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16

You have clearly given this a lot of thought. Unfortunately, as @adam.r said, you are laboring under certain misapprehensions. The quick answer is that each generation does not "improve" on the last. That is a common misconception. In a bit more detail: First of all, your copying metaphor is a bad one. There was no "perfect original", I expand on this ...


10

I think the issue with Intelligent Design is not so much that its patently proven wrong. On the contrary, the problem is that it not a scientific hypothesis and so it really isn't a scientific question. If I may, the basis of the scientific method, as formulated by Karl Popper, but commonly in use today, is that science is the putting forth of theories ...


8

This question is closely related, and the fascinating link posted by @JohnSmith is a good read. In short, with a four-base system, and a codon size of 1, you get four possible amino acids. Silly system. A codon size of 2 gives 16. Not too shabby, but not a lot of room for growth, and not enough for those 20 amino acids. Codons of size 3 gives 64 - ...


7

Abiogenesis, the development of living things from non living matter, is not something we know much about, since it happened about 4 billion of years before we were around and haven't reproduced it in the lab. My guess is that it's not easy. However, the Miller-Urey experiment and others have told us something about abiogenic production of organic compounds. ...


6

The smallest unit that can be selected is, of course, the single nucleotide. The most striking examples of this are Single Nucleotide Polymorphisms (SNPs), many of which confer selective (dis)advantages. To take a simple example, imagine a SNP that introduces a frameshift mutation, rendering a gene incapable of producing its protein. If that protein is ...


6

I’ll add a slightly different perspective, although terdon’s answer already contains the relevant facts. The thing that makes DNA endure in the face of imperfect copying is that, like computer storage, it’s digital. The relevant property of digital data here is that individual pieces of information aren’t given on a scale, they’re drawn from a strongly ...


5

I would recommend The selfish gene by Richard Dawkins. It is targeted at a scientifically interested audience, but well written and recognized by the scientific community. http://amzn.com/0199291152


5

We know about nuclear DNA having a mitochondrial origin mainly in two ways: (1) a sequence in the nucleus is found to closely match a sequence found in mitochondria, or (2) mitochondrial proteins are found to be encoded by the nuclear genome but not by the mitochondrial genome, and those proteins seem likely to have been necessary for sustaining life of the ...


5

Interesting question. I researched this a bit now and the phenomenon is termed "numt" for "nuclear mitochondrial DNA". This term descrives the transfer of cytoplasmic mitochondrial DNA sequences into the separate nuclear genome of a eukaryotic organism. It seems that most of these sequences are inactive. This list at pseudogene.net has a large number of ...


5

These equations describe how the haplotype frequencies will change over time due to a combination of recombination and natural selection. Before I proceed, I need to change your four $\delta X_i$ formulas above. Lewontin and Kojima (1960) writes the equations as: $$\Delta X_i = \frac{X_i(w_i - \bar w) \pm Drw_{14}}{\bar w}$$ where the minus sign is used ...


5

You either want a introductory book in evolutionary biology or a book that offers mathematical models of evolutionary processes. In my first class of evolutionary biology I had this textbook: Futuyama, Evolution I think it gives a good start to the field and offers a good overview of the difference subfields. If you think you already know enough about the ...


5

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

Recap of the question: Looking at a single locus trait ($A$) controlled by two alleles, $A_1$ and $A_2$, the phenotypic mean is only affected by inbreeding depression, $f$ (Wright's inbreeding coefficient), if there is some degree of dominance, $d$. Why? Answer: If we take inbreeding as a higher than expected frequency of homozygotes, such that if the ...


4

I would say the the topic is still very much under debate. This paper by Ferry and House (2006) briefly review the heterotrophic vs chemoautotrophic hypotheses. They include citations from proponents of each hypothesis. Interestingly, Ferry and House propose an "energy conservation" hypothesis that attempts to merge ideas from the other two hypotheses. ...


4

Start and stop codons are instructions for the ribosome to start and stop protein synthesis, respectively. The region between the start and stop codon (inclusive of them) is called ORF (open reading frame) or sometimes CDS (Coding sequence). Why does ribosome need explicit instructions for start and stop? Ribosome recognizes an RNA as a mRNA if it has ...


3

Even when you can live without Histone H1, its a widely distributed protein which you find in basically all living cells (except for some yeasts if I remember correct). This points to the fact that it must be available for quite a while. The same is true for the catalytic subunit of the DNA polymerase. Somatropin is still pretty important (and can be found ...


3

There are both chemical and electrical synapses in many organisms. The electrical synapses are called gap junctions. As you point out, the primary advantage of gap junctions is their speed, and they are commonly used in systems involving defensive reflexes. However, as AndroidPenguin indicates, chemical synapses allow for greater computational abilities ...


3

This is the coolest part. Those synapses are the reason the brain is so complex! Basically you've got the first part right, the neurones are quicker and they transmit messages from one end to the other. The other thing you have to do is analyse and calculate. Signals from multiple neurones feed into a single neurone using a chemical synapse. Similarly the ...


3

Lots of interesting questions! Let me try to address a few of them as I don't think I am qualified to answer them all but hopefully I can get this thread started. I am a graduate student in the biophysical chemistry field and have been following a little bit of the Crispr Cas9 craze in the last couple of years. So I am not an expert on Cas9 by any means but ...


3

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 ...


2

I think this book (The Story of Life, Southwood) would be just what you are looking for - it was one of my modules during my undergrad in Evolution and I think it touches on the basic geology too. It is quite an easy ready but covers the material pretty well, it also has good reviews on Amazon etc.


2

If sufficient time has elapsed, there will be a large number of transversions present between the original base and the final state. The initial state will therefore not matter. Say, you flip (turn over, not toss) a coin at random intervals. For short time and few flips, the initial state will matter. But if you go on flipping it for millenia, the final ...


2

When lactose is present in a cell, some of it is enzymatically converted by $\beta$-galactosidase from the $\beta(1,4)$ linkage (typical of lactose) to the $\beta(1,6)$ glycosidic linkage (becoming allolactose). Allolactose and other analogues can then bind LacI to induce the appropriate conformational change and unbind the lac operator (one such review ...


2

Everybody said it already, but there is none. The original HWE equation ($(p+q)^2=1$) works because you've got two variables and two equations ($p+q=1$) to work with (in reality, these are just one equation and one variable, since $q=1-p$ so $p+(1-p))^2=1$). Now you have three variables and still only the one equation ($p+q+r=1$) which is, mathematically, ...


2

Some elements of response to your question. First, something about tRNA frequency. Even if there are six codons for a given amino acid, they are not equivalent because some will correspond to abundant tRNA, while others correspond to very minor tRNA. This has significant influence on the traduction speed, as the traduction will dramatically slow down on ...


2

The problem with Intelligent Design is that it doesn't appreciate that the forces that shape species (and individual organism) have to be constant and ongoing or the species disappears. The past matters little, it's what happens right here, right now that keeps species in any particular form. Biological system are not static structures like a building. You ...


2

I would suggest the course of Coursera.org: Computational Molecular Evolution By Anders Gorm Pedersen Technical University of Denmark (DTU) PS: Do tell us if you found a better book!


2

Really interesting question. I am not sure, if the mutation rate is something "actively done" by the virus. I think its more a byproduct of vast replication after taking over the host cell. Mutations with a negative effect are deleted, those with neutral effects will be there, and those with positive mutations will be selected for. This paper looks ...


2

I'd like to add a few books to to the above suggestions. The book by Sean Rice "Evolutionary Theory: Mathematical and Conceptual Foundations" covers a lot of ground, including allele-based models, quantitative genetics, Price's formalism, and MLS. If you're interested in social evolutionary models, I found R. McElreath and R. Boyd "Mathematical Models for ...


2

I really good intro to evolution book is The Evolution of Vertebrate Design by Leonard Radinski. Also, for a more math based approach you could look into Narrow Roads of Gene Land. These are collected papers of W.D Hamilton.



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