Jorge Alves Audino

Ensaio opcional

What is universal in Molecular Biology?
The central dogma of molecular biology is claimed to be universal, including all possible ways to process biological information. DNA, RNA and proteins are the key sources to maintain and move information forward. Transfers are based on replication, transcription and translation, including well-known mechanisms and some less understood pathways. Since its original formulation, the concept was expanded to include multiple possibilities. Consequently, the power of dogma's universality is to predict information flow in any condition. Additionally, if the dogma is universal, comparisons among organisms are possible, providing bases for phylogenetic and evolutionary investigations. In contrast, the genetic code is not universal, thus different organisms exhibit distinct modes of translation for numerous reasons. However, what may be a problem to establish general patterns also addresses very interesting questions about the evolution of the genetic code in different lineages. Finally, if universal or not, these very solid patterns in molecular biology are the crucial background to understand and study the diversity of life.

Correção por Domingo:

A sentença introductoria não é muito explicativa. Durante a leitura do texto enteiro não queda muito claro qual é o tema principal do texto. Só queda bem claro quando lé o titulo.

O comprimento das sentenças é correito.

Quando usa a palavra "Transfer" na frase "Transfers are based on replication, transcription and translation, including well-known mechanisms and some less understood pathways." parece que esta a falar de algum proceso biologico especifico. Igual é melhor escrever "Biological information is transfered based on replication…."

Ensaio 1

DNA replication and dichotomy thinking
In a very complex dichotomy, DNA duplication is the molecular process to make two double-strand molecules from a single one. Other complex dichotomic examples are endless, including behavioral decisions, reproductive strategies and use of environmental resources. Could DNA replication be related to the role of dichotomy in our tree thinking? The answer to this question is not simple, but some aspects of molecular evolution can explore this issue. Firstly, replication process is vital to life maintenance, assuring two new copies from a single model. Secondly, dichotomy in cellular biology also plays vital role in cell division. Expanding this pattern, heritage can be conceived as sequential dichotomies where each new generation is doubled compared to the previous. In a phylogenetic perspective, lineages are split into two through time in a historical dichotomic process (cladogenesis), which is central to our view of evolution and historical reconstruction. In other words, DNA replication, even in a small scale, has crucial importance to vertical heritage. Consequently, the methods and premises we currently use for historical inference of life are deeply linked to this dichotomic process.

Comentários da Flávia:

Gostei muito das palavras que você usou para ligar as frases. Achei bom o tamanho das frases também, não muito longos.
Eu só começaria a primeira frase direto com "DNA duplication is…" pois acho que dá mais força a sua frase.
Achei muito didática a forma como você escreveu em geral, muito bom :)

Ensaio 2

The major roles of genetic drifting in molecular evolution
Neutral theory in molecular evolution provides a simple explanatory framework to high divergences of substitution rates. The theory does not evoke natural selection to explain most patterns of diversity at the molecular level. In contrast, it simply assumes that stochastic events are responsible to the divergence of nucleotides. At first, this assumption may be surprising, but several lines of evidence corroborate this view. As mutations are mostly neutral or nearly neutral, genetic drift determines the likelihood of fixation. Of course, natural selection plays crucial roles in purifying and selecting mutations that increase fitness. Nevertheless, this process is far more restricted in terms of genome remodeling. As predicted by neutral theory, genetic drift is the major process driving molecular evolution.

Comentários Ana Laura

Texto com frases curtas e claras.
Você deveria substituir na frase “…responsible to the divergence of nucleotides….” ´to´ por ´for´.
Acho a frase "…At first, this assumption may be surprising, but several lines of evidence corroborate this view…" desnecessária.
Gostei muito do texto.

Ensaio 3

Audience: graduate students of biological sciences
Implications of effective population size in genetic drift
Genetic drift is an evolutionary process which magnitude is deeply related to effective population size (Ne). Considering the stochastic nature of this process, alleles frequencies float randomly until fixation or lost throughout generations. According to Ne, the impact of genetic drift can be dramatic. When Ne is high, genetic drift is buffered and alleles take long time to become fixed or lost. This pattern is expected even when the initial frequencies are different. On the other hand, when Ne is low, frequencies rapidly change and soon become fixed or lost. Consequently, reduction of Ne profoundly affects alleles fate. In contrast to natural selection, which magnitude is imposed by fitness, genetic drift is severely changed by Ne. Finally, molecular evolution is mostly driven by genetic drift and, consequently, Ne should be taken into account as a key factor modulating the impact of genetic stochastic processes.

Correção por Lucas Denadai de Campos

As frases estão curtas e explicam bem sobre o assunto.
Do meu ponto de vista, na terceira frase: "According to Ne…". Quando você usa "According to" passa a impressão de estar falando de alguém e não sobre um conceito. Talvez trocar essa palavra por algum sinônimo.

Ensaio 4

Audience: graduate students of biological sciences
Historical reconstructions as methodological tools
Historical reconstructions comprise methodological strategies to infer evolutionary relationships based on available evidence. In a broad sense, this approach provides a phylogenetic framework, which assumes evolutionary characteristics, such as ancestry and cladogenesis. Applications are endless and widely explored in biological sciences. But what is the goal in applying historical reconstructions? No simple answer could resolve this question, but most studies converge to similar purposes. Firstly, topologies are currently fundamental to elucidate classification systems. In other words, proposing groups (taxa) is one of the most fundamental tasks in biological sciences. In accordance, phylogenetic methods, and trees ultimately, offer useful hypotheses to this process. Secondly, historical reconstructions provide conditions to analyze a plethora of biological questions, such as morphological evolution and evolutionary rates. In summary, evolutionary trees are not theoretical endpoints, but instead, they represent the pathways and sometime the starting point to investigate biological problems.

Corrected by Deyvid

Ensaio está bem estruturado e tem uma sentença tópico que mostra logo qual será o assunto do texto. Frases estão curtas e de fácil entendimento. Talvez, a frase "no simple answer…" possa ser substituída por "there is not a simple answer" ou algo do tipo para deixar a frase mais simples.

Ensaio 5

Audience: graduate students of biological sciences
Should similarity methods be still in use?
Methods based on similarity such as neighbor-joining (NJ) have been used in phylogenetic studies since the last decades. Nevertheless, the use of a phenetic approach might seem controversial and illogical at a first glance. Why such methods are still in use when phylogenetic systematics have established the current methodological paradigm? The starting point to this issue is understanding what NJ is able to do with a given data and how it could be used. Of course, the method is not the analytical endpoint for any investigation. Instead, NJ is used to a rapid analysis of the dataset, providing conditions to identify anomalous information. In addition, phenetic methods were never completed leave aside, for example, they are also used to start alignment processes. In other words, such methods are used as shortcuts to start further systematics analyses. The main reason is their mathematical simplicity with low computational power. In summary, while NJ is severely limited in historical reconstructions, it still represents a valuable tool in data analysis.

Correção por Flávia

Bom texto, gosto da sentença tópico e da sentença que fecha o parágrafo. O conteúdo está bem colocado, com fluidez no texto. Só tomaria cuidado, devido ao público alvo, ao colocar palavras com as quais eles podem não estar familiarizados (como phenetic na segunda frase) sem explicar o significado, além de outras palavras que acho que não se encaixam muito bem na construção da sentença ('since' em "have been used in phylogenetic studies since the last decades" na primeira frase). No geral, está muito bom :)

Ensaio 6

Audience: ungraduate students of biological sciences
Parameters in historical reconstructions based on maximum likelihood
Phylogenetic inferences based on maximum likelihood explicit consider a set of parameters that should be known. These parameters represent elements that comprise the evolutionary model included in the likelihood calculation. In its turn, the model is an attempt to represent and fit the dataset, i.e., the reality. Firstly, the model for nucleotide substitutions is a set of parameters estimating the rate and type of molecular changes. The parameter gama can also be included in the model as a complementary fit for variance. Secondly, a three topology is also considered for each likelihood calculation. Lastly, length branches are parameters estimated for each dichotomy based on previous assumptions. Altogether, these parameters are a crucial part of the likelihood estimation, thus relating the premises to the final fit and explanatory power of the hypothesis.

Comentários por Bruno F. Lima (26/05): Olá Jorge. Utilizando os parâmetros discutidos em aula pelo professor, considero que o seu ensaio segue as premissas estabelecidas por ele: é claro, direto e faz uso de frases curtas e "topic sentences". Apenas não tenho certeza sobre o uso do termo "comprise", na sentença "… elements that comprise the evolutionary model…". Não acredito que esse seja o melhor termo a ser usado nesse contexto. À parte esse detalhe, seu ensaio está muito bom e, como afirmado, segue os parâmetros da escrita científica. Abraços!

Ensaio 7

Tradeoff in model selection
Current methods and criteria to select models of nucleotide substitution consider the number of parameters and the fitness provided by additional ones. In any model, more parameters tend to improve how the model fits the dataset. In other words, numerous parameters provide a fine adjustment of the model to represent the properties and nature of a given dataset. Nevertheless, overparametrization is problematic and reduces the explanatory power of a hypothesis. In addition, more parameters will greatly increase the computational work. In this context, different methods were created to effectively quantify how parameters contribute to the model fitness. Some criteria, including AIC and BIC, calculate the likelihood and fitness of the model, explicitly considering the number of parameters included. Therefore, the criteria penalize additional parameters, ranking the models and excluding unnecessary parameters. Subsequently, the tradeoff between parameter numbers and contribution is overcame in model selection for phylogenetic reconstruction.

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