The Greatest Mystery - DNA - 2012 (just because people are searching 2012)
In a nutshell DNA is the building blocks of life. More like the blueprint actually. Elements such as carbon, oxygen, hydrogen, nitrogen, and a few others are the building blocks. DNA is the universe's answer to the concept of the Von Neumann Machine. An idea used in science fiction of the 50s after being elucidated in the 40s by John Von Neumann a Hungarian-American mathematician who contributed significantly to the architecture of computers before computers where the everyday machines they are today.
The idea that life as we know it is not unlike a machine is not a new idea. Descartes was said to talk about life as a complex machine.
Bacteria are probably the most "perfect" living Von Neumanns. If anything has achieved a level of perfection it is bacteria and their hitchhiking buddies the Viruses.
Regardless of what popularized science will tell you we know next to nothing about how DNA works. We have a very amateurish idea of what it looks like and its composition. Just in the last few days we have been told that contrary to popular theory the so called "junk" DNA is more important than we at first thought. Which came as no surprise to me and many others. Nice to know science eventually catches up.
The image behind my blog title is taken from one of my programs. It takes a data file from the Human Genome Project, filters out all the stuff I don't need, such as headers, credits, and other information they add to it and produces a stream of letters that represent the base pairs in our DNA. There are four bases for DNA and one is different when it is RNA. RNA being more or less the "working" template for protein synthesis by your cells. Lot's of viruses are RNA viruses. Perhaps that's how some viruses or all viruses got started. Which is one of the theories I am working on with my DNA Imaging programs. Perhaps the first viruses began as a section of DNA was being copied or DNA that got somehow opened up and became an organism of its own. A self contained "lifeform" with the tools to reproduce itself which is what viruses do. They reproduce, as far as we know, by attaching themselves to another organism's cell and borrowing its factories and spare parts to reproduce itself. It would not surprise me at all to find that viruses can reproduce and even evolve by methods we refuse to imagine. And I mean that. There are some things science just doesn't want to believe until they have no choice. See Alfred Wegener, Tesla, Einstein, Galileo, etc.
I admit my knowledge is rudimentary and I like it that way. I know enough to do what I want without getting so immersed in the jargon and theories that I lose sight of my goal which is to find patterns in DNA.
*As a side note. I am writing this blog as a means to put my thoughts and theories "out there" as a record of sorts. I think I said that before. So many times over the last few years I have seen ideas that I have had for a long time suddenly appear as new theories. While watching the show Through The Wormhole hosted by Mr. Smooth Voice himself, Morgan Freeman, I decided to start this blog because about half the novel ideas presented there are not that novel to me at all. You might think that is brag and that's okay. I don't require that you believe me. This blog on DNA on my research over the last few years with my imaging programs was sparked by the recent announcement of the change in the attitude toward "junk DNA" something I thought was a stupid idea from the first moment I heard the term. "Junk DNA" indeed. Just one more example how science is still just stumbling along until the next big idea. And if I record my theories and ideas right here right now then if we are still here in a decade or so I can look back and see how my ideas have evolved. Easier than keeping track of my notebooks. I am missing about 10 years of my early work. I think it's in the attic. I'll go look this winter when it is cooler up there. I will be curious to see if what I wrote down 20 years ago is anything like the landscape of science today. But I digress.
Here is a short primer on DNA as it is presented to us. Note that I don't necessarily believe all of it. For instance I don't believe they have actually sequenced the entire genome and in the article above in the Junk DNA link they say they have figured out or assigned functions to 80% of the Human Genome. This is bull. Just as it was bull 5 years ago when they said it was junk. Just because it is bioactive doesn't mean it serves a function but by the same token it also doesn't mean they know what it does. It's just hype like 80% of modern science stories.
DNA is Deoxyribonucleic Acid. First off note that the word acid does not necessarily mean what you think it means. As I go along I will make keywords into links and you can follow those links at your leisure. So as not to bore you to death I will be brief. The parts of DNA that are in the data of the Human Genome Project files are called bases. These bases are molecules and there are four of them in the case of DNA. Adenine, Guanine, Cytosine, and Thymine. When a protein or other part is needed a signal and/or mechanism is sent that tells/initiates the DNA to open up and a copy is made of that section of DNA. This copy is called RNA and it has the same four bases except Thymine is replaced with Uracil. These bases are held together by a "skeleton" if you will of sugars and phosphate groups. Sugar is another one of those words that means a considerable bit more than what you might think. But we won't go into that here. This isn't a chemistry lesson. Three years of chemistry was enough thanks.
These bases when taken in sets of three are called Codons. These codons are code for what are called Amino Acids. You are probably aware of that term. The amino acids when strung together form protein chains. Due to their electromagnetic properties they twist fold and turn until they eventually become a piece of what ever is needed. Blood cells, tissue, white cells, bones, what have you. That is the very very very short version. There are codons that tell the transcribing mechanism when and where to start and where to stop. In fact the regulations for the entire functioning of an organism must have codes for every function. Not necessarily codons but strings of bases that are or are not codons that give fairly complex instructions to the machines in the cell that do the work. The complexity is staggering to contemplate. So complex in fact that some people who have worked with DNA have gone from agnostics and atheists to believers because the idea that such a complex mechanism as DNA and its functions happened by chance is inconceivable to them. At least in the short time it happened here on earth. According to theory the earth had barely cooled before bacteria appeared. A lot of people who aren't creationists and know something about science find that hard to believe. Myself included. Although I don't necessarily understand why this would lead people to join any of the major religions that have spent most of their existence keeping man as ignorant of reality as possible, but to each his own I suppose.
My reasoning when developing the DNA IMAGER programs was fairly simplistic. My thinking was that a code designed to replicate a certain structure would be different from sequences of code for other structures and that these codes would have a repetitive quality to them. Repetition in data can be seen as a pattern. I had four "codes" to work with and my goal was to look at the patterns so I just assigned the arbitrary colors of red, green, yellow, and blue to the four bases. If you have read my other posts you know that I occasionally have moments where my scientific thought process is interrupted by sudden bursts of faux divinity. Such as developing the 444 system and then finding that the number is buried in such things as mathematics at it most basic levels. Pi, Square root of two, and the primes. When I figured out one day that the 12th prime was 37 and this equaled 444 I had one of those moments where you look up and grin into empty space. Not quite a Paul on the road to Damascus moment but one of those moments where you think you might be being coached by god.
I had one of those moments about a year into my imaging program development. I went to a library to find a book with the electronic structure of the bases. My thought, and it still is my thought, to build an imager based upon the electromagnetic properties of the molecules involved. I am a big believer in layers of coding. If you read my last post on the Giza pyramid you would know what I mean. In DNA there are different layers of coding for sure. The folding of proteins have primary, secondary, and tertiary properties. Just the coding of proteins from bases is multilayer. You have bases, three bases make a codon, several codons can code for the same amino acid, and the amino acid taken together are genes and genes can either code for proteins or for something else. The electromagnetic properties of these amino acid chains determine their bond angles and folding and this is a code in itself. While looking through the meager books on the subject at my backwoods library I came across a book that had something fairly similar to what I was doing with color coding the bases. They however were not imaging the entire Human Genome because it hadn't been released yet at the time of the book. But they had also seen the value of assigning colors to the bases in order to "see" them better. I recall looking up and feeling as if I was given "a sign". One of those moments when you realize people who get paid for this stuff are having similar trains of thought. This happens quite frequently to me actually. So much so in my younger days that I actually believed I was being coached, coaxed, or what have you. That was until I actually read the Bible and became a nonbeliever. At least in the Bible anyway.
So as not to turn this post into a short novel I am going to post some of the images and explain them and my thinking. Remember I believe in layers of codes so I am constantly looking at both natural and unnatural angles. But given what little we actually know about DNA and its origin or function it is hard to know what is natural or unnatural. And in case you are wondering based on my last post about the Giza Pyramid being a "message to the future" if looking for "unnatural" patterns in the DNA is the same thing as looking for a "message" you would be right. And when you get time, after finishing my blog of course you should check out the video I will be inserting by Lloyd Pye "Everything You Know Is Wrong". It is kind of long but pay attention at the part about Human and Ape Chromosomes.
So here come the pictures.
The first image is basically the original format I used when viewing the images. In the Human Genome files the bases are listed as a, c, g, t or the letter n when the base is not known yet. These files are so full of holes in the data that one of two things is true. Either they don't actually have the entire genome processed or they aren't releasing all of it. The conspiracy theorist in me is curious about both possibilities. Either it is a lie they have the whole thing sequenced or there are sequences they don't want us to see.
Imagine 4 possible colors of beads on a string. You put those beads on the string in the same way that the base that color represents is read from the genome file. Then you take those beads on a string and lay them down back and forth like a snake. You go a certain distance drop down one level then go back the other way and continue. In the case of some chromosomes that's hundreds of millions of beads. The patterns are formed depending upon the "matrix" you use. My program allows you to enter the matrix you want to image. This one goes 54 bases before it turns back the other way. This method is one of the so called natural methods since these bases would be one behind the other in the DNA strand. My first imager put down a certain number of beads then just started back over at the left. The difference in the patterns can be quite different but not totally different. I imaged all but one of these images with each version of my program using exactly the same DNA file. So this is the same DNA sequence viewed in different ways. I still don't know if patterns like the one you see in the wavy lines are genes or not. At first your "natural" inclination is that this would be a gene but you can't be sure. I am currently finding and filing away known gene files to see if I can find them among my images. I have also downloaded sequenced virus and bacteria genomes for the same reason.
The method below lays down the image much like the information on a CD. Concentric Circles. It begins in the center laying down the "beads". The black portions in the above image and in the one below are gaps in the data in the genome files. I used to have my program ignore them but now I leave them in as markers. Which will help while you are looking at this. If you are curious how the 2 dimensional image above relates to the one below you can find your "mark" in the black circles below. The gaps up top are the gaps below. The windmill effect is caused by using one of my favorite equations.
You can take the Pythagorean theorem and use it to plot arcs or
quadrants of a circle. Instead of A and B to find C you use
X and Y and the hypotenuse becomes a series of points for R. The hypotenuse is treated as the radius of the circle. If you keep the
radius constant and move x forward you plot a different value for y and
vice versa. At each point plotted a pixel was set to red, green, blue,
or yellow depending upon the letter of the base being read at that
moment from the file. The pattern is completely different. The only thing you can spot are the variations in the amount of a certain color which indicates the presence of a certain base.
On the right - This is the same data plotted across the surface of a rod like a dowel to simulate the helix quality of DNA. A true spiral on this scale would not be much more revealing than the same size circle being laid down on an imaginary rod. The shift would only be a little bit one way or the other but the pattern would be essentially the same. This image is if the rod were looked at straight on. This is also just one side of the rod. The other side would be hidden by the front view.
Below - is the same idea except the rod is split in half. You couldn't see both sides if the two halves weren't separated. Also the data is represented slightly differently. Instead of a single pixel the nucleotide base is represented by 3 pixels. Imagine a box of 4 pixels 2 x 2. The upper left, upper right, and lower left are on and the lower right one is left black. This method enhances the colors. As you can tell.
Below - is a screen shot of a program I call Helix Finder. This is not the same data as the others. I just included it to show a point about layers of coding. On the left in the image is a graph that plots points based on the average count of the bases in the line to the left. It works like this. 120 points are laid down. On average there would be 30 of each base in each line. Average is rarely the case with DNA. The line down the center in the graphs on the right represents the average. The point plotted is the distance from average, plus or minus, on either side of the line. Here is the layering point I am making. Look in the graph at the right. notice the red, green, and blue lines. You may be able to copy and enlarge if you need to see it better. What you will see is a helix like pattern. I discovered this completely by chance while trying to find a quicker way to look through the 3 gigabytes of data. I thought a graph might show me "hot spots" to come back and image. That idea didn't work out but it did produce this result. Note that this is just a numerical accounting of the occurrence of the bases not the actual bases. It seems even in the "math" of DNA there is structure.
Below - This is a very very very small sample of some of the "blips" found in the tens of thousands of panels produced by the very first method. I clipped and pasted them. These interesting patterns appear usually at the beginning and ending of a chromosome. The solid colors indicate strong math. Such as the exact same base occurring exactly in the same frequency over an extended period of time. The scaly looking sections have an interesting mathematics even more complicated than the solid colors. I haven't worked out the math of some of these patterns yet. My thought is to use known equations like the Fibonacci sequence and others like 2n +1 or whatever and see if I can find comparable patterns. It would not surprise me at all to find the Fibonacci sequence being used by DNA since it is used so much in nature. This set is taken exclusively from panels 54 bases wide. I have found interesting patterns using smaller matrices like 33 and larger ones like 121 or larger. I have one program that will image very large swaths thousands of bases across. This removes most patterns. Patterns seem to occur over a small range of bases. Each of these patterns persist for a few thousand bases. Some like the one at top persisted over 100s of thousands. You can see that in the numbers at the bottom of the screen which is a base count.
If you haven't figured it out yet the possibilities are infinite here. There are 3 billion bases to image in a myriad of different ways. I will admit the concentric circle idea seems to be producing nothing so I can probably drop that one. Looks cool on monochrome Pi and Phi images though. The rod imager doesn't seem to produce anything more interesting than the flat panels above. So I have set about imaging the entire genome using the first method. And that's why I happen to have all these panels 54 bases wide.
I haven't found anything like "HEY HUMANS WE WERE HERE" or an alien's face in the patterns but then again it takes weeks to generate one entire set of panels with all 23 chromosomes. When you have a regular job it takes a long time to look at all the data generated and that's just for a specific number like the above 54. Mix in blogging and writing Pyramid programs and working on about a hundred other different lines of inquiry and it has become apparent that if I ever do find the "EUREKA" moment the aliens may have already landed by then. In which case I suppose I could just ask them if they aren't busy vaporizing us for infesting a perfectly good planet with our stupidity.
Assuming aliens didn't write a message in our DNA or that we aren't a product of their genetic tampering the search for viruses in our genome is still a worthwhile endeavor. It is my theory that the points in evolution known as Punctuated Equilibrium are sometimes produced by viruses. This explains how species can take what appear to be monumental jumps in evolution. By jumps I simply mean significant changes not reaching higher levels. In fact it appears that humans may actually be kind of further down on the ladder than some of our ancestors but that is beside the point. The term punctuated equilibrium was coined to note those periods in the fossil record where an incredible change in the DNA of several species occurred.
The classic view of evolution is modification over time. A chance mutation occurs in the genome of a species and either produces a disadvantage, an advantage, or something neutral. Extreme changes in morphology that are not deadly are extremely rare. Mutations usually lead to deadly consequences if they produce a change. As I said before several different bases can be substituted in a given codon that produce the same amino acid so a mutation at this level has good odds of changing nothing. On the other hand a mutation in just the right place on a gene could cause the transcription of that gene and the subsequent folding of the protein it produces to be dangerous. Sickle Cell Anemia for example. But Sickle Cell also gives an advantage against malaria. Our advances in modern medicine have in fact increased the passing on of these mutated genes to the point where people who carry them are able to transfer them. Modern medicine is good for the individual but on the whole not for the entire species although some could easily argue that some people who have contributed greatly to the advance of mankind were carries of these genes. If we were to be pragmatic about the whole thing we could simply say that there are over 6 billion humans and that the number of those with the harmful mutations are a small percentage of the population and pose no threat to the entire human genome as whole. That entire discussion we will probably never have on this blog. Eugenics isn't a big winner with most people.
There is a way to look at genes themselves that is fairly novel. I didn't think of it and I don't remember where I heard it but it was one of those epiphany moments. The thinking goes like this. The same genes occur in several different species. Many species from chickens to humans have genes in common how do you suppose that happened? A common ancestor perhaps? This is where the sequencing of as many animals as possible turns out to be important, if you care about such things. We could map the genes we have in common and the genes we don't have in common and build a map of when our species diverged. Here is another way to look at evolution though. What if we look at it from the genes point of view.
Those genes that we all have in common or most of us (lifeforms on planet earth) have in common are most likely the oldest surviving genes. Animals have come and gone and the variety of life is amazing and these genes have survived since the time of our earliest common ancestors. It is the genes that are the survivors. Where as a gene might be mutated occasionally by chance in an individual it survives intact in everyone else unless that gene gives an advantage and is passed on. Could the different copies of these genes persist at the same time? Yes they do. Blue eyes and Brown eyes are an example as well as many others.
The biggest mystery perhaps is our supposed split from the apes. If we both descended from a common ancestor and the apes go back as far as we do and the apes have a total compliment of 48 chromosomes in the diploid state. Humans have only 46. This means that the haploid cells, or sex cells of apes have 24 chromosomes and humans 23. This is only one chromosome less than the apes but still IT IS ONE WHOLE CHROMOSOME difference.
How do you suppose that happens? An entire Chromosome difference in a few million years? Did they gain one or did we lose one? Or is there another possibility?
In my mind, if we leave out aliens, this is where viruses come in. Viruses can enter a host cell and stay there forever reproducing along with the cells of the host. Sometimes this causes illness and death. Sometimes its a mild illness and the host gets better. Sometimes it's cancer. And perhaps sometimes this self contained entity all its own can become a gene. Not likely an entire chromosome though lost or gained. But perhaps one mystery of evolution can be solved by the idea that viruses have caused punctuated equilibrium.
It may be just a matter of getting enough viruses sequenced until I start finding evidence of them in our DNA. But I also only have the one genome to examine and my computers aren't the fastest and I don't have the time to devote myself to the project more than a few hours a week.
Maybe someone out there who reads this blog. Assuming anyone ever reads this blog. Will see my theory, steal it, and develop it. If that happens and you make a few million how about sending a mil or two my way and I won't sue you and I can go to Egypt and spend my time on the pyramids. It's the least you could do. Frankly I would just like to know if I am right.
This isn't the whole story of my dance with DNA. I have more theories. I have more angles to approach the imaging. Perhaps I will find something maybe I won't. I have the method for imaging the DNA figured out but I am always thinking about new ones. In the mean time I will keep plugging away with the method I have and trying different matrices. If an alien face pops out of the data or a virus I will post it here first.
Enjoy the video. I found it very interesting.
The idea that life as we know it is not unlike a machine is not a new idea. Descartes was said to talk about life as a complex machine.
Bacteria are probably the most "perfect" living Von Neumanns. If anything has achieved a level of perfection it is bacteria and their hitchhiking buddies the Viruses.
Regardless of what popularized science will tell you we know next to nothing about how DNA works. We have a very amateurish idea of what it looks like and its composition. Just in the last few days we have been told that contrary to popular theory the so called "junk" DNA is more important than we at first thought. Which came as no surprise to me and many others. Nice to know science eventually catches up.
The image behind my blog title is taken from one of my programs. It takes a data file from the Human Genome Project, filters out all the stuff I don't need, such as headers, credits, and other information they add to it and produces a stream of letters that represent the base pairs in our DNA. There are four bases for DNA and one is different when it is RNA. RNA being more or less the "working" template for protein synthesis by your cells. Lot's of viruses are RNA viruses. Perhaps that's how some viruses or all viruses got started. Which is one of the theories I am working on with my DNA Imaging programs. Perhaps the first viruses began as a section of DNA was being copied or DNA that got somehow opened up and became an organism of its own. A self contained "lifeform" with the tools to reproduce itself which is what viruses do. They reproduce, as far as we know, by attaching themselves to another organism's cell and borrowing its factories and spare parts to reproduce itself. It would not surprise me at all to find that viruses can reproduce and even evolve by methods we refuse to imagine. And I mean that. There are some things science just doesn't want to believe until they have no choice. See Alfred Wegener, Tesla, Einstein, Galileo, etc.
I admit my knowledge is rudimentary and I like it that way. I know enough to do what I want without getting so immersed in the jargon and theories that I lose sight of my goal which is to find patterns in DNA.
*As a side note. I am writing this blog as a means to put my thoughts and theories "out there" as a record of sorts. I think I said that before. So many times over the last few years I have seen ideas that I have had for a long time suddenly appear as new theories. While watching the show Through The Wormhole hosted by Mr. Smooth Voice himself, Morgan Freeman, I decided to start this blog because about half the novel ideas presented there are not that novel to me at all. You might think that is brag and that's okay. I don't require that you believe me. This blog on DNA on my research over the last few years with my imaging programs was sparked by the recent announcement of the change in the attitude toward "junk DNA" something I thought was a stupid idea from the first moment I heard the term. "Junk DNA" indeed. Just one more example how science is still just stumbling along until the next big idea. And if I record my theories and ideas right here right now then if we are still here in a decade or so I can look back and see how my ideas have evolved. Easier than keeping track of my notebooks. I am missing about 10 years of my early work. I think it's in the attic. I'll go look this winter when it is cooler up there. I will be curious to see if what I wrote down 20 years ago is anything like the landscape of science today. But I digress.
Here is a short primer on DNA as it is presented to us. Note that I don't necessarily believe all of it. For instance I don't believe they have actually sequenced the entire genome and in the article above in the Junk DNA link they say they have figured out or assigned functions to 80% of the Human Genome. This is bull. Just as it was bull 5 years ago when they said it was junk. Just because it is bioactive doesn't mean it serves a function but by the same token it also doesn't mean they know what it does. It's just hype like 80% of modern science stories.
DNA is Deoxyribonucleic Acid. First off note that the word acid does not necessarily mean what you think it means. As I go along I will make keywords into links and you can follow those links at your leisure. So as not to bore you to death I will be brief. The parts of DNA that are in the data of the Human Genome Project files are called bases. These bases are molecules and there are four of them in the case of DNA. Adenine, Guanine, Cytosine, and Thymine. When a protein or other part is needed a signal and/or mechanism is sent that tells/initiates the DNA to open up and a copy is made of that section of DNA. This copy is called RNA and it has the same four bases except Thymine is replaced with Uracil. These bases are held together by a "skeleton" if you will of sugars and phosphate groups. Sugar is another one of those words that means a considerable bit more than what you might think. But we won't go into that here. This isn't a chemistry lesson. Three years of chemistry was enough thanks.
These bases when taken in sets of three are called Codons. These codons are code for what are called Amino Acids. You are probably aware of that term. The amino acids when strung together form protein chains. Due to their electromagnetic properties they twist fold and turn until they eventually become a piece of what ever is needed. Blood cells, tissue, white cells, bones, what have you. That is the very very very short version. There are codons that tell the transcribing mechanism when and where to start and where to stop. In fact the regulations for the entire functioning of an organism must have codes for every function. Not necessarily codons but strings of bases that are or are not codons that give fairly complex instructions to the machines in the cell that do the work. The complexity is staggering to contemplate. So complex in fact that some people who have worked with DNA have gone from agnostics and atheists to believers because the idea that such a complex mechanism as DNA and its functions happened by chance is inconceivable to them. At least in the short time it happened here on earth. According to theory the earth had barely cooled before bacteria appeared. A lot of people who aren't creationists and know something about science find that hard to believe. Myself included. Although I don't necessarily understand why this would lead people to join any of the major religions that have spent most of their existence keeping man as ignorant of reality as possible, but to each his own I suppose.
My reasoning when developing the DNA IMAGER programs was fairly simplistic. My thinking was that a code designed to replicate a certain structure would be different from sequences of code for other structures and that these codes would have a repetitive quality to them. Repetition in data can be seen as a pattern. I had four "codes" to work with and my goal was to look at the patterns so I just assigned the arbitrary colors of red, green, yellow, and blue to the four bases. If you have read my other posts you know that I occasionally have moments where my scientific thought process is interrupted by sudden bursts of faux divinity. Such as developing the 444 system and then finding that the number is buried in such things as mathematics at it most basic levels. Pi, Square root of two, and the primes. When I figured out one day that the 12th prime was 37 and this equaled 444 I had one of those moments where you look up and grin into empty space. Not quite a Paul on the road to Damascus moment but one of those moments where you think you might be being coached by god.
I had one of those moments about a year into my imaging program development. I went to a library to find a book with the electronic structure of the bases. My thought, and it still is my thought, to build an imager based upon the electromagnetic properties of the molecules involved. I am a big believer in layers of coding. If you read my last post on the Giza pyramid you would know what I mean. In DNA there are different layers of coding for sure. The folding of proteins have primary, secondary, and tertiary properties. Just the coding of proteins from bases is multilayer. You have bases, three bases make a codon, several codons can code for the same amino acid, and the amino acid taken together are genes and genes can either code for proteins or for something else. The electromagnetic properties of these amino acid chains determine their bond angles and folding and this is a code in itself. While looking through the meager books on the subject at my backwoods library I came across a book that had something fairly similar to what I was doing with color coding the bases. They however were not imaging the entire Human Genome because it hadn't been released yet at the time of the book. But they had also seen the value of assigning colors to the bases in order to "see" them better. I recall looking up and feeling as if I was given "a sign". One of those moments when you realize people who get paid for this stuff are having similar trains of thought. This happens quite frequently to me actually. So much so in my younger days that I actually believed I was being coached, coaxed, or what have you. That was until I actually read the Bible and became a nonbeliever. At least in the Bible anyway.
So as not to turn this post into a short novel I am going to post some of the images and explain them and my thinking. Remember I believe in layers of codes so I am constantly looking at both natural and unnatural angles. But given what little we actually know about DNA and its origin or function it is hard to know what is natural or unnatural. And in case you are wondering based on my last post about the Giza Pyramid being a "message to the future" if looking for "unnatural" patterns in the DNA is the same thing as looking for a "message" you would be right. And when you get time, after finishing my blog of course you should check out the video I will be inserting by Lloyd Pye "Everything You Know Is Wrong". It is kind of long but pay attention at the part about Human and Ape Chromosomes.
So here come the pictures.
The first image is basically the original format I used when viewing the images. In the Human Genome files the bases are listed as a, c, g, t or the letter n when the base is not known yet. These files are so full of holes in the data that one of two things is true. Either they don't actually have the entire genome processed or they aren't releasing all of it. The conspiracy theorist in me is curious about both possibilities. Either it is a lie they have the whole thing sequenced or there are sequences they don't want us to see.
Imagine 4 possible colors of beads on a string. You put those beads on the string in the same way that the base that color represents is read from the genome file. Then you take those beads on a string and lay them down back and forth like a snake. You go a certain distance drop down one level then go back the other way and continue. In the case of some chromosomes that's hundreds of millions of beads. The patterns are formed depending upon the "matrix" you use. My program allows you to enter the matrix you want to image. This one goes 54 bases before it turns back the other way. This method is one of the so called natural methods since these bases would be one behind the other in the DNA strand. My first imager put down a certain number of beads then just started back over at the left. The difference in the patterns can be quite different but not totally different. I imaged all but one of these images with each version of my program using exactly the same DNA file. So this is the same DNA sequence viewed in different ways. I still don't know if patterns like the one you see in the wavy lines are genes or not. At first your "natural" inclination is that this would be a gene but you can't be sure. I am currently finding and filing away known gene files to see if I can find them among my images. I have also downloaded sequenced virus and bacteria genomes for the same reason.
The method below lays down the image much like the information on a CD. Concentric Circles. It begins in the center laying down the "beads". The black portions in the above image and in the one below are gaps in the data in the genome files. I used to have my program ignore them but now I leave them in as markers. Which will help while you are looking at this. If you are curious how the 2 dimensional image above relates to the one below you can find your "mark" in the black circles below. The gaps up top are the gaps below. The windmill effect is caused by using one of my favorite equations.
On the right - This is the same data plotted across the surface of a rod like a dowel to simulate the helix quality of DNA. A true spiral on this scale would not be much more revealing than the same size circle being laid down on an imaginary rod. The shift would only be a little bit one way or the other but the pattern would be essentially the same. This image is if the rod were looked at straight on. This is also just one side of the rod. The other side would be hidden by the front view.
Below - is the same idea except the rod is split in half. You couldn't see both sides if the two halves weren't separated. Also the data is represented slightly differently. Instead of a single pixel the nucleotide base is represented by 3 pixels. Imagine a box of 4 pixels 2 x 2. The upper left, upper right, and lower left are on and the lower right one is left black. This method enhances the colors. As you can tell.
Below - is a screen shot of a program I call Helix Finder. This is not the same data as the others. I just included it to show a point about layers of coding. On the left in the image is a graph that plots points based on the average count of the bases in the line to the left. It works like this. 120 points are laid down. On average there would be 30 of each base in each line. Average is rarely the case with DNA. The line down the center in the graphs on the right represents the average. The point plotted is the distance from average, plus or minus, on either side of the line. Here is the layering point I am making. Look in the graph at the right. notice the red, green, and blue lines. You may be able to copy and enlarge if you need to see it better. What you will see is a helix like pattern. I discovered this completely by chance while trying to find a quicker way to look through the 3 gigabytes of data. I thought a graph might show me "hot spots" to come back and image. That idea didn't work out but it did produce this result. Note that this is just a numerical accounting of the occurrence of the bases not the actual bases. It seems even in the "math" of DNA there is structure.
Below - This is a very very very small sample of some of the "blips" found in the tens of thousands of panels produced by the very first method. I clipped and pasted them. These interesting patterns appear usually at the beginning and ending of a chromosome. The solid colors indicate strong math. Such as the exact same base occurring exactly in the same frequency over an extended period of time. The scaly looking sections have an interesting mathematics even more complicated than the solid colors. I haven't worked out the math of some of these patterns yet. My thought is to use known equations like the Fibonacci sequence and others like 2n +1 or whatever and see if I can find comparable patterns. It would not surprise me at all to find the Fibonacci sequence being used by DNA since it is used so much in nature. This set is taken exclusively from panels 54 bases wide. I have found interesting patterns using smaller matrices like 33 and larger ones like 121 or larger. I have one program that will image very large swaths thousands of bases across. This removes most patterns. Patterns seem to occur over a small range of bases. Each of these patterns persist for a few thousand bases. Some like the one at top persisted over 100s of thousands. You can see that in the numbers at the bottom of the screen which is a base count.
I haven't found anything like "HEY HUMANS WE WERE HERE" or an alien's face in the patterns but then again it takes weeks to generate one entire set of panels with all 23 chromosomes. When you have a regular job it takes a long time to look at all the data generated and that's just for a specific number like the above 54. Mix in blogging and writing Pyramid programs and working on about a hundred other different lines of inquiry and it has become apparent that if I ever do find the "EUREKA" moment the aliens may have already landed by then. In which case I suppose I could just ask them if they aren't busy vaporizing us for infesting a perfectly good planet with our stupidity.
Assuming aliens didn't write a message in our DNA or that we aren't a product of their genetic tampering the search for viruses in our genome is still a worthwhile endeavor. It is my theory that the points in evolution known as Punctuated Equilibrium are sometimes produced by viruses. This explains how species can take what appear to be monumental jumps in evolution. By jumps I simply mean significant changes not reaching higher levels. In fact it appears that humans may actually be kind of further down on the ladder than some of our ancestors but that is beside the point. The term punctuated equilibrium was coined to note those periods in the fossil record where an incredible change in the DNA of several species occurred.
The classic view of evolution is modification over time. A chance mutation occurs in the genome of a species and either produces a disadvantage, an advantage, or something neutral. Extreme changes in morphology that are not deadly are extremely rare. Mutations usually lead to deadly consequences if they produce a change. As I said before several different bases can be substituted in a given codon that produce the same amino acid so a mutation at this level has good odds of changing nothing. On the other hand a mutation in just the right place on a gene could cause the transcription of that gene and the subsequent folding of the protein it produces to be dangerous. Sickle Cell Anemia for example. But Sickle Cell also gives an advantage against malaria. Our advances in modern medicine have in fact increased the passing on of these mutated genes to the point where people who carry them are able to transfer them. Modern medicine is good for the individual but on the whole not for the entire species although some could easily argue that some people who have contributed greatly to the advance of mankind were carries of these genes. If we were to be pragmatic about the whole thing we could simply say that there are over 6 billion humans and that the number of those with the harmful mutations are a small percentage of the population and pose no threat to the entire human genome as whole. That entire discussion we will probably never have on this blog. Eugenics isn't a big winner with most people.
There is a way to look at genes themselves that is fairly novel. I didn't think of it and I don't remember where I heard it but it was one of those epiphany moments. The thinking goes like this. The same genes occur in several different species. Many species from chickens to humans have genes in common how do you suppose that happened? A common ancestor perhaps? This is where the sequencing of as many animals as possible turns out to be important, if you care about such things. We could map the genes we have in common and the genes we don't have in common and build a map of when our species diverged. Here is another way to look at evolution though. What if we look at it from the genes point of view.
Those genes that we all have in common or most of us (lifeforms on planet earth) have in common are most likely the oldest surviving genes. Animals have come and gone and the variety of life is amazing and these genes have survived since the time of our earliest common ancestors. It is the genes that are the survivors. Where as a gene might be mutated occasionally by chance in an individual it survives intact in everyone else unless that gene gives an advantage and is passed on. Could the different copies of these genes persist at the same time? Yes they do. Blue eyes and Brown eyes are an example as well as many others.
The biggest mystery perhaps is our supposed split from the apes. If we both descended from a common ancestor and the apes go back as far as we do and the apes have a total compliment of 48 chromosomes in the diploid state. Humans have only 46. This means that the haploid cells, or sex cells of apes have 24 chromosomes and humans 23. This is only one chromosome less than the apes but still IT IS ONE WHOLE CHROMOSOME difference.
How do you suppose that happens? An entire Chromosome difference in a few million years? Did they gain one or did we lose one? Or is there another possibility?
In my mind, if we leave out aliens, this is where viruses come in. Viruses can enter a host cell and stay there forever reproducing along with the cells of the host. Sometimes this causes illness and death. Sometimes its a mild illness and the host gets better. Sometimes it's cancer. And perhaps sometimes this self contained entity all its own can become a gene. Not likely an entire chromosome though lost or gained. But perhaps one mystery of evolution can be solved by the idea that viruses have caused punctuated equilibrium.
It may be just a matter of getting enough viruses sequenced until I start finding evidence of them in our DNA. But I also only have the one genome to examine and my computers aren't the fastest and I don't have the time to devote myself to the project more than a few hours a week.
Maybe someone out there who reads this blog. Assuming anyone ever reads this blog. Will see my theory, steal it, and develop it. If that happens and you make a few million how about sending a mil or two my way and I won't sue you and I can go to Egypt and spend my time on the pyramids. It's the least you could do. Frankly I would just like to know if I am right.
This isn't the whole story of my dance with DNA. I have more theories. I have more angles to approach the imaging. Perhaps I will find something maybe I won't. I have the method for imaging the DNA figured out but I am always thinking about new ones. In the mean time I will keep plugging away with the method I have and trying different matrices. If an alien face pops out of the data or a virus I will post it here first.
Enjoy the video. I found it very interesting.
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