The cryptography of DNA; And can an amatuer do genetic experiments

[Trurl]

Ok, for my background I am a college student. I confess to not knowing biology or genetics or even engineering for that matter. I have read some books on genetics and I am particularly interested in gene-therapy. But I have read that genetics is related in many ways to cryptography. I have tried here at SFN in a math post to solve the Prime-product problem. I have had little success so far. I have a polynomial which if you already know the Prime numbers proves true, but by itself I cannot solve the resulting equation. I have tried geometry and am currently looking at other methods.

 

My question is how do you read the genetic code chemically? I have seen some basic experiments in a Make biology book. Also what are the cytological algorithms? From my brief research the math problem is complex and differs from gene pattern to pattern. So not only do you have to solve a genealogic one-way-function, but you don’t know the algorithm that pattern is based on. And most gene knowledge is not shared due to the fact it is a big-money intellectual property. So with most researchers working alone it is no wonder mathematicians haven’t solved it.

 

My approach is to find a pattern that not only describes the RSA Key algorithm, but will find patterns where patterns don’t seem to exist. I believe in creation, but will not preach but list this to note something very important. A nonbeliever asked if God is so powerful can He make a bolder so heavy even he can’t lift. This sounds ignorant. The nonbeliever would say he isn’t all powerful if he can’t lift the bolder and if he can’t lift hit he can’t lift the heaviest boulder. I know it sounds like nonsense. But my question is can God make a function that cannot be reversed? Obviously I don’t know what God is capable of. There are easily one-way functions we cannot reverse. However I don’t see genetics as something that can’t be figured out. Some scientist, see genetics as chemical proof God does not exist. I believe the pattern just shows his work. The fact remains that knowledge of genetics is as dangerous as the fruit from the Tree of Life.

 

That is just my perspective. I don’t want to argue if genetics proves we evolved. I am just stating why I am interested in genetics. I want to find patterns in them. Obviously I am limited in what I can do. I don’t have a lab or biology background. But I found this article which described a one-way biological function.

 

Also you should check out my post in the math forum. Please share if you know any simple genetic experiments. I have the catalog of American Scientific’s “Amateur Scientist” columns. I have a professional microscope, power tools, Internet, cryptography books, and an impossible to solve polynomial. I’m not intending to cure cancer, but I want to look at patterns in DNA that could relate to cryptography.

 

http://www.asee.org/documents/sections/middle-atlantic/fall-2009/01-Biological-One-way-Functions.pdf

 

http://www.scienceforums.net/topic/95813-prime-products-just-one-last-time/

 

 

[Arete]

DNA sequencing technology is changing rapidly. The "standard method" is Sanger sequencing which would require a functional molecular lab. Most next generation methods would be cost and expertise prohibitive for a layperson with no training. One technique that may be approaching user friendliness attainable by a skilled citizen scientist is the Oxford Nanopore minION sequencer - but this still requires access to pipettes and for paired end sequencing, a thermocycler.

 

And most gene knowledge is not shared due to the fact it is a big-money intellectual property. So with most researchers working alone it is no wonder mathematicians haven’t solved it.

 

This is simply untrue - almost every scientific journal requires data to be made publicly available via NCBI or similar databases. Almost all the DNA sequence ever produced is open source, with data mining and collaborative study actively encouraged.

[ecoli]

DNA sequencing technology is changing rapidly. The "standard method" is Sanger sequencing which would require a functional molecular lab. Most next generation methods would be cost and expertise prohibitive for a layperson with no training. One technique that may be approaching user friendliness attainable by a skilled citizen scientist is the Oxford Nanopore minION sequencer - but this still requires access to pipettes and for paired end sequencing, a thermocycler.

 

OP seems to be asking about codon translation, not about sequencing. The algorithmic analogy would be a hash function. The 'God' part of the question is confusing, seems nonsensical so I will ignore it.

[Fallen Enigma]

Hi Trurl,

 

 

My question is how do you read the genetic code chemically? I have seen some basic experiments in a Make biology book.

 

Do you yourself want to know what a string of genetic code will turn into? Or do you want to know the process by which cells do it? If you yourself want to do it you can look at codons (https://en.wikipedia.org/wiki/DNA_codon_table) when you get to the mRNA stage, before this stage though (DNA and pre-mRNA) you can still have introns present, which can be functionally important, but redundant when trying to determine the end product of your genetic code as they're spliced out. To be honest this may be difficult as the redundancy of codons means several codons can lead to one amino acid. Yet this is precisely how ribosomes transcribe and translate the information in nucleic acids. Transcribing essentially gets the small part of information necessary (from the huge DNA molecule) out of the nucleus and allows it to be translated which allows ribosomes on the rough endoplasmic reticulum to utilise tRNA molecules (which have amino acids attached to them) and string them along next to one another in order to produce the primary structure of the protein (https://en.wikipedia.org/wiki/Transfer_RNA). Note these methods are extremely sensitive to shifts in point shifts etc where the code will be read one base off so on so forth.

 

Can God make a function that can't be reversed?

I am no mathematician, but regardless of whether or not a god has or hasn't done it would the translation step be non-reversible? It seems the paper you site states around 66% can be roughly recovered (if I read it right), but 33% of the information is still unknown. I don't know how far reversed you would consider a reversible code.

 

Hope this helps.

[Trurl]

OK, first off I’m sorry l haven’t replied sooner, but I have been busy.

 

Second, I think you guys overestimate my knowledge of biology and genetics. I want to look for patterns in the genetic code. I have did a little research and I don’t know what the information needs. I need a starting point. You guys gave me excellent information. But I cannot test the DNA myself. I have an upper-level chemistry book that says to place a specimen in a spectrophotometer. I have googled it and it is affordable. My chemistry book does not list steps however. It has theory then puts a list of 7 steps on what to do without a complete lab explanation.

 

I should explain more what I want to do. I want to look for patterns in genetics. As you guys stated that a lot of information is shared. I think it is like a networked science where the public looks at the data, like finding constellations in telescope pictures. I’m not claiming to be able to discover anything. I have tried to find patterns on the Prime factorization problem. I have found some patterns, but I don’t have a solution to the problem. As you can see from my math post on SFN.

 

So I suppose my question is can I do any meaningful experiments. And by meaningful I mean worth the price of a $500 spectrophotometer to do amateur experiments and have some fun.

 

I also have a question of the value of my own DNA. I was thinking of doing the Ancestry.com DNA test. But if I give my DNA do I compromise my privacy? I have DNA on record from being in the military. The military has a great DNA base of every member since approximately 1996. They are only supposed to use the DNA for identification, but imagine the information they collect on everyone with both nature vs. nurture. But I imagine a world where cryptography and identity will utilize the genetic information. Is it safe to give Ancestry.com genetic fingerprint?

 

BTW, when I was talking about God, it was not in a religious way. I was asking does a one-way function exist. If an all-powerful being can create a function can they reverse it? If they can there are no one-way functions. But if the being can’t reverse it, one-way functions exist. Either way some would say that either would mean they are not all knowing. The boulder problem is a non-religious person’s argument. But I mention this only as the meaning of a one-way function. It is not intended to prove any religious viewpoint right or wrong. It is just a conundrum.

[CharonY]

The nature of DNA sequences (not code, that refers specifically to sequences that are being translated into proteins, which, in eukaryotes is often only relative small fraction), makes it rather useless to look at by eye. There are a large number of computational approaches to train algorithms to find certain patterns (such as hidden Markov models). But either way that would be at the back end, after sequencing is done, which cannot be done at home. A spectrometer would only allow you to measure how much DNA you e.g. isolated from a sample (say, mouth swab).

 

Also note that if you have DNA information stored, it is not a full genome sequence, nor is it normally sequence at all. Rather, they amplify specific markers via PCR and based on the pattern (i.e. absence and presence of specific markers) they are used to identify you.

[Trurl]

https://soundcloud.com/quitteriel/connor-dickiesynbiota-synbio-experiments-for-all

 

 

What do you think of a kit like this? They start at $45.

 

 

Also from what you said. Is it safe to share my DNA with Ancestry.com? They give you access to the genome. But would I be able to analyze it?

[Endy0816]

Link is broken, but that is referring to genetic circuits.

 

https://en.wikipedia.org/wiki/Synthetic_biological_circuit

 

https://soundcloud.com/quitteriel/connor-dickiesynbiota-synbio-experiments-for-all

 

 

Ancestry only provides partial information. You may want to look into whole genome sequencing though even with the decreasing cost expect to pay $1K.

[Arete]

You may want to look into whole genome sequencing though even with the decreasing cost expect to pay $1K.

 

Even with in house pricing a paired end lane of Illumina HiSeq will run about $2k USD plus library prep. Of course the caveat is the data is worthless if you don't know how to analyse it or have the computational power - in which case the 23andme/ancestry/etc microrarrays are probably a better idea.

[Trurl]

I think the $100 price tag for 700,000 traits is a deal. I do wonder why 23andme compares to prehistoric man.

 

So, as I understand it, the genetic information is so vast it takes computer processing to find patterns. I don't know what kind of learning curve there would be. However, just by using N = p *q, I found 7+ patterns. All of which we found useless on this message board. But they were patterns even if they didn't solve the prime factoriation problem.

 

Now I am asking where to start looking for genetic patterns. Are there some classifications that are starting points, like N=p*q for RSA? I am good at looking for patterns. I don't have a biology background. But I have read about networked science where amateurs provide an extra perspective working to classify stars or find genetic patterns.

 

So please point me in the direction as to where to have a simple start to look for genetic patterns.

[Trurl]

Well I’ve been reading about genetics as a crash course. I am amazed at all the applications that bio-engineering has. But I did notice the intro chapter where there are arguments if bioengineering is safe or ethical. The book tries to be objective, but is really promoting the field. The author figures it has the same pro’s and con’s as any technology.

 

I don’t know that I agree. As for a pattern, I picture a chemistry problem. You don’t mix all the chemicals in the chemistry set together. Chemistry improves our lives dramatically. But that doesn’t mean someone doesn’t take nitrates in an oxygen source and make a bomb. But in the bio-world there would be a one-way function to disarm the bomb. The bomb is easy to make, but not easy to reverse, if the only way to disarm the bomb is to add more chemicals to the mix. In other words, if something is genetically altered and becomes dangerous, how would you reverse it if it multiplies.

 

I am not far enough in my study to find patterns in genes. But I just think of my chemistry example, where it is easy to add to a mixture of chemicals, but not as easy to neutralize the mixture of chemicals, by adding more chemicals to the solution.

 

I have seen interviews on TV of the guy who lead the mapping of the human genome. He claims that he just proved evolution. But I’m not convinced until he can explain all the patterns that exists and cures complex, genetic diseases.

 

So, if the math can be applied, and this isn’t the same math that says it’s a quintillion to 1 chance, like the March Madness bracket, I am going to ask the forum what are the simple strategies of finding patterns in genes?

 

As I learn more I will be able ask better questions.

 

 

[Trurl]

Ok so I posted here asking for how pattern in genes are found and if there are already mathematical problems in the experiments already found. No response yet, probably because I’m an amateur and asking silly questions.

 

But now I am going to up the ante. Reading only 2 chapters in the genetic textbook, this is a math pattern I believe needs investigated, if not already so. So the geometry of the genetic structure is a double helix. To me if I were going to map genes I wouldn’t be isolating single genes. I would look at the shape of the helix. It can’t be perfect. The connections would cause it to bend 3-dimentionally. The space between helixes could be measured and the slope in 3-axis could be measured.

 

I chose this not knowing what work is done in the field. But in my original cryptography amateur research, I stated that a pattern in Prime numbers could be found with a logarithmic spiral. To me I look at the helix and see a 3D shape that looks like it originated from a 2D logarithmic spiral. Now I never proved that Prime numbers can be described by a logarithmic spiral, but all patterns I found in the Prime factorization problem, are based on my theory of the logarithmic spiral.

 

So here is my theory. If you find the curve of the spiral that makes up the 3D Helix, then you can predict the size of the connections.

 

It seems simple not to be already thought of, but the theory is the easy part. Finding the exact mathematics will prove difficult. But I believe my work with the logarithmic spiral and cryptography in the Prime factorization problem shows patterns in the logarithmic spiral. My work may have nothing to do with DNA, but if I am looking for a pattern in genes and the resulting proteins, I wouls simplify the calculations by looking for a geometric pattern.

[Strange]

Ok so I posted here asking for how pattern in genes are found and if there are already mathematical problems in the experiments already found.

 

 

https://scholar.google.it/scholar?q=dna+matching+algorithm

 

There are software tools available for this, such as BLAST: https://blast.ncbi.nlm.nih.gov/Blast.cgi

 

https://en.wikipedia.org/wiki/BLAST

 

 

 

I would look at the shape of the helix. It can’t be perfect. The connections would cause it to bend 3-dimentionally. The space between helixes could be measured and the slope in 3-axis could be measured.

 

The DNA molecule is not a simple helix. It wouldn't fit in the cell if it were (the human genome is hundreds of kilometres long).

 

It is folded very compactly and the way it is folded changes over time to allow different parts of the genome to be accessed. This is a very active area of research.

 

 

 

So here is my theory. If you find the curve of the spiral that makes up the 3D Helix, then you can predict the size of the connections.

 

That is a hypothesis or guess. It could become a theory when you show the mathematics and the supporting evidence.

Edited March 26, 2017 by Strange

[Trurl]

Thanks Dr. Strange, those are some excellent links and what I need.