Flavia Akemi Nitta Fernandes

Ensaio Opcional - Aula dia 10/03/2017

The central dogma of molecular biology was proposed by Francis Crick in 1958 and then reanalyzed in 1970, after some misunderstanding in the scientific field. The main idea of the dogma is to explain the flow of genetic information in a biological system. One of its basic statements is that once genetic information is passed to the protein level it cannot be transferred to any other polymer (DNA, RNA or protein). Even though the core of the dogma is extremely simple, it has often been misunderstood due to the obscurity nature of some transfers. In this scenario, Crick reanalyzed his dogma in 1970, clarifying and reclassifying some events. He divided the genetic transfer events in three different categories: general transfers, special transfers and unknown transfers. The general transfers are the ones which occur in all cells (i.e. DNA→DNA, DNA→RNA and RNA→Protein). The special transfers, on the other hand, only occur in specific situations (i.e. RNA→RNA, RNA→DNA and DNA→Protein), such as the infection of a cell by a retrovirus. Finally, the unknown transfers are the ones which have never been identified before (i.e. Protein→DNA, Protein→RNA and Protein→Protein). This last category shows that is it impossible, from what we know, to transfer any information from the protein state to another polymer.

Correção por Jorge

Como previamente apontado, a ideia principal do texto está na segunda sentença. Sendo assim, esta poderia ser a primeira. Acho que talvez o ideal fosse juntar a parte histórica que está divida, combinando a primeira sentença com a que se inicia em "In this scenario, Crick…". Assim o texto se inicia com o que é o dogma, suas premissas e predições e então seu histórico. O restante do texto é muito claro e preciso, uma vez que primeiro você apresentou as três categorias e depois explicou cada uma separadamente. Na última linha, imagino que "it" e "is" estejam trocados acidentalmente. Eu também sugeriria que fosse usado "as far as we know" na última linha para reforçar a ideia de que há possibilidade da transferência, porém não está atualmente esclarecido como. Isso, claro, se houve essa intenção na sentença (como senti ao ler). Caso contrário, desconsidere.

Ensaio 1 - Aula dia 17/03/2017

The definition of species is one of the most controversial concepts in Biology. Even though the use of the word ‘species’ is widespread in the scientific literature, there are various acceptable definitions for this term. However, independently on the definition used by different authors, the main target of each study will determine the most preferable definition to be used. For instance, conservational studies usually focus on elucidating the diversity of taxa that can be found in a determinate location. Taxonomy studies, on the other hand, demand a more refined and detailed analysis, once the focus of this kind of research is to describe new species without the same urgency of the conservational ones. The different approaches chosen by each study represent the different scientific pressures the researchers are submitted to. Therefore, there is no right or wrong concept of species, only distinct definitions which explore different aspects of it.

Correção por Jorge

Novamente, acho o texto muito bem escrito e claro. Os seguintes comentários são pequenas sugestões para deixá-lo mais objetivo.
A sentença tópico está muito boa e precisa. Eu trocaria o "used" da segunda linha por "applied" para evitar a repetição da palavra que também é usada no final da oração (que, ao meu ver, poderia ser removida). "However, independently on the definition applied by different authors, the main target of each study will determine the most preferable definition".
Sugiro eliminar refined na linha 4, pois "refined and detailed" fica redundante. O resto da sentença poderia ser encurtada: "once the research focus is to describe…"
Finalmente, as orações finais deveriam ser idealmente divididas em duas, porém não consigo pensar em uma boa alternativa. Talvez elas estejam melhores juntas mesmo.

Ensaio 2 - Aula dia 24/03/2017

The neutral theory of molecular evolution postulates that evolution happens mostly in a stochastic way. A consequence of this statement is that genetic drift is much more common than natural selection as an evolutive force. This theory had a great impact in the scientific community once it was previously believed that natural selection was the main force taking place in the evolution of species. However, it is now known that almost all aminoacid and nucleotide substitutions take place due to genetic drift. The neutral theory of evolution does not annul the natural selection theory. Instead, it only conveys that various molecular events may have arisen and been fixated in a population by chance.

Analise por Livia
Texto claro a partir de uma frase tópico bem definida. No caso da avaliação de hoje, apenas um lembrete para que referencie as devidas colocações.

Ensaio 3 - Aula dia 31/03/2017

Target audience: Undergraduate students.

The effective population size (Ne) is an essential concept in the evolutionary study of populations. Evolutionary forces such as natural selection and genetic drift are extrictly dependent on the populations’ efective size. Genetic drift has a stronger effect in populations with smaller Ne. Therefore, alleles are randomly lost or fixated more rapidly (in fewer generations) than in populations with a bigger Ne. On the other hand, natural selection generates stronger consequences on bigger populations and is almost indistinguishable in smaller ones. However, only the response of the population to natural selection changes according to its effective size, while the strenght of the selection force keeps unchanged. For example, even though the fitness of a pair of alleles is the same in two different sized populations, the allele with better fitness might be lost by chance in the smaller one, once genetic drift has a stronger action in smaller populations. Then, knowing the effective population size is crucial to understand how to measure the evolutive forces in any biological system.

Comentários por Caio:

Achei o texto bem escrito e correto, com sentenças curtas e fluidas. Apenas 2 vozes passivas que podem ser mudadas:

"Therefore, alleles are randomly lost or fixated more rapidly (in fewer generations) than in populations with a bigger Ne." (Therefore, populations with smaller Ne ramdomly loose or fix an allele more rapidly (in fewer generations) than populations with bigger Ne.).

"… the allele with better fitness might be lost by chance in the smaller one …" (… the smaller one might loose the allele with better fitness by chance…).

Ensaio 4 - Aula dia 05/05/2017

Target audience: Undergraduate students

The misinterpretation of phylogenetic trees is a recurrent problem among graduate students and nonspecialists (Baum et al., 2005). There are two main explanaitions for this misinterpretation, both concerning the misunderstanding of the conceptual evolutionary relationship among the taxa. The first misinterpretation is about the topological position of the taxa on a tree, which represents the evolutionary proximity of two groups regarding their last common ancestor. Some students can interpret this proximity as a graphic way of showing similarities among the taxa and not with common ancestrality. The second misinterpretation is due to the wrong way of reading the tree, which can be incorrectly read from the tips to the root. When interpreting a tree this way, people are amiss reading the represented evolutionary history from the present to the past. The above reported problems show that there is a misunderstanding of basic and essential evolution concepts among nonspecialists and, therefore, represent an area of science which can also be incorrectly interpretated by other social institutions.

Comentario (juliano)

Bom texto. Está claro e com sentenças curtas e objetivo.

Ensaio 5 – Aula dia 12/05/2017

Target audience: undergraduate students

Neighbor-joining (NJ) is a controversial method of evolutionary distance inference due to the lack of reliability of its results. However, some researchers still use this method for checking their results and for infering trees. Studies that have successfuly applied NJ show that such method should not be desconsidered on the phylogenetic reconstruction (Wayne, 2012; Woese nad Fox, 1977). Even though the results generated by NJ are not completely reliable, they can be useful for studies with great amounts of data and for reconstructing deeper evolutionary relationships. As Woese and Fox’s study showed, the deeper clades on the phylogeny were correctly reconstructed, even though the more internal ones were incorrect. Thus, NJ can be used to generate a first general topology of a tree, but will not necessarily reconstruct all clades correctly. Another application for NJ could be for checking trees generated by other methods (i.e. maximum-likelihood, Bayesian). If the NJ reconstruction generates a highly discrepant branch, one can deduce that such branch should be reevaluated. Therefore, NJ is not a dispensable tool for generating phylogenetic trees, as it permits analyses in a scale that no other method could manage doing so far.

References:
Wayne, R.K., 2012. Evolutionary genomics of dog domestication. Mammalian Genome, 23(1-2), pp.3-18.
Woese, C.R. and Fox, G.E., 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences, 74(11), pp.5088-5090.

Comentários por Jorge

Assim como das outras vezes, acho seu texto muito bem escrito e com boas ligações. Eu, particularmente, evitaria evocar os pesquisadores, tentando dar ênfase ao estudo. Por exemplo, ao invés de "As Woese and Fox’s study showed", algo menos pessoal como, "As demonstrated for the relationships of the three domains…". Isso também deixa o texto menos "story telling" e mais objetivo. Mas isso é uma coisa de estilo, então fica por sua conta ;)
Considerando que o texto é para "undergrads", eu sugeriria acrescentar, em algum momento depois da frase tópico, o que é ou como funcionar o NJ. Isso porque você discorre sobre as aplicações e críticas ao métodos, mas seria legal ter falado antes "o método NJ faz isso e isso com base nisso". Não sei se fui claro…heheh
Espero ter ajudado.

Ensaio 6 - Aula dia 19/05/2017

Target audience: Graduation students.

The bootstrap is a method to estimate the confidence of your dataset in the reconstruction of a phylogenetic tree. Bootstrapping consists on resampling your dataset and inferring trees using these partial datasets. The percentage in which each clade is reconstructed in these trees is the bootstrap value (Soltis and Soltis, 2003). Even though the bootstrap was firstly proposed as a feature that shows the confiability of the chosen dataset, currently it has been used mainly to provide the confiability of the clade. This misunderstanding of the bootstrap concept can lead to wrong conclusions, such as the idea that a clade with a high bootstrap value is closer to representing the reality than a lower bootstrap clade. Low bootstrap values mostly indicate that the chosen dataset is not consistent enough for your analysis, and thereore, that you should change your data. However, relying on a high bootstrap value to infer that a clade is correct is an error. The high bootstrap value only means that the dataset used to reconstruct a clade is not completely inappropriate, but is does not indicate that the clade is reliable. Therefore, the bootstrap value is a useful method, but only when used for the correct analysis.

References

Soltis, P.S. and Soltis, D.E., 2003. Applying the bootstrap in phylogeny reconstruction. Statistical Science, 18(2), pp.256-267.

Análise por Livia Moura
Novamente achei seu texto muito bom e claro de se ler. Ele é fluido, "sem delongas" e está com referência da fonte principal de suas informações. Felizmente não tenho o que acrescentar.

Ensaio 7 - Aula dia 26/05/2017

Target audience: Graduation students.

The existence of sexual selection in plants is a controversial fact. One of the complications of this classification consists on the fact that even when the male structure is more attractive for pollinators, it does not imply on a widest range of pollination. In other words, the internal structure of the pollen will be more determinat to the reproductive success of the plant than the attraction of pollinatiors. This can be understood by the fact that a bigger number of pollinators do not necessarilly guarantee the fertilization. Therefore, comprehending the mechanisms of sexual selection in plants is not trivial, if htey are even existent. On the other hand, the concept of sexual selection is another questionable point, once it is not clear the limits between natural and sexual selection. Thus, this subject demands more study efforts and discussion to be better established.

Ensaio 8 - Aula dia 02/06/2017

Target audience: Graduation students.

The hill-climbing algorithm permits the search for the best tree in optimal methods of historical reconstruction (i.e. maximum likelihood – ML - and maximum parsimony - MP). The algorithm uses a previously generated tree as a basis (usually Wagner or NJ trees), and can be combined with the criteria which best fit your analysis. The basic principle of hill-climbing is that the algorithm searches of the tree with less steps (in the case of MP) or with the maximum likelihood (in the case of ML) in a a set of possible trees. The best trees are found when the algorithm reaches a hill top. However, some algorithms, such as the TBR and the SPR algorithms, do not come back down in the search of bigger hills (better trees) once they have reached a hill top. Therefore, rougher algorithms should be used as explorers of the set of trees, while more refined algorithms should be used only after you have a wider knowledge of your dataset.

Comentário por Livia Moura
Olá Flavia. Meu único conselho é referenciar suas ideias. De modo geral, ótimo texto.

Ensaio 9 – Aula dia 09/06/2017

Target audience: Graduation students.

Calibrating a phylogenetic tree is essential for the estimative of molecular clocks. The most usual way to calibrate trees is using fossil data. However, the use of this type of dataset should be adopted carefully, once fossils show some limitations. A fossil specimen can reveal a period in geological time when this extinct organism lived, but it cannot show the exact time when it appeared or was extinct. Therefore, the calibration should be followed by em error calculation or by a probability of the time span it englobed. Even with the error and/or probability estimates, it still is impossible to ensure an exact point of calibration. Anyway, it is important to have a model, to set a parameter of molecular clock analysis, even though the paleontological data is not the best one.

Ensaio 10 – Aula dia 23/06/2017

Reflexão sobre a disciplina

A disciplina correspondeu a minhas expectativas de forma mais positiva do que eu esperava. Eu esperava uma disciplina teórica na qual a grande maioria dos conceitos abordados em aula fossem familiares para mim, mas não foi o que aconteceu. Os conceitos em si eram familiares (na maioria das vezes), mas a forma como foram abordados foi muito mais interessante do que eu tinha imaginado. Gostei muito que víamos assuntos básicos sob um ângulo mais crítico e diferente do usual (para mim). Por isso, gostei muito da disciplina. O que foi mais positivo foi que comecei a questionar mais os conceitos e métodos que sei que vou usar durante meu projeto e durante a vida. O maior aprendizado para mim foi o questionamento em cima de tudo que falamos em ciência. Acho que o que mais gostei, na verdade, foi o fato de fazer uma disciplina em outra universidade que não a minha, com pessoas desconhecidas e com um backgroud muito diferente do meu, por termos formações diferentes. Este foi um dos motivos pelos quais fiquei mais satisfeita com essa experiência como um todo.
Quanto ao meu desempenho pessoal, sinto que comecei a questionar mais os conceitos e métodos que usamos em ciência no geral. Relembrei e aprofundei alguns assuntos. Ao longo da disciplina sinto que fiquei mais crítica tanto dentro como fora da sala de aula. Acho que melhorei algumas coisas que faço quando escrevo, como, por exemplo, não usar a retórica, que eu sinto que sempre usei muito (principalmente em introduções) e fazer frases mais curtas. O aspecto que eu poderia ter trabalhado melhor é quanto à participação em aula. Muitas vezes eu não me sentia a vontade de falar, principalmente porque muitos assuntos eram abordados de um ponto de vista completamente diferente do que eu tinha antes e, por isso, eu não conseguia raciocinar e elaborar uma pergunta, mesmo quando lia os textos antes da aula. Mas mesmo assim, deveria ter participado mais e lido mais textos antes da aula.
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