Physical question

How does science work? And what's all this about quantum mechanics?

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Hrvoje
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Re: Physical question

Post by Hrvoje » Thu Jul 04, 2019 3:52 am

Scott Mayers wrote:
Sun Jun 30, 2019 2:15 am
Except, I'm guessing, when those self-replicators are viruses?
I'm guessing that you are guessing that viruses lack intelligence? Well, it obviously depends on the definition of that word, but even they don't lack heuristic adaptive behavior, as well as any living or semi-living entities, so no, I would not single them out.
Scott Mayers wrote:
Sun Jun 30, 2019 2:15 am
Lossless compression is only functional if the ELEMENTS of information have repeats in patterns for a particular resulting whole. I'm not sure how it relates to DNA because it contains a lot of old information ('junk-DNA') that has its 'index' headers deleted but keeps the content of the 'files'. This is exactly why we 'defrag' computer drives.
I think it is compression simply because one molecule is a rather compact way of storing information about such an complex entity as any living organism is. I think it is lossless because it is sufficient to reproduce it exactly.
Scott Mayers wrote:
Sun Jun 30, 2019 2:15 am
The nature of repeating full copies of the DNA that acts as the information of the WHOLE but to EACH cell, is also over-redundant. Each cell only uses a very tiny percentage of the DNA at its core. This is definitely useful but NOT efficient and so is NOT 'compression'.
To confirm what Skepdick already said, the ability of cell differentiation or specialization is exactly what contributes most to the compactness of DNA code, so, a little bit of denormalization of data doesn't matter. Or, conditional compilation may be a better analogy to describe that feature, see this: https://ds9a.nl/amazing-dna/

Hrvoje
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Joined: Sat Jan 19, 2019 4:37 am

Re: Physical question

Post by Hrvoje » Fri Jul 05, 2019 3:29 am

And I don’t think that the fact that certain parts of DNA don’t code for anything, either because they are silenced in the process of differentiation or they don’t code anywhere because they are “junk”, that diminishes the fact of compression or losslessness. I mean, it is a kind of metaphor as all that happens is decompression of that information, but still, it is an illustrative metaphor.
Last edited by Hrvoje on Sat Jul 06, 2019 10:40 am, edited 1 time in total.

Scott Mayers
Posts: 1402
Joined: Wed Jul 08, 2015 1:53 am
Location: Saskatoon, SK, Canada

Re: Physical question

Post by Scott Mayers » Fri Jul 05, 2019 6:22 am

Hrvoje wrote:
Thu Jul 04, 2019 3:52 am
Scott Mayers wrote:
Sun Jun 30, 2019 2:15 am
Except, I'm guessing, when those self-replicators are viruses?
I'm guessing that you are guessing that viruses lack intelligence? Well, it obviously depends on the definition of that word, but even they don't lack heuristic adaptive behavior, as well as any living or semi-living entities, so no, I would not single them out.
Scott Mayers wrote:
Sun Jun 30, 2019 2:15 am
Lossless compression is only functional if the ELEMENTS of information have repeats in patterns for a particular resulting whole. I'm not sure how it relates to DNA because it contains a lot of old information ('junk-DNA') that has its 'index' headers deleted but keeps the content of the 'files'. This is exactly why we 'defrag' computer drives.
I think it is compression simply because one molecule is a rather compact way of storing information about such an complex entity as any living organism is. I think it is lossless because it is sufficient to reproduce it exactly.
Scott Mayers wrote:
Sun Jun 30, 2019 2:15 am
The nature of repeating full copies of the DNA that acts as the information of the WHOLE but to EACH cell, is also over-redundant. Each cell only uses a very tiny percentage of the DNA at its core. This is definitely useful but NOT efficient and so is NOT 'compression'.
To confirm what Skepdick already said, the ability of cell differentiation or specialization is exactly what contributes most to the compactness of DNA code, so, a little bit of denormalization of data doesn't matter. Or, conditional compilation may be a better analogy to describe that feature, see this: https://ds9a.nl/amazing-dna/
A 'virus' probably evolved initially as a communication mechanism between bacteria. It only contains information to make it function as a target to specific cell types (so the message only goes to the original intended cells of similar kinds). Then it injects its dna whereby it 'borrows' the host cell's normal operation that transfers DNA code into RNA. The DNA is encapsulated in a nucleus that restricts DNA normally to be used without CONTROL. RNA parts are copies of the larger DNA that are permitted to leave the nucleus so that it can be used to make proteins. But when viruses inject their DNA, it takes advantage of the RNA's function, and the cell's normal functioning goes into making copies of the virus. It continues to copy the guest as viruses that eventually overtake the cell then bursts out with many of those new copies.

So this is similar to those program's that Skepdick was mentioning. They are actually programs that still require a host machine to run the program and why I was relating that to viruses.

I'll look up your link and respond more later if need be.

Scott Mayers
Posts: 1402
Joined: Wed Jul 08, 2015 1:53 am
Location: Saskatoon, SK, Canada

Re: Physical question

Post by Scott Mayers » Fri Jul 05, 2019 7:06 am

Skepdick wrote:
Wed Jul 03, 2019 9:31 am
Scott Mayers wrote:
Sun Jun 30, 2019 2:15 am
Each cell only uses a very tiny percentage of the DNA at its core. This is definitely useful but NOT efficient and so is NOT 'compression'.
That's a reductionist view on the matter. Holistically it's far better to have it and not need it, than need it and not have it.

The cell is part of the whole. The whole needs it. To optimize for cell-efficiency at the expense of organism-efficiency is to miss the forrest for the trees. Economies of scale...

The Whole DNA copies for each cell are there because each cell begins as 'stems' or blank-slate type cells. It gets an initial 'tag' of information from its environmental cells once initiated that then tells WHICH part of of the DNA (genes) it will be using. Once that section is initiated, the cell transforms to its particular function and ONLY uses specific sections of the DNA to make RNA segments that then get used to make proteins. That is what I mean by the fact that the DNA's use in limited to a tiny part. See the comment on how viruses work above in my last comment. [What was the name of that program type you mentioned again, by the way?]
Scott Mayers wrote:
Sun Jun 30, 2019 2:15 am
Oh, by the way, 'defragging' is "lossless" compression.
If it's not reversible - it's not lossless.
Defragging only unfragments whatever is in its initiating 'table (of contents)'. OF that information uniquely, it then only takes all the links to the parts and brings them together 'lossless'. In DNA, I don't know if there is write-over in the same way as defragging but the example suffices RELATIVE to the function: it keeps all the information the drive has relative to that table; the 'junk' in a drive similar to DNA would be those complete segments similar to what occurs when a program is just deleted (but not wiped). The 'junk' in DNA is can be both segments partly overwritten (if this occurs OR to those parts that are just unlinked to it own type of 'table' relative to the type of function of that cell.

Hrvoje
Posts: 20
Joined: Sat Jan 19, 2019 4:37 am

Re: Physical question

Post by Hrvoje » Fri Jul 05, 2019 7:18 am

Aha, you were emphasizing their lack of ability to reproduce them selves independently of the host cell. Yes, I agree, the confirmation of superior intelligence I was talking about was to create the artificial intelligent self reproducible entities in our own image and likeness (like God created a Man), ie not like viruses.

Skepdick
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Joined: Fri Jun 14, 2019 11:16 am

Re: Physical question

Post by Skepdick » Fri Jul 05, 2019 8:18 am

Scott Mayers wrote:
Fri Jul 05, 2019 7:06 am
What was the name of that program type you mentioned again, by the way?
https://en.wikipedia.org/wiki/Quine_(computing)
Scott Mayers wrote:
Fri Jul 05, 2019 7:06 am
Defragging only unfragments whatever is in its initiating 'table (of contents)'. OF that information uniquely, it then only takes all the links to the parts and brings them together 'lossless'. In DNA, I don't know if there is write-over in the same way as defragging but the example suffices RELATIVE to the function: it keeps all the information the drive has relative to that table
Hence my point. Any process which destroys information is not lossless because the operation is not reversible.

This is the concept of undo/redo logging in relational databases. If you have enough storage to record every mutation - you can return the system to any prior state.

In practice - obviously we destroy information intentionally once it's no longer needed, or once we start to feel the storage/memory pressure.

Hrvoje
Posts: 20
Joined: Sat Jan 19, 2019 4:37 am

Re: Physical question

Post by Hrvoje » Sat Jul 06, 2019 11:19 am

These are both interesting analogies, disk defragmentation, and undo/redo logs in relational databases, with respect to junk DNA. But when I mentioned the analogy of DNA storing the information for the construction of a whole organism, in a very compact way, or compressed if you will, I didn't have in mind percentage of its information content that is not coding for anything, its origin or destiny, ie is it a source for future epigenetic changes or not. I just thought how throughout all copying of that information in the process of DNA replication, and its transcription and translation during protein synthesis, it constructs larger strings than are the original strings that code for it, and very numerous and varied strings, considering the compact original. It just looks like the whole organism gets "unzipped" during its development from the moment of conception when the original string of DNA was constructed, nuclear and mitochondrial. Although, as I said, there is no "zip", just copying and "unzipping", so maybe the analogy is not adequate.

Because, it is in fact a material construction, and the material is in the form of proteinogenic amino acids.

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