Thought Experiments in Biology

Unlike in physics, the category of thought experiment is not very common in biology. At least there are no classic examples that are as important and as well-known as the most famous thought experiments in physics, such as Galileo’s, Maxwell’s or Einstein’s. The reasons for this are far from obvious; maybe it has to do with the fact that modern biology for the most part sees itself as a thoroughly empirical discipline that engages either in real natural history or in experimenting on real organisms rather than fictive ones. While theoretical biology does exist and is recognized as part of biology, its role within biology appears to be more marginal than the role of theoretical physics within physics. It could be that this marginality of theory also affects thought experiments as sources of theoretical knowledge. Of course, none of this provides a sufficient reason for thinking that thought experiments are really unimportant in biology. It is quite possible that the common perception of this matter is wrong and that there are important theoretical considerations in biology, past or present, that deserve the title of thought experiment just as much as the standard examples from physics. Some such considerations may even be widely known and considered to be important, but were not recognized as thought experiments. In fact, as we shall see, there are reasons for thinking that what is arguably the single most important biological work ever, Charles Darwin’s On the Origin of Species, contains a number of thought experiments. There are also more recent examples both in evolutionary and non-evolutionary biology, as we will show. Part of the problem in identifying positive examples in the history of biology is the lack of agreement as to what exactly a thought experiment is. Even worse, there may not be more than a family resemblance that unifies this epistemic category. We take it that classical thought experiments show the following characteristics: They serve directly or indirectly in the non-empirical epistemic evaluation of theoretical propositions, explanations or hypotheses. Thought experiments somehow appeal to the imagination. They involve hypothetical scenarios, which may or may not be fictive. In other words, thought experiments suppose that certain states of affairs hold and then try to intuit what would happen in a world where these suppositions are true. We want to examine in the following sections if there are episodes in the history of biology that satisfy these criteria. As we will show, there are a few episodes that might satisfy all three of these criteria, and many more if the imagination criterion is dropped or understood in a lose sense. In any case, this criterion is somewhat vague in the first place, unless a specific account of the imagination is presupposed. There will also be issues as to what exactly “non-empirical” means. In general, for the sake of discussion we propose to understand the term “thought experiment” here in a broad rather than a narrow sense here. We would rather be guilty of having too wide a conception of thought experiment than of missing a whole range of really interesting examples

A Reproducible Study on Remote Heart Rate Measurement

This paper studies the problem of reproducible research in remote photoplethysmography (rPPG). Most of the work published in this domain is assessed on privately-owned databases, making it difficult to evaluate proposed algorithms in a standard and principled manner. As a consequence, we present a new, publicly available database containing a relatively large number of subjects recorded under two different lighting conditions. Also, three state-of-the-art rPPG algorithms from the literature were selected, implemented and released as open source free software. After a thorough, unbiased experimental evaluation in various settings, it is shown that none of the selected algorithms is precise enough to be used in a real-world scenario

Transcriptome analysis to investigate the link between obesity and its metabolic complications:type 2 diabetes and NASH

Wereldwijd zijn meer dan een half miljard mensen te dik. Dit is een enorm probleem, omdat zwaarlijvigheid vaak leidt tot ernstige ziekten zoals ouderdomssuikerziekte en Niet-Alcoholische SteatoHepatitis (NASH; soort leverontsteking). De oorzaak van de obesitas-epidemie ligt voor een belangrijk deel in de huidige “westerse” leefstijl. Maar ook erfelijke factoren (mutaties) in het DNA spelen een rol. UMCG-promovendus Marcel Wolfs ging op zoek naar genen die bepalen of iemand vatbaar is voor obesitas, ouderdomssuikerziekte en/of NASH. Voor zijn onderzoek verzamelde Wolfs negentig mensen met ernstige obesitas, van wie sommigen leden aan type 2 diabetes en/of NASH en anderen relatief gezond waren. Hij nam bij deze mensen vier soorten weefsel af die betrokken zijn bij het ziekteproces van type 2 diabetes en/of NASH: lever, skeletspier, subcutaan vet en visceraal vet. Op deze weefsels werd genoomwijde expressie analyse toegepast. Ook werden in deze mensen 1,2 miljoen DNA-mutaties in kaart gebracht. Wolfs identificeerde zes genen (THADA, PTPLB, MEST, CCNE2, NUCB2, ATP2B3) die hoogstwaarschijnlijk een causale rol spelen in het ziekteproces van ouderdomssuikerziekte. Ook bleek van drie genen (LEP, RARRES2 en ANGPT2) dat hun expressie in vetweefsel is gerelateerd aan NASH. Verder stelde Wolfs vast dat, in vetweefsel, expressie van genen betrokken bij het immuunsysteem is gerelateerd aan ouderdomssuikerziekte. Tenslotte vond hij een groot aantal verbanden tussen mutaties in het DNA en de expressie van genen. Vervolgonderzoek naar de functies van de bovengenoemde genen zal de kennis over ouderdomssuikerziekte en NASH vergroten, hetgeen kan bijdragen aan de ontwikkeling van nieuwe therapieën

Thought Experiments in Biology

Unlike in physics, the category of thought experiment is not very common in biology. At least there are no classic examples that are as important and as well-known as the most famous thought experiments in physics, such as Galileo’s, Maxwell’s or Einstein’s. The reasons for this are far from obvious; maybe it has to do with the fact that modern biology for the most part sees itself as a thoroughly empirical discipline that engages either in real natural history or in experimenting on real organisms rather than fictive ones. While theoretical biology does exist and is recognized as part of biology, its role within biology appears to be more marginal than the role of theoretical physics within physics. It could be that this marginality of theory also affects thought experiments as sources of theoretical knowledge. Of course, none of this provides a sufficient reason for thinking that thought experiments are really unimportant in biology. It is quite possible that the common perception of this matter is wrong and that there are important theoretical considerations in biology, past or present, that deserve the title of thought experiment just as much as the standard examples from physics. Some such considerations may even be widely known and considered to be important, but were not recognized as thought experiments. In fact, as we shall see, there are reasons for thinking that what is arguably the single most important biological work ever, Charles Darwin’s On the Origin of Species, contains a number of thought experiments. There are also more recent examples both in evolutionary and non-evolutionary biology, as we will show. Part of the problem in identifying positive examples in the history of biology is the lack of agreement as to what exactly a thought experiment is. Even worse, there may not be more than a family resemblance that unifies this epistemic category. We take it that classical thought experiments show the following characteristics: (1) They serve directly or indirectly in the non-empirical epistemic evaluation of theoretical propositions, explanations or hypotheses. (2) Thought experiments somehow appeal to the imagination (so a purely mechanical deduction or calculation from theoretical principles would not count as a thought experiment). (3) They involve hypothetical scenarios, which may or may not be fictive. In other words, thought experiments suppose that certain states of affairs hold (irrespectively of whether they obtain in the actual world or not) and then try to intuit what would happen in a world where these suppositions are true. We want to examine in the following sections if there are episodes in the history of biology that satisfy these criteria. As we will show, there are a few episodes that might satisfy all three of these criteria, and many more if the imagination criterion (2) is dropped or understood in a lose sense. In any case, this criterion is somewhat vague in the first place, unless a specific account of the imagination is presupposed. There will also be issues as to what exactly “non-empirical” means. In general, for the sake of discussion we propose to understand the term “thought experiment” here in a broad rather than a narrow sense here. We would rather be guilty of having too wide a conception of thought experiment than of missing a whole range of really interesting examples

Studies towards the total synthesis of Herbimycin A

Herbimycin A (1) belongs to the ansamycin family and is a 19-membered lactam with seven stereogenic centres, making it a synthetic challenge, which was first isolated in 1979 by Omura et al. Herbimycin A (1) exhibits a broad spectrum of biological activities: herbicidal, inhibitor of angiogenesis and of the maturation of growth factor receptor tyrosine kinases. Figure 1 - Herbimycin A (for figure see pdf) Since its discovery, only three total syntheses of Herbimycin A (1) have been described in the literature, along with the syntheses of advanced fragments. This thesis describes a new route to Herbimycin A (1), using a wide range of chemical reactions than those used in the previous routes from the literature. The main idea is to split Herbimycin A (1) into an aromatic fragment and an aliphatic fragment as shown below in Scheme 1. Scheme 1 - Retrosynthesis highlighting both aromatic and aliphatic fragments (for figure see pdf) The synthesis of aliphatic fragment (4) follows up the work of Ansell and Pietsch, past members of the Parsons group. Interesting results could be obtained and a wide range of Organic Chemistry reactions could be investigated

Deep Models and Shortwave Infrared Information to Detect Face Presentation Attacks

This paper addresses the problem of face presentation attack detection using different image modalities. In particular, the usage of short wave infrared (SWIR) imaging is considered. Face presentation attack detection is performed using recent models based on Convolutional Neural Networks using only carefully selected SWIR image differences as input. Conducted experiments show superior performance over similar models acting on either color images or on a combination of different modalities (visible, NIR, thermal and depth), as well as on a SVM-based classifier acting on SWIR image differences. Experiments have been carried on a new public and freely available database, containing a wide variety of attacks. Video sequences have been recorded thanks to several sensors resulting in 14 different streams in the visible, NIR, SWIR and thermal spectra, as well as depth data. The best proposed approach is able to almost perfectly detect all impersonation attacks while ensuring low bonafide classification errors. On the other hand, obtained results show that obfuscation attacks are more difficult to detect. We hope that the proposed database will foster research on this challenging problem. Finally, all the code and instructions to reproduce presented experiments is made available to the research community

The High-Quality Wide Multi-Channel Attack (HQ-WMCA) database

The High-Quality Wide Multi-Channel Attack database (HQ-WMCA) database extends the previous Wide Multi-Channel Attack database(WMCA), with more channels including color, depth, thermal, infrared (spectra), and short-wave infrared (spectra), and also a wide variety of attacks

A novel statistical generative model dedicated to face recognition

In this paper, a novel statistical generative model to describe a face is presented, and is applied to the face authentication task. Classical generative models used so far in face recognition, such as Gaussian Mixture Models (GMMs) and Hidden Markov Models (HMMs) for instance, are making strong assumptions on the observations derived from a face image. Indeed, such models usually assume that local observations are independent, which is obviously not the case in a face. The presented model hence proposes to encode relationships between salient facial features by using a static Bayesian Network. Since robustness against imprecisely located faces is of great concern in a real-world scenario, authentication results are presented using automatically localised faces. Experiments conducted on the XM2VTS and the BANCA databases showed that the proposed approach is suitable for this task, since it reaches state-of-the-art results. We compare our model to baseline appearance-based systems (Eigenfaces and Fisherfaces) but also to classical generative models, namely GMM, HMM and pseudo-2DHMM. (C) 2009 Elsevier B.V. All rights reserved

The impact of urban gardening on household food security: evidence from Makhanda East, Eastern Cape Province, South Africa

Urban gardening in townships is a common coping strategy employed by poor inhabitants to improve food security, earn income through sales, and generate cost-savings through home consumption of fresh produce. Food security is a cornerstone of human development and welfare, and the achievement thereof remains a global challenge. The majority of academic research and policy documentation traditionally positions food insecurity as a rural phenomenon. However, recent trends point to an increase in food insecurity in urban areas, particularly in low-income areas such as townships. In South Africa, rapid urbanization has led to burgeoning townships and rapidly expanding low-income informal settlements characterised by poverty, unemployment, and food insecurity. Research concerned with the role that urban agricultural production plays in contributing to the food security of poor households is scarce and not well understood. This research, therefore, aimed to contribute to the limited research which specifically examines urban food security, and the role urban agriculture play in the achievement of household food security. The study employed collective action theory and utility theory to firstly provides an in-depth examination of the determinants of participation in urban gardening using Probit regression modeling. The second research objective was to perform an impact evaluation of participation in urban gardening on selected household food security indicators including Household Dietary Diversity Scores (HDDS), the Household Hunger Scale (HHS) and the Coping Strategy Index (CSI) using Propensity Score Matching (PSM). Purposive and snowball sampling methods were employed to obtain a sample of 60 urban gardeners and a control group of 55 non-gardening households from Extension 6, 7 and 10 townships as well as Joza Location in Makhanda East, Eastern Cape Province. Households were surveyed using a structured household food security questionnaire. A focus group discussion was held with the Linomtha Community Garden members and key informant interviews were undertaken with important stakeholders such as the local extension officers. Descriptive analysis revealed that urban gardening households (UGs) had older household heads who were less educated, and that land and water availability were the dominant constraints to increases in agricultural production. Results from the probit and average marginal effects models showed that the likelihood of participation significantly increased when household unemployment and dependency increased and that households who were engaged in off-farm economic activity were more likely to participate in urban gardening. The impact evaluation was performed using PSM and Average Treatment Effect on the Treated (ATT). Analysis illustrated that participation in urban gardening does significantly reduce both the full CSI and Reduced CSI. Thus, participation in urban gardening improves the food security of participating households by significantly reducing the frequency of participating households (UGs) applying undesirable coping strategies such as sending children elsewhere other than the household, borrowing food from other households and reducing the number of meals eaten in a day due to food shortages. This study posits that urban gardening alone will not eradicate the rampant food insecurity and poverty which pervades in South Africa’s townships. However, urban gardening participation does contribute to the construction of a sustainable, urban livelihood by reducing the number and severity of the undesirable coping strategies that food insecure households employ by providing some nutritious produce as well improved social capital through gardening networks and supporting institutions. It is recommended that policy makers, at a national and municipal level, need to create a clearer directive for the integration of urban food production into the urban food marketplace thus increasing access to income generating channels for small-scale home, and community gardeners. Co-operation between private and public institutions for food security and urban gardeners needs to be fostered and awareness of opportunities to participate in urban gardens needs to be improved. Central to the developmental challenges that rapid increases in urbanization and food insecurity in poor urban areas, is the need for national and local governments to improve access to economic opportunities in township areas - both in urban agriculture and in other, skills intensive sectors.Thesis (MEcon) -- Faculty of Commerce, Economics and Economic History, 202