Bruno Fancio Lima

Ensaio opcional (10/03)

The discovery of the tridimensional structure of the DNA marked the beginning of the study of how this molecule can lead to the formation of a protein. Francis Crick proposed, then, the Central Dogma of Molecular Biology, which states a linear flux of the genetic information. Primarily, it is stored in the DNA molecule, that leads to the formation of a RNA molecule, which is “translated” by the ribossome into a protein by the use of a code, called “genetic code”. Crick received some criticism regarding the use of the word “Dogma”, because it was argued that it would be a “non scientific” word. However, researchs developed since the proposal of the Dogma confirmed the almost universality of the genetic code, along with some special cases, like the capacity of the RNA to form DNA or another RNA. Interesting and intriguing questions are still waiting to some response, like the universality of the code itself (that is, why it is universal) and how it could have arised and evolved.

Revisão:

Olá Bruno.
Aplicando os critérios sugeridos pelo Daniel, creio que sua primeira frase não vai direto ao ponto, não se enquadraria como um "topic sentence".
Suas sentenças são curtas e precisas, isso é bom.
No mais, o seu texto apresenta uma contextualização histórica da discussão em torno do dogma central que foi fácil de fácil entendimento.
Atenciosamente
Marcos

Ensaio 01 (17/03)

The mismatch repair is one of the most important mechanisms to fix the DNA strand. It consists in the substitution of a region that is near a mismatched base in the DNA sequence. The process begins when a protein complex recognizes a base that do not pair with the complementary base, located in the opposite strand of DNA. After that, a second complex cut the region that is neighboring this incorrect base. Finally, the DNA polymerase connects the correct nucleotides in the chopped strand. A special enzyme called ligase binds these newly added nucleotides together, restoring the DNA molecule. This mechanism is widely distributed in prokaryotes, although it can also be found in eukaryotes. It is proposed that, in these organisms, the mismatch repair mechanism originated via lateral transfer from mitochondrial genomes.

Revisão:

Oi Bruno! Em geral achei seu ensaio bem escrito. Você utiliza bem o "topic sentence", mas me deu a impressão de que às vezes a propria frase fica cortada por virgulas. Por exemplo: "It is proposed that, in these organisms, the…" Seguindo as sugestões do professor, seria bom repensar essa frase tentando evitar o uso das duas virgulas. Eu também tendo a escrever com muita virgula e percebi que é porque eu vou falando a minha ideia e escrevendo ao mesmo tempo, isso me leva a botar virgula cada que eu paro de falar… Talvez ajude!
Uma última dúvida: Será que ficou faltando um "WAS" nesta frase: the mismatch repair mechanism "WAS" originated via lateral…

Atenciosamente
Juan Manuel Vidal

Ensaio 02 (24/03)

The neutral theory of molecular evolution proposes that the majority of the mutations do not affect the phenotype of the organism (Kimura 1968, King & Jukes 1969). Kimura proposed this idea measuring the rate of nucleotide substitution of the hemoglobin gene. He discovered that this value is much higher than the expected. The only explanation is that the majority of this mutation can only be neutral. Before this finding, researchers thought that the mutations only fix in the genome due to its adaptive value. The proposal of the neutral theory lead to the development of the concept called "genetic drift". It proposes that stochastics processes drive the evolution of genetic sequences. In this sense, selection could have only the purpose of removing deleterious mutations. This type of selection is called "purifying selection".

References:
Kimura, M. 1968. Evolutionary Rate at the Molecular Level. Nature, 217:624.
King, J.L.; Jukes, T.H. 1969. Non-Darwinian Evolution. Science 164:788-97.

Achei que suas frases, são claras e bem diretas e apresentam uma idéia única. seu ensaio tem um pouco cara do "telegraph" e acho que pode trabalhar com conectivos para juntar ideias. Senti falta de uma conclusão, me deu a impressão de ter bastante informação, porem não muito desenvolvida.
e especificamente nessa frase : "The only explanation is that the majority of this mutation can only be neutral", achei muito determinista ou faltou referenciar.
Corrigido por Maila

Ensaio 03 (31/03)

A large set of parameters can determine the fate of a genetic mutation. These can be the adaptive value of the mutation, its initial frequency, or factors related to the population size under analysis. In this sense, the effective size of the population (Ne) is a very important concept. It is the number of individuals of a population contributing to the formation of the next generation (Charlesworth 2009). The population size can affect the strength of the genetic drift, which is the stochastic fluctuation of a mutation frequency across generations. This process is stronger in populations with reduced Ne. This can lead to the fixation of alleles that the natural selection can remove in large populations, with a lesser influence of the genetic drift.

References:
Charlesworth, B. 2009. "Effective population size and patterns of molecular evolution and variation." Nature Reviews Genetics 10.3: 195-205.

Comentário por Pietro Vicari (05/05)
Olá Bruno. Gostei das suas frases, sempre curtas e bem diretas. Apesar de não haver muitos conectivos as frases escolhidas dão fluidez ao texto. Não está com cara de telegráfo. Entretanto seria interessante trabalhar um pouco mais essa questão. Também senti falta de uma conclusão em seu ensaio. Ela pode conversar com a sequência tópico para dar um fechamento ao assunto tratado. Parabéns pelo seu desenvolvimento.

Ensaio 04 (05/05)

Systematics analysis is an important field in Evolutionary Biology. It has the objective of uncover the evolutionary relationships among biological entities. These relationships are based in the assumption that, due to evolution, living beings share common ancestors. The product of this analysis is the development of a phylogenetic tree, or cladogram. This diagram represents, graphically, the relationships among a certain group of individuals. However, there is some misunderstandings about the interpretation of these figures (Sandvik 2008). A major problem regarding the analysis of these cladograms is the developmental thinking. It is the view that evolution follows a tendency towards the appearance of human beings; in other words, it is the teleological idea that evolution has an objective (O’hara 1997). Some teaching strategies were developed to solve this problem, which is found between students of all levels of learning (Baum & Offner 2008).

References:

Baum D. A. & Offner S. 2008. Phylogenics & tree-thinking. The American Biology Teacher, 70:222–229.
O’hara R. J. 1997. Population thinking and tree thinking in systematics. Zoologica Scripta, 26:323–329.
Sandvik H. 2008. Tree thinking cannot taken for granted: challenges for teaching phylogenetics. Theory in Biosciences, 127:45–51.

Corrigido por Marcos

Olá novamente Bruno.

Cara, não encontrei nada que pudesse indicar para melhorar seu ensaio. Suas frases são curtas e precisas, suas ideias estão bem expostas e bem redondinhas. Muito bom, parabéns.

Ensaio 05 (12/05)

The number of possible phylogenetic trees (cladograms) increases exponentially with the rise in number of terminals. It turns unpractical to find all the possible trees in the case of a high number of taxonomic units under analysis. Because of this, search methods have arisen to find the most likely trees in the universe of all the possible trees. One of these methods is the exhaustive search. It is based in the reconstruction of all the possible trees given a certain number of terminals and the finding of the most correct one. However, the high number of cladograms make this exhaustive method very hard to apply. An alternative is the use of heuristic methods to find the most suitable tree. Instead of constructing all the trees and find the better one, a heuristic method builds only a certain number of trees. The trees constructed will be based on certain parameters, defined in algorithms. This reduces the number of possible trees and makes the analysis and the finding of the correct tree easier.

Comentários Giulia

Gostei muito do seu texto. Ele tem um objetivo bem claro e simples. Só tem algumas frases um pouco longas que talvez daria para dividir em duas.

Ensaio 06 (19/05)

Maximum likelihood is one method to estimate the reliability of a phylogenetic tree. This methodology constructs the tree that maximizes the likelihood of a data set, given a certain model of evolution. In this sense, a tree constructed by Maximum Likelihood reflects a topology that, additionally with a certain model, results in the data set. Different Models can be used, like: different rates of evolution according to the position of a base in the codon, different probabilities of substitution of one base to another or the dichotomization model of a phylogenetic tree. In resume, ML proves to be one important method to assess the certainty of a proposed cladistics reconstruction.

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