Biochemistry and Information Theory

[Vkothii]

Now that the subject has been declared, what is Biochemistry? What is Information Theory?

Does anyone agree that these subjects (that can be studied at centres of Scientific learning and research), are connected to something called Evolution?

(if not, some mod can bung this on the scrap-heap, and I won't bother with questions like this again, at this particular BB, anyway)

 

[Vkothii]

hmm, Step 2. Evolution: means (generally) some principle that we see in systems or spaces where "changes" occur. It's tied to a field of study called ergody, and to complex systems theory (like climate models, statistical markets).

So we see things "evolve". Physical systems can evolve (heat evolves from exothermic reactions).

Biological systems evolve representations, like eigenforms, or a resonant and stable phenomenological "geometry". But speciation isn't a stable phenomenon at all, in fact, organisms that can evolve quickly - like bacteria and mutable viral diseases like HIV and influenza and the rhinovirus "family" responsible for the "common" cold, seem to have more advantage over organisms that are specialised or adapted - like the polar bear or the manatee and dugong, or the Galapagos reptiles, etc.

OK so far?

So representations are things like symbols; in that sense, all organisms are symbolic, since they represent an "end product". Each of us "evolves" over a period of gestation (because we are sexually reproducing, placental mammals), from a single, specialised "start condition": the fusion of "gametes", the zygote.
Comparative embryology tells us that during development various structures emerge; as the cellular "matrix" grows and extends, each differentiating part eventually goes through apparent evolutionary phases that are common to other vertebrate (and invertebrate) embryology.
Although individuals exist with different amounts and complements of genes, they are only a step in a much longer journey, which can be imagined stretching back to the dawn of life itself: co-operating and replicating systems of chemicals in some sort of package or "bubble".
Classification and organisation into "families", "classes", "genera", and so on, is a human construct. Species and speciation isn't a static table, or picture, like the Periodic Table, it's an evolving process.

The process that results in a single-cell "seed number" becoming a human, is itself the result of "selection pressures", that act on genetic material's innate variability. These are the external circumstances that a particular specialisation - species, finds itself in, and how circumstances change, and especially feedback processes.

One feature of life and evolution (like the expansion of the cosmos) is that it must have evolved from an initial condition (set of conditions, in fact). To evolve, life has to change and respond to change. It must have developed this "evolutionary ability" alongside the ability to replicate and conserve certain information.
Life must have initially been a lot like we can see it now at the "lowest" branch of the tree - the oldest mycobacteria and slime molds, and the archaea.
It must have possessed variability and replicability nearly simultaneously - the alternative is that the earliest forms of life or "proto-life", must have rapidly developed the ability to replicate reliably and efficiently, so that critical information was conserved, and there must have been some "recording" mechanism, or persistent record as chemical information, that provided the physical means of conservation. That is, information as matter (some kind of polymer that "symbolised" an alphabet) along with agents, that were also conserved (catalysts of some kind), these would have had to be coded, eventually, into the polymer. Otherwise, after a few "accidental" divisions, there wouldn't be enough "organism" left to be alive. Early proto-life must have evolved rapidly, and diversely, i.e. it must have been able to present multitudinous versions, in order for selective pressure to result in "advantageous" evolution.

Today's "coding" polymers are ribo-nucleic acids, repeating units of ribose (a sugar), which forms a double-chain that twists (has chirality) - a double helix.
The earliest reproducing, evolving lifeforms must have had something that "settled" into this modern, efficient form via only those processes that are known to "push" the evolution process: natural selection and advantage (of variability).

 

[Vkothii]

OK, so life, in order to persist, has to not only have viable representations, it has to have a functionality that lets it replicate and inherit variable information (as structure). These are represented by the nucleic acids, the "coding", or message part of the DNA or RNA backbone.

So, the double helix is a stable polymer, which forms the carrier; it "carries" the messages (signals) called codons, that represent amino acids (the alphabet maps to 20 other "unit forms", and is redundant - in a symmetrical way). These molecules (AA units) get joined together by other structural "protein factories", and, as mentioned earlier, there is function in form (a shape alphabet): the proteins are folded, and variable forms are possible - i.e. a single gene message can be read a number of ways.

The principle of Biological Evolution (Darwinism), is that life varies, and is subject to selective pressure.
Life is both structure and agency; both are necessarily conserved (inherited), and, because of feedback (hysteresis, equilibrium), both also affect the environment, and result in changes in those selective pressures (amongst representations - genera, classes, and phyla). Life changes itself and its "world", the world also changes because of natural (tectonic, climatic) processes.

 

[kmguru]

Is there a question? or a supposition?

 

[Vkothii]

So, there's no argument with anything I've posted up there so far? I'm only trying to connect DNA and IT together. What do you know about Shannon entropy, or information entropy, or proteomics?

 

[kmguru]

Some of the items are way over my head as now I come from the Information Science world even though I studied BioChemistry long ago. I know a little bit about Proteomics - that is the study of Proteins, folds, 3D structure etc. I was involved in one project to develop a database to catlog these proteins using Massively Parallel Processors.

Where are you going trying to connect to IT? Have you found a method to catalog over 500,000 proteins in human body with its properties including mirror, folds etc?

Also are you thinking of simulating glycosylation,phosphorylation, protein degradation etc.?

 

[Hercules Rockefeller]

I'm only trying to connect DNA and IT together.

You don’t need to try; the link already exists. The use of DNA and proteins for information processing and data storage is hardly a new idea. People have appreciated the computing potential and information storage capacity of these biopolymers for a long time. If you go searching you will easily find examples of scientists utilising them for processing or storing data.

 

[Vkothii]

Well, there are research projects looking at neural models (or even modified neurons) as elements in some kind of "amorphous" computer. There are already DNA chips (and labs on a chip). MEMs have been around for a while. We're getting closer to linking the IT world with lifeforms (like bacteria or maybe amoeba) all the time.

But looking at information entropy of the whole show: I'm firstly interested in decomposing the DNA replication and ribosomal fabrication subsystems, basically making sure all the bits are there (the structure), then agency should "appear". once the gadgets are characterised.

Life is self-assembling (and disassembling), and relies on the tensions and surfaces it finds in molecular structure (and function). The dipolar character of good old H2O, and hydrogen bonding and the surface tension of aqeous/organic phases, are all important structurally, apart from protein structure.

But the whole is the sum of the parts - if all the parts work, and interconnect as they should, the car should be driveable.

Some of the items are way over my head

Can you be more specific - I'd like the discourse to be relatively straightforward, so what bits are "hard to follow" or whatever?

P.S. I'm aware that there are some gaps in the knowledge here - we know a lot about the DNA information model, but not so much about the fabrication side, except for some examples, and a general explanation of the transcription process.

 

[Hipparchia]

But speciation isn't a stable phenomenon at all, in fact, organisms that can evolve quickly - like bacteria and mutable viral diseases like HIV and influenza and the rhinovirus "family" responsible for the "common" cold, seem to have more advantage over organisms that are specialised or adapted - like the polar bear or the manatee and dugong, or the Galapagos reptiles, etc.

OK so far?

No. They only have more adavantage in a specific set of conditions, not a universal advantage. In simple lanaguage, there are swings and there are roundabouts.

 

[Vkothii]

Yes, thanks for the pointer; universal advantage is a misconception right there, though - no organism has any universally advantageous adaptation, never has and never will. The specific conditions are the specific environment, or niche.
I don't see where I imply that viruses and bacteria do have a universal advantage. Having advantage, is a universal trait of all lifeforms, the successful ones especially.

Cyanobacteria and blue-green algae have colonised a lot of "niches" however, including every ocean and freshwater system on the planet.

 

[Vkothii]

Still here, okey-diddly-kokey.
Evolution: a process with the following inputs:

* living things - varied and diverse representations of particular genomic classes and families of species;

* variability amongst individual members - a range or spectrum of different phenotypes from a particular genome;

* an environment: the "stage" upon which a particular genomic representative (species) evolves, this is also subject to external inputs
which include: one solar system with an average-size star that shines in an acceptable part of the spectrum (hold the gamma or x-rays, please); inner rocky planets, one of which is temperate and has liquid water; a nitrogen (neutral) atmosphere; tectonic processes actively forming new sea-floor and pulling and squeezing hardened plates of crustal matter around the surface of the rocky planet - continental plates (cratons), like bits of cracked and broken eggshell on the surface of a big "egg", floating on a plastic layer of basaltic rock.
These converge and disperse over timescales of hundreds of millions of years (orbits of the planet around the warm n'cozy little star). Any reversal usually involves a lot of volcanic activity, along the newly-forming subduction and fracture zones - large traps, of basaltic lava flows, periodically alter global climate, in synch with the end of a dispersal phase and the start of a "reassembly", of the continental crust (lighter minerals).

Life "needs" a planet warmed by a sun, that rotates with sufficient speed that the surface doesn't get too "toasty", and not so quickly as to cause violent storms and wild weather patterns.

It also needs all those other parts I've mentioned back up there in the earlier bits: structure, and a way to store the plans for it. Structure and function is what living things are all about. There is no function without structure. You can't send a message if the telegraph line is down.

So Life (with a capital), and its evolution, are the same package: there's no evolution without Life (and the background it "lives" on), and no life (successful adaptation) without Evolution. So what does evolutionary success mean? What results in a successful "process", in terms of the programming and the architecture - no sudden crashes or fatal bugs? What does Evolution output?

As biochemists and geneticists will remind us: there is no agency behind the "process" of Evolution - it's completely blind, it just throws the dice and spins the big wheel (after carefully shuffling the cards), and you get the hand you're dealt.
So a lifeform has to deal with "living", using the technology that has been developed for it, by its ancestry; obviously if this technology or toolkit is adaptive, then a lifeform will use it advantageously -indeed many random program changes have, down the ages resulted in a large collection of adaptive and useful tools - photosynthesis; multicellular plants & animals; the eye; feathers and hair; teeth and claws; lungs and gills; cortical neurons.
Just for example. Individual organisms, using and adapting the tools they have, and thanks to selection which sees the fittest and best adapted survive and pass on their genetic material (persist in the genome), are responsible for of all of them.

So that's Life & Evolution 101.

 

[kmguru]

You are not thinking about "A new kind of science" by Wolfram? Are you?

 

[Vkothii]

Who me?
Nope, just burbling away on my own here. I want to look at a couple of issues that Biologists have with the informational content of genetics, at least the bit we understand - but genetics isn't just RNA and DNA. There are actually some misconceptions amongst researchers and biologists with "information" - what it is and how to measure it.
Not trying to portray any great level of expertise here, but a bit more commentary from "others" would be OK.

I haven't really got into the IT side yet (by which I mean Information Theory, not computer science). You know - the characterisation of "static" patterns of information, and how it changes - information entropy.

Before charging into Shannon's ideas (and more recent ones about the "entropy" of information - something representable in the simplest numbers we know about: base2 or binary), I feel a need to expend a bit more effort on the topics of:

Selection Pressure and Variability.

Selection is a fairly simple idea: organisms are selected by the environment, and they reproduce - their genetic material contributes to the genome; those who aren't selected (are selected against), don't contribute - their genes die out, and get removed from the genome, or replaced with better (or better functioning) genes. Selection actually is against particular genes and alleles (genes can be recessive/suppressed, or dominant/expressed), and so against a particular set of genes: a genome.

Selection is an agency that is characterised by environmental conditions - because of feedback, and the changes that organisms make to the environment, the agency of "natural selection" is partly inorganic and partly organic, or partly (mostly, but not always) due to external (planetary, solar) changes, and partly to internal changes that result in environmental change - the internal or biogenic ecosystem changes also come from other lifeforms (genomes).

Selection pressures are: (cyclic) external conditions like circadian, orbit-precession, tectonic, geologic, atmospheric, and climatic changes; and inter-genomic competition and co-operation (co-evolution).
The first big environment change that the planet went through was the oxygenation of the (neutral) nitrogen atmosphere by newly-evolved phototropic lifeforms. As mentioned, these colonised liquid-water environments around the planet, and filled the niche rapidly, in evolutionary terms. Because of (our explanation) a key adaptation of some gene and the metabolic process it was part of, photosynthesis became part of the genetic toolkit. Chlorophyll and other kinds of pigments arrived on the scene.

Variability is also an agency, that changes the code or instructions for making stuff. Sometimes these changes are made by the enzymes that maintain genetic material, check for "copy errors" after cell division and so on, sometimes because of radiation that chemically alters a nucleotide base, so the codon triplet codes for a different AA, sometimes during meiosis (gamete production), the crossover of chromosome material can "go wrong". These are examples of ways that genetic material changes, there are others.

Oxidising chemicals and free radicals can "damage" DNA or RNA too. Then there are the virii, or viruses, if you don't speak Latin. Viral "packages" have been intruding into the genetic replication/transcription process for a long time (as long as bacteria have been around, maybe). Viral genetic material can be absorbed and eventually become part of the genome (following adaptation).

That's about it for how DNA and RNA mutate "normally", in Life's natural environment.

Note how Darwin's theory relies on the concepts of agency, rather than a static classification or schema - Life is a dynamic, shifting and extremely complex system. But fundamentally, it runs on basic principles that we can understand, just like we can understand how spark plugs, distributors and batteries work.

 

[Hipparchia]

I don't see where I imply that viruses and bacteria do have a universal advantage.

You are correct: you do not imply it, you state it clearly.
"But speciation isn't a stable phenomenon at all, in fact, organisms that can evolve quickly - like bacteria and mutable viral diseases like HIV and influenza and the rhinovirus "family" responsible for the "common" cold, seem to have more advantage over organisms that are specialised or adapted - like the polar bear or the manatee and dugong, or the Galapagos reptiles, etc."

You do not limit the circumstances in which this is the case. The bacteria and the viruses seem to have more advantage than big old eukaryotes. No qualification whatsoever.

 

[Vkothii]

You do not limit the circumstances in which this is the case.

Limit the circumstances? Advantage is an evolutionary principle - it's common to all life.
... so therefore having more advantage, for any organism anywhere on the big tree, is universally beneficial. It depends on what is seen (by us humans) as advantageous.

It's an advantage for organisms like bacteria to have a high rate of genetic variability. For more complex organisms, the goal is a stable genome. Or that's how we see it.

Advantage, goal, variability, purpose and adaptation, are things we see. That doesn't mean they're there, if you see what I mean.

Or if not, do you still see that I'm saying: "because viruses and bacteria can evolve quickly, this gives them a universal advantage - over other kinds of organisms, like mammals." It's only "half the story" isn't it?

This isn't what I'm implying, I'm implying they have an advantage in having the ability to evolve quickly - i.e. adapt to changes more "easily", than organisms who specialise.
However, specialised organisms (like the polar bear) have an advantage too - a more stable genome, which costs them the advantage (ability) of rapid adaptation.
If you look at it like a game of poker, say. I know that's over-simplifying it, but.

So, the advantage that mutable (rapidly evolving) organisms have, means they gamble on maximal diversity (what we see as species), and pay for it with genomic stability (the cost). Stable, specialised organisms have a stability advantage, but it costs them in variability terms. But bacteria can speciate more rapidly (in fact, bacterial species are very much a moving target); the sentence was about speciation, and I'm saying bacteria and so on have an advantage here (diversity-wise). But perhaps it should have been more balanced.

Maybe another view is that "simple" organisms "need" to gamble with diversity, and abandon stability. More "complex" communal-type organisms and eukaryotes (like the zooplankton), are "forced" by their complexity to gamble the other way.

So, the revised version:
"But speciation isn't a stable phenomenon at all, in fact, organisms that can evolve quickly - like bacteria and mutable viral diseases like HIV and influenza and the rhinovirus "family" responsible for the "common" cold, seem to have more advantage, speciation- or diversity-wise over organisms that are specialised or adapted - like the polar bear or the manatee and dugong, or the Galapagos reptiles, etc, that have more complexity and an evolutionary goal of stability within the species, not diversity"

 

[Vkothii]

Looking back over what I've put together so far, there are one or two contradictory things in it.

I've said that Evolution has "no agency" behind it. But then I say that variation and selection are the two agencies responsible for, or that "push" the process along.
Random changes to the genetic record aren't directed (except by probability), but other kinds of changes - like crossover errors during meiosis, are "directed" in a sense. And Darwin's theory invokes both random changes and the agency of selection.

So Evolution does have a chance factor - if some organism is "fortunate" to have its genome changed advantageously, that's "good", but a lot of changes aren't "good". What helps the "good" changes to persist, is obviously selection.

Life is information, in the sense it's a lot of structure (which is not static), and information also has structure.
Life is itself agency, in the sense that information can have agency, or information can be mapped. The mapping is also information.
Life is information gathering and "improving" itself - by improving the structure and the way it gets mapped.

Information entropy is kind of a misnomer. There's a rumour that Shannon first dubbed it "information uncertainty", but was advised that, since no-one understands what entropy is, he should call it information entropy, because no-one would argue that information can, or can't "have" entropy.

Another problem with information and entropy, is that physical entropy describes or measures a state of dispersal of heat, or energy. Information isn't "physical".
Nonetheless, information has a certainty/uncertainty or expectation, when it's analysed in terms of messages and channels.
Channels are straightforward enough, messages and expectation are a little trickier, and to understand Shannon's ideas, you have to disconnect from notions of meaning of messages - information is "meaningless", it's just a pattern.

The only significance is that there are potentially unlimited patterns of information - and they're all different. The differences and the expectation are connected.

 

[Vkothii]

So, now what? The Informatics side of Biology is humungous: there are gazillions of references to combinations of such words as: "bioinformatics" "DNA entropy" "information-theoretic" (googlemes).

An example of some gene, its representation and "informational entropy", could be the next thing to do here. But that alone implies gazillions of posts just to cover, say bacterial flagella (the evolution of motility).

There is a particular bit of information (a pattern) we can see with flagellum proteins and the MHC genes in humans and animals, or eukaryotes in general: an "interesting connection".

 

[Vkothii]

The advantage thing and the different aspects, as outlined above, point to the prokaryotes having a variability advantage, but the "goals" for prokaryotes are a bit different, they seem to be a simpler, less structured form of life than the eukaryotes.

Speciation is a "snapshot", that we humans have taken of the array of life forms, everywhere, even all over (and "inside") us. Without bacteria and the other "old guys", we wouldn't be here, because we depend on certain "classes", or what we call species, of them to stay alive. They live on us, and in our gut, and provide certain benefits in return (a symbiosis).

The prokaryotes outweigh "us guys", by a fair ratio, in terms of biomass. They got here first, and they have a few billion years head start on us. They've radiated absolutely everywhere there is any kind of energy source on, or under, or above, the surface of mother Earth.

Prokaryotes diversify, or they retain a high variability, and can evolve rapidly, gambling huge individual "losses" against the odds that some members in the range presented, will survive.
They achieve this via adaptation (genes get altered). The strategy is retention of high variability, in order to have some (even a very slight) chance of survival.
Only a single surviving individual (a "new" species that has endured a change in external conditions), is sufficient, the species persists, as a variation (like, on a theme).

 

[Hipparchia]

The strategy is retention of high variability, in order to have some (even a very slight) chance of survival.

There is no strategy. Strategies are teleological. The Modern Synthesis is not a teleological theory, therefore you are not talkning about evolution as currently understood by biologists.

 

[Vkothii]

Perhaps I should have put quotes around "strategy".
You're aware that there is evidence of co-operative and non-co-operative (i.e. cheating) behaviour in bacteria, like in ones that cause disease. And that they can gain advantage by cheating, by being filial, and so on, just like we do?

Lots of books about bacteria will imply that the different kinds have different strategies, for dealing with the changes in their environment, or even how ensporulation is a survival strategy. The development of resistance to antibiotics is strategic, in medical terms.