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531 results on '"Speijer, Dave"'

6. A Realistic Model under which the Genetic Code is Optimal

Author

Buhrman, Harry, van der Gulik, Peter T. S., Klau, Gunnar W., Schaffner, Christian, Speijer, Dave, and Stougie, Leen

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics
Abstract

The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic code which reflects the error robustness of that code. By comparing this value with a distribution of values belonging to codes generated by random permutations of amino acid assignments, the level of error robustness of a genetic code can be quantified. We present a calculation in which the standard genetic code is shown to be optimal. We obtain this result by (1) using recently updated values of polar requirement as input; (2) fixing seven assignments (Ile, Trp, His, Phe, Tyr, Arg, and Leu) based on aptamer considerations; and (3) using known biosynthetic relations of the 20 amino acids. This last point is reflected in an approach of subdivision (restricting the random reallocation of assignments to amino acid subgroups, the set of 20 being divided in four such subgroups). The three approaches to explain robustness of the code (specific selection for robustness, amino acid-RNA interactions leading to assignments, or a slow growth process of assignment patterns) are reexamined in light of our findings. We offer a comprehensive hypothesis, stressing the importance of biosynthetic relations, with the code evolving from an early stage with just glycine and alanine, via intermediate stages, towards 64 codons carrying todays meaning., Comment: 22 pages, 3 figures, 4 tables Journal of Molecular Evolution, July 2013

Published
2013
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14. How mitochondrial cristae illuminate the important role of oxygen during eukaryogenesis.

Author

Speijer, Dave

Subjects
*MITOCHONDRIA, *ELECTRON transport, *UNICELLULAR organisms, *MITOCHONDRIAL membranes, *OXYGEN, *ELECTROPHILES
Abstract

Inner membranes of mitochondria are extensively folded, forming cristae. The observed overall correlation between efficient eukaryotic ATP generation and the area of internal mitochondrial inner membranes both in unicellular organisms and metazoan tissues seems to explain why they evolved. However, the crucial use of molecular oxygen (O2) as final acceptor of the electron transport chain is still not sufficiently appreciated. O2 was an essential prerequisite for cristae development during early eukaryogenesis and could be the factor allowing cristae retention upon loss of mitochondrial ATP generation. Here I analyze illuminating bacterial and unicellular eukaryotic examples. I also discuss formative influences of intracellular O2 consumption on the evolution of the last eukaryotic common ancestor (LECA). These considerations bring about an explanation for the many genes coming from other organisms than the archaeon and bacterium merging at the start of eukaryogenesis. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Calmly coasting towards complete collapse.

Author

Speijer, Dave

Subjects
*EMERGENCY management, *POLITICAL philosophy, *BYSTANDER effect (Psychology), *BIOLOGISTS, *SUSTAINABILITY
Abstract

The editorial in BioEssays discusses the urgent need for action in the face of ecological, climate, and societal disasters. The author highlights psychological aspects contributing to our dangerous inertia, such as diffusion of responsibility and the bystander effect. Powerful forces, including tech bros and media moguls advocating for unsustainable consumption, are identified as obstacles to change. The author calls for a reduction in consumption and population growth, emphasizing the importance of spreading scientifically based insights and combating misinformation to secure a sustainable future. [Extracted from the article]

Published
2025
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24. Protease resistance of food proteins: a mixed picture for predicting allergenicity but a useful tool for assessing exposure

Author

Akkerdaas, Jaap, Totis, Muriel, Barnett, Brian, Bell, Erin, Davis, Tom, Edrington, Thomas, Glenn, Kevin, Graser, Gerson, Herman, Rod, Knulst, Andre, Ladics, Gregory, McClain, Scott, Poulsen, Lars K., Ranjan, Rakesh, Rascle, Jean-Baptiste, Serrano, Hector, Speijer, Dave, Wang, Rong, Pereira Mouriès, Lucilia, Capt, Annabelle, and van Ree, Ronald

Published
2018
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31. "Social Darwinism" revisited.

Author

Speijer, Dave

Subjects
*NATURAL selection, *GENETIC drift, *BIOLOGICAL evolution, *TOP predators, *LIFE (Biology)
Abstract

The article discusses the misuse of the terms "Darwinian" and "Darwinism" in public discourse, particularly in relation to the concept of "Social Darwinism." The author argues that this limited understanding of evolution fails to acknowledge the role of symbiosis, cooperation, altruism, and empathy in the process. The article also highlights the importance of chance and luck in evolution, emphasizing that these factors are often overlooked in favor of selection. The author suggests that a correct understanding of nature could help combat societal issues such as racism and sexism, and criticizes the belief that wealth and success are inherently deserved. [Extracted from the article]

Published
2024
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42. How germline genes promote malignancy in cancer cells.

Author

Bruggeman, Jan Willem, Koster, Jan, van Pelt, Ans M. M., Speijer, Dave, and Hamer, Geert

Subjects
CANCER cells, GERM cells, MEIOSIS, GENES, CANCER genes, CARCINOGENESIS
Abstract

Cancers often express hundreds of genes otherwise specific to germ cells, the germline/cancer (GC) genes. Here, we present and discuss the hypothesis that activation of a "germline program" promotes cancer cell malignancy. We do so by proposing four hallmark processes of the germline: meiosis, epigenetic plasticity, migration, and metabolic plasticity. Together, these hallmarks enable replicative immortality of germ cells as well as cancer cells. Especially meiotic genes are frequently expressed in cancer, implying that genes unique to meiosis may play a role in oncogenesis. Because GC genes are not expressed in healthy somatic tissues, they form an appealing source of specific treatment targets with limited side effects besides infertility. Although it is still unclear why germ cell specific genes are so abundantly expressed in cancer, from our hypothesis it follows that the germline's reproductive program is intrinsic to cancer development. [ABSTRACT FROM AUTHOR]

Published
2023
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