What's a virus, anyway? The bare-bones basics
scopeblog.stanford.edu
scopeblog.stanford.edu
^ here is the link. Pretty great animation. Thanks for the recommendation.
All you have to do is go to a pond or creek scoop out some weeds, dirt and water and stick it in a jar and there is hours of exploration in front of you. Once you start looking its like seeing an evolutionary world in front of you, everythings eating each other and trying to not be eaten. If you're thinking of getting a telescope (I had one), think of a microscope they open up a new world, its incredibly easy to see things - I thought it would be a lot more work.
Probably there's so many on line resources now to - this guy is a great start - microbe hunter https://www.youtube.com/channel/UCDpKY8-oz5PWlBPNzNsbLug
In short, energy gradients (ie, on hydrothermal vents) can cause matter to organize itself into structures that more efficiently dissipate this energy. You can see how the creation of this structure would in turn enable the creation of a new kind of structure that lives on top of that.
and your last statement isn't getting to why. it's just what happens.
every living organism has some way of perpetuating itself, either by growing indefinitely or by making copies of itself. there's no reason "why", other than that organisms that can't do this get filtered out very early in the game. this implies having some sort of "strategy" for traveling up the energy gradient.
short of somehow evolving the biological capability to fuse/split atoms, all the usable energy on earth comes from the sun. so the first link in the chain has to be something like photosynthesis, where you collect and store energy directly from the sun (ie, "building a house"). but in doing this, you change the gradient, creating an opportunity for other organisms take your stored energy for themselves. in some sense, it's much "easier" for a rabbit to eat a plant in one minute than it was for the plant to collect all that energy over its entire life. there's only so much solar radiation per square meter, which limits a plants energy budget. a rabbit can eat many plants in a day, effectively multiplying the area of the solar radiation it can capture (and spend on acquiring even more). but then the rabbit creates an opportunity for a predator to harvest its stored energy and the cycle continues...
it seems like you're maybe asking "why can't all life just cooperate"? this would probably look like a planet full of plants (or a similar lifeform at a different scale). the problem is that this leaves a huge opening for the first "defector"; it's an unstable equilibrium. life does not evolve to leave opportunities on the table.
Organisms that consume plants are capable of more complex behaviour and growth because the amount of energy and nutrients etc. is greater that they receive by conauming things that photosynthesize.
Anyway... The 'why' is trivial-seeming to me. Once one organism can consume ready-made nutrients from another organism for less energy cost than producing, it will, or it will be out competed by others who do. So carnivores exist everywhere. Even deer happily eat baby birds that they come across, and rabbits eat their own.
Almost Tragedy of the Commons?
This animation enables one to visualize a single SARS-CoV-2 virion binding with the ACE2 enzyme, entering the host cell, and replicating 4-5 new virions.
One SARS-CoV-2 virion is 125 nanometers wide. By the time it shows up on a CT scan we are talking many, many billions.
It's seems impossible anyone could test positive and still be asymptomatic.
DNA based viruses don't have that unique mechanism but the result is conceptually the same: you get a virus that is extremely hard to completely cure/remove due to it being present in some of your own DNA. Herpes is a DNA based virus and that's why you can't ever be fully cured from it.
That's also why retroviruses like HIV can only be suppressed. It's also why antiretroviral drugs try to inhibit the replication phases of the virus, which makes managing the disease possible but can't remove the virus itself. Still, a cocktail of those inhibitors is an amazingly powerful treatment against AIDS and leads to HIV becoming basically dorment in the body.
A ribovirus (which is what coronaviruses are) is RNA based but it doesn't embed itself into our genome. It never translates it's RNA and since RNA is fundamentally less stable of a molecule than DNA, you get really high mutation rates. That "instability" is caused by the lack of a built in error checking mechanism in RNA. Those random mutations are part of why Influenza is hard to build immunity against. But it's also why RNA based viruses are generally either too virulent and mortal to allow for effective spread, or rapidly evolve towards less lethal forms.
Keep in mind that I've generalized a lot and that there are a lot of exceptions and outliers when it comes to viruses. For example, Hepatitis C is a ribovirus but it has a special protection mechanism that protects it's core genetic material from mutations even if it's RNA based.
The coronovirues have a proofreader mechanism, which is interesting.
And influenza has more potent evolved countercountermeasures than just high mutation rates: https://en.wikipedia.org/wiki/Antigenic_shift
One of the distinguishing trait of CoVs are their special RNA replication/transcription mechanisms that results in less errors, which is really important considering the large size of their genomes compared to other RNA based viruses. Though, and correct me if I'm wrong, aren't they still extremely less stable than DNA viruses? Which is why only short/medium term immunity is usually possible? I don't know a lot about the synthesis of coronavirus RNA but it looks super interesting
That's correct. Worse, the proofreader doesn't have to protect all parts equally...
> Which is why only short/medium term immunity is usually possible?
No. For some viruses active immunity just doesn't last particularly long for reasons we don't understand (or at least it was described as not understood in every paper I've seen on the subject). For some viruses you can be reinfected months later with exactly the same virus. This is the case for several cold causing viruses.
Why? Most symptoms are part of the body's response switching into overdrive and not a direct consequence of cells getting subverted into virion farms. If the immune system wins without resorting to state of emergency measures like a fever you won't notice, but in the meantime there is a phase of viral replication in the throat.
With SARS-Cov-2 there is even the pattern that detection drops already in the throat of patients that still have a pneumonia raging in their lung (probably because the throat, as a battlefield in this war, somehow favors the immune system more than the lung?), so it's not even a subset/superset relation between symptoms and positive throat PCR, it's a partial overlap.
Comorbidity is the issue with SARS-CoV-2. It is interesting that some patients testing positive report losing the sense of taste and/or smell while others report digestive problems prior to the onset of acute respiratory problems or even sore throat.
https://www.youtube.com/watch?v=7Hk9jct2ozY
https://www.youtube.com/watch?v=B_zD3NxSsD8
The GP is right in that our intuitions aren't cutting it down at the bottom.
All these animations tend to edit out the water molecules so that the audience can understand better. The proteins aren't colored blobs at all. At these scales you'd clearly see individual atoms instead of blobs. But watching a bunch of really detailed atomic ball-stick models would be confusing. And not only are the H2Os battering everything like TIE fighters in the Hoth asteroid field [0], there are ions in there too (Na, K, Cl, etc) that really effect the cell. The membranes are also edited, as many cells are porcupined with receptors like an over crowded wave pool [1]. In addition to the water/saline being edited out, most of the other proteins, vesicles, and interior membranes are also gone for the sake of clarity. There is nearly no free 'space' in the cell, think of a really crammed subway car [2], with the air being like the water/saline. But only much much tighter.
The cell is more like a frantically efficient liquidy crystaly thingy than a wonky wobbly blobby poofed-up juice box. And each one is utterly deeply profoundly fascinating.
[0] https://www.youtube.com/watch?v=C_DnrceDEI8
https://ccsb.scripps.edu/goodsell/machinery-of-life-reducedi...
Here's an interview with him, explaining and showing his process:
https://www.youtube.com/watch?v=f0rPXTJzpLE
Here's his recent painting of a coronavirus protease:
https://pdb101.rcsb.org/motm/242
The other thing missing from those videos is any indication of how random these processes are. At one point, an actin filament assembles by having monomers fly directly at the tip and stack neatly together. It's not like that. In reality, there are all sorts of molecules just randomly moshing around, and occasionally, an actin monomer will bump into the tip of the filament and stick, because it has a binding site. But sometimes one will bump into the tip and not stick! Sometimes, the tip of the filament will fall off! The growth is purely statistical: monomers are more likely to stick than to fall off, and more likely to stick than some random unrelated protein is to stick.
Because of Richard Smalley that money went towards material science and chemical research instead of the molecular manufacturing it was promised for. Even though, as you point out, in terms of fact the critique only applied to life-like bionanotechnology.
The history of this is laid out pretty well—with a surprisingly minimal amount of sour grapes—in Drexler‘s book Radical Abundance.
Another interesting thing: cells are packed so tightly (not just a bag of water) that proteins grind against each other and against their ligands, increasing the "activity" (even the free energy of ATP hydrolysis isn't the standard 7.3kcal/mol.
Yes, macro-scale intuition isn't great (although people pierce cell walls with tiny needles all the time), but if you spend enough time looking at cells under a microscope, you start to build an intuition about cell and molecule behavior.
Many vulgarization sources say that DNA is like the source code of life. But they mostly skim across the issue and go to conclusions like "this gene or set of genes are responsible for that outcome".
But coming from a CS background that sounds a bit like non-sense. I feel like it is like saying that "this processor instruction is responsible for that outcome". But in the end what is important is not the individual instruction but the interaction between them and the environment (Input / Ouput).
Regarding the genes and central dogma, he gives a LOT of detail about how for instance it was discovered that codons work in threes (not twos or fours). Also how it was discovered that DNA is the thing with the code, how the transcription process works, how the different kinds of RNA are involved, all the way to how the protein comes out.
The audiobook also comes with a downloadable book in case you'd rather read it.
I absolutely love the series, and the one you're describing definitely sounds like one I would like to listen to.
Essentially, everything is in the service of increasing order. And maintaining it.
Polymerase creates more genetic code out of raw ingredients.
Genetic code creates proteins.
Proteins perform all kinds of functions by leveraging physics and chemistry.
Membranes prevent all of this from being blown away and scattered in the chemical equivalent of a slight breeze.
... so, as you ask, 'Why genetic material in the first place?'
And to that, something of a tautology: because reproducing order reproduces.
Randomly assembled self-assembling assemblages constitute the major components of our environment, because everything else... didn't.
A rock is still one rock. Water is still water.
A blade of grass is now a meadow. A tree, a forest. A slightly intelligent primate, civilization as we know it. And a single mutated coronavirus, a pandemic in every country on the globe.
Gene A is responsible for property A is way way way too simplified.
Which is to say, you can use quantum mechanics to augment Newtonian physics, but the latter dominates results in most usages.
Biology does have the quirk that sometimes (I guess because exponential growth / propagation?) nuances dominate observed result.
But usually things proceed as expected. Otherwise, we'd be killing people left and right with pharmaceutical side effects!
In very broad terms, the segments of code in DNA/RNA acutally provide a template for specific molecules and enzymes.
For context, imagine if I as a biologist asked you, what's a good read on CS for a biologist? And generally how algorithms, data science, AI, and operating systems work?
You can understand why it would be difficult to recommend any readings on it. For me to learn to code at any level, I had to spend the time learning it from the fundamentals, and it was worth spending the time for me as it was far more rewarding than trying to wrap my mind around something like "so imagine source code is this thing that's like DNA + epigenetics + dna topology that codes for the information you want, but instead of a complex set of chemical and physical interactions, it's math, and you can change it at will and nothing is leaky on purpose, and the code you write doesnt evolve unless you tell it to which you might want to do sometimes for AI stuff, but usually not."
I think the best analogy is DNA is a series of automated assembly lines. The workers, raw materials, and signals to turn sections on or off are separate. Each nucleotide station is called A, T, C, or G and adds a single element at a time to long chains which then get folded up into useful tools. DNA can also be used to manufacture either more stands of DNA or to do very simple repairs.
Alternatively, a stack of computer punch cards with a program on them. In that it’s a standard format for information transfer that is physically altered by the message it carries. Further, on it’s own nothing happens but connected to the right machinery it’s useful.
The second analogy is ok, but again not really great if you want to understand what's actually going on. If you just want to get an intuition that DNA has something to do with storing information, as long as that comes with an understanding that information evolves (biology is really the study of evolution in many ways), that's probably more than enough for a layperson. But it's a dangerous understanding if you plan on using it as a foundation to try and explore more complicated topics in biology. There's no need to do so, but if you are going to, it's far far better to spend the time getting the correct first-principles understanding and get rid of this idea of "DNA as source code" so you can better grapple with the subject.
I don't think the first analogy makes much sense since it makes nucleotides the sort of active agents here and needlessly focuses on individual nucleotides when codon triplets are what are involved in coding for proteins (probably better to, if you have to use an analogy, treat nucleotides as letters instead of words). And, especially in the context of this thread, neither analogy build the understanding needed to really dive into what RNA is, which is important for understanding what RNA viruses are, and what the coronavirus is.
Also, you really should include activation sites etc, but soon your out of the realms of analogy and just describing the details.
I guess we could visualize it as a series of drains, where the size of the hole can be modulated. Since gene expression can decrease or increase the rate at which DNA is transcribed
> The workers, raw materials, and signals to turn sections on or off are separate.
People are used to the idea of thermostats using on/off to maintain temperature which is not a terrible association. As you say gene expression is different, but I can’t find a better analogy.
For example, the covid-19 virus's RNA ends with AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA (33 As) which, as someone pointed out, looks suspicially like a "NOP sled"[1] (i.e. so that a protein coming in hot can hit anywhere on the sled and then slide down to the actual information)
Definitely nothing wrong with trying to find things that look similar across fields and try and gain differentiated insights, it's certainly an admirable thing and an important part of making many discoveries. But a first principles understanding of the structure of DNA, what a 5' end and a 3' end is, and how transcription/translation works (all bio 101 type stuff) would provide a much better foundation to do that with. You don't need a degree in biology to know the basics, just like you don't need a degree in CS to know the basics, but it's worth learning the basics if you want to get an understanding of the field or work with it.
I think most of the discussions I've had have been journal clubs during lab meetings. An hn style website for virtual journal clubs would be super cool...
The nature of biology is much like classes and data floating around and all seemingly randomly interacting with each other, because ultimately this is just chemistry with thousands of unique compounds, which makes things messy.
But through natural selection it seems to work. Like a totally incomprehensible compression algorithm learned by neural nets or evolved by genetic code. There should be a source somewhere around here...
Once I tried to learn this stuff by asking a biochemist, but I soon became frustrated because it seems there are no 100% rules, only "it is usually like this" all the way down.
Like, did they teach you at school that eukaryotes have two sets of chromozomes, one from each parent? Yeah, "usually". But then also: https://en.wikipedia.org/wiki/Polyploidy
And similarly with everything.
It should be noted that biological systems were one of the exlicit inspirations for extremely dynamic and object oriented languages like smalltalk.
Far from being a negative aspect the 'centerless' design and high degree of decentralization is messy, but also extremely robust.The internet as a whole is another example of a human technology that utilizes that sort of design.
https://www.amazon.com/Touchstone-Life-Information-Communica...
The various proteins that are built are actually interacting with the environment.
So, your desire to look at interaction with the environment might be better captured by a field other than genetics: maybe proteomics or molecular biochemistry.
The complicated part is that a lot of genes actually control for eye color - that is where the complications come. Each gene interacts with every other gene in a unique way.
When talking about how DNA is an instruction for making a protein, that protein is your data structure or a function. The next level of fundamental building block. Genes can contain a lot of information or non-information for proteins. Just like a program might have a lot of functions or data. The way they work together and interact is what creates a larger effect.
I think maybe the best starting point for understanding biology is learning about enzymes up close. They are proteins that act as “machines”. It gets down to physics and chemistry to determine how they work, so that’s probably when to drop the analogies.
Eye colour is modulated by several genes which haven't necessarily been identified - I understand this to be an open question.
I can give an example, though:
Eye colour is a function of what pigments are present in the iris, the most relevant pigment (in humans) being melanin, which also contributes to dark skin and tanning.
So, melanin is produced via the biochemical pathway 'melanogenesis'.
Among other things, the process of melanogenesis requires the enzyme tyrosinase, a protein which has a decent length wikipedia page.
If you are missing the TYR gene which codes for the protein tyrosinase, then you will likely be albino. This won't only affect your eyes, then.
I say you will 'likely' be albino only because it's hypothetically possible that a lack of tyrosinase could be compensated for with another biochemical pathway. And, of course, albinism could come about by some other break in melanin production.
The solution to this is narrow your scope: is there a particular subtopic that interests you?
https://en.wikipedia.org/wiki/Central_dogma_of_molecular_bio...
Proteins are built out of a chain of aminoacids. There are 20 different kinds of aminoacid, and the particular sequence of aminoacids determines the shape of the protein, and therefore its biological function.
https://en.wikipedia.org/wiki/Amino_acid
To build a protein, the cell uses a strand of RNA as template. The RNA consists of a sequence of 4 kinds of bases (A=Adenine, C=Cytosine, G=Guanine, U=Uracyl) and there is a genetic code that maps each group of 3 RNA bases into one aminoacid. For example, "AGC" corresponds to serine, "AAG" means lysine, and "AGCAAG" means serine followed by lysine.
https://en.wikipedia.org/wiki/Genetic_code
DNA is built of similar pieces as RNA. The main difference is that RNA is single stranded, while DNA is double stranded with that famous double helix structure. Additionally, DNA uses T=Thymine in place of U=Uracyl.
DNA acts a store of information. Each gene contains the genetic sequence that describes how to build one protein. When a gene is active, the cell copies that part of the DNA into a messenger RNA, and then uses that RNA as a template to build the protein in question.
Every cell in the body has the exact same set of genes, but they differ in what genes are active at each time.
------------------------------------
Now on to viruses...
The Coronavidus is an RNA virus. Each individual virius is a little ball made of proteins and lipids, encasing a genome made of RNA.
By itself the virus is inert, but once that RNA finds its way to inside a human cell, it behaves like a fork bomb. The cell translates the viral RNA into proteins, just like it would with our own RNA. One of the proteins is a polimerase enzyme, which then makes even more copies of the viral genome. Soon, there are thousands of copies of the virus. Additionally, the viral genome also encodes the structural proteins for the capsule of the virus, including the "spike" protein that gives coronaviruses their signature look.
The Virus reproduces using a fork bomb but for us it's deadly.
https://en.m.wikipedia.org/wiki/RNA-dependent_RNA_polymerase
That kind of thing doesn't normally happen to us because we don't have those enzymes that can make copies of their own messenger RNA. Putting those fork bombs in production would be asking for trouble :)
If you ever wanted to get deeper into biology than reading news articles, I cannot recommend this course enough.
https://www.khanacademy.org/science/high-school-biology/hs-m...
Also here, the three sections starting with “DNA as the genetic material”:
https://www.khanacademy.org/science/biology
An introductory biology textbook would be good too. Any AP biology textbook should cover it all.
I feel like information is the mother of all sciences and computer science has developed powerful tools for dealing with certain aspects of it.
I don’t see why it can’t address certain fundamental issues in biology either.
For example, in eukaryotes, the same piece of DNA can can produce different amounts of different proteins (i.e. with different amino acid sequences and different post-translational modifications), depending on things like DNA methylation (there's a number of different types), genomic location, accessibility, transcript methylation, multiple mRNA isoforms - the list goes on. A combination of these and other still unknown factors produces the final product, which may vary within a cell, between cells in a tissue, and between tissues.
Things behave consistently and predictability, except when they don't. Makes the field interesting and frustrating.
- DNA: code in your repo
- RNA: code in your working directory
- transcriptase: 'git fetch'
- ribosome: compiler
- proteins: executable object code (ribosomes are also proteins, mostly)
- epigenetics: build config options
- promoter site: `ifdef
First, imagine a system where every time you compile something, the object code is immediately launched in its own thread executing truly in parallel with all the others.
The overall behavior of the cell is the interaction of all these threads. A gene is a single block of code. They can do lots of things, including changing build options and enabling/disabling the generation of other blocks of code. We say a particular gene causes a particular effect, but really it's the aggregate interaction that does things. Most traits require the cooperation of many genes to express. If we associate a gene with a particular trait, it's usually because it is a critical component of that trait; necessary so if you break the gene the normal aggregate behavior goes away, but not sufficient - it still needs a lot of other working genes to have the right effect.
Now imagine that some of those threads run a constant cleanup process that kills running threads, delete your object code and delete files in your working directory (largely at random) while another set of threads are constantly fetching (transcriptase) and recompiling (ribosomes) code to launch new threads to keep the system working and your services up. During this process the relative number and type of running threads will change according to a combination of code and the environment.
Viruses are a tiny executable (protien coat) that copies some rogue code (RNA) into your working directory, so that constant recompilation will generate new instances that copy more code, etc.
Too many running virus instances will crash the system (kill the cell) by starving/corrupting normal processes. The random deletion and constant fetching from the repo slows the virus replication down however, and may stop it entirely.
_Retro_viruses have an additional piece:
- reverse transcriptase: 'git commit; git push'
which will copy the virus code back into your repo. Now the regular 'fetch' will copy the virus code back into your working directory.
Your immune system has processes which run around checking object hashes for threads. There's a whitelist for expected hashes (normal threads). If the same unexpected hash shows up too many times, it goes on a blacklist and you start generating antibodies- special threads that go around searching for a specific object hash and tagging that thread for deletion. If too many bad hashes are found in the same place, a white blood cell nukes the whole site from orbit.
Once you generate enough antibodies, the virus threads start getting killed before they can replicate and you're immune. If the virus mutates, the hash may not match anymore and you'll be vulnerable to the new strain. Things like the common cold and influenza mutate all the time, so you can very them over and over while chicken pox rarely mutates and youth can usually only get it once.
Vaccines are a bunch of copies of (usually inactive) threads with a particular hash, to encourage your immune system to put that hash on the blacklist.
Autoimmune diseases happen when valid code accidentally gets on the blacklist.
Cancer (a fork bomb) tends to evade the immune system because its code was already on the whitelist.
But... this is a super simplified version of how things work, and really only applies to mammals. Do not take these analogies too far.
Biology is fascinating, and definitely worth deeper study.
https://www.youtube.com/watch?v=xJFqqxxtbRY
Gives you enough pointers to be able to start googling from there.
This algorithm is allowed to run for 4.5 billion years, and it has produced, through random iteration, a very good CMS.
The CMS works great most of the time, but there's a bug which rarely happens, which crashes the whole system.
This bug has been correlated with lines 4632486 and 434876365 in module132413.pl being executed, but it is not exactly clear how.
Your job is to figure out what these lines of code do, and how they cause the bug. Here they are, and you can download the whole source on github:
module132413.pl:4632486: $a4918732 = $b13rqw9 && chomp $dfadfaadf4r;
module132413.pl:434876365: print;
Good luck with the debugging!
DNA truly is a blue print. (almost) Every cell in your body has the source code for your entire body.
"this gene or set of genes are responsible for that outcome" is generally going to be a true statement.
The equivalent wouldnt necessarily be a processor instruction.
If you wanted an analogy, a cell is like an entire minimal computer. Power supply, processor, memory, and I/O. Each computer can run different parts of the code, but every computer has the entire code base.
Within the computer are specialized "organelles" for storage, graphics, network, etc. These are comparable to organelles such as mitochondria, nucleus, endoplasmic reticulum etc.
DNA acts like code in that it produces outputs (messages) and receives inputs. Proteins are also like code in that they produce outputs and receive inputs.
It might be that DNA is like the executable source code that is stored as files and proteins are more like in memory processes such as services and actively running programs that get spawned from the files to perform various tasks.
Viruses are like hostile code in bound in an email or coming through as tainted packets. They cant actually do anything on their own - they are inert, but once the processor starts executing the code, they hijack the processor. Sometimes to spawn more malicious code to other computers in a trusted network
To carry the analogy further, departments in a company are a bit like organs. The computers in that department all roughly do the same thing. Imagine if IT imaged every computer in the company the exact same way, but what software was actually used would be based on your department.
One really simplified model (inaccurate, but useful) of the computational state and evolution of the cell involves DNA methylation. DNA is methylated to shut it off, demethylation turns it on. To turn some DNA off or on, either DNA methyltransferase (DNMT3a/b) for methylation or one of the Tet proteins for demethylation needs to be guided to that region of DNA, usually through the assembly of some transcription factor complexes. The assembly of these complexes is combinatorial and performs logical addressing depending on the cell state. For example the cell may be expressing TF's A, B, and C, and these guide DNMT3a/b to DNA locus 3xq3945 (made up, whatever) if beta catenin translocates to the nucleus as a response to Wnt signaling, to turn something off. If TF's A, B, and D are expressed, it may bring it to a different location, and may bring Tet there instead, for demethylation.
Anyways, that's an example of "computery" description of cell biology. I don't really like how other responders shot your question down, I think the computer science mindset is really relevant to biology.
DNA is source code. RNA is an intermediate representation. Enzymes compile DNA into mRNA. Ribosomes compile mRNA into proteins which can actually execute a wide variety of functions.
Proteins may require post-processing before they're usable. The output of a ribosome is a primary protein: a linear, one-dimensional structure. By interacting with itself and other cell machinery, the protein could be folded into three-dimensional secondary and tertiary structures. Several of them might be assembled into a quaternary protein.
https://en.wikipedia.org/wiki/Protein_structure
The final result could be a simple peptide or some huge machine like this thing:
https://en.wikipedia.org/wiki/Type_three_secretion_system
The mitochondrion and the ATP synthase are like a hydroelectric power plant. The electrochemical gradient is the gravity, the hydrogen is the water and the enzyme is the turbine.
https://en.wikipedia.org/wiki/ATP_synthase
Enzymes transform substrate into product. They're like functions. When one enzyme's product is another's substrate, a pipeline is formed. Metabolism is a parallel process. I've written about metabolism as a programming metaphor before:
https://news.ycombinator.com/item?id=21562716
Sometimes bacteria save useful snippets of their own source code into gene cassettes. This allows the code to be exported to other bacteria via horizontal gene transfer.
https://en.wikipedia.org/wiki/Gene_cassette
Developed an awesome antibiotic-destroying enzyme? Make copies and send them to friends through a pipe. Didn't manage to survive? Said friends might be able to absorb the DNA from the environment anyway. They can obtain the fallen's powers just like Mega Man.
DNA is a tape archive of files (genes). They are not binary (base-2) encoded, but base-4 encoded. A reading head (polymerase) reads sections of the tape and copies them into working memory. A 3D printer (ribosome) receives these sections from the working memory and prints nano machines (proteins) based on these tape snippets. DNA is not source code, it does not contain conditions or jumps (loops), it's data for the 3D printer. (Actually it's just a 1D printer, but the result folds into a 3D shape).
Molecular Biology Made Simple and Fun https://www.amazon.com/dp/1889899070
I remember 20 year ago, at school, when the biology teacher was presenting this dilemma. Ever since, when I hear someone saying "doing this will kill the virus", it triggers my brain into this subject, since you can't kill something if it's not alive ;)
Somewhat related, I also like the concept of the "Viruses of the Mind" [1], which makes an analogy between the spreading of a biological virus and the spreading of an ideology.
Anything can be said to have, or not have a purpose, depending on how broadly or narrowly you scope the definition.
For use in this conversation, I think it's self evident that the level of purpose exhibited by higher-complexity organisms is several orders of magnitude different than that of basic organisms.
Wasn't sure if original poster would agree / disagree.
The word purpose has lots of usages, but the one that seems to be discussed here is some intrinsic purpose that an object or creature has for existing.
I can perform an action with a purpose, which is different to my (personal) purpose for being alive, which is different again for some intrinsic purpose for why I am here in the first place.
It's this last purpose that daseiner1 was referring to when they asked "what’s the purpose of an amoeba? or a mosquito? or a duck? or a chimpanzee?"
They are questioning if that kind of purpose even exists.
Your argument is:
Some things have more purpose than others.
Therefore purpose exists.
In this next response you get closer to defining what purpose is - "level of purpose exhibited by higher-complexity organisms" - but we haven't really established what that purpose is or what it means to have more purpose. At best you seem to be equating complexity of behaviour to level of purpose, but I see no reason why complex behaviour should imbue some kind of purpose; all usages of the word purpose imply intent of some kind, and there are many complex processes that have no intent.
I will say that complex animals seem to be more purposeful than simple creatures, but that just means that they perform actions with more intent than simpler creatures, not that they have some intrinsic purpose themselves.
I was using purpose in my sense. Daseiner1 may use the same definition, or they may be using another. As with you.
It's useless to debate anything else until we figure that out.
---
My definition is contained in my original statement "reproduction without purpose is not life." I do not consider reproduction a purposeful action, as I define it.
It's hard to be intentional about something that forms the minimum bar of existence (immortal organisms aside).
It’s also not clear if you are discussing “why I do something” (purpose of an action) or “why am I?” (purpose of me).
I would argue that's a false dichotomy. In your terms, there can be no purpose of me without purpose of action. And purpose of action requires selection from multiple viable options.
I'm not sure that there is any intrinsic purpose to anything, only ever purpose imbued.
I understand the word gets used that way, to describe some intrinsic meaning to a life, but the word being used that way doesn't mean the thing it describes exists.
To try and be a bit clearer let me write out the three usages I am aware of and you can say which you are talking about.
1. I picked up the apple with the purpose of eating it.
2. My purpose in life is to enjoy it and leave the world a better place than when I found it.
3. The purpose of humans is to colonise the universe.
1 is purpose of an action (the action is done for a reason), 2 is purpose I give myself (I choose what gives me meaning), 3 is intrinsic purpose (regardless of what anyone wants or thinks).
It is 3 which I think we have no evidence for.
Viruses also provide a mechanism for horizontal gene transfer. A protein that is critical to the formation of the human placenta has a viral origin.
Viruses have a massive impact on life, but we're just now starting to realize it.
The virus has no intentionality in doing them. They're a consequence of replication.
In contrast, I think a much stronger case could be made for a chimpanzee, duck, mosquito, or even amoeba evaluating multiple options, choose one to the exclusion of others, and pursueing it.
I'd go as far as to say if you kill the ability to fork, a lot of processes would go extinct and be replaced.
The purpose of a bacteria is to replicate. They just do it the complicated way.
That goes up all the way to modern humans; on a ground level, life is about replicating your genetic information. What you do beyond that is on you.
It can be considered a toxin that a cell reacts to by creating more of the toxin.
It can be considered a collection of atoms that modifies its surroundings in a way to create similar collections of atoms.
I kind of see the point of not calling a virus a living thing. But if viruses aren't even "active" I don't really know why a cell (or even a dog) would be "active".
We also analyze and modify our representations in various ways, both consciously and unconsciously. Science is one of the more explicit processes for doing so.
Of course, much of reality is lost and distorted in the process. But we do the best we can :) I like to think we make better maps of reality now and then.
I suppose, at the very least, some of the maps we currently possess can be used to enact more dramatic change in the world around us than ever before, which must say something about their truthiness.
It seems pretty simple to me: viruses are not living. They are able to co-opt living systems into making more of themselves.
A virus may gain life while it is inside of a cell, but why is that any different than the organic molecules which gain life when assembled into a cell? We don't say carbon is alive.
I think the distinction between what is doing the replication is spurious. The fact is even living replicators need some sort of base resource to exploit to pull off the feat. I could say that animals aren't replicators, because they inherently require other living creatures to be eaten in order to replicate.
The SCP wiki started these terms to refer to objects which present anomalous properties when you're exposed to them, such as what the foundation regularly employs to protect articles; "memetic kill agents", basically information that kills if you consume it.
What definitions of "billion" and "trillion" are they using? 10 to the 31st would be only ten million trillion trillion, going by the common definition of million as 10 to the 6th and trillion as 10 to the 12th.
4 x 9 + 4 x 12 + 3 = 87
4 x 3 + 4 x 4 + 3 = 31.
[1] in the US system. In Germany and historically the UK, apparently, it’s 1000,000^N = 1000^(2N), which I personally prefer.
> Try multiplying a billion by a billion, then multiply that by ten trillion, and that (10 to the 31st power) is the mind-numbing estimate of how many individual viral particles are estimated to populate the planet.
(I can't find a "correction" notice... It's Stanford Medicine, not a proper newspaper.)
Maybe Virus is akin to a SEED. Seeds are inert/dead by themselves, but it carries as all the code/DNA/instructions needed to spring to life, flourish & even reproduce infinitely when put in an friendly environment (nourished soil with water, O2 etc)
Some viruses don't directly cause the host to create new viruses. Instead they direct the creation of virus creating factories, which create the virus.
Then you get virophages which are even tinier than normal viruses, which infect the virus factories of other viruses.
I hope nobody complains "but he shakes the flask" -- because that is exactly what the temperature is -- how fast the particles "jiggle" as Richard Feynman would that describe:
Interesting for coders/hackers
First in the series here: https://youtu.be/8vWaawiUteM
When you see a biologist draw a system in biology, say, how a protein interacts with a cell membrane and then causes a change in expression within the nucleus, it can look relatively simple.
Well, it's about as simple as drawing how an airplane works. In this example, you have the "flightosome", which is made up of fuselage, wings, cockpit and landing gear. That's what transports passengers from one airport to another.
Simple right? Well even the landing gear component is complex and with biology, we have very little understanding of it at all.
[1]https://blogs.sciencemag.org/pipeline/archives/2017/02/01/th...
https://blogs.scientificamerican.com/observations/watch-the-...
DNA is a molecule, made out of 4 amino acids. ACTG. There are 18 different kinds of amino acids. Amino acids are made out of carbon, nitrogen, hydrogen, oxygen. Amino acids make proteins. Proteins are the structural bricks (like LEGO) that are combined in various sequences by enzymes to build more complex machinery.
The proteins make up cell organelles, which make up cells.
How much of how DNA turns into proteins and different proteins build different structures is understood? Do we have a DNA simulator where I can write ACTG code and it tells me what kind of proteins will be made, how those proteins will interact to build complex structures?
How close are we for computer science folks to actually start writing compilers, debuggers, frameworks and simulation tools for DNA and man made cell machinery ?
How far away are we from making custom DNA + cells that act like 3D printers taking collagen and building nanometer precision complex structures?
It seems our cells already do nano manufacturing and computation, how do I tap into that ?
How DNA -> proteins is well understood. Protein folding though is incredibly complex to model.
It is easy to know the amino acid sequence, but hard to know how the protein will end up folding.
And the protein coding sequences are coded into proteins, except when there are alternative splicing sites, or anti-sense RNAs.
And then the protein sequence folds into their minimum free energy state, except when they are assisted by other proteins, or when they exist as disordered proteins.
And it's not always DNA -> protein. Sometimes proteins make other proteins, for example circular proteins can only be made from other proteins.
Then there are post-translational modifications, which change the RNA sequence between DNA to RNA and RNA to protein. And then there's RNA interference, where miRNAs interfere with RNA to protein translation.
And then there's epigenetics such as DNA methlyation or histone modifications (histones are protein which compress DNA) which change what genes can be expressed when.
Really, for every rule that you've been taught, there is an exception. Biology is so much more complicated than we understand. And understanding how to make a biological computer (different from the biological computing of Adelman, yes the same Adelman as RSA) would involve understanding how all the pieces fit together.
Determining the physical structure of a protein from the amino acid sequence is NP-Hard : https://ieeexplore.ieee.org/document/6965037
Without a very significant breakthrough either in computation or some biological discovery that gives a shortcut I don't think a "DNA compiler" will be available anytime soon.
At least for me, I had tons of pedestrian questions, as I haven't taken a biology/chemistry course since high school.
A search for virology on the youtoobs led me here: https://www.youtube.com/watch?v=8_bOhZd6ieM
I found it to be a homerun in all but addressing my 20-30 questions in these times just in the first ten minutes. To the point. Without the current yt culture of gratuitous cuts and FX.
Losartan is currently in clinical trials for this new usage.
I've also heard conflicting reports about Ibuprofen. I don't think anyone knows for sure.
On the flip side, NSAIDs do reduce inflammation and inflammation is part of the body's response to various stressors; I could see that lowering our response leads to worse outcomes when sick. I have always thought that cold medication increases the duration of a cold just from my own observations, so I do find it at least plausible.
I agree on the high blood pressure, if you are on it that means you have hypertension and are likely in poorer shape than someone who does not take it. I can somewhat see diuretics having an impact though as those can flush needed minerals out of your body when your body is in need. They also dehydrate you, so if you are on one and don't get properly hydrated and have a proper mineral balance, I can see that being a big negative.
https://www.thelancet.com/journals/lanres/article/PIIS2213-2...
I think with SARS-CoV-2 the pathogenesis is still not properly understood. For e.g. if you take a look at the ACE-2 expressing cell distribution, the tongue and oral cavity are very high on the list. And yet, there is no current guidance on disinfecting food before eating it, even though its a potentially high-risk route of infection.
A few videos that blows my mind on what really happens inside your cells - https://youtu.be/bee6PWUgPo8