Biology - Rudy Garns on Diigo

Apr

20

2012

Species Concepts | EvoEcoLab, Scientific American Blog Network

blogs.scientificamerican.com/...species-concepts

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species concepts evolution biology

Dec

5

2011

Biological Information (Stanford Encyclopedia of Philosophy)

plato.stanford.edu/...information-biological

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information biology gene evolution

Many biologists think of the developmental processes by which organisms progress from egg to adult in terms of the execution of a “developmental program.
major transitions in evolution depend on expansions in the amount and accuracy with which information is transmitted across the generations.
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- an informational “domain” that exists alongside the domain of matter and energy
- anything is a source of information if it has a range of possible states, and one variable carries information about another to the extent that their states are physically correlated
- although contemporary mainstream biology is an overtly materialist field, it has come to employ concepts that philosophers will recognize as intentional or semantic ones, concepts
- Genes are crucial to both explaining the development of individual organisms, and to explaining the inheritance of characteristics across generations.
- the familiar chart representing the “genetic code,” that maps triplets of the DNA bases (C, A, T, G) to individual amino acids, which are the building blocks of protein molecules.
- In the weaker sense, informational connections between events or variables involve no more than ordinary correlations (or perhaps correlations that are “non-accidental” in some physical sense involving causation or natural laws).
- For Shannon, anything is a source of information if it has a number of alternative states that might be realized on a particular occasion. And any other variable carries information about the source if its state is correlated with the state of the source.
- there is no sense in which biological processes are being explained in terms of the use or manipulation of information
- The appeal to information has an inferential use that is no way explanatory.
- The term “causal” information is also sometimes used to refer to this concept, and it is essentially the same as what Grice (1957) referred to as “natural meaning” in his work in the philosophy of language.
- The more contentious question becomes whether or not biology needs another, richer concept of information as well. Information in this richer sense is sometimes called “semantic” or “intentional” information.
- In mammals, for example, chromosome structure predicts the sex of the adult animal.
- For environmental factors, not just genes, “carry information” about phenotypes, in Shannon's sense.
- if we are using Shannon's concept, then the informational relationship between genotype and phenotype is symmetrical.
- In addition, a message that carries “semantic information,” it is often thought, has the capacity to mis-represent, as well as accurately represent, what it is about. There is a capacity for error.
- Genes carry a message that is supposed to be expressed, whether or not it actually is expressed.
- a prescriptive or imperative content, as opposed to a descriptive or indicative one.
- When an entity has been subject to and shaped by a history of natural selection, this can provide the grounding for a kind of purposive or normative description of the causal capacities of that entity.
- the proposal of Sterelny, Smith and Dickison (1996), supposed that there is an intimate connection between evolutionary function and semantic properties in the case of biological structures that have been selected to play a causal role in developmental processes.
- Some non-genetic factors have the same status.
- ne problem is that any causal relation can look “arbitrary” if it operates via many intervening links, for there are many possible interventions on those links which would change the product of the causal chain.
- a producer and an consumer device
- In the case of an indicative signal or representation, the representation is supposed to affect the activities of the consumer in a way that will only further the performance of the consumer's biological functions if some state of affairs obtains. In the case of an imperative representation, the representation is supposed to affect the activities of the consumer by inducing them to bring some state of affairs about.
- genes “code for” the amino acid sequence of protein molecules, in virtue of the peculiar features of the “transcription and translation” mechanisms found within cells.
- This process makes eukaryotic DNA a much less straightforward predictor of the protein's amino acid sequence than it is in bacteria
- the standard genetic code is turning out to have more systematic and non-accidental structure than people had once supposed
- hormonal signaling systems, and other mechanisms by which one part of the body conditions the activities of another by means of an intermediate molecule.
- A central feature of this schema is the distinction between some mechanism that reads or consumes the signal, and the signal itself. The very notion of a “receptor,” seen so often in cell biology, suggests this schema. This explains why hormones seem to be such good candidates for a semantic characterization.
- proceeds reliably and predictably without any central control of the development
- genes can be said to code for protein molecules but not for anything further downstream.
- explanatory illusions and distortions
- these concepts distort our understanding of the causal processes in which genes are involved
- Preformationism, in its original form, in effect reduces development to growth
- informational models of genes and gene action make it very tempting to attribute a kind of causal primacy to these factors, even when many other causal factors are essential players in the process in question
- in biological systems the causal role of genes is in fact tightly interconnected with the roles of many other factors (often loosely lumped together as “environmental”)
- it is highly misleading to treat genes and only genes as carrying “messages” that are expressed in their effects.
- the idea of internal genetic messages may also foster a tendency towards a kind of essentialist thinking;
- information is a non-material posit masquerading as a high-level physical property
- Jablonka and Lamb hold that one of the useful features of informational descriptions is that they allow us to generalize across different heredity systems, comparing their properties in a common currency.
- intricate but orderly and well-coordinated nature of many processes in biological systems
- there is an informational “domain” that exists alongside the physical domain of matter and energy.

Jan

7

2012

Phil 2890: Philosophy of Biology

joelvelasco.net/2890

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biology philosophy

Dec

5

2011

Adaptationism (Stanford Encyclopedia of Philosophy)

plato.stanford.edu/...adaptationism

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philosophy biology adaptationism

the importance of natural selection in the evolution of organisms, in the construction of evolutionary explanations, and in defining the goal of research on evolution.
natural selection among individuals within a population
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- only important cause of the evolution of a trait
- the evolution of adaptations
- “pluralism”, invokes historical contingency and developmental and genetic constraints, in addition to natural selection, as important causes of the evolution of a trait
- “flavors” of adaptationism
- standards of evidence
- potential role of non-selective influences on trait evolution
- Ronald Fisher and Sewall Wright
- invokes only natural selection as an important causal explanation of the trait
- neutral theory in population genetics, which posits that natural selection plays little or no role in determining DNA and protein sequence variation in natural populations
- little more than “the attempted intellectual lynching” of sociobiology
- “empirical” adaptationism, is the view that natural selection is ubiquitous, free from constraints, and provides a sufficient explanation for the evolution of most traits, which are “locally” optimal, that is, the observed trait is superior to any alternative that does not require “redefining” the organism
- the realized influence of natural selection on the evolution of traits
- “explanatory” adaptationism, is the view that explaining traits as adaptations resulting from natural selection is the central goal of evolutionary biology
- “methodological” adaptationism, is the view that looking first for adaptation via natural selection is the most efficient approach when trying to understand the evolution of any given trait.
- “Natural selection is a powerful and ubiquitous force, and there are few constraints on the biological variation that fuels it. To a large degree, it is possible to predict and explain the outcome of evolutionary processes by attending only to the role played by selection. No other evolutionary factor has this degree of causal importance.”
- natural selection governs all important aspects of trait evolution
- the order in nature is a consequence of natural selection
- Many proponents of empirical adaptationism concede that important aspects of the evolution of DNA and protein sequences are little influenced by natural selection.
- “The apparent design of organisms, and the relations of adaptedness between organisms and their environments, are the big questions, the amazing facts in biology. Explaining these phenomena is the core intellectual mission of evolutionary theory. Natural selection is the key to solving these problems; selection is the big answer. Because it answers the biggest questions, selection has unique explanatory importance among evolutionary factors.”
- it organizes research to understand how natural selection underlies the world around us.
- Dennett and Dawkins argue that this perspective counters the natural theological argument from design and vindicates a secular humanist perspective.
- many systematists believe that describing the history of life is the central mission of evolutionary biology;
- “The best way for scientists to approach biological systems is to look for features of adaptation and good design. Adaptation is a good ‘organizing concept’ for evolutionary research.”
- a mixture of distinct approaches is superior at advancing knowledge as compared to a single approach
- including comparative and molecular data
- the truth of empirical adaptationism is a possible outcome of testing of optimality models, as opposed to being something that is decided a priori.
- ensemble test,
- Species with a recent common ancestor may have inherited the same trait from the ancestor, as opposed to evolving it independently of one another.
- Optimality models put the contingencies of history and developmental and genetic constraints in to the background so as to focus on natural selection.
- evolutionarily stable strategy
- This is often justified on the grounds that there exists a “good fit” between the trait and its current function (Maynard Smith 1978) or that natural selection is ubiquitous in nature
- Gould and Lewontin (1979) view constraint hypotheses as competing with adaptive hypotheses as explanations of traits.
- developmental and genetic constraints on variation and transmission
- Advocates of optimality models treat constraints as presupposed by adaptive hypotheses.
- Developmental processes may limit the spectrum of evolutionary trajectories available to a lineage.
- the concept of optimality is a poor tool for answering their research questions.
- If explanation amounts to identifying causes, then constraints must be causes to explain evolutionary outcomes. But how can impediments have a causal influence on the evolutionary trajectory of a lineage?
- background
- the constraint set is presupposed
- Constraints are defined as biases or limitations on the production of variation.
- it is essential to precisely specify the rival evolutionary hypotheses.
- As adaptationists point out, any evolutionary hypothesis must assume some constraints, so the accusation that optimality models fail to include constraints is incorrect. But pluralists are right to argue that in some cases constraints may play a significant role in the evolution of some trait, and that the correct evolutionary explanation may not even include natural selection for the trait.