Has God's Signature been found in the Genetic Code

[Craig.Paardekooper]

So far the best result I have obtained is 19 different consecutive aminoacids with a stop signal. The largest genomes are more likely to contain the full alphabet. Currently the largest genome is in a plant or tree - its genome is about 50 times larger than the human genome. It would be interesting to see if this plant holds the key.

I have amended the computer code now, so that it searches all three reading frames. It translates the codons in the first reading frame into the corresponding 22 amino acids, then searches for a string of 22 different consecutive amino acids. On completion it translates the second reading frame into the corresponding amino acids, then searches for a string of 22 different consecutive amino acids. Finally it does the same for the third reading frame.

I am running it on a slower computer that is less likely to get overheated. It will take about 200 hours to complete the entire Y Chromosome and 600 hours (approx 1 month) to complete the entire X Chromosome - with the computer running 24 hours. I have delegated one computer completely for this task, and this task only. This means that I can get on with investigating other ideas on my other computers.

[Craig.Paardekooper]

Description
Here is a software program that I created. It reads any DNA sequence and divides it up into codon triplets. These are then converted to an aminoacid sequence. It then searches the sequence for a string of different consecutive aminoacids.

The codons are overlapping eg ACCTGATTAGCT would produce ACC + CCT + CTG + TGA + GAT + ATT + TTA + TAG + AGC + GCT


Instructions

1. The Input file should be in .txt or .fa format.
2. The input file should consist of a sequence of As, Cs, T, and Gs

3. You must stipulate the start and length of the DNA segment that you want to search - otherwise it will default to a start index of 0 and a length of the entire DNA sequence (which might take months to process). Try smaller segments of length 1000000 to start with.

4. You must set the length of the alphabet string that you are searching for. Do not go lower than 10 or you will produce too much output. Try 15 - 22.


Download

There are two software programs. The first is for non-overlapping codons. The second is for overlapping codons -

A. http://www.craigdemo.co.uk/DNAsetup.zip

B. http://www.craigdemo.co.uk/OverlappingCodonSetup.zip

Extract from zip then in the dialog that appears click NEXT - EVERYONE - NEXT - NEXT.

Note : If you do not have the dotNet 4.0 framework installed on your computer already, you may need to install that also. Contact me if you need help. craig_pkooper@yahoo.com

[luke1978]

Hi Craig,

Do you think there is any correlation between the signature you are looking for and the 22 letters used in the hebrew alphabet?

Keep up the good work. I have a copy of 373 proof set in stone and a printout of Peter Bluer's work with DNA in the genetic code.

I still cannot get my head around the boulay hypothesis?

http://jean-yves.boulay.pagesperso-o...enucleon1.html

Doesn't the symmetry fall apart without swapping a proton and neutron or something like that?

regards

Luke

[Craig.Paardekooper]

Hi Luke,

The signature I am looking for is a string of 22 different aminoacid letters, all occuring consecutively. This MAY correspond to the 22 letters of the alphabet, hence providing an inbuilt KEY for translating non-coding DNA into spoken language. Once a string of 22 different aminoacids is found, then it's value as a key will be judged solely upon it's ability to translate DNA into meaningful language. I would also expect a genuine key to occur in multiple places.

An effort to find this key is currently underway. 3 days ago I set in motion a software program that is slowly proceeding through the X Chromosome in search of potential keys. It will take an estimated 200 hours to complete analysis.

I have not looked at Boulay's theory yet. Though I am persuaded by Shcherbak's and Rakocevic's. Research is advancing all the time, and you might like to search Pubmed to see what advances have been made.

Isolating Coding from Noncoding Areas

I have worked out a way of identifying WORDS within NonCoding DNA. However, to implement this, I first need to isolate the non-coding DNA areas from the coding areas.

Here is the computer code that I will use to isolate the non-coding DNA -

1. Create an array of all the non-overlapping codons within a sequence

2. Create the variables that we will use
Dim IndexA as Long = 0
Dim IndexB As Long = 0
Dim n as long = 0
Dim Start as Integer = 0
Dim NonCodingDNA as String = ""
Dim CodingDNA as String = ""

3. Next we loop through the array detecting ATG (Start codons) and TAA, TAG, TGA (Stop codons)

For Each codon in CodonArray
If codon = "ATG" then
IndexA = n
Start = 1
NonCodingDNA &= DNA.Substring(IndexB, IndexA - IndexB)
End If

If (codon = "TAA" or codon = "TAG" or codon = "TGA") and Start = 1 then
If n - IndexA > 100 Then
IndexB = n
Start = 0
CodingDNA &= DNA.Substring(IndexA, IndexB - IndexA)
End If
End If

n += 1
Next
This code will isolate all noncoding areas and coding areas based on the criteria that a coding sequence -
1. starts with ATG
2. ends with TAA, TAG or TGA
3. is atleast 100 codons long

Once I have separated out the non-coding areas, then I can convert the codons in these areas into single letter aminoacids.
This should speed up the search for the 22 letter alphabet, since I can concentrate the search on non-coding areas.

Now, what I could also look for are actual words made out of aminoacid letters.

For example, if we took a string of letters such as THECHURCHWASFULLONSUNDAY, then potential 6 letter words would be THECHU, HECHUR, ECHURC, CHURCH etc.

So I can create a list of all possible 6 letter words by looping through the aminoacid letters, incrementing the start position by 1, and length fixed at 6.

So how will we know that any of these words represents a real word such as CHURCH, or is just nonsense such as HECHUR? Well we could see if the frequency of occurrence of a word stands out from the frequency of occurrence of other words.

We would expect real words to have a higher frequency than nonsense.

So I will have to create a separate program that can store all 6 letter words, for example, and then record the frequency of each.

Once we have identified such a "word", then we will have to match it to a spoken word that occurs with similar frequency. It will be a bit like a cross word puzzle. The more "words" we have, the more their letters will overlap, and help in solving the puzzle.

Anyhow, the discovery of an alphabet key would be much faster than this word search, so that is what I am engaged in at present.

[luke1978]

Hi Luke,

The signature I am looking for is a string of 22 different aminoacid letters, all occuring consecutively. This MAY correspond to the 22 letters of the alphabet, hence providing an inbuilt KEY for translating non-coding DNA into spoken language. Once a string of 22 different aminoacids is found, then it's value as a key will be judged solely upon it's ability to translate DNA into meaningful language. I would also expect a genuine key to occur in multiple places.

An effort to find this key is currently underway. 3 days ago I set in motion a software program that is slowly proceeding through the X Chromosome in search of potential keys. It will take an estimated 200 hours to complete analysis.

I have not looked at Boulay's theory yet. Though I am persuaded by Shcherbak's and Rakocevic's. Research is advancing all the time, and you might like to search Pubmed to see what advances have been made.

Isolating Coding from Noncoding Areas

I have worked out a way of identifying WORDS within NonCoding DNA. However, to implement this, I first need to isolate the non-coding DNA areas from the coding areas.

Here is the computer code that I will use to isolate the non-coding DNA -

1. Create an array of all the non-overlapping codons within a sequence

2. Create the variables that we will use
Dim IndexA as Long = 0
Dim IndexB As Long = 0
Dim n as long = 0
Dim Start as Integer = 0
Dim NonCodingDNA as String = ""
Dim CodingDNA as String = ""

3. Next we loop through the array detecting ATG (Start codons) and TAA, TAG, TGA (Stop codons)

For Each codon in CodonArray
If codon = "ATG" then
IndexA = n
Start = 1
NonCodingDNA &= DNA.Substring(IndexB, IndexA - IndexB)
End If

If (codon = "TAA" or codon = "TAG" or codon = "TGA") and Start = 1 then
If n - IndexA > 100 Then
IndexB = n
Start = 0
CodingDNA &= DNA.Substring(IndexA, IndexB - IndexA)
End If
End If

n += 1
Next
This code will isolate all noncoding areas and coding areas based on the criteria that a coding sequence -
1. starts with ATG
2. ends with TAA, TAG or TGA
3. is atleast 100 codons long

Once I have separated out the non-coding areas, then I can convert the codons in these areas into single letter aminoacids.
This should speed up the search for the 22 letter alphabet, since I can concentrate the search on non-coding areas.

Now, what I could also look for are actual words made out of aminoacid letters.

For example, if we took a string of letters such as THECHURCHWASFULLONSUNDAY, then potential 6 letter words would be THECHU, HECHUR, ECHURC, CHURCH etc.

So I can create a list of all possible 6 letter words by looping through the aminoacid letters, incrementing the start position by 1, and length fixed at 6.

So how will we know that any of these words represents a real word such as CHURCH, or is just nonsense such as HECHUR? Well we could see if the frequency of occurrence of a word stands out from the frequency of occurrence of other words.

We would expect real words to have a higher frequency than nonsense.

So I will have to create a separate program that can store all 6 letter words, for example, and then record the frequency of each.

Once we have identified such a "word", then we will have to match it to a spoken word that occurs with similar frequency. It will be a bit like a cross word puzzle. The more "words" we have, the more their letters will overlap, and help in solving the puzzle.

Anyhow, the discovery of an alphabet key would be much faster than this word search, so that is what I am engaged in at present.

Hi Craig,

My programming knowledge is limited to C++, VB(Haven't done the previous in years) and batch files!

However I can see the logic in what you are doing and I understand that coding to a certain degree. What language is that?

I was thinking about your project and maybe the first and last letters of the hebrew alphabet will correspond to the Start and Stop codons(Is there 3 different stop codons? - Last letter may work for all 3)

So if you find a whole string of 22(Start,Stop and 20 Amino acids) that may be a key?

Maybe you just need to find 20 Amino acids and can assume the places of the first and last letter?

I am probably not fully understanding your project but I hope these ideas are helpful. You will give CERN a run for their money! - Very exciting work you are doing and if the code is there I think you are God's man to find it. Keep us all updated.

Thanks for your work. I'm glad someone is looking.

regards

Luke

[Craig.Paardekooper]

Hi Luke

There are 20 amino acids and three stop signals generated from the 64 codons via the genetic code. However sometimes, two additional aminoacids are generated instead of two of the stop signals, bringing the total to 22 amino acids and one stop.

Twenty-two amino acids are naturally incorporated into polypeptides and are called proteinogenic or natural amino acids.[10] Of these, 20 are encoded by the universal genetic code. The remaining 2, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms. Selenocysteine is incorporated when the mRNA being translated includes a SECIS element, which causes the UGA codon to encode selenocysteine instead of a stop codon.[22] Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded for with the codon UAG, which is normally a stop codon in other organisms.[23] This UAG codon is followed by a PYLIS downstream sequence.[24]

[Craig.Paardekooper]

While the software is busy searching DNA for an alphabet key, I thought it would be interesting to convert DNA into binary code, (ie a list of 1s and 0s).

Kraker suggested that the binary format might reveal some interesting patterns when converted into a picture made of pixels where a dark pixel stands for 0 and a light pixel stands for 1.

Anyway, I thought I would give this a shot and see what appears.

DNA has a natural binary structure because there are 4 nucleotides - A, C, T, G.

C always binds with G, and A always binds with T, so DNA could be thought of as having only two pairs which could be replaced by a 1 or a 0

So the nucleotides G and C will be replaced by 1 and the nucleotides A and T will be replaced by 0.

Here is the software that I will use to do this

[luke1978]

While the software is busy searching DNA for an alphabet key, I thought it would be interesting to convert DNA into binary code, (ie a list of 1s and 0s).

Kraker suggested that the binary format might reveal some interesting patterns when converted into a picture made of pixels where a dark pixel stands for 0 and a light pixel stands for 1.

Anyway, I thought I would give this a shot and see what appears.

DNA has a natural binary structure because there are 4 nucleotides - A, C, T, G.

C always binds with G, and A always binds with T, so DNA could be thought of as having only two pairs which could be replaced by a 1 or a 0

So the nucleotides G and C will be replaced by 1 and the nucleotides A and T will be replaced by 0.

Here is the software that I will use to do this

Hi Craig,

Do all humans have the same DNA?

As an example does an Asian person have slightly different DNA then a Caucasian person?

I'm asking this question as I'm wondering if there are slight variations in DNA how do you come up with a standard to use?

I believe the Mitochondrial DNA is all the same?(37 Genes)

I am following your work with interest.

[Craig.Paardekooper]

Hi Luke,

I found some samples of human mitochondrial dna here - http://www.mtdb.igp.uu.se/

Though all of these samples are only 16568 bases long. So it was easy to analyse them for an alphabet sequence.

Here are the results for overlapping codons

1. : Reading Frame = 0 : at 6883 : PHTRGEKSAQNIYMU

2. : Reading Frame = 0 : at 7369 : HI1KNTPLWGESVUD

3. : Reading Frame = 0 : at 8354 : FLYTQSVUEKNMCAP

Here are the results for non-overlapping codons

1. : Reading Frame = 2 : at 1117 : QWHS1CLPNEKFOAI

2. : Reading Frame = 2 : at 1118 : WHS1CLPNEKFOAIY

So this sample of mitochondrial dna does not contain an alphabet primer - atleast not one of 22 letters. The longest sequence was only 16 aminoacids long, and this sequence occurs only once.

[Craig.Paardekooper]

Here is a link to a simple program that I created for isolating coding areas of DNA from non-coding areas -

http://www.craigdemo.co.uk/CodingRegionsSetup.zip

The software isolates all coding regions that start with ATG and end with TAA, TGA or TAG

Because there are three possible reading frames, depending upon where you start reading a codon from, you can access the other reading frames by entering either 0, 1 or 2 in the reading frame box. The default is 0.

To run the software simply choose a text file containing the DNA sequence
This software works best with microbes - because microbes have a simple DNA structure that follows the START-STOP coding pattern. It also works will with cDNA and mRNA of higher organisms, since these do not contain introns.

Vertebrate DNA has a more complicated structure - and requires the identification of SPLICING SITES in addition to the STARTS and STOPS. I will develop the software to work better with higher vertebrates.