Edgar Gamero Mora

Ensaio Opcional (03/10/17)

One of the most remarkable characteristics of the genetic code is their capacity of redundancy, meaning that most amino acids can be encoded by more than one three-base pair codon. Nucleotide base substitution occurs at different rates and have different consequences; thus, changes in the third codon base are most frequent than substitutions in the first and second positions. Commonly, a change in the third position does not lead to changes in the encoded amino acid. On the other hand, changes in first and second positions are always critical -specially in the second-; since they can originate point mutations, by encoding a different amino acid or by the appearance of stop codons, that may result in the translation of non-functional proteins. Since codon degeneracy is a natural mechanism to protect the genetic information against mutations and it is present in all living systems, this variation in the frequency of substitution has allowed to recover the phylogenetic signal for the reconstruction of evolutionary relations of organisms.

Comentário por Pietro
De forma geral eu considero o ensaio muito bom. A escrita está direta; a maior parte das frases apresentadas são curtas e diretas. Também pude identificar a ideia sentença tópico no começo do ensaio. Eu sugiro que se divida a primeira e a última sentença do ensaio em duas para que a escrita fique mais direta. As demais sentenças do ensaio estão boas e de acordo com esse conceito de escrita.

Ensaio 1 (03/17/17)

Before cell division occurs, DNA must be duplicated in order that each one of the daughter cells holds a copy of genetic material. The mechanism by which DNA is duplicated is called replication, and it is a semi-conservative process. DNA replication is referred as semi-conservative, because of one DNA molecule are created two identical replicas; each one conserving an original strand and a new one, which is synthesized by adding nucleotides that complement the template strand. DNA replication is not bug free, and errors can lead to mutations that can trigger different genetic diseases. It is therefore, that cells have mechanisms to check and repair faults during and after replication. Different pathways for DNA repair are present in all extant lineages, and they are vital for maintain the accuracy of replication, and with that life prosperity.

Comentários por Stefany A. de Angelis:
Senti falta de uma frase introdutória. Algo como "No Sign in as Wikidot user processo da Replicação genica[…]. Antes da divisão ocorrer[…]."
Nesta frase "DNA replication is not bug free[…]", eu escreveria: "This process is not bug free […]". Pois já está subentendido sobre o que o texto está falando, descrito anteriormente. Então para não ficar repetitivo, eu colocaria desta forma.
No mais, entendi perfeitamente!

Ensaio 2 (03/24/17)

Evolution is propelled for different forces. Nevertheless, it is usually associated only with one of them, the natural selection. That, as result of the big influence of Darwin in the understanding of the evolution theory. In this way, it can be difficult to think in evolution as result of other mechanisms than those inherent to adaptive values. However, between the processes that propel evolution, there are one of them more likely to occur, the genetic drift. The genetic drift is non selection-driven. Instead, it generates variation in allele frequency in a stochastic way, without any allele’s adaptive value. So that, it can result in the loss or fixation of alleles, even if they are harmless or not for populations. Today it is known, that there are so many variations generated by genetic drift, that most of them should be neutral. On the hand, variations by natural selection are less frequent. But, commonly with a greater probability of cause impact on the evolutionary history of organisms. Whatever the mechanism of evolution of which we speak, it is important to highlight they are not mutually exclusive. So, the interaction of different evolutionary forces influences the way in which history of populations is shaped.

Comentarios de Stefany A. de Angelis:
Consegui encontrar em seu texto os padrões de redação que estamos aprendendo em sala. Isso é muito bom. Torna o texto bem mais claro.
Só falta citas referências agora. Tanto no texto, para informar de onde veio aquela ideia, teoria ou hipótese. E também a referência no final, complementando a informação citada na redação.

Ensaio 3 (31/17/17)

Audience: graduate students

The effective population size can be defined as the part of a population that contributes genetically to the next generation. So, if all organisms of a populations were able to transmit their genetic information to next generation, the effective population size will be equal to the number of censored organisms. However, in order all the organisms of a population reproduce, the population should met certain requirements. For example, the number of males and females should be equal, all the organisms should have the same opportunity to reproduce themselves, and the generations must not have overlapping reproduction. Since it is impossible to fulfill all those assumptions. A long the years it has been developed different methods to estimate the effective population size; each one of them adapted to reduce the effect of the violated assumption.

Comentários Alfredo:
- "However, in order all the organisms" -> However, in order to all organisms";
- Boa escolha de tema;
- Foi bem escrito, frases curtas e claras;
- Assunto bem trabalhado;
- Condiz com o grupo alvo.

Ensaio 4 (05/05/17)

Audience: biology ungraduate students

Historical reconstructions in a phylogenetic context are used base on the fact that all linages descent from common ancestry. Nowadays, there are various methodologies developed to construct them based on different types of logical inferences. Independently of the optimality criterion used to create those tree, the results usually conclude with the graphical representation of those phylogenetic relationships. Namely, they have simply the aim to propose a classification. Even when it would be interesting that the results goes beyond to define terminal groups. It is undeniable that those results can be the base to solve other types of inquiries: such as, ancestral character state reconstruction or phylogeographic approaches. Representing then the starting point for other types of approaches according to the aim of the research.

Comentários de Lyslaine Sato:
O texto foi escrito com linguagem clara e objetiva. A topic sentence destaca o assunto tratado no parágrafo. O texto atende o público alvo.

Ensaio 6 (19/05/17)

Selfish genetic elements are different types of DNA sequences that can exist in the genome of any organism (e.g. homing endonuclease genes and transposons). All those elements perform self-replication for guarantee their persistence in the genome of their hosts. Also, they are able to use the cell mechanisms to proliferate. In this sense, one of their strategies is to cleave at homologous chromosome and trigger homologous recombination. Being therefore capable to survive processes that can eliminate them during DNA proofreading and repair. These are mobile elements and can move themselves to different positions in the genome, being this one of their mechanism of dispersion. Aspects such as their origin are still uncertain. However, nowadays it is known that these elements don’t have any contribution to the fitness of their hosts, but can have slightly deleterious effects on them.

Comentários Rosana Cunha:
- Texto muito bom Edgar, parabéns!
- Sua "topic sentence" está bem clara e objetiva.
- Sua linguagem, apesar de telegráfica, utilizou os elementos conectivos apropriados que deram fluidez à leitura.
- As ideias estão numa ordem de fácil entendimento do assunto pelo leitor.
- A única critica: na escrita formal não se deve usar a forma reduzida "don't" e sim "do not", ok!


Ensaio 7 (26/05/17)

Models of evolution in phylogenetic systematics
The development of methodologies to infer phylogenetic relationships using molecular data came with the implementation of mathematical approaches (e.g. Maximum Likelihood). In this sense, probability models have been used to estimate evolutionary rates of nucleotide and amino-acid substitution. Models of evolution can be as complex as the number of parameters they consider. In the case of nucleotide substitution models, only the number of transition and transversion provides 12 parameters. Although the use of most parameter rich model may help to get a best fit model. It is a fact that more parameters represent more assumptions in our reconstruction, which increase the number of requirements for ad hoc hypotheses. In this way, there are different methods that allow us to compare models (e.g. AIC, BIC). Those methods, give as output a list with a score for each one of the models on the set. Being on the top of the list, that one that only considers informative parameters.

Comentarios de Stefany:
-O texto está bem estruturado. Parabéns :)
-Eu fiquei com duvidas em pequenos trechos, como: "In the case of nucleotide substitution models, only the number of transition and transversion provides 12 parameters.", mas que não me impediu de compreender o restante do texto e nem o geral do que estava explicando. E eu considero isso um ponto positivo.
- Algumas virgulas eu não usaria. Mudaria a frase pra deixar a leitura mais fluida e sem essas pausas. Por exemplo " In this sense, probability […]"; 'In this way, there[…]"; " Those methods, give as output[…]"

Ensaio 8 (02/06/17)

Tree searching using algorithms
In order to determine the best topology, methods such as parsimony or maximum likelihood use an optimality criterion. So, the parsimony criterion helps to detect the the shortest tree; while, likelihood criterion serves to find the tree with the maximum value of likelihood. Since the number of possible results increase with the amount of terminals and characters employed in the analysis. It has been necessary to develop algorithms that reduce the computational time needed to find the best result. In this sense, a traditional algorithm used is the called Hill-Climbing (HC). This algorithm usually starts the search with a phylogeny created by neighbor joining. Then, the algorithm improves the above-mentioned reconstruction modifying one element by time. If that modification gives better results, a new modification is made. And so on until there are no possible improvements. However, it should be noted that HC can lead to problems. For example, always exist the risk to get stuck in a local optima. It is therefore, that usually the tree obtained by HC is used for subsequent refinement. The refinement stage includes the use of heuristic algorithms for tree rearrangements (e.g. SPR and TBR); which, perturb the HC result with the aim to ensure the arrived to a global optima.

Comentários por Juan Manuel

Olá Edgar!

Em termos gerais achei seu texto muito bem escrito. A sua frase inicial é uma boa indicação do que foi tratado no resto do texto. Você conseguiu utilizar frases curtas, mas sem deixar o texto muito cortado. Tal vez poderia tirar a pontuação que tem no final da segunda linha e começo da terceira: “…employed in the analysis. It has been…” Sera?
Só um errinho de digitação no final da primeira linha, tem um “the” repetido.
Parabéns pelo texto.

Juan Manuel

Ensaio 9 (09/06/17)

The neutral theory holds that evolutionary substitutions at the molecular level follow an approximately constant rate. This means, that divergence between two lineages increase as the time since they shared a common ancestor progress. This property, led some authors to conceive the idea that the degree of sequence divergence among species can be us as a molecular clock. In the field of systematics, it has been mainly used to date evolutionary transitions and for estimating divergence times. Some of the problems associated with the use of molecular clock are related with the disparity in rate of molecular evolution among taxa. To handle the different problems associated with the use of molecular clocks, there have been developed different kinds of methodologies for molecular clock calibration. Including the use of statistical approaches (such as maximum likelihood); which allowed the development of relaxed molecular clocks. Those models, take into account rate variation across lineages for obtaining better estimations of divergence times.

Ensaio 10 (23/06/17) Reflexão sobre a disciplina e auto-avaliação

Eu fiz a disciplina esperando aprender sobre princípios de evolução molecular. Fique conforme porque agora consegue entender sobre as implicações da evolução molecular nas reconstruções filogenéticas, e assim obteve as ferramentas necessárias para continuar estudando pela minha conta. Além disso, reafirmei os conhecimentos que tinha sobre sistemática filogenética e terminei por compreender alguns que não entendia. Achei boa a inciativa de incentivar a os estudantes a escrever toda aula, melhorei minha escrita. Disponibilizar os textos para toda a turma foi uma ótima ideia. Isso, porque mediante sua leitura, eu consegui entender de melhor forma alguns tópicos explicados na aula. Ainda quando perdi uma aula, eu li o material disponibilizado no site. Comparando o que eu sabia antes do curso e o que eu sei hoje em dia, considero que aproveite a disciplina. Portanto, minha autoavaliação é 1.

Com respeito a como poderia se melhorar a disciplina: as ultimas leituras poderiam ter sido disponibilizadas com mais antecedência. Ainda quando li textos por minha conta, algumas vezes não consegui entender totalmente as leituras obrigatórias, justamente por falta de tempo. Teria sido bom continuar recebendo observações gerais sobre a escrita durante o curso inteiro. Com respeito a os seminários, nalguns casos eu achei que a gente não conseguiu abordar o tópico desde uma perspectiva de evolução molecular.

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