminated contact lens solution infected with two bacteria, a giant virus, a virus within this virus, and a transposon. Smacks of hierarchical endosymbiosis to me.

http://arstechnica.com/science/2012/10/contact-lens-solution-hosts-giant-virus-ecosystem-of-parasites/

What lit the fuse for the Cambrian explosion?

For most of the course of evolution, life has existed as some form of bacteria and nothing else. The first signs of life were as early as 3.8 billion years ago and little changed until the Cambrian explosion 542 million years ago. That is a span of 3308 million years prior to any signs of complex multicellular life!  Somewhere within the Cambrian, life exploded into all the major animal phyla within a geologic span lasting no longer than 54 million years and perhaps even less!

This means the evolutionary rate suddenly increased to a minimum of over 61 times what it had been during the Precambrian. There is no adequate way to explain this in terms of simple, incremental mutations, because such mutations had been going on for over 3308 million years prior to the Cambrian. Something else had to have taken place to generate such a rapid shift in the evolutionary rate.

This blog suggests that what fueled that increased rate was the phenomenon of endosymbiosis, whereby large cells incorporate smaller cells and utilize their DNA to upgrade their own.  Evolution is a race for survival, and the cells or animals with the most adaptable genomes will usually come up as the winners (barring unforeseen circumstances such as an asteroid attack).

There are two kinds of endosymbiosis: serial endosymbiosis and hierarchical endosymbiosis.  One follows an arithmetic progression and the other is geometric. Cellular evolution that follows a geometric progression will blow the other kind out of the water every time. To better understand this statement, please click on the following thumbnail:

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

We’ve all seen this tired old movie before, folks. It’s kind of like watching a “new” hyped up, fresh faced, slick, computer enhanced show on TV that tries to hide the fact it is using the same old moth-eaten, battered up script used innumerable times before. Creationists use the Cambrian explosion and lack of intermediate fossils to blast away at evolutionary theory. Evolutionists provide assistance to them by insisting that evolution only occurs in incremental steps, one little mutation or gene duplication at a time. They claim that given enough time, genetic drift, and natural selection, all things are possible.  However, the time frames for the appearance of new complex species and the glaring lack of intermediate fossils leading up to them strongly suggest otherwise (score one for the creationists).

So who’s “right” here?

Well, the creationists are not going to change their position any time soon, that’s for sure. So maybe the evolutionists need to take a long hard look at what they are trying to sell here and defer to the idea that the creationists may actually have a point. How in the world did complex life evolve as rapidly as it did?  How can single cells or even colonies of cells, exploit simple incremental  mutations to form complex tissues, organs, systems, and animals that display a vast array of complex behaviors? The short answer is that this is highly improbable, if not altogether impossible.

So does this spell the end of evolutionary theory? It could, if evolutionists refuse to evolve themselves. Evolution is not simply about serial incremental changes over vast expanses of geologic time. Dramatic evolutionary change can occur whenever two cells from different species fuse together and generate a genetically stable, viable organism capable of producing fertile offspring. This happens in plants and it can lead to a new species incapable of breeding with either of the original species that generated it. This is an example of speciation via punctuated equilibrium.

Main keywords in this blog are mutualism, symbiosis,  endosymbiosis, and hierarchical endosymbiosis.  Hierarchical endosymbiosis states that evolution can also be a geometric event occurring within a very brief period of time, an instant of time in geologic terms.

The driving force behind the Cambrian explosion was not simple genetic mutations over large periods of time. Such changes had already been going on for eons with no real substantive results that show up in the fossil record. The real driving force was cooperation (mutualism) between non-related cells. Such cooperation could result in horizontal gene transfer on a massive scale, allowing formerly non-related cells with complementary attributes to essentially co-exist within a single cell (zygote).  These different attributes would be turned on in multicellular organisms as the need arises, i.e. during cellular differentiation.

For example, assume the existence  of two non-related cells: one cell is highly motile but is incapable of predation (molecular feeder) the other larger cell is capable of phagocytosis but is slow moving. The highly motile cells may attach to the surface of the larger cell, providing it with greater motility while absorbing nutrients from the larger cell through cell membrane adhesion sites. Over time, some of these ectosymbionts may become phagocytosed without being destroyed. This occurs frequently with pathogenic microorganisms that invade cells. Such cells may have initiated the formation of a permanent internal structure, the cytopharnyx as seen in protozoa like ciliates. The longer these endosymbionts remain within the larger cell unharmed, the greater the likelihood of a  horizontal gene transfer. Over time, redundant genes (housekeeping genes) not unique to either of the original genomes are deleted out or inactivated by mutations.  In anthropomorphic terms, think of business mergers and downsizing.

The glaring fact that mitochondria and chloroplasts have not been absorbed by the nucleus belies the nature of their endosymbiotic relationships: They cannot perform their primary tasks of respiration and photosynthesis without the presence of extranuclear membranes. Nonetheless, some horizontal gene transfer has occurred, indicating some nuclear regulation over their interactions within the cell.

To get an idea of what I am talking about, please scroll way down to the bottom of this post and begin there.

The evolution of mitosis

The evolution of mitosis may have greatly facilitated the uptake of genome-sized exogenous DNA’s into early eukaryotes. Click here to view models that may explain how mitosis may have evolved from prokaryotic symbiotic relationships.

Could our DNA have evolved from simple viruses?

In this blog, I discuss the evolution of complex organisms from more primitive ancestors. When I do this, I go way, way, way back in time.. before mammals, dinosaurs, fish, simple sponges, one celled protozoa, and even before the first bacterium! I start with the first replicons. A simple replicon is a single piece of circular DNA like a virus, a plasmid, or a transposon (jumping gene). In today’s world, replicons cannot exist outside of a cell because they lack the machinery required for self replication, i.e. the proteins required for DNA synthesis. However, they may have been able to exist and evolve as parasites within primitive cellular hosts whose genome was composed of RNA that functioned both as  hereditary material and as enzymes. The stability of these circular DNA structures may have provided an evolutionary advantage to these primitive hosts, paving the way for the first phase in a process I call hierarchical endosymbiosis. This phenomenon may have allowed life to rapidly evolve through a series of geometric integrations of DNA cassettes in roughly the following sequence of events: virus, bacterium, simple eukaryote, and complex eukaryote. All of these integration events may also be occurring simultaneously.

I present models to explain how these integration events may have occurred at the molecular level, beginning with simple replicons and ending with complex eukaryotic chromosomes. There are also models to explain how transcription is enabled via differentiation and how introns are spliced out of the final mRNA product. These models can be viewed directly at this blog by clicking here or going to the original website that describes them and other processes in considerably more detail.