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Do cells use passwords?

structure of an animal cell/royroydeb (CC BY-SA 4.0)

Sloan Kettering molecular biologist argues that this may not be semantics. What if that’s what they are actually doing, in effect? One wonders, how would it affect cancer treatment?

Abstract: Living organisms must maintain proper regulation including defense and healing. Life-threatening problems may be caused by pathogens or an organism’s own cells’ deficiency or hyperactivity, in cancer or auto-immunity. Life evolved solutions to these problems that can be conceptualized through the lens of information security, which is a well-developed field in computer science. Here I argue that taking an information security view of cell biology is not merely semantics, but useful to explain features of cell signaling and regulation. It also offers a conduit for cross-fertilization of advanced ideas from computer science, and the potential for biology to inform computer science.

First, I consider whether cells use passwords, i.e., precise initiation sequences that are required for subsequent signals to have any effect, by analyzing chromatin regulation and cellular reprogramming. Second, I consider whether cells use the more advanced security feature of encryption. Encryption could benefit cells by making it more difficult for pathogens to hijack cell networks. Because the ‘language’ of cell signaling is unknown, i.e., similar to an alien language detected by SETI, I use information theory to consider the general case of how non-randomness filters can be used to recognize (1) that a data stream encodes a language, rather than noise, and (2) quantitative criteria for whether an unknown language is encrypted. This leads to the result that an unknown language is encrypted if efforts at decryption produce sharp decreases in entropy and increases in mutual information. A fully decrypted language should have minimum entropy and maximum mutual information. The magnitude of which should scale with language complexity. I demonstrate this with a simple numerical experiment on English language text encrypted with a basic polyalphabetic cipher. I conclude with unanswered questions for future research. Alex Root, “Do Cells use Passwords? Do they Encrypt Information?” at bioRxiv

He is throwing out ideas to start discussion, but it is a serious one.

See also: Decidedly unDarwinian admissions re proteins

Who was it that posted recently on Mutual Information? Found him, Eric Holloway, posted here on an interesting discussion that eventually led to more conversation off of UD with Professor Swamidas, Eric and Durston. the follow up paragraphs leading to Mutual Information. Sorry, one long paragraph...
Williams and colleagues found that Zipf's law held more generally for phrases in English than words, which is intriguing because phrases are "the most coherent units of meaning in language61." Language has additional structure that can be captured through analysis of pairwise and higherorder interactions62. One measure of association is Mutual Information6. It can be defined between two sets of variables X and Y, e.g., adjacent letters in the English alphabet as MI(X,Y ) = H(X)+ H(Y )? H(X,Y ), (3) where H(X,Y) is the joint entropy between the X and Y, which is defined as H(X,Y ) = ? p(x, y)log2 p(x, y) y?Y ?x?X?. (4) When X and Y are statistically dependent, the joint entropy H(X,Y) is lowest and the Mutual Information is maximized. Doyle and colleagues describe the search for extraterrestrial intelligence (SETI) as fundamentally applying Zipf's law and higher-order information-entropic filters to received sources of electromagnetic radiation63. Cell signaling and gene expression have been shown to pass both of these non-randomness filters6,64. These non-random filters can also be applied to any sort of data stream to check if it is non-random. If a simple substitution cipher is applied to an unknown language, the frequency distributions of letters, words, and phrases do not change, and therefore, given enough text would be recognizable as language, although perhaps untranslatable. For a more complex cipher, e.g., a polyalphabetic cipher, the entropy will increase and frequency distributions will deviate from Zipf's law. In other words, if SETI receives a long stream of an alien communication that is encrypted by relatively simple methods, its non-randomness filters should recognize it as a language. If the alien language is encrypted with a polyalphabetic cipher, which was subsequently decrypted, the plaintext would have lower but non-trivial entropy. A quantitative test for whether a text is encrypted is whether there is a decryption, such that: argmax d?D (MI(E),?H(E)) (3) Where d is a decryption out the set of all possible decryptions D, E is the decrypted plaintext, and MI is the Mutual Information in the decrypted plaintext, e.g., the mutual information in adjacent letters, and H is the entropy of the decrypted plaintext, e.g., per letter. In other words, a signal stream is encrypted if a decryption can be found, such that the entropy is minimized and the Mutual Information is maximized.
Fascinating, he goes on to say this is a suggestion and not direct evidence...
While I have not presented direct evidence for cell passwords, encryption, or other security measures, I suggest that they may exist and provide fragments of theory and criteria that the community can use to look for patterns that may demonstrate their existence.
Certainly an area to look at with regards to Chromatin, Transcription Factors, Compression and Open or Closed Access. What signal cascades are required for success and are there more IDPs involved at this level possibly? As "flexible keys(folds)" to unlocking the "Locked States"? . DATCG
From the text of the paper...
Organization of chromatin into highly compact, inaccessible regions, and open, accessible regions appears on its face to be a form of cellular information security because some genes are "locked" and therefore, cannot be transcribed. Chromatin is frequently characterized as being in "open" and "closed" states that must be unlocked for cell differentiation by pioneer transcription factors. Exactly, they are compressed and only made available upon correct signal.
This appears to be a potential case where cells use passwords. There are multiple algorithms to predict combinations of transcription factors to reprogram human cells from one type to another with the number of successful conversions being relatively low, reviewed by Kamaraj and colleagues51. If not a "password" then a specified sequence of tumblers per say of events that cascaded in line with specific actions for specific "unlocking" Chromatin to an "open" state for access.
The systems work by engineering overexpression of Transcription Factors, rather than as it happens normally in development through extracellular signaling molecules that signal to transcription factors to achieve the rewiring.
Note in order to "rewire" this needs prior knowledge and cannot blindly hit upon a lucky outcome, or it all tumbles, degrades and ultimately fails.
To our knowledge, no one has attempted to predict upstream combinations of signals, e.g., growth factors, hormones, adhesion contacts, etc. that would trigger the right combinations of transcription factors.
Ooooooooh... sounds like great ID work. Because by untangling this, we will see if it's guided or unguided, blind or prescribed to limit failure and aide error correction. Error Correction is a mark of intelligent design, not blind, unguided events. Error Correction alone should kill any thought of blind, unguided Darwinist conjecture.
Sampattavanich and colleagues demonstrated that FOXO3 dynamics can code for different growth factors and their concentrations, which are under combinatorial control of ERK and AKT pathways54.
Note how this dynamic interplay is still under restrictions and controlled systems architecture, of which any Protein Complex fault, could lead to disease or catastrophic results.
One simple way to conceptualize this is that it takes the right combination of transcription factors to unlock the epigenetic code to transdifferentiate cells, i.e., it might require an initiation sequence and therefore, a password.
I don't know about a "password" per say, but a series and combinations of cascading events that initiates a Key or Lock for the correct folding and unfolding process to start, or to Open Access. Any one of these events could by mutation cause deleterious outcomes, or a prescribed change that works for subtle requirements.
This is distinct from simply requiring a series of events. If the reprogramming transcription factors are active during the entire reprogramming process, then they are not performing an initiation sequence and therefore, not entering a password. Similarly, if only one member of the combination can partially reprogram cells then it would seem inappropriate to conceptualize the mechanism as a password. I predict that password-length, i.e., the complexity of the reprogramming initiation is directly proportional (to) the fitness cost posed to the organism from the conversion. For example, because stem cells have greater replicative potential, they might pose greater risk to develop into cancer and consequently, require a more complex password for reprogramming.
Do cells encrypt information? If cell signaling networks use encryption, how might we know? Put another way, if we do not know the underlying language, i.e., the unencrypted information, how can we recognize encrypted information? To explore this question, several concepts from information theory are useful. The Shannon entropy is defined as55: H = E[I(X)] = ? p(x)log2 (x) ?x?X (1) where H is the entropy in bits, defined as the expected information of a distribution of random variables X. The entropy can be thought of as how predictable the next character in a transmitted message is. A message that is purely random characters and therefore, not meaningful language, will have the highest entropy55. Considering only the 26 letters in the English alphabet, the maximum entropy is log2(26)=4.7 bits. Shannon analyzed words of size N up to 8 letters and found the entropy of the English language to be roughly 2.3 bits per letter, a 50% reduction over random56. The English alphabet could eliminate the letter c with either k or s without any meaningful effects. Moreover, English text can be re-coded and stored in smaller file sizes without loss of information (lossless compression) using sophisticated algorithms55. Entropy provides a limit on lossless compression55. A related concept to entropy is Zipf's law, which states that a word's probability is inversely proportional to its rank and has been found in English language phrases, and also other fields, e.g., city sizes, firm sizes, and neural activity57. Frequency ? 1 / Rank (2) A large number of explanations has been proposed for why Zipf's law exists, which are reviewed by Piantadosi58. Purely random texts do not follow Zipf's law59. Salge and colleagues found that Zipf's law emerges through minimization of communication inefficiency and direct signal cost60.
So intreesting, this eventually leads to another aspect he covers on Mutual Information. See next comment. DATCG
... Chuckles, "Spread the Love" just make sure it's encrypted with a key ;-) lest the bonds be broken and folds unfolded. Good stuff, great thinking and very real application of reason to the issue of communications and information control systems related to Chromatin, compression algorithms, access and cell signaling. And agree with Tom Robbins thoughts. A communication system between sender and receiver in order to be efficient must 1) be compressible, 2) recognized and tagged with 3) keys or encryptions. In the case of DNA, for example like Ubiquitin tags and the UPS act as regulators along with other Transcription Factors. You see the use of flexible folds(Intrinsically Disordered Proteins - IDPs) that can match a variety required shapes for modular interface and likely that is a "key" in communications systems in cells. A cascade of signals must unfold for authority to final release and/or form final gene expression. And reactions of correct sequences must unfold, leading to appropriate Protein Complexes and Reactor agents as a reply to ongoing developmental processing, or as signaled responses to internal and external cues. The Code enforces the adjustments, often upon unfolding and differing angles to unlock or keyed recognition events. DATCG
Synapses are ALL about passwords. Each axon emits a cloud of neurotransmitter molecules, and the surrounding dendrites only let in the molecules that have the key to fit their lock. Hacker molecules that fail to penetrate any dendrites are later sucked up by glial janitors. polistra
Cellular TCP/IP, anyone? ET
Well you did have an article where the cell employs a very real kind of chemical encryption but I don't recall the exact part of the cell that employed it- if I recall correctly, there is a process where a chemical tag, acts like a kind of key as in a public or private key - I am in IT and now Cloud computing work, have been for a very long time. And basically if you have a enzyme or protein (lets say) that requires access to another resource like a molecular machine , in order to obtain access to the resource, it holds a chemical market that is equivalent to a public key (given to all enzymes that require "access") - it is not given a public key UNLESS it has been approved for access - then this match up with the molecular machines private key - these keys are generated through an algorithm, and if the Public key is correct, putting it together with the private key, opens the "lock" by giving a certain result that resolves the algorithm (sometimes known as a HASH number), then it is securely accessed. This can be either with data in "flight" (like data between your browser and a server on the internet, that uses HTTPS certificate encryption to validate to the client that the site is indeed who they say they are, generated by a certificate issuing authority, who insures the website belongs to the identity recognized. OR it can be used at rest, where the data sits on a disk, literally scrambled, and can only be accessed if the Public key is produced, and the algorithm can then decrypt the data. I will have to look up that older article - it may be in the link above. Tom Robbins

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