Publications - Gabriel Dall'Alba

[Feature Article] When we Become the Seekers

Gabriel Dall'Alba*, Guilherme Brambatti Guzzo* (* equal contribution)

Free Inquiry 2025

In this article, we explore the fascinating case of Leon Festinger's "When we Become the Seekers". It serves as a scaffold to reason philosophically about our beliefs and how to navigate them. We dive deeply into the story of the so-called Seekers, and tackle ideas such as "A belief is a part of me, so what?". This article was featured and also is available in Audio edition.

[Feature Article]

[Feature Article] When we Become the Seekers

Gabriel Dall'Alba*, Guilherme Brambatti Guzzo* (* equal contribution)

Free Inquiry 2025

In this article, we explore the fascinating case of Leon Festinger's "When we Become the Seekers". It serves as a scaffold to reason philosophically about our beliefs and how to navigate them. We dive deeply into the story of the so-called Seekers, and tackle ideas such as "A belief is a part of me, so what?". This article was featured and also is available in Audio edition.

[Feature Article]

[M.Sc. Thesis] Toward a comprehensive understanding of early metazoans : reannotation for enhanced completeness of the ctenophore Mnemiopsis leidyi genome

Gabriel Dall'Alba

University of British Columbia 2024

The genome of the ctenophore Mnemiopsis leidyi, a marine species of gelatinous zooplankton, was recently re-analyzed to obtain a more complete and gap-free DNA sequence. This updated survey uncovered an additional 50 million base pairs, expanding the known genetic material of this organism. Using state-of-the-art methods, we systematically labeled and interpreted different regions of the genome. We explored the repetitive sequences within the genome, providing insights into the evolutionary trajectory of ctenophore genomes. In addition, we successfully identified previously missing genes and analyzed complex regions of the genome that are traditionally difficult to resolve. Finally, through genomic comparative studies, the present M. leidyi assembly and annotation results are consistent with previous research placing the ctenophore as the earliest branching lineage in animal evolution.

[Thesis]

[M.Sc. Thesis] Toward a comprehensive understanding of early metazoans : reannotation for enhanced completeness of the ctenophore Mnemiopsis leidyi genome

Gabriel Dall'Alba

University of British Columbia 2024

The genome of the ctenophore Mnemiopsis leidyi, a marine species of gelatinous zooplankton, was recently re-analyzed to obtain a more complete and gap-free DNA sequence. This updated survey uncovered an additional 50 million base pairs, expanding the known genetic material of this organism. Using state-of-the-art methods, we systematically labeled and interpreted different regions of the genome. We explored the repetitive sequences within the genome, providing insights into the evolutionary trajectory of ctenophore genomes. In addition, we successfully identified previously missing genes and analyzed complex regions of the genome that are traditionally difficult to resolve. Finally, through genomic comparative studies, the present M. leidyi assembly and annotation results are consistent with previous research placing the ctenophore as the earliest branching lineage in animal evolution.

[Thesis]

[Feature Article] Science Does Not Have All the Answers—and This Is Not a Problem

Gabriel Dall'Alba*, Guilherme Brambatti Guzzo* (* equal contribution)

Skeptical Inquirer 2024

In this article, we explore the philosophical framework that claiming "science does not have all the answers" as an argument against the validity of a scientific idea is misleading. Instead, we argue that it is part of the ethos of science to not have all the answers.

[Feature Article]

[Feature Article] Science Does Not Have All the Answers—and This Is Not a Problem

Gabriel Dall'Alba*, Guilherme Brambatti Guzzo* (* equal contribution)

Skeptical Inquirer 2024

In this article, we explore the philosophical framework that claiming "science does not have all the answers" as an argument against the validity of a scientific idea is misleading. Instead, we argue that it is part of the ethos of science to not have all the answers.

[Feature Article]

[Book Chapter] Nature's Imposters: Mimicry.

Diego Castellan Elias*, Gabriel Dall'Alba* (* equal contribution)

E-Book - Science to be read in schools 2023

We propose a K-12-level activity to teach mimicry as a fascinating example of evolutionary principles. Students are set to think critically and scientifically on grounds of natural selection, phenotype, genotype, populations, and more in a simple exercise.

[E-Book]

[Book Chapter] Nature's Imposters: Mimicry.

Diego Castellan Elias*, Gabriel Dall'Alba* (* equal contribution)

E-Book - Science to be read in schools 2023

We propose a K-12-level activity to teach mimicry as a fascinating example of evolutionary principles. Students are set to think critically and scientifically on grounds of natural selection, phenotype, genotype, populations, and more in a simple exercise.

[E-Book]

[Book Chapter] Clustering for bacterial promoter sequences: DNA Sequences Clusterizer tool

Gabriel Dall'Alba

E-Book - From Biology to Biotecnology 2023

I provide a in-depth tutorial on how to use a clustering tool called DNA Sequences Clusterizer, created at the University of Caxias do Sul, and that I have extensively used during my undergraduate studies. It pipelines from data extraction to results analysis in a user-friendly way, with no coding needed.

[E-Book]

[Book Chapter] Clustering for bacterial promoter sequences: DNA Sequences Clusterizer tool

Gabriel Dall'Alba

E-Book - From Biology to Biotecnology 2023

I provide a in-depth tutorial on how to use a clustering tool called DNA Sequences Clusterizer, created at the University of Caxias do Sul, and that I have extensively used during my undergraduate studies. It pipelines from data extraction to results analysis in a user-friendly way, with no coding needed.

[E-Book]

[Review] A Survey of Biological Data in a Big Data Perspective

Gabriel Dall'Alba*, Pedro Lenz Casa*, Fernanda Pessi de Abreu, Daniel Luis Notari, Scheila de Avila e Silva (* equal contribution)

Big Data 2022

In this article, we look at the literature to explore how big data technologies are being applied in biology. With the continuous growth of available data, the concept of big data has gained importance, supported by technologies like cloud computing for infrastructure and NoSQL for storage. We examine how machine learning methods—such as decision trees, support vector machines, neural networks, and clustering—are used for data analysis. Our goal is to provide a clear overview of how information technology concepts (like storage, analysis, and data sharing) are connected to and applied within biological research.

[Paper]

[Review] A Survey of Biological Data in a Big Data Perspective

Gabriel Dall'Alba*, Pedro Lenz Casa*, Fernanda Pessi de Abreu, Daniel Luis Notari, Scheila de Avila e Silva (* equal contribution)

Big Data 2022

In this article, we look at the literature to explore how big data technologies are being applied in biology. With the continuous growth of available data, the concept of big data has gained importance, supported by technologies like cloud computing for infrastructure and NoSQL for storage. We examine how machine learning methods—such as decision trees, support vector machines, neural networks, and clustering—are used for data analysis. Our goal is to provide a clear overview of how information technology concepts (like storage, analysis, and data sharing) are connected to and applied within biological research.

[Paper]

[Original Book Review] LAATS, A.; SIEGEL, H. Teaching evolution in a creation nation. Chicago: The University of Chicago Press, 2016.

Guilherme Brambatti Guzzo, Gabriel Dall'Alba

Revista Conjectura 2022

We review the book Teaching evolution in a creation nation, by Harvey Siegel and Adam Laats (https://press.uchicago.edu/ucp/books/book/chicago/T/bo22541379.html). We discuss how the book adds valuable insights that are helpful to the fostering of philosophy of education discussions, as it tackles a most controversial topic in its nature: the teaching of evolution in face of stonewalls placed by fundamentalist religion. The authors argue, and we agree, that teaching in scientific grounds must be made according to the strength of evidence in favour of an idea, not due to social or cultural reasons. And claiming that introducing evolution in schools is a social, not a scientific matter, is controversial.

[Direct download]

[Original Book Review] LAATS, A.; SIEGEL, H. Teaching evolution in a creation nation. Chicago: The University of Chicago Press, 2016.

Guilherme Brambatti Guzzo, Gabriel Dall'Alba

Revista Conjectura 2022

We review the book Teaching evolution in a creation nation, by Harvey Siegel and Adam Laats (https://press.uchicago.edu/ucp/books/book/chicago/T/bo22541379.html). We discuss how the book adds valuable insights that are helpful to the fostering of philosophy of education discussions, as it tackles a most controversial topic in its nature: the teaching of evolution in face of stonewalls placed by fundamentalist religion. The authors argue, and we agree, that teaching in scientific grounds must be made according to the strength of evidence in favour of an idea, not due to social or cultural reasons. And claiming that introducing evolution in schools is a social, not a scientific matter, is controversial.

[Direct download]

[Original Research Paper] The importance of qualified communication of ideas on science education

Gabriel Dall'Alba*, Guilherme Brambatti Guzzo* (* equal contribution)

Revista Interdisciplinar de Ciência Aplicada 2022

Science education involves several features that are beyond the so-called products of science: ideas, theories, hypotheses, laws, and results. Any education that aims the full comprehension of science as a human endeavor should incorporate epistemic qualities of the nature of science in the teaching of scientific content. One strategy for promoting the transmission of these features is the formal employment of qualification of ideas through guarding terms. Here, we discuss some of the epistemic features of science and their connection to the qualification of ideas in classrooms: epistemic fallibilism, open-mindedness, and the ongoing review process. We argue that the employment of terms and sentences that better reveal the strength of the existing evidence for a given idea can better reflect the presence of those science features on the scientific process. The substitution of terms such as “proven” or “it was proven that” by “probable” or “evidence suggests that” can better describe the epistemic status of scientific ideas, which are not fixed between true or false, but contained in a complex spectrum of likelihood. Strengthening science education with emphasis on the understanding of the nature of science can help to fix modern problems, such as the increasing distrust in science and in their products, such as vaccines and pharmaceutical drugs, as well as helping to reasonably dose the strength of the belief on those ideas.

[Paper]

[Original Research Paper] The importance of qualified communication of ideas on science education

Gabriel Dall'Alba*, Guilherme Brambatti Guzzo* (* equal contribution)

Revista Interdisciplinar de Ciência Aplicada 2022

Science education involves several features that are beyond the so-called products of science: ideas, theories, hypotheses, laws, and results. Any education that aims the full comprehension of science as a human endeavor should incorporate epistemic qualities of the nature of science in the teaching of scientific content. One strategy for promoting the transmission of these features is the formal employment of qualification of ideas through guarding terms. Here, we discuss some of the epistemic features of science and their connection to the qualification of ideas in classrooms: epistemic fallibilism, open-mindedness, and the ongoing review process. We argue that the employment of terms and sentences that better reveal the strength of the existing evidence for a given idea can better reflect the presence of those science features on the scientific process. The substitution of terms such as “proven” or “it was proven that” by “probable” or “evidence suggests that” can better describe the epistemic status of scientific ideas, which are not fixed between true or false, but contained in a complex spectrum of likelihood. Strengthening science education with emphasis on the understanding of the nature of science can help to fix modern problems, such as the increasing distrust in science and in their products, such as vaccines and pharmaceutical drugs, as well as helping to reasonably dose the strength of the belief on those ideas.

[Paper]

[Book Chapter] Science as a process: Critical Thinking and Scientific through the lens of Biotechnology

Gabriel Dall'Alba

Biotechnology in Schools: Educational Practices for Basic Education 2022

I explore the overlap between teaching practices in science classrooms with classic biotechnology examples. I first explore the philosophical background of science education and what epistemic virtues are best candidates to be integrated in classrooms. Then, I propose the activity of "thinking like a scientist", using insulin as a classic example of biotechnology advancements that allows students to step into the shoes of seasoned scientists. I finish with a philosophical reasoning exercise of why the activity is beneficial to the teaching of science.

[Book]

[Book Chapter] Science as a process: Critical Thinking and Scientific through the lens of Biotechnology

Gabriel Dall'Alba

Biotechnology in Schools: Educational Practices for Basic Education 2022

I explore the overlap between teaching practices in science classrooms with classic biotechnology examples. I first explore the philosophical background of science education and what epistemic virtues are best candidates to be integrated in classrooms. Then, I propose the activity of "thinking like a scientist", using insulin as a classic example of biotechnology advancements that allows students to step into the shoes of seasoned scientists. I finish with a philosophical reasoning exercise of why the activity is beneficial to the teaching of science.

[Book]

[Original Research Paper] Science as a process: epistemic lessons from the pandemic

Guilherme Brambatti Guzzo*, Gabriel Dall'Alba* (* equal contribution)

Actio - Docência em Ciência 2021

Studying science means more than simply coming into contact with its products—that is, with ideas, hypotheses, theories, and scientific conclusions. It also involves understanding the processes through which scientific products are proposed, justified, evaluated, revised, established, or discarded. One of the most prominent ways to approach science as a process is through the study of historical cases. In this article, we argue that the novel coronavirus pandemic constitutes one such case, as it offers an interesting glimpse into at least three fundamental elements of scientific processes and, more broadly, the nature of science: the social character of the scientific enterprise, the caution required when dealing with claims of authority, and epistemic fallibilism. We identify and reflect on these three elements based on the work of scientists during the COVID-19 pandemic and, finally, offer suggestions on how they can be incorporated into science classes at schools and universities.

[Paper]

[Original Research Paper] Science as a process: epistemic lessons from the pandemic

Guilherme Brambatti Guzzo*, Gabriel Dall'Alba* (* equal contribution)

Actio - Docência em Ciência 2021

Studying science means more than simply coming into contact with its products—that is, with ideas, hypotheses, theories, and scientific conclusions. It also involves understanding the processes through which scientific products are proposed, justified, evaluated, revised, established, or discarded. One of the most prominent ways to approach science as a process is through the study of historical cases. In this article, we argue that the novel coronavirus pandemic constitutes one such case, as it offers an interesting glimpse into at least three fundamental elements of scientific processes and, more broadly, the nature of science: the social character of the scientific enterprise, the caution required when dealing with claims of authority, and epistemic fallibilism. We identify and reflect on these three elements based on the work of scientists during the COVID-19 pandemic and, finally, offer suggestions on how they can be incorporated into science classes at schools and universities.

[Paper]

[Book Chapter] Applications of Neural Networks

Rafael Vieira Coelho*, Gabriel Dall'Alba*, Scheila de Avila e Silva* (* equal contribution)

E-Book - Bioinformatics: Computational Context and Applications 2020

We provide a detailed overview of Artificial Neural Networks applied to Bioinformatics research, with emphasis on prokaryote sequence prediction, including existing approaches, limitations, and future outcomes of the field.

[E-Book]

[Book Chapter] Applications of Neural Networks

Rafael Vieira Coelho*, Gabriel Dall'Alba*, Scheila de Avila e Silva* (* equal contribution)

E-Book - Bioinformatics: Computational Context and Applications 2020

We provide a detailed overview of Artificial Neural Networks applied to Bioinformatics research, with emphasis on prokaryote sequence prediction, including existing approaches, limitations, and future outcomes of the field.

[E-Book]

[E-Book] Bioinformatics: Computational Context and Applications

Gabriel Dall'Alba*, Scheila de Avila e Silva*, Daniel Luis Notari* (* equal contribution)

EDUCS - Caxias do Sul 2020

We organized this book with the aim of bringing students and professionals from biology, computer science, and related fields closer to Bioinformatics, offering an overview of its concepts and applications through the expertise of professors and researchers from its various domains. We divided the book into two sections: Computational Foundations and Applications. Thus, the reader will first find a technical conceptualization of computational methodologies and approaches, followed by the ways in which these are employed in academic research. Additionally, the reader will find an up-to-date and exemplary reference from the literature on Bioinformatics. We hope that this book will further foster interest in Bioinformatics and serve as both an example and a theoretical reference regarding the important role this field has played — and will continue to play — in research, as well as its potential.

[E-Book]

[E-Book] Bioinformatics: Computational Context and Applications

Gabriel Dall'Alba*, Scheila de Avila e Silva*, Daniel Luis Notari* (* equal contribution)

EDUCS - Caxias do Sul 2020

We organized this book with the aim of bringing students and professionals from biology, computer science, and related fields closer to Bioinformatics, offering an overview of its concepts and applications through the expertise of professors and researchers from its various domains. We divided the book into two sections: Computational Foundations and Applications. Thus, the reader will first find a technical conceptualization of computational methodologies and approaches, followed by the ways in which these are employed in academic research. Additionally, the reader will find an up-to-date and exemplary reference from the literature on Bioinformatics. We hope that this book will further foster interest in Bioinformatics and serve as both an example and a theoretical reference regarding the important role this field has played — and will continue to play — in research, as well as its potential.

[E-Book]

[Original Research Paper] Toward Algorithms for Automation of Postgenomic Data Analyses: Bacillus subtilis Promoter Prediction with Artificial Neural Network

Rafael Vieira Coelho, Gabriel Dall'Alba, Scheila de Avila e Silva, Sergio Echeverrigaray, Ana Paula Longaray Delamare

OMICS: A Journal of Integrative Biology. 2020

There is a great unmet need for automation and algorithms to aid in analyses of big data, in biology in particular. We report here an original neural network approach for recognition and prediction of Bacillus subtilis promoters. The artificial neural network used as input 767 B. subtilis promoter sequences, while also aiming at identifying the architecture, provides the most optimal prediction. Two multilayer perceptron neural network architectures offered the highest accuracy, one with five, and another with seven neurons in the hidden layer. Each architecture achieved an accuracy of 98.57% and 97.69%, respectively. The results collectively indicate the promise of the application of neural network approaches to the B. subtilis promoter recognition problem, while also suggesting the broader potential of algorithms for automation of data analyses in the postgenomic era.

[Paper]

[Original Research Paper] Toward Algorithms for Automation of Postgenomic Data Analyses: Bacillus subtilis Promoter Prediction with Artificial Neural Network

Rafael Vieira Coelho, Gabriel Dall'Alba, Scheila de Avila e Silva, Sergio Echeverrigaray, Ana Paula Longaray Delamare

OMICS: A Journal of Integrative Biology. 2020

There is a great unmet need for automation and algorithms to aid in analyses of big data, in biology in particular. We report here an original neural network approach for recognition and prediction of Bacillus subtilis promoters. The artificial neural network used as input 767 B. subtilis promoter sequences, while also aiming at identifying the architecture, provides the most optimal prediction. Two multilayer perceptron neural network architectures offered the highest accuracy, one with five, and another with seven neurons in the hidden layer. Each architecture achieved an accuracy of 98.57% and 97.69%, respectively. The results collectively indicate the promise of the application of neural network approaches to the B. subtilis promoter recognition problem, while also suggesting the broader potential of algorithms for automation of data analyses in the postgenomic era.

[Paper]

[Original Research Paper] Bibliometric Study on Bioinformatics: A Survey in the Brazilian Library of Theses and Dissertations

Gabriel Dall'Alba, Gustavo Sganzerla Martinez, Nicole Anne Modena, Morgana Menegotto, Rosiendi Polesello Menin, Pedro Lenz Casa, Scheila de Avila e Silva

NBC, Periódico Científico do Núcleo de Biociências 2019

This paper aims to present an analysis of publications related to Bioinformatics found on the Brazilian Biblioteca Digital de Teses e Dissertações (BDTD). In order to do this, we conducted a bibliometric study of quantitative nature and descriptive character. A total of 594 records were collected and quantified by the amount of publications, their type and the institution of origin. We identified that the main source of bioinformatics publications takes shape of master theses in the country. Also, biological structures prediction was the main topic found among the studies.

[Currently Unavailable (email me for a copy)]

[Original Research Paper] Bibliometric Study on Bioinformatics: A Survey in the Brazilian Library of Theses and Dissertations

Gabriel Dall'Alba, Gustavo Sganzerla Martinez, Nicole Anne Modena, Morgana Menegotto, Rosiendi Polesello Menin, Pedro Lenz Casa, Scheila de Avila e Silva

NBC, Periódico Científico do Núcleo de Biociências 2019

This paper aims to present an analysis of publications related to Bioinformatics found on the Brazilian Biblioteca Digital de Teses e Dissertações (BDTD). In order to do this, we conducted a bibliometric study of quantitative nature and descriptive character. A total of 594 records were collected and quantified by the amount of publications, their type and the institution of origin. We identified that the main source of bioinformatics publications takes shape of master theses in the country. Also, biological structures prediction was the main topic found among the studies.

[Currently Unavailable (email me for a copy)]

[Original Research Paper] Analysis of the nucleotide content of Escherichia coli promoter sequences related to the alternative sigma factors

Gabriel Dall'Alba, Pedro Lenz Casa, Daniel Luis Notari, Andre Gustavo Adami, Sergio Echeverrigaray - Scheila de Avila e Silva

Wiley - Journal of Molecular Recognition 2019

Currently, promoter prediction still poses many challenges due to the characteristics of these sequences. In this paper, the nucleotide content of Escherichia coli promoter sequences, related to five alternative σ factors, was analyzed by a machine learning technique in order to provide profiles according to the σ factor which recognizes them. For this, the clustering technique was applied since it is a viable method for finding hidden patterns on a data set. As a result, 20 groups of sequences were formed. Evidence was found of an overlap between the functions of the genes regulated by different σ factors, suggesting that DNA structural properties are also essential parameters for further studies. These found patterns should be considered for implementing computational prediction tools.

[Paper]

[Original Research Paper] Analysis of the nucleotide content of Escherichia coli promoter sequences related to the alternative sigma factors

Gabriel Dall'Alba, Pedro Lenz Casa, Daniel Luis Notari, Andre Gustavo Adami, Sergio Echeverrigaray - Scheila de Avila e Silva

Wiley - Journal of Molecular Recognition 2019

Currently, promoter prediction still poses many challenges due to the characteristics of these sequences. In this paper, the nucleotide content of Escherichia coli promoter sequences, related to five alternative σ factors, was analyzed by a machine learning technique in order to provide profiles according to the σ factor which recognizes them. For this, the clustering technique was applied since it is a viable method for finding hidden patterns on a data set. As a result, 20 groups of sequences were formed. Evidence was found of an overlap between the functions of the genes regulated by different σ factors, suggesting that DNA structural properties are also essential parameters for further studies. These found patterns should be considered for implementing computational prediction tools.

[Paper]

[Book Chapter] Synthetic Biology and Metabolic Engineering for Developing Solutions in Biotechnology

Mauricio Schiavo, Gabriel Dall'Alba, Mauricio Moura da Silveira, Sergio Echeverrigaray

Atena Editora - Biological Sciences in Healthcare and Contemporaneity 2 2019

Advances in molecular biology, bioinformatics, and omics sciences have driven the development of synthetic biology and metabolic engineering, two fields with transformative potential in biotechnology. These technologies are being applied across industries—from reducing costs and environmental impact in biorefineries, to enabling gene therapies in medicine, and producing nutrients and additives in food through engineered microorganisms. This work aims to organize recent developments and applications in both fields, highlighting current innovations and future prospects that may shift technological and societal paradigms.

[Book Chapter]

[Book Chapter] Synthetic Biology and Metabolic Engineering for Developing Solutions in Biotechnology

Mauricio Schiavo, Gabriel Dall'Alba, Mauricio Moura da Silveira, Sergio Echeverrigaray

Atena Editora - Biological Sciences in Healthcare and Contemporaneity 2 2019

Advances in molecular biology, bioinformatics, and omics sciences have driven the development of synthetic biology and metabolic engineering, two fields with transformative potential in biotechnology. These technologies are being applied across industries—from reducing costs and environmental impact in biorefineries, to enabling gene therapies in medicine, and producing nutrients and additives in food through engineered microorganisms. This work aims to organize recent developments and applications in both fields, highlighting current innovations and future prospects that may shift technological and societal paradigms.

[Book Chapter]

[Original Research Paper] What is an ideal critical thinker expected to conclude about anthropogenic global warming?

Guilherme Brambatti Guzzo*, Gabriel Dall'Alba* (* equal contribution)

Philosophical Inquiry in Education 2017

Critical thinking involves the ability to properly assess statements and actions, and it also requires a permanent disposition to appropriately use cognitive skills in the evaluation of any claim. In the present paper, we discuss the characteristics of an ideal critical thinker, and apply them to a contemporary problem, namely anthropogenic global warming (AGW, a hypothesis that accounts for the increase of the average temperature of Earth as a consequence of human activities), in order to discuss what an ideal critical thinker is expected to conclude about the occurrence of this phenomenon. We assume that an ideal critical thinker is able to find out where the most reliable information regarding a certain issue is, is competent to reasonably evaluate it, and has an inclination to calibrate her beliefs according to the results of the inquiry. We thus conclude that an ideal critical thinker is expected to accept the current scientific consensus that AGW is occurring, albeit considering this issue, as well as virtually any other idea, open to revision. The fact that in many occasions people are selective in using critical thinking skills, such as when they reject the massive evidence of AGW, should be a cause of concern for educators, who should motivate their students to think critically about any problem and question they encounter; this, in turn, could help the students to develop a better understanding of the world, take more reasonable courses of action, and be protected against misinformation.

[Paper]

[Original Research Paper] What is an ideal critical thinker expected to conclude about anthropogenic global warming?

Guilherme Brambatti Guzzo*, Gabriel Dall'Alba* (* equal contribution)

Philosophical Inquiry in Education 2017

Critical thinking involves the ability to properly assess statements and actions, and it also requires a permanent disposition to appropriately use cognitive skills in the evaluation of any claim. In the present paper, we discuss the characteristics of an ideal critical thinker, and apply them to a contemporary problem, namely anthropogenic global warming (AGW, a hypothesis that accounts for the increase of the average temperature of Earth as a consequence of human activities), in order to discuss what an ideal critical thinker is expected to conclude about the occurrence of this phenomenon. We assume that an ideal critical thinker is able to find out where the most reliable information regarding a certain issue is, is competent to reasonably evaluate it, and has an inclination to calibrate her beliefs according to the results of the inquiry. We thus conclude that an ideal critical thinker is expected to accept the current scientific consensus that AGW is occurring, albeit considering this issue, as well as virtually any other idea, open to revision. The fact that in many occasions people are selective in using critical thinking skills, such as when they reject the massive evidence of AGW, should be a cause of concern for educators, who should motivate their students to think critically about any problem and question they encounter; this, in turn, could help the students to develop a better understanding of the world, take more reasonable courses of action, and be protected against misinformation.

[Paper]

[Original Research Paper] Science and Education: A Perspective of Didactic Transposition with Bioinformatics Concepts

Gabriel Dall'Alba, Guilherme Brambatti Guzzo, Scheila de Avila e Silva

International Journal for Infonomic 2016

This paper emerges as a follow up from my presentation at the 2016 Canada International Conference on Education (https://ciceducation.org/). The large amount of scientific information available nowadays challenges the capacity of students to deal appropriately with it. This may result in a loss of interest on the subject and, thus, create a gap between scientific ideas and the students. In order to avoid this, didactic transposition and interdisciplinary methods might bring in new thoughts on how science education can be improved. In this paper, we discuss the application of those ideas by using Bioinformatics as an example, as it has been an emerging field that is based on interdisciplinary approaches. By improving the teaching of complex ideas and theories, it is possible that the student’s relationship with science, as well as with the educators, may be improved.

[Article]

[Original Research Paper] Science and Education: A Perspective of Didactic Transposition with Bioinformatics Concepts

Gabriel Dall'Alba, Guilherme Brambatti Guzzo, Scheila de Avila e Silva

International Journal for Infonomic 2016

This paper emerges as a follow up from my presentation at the 2016 Canada International Conference on Education (https://ciceducation.org/). The large amount of scientific information available nowadays challenges the capacity of students to deal appropriately with it. This may result in a loss of interest on the subject and, thus, create a gap between scientific ideas and the students. In order to avoid this, didactic transposition and interdisciplinary methods might bring in new thoughts on how science education can be improved. In this paper, we discuss the application of those ideas by using Bioinformatics as an example, as it has been an emerging field that is based on interdisciplinary approaches. By improving the teaching of complex ideas and theories, it is possible that the student’s relationship with science, as well as with the educators, may be improved.

[Article]

[Original Article] The Role of Educators in Desacralizing Ideas

Guilherme Brambatti Guzzo*, Gabriel Dall'Alba* (* equal contribution)

Humanist Perspectives - 197 2016

From the Editorial: "All of us, at some point or another, have been (or are, or will be) wrong in a belief. Sometimes the correction is quick and painless, but sometimes – often in cases where the belief has become a pillar of personal identity – it is neither. Sometimes these beliefs are considered sacred and not up for discussion. So how do we discuss the undiscussable? Guilherme Brambatti Guzzo and Gabriel Dall’Alba tackle this question in their article “The Role of Educators in Desacralizing Ideas,” on page 8. (Sneak preview: Do it gently!)".

[Article]

[Original Article] The Role of Educators in Desacralizing Ideas

Guilherme Brambatti Guzzo*, Gabriel Dall'Alba* (* equal contribution)

Humanist Perspectives - 197 2016

From the Editorial: "All of us, at some point or another, have been (or are, or will be) wrong in a belief. Sometimes the correction is quick and painless, but sometimes – often in cases where the belief has become a pillar of personal identity – it is neither. Sometimes these beliefs are considered sacred and not up for discussion. So how do we discuss the undiscussable? Guilherme Brambatti Guzzo and Gabriel Dall’Alba tackle this question in their article “The Role of Educators in Desacralizing Ideas,” on page 8. (Sneak preview: Do it gently!)".

[Article]

[Original Research Paper] In silico analysis of Escherichia coli promoters recognised by the σ28 factor

Gabriel Dall'Alba*, Scheila de Avila e Silva*, André Gustavo Adami, Sergi Echeverrigaray (* equal contribution)

SaBios - Revista de Saúde e Biologia 2016

Prokaryotic gene transcription is tightly regulated, with σ factors like σ28 guiding RNA polymerase to specific promoters related to bacterial motility and pathogenicity. This study applied k-means clustering to group E. coli promoter sequences recognized by σ28 and analyzed the clusters using WebLogo, STRING-DB, and Gene Ontology. The resulting clusters showed promoter sequence compositions that diverge from the canonical biological pattern, and protein-protein interaction analysis indicated that cellular function is not directly linked to promoter nucleotide structure. These results highlight the complexity of transcriptional regulation and suggest that promoter sequence alone may not predict functional protein associations.

[Paper]

[Original Research Paper] In silico analysis of Escherichia coli promoters recognised by the σ28 factor

Gabriel Dall'Alba*, Scheila de Avila e Silva*, André Gustavo Adami, Sergi Echeverrigaray (* equal contribution)

SaBios - Revista de Saúde e Biologia 2016

Prokaryotic gene transcription is tightly regulated, with σ factors like σ28 guiding RNA polymerase to specific promoters related to bacterial motility and pathogenicity. This study applied k-means clustering to group E. coli promoter sequences recognized by σ28 and analyzed the clusters using WebLogo, STRING-DB, and Gene Ontology. The resulting clusters showed promoter sequence compositions that diverge from the canonical biological pattern, and protein-protein interaction analysis indicated that cellular function is not directly linked to promoter nucleotide structure. These results highlight the complexity of transcriptional regulation and suggest that promoter sequence alone may not predict functional protein associations.

[Paper]