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14

The answer is chance or, even better, contingency. About your calculations, it is true that the theoretical sequences are almost unlimited, but the basic scaffolds are not. Very different sequences can fold into the same basic scaffold and have a similar reactivity/function. So, even if not all the sequences have been explored on this planet, most of the ...


9

The current hypothesis is that RNA came first, DNA and proteins came later. So the reason that four bases are used might be related to the initial RNA world, and then DNA just reused the already existing RNA bases in a slightly modified form. In the RNA world, all functions had to be performed by RNA. Having more bases available than two would likely be ...


6

One reason is that an intermediate like mRNA allows for higher amounts of protein expression. You can have multiple mRNA molecules that are translated simultaneously. If you read directly from DNA you can have at most two translations in parallel. I'm not sure about this, but I would imagine that having to unwind the DNA double strand every time for ...


4

I don't have a lot of references for this, but it's too long for a comment. Separating the roles of RNA and DNA helps to better control protein production and gene replication. If ribosomes worked directly on DNA, it would probably be very hard to replicate that DNA, as the DNA polymerases would collide with the ribosomes. You'd have to stop protein ...


4

This is actually a very interesting yet difficult question to give a single precise answer to. I will try and summarize for you a "meta answer": Complexity Science Some consider complexity not to be a Biological topic as such, since it is a property that accumulates in non-biological systems e.g. economics, technology, music, language - in fact anything ...


4

Unfortunately the answer is highly dependent on what you mean. In the simplest terms, comparing it directly to how we measure data storage in digital media, the number of different states of a DNA string of length $n$ can have is simply $4^n$. A byte holds $2^8$ different states so the number of bytes in a DNA string of length $n$ is $\frac{n}{4}$. Of course,...


3

Why does nature use a 4-level system (DNA) to encode information? Short answer: Ease of manufacture, simplicity of matching, sufficiency for requirements. Fewer simple bases take less effort to create, provide fewer possible matches, yet is complex enough to code what is required while retaining sufficient degeneracy for success. Also it was the coincidence ...


3

John Harte's work on applying the mathematical theory of maximum entropy to ecology is certainly one of the better known examples of the application of this area of mathematics to science, in part because he literally wrote the textbook: Maximum Entropy and Ecology: A Theory of Abundance, Distribution, and Energetics (Oxford Series in Ecology and Evolution) ...


2

You might also be interested in this paper from EMBL-EBI about storing data on DNA. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA They show they can get 757,051 bytes or a Shannon information 10 of 5.2 × 106 bits onto 153,335 strings of DNA, each comprising 117 nucleotides (nt). George Church had a similar paper ...


2

Is it interesting? Perhaps, but "complexity" is a vague notion. If you want to simplify and just say "variation" then sure, sex increases variation. But so does that random mutation you brought in. Really, all you need for increased variability is some difference between generations and genetic Drift will take care of the rest. Mutation is enough, which ...


2

I'm not sure I understand the question. You've elegantly demonstrated that only a tiny fraction of all protein sequences could possibly exist, but then asked why only a tiny fraction of all protein sequences do exist. Your conclusions about independent origins of life having no proteins in common are accurate, but also consider that you as a human being have ...


2

You are misinterpreting the meaning of that inequality and confusing information and entropy (there are other logical errors but this one is the first and most obvious, and makes all the others unimportant by comparison). $I(X;Y) \geq I(X;Z)$ is referring to the mutual information between X and Y compared to the mutual information between X and Z. ...


2

The number of parameters depends both on the number of taxa and model of sequence evolution. The topology is not typically considered a parameter in the usual sense of statistical inference (as it is the a priori specified topology the likelihood was calculated on). So, for example, if you infer a tree from nucleotide data for 25 sequences under the ...


1

The leading contender of "why" in my former lab, is that if a chromosome becomes too long, a cell cannot fully isolate the chromatid to a daughter cell. Ie in a giant chromosome, the chromosome arms trail so far behind centromere, that the arms are of two sister chromosome are still touching each other even through the centromere have reached the opposite ...


1

I think this is missing the elephant in the room, namely that you need to have selection (natural or otherwise) for evolution to happen (in a reasonable time). And selection (unlike mutation) is not a local operation on the DNA strands as required by the data processing inequality. Selection tosses out some individuals carrying certain strands in relation to ...


1

General answer The use of binary in computers arose primarily from practical considerations of how to represent digits using electric current or voltage (i.e. either ‘on’ or ‘off’ is the least equivocal). Such representation was not only — or even primarily — for storing information of different numerical types, but for programming logic using Boolean ...


1

DNA is a code that occurs via stepwise polymerization, like all major macromolecules. In respects to DNA, it is Nucleic Acid sequences that polymerize to create the DNA. In eukaryotic cells this happens at multiple replicons (regions of replication). So you can look DNA as code for itself. You also have rRNA, mRNA, and tRNA. All of these code for and do ...


1

A concrete theoretical version of my model could be a population of random computer programs or Turing machines. I would define the complexity of a computer program as its run time not the size of its code. Mutating programs will have varying run times whose logs just perform a random walk. But if you allow pairs of those programs to occasionally combine ...


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