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Before cancer kills, it cheats

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Re: Before cancer kills, it cheats

#51

Post by domnomnom »

smallhands wrote: post #10
domnomnom wrote: post #6

Here are some ideas: Look at the functional call stack. Its a slice of the linear address space that’s actively being used and it is strikingly similar to the promoter regions of the genome. Like some pathogens, hackers randomly try to hit that sweet spot that will jump to the special program. Operating systems are like simple biological organisms that evolve in response to various influences (cybersecurity it seems…

I have no idea what you are talking about but does human biology have computation at the core? Any papers on these?

Well all info can be encoded as bits (Shannon’s theory of information) and the genome isn’t very far from that encoding. You can divide with bitshifts with computers, it’s possible it could be occurring in biology(this area has been looked over in analysis until recently).

The properties of the genome are similar to the storage memory in a computer in that malicious code is inserted into the path of the biological interpreter. Early during human embryonic development (and only during this time for the human) you have a sudden increase of retrotransposon activity. The DNA itself is like stored polymorphic computer virus with a compiler and code to interface with the environment. It’s very unusual the timing and genes carried around by this circular process are vital for life. That is my basis for the comparison to ASLR. There also exists 2 factor authentication, signature based intrusion detection, intrusion prevention systems.

Here is an interesting paper on an organism that has high rates of this DNA recombination..read the motivation section and you decide if this is computation.

https://ac.els-cdn.com/S0166218X09002534/1-s2.0-S0166218X090...

Re: Before cancer kills, it cheats

#52

Post by domnomnom »

nnq wrote: post #13
domnomnom wrote: post #6

Here are some ideas: Look at the functional call stack. Its a slice of the linear address space that’s actively being used and it is strikingly similar to the promoter regions of the genome. Like some pathogens, hackers randomly try to hit that sweet spot that will jump to the special program. Operating systems are like simple biological organisms that evolve in response to various influences (cybersecurity it seems…

Not sure how much ASLR would be relevant w.r.t. genomes and cancer... Malicious hackers are on the one side very smart (the cancer genesis process is not smart at all ), but on the other side they make poor use of evolutionary strategies, mainly because human hackers can't easily spawn "an army of clones of their mind" (cancer otoh is all about evolutionary strategy ). Since the information about "what mutating a cod…

At one point during the cancer progress process the cancer is characterized by genomic instability (high mutation rate) and extremely high metabolism(high replication rate). The immune system is actually attacking the cancer cells successfully(in generalizing here in regards to cell types), and this may lead to an optimization process where the immune system is selecting for a cancer cell able to avoid the immune defenses. This interplay creates a microenvironment which is as you described, evolutionary in nature.

As for cryptography, I would argue the biology contains hash signatures and other configurations common to cybersecurity(blockchain turns one problem into many IMO). While there may not be asymmetric cryptography, there is also no pseudorandom business.

Re: Before cancer kills, it cheats

#53

Post by jldugger »

smallhands wrote: post #10
domnomnom wrote: post #6

Here are some ideas: Look at the functional call stack. Its a slice of the linear address space that’s actively being used and it is strikingly similar to the promoter regions of the genome. Like some pathogens, hackers randomly try to hit that sweet spot that will jump to the special program. Operating systems are like simple biological organisms that evolve in response to various influences (cybersecurity it seems…

I have no idea what you are talking about but does human biology have computation at the core? Any papers on these?

IDK about papers per se, but as a computer scientist who took classes in bioinformatics, there are parallels. At the base level, cells are machines for constructing proteins, and information on that process is encoded in DNA. Silicon uses 2 bits, DNA has 4 base pairs. Those base pairs groups in sets of 3 called a codon, kinda similar to a byte. Word size is normally a multiple of 8 for computers, but the 6 bit word in DNA is more than sufficient to cover the 20 amino acids, leaving room for both a stop sequence, and some rudimentary error correction -- a mistake in copying DNA somewhere might not end up changing the resulting protein.

There's also a level of programmatic structure in terms of transcription promotors and gotos, and probably some level of conditionals. DNA is also special in that it can be read forwards or backwards, and the base pairing means you always have two potentially transcriptable sequences, each starting from one of 3 offsets. Imagine if busybox implemented all of coreutils in one binary by shifting the word alignment 1 bit to produce a completely different program.

Finally, at the intracellular level, we have a whole host of message passing between cells using hormones and other signaling molecules, and organs like the pancreas that try to regulate a system using them.

As far as 'computation' I don't think the system is Turing complete, and the systems aren't designed to answer decision problems, just construct things, possibly in response to an environmental factor.

Re: Before cancer kills, it cheats

#54

Post by domnomnom »

thraway180306 wrote: post #11
smallhands wrote: post #10

Earlier quoted context omitted.

I have no idea what you are talking about but does human biology have computation at the core? Any papers on these?

biology have computation at the core? Doubtful. You can to computing with DNA http://dna.caltech.edu but it is still debated if the actual role of DNA is being a code (some recently weasel out form that stance by saying it's an “app”, like there's a difference, machine code being a code). Coding theory applied to DNA yields inconclusive results. Galois theory usually has power over any kind of information encoding, c…

DNA compilation is pretty Read Eval Print Loopy to me...

Re: Before cancer kills, it cheats

#55

Post by domnomnom »

Cybiote wrote: post #39
thraway180306 wrote: post #11

Earlier quoted context omitted.

biology have computation at the core? Doubtful. You can to computing with DNA http://dna.caltech.edu but it is still debated if the actual role of DNA is being a code (some recently weasel out form that stance by saying it's an “app”, like there's a difference, machine code being a code). Coding theory applied to DNA yields inconclusive results. Galois theory usually has power over any kind of information encoding, c…

Linking biology to specific concepts in computer architecture or worse, with OS design, is indeed a stretched analogy but biology is rich with computation. I'll try to be short. A cell must sense and respond to its environment. One aspect of this is regulation of gene activity by interactions of for example, transcription factors. When interaction types can be well enough approximated as either of inhibition or activ…

Can you explain how the analogy is stretched? It’s my personal belief that biologists tend to be fairly implementation focused from how they learn about the systems involved.

In biology there is 2 factor authentication to protect against parasitic spoofing, intrusion detection systems, protected kernel memory, memory hierarchy, policy based permission. It a very nice operating system IMO.

Re: Before cancer kills, it cheats

#56

Post by domnomnom »

klmr wrote: post #15
untilHellbanned wrote: post #2

Professor at a med school here. Regardless of whether you think the specifics presented in this article (e.g., NSAIDS-esophageal cancer) are right, it’s great to see this kind of philosophical approach to biomedical research. We need more people like this professor. That she started with a plant and that made her think about humans was a great insight. She rightly recognizes the key role of cell autonomous vs. cell n…

> She rightly recognizes the key role of cell autonomous vs. cell non-autonomous processes in how multicellular organisms work. This is an odd comment: This realisation is quite literally at the core of cancer research, and every researcher in the field recognises this. Heck, it’s implied if not mentioned outright in the seminal Hallmarks of Cancer paper [1] that every cancer researcher (and probably generally most h…

I was talking to a friend in med school, and I feel the difference between what exists in biology as we understand it currently, and what is clinically relevant is gigantic. That paper definitely educated a generation.

Re: Before cancer kills, it cheats

#57

Post by agumonkey »

domnomnom wrote: post #54
thraway180306 wrote: post #11

Earlier quoted context omitted.

biology have computation at the core? Doubtful. You can to computing with DNA http://dna.caltech.edu but it is still debated if the actual role of DNA is being a code (some recently weasel out form that stance by saying it's an “app”, like there's a difference, machine code being a code). Coding theory applied to DNA yields inconclusive results. Galois theory usually has power over any kind of information encoding, c…

DNA compilation is pretty Read Eval Print Loopy to me...

dna replication is very map-ish. then they can fold back to a reduced state

Re: Before cancer kills, it cheats

#59

Post by artsnail »

How accurate is the comparison with plant fasciation, for anyone who knows more? My experience with owning/growing fasciated succulents (usually referred to as "crested" by growers and collectors) has been that they're more challenging to grow in terms of risks of things like overwatering, but as far as I know that behavior doesn't necessarily impact their overall lifespan. Sometimes a crested specimen can also revert back to normal growth. Maybe that's tangential to the article itself, but it's something I'd be curious to find more information about.

Re: Before cancer kills, it cheats

#60

Post by 2chen »

wobbly99 wrote: post #36
gshubert17 wrote: post #26

Earlier quoted context omitted.

Agreed. What can society, which creates corporations, do to limit the likelihood that they will "go rogue" to harm society?

Regulate them, limit them and in extreme cases kill them. And the thought that corporations are cancers of human societies that cheat is not a new.

Corporations are more multicellular organisms than cancer. They are capable of achieving far more than a single cell or person, for better or for worse.
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