Jessica

Ensaio opcional 12 de março de 2019

Understanding the central paradigm of molecular biology was the first step to uncover the evolutionary history of life. Francis Crick proposed in 1970 a simple model to explain how genetic information flow (DNA>RNA>Protein) occurs in a biological system. Such knowledge allowed the remarkable advance in several fields evolutive biology. In its unveiling the way as most organism works at molecular level, Crick provided evidence of Darwin’s premise of common ancestry. It made possible scientists use DNA or protein sequences as a powerful tool to reconstruct evolutionary history through phylogenies (i.e. tree life) at the last 30 years. Today we are more prone to obtain a more robust picture of the relationship among organism and answer questions about the origin, maintenance, and future of different living organisms.

Correção Ensaio Opcional

Correção feita por Tamires Andrade

Understanding the central paradigm of molecular biology was the first step to uncover the evolutionary history of life. Such knowledge allowed the remarkable advance in several fields evolutive biology, in its unveiling the way as most organism works at molecular level. It made possible scientists use DNA or protein sequences as a powerful tool to reconstruct evolutionary history through phylogenies (i.e. tree life) at the last 30 years. Nowadays, we are more prone to obtain a more robust picture of the relationship among organism and answer questions about the origin, maintenance, and future of different living organisms.

Comentários:
Olá Jéssica, gostei muito do seu parágrafo e fiz apenas pequenas alterações. Retirei algumas frases que acho que não são necessárias neste contexto e juntei outras, deixando assim o parágrafo mais suscinto.

Ensaio 4- 2 de abril de 2019

Effective population size

Effective population size (Ne) determines the affect of genetic drift and natural selection. Ne represents the number of breeding individuals that effectively contribute to the next generation. It is responsible to maintain the genetic variability of a population. While the genetic drift and natural selection are mechanisms for evolution that change allele frequency over time. Genetic drift generates stochastics change on allele frequencies, whereas natural selection leads to deterministic changes due to organisms’ fitness. The fate of neutral, harmful and nearly advantageous alleles depends on population size. In general, small populations undergo a bigger effect of genetic drift decreasing the genetic variation over time and consequent potential adaptive. Thus, nearly advantageous alleles can be lost by chance, while neutral and harmful ones can spread and become fixed in a population. On the other hand, when small populations are substructured the genetic drift tends to increase the genetic variability among them upon which speciation can operate. In contrast, large populations have the capacity to buffering the genetic drift force. In this case, natural selection takes over the main role in the maintenance and elimination of alleles. Therefore, we need considers how the Ne influences the interplay between these evolutionary mechanisms to think about molecular evolution and variation.

Ensaio 5-l 30 de abril de 2019

What is a species?

Taxon description is not a fact, but a testable hypothesis. Species represents a taxonomic category that seeks to depict an attempt of "real biological entity". Species delimitation has long been a theme of intense debate among researchers. It because two questions of different nature had mixed: the species category definition (ontological question) and the adequacy of criteria (epistemological question) used in the definition of taxa classified as species. That is, the delimitation of species has been confused with the concept of species itself. Several species concepts could be found at the literature (e.g., ecological, biological, phylogenetic, etc) which disagree on the adoption of different properties acquired by the lineages during speciation (e.g., ecological niche, reproductive isolation, monophyly, etc)- a species criteria. Despite the differences among the alternative species concepts, all exhibit a common conceptual unit that provides the basis for a unified species concept: separately evolving metapopulation lineages; which is the only property necessary for species definition. Thus, the incompatibilities of properties created among alternative species concepts are reinterpreted as properties of species categories. Those properties constitute a secondary species criteria, serving as operational criteria or lines of evidence to assessing lineages separation. This allows the clear separation between the theoretical species concept from operational criteria used for its empirical application.

Correção Ensaio Opcional 07/05/2019

Correção feita por Alvaro Doria

Olá, Jessica. Adorei o seu texto e as suas idéias. Segue abaixo algumas sugestões que poderiam melhora-lo.

Taxon description is not a fact, but a testable hypothesis. Species represents a taxonomic category that seeks to depict an attempt of "real biological entity".
(Acho que a sua primeira frase pode ser unida com a segunda formando uma topic sentence mais completa)
Species delimitation has long been a theme of intense debate among researchers.
It because two questions of different nature had mixed: the species category definition (ontological question) and the adequacy of criteria (epistemological question) [used in the definition of taxa classified as species] (acho que este final pode ser retirado pois já esta subentendido pelas suas idéias anteriores que você está falando que estes conceitos são utilizados na delimitação de espécies)
That is, the delimitation of species has been confused with the concept of species itself.
Several species concepts could be found at the literature (e.g., ecological, biological, phylogenetic, etc) which disagree on the adoption of different properties acquired by the lineages during speciation (e.g., ecological niche, reproductive isolation, monophyly, etc)- a species criteria.
Despite the differences among the alternative species concepts, all exhibit a common conceptual unit that provides the basis for a unified species concept: separately evolving metapopulation lineages (seria legal citar o Queiroz ); [which is the only property necessary for species definition.] (Acho que esta frase pode ser removida pois parece ser uma idéia repetida.)
Thus, the incompatibilities of properties created among alternative species concepts are reinterpreted as properties of species categories. (Voz passiva)
Those properties constitute a secondary species criteria, serving as operational criteria or lines of evidence to assessing lineages separation.
This allows the clear separation between the theoretical species concept from operational criteria used for its empirical application. (E como essa conclusão pode ser remetida a sua topic sentence?)

Ensaio 14 de maio de 2019

Write thinking

A escrita científica deve ser clara e objetiva. O processo de amadurecimento das ideias, construção do pensamento e transposição do conhecimento em forma de texto requer tempo. Tempo é um fator limitante e muitas vezes autores acabam pulando etapas essenciais para sua construção. Um dos elementos fundamentais para escrita é propor um planejamento sobre o conteúdo, objetivo e estrutura do texto em questão. A estrutura do texto com apresentação de ideias que desencadeiam uma ordem de pensamento até chegar à conclusão é um dos principais desafios encontrados nos ensaios… Falar brevemente da estrutura e concluir (alterar texto pro inglês).

Ensaio 21 de maio de 2019

Maximum likelihood applied to phylogenetic

Maximum likelihood is an approach generally used to infer the phylogenetic tree. This statistical method estimate parameters through of a function of probability estimated from data given a model. For example, rate of nucleotide substitution, differential transformation costs, the phylogenetic tree, and its topology. Such method suggested what function maximize (explain) the likelihood of observed data. However, when the topology is calculated all possible models are tested, but the topology itself cannot be maximized because it does not have an expected distribution. The bootstrap seeks to measure this distribution for a rough notion. So, although maximum likelihood has some limitations, it still is an appropriated method to analysis with DNA sequences given that allows incorporating stochastic models of knowledge molecular evolution.

Outline 28 de maio de 2019

Tema: "Guia prático e rápido para calibração molecular"

Objetivo: ajudar leitor escolher melhor o modelo de relógio molecular conforme seus dados

Introdução (1 parágrafo):
O que é RM?
Validade para aplicação em análises filogenéticas.
Gama de relógios e métodos.
Desafio: Qual escolher?
O que será abordado no texto.

Desenvolvimento (alguns parágrafos):

Preparo prévio dos dados
Tipos de calibração: taxas ou idades baseadas em fóssil, evidências geológicas, etc.
Tipos de ditribuição
Os relógios: strict vs relaxed (dando exemplos)
global vs local
autocorrelated vs uncorrelated

Conclusão (1 parágrafo):

Fechamento e desafio era do bigdata

Mudanças de plano 04 de abril de 2019

Pretendo escolher um desses assuntos:

-Relógio molecular na Era Genomica: podemos afirmar que estamos mais próximo em conseguir obter uma estimativa mais próxima da real?
-Como localização dos pontos de calibração em diferentes locais da filogenia são afetadas;
-Desafios para calibração secundária;

Auto-avaliação 11 de junho de 2019

A disciplina aprofundou minha visão crítica a respeito do tema. Embora já tenha conhecimento sobre alguns dos assuntos, apenas aqui tive a possibilidade de questionar outros aspectos até então não pensados. Amei o primeiro bloco pois nunca havia lido com mais carinho sobre as questões básicas envolvidas na evolução molecular. A prática de escrita e revisão dos textos de colegas foi de suma relevância, gostaria de ter feito mais. Como nota da auto- avaliação sugiro 0.85.