Questions tagged [molecular-evolution]

The study of evolutionary mechanisms in operation at the molecular scale, primarily DNA, RNA, and proteins.

Filter by
Sorted by
Tagged with
31
votes
3answers
52k views

Why is ATP the preferred choice for energy carriers?

Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?
20
votes
3answers
6k views

Do animals other than humans have different blood types?

Humans have the ABO and Rhesus blood typing systems. I have two questions about it: Why have we evolved these blood types? Do other animals have different blood types as well?
13
votes
3answers
355 views

Formation of Life

Originally, life evolved from non-living matter. Why is life only generated from other life nowadays, and why doesn't it evolve from inanimate matter, like it did originally billions of years ago, ...
13
votes
1answer
654 views

When did CRISPR/Cas9 evolve and what is the likelihood that a superior system for live cell genome editing has already evolved on earth since then?

I've read that CRISPR/Cas9 is currently being implemented and tested for its ability to edit genomes in live cells, and that it is supplanting other genome editing tools in labs, such as TALENs and ...
12
votes
3answers
2k views

How did the genetic code evolve?

The genetic code is redundant, there are 20 amino acids for 64 possible nucleotide combinations (triplet codons). Therefore some amino acid are coded by several different codons. While leucine is ...
11
votes
2answers
984 views

Why, specifically, does each generation, on average, improve upon the design of the species rather than degrade it?

In every non-life example I can envision, a copy of a copy is always a degraded or less pure version of the original unless some outside influence acts to correct the copy back toward the ideal ...
11
votes
1answer
244 views

A question about the intersection of evolution and thermodynamics

From this 2014 article in Quanta magazine by Natalie Wolchover there is a quote from a physicist with an intriguing idea about evolution: “You start with a random clump of atoms, and if you shine ...
9
votes
3answers
1k views

Why do (almost) all energy carriers contain adenine?

Unlike this question which is specific to just ATP, this one includes all energy carriers. When thinking of common energy carrying molecules, I can think of Adenosine triphosphate (ATP), Nicotinamide ...
9
votes
1answer
354 views

Evolution of the Redundancy of the Genetic Code

In short Looking at the genetic code, it appears that most redundancy is on the third letter rather than on the first or the second letter of the codon. Why has it evolved this way? Longer version ...
9
votes
2answers
1k views

Evidence & discussions of hard polytomy

Phylogenetic trees with >2 branches on a node are polytomic, and polytomy can appear on trees for two reasons. Firstly a lack of information in the data prevents proper resolution within a clade, ...
9
votes
4answers
1k views

Why and how does complexity usually tend to increase through time?

The question of complexity is classic in the very first lectures of evolutionary biology where the teacher usually tries to tell the students that complexity does not necessarily increase and that ...
9
votes
0answers
217 views

Do ring species exist?

In trying to understand evolution better, I have been looking at examples of speciation, and have thus come across the topic of ring species. I have tried to find concrete examples of how these work, ...
8
votes
3answers
2k views

Why do neurones use chemical signalling at synaptic junctions?

When a neurone fires, it sends an electrical signal that jumps down the axon via the nodes of Ranvier very rapidly. At a synaptic junction, chemical Brownian diffusion signalling with receptor surface ...
8
votes
4answers
721 views

What is the viability of Intelligent Design as a supplement to chemical abiogenesis and Darwinian Evolution?

First of all I am not endorsing Intelligent Design (Wikipedia link); I'm asking this because I (someone who does not have a background in biology, organic chemistry, or philosophy) got into a ...
7
votes
1answer
3k views

Smallest unit on which selection can act

Traditionally, the individual was considered to be the smallest unit on which Natural Selection (NS) acts. Today, we usually consider the gene as being the unit of NS. Of course, we should also ...
7
votes
1answer
139 views

Selection on linked loci in a diploid population

Let’s consider two linked loci $A$ and $B$ that are both bi-allelic. In consequence, we have four different possible haplotypes $A_1B_1$, $A_1B_2$, $A_2B_1$, $A_2B_2$, which frequencies are $X_1$, $...
7
votes
1answer
174 views

Book suggestion on computational molecular evolution

I'm currently reading Computational Molecular Evolution by Yang. Can you recommend alternative books? I am finding it to be lacking on conceptual discussion (it's more focussed on the mathematics and ...
6
votes
3answers
14k views

Why is mRNA needed in the Protein translation?

The original question was to predict the basic requirements for information storage. Then the discussion moved to why is it necessary to include mRNA in the protein translation process. Why can't ...
6
votes
2answers
219 views

How much DNA of mitochondrial origin is incorporated in main cell's DNA?

And especially three points : in which chromosomes is it located (especially for the human case) ? how do we know about it ? does the proportion and composition vary a lot from one eukaryot to ...
6
votes
1answer
1k views

What came first? The DNA or the DNA polymerases?

I know this sounds a lot like chicken and egg question and while the latter has an answer, I am intrigued about the former. A modified form of the question would be, in the course of abiogenesis, ...
6
votes
1answer
210 views

How did genome duplication in jawed vertebrates allow gene specialization?

I am currently reading from Chapter 15 in Principles of Life, 2nd Edition: Many gene duplications affect only one or a few genes at a time, but in some cases entire genomes may be duplicated. When ...
6
votes
1answer
315 views

The origin of molecular machines

DNA holds genetic information and holds the key to the evolution of living organisms. Transcription and translation mechanisms enable living cells to process information encoded in DNA. To that end, ...
5
votes
3answers
581 views

Good book on Origin of Life [closed]

What is a book that goes into reasonable detail (but isn't textbook-level technical) about the origin of earth and in particular the origin of life on earth? Something intended for a broad audience, ...
5
votes
1answer
144 views

Learn Bioconductor the hard way!

I came to analyzing population genetics data from the background of a theoretician and a computer biologist but not with the standard tools that a bioinformatician (or empiricist in population ...
5
votes
1answer
6k views

Why is allolactose the LacI inducer?

For what reason(s) is allolactose, instead of lactose, the "natural" inducer of lac operon repressor?
5
votes
2answers
347 views

How do I know whether or not a nuclear gene is single copy?

As a part of a phylogenetic study, I need to find a nuclear gene that meets the following requirements: Single copy gene; Highly variable gene; Gene longer than 400 bps; Gene that gives information ...
5
votes
2answers
634 views

Non Coding DNA and its effect on evolution

I had a discussion with a friend of mine; from his understanding, bacteria and other small organisms have higher amounts of "coding" DNA and, as such, are able to evolve much faster than organisms ...
5
votes
0answers
172 views

At what rate do chromosomal rearrangements occur?

How often do chromosomal rearrangements occur? I am interested about these kind of chromosomal rearrangements that are passed on to the descendants, i.e. germ line chromosomal rearrangements. The ...
4
votes
3answers
323 views

Book recommendations for evolutionary models

I was recently working on getting a statistical model of a DNA sequence. To do this I found that understanding evolution quantitatively seems to be quite important. I would really appreciate any book ...
4
votes
2answers
279 views

Can estimating the likelihood of protein sequences adopting functional enzyme folds show life is too complex for evolutionary timescales?

An acquaintance provided me with this article1. I can't understand for sure what it is about. My acquaintance said that it proves that time for generation of even the simplest proteins is on a ...
4
votes
2answers
177 views

Why would low complexity regions be linked with relaxed selection?

I'm reading a text (Wagner, 2007) on identifying positive selection. In the paper, the author says that low complexity regions are known to be associated with the relaxed selection. I'm trying to ...
4
votes
2answers
154 views

Is there selection against long proteins and long genes?

Background thought Titin and TTN Titin is the largest protein in the human genome with 33423 amino acids. Titin is coded by the gene TTN that must be at least $3 \cdot 33423 \approx 100kb$ long. ...
4
votes
1answer
346 views

Is the heterotroph hypothesis universally accepted?

I was wondering whether there are hypotheses that take a different approach that is contrary to the heterotroph hypothesis. The heterotroph hypothesis states that autotrophs evolved from heterotrophs ...
4
votes
1answer
138 views

Polymorphism in number of chromosomes?

The answer to this question, saying that Down Syndrome - a trisomy of human chromosome 21 - is caused by de novo mutation (rather than resulting from standing variation) made me think about ...
4
votes
2answers
224 views

How can (or did) Deinococcus radiodurans continue to evolve after developing resistance to mutation?

Deinococcus radiodurans has a remarkable ability to resist damage to its DNA due to radiation, dehydration or (to my knowledge) any other source. It keeps multiple copies of its genome and has a ...
4
votes
1answer
182 views

CRISPR/Cas9: What are the main differences between sgRNA and the Cr:TracrRNA ?

So from what I understand, in gene editing, the CRISPR vector expresses a small RNA sequence comprised of a small guide-RNA that is complementary to your target sequence. The sgRNA comprises a 20 Bp ...
4
votes
3answers
139 views

Does the genome make sense without knowledge of the ovum?

Much of the literature for laypeople seems to consider (and to spread the idea) that an animal (or a plant, I guess) is characterised by its genome. I do not know whether the same goes for more ...
4
votes
0answers
63 views

Mechanisms of genotype*sex interactions [closed]

I'm looking for suggestions of the mechanistic level at which genotype*sex interactions can occur. These give different phenotypes from the same genotype dependent on the sex they are expressed in. ...
3
votes
4answers
14k views

Why are there both stop and start codons?

Based on my understanding from wikipedia, there is the (RNA) start codon AUG and the stop codons UAA, UGA, UAG. AUG can also encode Methionine, I'm assuming if it appears in the middle of a mRNA ...
3
votes
1answer
168 views

Text Book Recommendation: Organic Evolution

I was wondering if anyone could point me in the direction of any text books on organic evolution? I have recently become interested in the subject and would like to know more. I think an undergrad ...
3
votes
1answer
124 views

How did mitochondria make energy long ago?

I've learned that mitochondria is thought to have been eaten by a larger cell, resulting the mitochondria to be part of a bigger cell. Well, here's my Q. If you look at how mitochondria works, you ...
3
votes
1answer
212 views

Inbreeding depression and dominance

From this article, second paragraph of the second page A classic theoretical result is that the mean of a character controlled by a single locus i with two alleles Ai1 and Ai2 is only affected by ...
3
votes
2answers
138 views

What is the evolutionary relationship between heme, chlorophyll and other tetrapyrroles?

As a non-biologist, I have searched the Internet and found dozens of papers discussing the similarity between the structures of heme and chlorophyll molecules, but I could not find any discussion of ...
3
votes
2answers
57 views

Heterochromatin production limitations

Currently playing with some ideas for a project and needed some guidance. I am wondering, both in Drosophila melanogaster and in general, is the amount of heterochromatin a cell/nucleus can produce ...
3
votes
1answer
303 views

Mutation rate in viruses

Mutation rate is a phenotypic trait that evolves. The process of evolution of such kind of traits are often referred to as evolvability. I am wondering about the evolution of the mutation rates in ...
3
votes
1answer
97 views

Evolutionary conservativeness

List the following proteins in the order of decreasing evolutionary conservativeness of their primary structure: Somatotropin. Catalytic subunit of a DNA – polymerase. Histone H1. ...
3
votes
1answer
125 views

Why did translation develop a specific codon for initiation?

The translation of mRNA is initiated by a specific methionine-accepting tRNA at a specific initiation codon, usually AUG (complementary to the tRNA anticodon). However translation at suitable (albeit ...
3
votes
2answers
4k views

Identity By Descent vs Identity By State

Background The concepts of Identity By Descent (IBD) vs Identity By State (IBS) are central in population genetics, yet I fail to fully wrap my head around the definitions. You can find examples ...
3
votes
1answer
73 views

Book Recommendation: Complex Traits and Complex Genetic Architecture

I am looking for a book (or any good source of information) that offers an in-depth discussion and models about the evolution and analysis of complex traits and complex genetic architecture. Do you ...
3
votes
1answer
117 views

Nucleotide frequencies in Kimura's two-parameter model

Here's an excerpt about Kimura's two-parameter model from Felsenstein's Inferring Phylogenies: "The model is symmetrical, and one can immediately see that, after enough time has elapsed, it will ...