I have some promising DNA work I have been doing in my spare time. I have found a sequence that appears to repeat itself quite often within a chromosome. So far I have only done Chromosome 19. My belief is that there is not just a single simple codon that denotes where transcription of a gene begins. This seems somewhat ridiculous. The start sequence and end sequences must be longer. Also how does the cells mechanisms determine so called 'junk DNA" from useful and still essential DNA. I am exploring a sequence with the bases agggagggaggg. This has shown some promise. I am testing other 12 base combinations for frequency. I think if I find that almost any 12 base sequence occurs with near or equal frequency I will be even more surprised. So that's where the DNA work is for now. Still working with only a couple computers so it will take some time. I think that we would find that the "apparatus" that uses the template string to create a protein chain has a liking for agggagggaggg or something similar. I think DNA research should move into the area of examining the DNA in different cell types, such as muscles, nerves, etc to see if they can find through analysis where the DNA for that particular kind of structure is coded in the DNA.
Contained within the DNA is not only the necessary blueprint for cellular life but for cellular maintenance, building, and replication. Life is an example of a Von Nuemann Machine. It is not difficult to understand how some researchers who immerse themselves in the complexity that is DNA become spiritual. The idea that such a machine built from basic molecules and capable of replicating and installing most of the software it takes to cause the product to grow and reproduce is amazing to say the least and the idea that it happened by chance is just as ridiculous to me, an agnostic, as most religion is to me.
It makes sense that the sequence I am looking for would be a pattern. It would have a symmetry to it. This idea is based on the premise that DNA and DNA transcription is an electrical process which all chemical reactions ultimately are. Cellular machines would have symmetry I suspect to create their "tools". If you look at the machines we make you will see symmetry and repetition. So it stands to reason the secrets of DNA lie in the patterns and symmetry. That is the state my DNA research is in.
And in a couple weeks I will be working on reroofing my shop and starting my part time, hopefully and eventually full time business. I will probably not discuss that in my blogs except perhaps a photo gallery of my more artistic work. But that is later.
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I began writing the above a few weeks ago. Since then I have roofed my shop and had my house roofed. It took pretty much my last dime so I guess my own business will be on hold for a few more months. But at least most of my roofing is done.
In the interim I have been giving some thought to the entire DNA paradigm. The complexity of DNA is such that it almost makes an agnostic believe in something else. Think about it. Contained within the 3 billion or so bases of the human genome are the instructions to begin reading and utilizing the instructions. Contained within the DNA is the blueprint for the body and its many organs and tissue types. But also contained in that information is the code for enzymes, hormones, and other molecules. For example the process performed by the Golgi Apparatus.
This organelle has several functions. It takes up products from another amazing organelle known as the Endoplasmic Reticulum and puts the finishing touches on it and then ships it inside or outside the cell what ever the coding has told it to do.
That is far more amazing than you might think. We have in our DNA the code to build this "device" then once built this device itself knows its job based on what? How does the Golgi Apparatus know what to do with the products of the Endoplasmic Reticulum? How did such a small assembly line way station ever come to be over only five or six hundred million years? I will try to give you an idea of how complex and unlikely this is.
We don't know, or at least I don't know, where the sequence or sequences are that tell the other little molecules that have formed into little machines how to form this structure from a string of bases, which code for amino acids, which form proteins is but lets imagine it is something about a hundred thousand bases long and looks something like tactggtagtagtcctctctccccaatctaatctactagactagactag.....etc
This is just a representation of a hundred thousand molecules that when processed in sets of three tell the processor to make corresponding amino acids which in turn then come out of the processor, which is the Endoplasmic Reticulum which looks something like this
Along the way the DNA has contained the instructions for the entire process within itself. Then it contains the instructions also to make more of itself. When you think about it you and I and everyone else as well as every living thing is a set of molecules put together in such a way as was dictated by a complex set of molecules before it. Every individual cell type in your body is produced by small factories
The idea that this complexity could form in 600 million years as in the case of larger multicellular lifeforms is far more mysterious and unlikely than science would have you believe.
Take the mystery of the divergence of homo sapiens from their distant ape cousins. Apes have 48 chromosomes. Humans have 46. In other words apes have 24 pairs and humans who split off the same distant branch at the same time have 23 pairs. So did the apes pick up a single chromosome during the gamete phase (sperm and egg) or did humans lose one? I Say gamete phase because that is the easiest moment for mutation to occur. Actually unless it does happen at the sperm/egg phase it more likely becomes cancer than a new species. A single mutation in one or a few of your cells won't do anything to change your entire genome. The mutation would have to occur during the time when you have a single set of haploid chromosomes. Diploid being the full set when the haploid set from the egg and the haploid set from the sperm combine.
One of the current theories how this reduction in chromosome pairs occurred was a joining of two chromosomes that then became a single chromosome leaving you with 23 pairs. But this would have to happen almost immediately after fertilization perhaps during a process known as transposition. During this phase the same segments from the egg haploid genome and the sperm haploid genome change places. Perhaps an entire chromosome was some how grafted onto another chromosome before the first mitotic division instead of just two segments swapping places.
I am a big fan of viruses being the impetus for much of the changes that have occurred in evolution. Especially those changes on a large scale. Those moments known as Punctuated Equilibrium. A virus already has the machinery to manipulate DNA. Also it's goal in many cases is to have a living host to reproduce in. By inserting its genome into the genome of the host it will be replicated every time the host cell is duplicated.
It is not unbelievable that these master DNA manipulators could stitch together two pieces of DNA or perhaps even make themselves the nexus of the joining. It is also possible that many of the genes we carry to this day were once viruses that got absorbed by our genome. Perhaps still active maybe now serving as a different function than they originally served the virus.
The problem with the fusing of two chromosomes, regardless of the stage of development, is that it would have to happen to a population. Even if a single mutation occurred in a female during very early gestation and she had a set of twins who could then turn around and reproduce this would have created such a bottle neck for our species at that point as to defy the odds of them and their offspring continuing on. The virus theory is actually better because the virus could be such that one of its side effects is this stitching together of these two particular chromosomes at some particular point after fertilization. Can you imagine the look on the faces of those parents when an entire troop gave birth to such different children?
When I first started studying biology back in the early 90s one of the very first thoughts I had was that viruses cause cancer. Cancers grow like an organism all their own. It is not a leap to imagine that out of the thousands if not millions of cancers and defects that have occurred over the millions of years that occasionally the manipulation turns out to be something beneficial.
* This entry took several months to write. I have been very busy. I also tend to burn out on all these things until I find a new angle to go at them with. I have been contemplating lately the idea of Intelligent Design. In my next blog entry, unless I come across something more interesting before I am finished outlining the case for or against intelligent design, will be The Case For Intelligent Design. Before I end this entry let me point out that Intelligent Design is real. It is happening right now. We are designing crops and organisms for purpose they did not evolve naturally. So who is to say it wasn't done before since we already know it happens?
*As a side note. This fusion of chromosomes occurs in other species as well. Mice for example. Apparently it is not uncommon and apparently not detrimental at least to humans and mice.
