Deyvid Emanuel Amgarten

Hello world!
Welcome to my personal page for the course PEMARF.
Have fun :P

Optional Essay - March, 9th

Viruses and the central dogma

The flow of information from DNA molecules to RNA and thereafter to proteins is known as the Central Dogma of Molecular Biology, as first stated by Francis Crick in 1958 [1]. This dogma was the epicenter of plenty of debate in the scientific community and new directions to the flow of genetic information are now well described. Viruses are remarkable exceptions in this regard, since several studies have demonstraded RNA viruses that replicate themselves through a DNA intermediate (Retroviruses) and self-replicating RNA genomes from single and double stranded RNA viruses. Another noteworthy case refers to viruses that carry methylation proteins in the virion to target bacterial DNA and stop host transcription once and for all. This last example could be characterized as an Unknown case of transfer (Protein -> DNA), as hypothesized by Crick in 1970 [2]. As a result of the diversity of genome forms and replication mechanisms, viruses have a unique capacity of shedding light to a complete picture of the Central Dogma of Molecular Biology.

1. Crick, Francis. "On protein synthesis." Symp Soc Exp Biol. Vol. 12. No. 138-63. 1958.
2. Crick, Francis. "Central dogma of molecular biology." Nature 227.5258 (1970): 561-563.

Analisado por Livia Moura: Dado que o objetivo desse exercício é ser sucinto e direto na informação que se quer transmitir: + a primeira sentença vem com a informação principal de antemão, antes da histórica ( :D ); + creio que a segunda sentença poderia ser descartada; + na terceira sentença a frase ficou estranha, como precisando de uma finalização (n seria o "that" substituido por "can" ou similar?… posso estar enganada). + As demais ficaram boas :)

Essay 1 - March 17th

The avalanche of genomic information that scientists have been experience in the last decade is revolutionizing several areas of biology. Taxonomy and species definition are special cases in this context, since both fields are subject to classical taxonomic rules and descriptions. Techniques of environmental sequencing allow researchers to obtain entire microbial genomes without the isolation of the organism in vitro, with many completely new species been unveiled every day in all parts of the globe. Therefore, taxonomy and species definition should change to embrace genomic data and rules should be redesigned in a way that genomic/molecular data and classical descriptions could both be used in this new scenario. Biology since its very beggining is changing from exclusively descriptive approaches to include computational and quantitative methods [1], and so should do its taxonomy field.


1. Markowetz F. All biology is computational biology, 2017. PLOS Biology 15(3): e2002050. doi: 10.1371/journal.pbio.2002050

Primeira Frase, OK : Achei direta e objetiva, uma idéia clara.
Segunda frase também Ok, tem duas idéias, mas bem ralecionadas.
Terceira frase, muito longa, quebraria em duas: "Techniques of environmental sequencing (…) the organism in vitro. Therefore many new species (…)."
Frase seguinte também está longa, como já usei um "Therefore" antes começaria direto com: "Taxonomy and (…) genomic data. The rules should (…) in this nex scenario."
Ultima frase, OK.

Correção Maila

Essay 2 - March 24th

Student's understanding of the neutral theory

It is interesting to think about the bias that most scientists have regarding the importance of Darwinian selection in the evolution landscape. It is contra intuitive to think that stochastic processes (genetic drift) could be responsible by most of features we now see fixed in different populations. Darwin’s natural selection teachings permeate most undergrad courses and there is a constant repetition of its importance to evolution and biology in general. On the other hand, the neutral theory and its agent are only taught in evolution classes and/or more advanced graduation classes. This causes students to contest ideas that for them are not intuitive. The diversity arises from random mutations and the ones that are truly adaptive are thought to be very rare. Nevertheless, the majority of substitutions are thought to be neutral and they are fixed in populations through genetic drift, as many studies have shown[1,2,3]. Thus, early evolution courses in undergrad could be a way of solving this problem and make students more familiar with the neutral theory since the very beggining.


1. Kimura, Motoo (1968) Evolutionary Rate at the Molecular Level. Nature, 217:624.
2. King JL, Jukes TH. (1969). Non-Darwinian Evolution. Science 164:788-97.
3. Kimura, Motoo (1991). The neutral theory of molecular evolution: a review of recent evidence.. Jap. J. of Genetics.

Essay 3 - March 31st

Infinite size populations

Species with assumed infinite population sizes may pose as exceptions to the neutral theory of evolution. Most of substitutions observed in different populations are thought to be fixed by random drift of the allele’s frequency, as first stated in [1]. However, the effective population size modulates how genetic drift and natural select act upon the frequency of alleles [2]. Species with enormous population sizes (e.g. bacteria and viruses) may amplify the effects of selection upon alleles that confers differential fitness to the organism. Thus, different from small size population, most of diversity observed in bacterial and viral populations would be a result of natural selection action. Nevertheless, what seems to actually occur is that most of modifications slightly decreases or increases the fitness of its carrier [3]. In this context, selection is more pronounced in infinite size populations when compared with small size populations. In other words, we are more likely to see nearly neutral (increasing or decreasing the fitness) modifications in small size populations than we are of seeing slightly deleterious modifications in infinite size populations.


1. Kimura, Motoo (1968) Evolutionary Rate at the Molecular Level. Nature, 217:624.
2. Charlesworth, Brian. "Effective population size and patterns of molecular evolution and variation." Nature Reviews Genetics 10.3 (2009): 195-205.
3. Ohta, Tomoko (1973-11-09). "Slightly Deleterious Mutant Substitutions in Evolution". Nature. 246 (5428): 96–98

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