Question Submission 6

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It strikes me that natural selection is in the drivers seat of the debate between Griesemer and Godfrey-Smith. That is to say, each wants an account of reproduction that captures the class of things on which natural selection acts. I'd like to explore why this an ideal for a successful account of reproduction. It seems that Griesemer can escape Godfrey-Smith's criticisms by saying that natural selection acts on a class of replicators broader than the class of reproducers, but that the distinction between replicators and reproducers nonetheless captures an important distinction between the types of things that produce offspring. My question is then twofold:

1. What is the basis of the assumption that a successful account of reproduction capture all things on which natural selection acts?

2. Would rejecting that assumption give Griesemer a response to Godfrey-Smith's critique that can potentially do some other useful work?

In reading "Darwinian Populations & Natural Selection" by Peter Godfrey - Smith I found myself focusing on the distinction made between the Tree of Life understanding of Evolutionary Biology and the account of how change occurs within populations and species in respect to Evolutionary Biology.
To me it feels as though these are two descriptions of the same thing but at a different scope or level, and maybe this is the intention?!
ie: the shape of the tree of life is dictated by Genealogical relationships between species but HOW can we even have different branches, and relationships between branches if there is no say, natural selection, offering say, differential reproductive success amongst and thus between species.

ie: how can we understand variance arising in a population if we say it arises "haphazardly"? Is it not the case that we should instead be looking more into the relationships between species? And then from examining the interconnectedness of species try to identify how their differentiation occurred? aka trying to look back to find where the variance came from, giving us a better idea of how it developed the variance...

Griesemer discusses Darwinian evolution in his manuscript. Griesemer begins by saying that traits must be heritable, and these heritable traits must effect reproduction. Therefore, the species with the most desirable traits will reproduce in greater numbers and thus effect evolution. My confusion begins when Griesemer distinguishes between “evolution by means of natural selection” and “adaptive Darwinian evolution.” It seems to me that the difference between these two paths of evolution are that with “adaptive Darwinian evolution” the trait effecting reproductive success must be “causally related” to its environment. What does Griesemer mean by “causally related” to its environment? Is this relationship with its environment different from the evolutionary process of natural selection? If they are different, how so? Or are they part of the same concept?

In lecture on Thursday, Professor Griesemer was clarifying his views of material overlap after Godfrey-Smith had said it was too narrow. To do so, he discussed that there are different resolutions (low and high) to looking at the issue. He then gave the examples of both retrovirus and humans in the low resolution showing that there is no material overlap. He then showed them in the high resolution showing that material overlap occurs in both of them. Professor Griesemer said that Godfrey doesn't believe there is material overlap in retroviruses (which would lead to believe he is looking at low resolution) but believes there is material overlap in humans (looking at high resolution). So I'm wondering if he believes in looking at the issue in terms of resolution or not? And if so, which resolution? Professor Griesemer makes Godfrey-Smith's views to be contradicting/confusing, and I don't know if that is really the case. (He may have a very clear view against Griesemer's ideas but they were not communicated to me clearly)

In lecture on Thursday, Professor Griesemer was discussing his counter points to conditions that Godfrey-Smith had brought up, mainly involving low/high resolution. When discussing these he explained that if the other person was able to come up with an example to their ideas, that neither would change their opinions or work. If this is true than why is it necessary for either to produce examples, counter examples or even discuss the others work at all? Is it due to the reflections and opinions of the scientific community rather than that of the individuals in the debate?

I have several questions that all have to do with material that Griesemer taught this past week. The first has to do with reproduction in living species, and what is reproduction. Since all living beings have DNA, can't we just call reproduction the actual act of replicating the DNA which leads to a new organism? I know Prof. Griesemer talked about several different species that have what we would consider abnormal methods of reproducing, but don't these species still replicate DNA to reproduce? Am I trying to oversimplify this idea of reproduction? After hearing the Prof's argument, I still am not 100% sure why he considers development part of reproduction. Can't we simplify it and say that reproduction is simply the beginning of a new organism that either via material overlap or not (in the case of the retrovirus) has the same DNA as the organism(s) deemed the creator(s)? Are there any examples that would make my definition of production not work?

Godfrey-Smith poses an interesting idea in Chapter 4: Reproduction and Individuality by way of critiquing the "common sense" notion of reproduction. Specifically, he spells out how the dilemma of "growth versus reproduction" and "collective entities" stresses our intuitive notion of reproduction and, I would argue, this further points out a tension for our (unconscious?) imposition of the "right" unit of selection on the "right" level of reproduction. It seems that for any given individual, the higher this individual is on hierarchy of organization (or in the case of the "runners" where some of the levels on the hierarchy seem maybe to collapse), the more dynamics there are for any analysis to take account of when trying to explain selection (thus also evolution). With every additional dynamic, a complete explanation (of evolutionary units or the appropriate level of selection) appears to be less and less tenable, yet is this not (ironically) the strength of the theory of evolution? I guess I'm wondering why adaptation doesn't presuppose an inability to have an all-encompassing theory of evolution (I mean specifically its units and anything narrower than generalizations)? This also seems to pose a problem for a supervenience schema regarding the hierarchical organization of life: in the course of evolution for an individual (defined broadly), can the adaptations gained at a lower level be lost over time due to the adaptations on a higher level, thus rendering supervenience at least partially inaccurate? Or is this the "maximum requirement" for adaptation and evolution?

For the last week, I've been thinking about agricultural communities as Griesemerian reproducers. The following concepts are especially intriguing when applied to the agricultural organism: material overlap, alternating generations, inheritance of developmental capacities (especially in cases of genetic modification) and coadaptation between humans, crops and livestock. Should an agricultural community be considered an evolutionary unit?

Agriculture is my research focus, so any and all feedback would be greatly appreciated.

Professor Waters’ depiction of Morgan and co.’s experimental procedure states that it didn’t ‘depend on indentifying the material make-up, mode of action, or general function of the underlying purple gene (Waters, manuscript pg. 6).’ Rather, Morgan’s approach was only concerned with the idea that genes were heritable, located on chromosomes, and that differences in a gene (+ vs. pr) resulted in different phenotypes. To me, this can be translated as saying that Morgan was unsure as to what led a gene to produce a particular phenotype, but he knew that circumstance A (the possession of + vs. pr) resulted in circumstance B (red or purple eyes), without any knowledge of the intermediate processes. Additionally, it’s worth noting that although Morgan and co. didn’t know the make-up of a gene (other than its location), they were aware that multiple genes could have a combinational effect on a particular phenotype such as eye-color, as is described in Prof. Waters’ manuscript. However, on pg. 7 it states that ‘Many genes are potential difference makers with respect to eye color. Morgan’s group had already identified 25 by the time they reported the experiment described here. But in this experiment, genes were controlled via breeding regimens so that only one of them (the purple gene) actually caused eye color to differ among the experimental organisms.’ This statement raises a flag for me – while it’s true that Morgan and co. bred flies that would produce phenotypic differences, they were unaware as to what combination of factors might produce these phenotypes. With that being said, is it contradictory to say that Morgan and co. controlled the experimental conditions to ensure that only one gene would be causing the phenotypic differences amongst offspring, when at the same time they had no idea whether it was this single gene, a combination of genes, or other factors that ultimately resulted in the phenotypic differences? How can you ensure that only one gene is causing the phenotypic differences when you aren’t sure as to what the other involved mechanisms might be?

After reading the recommended part of the introduction and chapter 2 of Prof. Waters' manuscript, I am confused about why we must be anti-realists.

First, I agree that if a scientific practice correctly describes some entity, then this entity need not be "fundamental." In this way, it would not be appropriate to account for the success of science with some fundamental/grand/unifying theories that get the world right in a fundamental way. Then, we are fundamental anti-realists.

However, Prof. Waters says that the success of experimental science is explained by practices that generate better methods for manipulating the world, and theoretical constructs that explain the results of those manipulations. And, eventually all this manipulation and investigation will eventually provide "piecemeal" explanations of a wide range of phenomenon. Here, I digress to ask the following. What makes a "piecemeal explanation" different from another "basic theory?"

A range of phenomenon cannot be explained by the basic theory originally employed as a tool in the investigation. But, taking all of this together, we end up using one basic theory as a tool to determine another basic theory that pertains to an additional specific/local phenomenon. Though, none of the theories are fundamental. Then, isn't the success of scientific practice equally explained by the fact that these local/basic/specific theories get the world right (correctly describe a real entity or process in the world) in local/specific contexts? So, is the success of science, when looked at from the perspective of scientific practice, still accounted for by theories, albeit piecemeal/local ones?

On pages 23-24, Waters discusses the importance of recognizing the connections between individual populations and the types of difference makers. He states on page 24, “The intricacies of these kinds of relationships have important implications for the exportation of casual knowledge from one population to another, especially from laboratory populations to natural populations.” I conduct genetic epidemiology research on very rare pediatric cancers. In one of my studies, roughly 300 children in the US are diagnosed annually with a specific form of cancer. Being that my population base is quite small and we have obtained data for roughly 60% of these potential subjects within the time frame of our study, are the implications greatly reduced when applying the causal results to the rest of the specified population base since data was collected on a majority of the population? I assume the more difficult extrapolation would occur when trying to connect “an” actual difference maker from this population (a subset of the whole population) to a population of another type of cancer (each cancer population would be mutually exclusive) or to the population as a whole?

During Professor Griesemer's lecture on Thursday, he spoke about the idea of looking at material overlap in terms of resolution. When one looks at the retrovirus in terms of high resolution, there is overlap, but when one looks at the retrovirus in terms of low resolution there is no overlap. In cases like the retrovirus, where at different resolutions you see different things (i.e. overlap/no overlap) ,which is the correct way to view them? Is the high resolution the correct way because it looks at the subject at hand in a more focused, zoomed view? Is there a way to view them at both high and low resolutions at the same time to get a sort of "overall" view? It seems to me that if a person wants to see overlap, they can just speak in terms of high resolution, and if a person wants to see no overlap they can just speak in terms of low resolution. The person can look at the issue at a high or low resolution depending on what they are arguing for/want to see.

My question is from Prof. Waters' manuscript and subsequent lecture on Gene-Causation and the Transmission Theory of Classical Genetics.

I am very sympathetic with a research program that focuses on the practice of science. As Prof. Waters' frames the questions 'how does scientific practice work?' and 'what kind of knowledge does it produce?'. And it seems to follow that in pursuing these kinds of questions, one must inevitably leave the grand sweeping explanatory theory talk behind. However, it seems to me that it is not at all clear how to separate out representations, models, heuristics, bench theories, or informed theoretical conclusions from some of what eventually becomes the explanatory theory in a given scientific project.

I understand that a definitive step in Waters' project is to examine sources which serve to help recreate the experimental processes, and that such 'raw' sources in the case of classical genetics deviate sharply from the picture of theory-driven picture. What I don't understand, however, is how we continue chipping away at theory-driven perspectives. What is the difference (are the differences) between "basic theoretical and causal reasoning" and the misconceived larger theories that are oftentimes thought to drive the sciences?

Prof Waters suggests that many developments in science occur not as a result of theorizing & discussions about theory as well as possible/plausible accounts for observed phenomena; but rather, as a result of pragmatic moves/techniques/ made by the practitioners (read: experimenters) that enable them to track whatever it is they are interested in tracing. Thus, success in scientific practice directly follows from material culture (the tools, and techniques available to lab groups). Waters appeals to a change in how we ought to think about concepts in their fields: instead of trying to discern "what is a molecular gene"; Waters wants to ask "how can genes be usefully conceived at the molecular level.

I wanted to elicit for further elaboration on who should think this way; that is who should undergo this conceptual change when considering science: should philosophers change their approach to the philosophy of science and take a more pragmatic view; should politicians adopt a more nuanced view of science thus recognizing that scientific knowledge is continuously challenged and in the process of revision in order to provide descriptions of ever increasing accuracy; should historians adopt this view and thus recognize the role of experiment, material culture, and 'explanatory power' in the development of science; should scientists adopt this view in oder to think more clearly about their work, presumably, thinking about ideas as pragmatic holders as opposed to metaphysical certainties can provide scientists with greater focus (knowing when to apply certain constructs or change the manner in which these concepts are used?); should citizens adopt this approach when thinking about whether to get vaccinated or follow the advice of doctors and/or scientists? Or can embracing a view which implies the fluidity of concepts stifle the development of some of these disciplines by hindering the practitioners adherence to theories and/or models which arguably, as presented by Prof Wimsatt, can result in the formulation of theories of ever increasing accuracy?

I have two questions from this week's reading.

On p. 2 of Chapter 1, Waters says, "This epistemology is developed in the context of experimantal sciences centered on DNA, but has something to say about the nature of scientific knowledge more generally." This quote references a worry that I have had throughtout this course. It seems that we are looking at very specific moments in scientific history and trying to make general claims about scientific practice. I worry that we may be overgeneralizing. Are there counter-examples to the claims that we are making about scientific practice? Are there different practices in different areas of science or even biology?

My second question relates to Chapter 2 and causation. Has anyone considered using different cause values? I am thinking about this in relation to the idea that some people have in logic that there should be more than just true and false as truth values. Should we have more than just "the cause" and "not the cause" (i.e. "this event has cause values 1 while this other event has cause value 4")? I am not sure how much this would help our situation but it is just a question.

Looking through an epistemological lens while questioning how much science truly knows about biology and how much science thinks it knows, it is evident that the theories, and even models, that modern scientists use to understand the natural world are often derived by romanticized notions of science derived from incomplete accounts of certain processes, where gaps in knowledge are often conveniently bridged with misguided assumptions of intuition.
My question is, while looking through this epistemological lens, does a reductionist account of science lend anything in terms of advancing knowledge? I ask this question from a perspective of realization that a reductionist account is flawed and, at best, incomplete, but wonder if it can serve a purpose in formulating scientific explanations if only to serve as a sort of temporary scaffolding for ideas; or does it just hinder our quest for knowledge?

I am having trouble accepting Professor Waters' account of causation which he proposes in Chapter 2 of his book (and described in lecture). Though it does nicely solve the problem posed by Mill, it seems to me that it will have trouble with higher level causes, not simply dealing with simple causes like gene differences and the position of a gas pedal in a car. For example, if a person is killed by being shot, would Professor Waters' account say that the position or trajectory of the bullet caused the death? In some sense this seems true, but it also seems true that the shooter caused the death of the person in question. This is not obviously accounted for in the account. Is this a misreading of Waters' theory of causation? Or is saying that the shooter caused the death just not a prescise way of speaking in this case?

In section 2.4 of Walters reading, he discusses Woodward’s interventionist theory. On p.14 he states “a causal relationship exists between two variables, X and Y, when: for at least some individuals there is a possible manipulation of some value of X that they posses which, given other appropriate conditions (perhaps including manipulations that fix other variables distinct from X at certain values), will change the value of Y or the probability distribution of Y for those individuals.” On the same page, he sums up this passage by saying “[Woodward] is claiming that if the manipulation of X has or will occur, then this manipulation has or will change the value of Y.” My question is does he take into consideration the possibility of X changing but not having an effect on Y? In my experience, there are cases in research where you will change a variable X and examine the change of Y, but there are times when there appears to be no change. Sometimes you can change X, for example deleting a gene, and Y will still be functioning and normal with no phenotypic changes. How would Woodward account for this in his theory? Or would he? Would my point fit into anyone’s theory discussed in Waters paper?

In class was discuss the Morgan paradox which say that “one gene alone has produced this effects. … but the effects is produced only in conjunction with all the other.” Could the example of albinism can fit with Morgan paradox? There are several genes that could cause albinism but it only take one mutation in the whole process to cause albinism. And from the fruit fly experiment did it actually one gene change that can cause the eye color change or it is know by now the other factor that can cause the change?

My question comes from chapter 2 of professor Waters "Why Genetics Succeed..." when he talks about how Morgan had the notion that one-gene one-characteristic seemed unlikely. This leaves me to question what professor Waters was talking about with the Gas pedal scenario in lecture. If there are many gene combinations (genes not identified as eye color genes are included) that could possibly effect a characteristic such as eye color, how is one ever supposed to find those links? In my opinion it seems that there are too many variables, and I just don't understand how the position of the "Gas Pedal" will help us figure out what we are looking for.
 

This question is based on Waters' 'Why Genetics Succeeds'.
I wonder about the connection between warranted belief and knowledge in the context of classical genetics. Waters argues in Ch2 that only the minimal, classical gene concept warrants belief. I assume that the contrast to warranted belief is knowledge, and that knowledge is something like warranted true belief.
My question is whether Waters thinks of the gene concept as the kind of thing that could be true? A worry I have is that the thought that the way scientific representation works rules out the gene concept from being even possibly the case makes it unclear what we are warranted in believing. If we are warranted in believing the classical gene concept, is not the belief warranted that the gene concept is correct or true?
I guess that a more general confusion I have is whether we should be anti-realists about just fundamental theorizing or about basic theories too.

Waters' account of difference makers applies only to contrastive classes, not to single instances. He makes this clear in Ch2 p26. He says, "In the case of a singular effect, it would indeed be a fool's errant to identify the actual difference maker." You need a population, either multiple individuals at a time or one individual across time (p19), in order to speak about difference makers.

I suppose though that you might formulate your worry in terms of the population being the one individual at different actual times and ask why was it that he died when he did and not any other time. I might be confused here too, but here we might be able to say that the bullet was the actual difference maker.

In "Why Genetics Succeeds," Prof. Waters claims that Bridges & Morgan's work in classical genetics explained contrasts in characteristics among an entire population of flies, rather than singular characteristics of individual flies. In other words, it explained why a certain ratio of the flies in the population had purple eyes and why a certain ratio had red eyes, but not why a certain individual had developed red or purple eyes. My question is: would Prof. Waters claim that developmental research explains singular characteristics? It seems that developmental research is also dependent on the context of a population. For example, to explain the development of one fly's eye color, wouldn't developmentalists contrast that fly's development with that of another fly who developed a different eye color? It seems to me that it would be difficult for scientists to explain any characteristic without making comparisons between organisms.

It is interesting that so much thought and effort is put into examples and counter examples and rarely do people producing these examples change their mind. The reason for these examples/counter-examples, I believe, relates to the general reason for philosophy. By pondering a theory and dedicating time to coming up with examples and counter-examples it allows one to possibly expand on current ideas and come up with new ideas. Even if someone is not willing to change their mind on a particular thought, carefully examining it may lead them to develop new thoughts/theories. The process of discussion can generate new ideas and expand knowledge.

I think your question is interesting because your use of the example of albinism is one that seems to fit the Morgan Paradox.
With that said, I also find myself very confused if this is a GOOD example to fit with the Morgan Paradox. As I explore this idea in my head I soon become roadblocked by the lack of my knowledge in the field of mutation and genes... I see a difference in your example of albinism from the flies Morgan used but when I try to express specifically why there are differences it seems that I am not knowledgeable enough in the realm of mutations, genes, and their role(s). But what I have goes something like this...
The flies were looked at under very specific "conditions". I mean Morgan knew what flies had what genes. Because of this detail I somehow find it hard to compare with albinism simply due to the fact that I do not know of any back crossing that can be done to find what gene produced the mutation that caused the albinism...
I think many factors can affect the eye color of the flies and I think that Morgan's experimental design was aimed at identifying what factors, or the location of the factors that led to phenotypic changes in the flies eye color.

Since you're referring to a causal relationship within a small population group that contains specific characteristics, I think it would be extremely difficult to apply those relationships to any population that contains a different set of characteristics. Your group of interest has both different causal factors and effects when compared to the rest of the population - even different populations of cancer groups. Because of this, the causal relationships you discover in the group of interest wouldn't necessarily be transferable to a different group. Since you're dealing with pediatric groups, that implies that there is a different set of underlying factors when compared to the rest of the population. If you were dealing with a type of cancer that occurs in adult populations, you'd be able to cross-examine the causal factors in that cancer population with a population of normal adults to determine if the causal relationships could be applied outside of the cancer group, if the causal factors were determined to be things that were common in most individuals. But since you're dealing with pediatrics, I'd say the application of any causal relationships would be limited to a younger age group, since they would be the only populations that would share such causal factors. Good luck with your research, it seems like a pretty interesting topic that definitely has important implications.

It is true that counterexamples to a theory rarely change the mind of the philosopher who put forth that theory. However, if enough counterexamples accumulate against a theory, it certainly changes the reputation of the theory in the philosophical community. I do not think the primary purpose of counterexamples is to change an individual's mind, but rather to call into question the validity of the theory for other philosophers.

Prof. Griesemer's discussion of counter-examples is illuminated as follows. Prof. Griesemer does not attempt to give an in principle analytic claim about what it must be for anything to be a reproducer. That is, he is not saying that his idea will necessarily capture ever reproducer. One obscure counter-example is not detrimental to the account. It is an illuminating special case that warrants description, but since his account is not some unchanging analytic definition, his definition need not be dismissed in light of the counter-example. It is important to note, that the concepts may require qualification or clarification in the light of counter-examples, but this is not outright dismissal.

Think of his concept of reproducers as a heuristically useful identification in the sense Prof. Wimsatt discussed. If it is good, it gets a lot right. This not to say that counter-examples are not important. They are valuable if we want to investigate the whole "tropical rain-forest," but we should not throw away incredibly useful concepts in the face of minor counter examples.

Additionally, the philosopher still wishes for his idea to be as powerful (read for Griesemer, Wimsatt: as heuristically productive/robust (hopefully indication of reality), even if local). So considering counter-examples is valuable to examine just how much the concept captures. If the concept captures relatively little in the face of a massive barrage of counter examples as Katie explained, then the whole concept will likely be dismissed. But, if it explains a lot, but misses two cases, we do not throw the entire account away.

You bring up a good question about what reproduction is. I don't think that, "calling reproduction the actual act of replicating the DNA which leads to a new organism" is an oversimplification of reproduction. It seems to me that, instead of oversimplifying, you'd be looking at reproduction at a high resolution. Like Professor Griesemer said about seeing overlap when viewed from a high resolution, getting down to the actual replication of DNA would be a matter of being at a high enough resolution. I'm not really sure about the idea of development being a part of reproduction and would like some clarification.

Chris' question: Prof Waters suggests that many developments in science occur not as a result of theorizing & discussions about theory as well as possible/plausible accounts for observed phenomena; but rather, as a result of pragmatic moves/techniques/ made by the practitioners (read: experimenters) that enable them to track whatever it is they are interested in tracing. Thus, success in scientific practice directly follows from material culture (the tools, and techniques available to lab groups). Waters appeals to a change in how we ought to think about concepts in their fields: instead of trying to discern "what is a molecular gene"; Waters wants to ask "how can genes be usefully conceived at the molecular level.

I wanted to elicit for further elaboration on who should think this way; that is who should undergo this conceptual change when considering science: should philosophers change their approach to the philosophy of science and take a more pragmatic view; should politicians adopt a more nuanced view of science thus recognizing that scientific knowledge is continuously challenged and in the process of revision in order to provide descriptions of ever increasing accuracy; should historians adopt this view and thus recognize the role of experiment, material culture, and 'explanatory power' in the development of science; should scientists adopt this view in oder to think more clearly about their work, presumably, thinking about ideas as pragmatic holders as opposed to metaphysical certainties can provide scientists with greater focus (knowing when to apply certain constructs or change the manner in which these concepts are used?); should citizens adopt this approach when thinking about whether to get vaccinated or follow the advice of doctors and/or scientists? Or can embracing a view which implies the fluidity of concepts stifle the development of some of these disciplines by hindering the practitioners adherence to theories and/or models which arguably, as presented by Prof Wimsatt, can result in the formulation of theories of ever increasing accuracy?


I think this is a good question; however, it also seems to be more of a moral question than anything else. It seems as though stifling knowledge would be immoral on many levels. Perhaps the question that we should be asking is: what can be gained from sharing this knowledge? Perhaps having a better knowledge of how scientific experiment actually works will help scientific research progress.

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I found this comment about how providing evidence for one's opposing argument would not change the opposing scientists viewpoint. Right now I am discussing the social construction of science in another philosophy of science course and this to me seems like a perfect argument for the social constructivists. Even if solid evidence exists for some of these theories, society is allowed to accept or reject them as a whole. This makes little sense to me as I always think solid evidence for a counter argument should cause the original theorist to reconsider their argument.

After reading Griesemer’s paper, I found myself also questioning to what level the concept of an evolutionary unit applies. An important component to Griesemer’s case regards the definition of an evolutionary transition, which are, to quote Maynard Smith and Szathmary, “entities that were capable of independent replication before transition can replicate only as part of a larger whole after it.” Griesemer’s lecture notes included a table of major evolutionary transitions, which include transitions between species (i.e. primate societies to human societies). The idea of whether selection can occur at or above the species level remains controversial, so I personally don’t believe a community of any kind should be regarded as an evolutionary unit. Though Griesemer believed Dawkins’ argument was too constricting, I believe his argument is too all-encompassing.

To answer this question I believe it is important to take a look at the idea that the biological community struggles with this question. We must note that just because something fits to a model doesn't mean it wasn't manufactured to fit a model

I would argue that you cannot have a truly (r)evolutionary understanding of biological entities without taking all "individuals" seriously, across all scales. The attempt to identify a single evolutionary unit is an ill-advised endeavor from my perspective. It is our responsibility as members of the scientific community to approach the topic from whichever angle is most interesting to us. In Griesemerian terms, we must commit to our own ontological commitment about the nature of evolution. No one approach has privileged access to the reality of evolution, so let's embrace the all-encompassing definition of "evolutionary unit" and share our knowledge as we go along. The robustness of information provided by this collective effort will provide us with a more sophisticated understanding of the nature of biological life.

I asked a related question to Troy's the other week. After thinking about it and now his I thoroughly believe that the inherent flaws reductionist theories tend to have act like navigational tools to the sciences. Scaffolding is a great analogy for this. The building is not made of scaffolding, but scaffolding allows us to make better buildings. And as scaffolding is always disassembled when the building is finished, reductionist theories are always replaced once the phenomenological ones are assembled. Reductionist theories help the sciences formulate explanations while simultaneously providing the direction for further research by exposing the gaps in our knowledge, caused by its inherent flaws.

I think this is a really interesting perspective, especially in light of Water's explanation of Mill's critique of causality. It would seem (at least in terms of an evolutionary perspective) causality should be seen in light of a totality. Perhaps within the laboratory the relationship between specific "causes" can be isolated, but in terms of natural selection a single dynamic (or a unit) is vastly insufficient for explaining what actually unfolds before our eyes. With the development of social activity, what does it mean if the success of an "agricultural community" not only sustains itself over time, but actually expands? Or even more profound, what if of a given agricultural community's technique proves truly robust? You could count on its methods being copied or transferred to other communities. This "transfer" presupposes the existence of life (even in the most narrow biological sense), if it doesn't count as a unit of evolution how else must it be analyzed? Specifically, if this is not part of evolution, or a unit thereof, wouldn't you be forced to argue that entities of this nature are a byproduct (I mean something like a waste product) of life, and not actually a part of it?

This is the same point that I was making in my question. I don't completely understand it either. I don't think there is a "correct" way to look at them. It is basically if you believe there is depends on what side of the issue you are one. That is an interesting question about looking at both high and low resolution to get an overall view. That would be interesting to find out. The thing that I don't understand is how Godfrey-Smith doesn't believe there is material overlap in things such as retrovirus which would imply that he is looking at a low resolution but believes there is material overlap in humans, which would be high resolution. I think you either have to believe there is material overlap in all species or none so you are looking at just one resolution (unless there is a way to get an overall view).

Is a reductionist view really flawed, or just incomplete? I think reduction is a useful tool in many cases, like molecular genetics, but it also requires a higher level underestanding of system function at the component level to achieve true accuracy when defining biological systems. I see both reductive reasoning and phenomenological reasoning as incomplete models of reality, I dont think I would go so far as to call them flawed because they are incomplete.

I don't think agricultural entities are restricted to actions like expansion or transference; they are truly reproducers. At a certain size (just like with conventional biological organisms) the nutrients cannot be dispersed efficiently, so a gamete (in the form of a human-nonhuman team: farmer and seed, perhaps) leaves to find another hospitable environment to grow another agricultural organism. It is interesting to think about "agriculture" as an aggregation of cultures, a collection of organically developing organisms. Those individuals form a truly collective organism, none of which could exist independently from one another.

From a permaculture perspective (permaculture being the form of agriculture which most clearly exemplifies a healthy agricultural organism) the concept of "waste" and "byproduct" doesn't make any sense. On a permaculture farm (or in any self-sustaining ecosystem) wastes are resources, byproducts are products, everything is part and parcel to the collective unit. Permaculture practices are developed on a cyclical, dynamic, interactive conceptual framework, not a linear one. The ontological commitment to circularity, instead of linearity, breaks down the waste-resource dichotomy and recognizes the value and utility of all forms of material and energy.