Just Thinking Aloud - Sorta

I was at work today writing notes as I go on which topic to explore next.  I am off the Pyramid kick for the moment.  Although today I had an idea about how the information, if any, is organized in the mathematics of the Giza Pyramids. Which I believe are Mesopotamian/Sumerian in origin. Not Egyptian.  The Egyptians probably began as a split off of the Sumerians or Akkadians but the pyramids after the first few pyramids show a decline from high engineering to a dwindling of knowledge and skill.  So that is the state of my thoughts on Pyramids. If you haven't read what I have posted so far check the earlier blogs.

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.

Wrapping Your Mind Around Time

It is truly difficult to quantify time.  It's like a congressman once said about porn. " I know it when I see it."  We have clocks to tell us the time of day but when you look at a clock exactly what are you looking at?  And how important is keeping track of time anyway?  And in keeping track of time what are we learning about it in the process?

You have heard that time is the fourth or fifth dimension I am sure. I don't believe that time is a dimension.  Then it is explained that the level of dimensions proceed as such.  You have a point in space with no width or depth. That's one dimension. You have two of these and you have a line.  A line is two dimensional or so you would think.  Actually you don't. Even with multiple points you still only have one dimension as long as no points lie outside that line. Even at just two points the problem becomes as much metaphysical as it does mathematical.  Do you really have a line or just two points in space.  You really wouldn't even get that far in this discussion since if these two points or even a single point existed "in space" then you already have dimensionality because of the space that contains them.  What if you have a thousand points all lined up?  Do the number of dimensions jump? Intuitively you say no.

Most people would agree that a plane, such as a sheet of paper with no thickness would be two dimensional. To form this geometric construct you would need a minimum of three points and one must not be in line with the other two.  So when you think about it any two points of any triangle are lines but you need all three points to define a plane.

If you build on this idea in a minimalist fashion and ask yourself how many points you need for three dimensions you realize you need four but this is only a geometric construct it doesn't actually represent reality. For this "space" to contain points then it must already have dimensional characteristics so the points do not define the "first" dimensional construct the space that they occupy must first. That is unless your construct is the only thing that exists.  Furthermore couldn't two planes exist with each having its own set of points without the two being connected and therefore not achieving dimension?  If so then would the two separate planes need to occupy the same plane and would just be segments of a larger plane?

As you can see by the time you reach any discussion about a fourth and fifth dimension and the property of time you aren't talking about anything you know with any degree of certainty.  To call time a dimension wouldn't even make sense in this context.  If time existed in a universe with two geometric dimensions like a sheet of paper would time add a third dimension? And which dimension comes first?

In this thought experiment lets say that time is not a dimension thus saving ourselves the trouble of trying to define its rank in the universe. The very idea of "dimensions" is a human construct and therefore not necessarily a true representation of "nature's reality" as opposed to those things that are "human realities"

So what is time as we know it?

We experience time as the property of the universe that does not allow for everything to happen all at once which would destroy the universe? We only experience anything that we experience due to the property of the passage of time.  I have to admit I am having trouble forming a sentence to describe time without using the word time. As I said it's one of those things you know when you see it but I don't think we have the language to explain it we can only quantify it.

Measuring Time

 


<===synchronous




       digital===>






<==== cesium atomic


strontium atomic===>





The first clock above (synchronous) works on the fact that the power grid has a certain frequency.  AC current in America is kept as close to 60 hertz, or 60 back and forth cycles,  as possible for this reason originally.  This is averaged out over the course of a day. This method of time keeping is more a counting of the oscillation of the power supply than it is a time keeping device.

The second clock (digital) works on the same principle.  Again a counter of pulses or oscillations is used.

Atomic clocks are similar in that they are merely counters. In the case of Cesium the oscillation is the radiation emitted from an electron jumping from one energy level to another very rapidly. How this is achieved is simple if you are a physicist but the rest of us will just take their word for it.

The second is defined as 9,192,631,770cycles of this radiation.  Note that radiation does not always mean something deadly.
Radiators in your home "radiate" heat.  Again we are counting something and defining what that means. A more 
detailed account is found in the following link. This probably seems odd that this is the number used and it matches a second
except the second was already a pretty defined length of time. This is "backward engineering" in that the second existed
and they found a number that suited their needs.  If they had chose 9,192,631,771 the difference would only show up after 
9,192,631,770 seconds which is over 12 years and then you would only be off by a second.  An Atomic Second anyway.

 http://www.popsci.com/science/article/2010-11/where-international-standard-units-come-part-two-second

In general terms the length of a second is 60 x 60 x 24 parts of a day or 86,400 seconds in a day.  This is what matches our clocks.  This is a day divided into 24 hours and hours into 60 minutes and minutes into 60 seconds. This is somewhat "natural" as is the first clocks used.  Water clocks and then pendulum clocks were "natural clocks".  But even then the length of the pendulum used had to be determined to make a number of swings that matched the possibly arbitrary division of the day into 86,400 seconds.

There are a few books on the measurement of time. I would suggest  Deep Time by Gregory Benford and In Search Of Time by Dan Falk. And many others I have read that I don't recall right now.

Given the volume of books on the subject I could not possibly go into all the aspects of time but my hope is to actually get you interested in looking for yourself.  For instance why do you need a clock as accurate as over 9 billion parts per second as demonstrated in the Cesium Atomic Clock.  What could you possibly need with that kind of accuracy?

One answer is GPS.  We owe a lot of our modern transportation, especially on the ocean, to the use of GPS. Global Positioning System. We also owe our ability to wage war with precision guided weapons to this system. But we also use it to measure the height of volcanoes to see if they are growing and combined with lasers could measure the movement of fault lines.  For this to be possible the signals from the satellites to a receiver on the ground and between the satellites have to know exactly what time it is and not just any old time.  The signal between two satellites or the time between signal from and to the ground needs to be measured very accurately.  Radio signals travel at the speed of light just like well just like light does.  To measure something with the accuracy of say 30 feet is a pretty remarkable feat.  A foot is roughly 1 / 11,784,960,000 the distance an electromagnetic signal travels in a second.  Thus 30 feet is a calculation roughly of 1 in 392 millionths.  In atomic clocks time that is about 23 or so super super small ticks of the atomic clock. It is easy to see that over greater distances even an atomic clock would eventually lead to large inaccuracies.  And we haven't even factored in the speed of the satellites at nearly 9,000 miles per hour not to mention the effect of time dilation on moving objects etc.

On a more general level we have an idea what the greatest amount of time is. We already know or believe the universe to have existed for nearly 14 billion earth years which is odd when you think about it since the earth has only been around about a third of that.  Which leads me to the point that the measurement of time is a totally human endeavor. However it would not be surprising to find out that if an alien race were to ever visit humankind that they too invented Cesium Atomic Clocks and Quartz Clocks both of which use natural phenomenon to achieve accurate oscillations to count. But their definition of what a standard unit of time like the second would be different and probably based upon the orbit and rotation of their home planet at first. As I mentioned in a previous blog when you use nature as your units of measure a species not "from here" would, if they had science, encounter the same universal properties that we do and thus science and math would be our common language. What their language and imagery means would be more difficult to decipher but math is math and a pendulum is a pendulum no matter where you are.

So what is the smallest amount of time?  A much harder question to answer.  Max Planck sought to answer that with the idea of Planck Time.  For a decent article on this subject check out the following link.
 http://www.universetoday.com/79418/planck-time/   basically Max Planck did what I would do, if I may be so bold, is to reduce time, velocity, size, etc into a system based on the observed universe where the fasted thing we know is the speed of light and the smallest thing we know is in the smallest sub sub atomic particles. A Planck length is the point at which two points are distinguishable. Below this measurement any two points, if they existed independently of each other, would be indistinguishable.  This of course cannot be proven at present.  The distance is on the order of 1 x 10 to the minus 20 which is very very small. And it may turn out that you can't have two points indistinguishable from each other and still have two points until you bring in string theory or some such thing.  Something I don't pretend to understand or necessarily believe.

The use of atomic clocks in a way divorces us from nature.  The number of cycles 9 billion or so is only the way it is because it closely matches the second we have become accustomed to a second that goes all the way back to the earliest civilizations who divided time by 12s and 60s for whatever reason we can only guess.  Is it because circles divide easily into 60s?  Would this even matter in a time when there were no clock faces?  Probably not.  So why those numbers?  It's a mystery lost to time. Why did people with 10 fingers decide to stop counting at 60 discrete numbers and then use multiples of that number?  70 becomes 1 x  60 + 10 not just plain old 70.

Here is a quick quiz of course only you will know if you get it right. What are the first 10 numbers?  Did  you say 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ?   Look closely.  How did you get 10?  You just stuck a zero after a 1.  But where did you get a zero?  The actual first numbers or digits are the same as above except you start with 0 and end with the 9.  As you count higher and higher you just move numbers around. 10, 20, 30  or 100, 200, 300, etc.  Easy enough to figure out unless you don't believe in 0.  You don't have 0 fingers. Hopefully.  So it is kind of understandable that some people may not believe or understand 0. But still why 60?

The actual day, expressed in seconds, is 23 hours 56 minutes and 4 seconds. This is how long it takes for the earth to rotate once but based on what?  In this case for the sun to reach its highest point on two successive days but this is somewhat arbitrary and changes depending on the season as much as 146 seconds from least to greatest.  There is also the sidereal day or the time for the earth to rotate enough to have a distant star in the same place two days in a row. Or two nights anyway.  While you are thinking about that think about this.  At the same time the earth is rotating it is also moving around the sun slightly less than 1 degree per "day" but which "day".  Once the concept of days became known to some degree of accuracy and "fixed" as a standard it became apparent over time that things didn't quite appear where they should appear in the daytime or nighttime sky.  This is why we have a leap day every 4 years, but not in 3 successive years that fall on a century,  and one extra every 4th century.  Example 1700, 1800, and 1900 were not leap years but 2000 was.  Also 2100, 2200, and 2300 will not be but 2400 will.  These account for the "decimals" in the numbers.  A "year" turns out to be 365.242 rotations of our planet or "days" and therefore in four years you get an extra day on the calendar but over four centuries this turns out to add 3 days too many so you keep them out at three century years but include it on the fourth century year.


If you really want to cook your brain follow this link.  http://www.universetoday.com/14700/how-long-is-a-day-on-earth/

There are obviously lots of things to consider when we consider time or at least the marking of time.  Over the thousands of years that man has been marking time it was the use of astrology and then astronomy and ultimately physics that lead us to the understanding that time is slippery in that when you seek to measure it at some point you are going to be wrong and at some point you realize that time is relative to the observer. Even at the smallest level Planck Time is not the smallest unit of time but the smallest measurement.

The whole point of this blog entry is to get the reader interested in the history of telling time.  How man arrived at his measurement of time from sundials, to water clocks, to the pendulum, to synchronous, to quartz, and ultimately to atomic clocks  is story of deep and clever thinkers.  Just think about this.  Currently there is a camera in existence that can actually take an image of a light beam as it strikes an object so quickly that you can tell where the light ends and begins and this method could produce some scientific discoveries we can't imagine yet. Machines and the use of time has enabled mankind to peer into worlds we could not possibly see on our own because we simply are not capable. Already the "slowing" of time by using cameras has enabled us to image the wings of insects in flight and create our own mechanical insects that fly as well as toy birds. Before the invention of digital movie making, it took only 16 frames per second of still photographs, taken in succession, to trick you into realizing the illusion known as the motion picture. Only 16 per second.  Lots of things can happen in a 1/16th of second especially inside an atomic clock.

And now I am out of time.  I will leave you with one of the most profound quotes that I have ever heard in my life and they come from a Star Trek movie no less.  In the movie Generations Malcolm McDowell is talking to Captain Picard and he says "time is the fire in which we burn" and later "time is the ultimate predator".  And when you think about it both of those things are true. Time eventually wins. After the last star burns out in trillions and trillions of years and the blackholes evaporate and perhaps the universe expands into a substance so thin as to not even have gravity anymore time will still exist. Time will be the very very last fundamental force/law of nature to exist long after the rest are gone.

And we didn't even get into the fact that our orbit around the sun isn't a circle or even an ellipse.  Not really. Here is another link to upset what you thought you knew about reality.   http://aa.usno.navy.mil/faq/docs/seasons_orbit.php


Goodbye

A Day Of Video Enlightenment an answer to Conspiracy Theorists who may be right.

Below is a collection of videos every American should be watching. Countries around the world are currently being robbed with the help of other governments and if you think for second it won't happen here you don't recall the history of America very well. Which is understandable since you were never actually taught anything.

Rich kids shouldn't run countries because they are rich.

Most Americans aren't smart enough to vote.

More examples of voter ignorance

This guy votes on legislation that affects you.

Why we need IQ tests for politicians.

Anarchy - AWESOME Speech

You will have to type in the above title to see the  video I have selected. Youtube doesn't allow you to copy and paste the URL.  I wonder why.

Zeitgeist - long movie. I don't agree with everything in it but you would do yourself a world of good to watch it.

  Lloyd Pye - Again I don't agree with everything in this video but he brings up some interesting points about the ethics and believability of science just because you don't understand science doesn't mean the people who do are telling you the truth.

OIL - Current News

You can watch a thousand videos with numerous viewpoints and still be confused but here is what you should know and remember.  A few months ago someone said Gold was worth nearly $2,000 and today its in the $1300 - $1400 range and everyone that believed it was worth nearly $2,000 just lost a lot of money.  Before 2008 the Media arm of the banks and corporations made TV shows that told you to buy houses and flip them and double  your money. They used regulations that had lay dormant for over a decade to rationalize giving loans to millions of people they knew couldn't pay it. Then they crashed the market with millions of people's names still on the dotted line and turned what your appraiser/bank said was a $300,000 home into one worth $175,000 almost over night.  Silver reached nearly $50 in April of 2011 and is now worth less than $23.  Why?

If you didn't watch all the videos but skipped down here to read this message go back up and watch the videos.  Take a day and watch the videos.  And if you don't agree with all of them that is fine but what you should be taking away from all this is that every single day of your life and for your entire life you have been lied to and almost none of what you think is true has anything to do with reality.

Humans should be better than this.  We may be the only intelligent life in the history of the universe and we are letting ourselves be run by people who will poison and destroy the planet just to have what they want in their short and pointless lives.  You people better wake up before it is too late. And before you think about listening to those people out there selling gold and silver on their radio shows and in youtube videos because ECONOGEDDON is coming. Just remember. If the American Dollar collapses you can't eat metal

Think about that

DNA IMAGER

I have been writing programs for about 28 years now beginning with Basic on TRS-80s which had about as much memory as a cheap solar calculator you find these days.  One of the first things I used a computer for was to turn data into images I could look at. I have always believed in the cliche that a picture is worth a thousand words.  We perceive more data through vision than any other sense. We see patterns that we wouldn't otherwise detect by other means.  The Human Genome Files have their data as a giant set of text containing the letters A, G, C, and T.  I like to use the files with the extension FA.  These are easiest to convert for my use although I have written several programs that will seek out the lines of a, c, g, and t in the other file formats.  The program won't start imaging the data until it gets an entire line of just those four letters thus a regular sentence such as those typed here won't fool the program.  If 40 a, c, g, and t's don't appear side by side it won't use the data at that point.   FA files eliminate the need for The Sifter as I call it.

I have imaged the entire Human Genome Set.  The last set I used was from February 2011 and isn't complete. I am not sure what this means. Is some of the data in doubt?  Is some of the data being withheld? Is it just actually incomplete?  We were all told that the entire human genome had been sequenced.  Be that as it may those missing lines of data are denoted in the Human Genome files with the letter N.  These appear as the black regions in the images. I originally excluded that data from my imaging but realized it would mess up the accounting part of the program. Not only am I imaging the entire genome I am testing the frequency of the bases in each chromosome as well as combinations of the bases such as the how often one letter/base occurs next to another and so forth.

The imaging is simple. A small bmp file 2 pixels by 2 pixels stands in for the letters in the files. Adenine is red, Guanine is blue, Cytosine is green, and Thymine is yellow. Instead of setting all four pixels in a 2 x 2 block I just set 3 leaving 1 pixel black. This gives contrast to the image.  Using small bmp files I am able to use images of small spheres, ovoids, or anything I want to represent the bases.

If I want to look at very large patterns on my largest computer screen with a resolution of 1400 x 900 I can use individual pixels for each base.  This gives me a larger section of the data I can look at at one time.

I have found a multitude of patterns.  I expect it will take me years to sift through all the data. Each chromosome, especially the larger ones, have as many as 250 million bases in them and generate several gigabytes of image files.  I have done only a quick look through the entire set and pulled out those patterns that caught my eye.  Originally I wasn't going to blog/publish any of these results thinking I may be on to something. My thought is to ultimately get crowd source funding to continue the work assuming someone doesn't just steal the work if they find it useful and call it their own. It wouldn't be the first time someone nearly anonymous got ripped off in the field of DNA research. Read the story of Rosalind Franklin if you are curious about that comment.

The first two panels below show a pattern I have seen across the entire genome all 24 chromosomes. That's 22 numbered chromosomes and 2 sex chromosomes X and Y.  In the panel below is a pattern I call Red and Green Banding.  All this work is preliminary so I don't know what it means yet except that it is an obvious strategy employed in every chromosome. Off the top of my head I am thinking it is like file folders in Windows.  Perhaps these sequences, which are folded in the chromosome, emit a magnetic signature that is like an index card along the sequence. Since it is my contention that all processes are based on electromagnetic properties I call profiles.  This is in line with the study of Protein Folding. The imaging idea is loosely based on the idea of a Beta Pleated Sheet. The image is laid down left to right and then depending upon the matrix it doubles back on itself like a snake winding its way down the screen.  To save hard drive space and to facilitate side by side comparisons I wrote a feature of the program that determines how many patterns can be put on a single screen, minus the control buttons on the side you can't see in the screen shots. This folding would not occur in nature because the particular EM properties of the bases would not allow such an arrangement if only because my representation is 2 dimensional and these molecules would be in 3 dimensions. This doesn't matter since I am looking for patterns in the bases. A similar string of bases, as you will see, will show a similar pattern

Red and Green Banding in the number 5 Chromosome.  An arbitrary distinction made up by the earlier scientists in the field. I don't believe there is any particular order of chromosomes although this research, when I really get down into the patterns, may prove otherwise.







Red and Green Banding in the number 3 Chromosome.  Having looked through the thousands upon thousands of images my programs have generated I have noticed that the red and green bands are "tighter".  There are also Orange and Aqua colored bands as well. These bands are more drawn out and not as "tight".






I expect these images to expand quite a bit when the viewer clicks on them. I am working with blogger while it is acting up so I am not sure what it is going to do.  Assuming it works correctly the user will see in the next panel what I call Red Blue Jean Pattern and in the same image what I call the Slanted Pattern.  The red blue jean pattern is fairly unique. This is the largest example of it. The slanted pattern occurs in half of the chromosomes which is interesting to me.  Of course the orientation of the pattern is affected by the matrix used. The matrix being the point at which the line of pixels, beads, or what ever colored image I am using loops back on itself.  This particular panel has a matrix of 54.

I wrote a program that I could change the matrix in real time while the image was being painted on the screen.  The range of 50s to 70s produces some very striking patterns. In the pixel form of this program which sets a single pixel per base the matrix 121 is interesting. I am imaging the entire genome again using that method and comparing these areas. Changing the matrix changes patterns and reveals new ones the other matrix didn't.

 The Red Blue Jean panel shows another pattern similar to the next two image panels above this sentence.  This feature is the slanted pattern and in some chromosomes is found in the middle of the data and continues for hundreds of thousands of bases. The two panels above are from chromosomes 3 and 5.  At the bottom of all the panels  you will see numbers in white blocks.  These are reference numbers for my continuing work.  Another program I have written allows me to start imaging from any point within a file from the Human Genome set.  These numbers help me to approximate where to start looking for patterns I find interesting.  Since I have completed the entire imaging of the genome using a single matrix, 54, and  have sifted through all the images I am now writing the program that will isolate these patterns and their associated representation in the data files. Then I can begin to classify them.

The next panels show a pattern I found in chromosome 19 that prompted me to post these findings. If you look  you will see a pattern repeated in small chunks through out this data set. Panel 1 shows one type of this pattern and panel two shows another. By type I mean in the first panel the slants are in sets of 2 where as in panel 2 they are in sets of 3. The patterns are similar but different.  What causes them to be a group is that this pattern occurs as many as 200 times within the data file for chromosome 19.

Chromosome 19 is the oddest of the chromosomes I have imaged yet.  After viewing all the other chromosomes using this method I got the feeling I was looking at the Frankenstein's Monster of the human genome. A chromosome that looks as if it is a hodge podge of the features of the other 23. Chromosome Y is pretty interesting as well but I will keep that to myself for now until I develop this idea further.

I have an ultimate theory which is the reason I am doing this work.  This is not my job this is my hobby. I enjoy science for its own sake but I think this method may be of use in finding patterns we wouldn't otherwise come across. The imaging method uses the advantage that the human eye offers for finding patterns. More correctly the human brain. I do realize that we also see patterns that aren't necessarily there. For instance I have a picture of a coffee stain on a coffee pot that looks just like the Coca Cola Polar Bear and one of mold in a coffee cup that looks just like the Egyptian Sphinx. So I am not oblivious to the fact that I may see and interpret things that are not necessarily really there.

This is why this work has gone on for several years now. To be sure I am seeing something that is persistent and not a transient effect of screen resolution or another problem I once encountered while imaging large number files like Pi.  I am collecting the data for my larger hypothesis that has to do with the mechanism for evolution. Here is a hint. It deals with the phenomenon called Punctuated Equilibrium. I believe I know how it is possible and this is how I am going about looking for it.

Along the way I am hoping to find what I call structures and sub structures. In a few days I will be going to the crowd sourcing sites looking for funding to complete at least one project from this research. Even if this turns out to have little or no scientific value it has art value. And the completion of the art project I have in mind would also be useful in the scientific aspect of the work.  I would like to image and print the entire human genome and lay the images end to end on a giant white wall and stand back and see what I see.  A look at the entire Human Genome at one time. There may be a super structure there that we cannot see without imaging the entire thing.

Since I do this in my spare time the work is going to be slow.  So far the work keeps generating more experiments of which I have only completed one. The imaging of the entire genome with a single matrix. My computer screen size limits the size of a panel I can produce. With some time and effort I could manipulate the program to produce a block image of an entire chromosome. Even pixel by pixel this block would be several feet by several feet but laid out on a large wall might reveal something we didn't expect.  I can think of 10 good experiments that can be done using this and other genome data.  If you could use this technique to find a gene signature image or enzymes wouldn't that be very interesting?

I also have a version that converts the codons that code for amino acids into images. It is at a very early stage. Finding 20 unique colors or tiny images to represent the 20 usual amino acids formed from the 64 possible combinations of 3 letter codons isn't easy but the  preliminary work shows that some of patterns hold up and some don't which is very interesting. This is made more interesting by the fact that different codons code for the same amino acid. This also has ramifications in the the accounting program and in evolution itself. A single or even multiple mutations may not cause a change in amino acids and hence the protein it forms if the mutation is in the same set as the ones that already code form that amino acid. For instance cct, ccc, cca, and ccg code for the amino acid proline. If there is a change in the third base from any one base to another the same amino acid is coded for so the question is does it make a difference?  Are there "flavors" of the same amino acid? Electrochemically I am sure there are.

A person could spend a life time at this I suspect.  I would need 20 computers and several printers and about 20 years to run just the experiments I have thought of so far. It would have to become my job. Doing this piece meal won't get results very fast.

Below is another pattern found in chromosome 19. I thought I would throw it in for fun. This panel is actually a center panel of 3. In the data on either side of this panel the pattern continues. If you notice it is similar in color scheme to the panel directly above.  These are imaged at the same matrix so apparently the "math" internally is different or it would have produced slants. The arrangement that produces an orderly slanted pattern above produces these "swiggles below". Until I get into the file itself and look at the arrangement of the a, c, g, and t's I won't know what is going on.  Stay tuned for that post if you are interested.

Finally you will see below a panel I have made by using a photo editing program. These are crops from various chromosome images.  Another theme I have found is that at the beginning and ending of nearly every chromosome you find these strong vivid images. Some are what I call primary color bars, scales, waves, and interference. Collecting these snippets out of each image set is a little like bug collecting.  I have to go through each image set for each chromosome panel by panel and crop and paste. During this operation I noticed that some of these same patterns appear in more than one chromosome.  I haven't bothered to keep track of them yet. Like I said, since this is a hobby and not something that pays the bills I have to focus on my primary theory in the bulk of my work.

I just took the time out to post these images for any viewers who might be interested in the subject.

In conclusion I always like to do a recap in case anyone is actually reading this blog and becomes confused about some of the content.  This research is based on a pet theory I have about Punctuated Equilibrium and its mechanism. I believe I know how it is possible that we find sudden dramatic changes in a species within just a few layers of the fossil record.  The classic view of Darwinian Evolution puts forth the idea of change over time by a build up of mutations and selection but according to the fossil record sometimes this occurs so fast as to seem impossible based on the slow mutation/selection method but it does appear to happen.  I think I know why and the answer is actually kind of simple.


Until next time. Enjoy the post.  I will edit and spell check it later as always.

And that's what's inside my brain for today.