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Old 2021-03-23, 08:23   #34
Batalov's Avatar
Mar 2008

270316 Posts

Originally Posted by jwaltos View Post
Some questions:
(because the margins of this book are too narrow to contain a full answer, I will try to give a very terse answer and a few links if I can... and the answers are going to be simple and incomplete):

• Is the study of genomics primarily within the realm of biology affiliated with chemistry..etc..or is there a different and unique characterization of such studies that straddles the life sciences and things non-living?
> Chemistry, biology (cell biology, mol biology), computational biology (including bioinformatics and biostatistics), and importantly – medicine. That’s what I love about this field – you have got to know and constantly learn a lot of everything.
> With sequencing a genome of a sick person now becoming comparable to an MRI test in price, more and more hospitals do it, and then at average 25-35% success the genetic wound can be identified and in 50-70% of those the differential diagnosis becomes straightforward all the way to treatment (imagine Dr.House ordering a genome sequence in every episode and then saying “Boring! Case solved!”).
• Are A,C,T,G and U the only nucleotides?
> No, there are 4 basic nucleotides for DNA – A, C, G, T (yes there exist some exotic ones, as well as humans made synthetic nucleotides that do nothing in living cell but are instrumental for sequencing). DNA is like a magnetic tape, contains instructions, but to perform instructions it is first transcoded into RNA which uses A, C, G, U nucleotides. The mRNA vaccines contain pre-recorded instructions for making protein that only makes for the spike protein of the SARS-Cov2 virus and nothing else, so a person who gets these shots is not burdened with the rest of the virus and among other benefits, that fragment has no way of becoming alive – it only serves as a boxing punching bag for the immune system.
> there are some specialized scientists who study bacteria and other organisms - those use a few more nucleotides (e.g. "I" and some others; the also use various transcoding code "tables"; it is a vast area, I cannot cover it). I only know reasonably well the mammalian genomics.
• Is there any correlation with this encoding and the Base 10 number system? I've seen questionable works on this but is there anything of substance?
> not really.
• Is there an underlying structure that is sub-atomic in nature that provides the "encoding" for the genetic process? That is, is there a precursor "code" to the genetic code? If there is, is there an antecedent to the sub-atomic structure?
> not really. there is instead a super-molecular layer, i.e. modifications atop of the genetic code, referred to as epigenetic
• I posted something in my blog area (since effaced) regarding a possible goal oriented process of genetic evolution. do you have any opinions or pointers on this?
> What happens inside each one of us is constant evolution. Unfortunately, viruses also undergo evolution. So does cancer. There is no single process that would be cast in stone and you solve it and you are done (e.g. while developing a drug) – the living thigs that you are stopping by applying the drug, evolve to survive and drug stops working. Slowly though, so the drug development is not futile. It is just ...a constant work to keep up, year after year.
• In my virtual library I have numerous texts on many topics including bio-informatics. Which text within this field best exemplifies creativity and imagination rooted in fact? One possible tendril in this regard is AI married with Quantum computation.
> Bioinformatics itself evolved so much since ‘90s that there are many bioinformaticists that have literally nothing to talk to each other about. It is too loose a word.
• Why are you interested in computing large primes and how does integer factorization factor into this (pun intended).
> No connection. I also hike on weekends and that helps in the same way: exercise that keeps my body and mind fit for hard work.
• Regarding solutions/answers to any questions of import, the answers are ancillary to the conceptual foundations that are the well-spring for those answers. What genre(s) of mathematics are capable of expressing most comprehensively what is to be known about genomics and does such a toolkit presently exist?
> there are amusing connections to information theory (and in particular to compression), B-W algorithm for example completely changed the way genome similarity computations were done initially in the 70s through 90s (at that time, people readapted dynamic programming to the DNA and protein query-to-database alignments, allowing for errors and (again) for evolution), and in 2000s B-W not only resurrected in compression (cf. bzip) but also in DNA alignments! It is remarkable. Evolution of computational methods and survival of the fittest implementations in a matter of a few years made all methods except those that used B-W ...obsolete! it is just one tiny example, but the computational biology is full of many more examples. Gamification made huge strides just recently (cf. Folding @ Home as well as human-assisted bottleneck in folding solutions). it is along story.
• Finally, what must I learn AND understand to ask better questions?
> Well, a bit of everything. I learn something new every day!

Re: DNA fingerprinting. It is an amazing pragmatic development. Very practical science. There are just a handful of genomic positions that are used there (most frequently just 24), and because it was contracted by FBI/police/Interpol and millions of these tests need to be done in the minimal amount of expense - people optimized the heck of it. It now in bulk costs just a few bucks. The pharmacies have the paternity tests for sale - those are actually the same. And that's how you can see the price argument - even after the markup that goes to distribution chain and to the labs, it is like 60 bucks (which is 3 tests in a bundle - kid, mother and father) / 3 = $20 per test! It is similar to 90%+ of people driving cars not knowing the physics of combustion engine or oil->petrol conversion science. Or people using cell phones+GPS not knowing that they are using "general relativity theory" in their hands. They don't have to know science! It had been commoditized into products.
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Old 2021-03-23, 09:20   #35

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When I was in French Guyana I recall we had to shepherd some Merck researchers into some of the deeper micro-climates of the forest. Equatorial jungle is a very interesting place and I learned my share of tropical pathology/toxicology along with many other things.

A friend of ours who was an urgent care RN and who is now one of the directors for infectious disease control (you need special genes to work in this field) in the area has her hands full on a daily basis...and then some. Anyone engaged in an occupation dedicated to the well-being of others including those beings with hide, hair, feathers or scales is on the right side of things. Thanks for being part of that group..and this one. may need to have a chat with Tim Berners-Lee regarding those margins..

Last fiddled with by jwaltos on 2021-03-23 at 09:35 Reason: Reference Toulousain
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Old 2021-03-23, 18:37   #36
CRGreathouse's Avatar
Aug 2006

5,987 Posts

Originally Posted by jwaltos View Post
Are A,C,T,G and U the only nucleotides? Is there any correlation with this encoding and the Base 10 number system? I've seen questionable works on this but is there anything of substance?
There are lots of synthetic nucleotides out there beyond the standard ones.
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Old 2021-03-30, 22:07   #37
Batalov's Avatar
Mar 2008

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(it is a single symbol (UTF u'\360\237\247\254')... I am not sure but looks like a candy. )
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Old 2021-03-31, 05:34   #38
MattcAnderson's Avatar
"Matthew Anderson"
Dec 2010
Oregon, USA

49A16 Posts

I am glad that April 25th is DNA day. We need that.
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