Question Submission 7

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My question involves the term "robust" as it applies to biological systems. I have heard the word used in discussion several times, and it seems to me synonomous with fitness. Is "robustness" simply a magnitude of fitness? The definition of a robust biological system given by several websites defines robust as "the extent to which an organism's phenotype remains constant despite mutation." If robustness describes the threshold at which an organism's phenotype will be altered, how can one determine an organism's "robustness" when the expression of genes is such a complicated process? To clarify, sometimes few mutations may drastically alter phenotype and sometimes major mutations wont. Doesnt then robustness depend on the specific location of mutation in the genome?

In his introductory chapter, Prof. Waters calls out the dissonant gap between the practical scope of a successful science and the scope of the overarching theories which that practice is operating under. In essence, when the scientist is deeply mired in their work in the lab/field the range of the phenomena they are interacting with is greater than what can be explained by the theories that science is producing. In the explanatory void that exists between practice and theory, Waters suggests that 'speculative theorizing' or hyperbolic guesswork is all too commonly used to fill the empty space. My question concerns the worth of this speculative theorizing. One of the things I found to be most intriguing about Kuhn's The Structure of Scientific Revolutions was his descriptions of the revolutionary scientist. In the very enigmatic transitional stage from a paradigm to another Kuhn's description of what occurs breaks down into descriptions of scientists as artists or fecund creators who guide scientific research not through means of mature scientific practice but through some other obscure source. What worries me about an epistemology of scientific practice is the concern that science can sometimes be guided by unscientific means and practices and that these means can have large ramifications. It doesn't matter where an idea is generated, if it can still be subjected to rigid scientific experimentation than it has the same shot at validity as something that is the product of a successful scientific lab. Isn't it possible that this explanatory void is an important aspect of the scientific endeavor and allows the scientist yet another tool to alter the focus of their practice?

My question comes from Water's Chapter 2 and discussion on the transmission theory of classical genetics. When Morgan developed the Chromosome Theory of Inheritance and was working on transmission theory, how much was actually understood on say a biochemical/molecular cellular biology level? I know that both Morgan and Mendel had theories about independent assortment and segregation in regards to transmission of genetic material, but using microscopes were they able to see mitosis and meiosis? I guess that I don't know enough about the history of genetics and science to say when microscopes were produced that were able to show these actions on a cellular level. I am just wondering that since most of the work in classical genetics was done experimentally whether or not they were able to see it on a cellular level, or whether this experimental research was done mostly on a macro level such as analyzing phenotypes of plants in Mendel's case or Flies in Morgan's case. It seems rather remarkable to me that without advanced technology their theories were so accurate and did a good job (for the most part) of explaining transmission of genetic material.

In class, I asked Prof. Waters to re-describe what he meant by the "success" of classical genetics. That answer is clearly found in the following quote, "The success of experimental science involves establishing practices that generate better and better methods for manipulating the world..." In later sections and lecture, Prof. Waters emphasizes how classical genetic investigative strategies in combination with transmission theory was often unsuccessful in providing new explanations about phenomenon in the "investigatory scope" of classical genetics. However, this seems to contradict the remainder of the quote I began above, "...and that provide a theoretical basis for predicting and explaining the results of these manipulations."

Would it be correct then to say that the scientific knowledge of this domain is largely the "know-how" of manipulations? Then, how successful is that "know-how" if it largely fails to result in an explanation of an investigated phenomenon? I am probably begging the question about what I think scientific knowledge and success is. But, it seems that those piecemeal theoretical explanations account for just as much of the success of science as does the practical "know-how." That is, if science is successful because the manipulations are successful, and the manipulations are successful because they provide some limited theoretical knowledge, isn't scientific knowledge equally grounded in just that limited theoretical knowledge? So can't we account for the success of science with this brand of theory bias? Why is it that theory bias is only "grand theory" bias, assuming scientific theories are used in the multiple ways described in chapter 3? I'm not sure how much of that I believe but at the very least any answer should clarify what it really means to be theory-biased and what underlies the success of experimental manipulations.

In Chapter 3 of Prof. Waters’ manuscript, differences are drawn between theory-driven research and exploratory research. Theory-driven research is set up in a way that restricts the ranges of intervention by the experimenter(s) and seeks to relate the observed phenomena to the theory which drives the research. Alternatively, exploratory research is set up in a way to allow experimenter(s) to intervene in many ways and, as described by Burian, ‘comes into play when theory does not provide expectations about what investigators will find (p.10).’ Although the goals of exploratory research do not involve the confirmation or application of a pre-existing theory, ‘exploratory experimentation is not (typically) theory free (p.10),’ as it relies on pre-existing theories to set up experiments and draw conclusions. Therefore, it seems logical to say that pre-existing theories provide a foundation for exploratory research to take place, even if that research does not attempt to confirm or apply those theories which provide the foundation.

My question is: even if exploratory research is not theory-driven, would the resulting experimental conclusions at some point need to tie in pre-existing theories (the foundation for the research) in order to make observed phenomena relatable to the relevant scientific domain? This doesn’t mean that the pre-existing theories will be directly involved in the observed phenomena, but would rather serve to bridge the gap between what was already known and what was observed in the exploratory research. If you’re answer is ‘no’ to the question, how would you suggest expanding the scientific domain to include both of these bodies (the foundation and the exploratory findings) rather than having two disconnected entities?

My question is from Chapter 3 of Professor Waters' manuscript. Professor Waters states that, "The research program of classical genetics can't be understood by viewing it through a theory-biased lens of traditional epistemologies of science. Then from class on Tuesday, I got the notion from Professor Waters that scientific exploration revolves around theories. If nothing in science is free from theories, how is one supposed to, like in the case of classical genetics, not view it through a theory-biased lens? How should it be viewed? Because theories guide research, it seems like a scientist would always be looking at their science through a certain theory-biased lens, depending on which interpretation the scientist is working towards.

Professor Waters explain how the vantage points of the preformation interpretation and the transmission interpretation are flawed because they both possess a theory bias; that is, they rely and build upon an incomplete and certainly imperfect theoretical account of science. This concept seems clear and reasonable to me and I generally agree with the notion that science does not know even close to as much as is claimed. But, my question is, does the fact that science is less knowledgeable of the world that they appear or claim to be really pose a problem to the discipline of scientific study? I mean, the way scientist view their account of the natural world—as high horsed as they may be—has proven to work well so far as the discoveries and implantation of these (albeit incomplete) discoveries has yielded such a vast amount of practical information that is used to save lives (in the medical sciences for example) that maybe we shouldn’t rock boat in fear of stifling progress. ( I realize this question has the potential to upset the common philosopher.)

This question is from Kitcher's "1953 and all That. A Tale of Two Science". On page 352 he says, "Second, we think of genetic theory as something that persisted through various versions: what is the relation among the versions of classical genetic theory accepted at different times (the versions of 1910, 1930 and 1950, for example) which makes us want to count them as versions of the same theory?"

I think that this is a great question...so I am adopting it as my own! In the brief section of the recommended reading, I did not see an attempted answer from Kitcher. Perhaps he does this elsewhere and I would like to be pointed in that direction. However, I would also like to extend this question more generally to ask how do we decide which scientific thoughts and evolutions fall under the same "theory"?

**sorry about the grammatical typo that snuck past me ;')

My question is more of a clarification for my own understanding. In chapter 3 of Professor Waters manuscript, he states "The second point is that exploratory experimentation is not (typically) theory free. All kinds of background theories are used to set up experiments, generate data, and draw conclusions (as Kuhn’s remark about Coulomb’s apparatus attests). Exploratory experimentation is embedded within scientific inquiry that relies on a lot of theory. The point of difference, Burian (1997) and Steinle (1997) suggest, is that the experiments are not “directed” by the aim to test, develop, or otherwise articulate an existing theory or hypothesis."

Despite the numerous explanations, I am still having trouble seeing the difference between 'exploratory' and 'theory-directed' experiments. It says that the experiments are not "directed" by the aim to test etc. What if a researcher was to discover through an experiment that two proteins interact. Based on that one experiment they form a theory that the two proteins interact, but then to prove their theory they must create and design experiments that will support their other data about the proteins. Would this be exploratory or theory-driven? And how do these definitions apply in a practical sense?

Water's certainly cast a tremendous amount of doubt on the capabilities of the current paradigm for understanding classical genetics. "Historical and philosophical accounts that presume classical genetics was structured by an overarching theory of preformationism or of gene transmission fail to engage the reasoning that guided much of the experimental research...
We simply need to acknowledge that [classical genetics] was a system for explaining a broader domain of biological phenomena (including crossing over, gene action, and speciation)." In doing this he does well to draw attention to his focus on the practice of classical genetics. While he concurrently assures us that theory does have a part to play in organizing our thoughts about classical genetics. "[One] cannot understand the experimental strategies that geneticists’ employed to advance their agendas without understanding their theoretical reasoning about transmission." I wonder whether or not it is even possible to perceive classical genetics through its methodology. We can understand the meticulous reasoning that contributed to experimental design, and the exceptional foresight the Morgan school was able to derive from their findings. But what epistemological evidence will this provide? Knowing how they knew, should help us how to know. But how does knowing how they knew change what we know now?

Exploring the theory of practice is certainly a worthwhile venture. I just have reservations about the perceived rewards such research will provide. Because, in response to advancing techniques, practice is in continual flux, is it not? If it is, does that not necessitate the value of understanding practice as being context specific and only applicable to contemporary studies?

In Prof. Waters' chapter "The Practice of Classical Genetics," he differentiates between "exploratory" experimentation and "theory-driven" experimentation. This struck me as a departure from the conception of science that students are taught from a very young age. A great deal of emphasis is placed upon the "scientific method," which would indicate that a theory is always being tested in scientific investigation. Would Waters suggest that there are alternative "scientific methods" that are followed when scientists perform exploratory experimentation? Or would this exploratory experimentation fit into the "preliminary/background research" step of the scientific method? I guess what I'm asking is, when this exploratory research is performed, is the ultimate aim always to generate new hypotheses to be tested?

My question if about prof. Water diagram. The diagram was explaining how theory could explain some aspect of the world and create a explanatory range. Then from that explanatory range domains are create. My question is, how could the same theory lead to different domains? For example Darwinian theory it is use to explain some aspect in the biology and social science leading to two different domains.

After reading chapter 3 of Prof. Water's manuscript, I find myself slightly confused on the significance of theory-driven and exploratory driven experiments. I understand that the idea of a exploratory is that it isn't based directly off a theory (It is not trying to test a theory) However, the way Prof. Water's explains exploratory experiments has me questioning if scientists really do exploratory experiments in the area of genetics (for example), because there seems to already be to many theories in this area for there to be an experiment that isn't based off a theory. Also, it seems like there has to be some base for one to build an experiment on, which requires some prior knowledge or understanding of the subject matter.

In Tuesday's Lecture Prof. Waters presented his aw-inspiring diagrams that showed knowledge (scientific) on one side and aspects of the world on the other.
I can see how the domain of science is equal to the explanatory range in the traditional theory-centric conception of domain. I also see how in Waters's practice conception, the scientific domain is equal to the investigative reach.
My question is...
What is the investigative reach of the theory-centric conception? Is it located on the knowledge side of the diagram or where does this fit in?
Is the investigative reach in the theory-centric conception limited to the explanatory range provided by the theory?

I am interested in how different theories might overlap domains in Waters' account of scientific knowledge and the implication of that overlap. (This is under the assumption that theories ideally could explain all phenomena, which, though it does not mesh with Waters' goals necessarily, seems plausible and applicable to any account of scientific knowledge.) Would the explanatory void left by a particular theory be a place where a separate theory is needed to explain phenomena? If so, would the overlap in domain suggest that these theories might be aspects of a single theory (though perhaps fully fledged theories themselves)?
Theory succession is common in all sciences, so this seems like an account of that phenomena that Waters' epistemology deals with very well if I am understanding it correctly (which is not certain). I would like to know if Waters would consider this interpretation sensible under his account, or a misuse or misapplication.

At the beginning of chapter two, Professor Waters talks about the development of classical genetics. He describes the transmission theory as explaining characteristic inheritance while being able to avoid the topic of “how these characteristics were produced in the development of individual organisms.” Transmission theory was highly used by Thomas Hunt Morgan to separate heredity and development. Waters mentions this separation being controversial and difficult to prove – why was it considered controversial? Why was it so important for Morgan to separate heredity and development? Waters mentions that he was never able to fully separate the two, and genetics knowledge has been influenced ever since. How would our current knowledge of genetics be different today if Morgan had been successful at separating heredity and development?

Tuesday's second diagram shows that there is a distinction between the range of explanation and the investigative reach. I found it particularly interesting that the knowledge column was broken up into several entries. Professor Waters made the claim that the parts of our knowledge which are not included in "theory" can still possibly inform us as to what is in the "explanatory void"; however doesn't this entail more theory? I guess I'm wondering why things like "strategy and investigative principles", "methods", and "concrete information" are not strictly limited explaining the function of a theory, and not so much aspects of the real world? It seems to me that any attempt to explain aspects of the real world would have to be through the lens of a "theory", which in turn is based on other epistemic foundations.

In Tuesday's lecture, Professor Waters was describing the different
scientific domains (theory centered and practice conception). For the
theory centered domain, there is some theory that that can explain a wide
variety of problems. Water's practice conception, consists of a theory that
has a very small explanatory range with a large explanatory void.

I find myself disagreeing with Professor Waters' view. I don't understand
why you would want to have an explanatory void instead of a theory to have
a large explanatory range. I am confused as to how his view helps
understand science rather than trying to figure science out. I do not agree
with the view of preformation, but I do like the ideas behind their theory
centered domain. They widen their theory so that it has a wider explanatory
range. Would another possibility be to "add together" the preformation
interpretation (theory centered) and the transmission interpretation
(theory centered) to be able to expand the range even more? I also don't
understand why Waters is trying to make the theory narrower, because that
seems to not help science and make it necessary for more theories to be
developed. Also, Waters talked about the role of theory of practice, wouldn't his idea of theory informed (use basic knowledge to apply to other topics) support the idea of a theory centered scientific domain? I am wondering if somebody can clear up my thoughts and explain
to me why the practice conception view is "better" than the theory centered
domain.

The difference between the "traditional, theory-centric" epistemology and Waters' new "practice"-based epistemology seems to hinge on what it means to have explanatory power. Waters' representation shrinks the explanatory scope of scientific theories, but couldn't the old paradigm remain intact with a more widely encompassing conception of "explanation"?

This is an interesting point Emily. As I have been listening to Professor Waters explain practice-based epistemology, it seems to me that many of his examples could be included in theory-based epistemology. Perhaps the reason the two are separated is not to say that they couldn't overlap, but rather, to emphasize one more than the other in an effort to illustrate its significance.

I think a homespun proverb may be in order:

"In epistemic darkness, the precision of laser doesn't disprove the utility of a bare light bulb."

Emily writes, "Waters' representation shrinks the explanatory scope of scientific theories, but couldn't the old paradigm remain intact with a more widely encompassing conception of "explanation"?"

Here, I wonder what exactly you mean when you call for a more encompassing concept of explanation. What does this concept look like and what reasons do we have for adopting a more encompassing view of explanation? I'm sure there are more reasons than just the need to keep the old theory-biased paradigm in tact. But, I'm curious as to what exactly it is.

It is clear that this new concept of explanation would include whatever it is the practical manipulations explain. How would you work that into your account of explanation in a way that preserves the theory-biased account? What aspects of the world do the successful manipulations explain beyond themselves, partial verification of the transmission theory, and those limited successful piecemeal theories (if even those)? That is, if we are successful in investigating a local phenomenon, then was it the manipulation itself that did the explaining?

Or, is it that you are willing to give up the theory biased account, and grant that more is explained than just that which is explained by these theories? I would be careful to preserve the investigatory scope of classical genetics as a genuine structural component of the science, which left much unexplained even though the manipulations themselves were successful. Beyond that point, I'm trying my best not build my own answer into these questions, because I am genuinely interested in your account.

Lastly, Prof. Waters is not getting rid of theory entirely in his account, nor is he even trying to limit its importance. Theory works. What he is trying to do is to stress the equal (if not greater) importance of understanding the practice as a way to understand the knowledge.

I think your question is interesting because the application of one theory can indeed give a wide variety of domain(s). I also liked your question because it raised more questions in my mind like: what exactly a domain is, considered singularly... and how do these domains change when overlap occurs with other domains ...
But to be more specific in answering your question, I think that the same theory can lead to different domains. Furthermore, I believe that this is a result of the way human knowledge has been (and is) constructed in our attempt of understand. And that we have tendencies as humans to apply successful 'theory'(what we know works) to systems that we do not understand in our attempt to explain what we do not know in terms of the established, "mature" form, even though the theory originally explained something else entirely.

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Brooke's question:

In Tuesday's lecture, Professor Waters was describing the different scientific domains (theory centered and practice conception). For the theory centered domain, there is some theory that that can explain a wide variety of problems. Water's practice conception, consists of a theory that has a very small explanatory range with a large explanatory void.

I find myself disagreeing with Professor Waters' view. I don't understand why you would want to have an explanatory void instead of a theory to have a large explanatory range. I am confused as to how his view helps understand science rather than trying to figure science out. I do not agree with the view of preformation, but I do like the ideas behind their theory
centered domain. They widen their theory so that it has a wider explanatory range. Would another possibility be to "add together" the preformation interpretation (theory centered) and the transmission interpretation (theory centered) to be able to expand the range even more? I also don't understand why Waters is trying to make the theory narrower, because that seems to not help science and make it necessary for more theories to be
developed. Also, Waters talked about the role of theory of practice, wouldn't his idea of theory informed (use basic knowledge to apply to other topics) support the idea of a theory centered scientific domain? I am wondering if somebody can clear up my thoughts and explain to me why the practice conception view is "better" than the theory centered domain.


Waters is not trying to describe what he wants scientific knowledge to look like but, rather, what he thinks scientific knowledge looks like right now. Clearly, if it were up to our decision, there would be no explanatory void at all.
While examining these theories may help scientists to alter their practice in order to make it more like the theory that they want to have, Waters' main goal is descriptive. What we mean by "better" in this case is "more accurate". The model that Waters developed seems to more accurately describe how we come to scientific knowledge better than the theory-centric model does.

I would say that Waters' deflation of scientific knowledge would not stifle the practical benefits of scientific endeavors. Simply admitting that there is less knowledge in science than was formerly presumed would not change the fact that (as Waters has stated in class) that scientists can manipulate the natural world in amazing and predictable ways. The lack of explanations for why that is so does not eliminate the ability to do this or to build further from it.

I was glad you asked this question because that was something that I was finding confusing as well. I think it was nice for him to use some students' example questions because I usually find that if someone has a question, I usually have that question too. I thought it was really helpful for him to go over the diagram again and show how investigative reach fits into the domain.

I believe that the notion that “experimental conclusions at some point need to tie to pre-existing theories” relies on an assumption that I don’t believe one has enough evidence to make; that is, the premise that there needs to be pre-existing theories. Although there does exist in science evidence that one could interpret as suggesting that all phenomena can be described by some rule, law, or principle of the physical world—regardless of whether or not these rules are known in part, completely, or not at all—it seems entirely possible that such a theory needn’t must apply to the all phenomena it describes unrestricted and in toto. I don’t believe we have proof of that all-encompassing theories must exist. It may be convent if this were the case, and provide organization allowing the natural world to be comprehended by humans, but I think it is a reflection of our desire for simple and straight forward explanations of the world and not a reflection of the natural world itself.

I don’t actually believe an epistemological approach to science would hinder science in the direct sense; I really meant it as a rhetorical question eliciting a prompt rebuke... with a tinge of cynicism. But now I’ve thought about it, there does seem to be the potential of an indirect consequence with negative implications. And I think professor waters alluded to it during Tuesday’s class: if those in charge of distributing public funding for scientific research become privy of the possibility that science may not actually know squat about science, it may affect how they allocate funds.

I don't think that fact poses a problem to the discipline of scientific study. Even though science may be less knowledgeable than they put on, we are still able to do great things with it. Like you said, lives have been saved because of scientific advancements. I think science should keep doing what it has been doing. I think it's also a good thing for the scientific community to recognize that they don't know as much as they think they do, so they will strive to get at answers instead of sitting back and being content with their "knowledge."

“In epistemic darkness, the precision of laser doesn't disprove the utility of a bare light bulb.”

I think that this fine proverb makes a worthwhile point by highlighting the metaphorical utility of both a laser and a light bulb. Scientific practice and theorizing are tools that have a certain utility which help us comprehend the incomprehensible world. An epistemology that denies an aspect of speculative theorizing as integral to science might be putting aside a useful tool. There doesn't seem to be a way to separate theorizing with practice so it is not as though speculation simply has the same epistemological weight as practice-produced theory or even practice itself, but it is an important tool that can act as a more expansive, if dimmer, source of light. Doesn't it sometimes give us an idea of where to shine the laser?

From my limited knowledge of the history of Morgan, I believe his attempts to separate heredity and development were deemed controversial because of other relevant work that emerged during that time. Mendel’s work was rediscovered, Boveri & Sutton’s work provided significant links between heredity and development, and scientists were attempting to disprove Darwin’s theories. I believe Morgan initially disregarded these theories and sought ways to explain heredity in a different way. The knowledge of genetics has been influenced by Morgan’s work because though he attempted to separate heredity and development, even Morgan realized the two are difficult to isolate. As a result he was able to provide the foundation for genetics that was able to explain Darwin’s natural selection.

I hate to be the dissenting voice as to the intrinsic value of science, but given that this comment has had several replies to it that hold a similar tone, I can't help but think this needs to be addressed: science cannot be evaluated as good or bad, and I don't think it is very difficult to cite, one for one, the evils of science in ratio to science's "good-doings". I mean, just looking at modern warfare: humans can kill a whole lot more people in a lot less time than we used too. Or, think about any dilemma regarding human's causal role of environmental disasters: the use of "science" is absolutely essential in bringing things of this nature about. I think its important to recognize that science is more akin to a conceptual tool that helps explain what we see around us, but nothing more; it expands our ability to manipulate, but, I don't think it tells us much about how we "ought" to manipulate. I don't want to sound like a broken record, because I've brought up this "branch" of "science" before, but I think that it is key to remember that eugenics was considered a "science" at one point in time. As the saying goes, "hindsight is 20/20", but this doesn't do us much good when trying to grapple with the present...