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I really like this question as it is such a fundamental underpinning of all life on the planet, yet there is such sparsity of actual information on its origins and why selection rewarded ATP use over anything else. Here I am talking generally since no specific studies exist in ATP vs other candidates. A lot of the below information is taken from a ...


28

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 theme ...


13

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 ...


11

I don’t like this sort of question because I don’t think it can really be answered and I’m very suspicious of arguments that seem to claim ATP is the only or even the best solution to the problem. Nature generally demonstrates that there is more than one way to kill a cat, but if one way works adequately you don’t always need to look for another. This is ...


10

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 - ...


9

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 ...


8

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. ...


8

The straight forward answer is: we don't know. We don't have any direct evidence for what happened at that time nor any completely developed and coherent theories for how it worked. The widely believed hypothesis is the "RNA World" hypothesis. RNA, unlike DNA, is capable of spontaneously folding to form catalytic molecules and thus avoids the needs for ...


7

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 ...


7

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 ...


7

There are two types of synapses: Chemical synapse Electrical synapse The first one is the one you are asking about. The second one corresponds to the faster synapse you are imagining. It consists of two neurones connected by a gap junction. Gap junction form a cytoplasmic bridge between the neurones and thereby allow electrical signal to directly go from ...


7

The flaw in his argument, from what I can see in your quotes, is to equate evolution to natural selection. Natural selection was never proposed to explain all evolution, nor how advantageous traits arise, but was proposed to explain how advantageous traits spread. Ultimately, why adaptation is so prevalent? The modern theory of evolution is so much more ...


6

There are indeed 'gap junctions' which pass current directly from one cell to the next. So what advantages do we get out of chemical synapses that gap junctions do not provide? Asymmetry. Synapses do not operate in reverse, thus the postsynaptic cell cannot generate currents in the presynaptic terminal (although there are secondary forms of communication ...


6

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 (...


6

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 ...


6

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 ...


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 ...


6

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 ...


6

As @canadianer comments, this question is unanswerable, and it verges on being classified as ‘opinion-based’. However, because I do not find the answer from the OP appealing, I’ve set out a few points of my own. Hardly an answer — more a list of alternatives as food for thought. I can imagine adenine being chosen for one of the following reasons (others ...


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

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

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 ...


5

To fully comprehend the concept of wobble base-pairing we need to consider the nucleotide sequences of the anti-codons in the tRNAs that have to "read" the genetic code when the mRNA is being translated on the ribosome. The nucleotide in the anti-codon's wobble position is, for example, often inosine. Under the rules for wobble base-pairing an Inosine can ...


5

Hummingbirds were not created, they evolved. Ancestors of a modern species need not be that morphologically different from their progeny, even over a time span of millions of years. And organism will fill a niche based on its fitness to survive in the niche. If there are strong selective pressures in the environment to maintain the traits that we see today,...


5

You are asking a very interesting question. As you correctly mention, the substrates of mitochondrial metabolism (TCA or Krebs Cycle) are pyruvate and NADH, and, through oxidative reactions, ATP is produced. Indeed, it seems unrealistic that when the "mitochondria" were by themselves there was pyruvate and NADH in the environment. Let's take a step back. ...


5

I think your acquaintance is trying to fit real science to some of his personal beliefs (that are obviously wrong). If you read the article you'll see that it's not about evolution at all, but about protein folding and what proportion of possible sequences gives a working protein. It turns out random sequences are not that likely to fold, which leads to ...


5

Organic Evolution - Definition 'Organic evolution' was a common term. It is just rarely used today. Today, we just say 'evolution' or 'evolutionary biology' when referring to the field of study of 'evolution' (or of study of 'evolutionary processes'). Book recommendation Math oriented As you are used to work in applied mathematics, you'll definitely be ...


5

Serine Protease Catalytic Triad This is classic example of convergent evolution in catalytic mechanisms. Shown below are chymotrypsin (4CHA, green) and subtilisin (1ST2, blue) aligned on their catalytic triads (Ser/His/Asp, darker colours). There is no obvious sequence or structural similarity. You can check out the MEROPS database for a list of protease ...


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