Biological Thinking Research Articles

Using Research in a First Year Biology Class to Promote Critical Thinking

In their first semester students interested in majoring in the life sciences take an "Introduction to Biological Thinking" class to expose them to critical thinking and research questions and skills as well as some basic chemistry and biology. In the early part of the semester students are also introduced to the primary literature. Using National Science Foundation funded research on Malate Dehydrogenase, students learn how to analyze clustal results, develop a hypothesis and design a mutant to test the hypothesis. The students write a proposal and conduct the research before giving a presentation of the outcomes of the work. In the early part of the course and at the end of the course students are assessed for their understanding of what it takes to develop a hypothesis and design appropriate experiments to test the hypothesis and on their ability to use the primary literature. Significant gains in these skills are found. A number of the students go on to start independent research projects with faculty, and over 90% of the students indicate that they have a much better appreciation for what it takes to do science.This research is supported by a Grant from the National Science Foundation: MCB 0448905 to EB

Is cultivating “biological blindness” a viable route to understanding behavioral phenomena?

AbstractMitchell et al. propose that associative learning in humans and other animals requires the formation of propositions by means of conscious and controlled reasoning. This approach neglects important aspects of current thinking in evolutionary biology and neuroscience that support the claim that learning, here exemplified by fear learning, neither needs to be conscious nor controlled.

When the exception becomes the rule: The disappearance of limiting similarity in the Lotka–Volterra model

We investigate the transition between limiting similarity and coexistence of a continuum in the competitive Lotka–Volterra model. It is known that there exist exceptional cases in which, contrary to the limiting similarity expectation, all phenotypes coexist along a trait axis. Earlier studies established that the distance between surviving phenotypes is in the magnitude of the niche width 2 σ provided that the carrying capacity curve differs from the exceptional one significantly enough. In this paper we studied the outcome of competition for small perturbations of the exceptional (Gaussian) carrying capacity. We found that the average distance between the surviving phenotypes goes to zero when the perturbation vanishes. The number of coexisting species in equilibrium is proportional to the negative logarithm of the perturbation. Nevertheless, the niche width provides a good order of magnitude for the distance between survivors if the perturbations are larger than 10%. Therefore, we conclude that limiting similarity is a good framework of biological thinking despite the lack of an absolute lower bound of similarity.

Megaphylls, microphylls and the evolution of leaf development

Originally coined to emphasize morphological differences, 'microphyll' and 'megaphyll' became synonymous with the idea that vascular plant leaves are not homologous. Although it is now accepted that leaves evolved independently in several euphyllophyte lineages, 'megaphyll' has grown to reflect another type of homology, that of euphyllophyte leaf precursor structures. However, evidence from the fossil record and developmental pathways fails to indicate homology and suggests homoplasy of precursor structures. Thus, as I discuss here, 'megaphyll' should be abandoned because it perpetuates an unsupported idea of homology, leading to misconceptions that pervade plant biology thinking and can bias hypothesis and inference in developmental and phylogenetic studies. Alternative definitions are needed that are based on development and phylogeny for different independently evolved leaf types.

Community-based Inquiry Improves Critical Thinking in General Education Biology

National stakeholders are becoming increasingly concerned about the inability of college graduates to think critically. Research shows that, while both faculty and students deem critical thinking essential, only a small fraction of graduates can demonstrate the thinking skills necessary for academic and professional success. Many faculty are considering nontraditional teaching methods that incorporate undergraduate research because they more closely align with the process of doing investigative science. This study compared a research-focused teaching method called community-based inquiry (CBI) with traditional lecture/laboratory in general education biology to discover which method would elicit greater gains in critical thinking. Results showed significant critical-thinking gains in the CBI group but decreases in a traditional group and a mixed CBI/traditional group. Prior critical-thinking skill, instructor, and ethnicity also significantly influenced critical-thinking gains, with nearly all ethnicities in the CBI group outperforming peers in both the mixed and traditional groups. Females, who showed decreased critical thinking in traditional courses relative to males, outperformed their male counterparts in CBI courses. Through the results of this study, it is hoped that faculty who value both research and critical thinking will consider using the CBI method.

Superposition of Transcriptional Behaviors Determines Gene State

We introduce a novel technique to determine the expression state of a gene from quantitative information measuring its expression. Adopting a productive abstraction from current thinking in molecular biology, we consider two expression states for a gene - Up or Down. We determine this state by using a statistical model that assumes the data behaves as a combination of two biological distributions. Given a cohort of hybridizations, our algorithm predicts, for the single reading, the probability of each gene's being in an Up or a Down state in each hybridization. Using a series of publicly available gene expression data sets, we demonstrate that our algorithm outperforms the prevalent algorithm. We also show that our algorithm can be used in conjunction with expression adjustment techniques to produce a more biologically sound gene-state call. The technique we present here enables a routine update, where the continuously evolving expression level adjustments feed into gene-state calculations. The technique can be applied in almost any multi-sample gene expression experiment, and holds equal promise for protein abundance experiments.

El «factor humano» y la distribución sexual del trabajo en el discurso de la organización científica del trabajo (España, 1922-36)

During the first third of the twentieth century, and especially after the 1920s, a discourse on occupational hygiene and safety began to develop in Spain. This discourse, without rejecting the value of the work carried out in the factory environment, particularly stressed the need to take into account what was called the "human factor." Promoted mainly by the budding occupational doctors and psychologists, this discourse became part of both the lines of biological thinking of constitutional pathology as well as the economic ideas of the so-called OCT, and it expounded the need to take the somatic and psychic characteristics of people into account in order to carry out "rational" distribution of the same in the workplace. The article aims to highlight the way in which this discourse contained elements that would help to attribute specific roles within the workplace based on the biological and psychological characteristics of men and women, so facilitating the legitimisation of a sexual distribution of work which helped to reinforce the social organization of gender at that time.

Tree thinking cannot taken for granted: challenges for teaching phylogenetics.

Tree thinking is an integral part of modern evolutionary biology, and a necessary precondition for phylogenetics and comparative analyses. Tree thinking has during the 20th century largely replaced group thinking, developmental thinking and anthropocentricism in biology. Unfortunately, however, this does not imply that tree thinking can be taken for granted. The findings reported here indicate that tree thinking is very much an acquired ability which needs extensive training. I tested a sample of undergraduate and graduate students of biology by means of questionnaires. Not a single student was able to correctly interpret a simple tree drawing. Several other findings demonstrate that tree thinking is virtually absent in students unless they are explicitly taught how to read evolutionary trees. Possible causes and implications of this mental bias are discussed. It seems that biological textbooks can be an important source of confusion for students. While group and developmental thinking have disappeared from most textual representations of evolution, they have survived in the evolutionary tree drawings of many textbooks. It is quite common for students to encounter anthropocentric trees and even trees containing stem groups and paraphyla. While these biases originate from the unconscious philosophical assumptions made by authors, the findings suggest that presenting unbiased evolutionary trees in biological publications is not merely a philosophical virtue but has also clear practical implications.

Field and Transformation in Relation to Biological Form

Ideas about field and transformation are especially important in modem physics and have also made an impact of biological thinking in various ways. The purpose of this paper is to look at some integrative ideas in biology that access field and transformational thinking, particularly in relation to form. The paper begins with a brief consideration of some philosophical schools of thought that may and do influence thinking about form. This is followed by a consideration of relations between field and form in the work of Gurwitsch and Thompson. Finally, Thompson’s transformational approach to comparative forms is considered with regard to interactions between biological forms and their environments.

Brandom’s Demarcation of Logic

In my dissertation (which I wrote under Brandom's supervision), I argued that in order to understand the confused state of contemporary debates about the demarcation of logic, one has to go back to Kant.2 Following tradition, Kant thought of logic as a normative discipline, with the job of identifying norms for thought. On this broad construal, it makes sense to talk of (say) the logic of jurisprudence, or of geometrical thinking, or of biological thinking. Kant called these logics. But in addition to all the special logics, which provide of correct thinking as regards a certain kind of object, Kant recognized a logic, which provides rules for thought as such , regardless of its objects (and even regardless of whether it has an object). When Kant made his critical turn, the notion of general logic posed a serious problem for him. He held that concepts could have representational content (objective validity) only insofar as they applied to some object that could be given to us

Senescence Viewed through the Lens of Comparative Biology

Although mortality and longevity are inherently biological phenomena, their study has historically been the purview of demography and the actuarial sciences. An infusion of biological thinking into these disciplines transforms demography into biodemography and provides expectations and coherency to observations on age-determined mortality that would not be explainable otherwise. Comparative biology teaches us that reproduction is life's solution to the inevitability of death in the hostile environments of Earth. That solution, however, places a higher priority on investing physiological resources into reproduction that could otherwise have been used to maintain the soma (body) longer. As such, aging is an inescapable but inadvertent byproduct of imperfect maintenance and its attendant surveillance and repair. Biology also reveals that while bodies are not designed to fail, neither are they designed for extended operation. In other words, bodies are subject to biological warranty periods for normal operation. For sexually reproducing species, that warranty period includes the time from conception to sexual maturity, the production and nurturing of offspring, and a period of grand-parenting in some species. Humans are the only species capable of exploiting the loophole in the biological contract of life (bodies that are not designed to fail). Human ingenuity (science, medicine, public health) has produced interventions that manufacture survival time by delaying death, and in so doing, has created a phenomenon never before seen in the history of life-population aging (and all the societal and health consequences that go with it).

New Insights into Thyroid Stem Cells

Stem cells exhibit an extraordinary ability for self-renewal. They also give rise to many specialized cells. The potential of stem cells in regenerative medicine, developmental biology, and drug discovery has been well documented. Although advances in stem cell science have raised broad ethical concerns, it is clear that stem cell technology has revolutionized our thinking in modern biology and medicine and provided the basis for understanding many of the mechanisms controlling basic biological processes and disease mechanisms. This review details the nascent field of thyroid stem cell research, exploring the current status of thyroid stem cell differentiation from the perspectives of both developmental biology and cell replacement therapy. It highlights successes to date in the generation of thyroid follicular cells from embryonic stem cells in the laboratory and the identification and characterization of adult stem cells from human thyroid glands and thyroid cancers. Finally, it outlines future challenges with a focus on potential stem cell therapy for thyroid patients.

Systemic Metaphors and Integrative Biology

The purpose of this paper is to provide a conceptual framework for examining and integrating systemic thinking in biology through the analysis of a number of systemic metaphors. After a brief examination of the roles that systemic metaphors can play in model development, a general framework is presented for integrating a range of key constructs such as hierarchy and organisation as well as the scope for use of the ecosystem metaphor. The idea of an ecology of biological information is used to encapsulate general thinking about networks, hierarchies and nestings at various scales and times and this leads on to the role played by the cognitive system metaphor. After a discussion of a number of occurrences of the cognitive metaphor a complementary systemic metaphor - verb-glue-text - is discussed. The paper concludes with a brief look at some of the conceptual constraints related to this metaphor. In order to make the paper integrative a broad range of biological examples are discussed from molecules to ecosystems.

MODEL WEIGHTS AND THE FOUNDATIONS OF MULTIMODEL INFERENCE

Statistical thinking in wildlife biology and ecology has been profoundly influenced by the introduction of AIC (Akaike's information criterion) as a tool for model selection and as a basis for model averaging. In this paper, we advocate the Bayesian paradigm as a broader framework for multimodel inference, one in which model averaging and model selection are naturally linked, and in which the performance of AIC-based tools is naturally evaluated. Prior model weights implicitly associated with the use of AIC are seen to highly favor complex models: in some cases, all but the most highly parameterized models in the model set are virtually ignored a priori. We suggest the usefulness of the weighted BIC (Bayesian information criterion) as a computationally simple alternative to AIC, based on explicit selection of prior model probabilities rather than acceptance of default priors associated with AIC. We note, however, that both procedures are only approximate to the use of exact Bayes factors. We discuss and illustrate technical difficulties associated with Bayes factors, and suggest approaches to avoiding these difficulties in the context of model selection for a logistic regression. Our example highlights the predisposition of AIC weighting to favor complex models and suggests a need for caution in using the BIC for computing approximate posterior model weights.

‘A Dispassionate and Objective Effort:’ Negotiating the First Study on the Biological Effects of Atomic Radiation

The National Academy of Science's 1956 study on the Biological Effects of Atomic Radiation (BEAR) was designed to provide an objective analysis to assess conflicting statements by leading geneticists and by officials in the Atomic Energy Commission. Largely because of its status as a detached, non-governmental evaluation by eminent scientists, no studies have had a broader impact on the development of biological thinking in regard to nuclear policies. This paper demonstrates that despite the first BEAR study's reputation as an objective and independent study, it was the product of careful negotiation between Academy scientists, the Atomic Energy Commission, and Britain's Medical Research Council. This paper also reveals the fragility of the consensus that produced the Academy's report, the range of political uses of the report, and the subsequent disaffection of the scientists who took part in it.

From Cowards and Subversives to Aggressors and Questionable Allies: US Army Perceptions of Zionism since World War I

For most of the twentieth century, the attitudes and policies of the US army were consistently anti-Zionist. From World War I into the 1950s, army anti-Zionism was inextricably interrelated with a mutually reinforcing anti-Semitism that ranged from political and ethnic bias to extremist versions of biological racial and conspiratorial thinking. Army officers perceived Zionist objectives in the Middle East as detrimental to America's national interest regarding wartime security and geopolitical stability in a crucial region, as well as concerning oil resources and communist containment. In supporting Zionism and later Israel, America Jews revealed their suspected disloyalty. Although anti-Semitic concepts gradually disappeared from official army analyses, striking continuities remained in the army's anti-Zionist position. Until the end of the Cold War, the army rejected the “special relationship” argument based upon shared values or Israel as a military asset. The image of the cowardly, weak Jew incapable of establishing and defending a Jewish state in Palestine had been replaced by that of a militarily superior, potentially aggressive Israel destabilizing a strategic area.

What is healthy aging in the 21st century?

In the coming years, human aging will be one of the biggest challenges faced by industrialized countries. The average life expectancy is continuously increasing and we may be faced with spending more years in poor health. Because aging is a relatively modern phenomenon, we lack knowledge for a proper understanding of this process. Current biological thinking emphasizes that organisms are encoded for early survival and reproduction, humans not excluded. Aging is not programmed nor is it inevitable. Life span is the result of the interactions between genes and the environment in which we live. In the original habitat, genes encoding early survival and reproduction were optimized in an everlasting attempt to increase fitness and prevent the species from extinction. Aging is best explained as a cost of optimizing fitness because investments in body maintenance and repair cannot be maximized. The environment also determines how a gene influencing life span is expressed over a lifetime. When the conditions in which we live significantly improve, mortality decreases, evolutionary pressures for early survival and reproduction relax, and further resources can be invested in body maintenance and repair, which increases both average life expectancy and maximum life span. Increasing our understanding of the aging process and applying available interventions will help to protect and preserve healthy aging.

How Many Nodes Are Enough? The Breast Surgeon’s Dilemma

For most of the 20th century, surgeons believed axillary lymph node dissection (ALND) to be a therapeutic procedure for breast cancer, according to Halsted s notion that breast cancer metastasizes in series from the breast to the nodes and then from the nodes to distant organs. The ALND was thought to limit malignant spread by eliminating a critical pathway for cellular migration from the breast to distant sites. On the basis of the rationale that ‘‘bigger must be better,’’ surgeons considered the adequacy of their ALND to be measured by the degree to which the dissected axilla was left devoid of lymphatic and adipose tissue. Considered a necessary evil of proper surgical cancer care, lymphedema was largely ignored by the surgical community. This conceptual framework, while intellectually plausible, proved to be biologically flawed. Bernard Fisher in the United States and Umberto Veronesi in Europe led the groundbreaking randomized trials that have unequivocally proven breastconserving surgery to be equally effective to more extensive breast cancer resections in the reduction of breast cancer mortality. The breast-conservation trials were initially rejected by surgeons as counterintuitive and dangerous, because everyone ‘‘knew’’ that patients should undergo cancer surgery as soon as possible and with the largest feasible resection, ‘‘before the cancer spreads.’’ As surgeons gradually came to accept breast conservation, a new paradigm evolved in cancer biological thinking. It became obvious that cancers metastasize, not in series through the nodes to distant sites, but rather in parallel to the nodes (via lymphatics) and to distant organs (via the circulation). Realizing that hematogenous micrometastasis occurs early in the course of the disease, Fisher came to describe breast cancer as a fundamentally systemic disease. In line with the shifting biological paradigm, Fisher and others questioned the value of ALND other than for the purposes of cancer staging. Since then, the role of the ALND has been debated extensively, and no definite winner has been declared. ALND advocates have argued that lymphadenectomy still has therapeutic benefit for breast cancer patients because ALND facilitates regional control of axillary disease. Supporters contend that surgical extirpation of microscopic nodal metastases is curative without adjuvant chemotherapy in a subset of patients. Conversely, ALND dissenters maintain that overall survival, depending on the development of distant metastases, is not influenced by ALND in most patients. These opponents suggest that patients with microscopic axillary metastases can be cured by adjuvant chemotherapy, nodal irradiation, or both, without axillary dissection. The debate regarding the therapeutic benefit of ALND was rekindled with more recent reports based on Surveillance, Epidemiology, and End Results data suggesting that the number of removed nodes is associated with crude survival in patients with no or one to three positive nodes and that in node-negative patients, examination of fewer nodes is associated with an increased risk of death due to breast Received September 1, 2005; accepted September 8, 2005; published online January 30, 2006. Address correspondence and reprint requests to: Benjamin O. Anderson, MD, FACS; E-mail: banderso@u.washington.edu.

Who was the first genetic engineer?

This paper discusses how Gregor Mendel discovered the predictive law on the characteristics of the offspring through his power of observation and patience. Mendel's law, which has had a tremendous influence on medical and biological thinking, postulates that in the generation of hybrids one half of the progeny will breed true to the parental characteristics and the other half will be equally divided between offspring possessing only the dominant or the recessive characteristics. Mendel lived at a time when the first engineering schools were being created and the only degree granted was in civil engineering. However, if Mendel had lived at a time when bioengineering existed, he would undoubtedly be the first genetic engineer.

Curious Parallels and Curious Connections—Phylogenetic Thinking in Biology and Historical Linguistics

In The Descent of Man (1871), Darwin observed "curious parallels" between the processes of biological and linguistic evolution. These parallels mean that evolutionary biologists and historical linguists seek answers to similar questions and face similar problems. As a result, the theory and methodology of the two disciplines have evolved in remarkably similar ways. In addition to Darwin's curious parallels of process, there are a number of equally curious parallels and connections between the development of methods in biology and historical linguistics. Here we briefly review the parallels between biological and linguistic evolution and contrast the historical development of phylogenetic methods in the two disciplines. We then look at a number of recent studies that have applied phylogenetic methods to language data and outline some current problems shared by the two fields.