Manuel

Ensaio opcional - Aula 1

In the article Central Dogma of molecular Biology, 1970, Crick shows the weak points of his previous text on the Central Dogma. At the time he wrote the article, many of the possible replications, transcriptions and translations were not yet tested. Crick confirms the importance of the transfers among the three families of polymers - DNA, RNA and proteins - but sets DNA to DNA, DNA to RNA, RNA to RNA and RNA to proteins as probable and all other situations as hipotecally possible. Nowadays, the Central Dogma is well tested, accepted and fully used as a tool for phylogentic inference, for the DNA represents the morphology of any living creature, provides many more caracters to be evalueated and is not subjective.

Ensaio 1 - 19/03/2019

Correção do ensaio opcional de 12 de março por Arthur

In his article entitled “Central Dogma of Molecular Biology”, Crick (1970) shows the weak points of his previous contribution on this topic (Crick 1958). At the time he wrote the first article, many of the possible replications, transcriptions and translations were not yet tested. Crick confirms the importance of the transfers among the three families of polymers - DNA, RNA and proteins - but sets DNA to DNA, DNA to RNA, RNA to RNA and RNA to proteins as probable and all other situations as hipotecally possible. Nowadays, the Central Dogma is well tested, corroborated and widely used as a tool for phylogentic inference; DNA represents the morphology of any living creature, is not subjective and provides many more characters to be evaluated.

Ensaio 2 - 26/03/2019

The theory of natural selection alone is not able to explain the high ratio of substitutions in DNA coding genes. The ratio of substitutions is always higher than the expected. These substitutions are in most cases neutral, generated stochastically and with no effects in the organism. The neutral theory of molecular evolution enabled tests of evolution hypothesis. The ratio between synonymous and non synonymous substitutions can predict neutral or positive signals and sweep population.

Correção do ensaio opcional de 26 de março por Bárbara Brito

The theory of natural selection alone is not able to explain the high ratio of substitutions in DNA coding genes. The ratio of substitutions is always higher than the expected. These substitutions are in most cases neutral, generated stochastically and with no effects in the organism. The neutral theory of molecular evolution enabled tests of evolution hypothesis. The ratio between synonymous and non synonymous substitutions can predict neutral or positive signals and sweep population.

The natural selection theory is (……) not able to explain the high ratio of substitutions in DNA coding genes [Bibliography]. Vast majority of randomly substitutions rates occurs higher than expected (?) These substitutions are in most cases neutral and with no effects in the organism.The neutral theory of molecular evolution enabled tests of evolution hypothesis. [Bibliography]. Tests can predict neutral mutations or sweep on population trough synonymous and non synonymous substitutions rates calculations.

1) On the first phrase, maybe it is better to substitute "alone".
2)I could not understand the second phrase. Substitutions are always been seen randomly during the evolution course. Whats is higher than expected is the neutral rate of them, which can be seen on the third phrase.
3) all substitution are stochastic, so this "generated by stochastic events" could be removed
4) On 4th phrase it is important to introduce neutral theory, on the context of your text.
5) It is also important to remember to connect your phrases.

Ensaio 3 - 30/05/2019

The cladogram is a scientific tool able to explain the relation among species. The introduction of an outgroup enables cladograms to predict the direction evolutionary substitutions occurred. Thus, analyzing phylogenetic trees it is possible to answer whether morphological characters in different taxa had losses or gains as well as infer the geological era. The importance of understanding phylogenetic trees is so strong that the expression "tree thinking" was created.

Correção do ensaio 3 realizada por Igor Salles de Oliveira.

Notes:

The essay demands more accuracy and pre-writing time.

1) Try to maintain a direction in your essay. The first sentence gave me the impression that your essay will show facts and examples which demonstrate the use of cladograms to elucitade the relationship among species. However, I didn't notice it through all your paragraph.
2) Rewrite the sentence "Thus, analyzing phylogenetic trees …" = You could exposed the ideia in a concise way: Analyzes of phylogenetic trees allows the inference of losses or gain of characters in different taxas and molecular dating of the vicariances events.

Ensaio 4 14/05/2019

Dificuldade própria:
Eu notei o uso excessivo de voz passiva apesar de não ser o meu maior problema. Tenho bastante dificuldade em ligar as ideias que pretendo passar. Meu texto parece confuso e um monte de retalhos. Eu consigo pensar em três motivos que geram isso: (1) usar frases curtas, (2) falta de conhecimento científico, e (3) tentar passar tudo em um único parágrafo.

Dificuldade comum:
Quando leio os textos dos outros alunos noto que eles têm dificuldade de escrever frases curtas e ligar umas nas outras. Esse problema ainda ocorre, apesar de diminuir ao longo do curso.

Ensaio 5 - 21/05/2019

Maximum likelihood is a statistical method widely used to infer phylogeny. This method takes into account all the information the data provides. Likelihood depends on the choice of an evolutionary model. These models have different rates of substitution. The correct model can reproduce a tree that corresponds to the historical relationship of the data. However, when used a mistaken model a false tree can be generated. A possible method to confirm the consistence of the tree is the use of bootstrap. Although the tree can be the correct one, the data should be revised when bootstrap result is low.

Ensaio 6 - Outline - Tema: 2 - Utilização de modelos em ciência com enfoque na reconstrução histórica.

How worth is to select a specific model for phylogeny?

- Explicar a necessidade de modelos em verossimilhança.
- Citar os principais modelos e quais parâmetros eles adotam - MODEL SELECTION IN PHYLOGENETICS - Jack Sullivan and Paul Joyce.
- Tentar achar um comparativo com tamanho da matriz e o modelo adotado. Talvez, depende do tamanho do texto.
- Citar o artigo - Model selection may not be a mandatory step for phylogeny reconstruction - Shiran Abadi, Dana Azouri, Tal Pupko & Itay Mayrose - e o uso do GTR+I+G.
- Usar o artigo dos opiliões - Phylogeny of harvestmen family Gonyleptidae inferred from a multilocus approach (Arachnida: Opiliones)- para comparar o modelo assumido com o GTR+I+G.
- Concluir se a árvore modificou.

Ensaio 7 - 04/06/2019 - Topic sentences

The maximum likelihood (ML) method is depend of a model that suits the data.
The most commonly models for phylogenetic reconstructions are: (1) Jukes and Cantor (1969), (2) Kimura (1980), (3) Blaisdell (1985), (4) Felsenstein (1981) and (5) Lanave et al. 1984.
The model search necessity has not been questioned to date. Sullivan & Joyce, 2019 assume that GTR+I+G performs a reasonable solution for topologies of all data.
Tests with different models in the same data might show how different the topologies are.

https://genome.cshlp.org/content/8/12/1233.long#ref-15
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674669/

Auto Avaliação 11/06/2019

Minha intenção nesse curso foi de voltar a estudar com mais responsabilidade do que a de um aluno especial. Eu queria sentir como seria começar um mestrado. Se é possível levar comitantemente com o trabalho. Eu acredito que sim mas preciso adiantar mais créditos antes de ingressar na pós. Aprendi muito como o curso. Aprendi as noções da escrita científica e percebi que eu fazia muito errado. Aprendi muito sobre os tópicos das aulas e os seminários. Passei a pensar de maneira mais completa sobre muitos assuntos. Achei que eu conseguiria participar mais durante as aulas mas não perdi a timidez. Em muitas horas eu queria opinar mas não consegui. Me diverti muito voltando a fazer um seminário após 12 anos mas nem um pouco na hora de apresentar. Devido a minha fraca participação nas aulas eu me dou 0,6.