Question Submission 11

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1) Beadle and Tatum's theory that every gene coded or was responsible for a protein seems compelling in some cases; however, as some of the research of biometricians and the Morgan school suggested things were more complicated. Further, the Morgan school had apparently found that certain mutations had a diverse set of effects (what we would now call pleiotropy). Or that proteins could be the result of several genes? (pg27). If so was this recognized by Beadle and Tatum and their followers? If so, did they follow, what would appear to the logical conclusion today, that a change in one protein is responsible for all the observed effects? And was there compelling evidence to take this position given the absence of knowledge about DNA? Further, were there compelling reasons to belief that simple and complex traits (or rather traits produced by simple and complex processes) develop similarly (or through similar mechanisms?)?

2)Morange appears to agree with Avery's collaborators that Avery's experiment should receive greater praise than Hershey/Chase's experiment. Morange argues that even text book portray these experiments as being equals despite the fact that they took place eight years apart (pg 48). To what an extend is a scientist work recognizable if it gets what is now perceived to be the right answer for the wrong reasons? Not to say that Avery did not have compelling reasons to think that DNA was the material which imbued organisms with their traits but as Morange points out there were reasons to be sceptical of such claims. Can we suggest, that experiments which seeks to test a "result that may already be known" (pg 47) are more important than ones that try to establish 'new' knowledge as they are able to test whether a theory can explain an observed phenomena or not. That they are able to test whether a theory works or not and that through more thorough investigations they can assert whether a theory can explain said phenomena or not. Or are theories only to be considered proper theories once a number of experiments' result converge onto the same conclusions (in the case of Avery's experiment it could only be accepted given X-ray work on phage, Hershey-Chase investigation, etc).

On page 332 of the Schaffner article, he says, "When reductions between theories occur, terms in the reducing and reduced theories often change their meaning: they now have new connections and the referents are characterised in a more general way."

I am very interested in the development of definitions? How do definitions develop in biology?

As I am reading about the attempted reduction of biology to chemistry and physics, I see a clear parallel in a discussion I just had in a conservation biology course. The buzz word in conservation is "biodiversity" and we read several articles that argue that high biodiversity causes ecosystems to function. In order to make biodiversity quantifiable, ecologists reduce biodiversity to genetic diversity and ecosystem function has been reduced to either biomass creation (goods) or nutrient cycling (environmental services).
In the words of Donna Haraway, "What money does in the exchange orders of capitalism, reductionism does in the powerful mental orders of global science." Modern ecology and conservation biology has attempted to reduce biotic agents to genetic capital and their communities to producers of goods and services. I felt that the methodology and ideology behind many conservation projects are rooted in capitalism and industrialism, at least in part because these projects are funded by institutions seeking to profit from ecosystem management (to gain goods and services from nonhuman biotic systems). When I voiced this opinion, a classmate said, "This is science. Science is not informed by social ideologies. Science is objective." (paraphrase) The professor and the rest of the class vehemently agreed.
Considering I am taking also taking courses in philosophy of science and history of ecology this semester, I am having a really hard time sweeping these pressing issues under the table. The course is meant to show how scientific evidence informs policy, but they refuse to recognize what science is informed by. How can I present these challenges to "objective science" without evoking confusion and indignation in my classmates? More importantly, do you believe there is there an ethical imperative to bring philosophical issues to light if they can profoundly effect public policy?

Schaffner talks about the first attempts at constructing reduction functions and how connections between entities in two theories are introduced at first, while others are introduced later as the reduction is further developed. He states, "This non-simultaneous establishment of reduction functions is further complicated by the fact that not all of the problems that fall with in the province of the secondary science may have been solved by the secondary theory. Such a distinction between 'science' and 'theory' is one of the reasons why I sometimes use one term, sometimes another, as the context demands." Is Schaffner saying that science and theory are the same thing? Can science be reduced to all theory? Is the whole point of scientific inquiry to get at the theory?

In Schaffener it explain that it been a reduction of biology to physic and chemistry by the discovery of molecular biology. There been given a variety of example in class like the use of x-ray, the use of electrophoresis, chromatography and other. These are apportion that these field have made to biology but what apportion those biology make to these fields (is there are any) and in which ways does these apportions have change the way science is made in these field?

Schaffner (1969) states that the goal of his paper is ‘to argue that the development of the implications of the Watson-Crick model have given us persuasive scientific reasons for believing that biology is nothing more than chemistry (p. 326-7).’ Although one could reduce biology down to the level of chemistry, Schaffner believes that ‘the chemical systematization of the chemical elements plays a most important role (p. 327)’ and that carrying out this reduction ‘does not entail the consequence that living organisms can only be fruitfully studied as chemical systems (p. 346).’

While reading Schaffner’s argument, it may be difficult to separate the level of biology from the level of chemistry when dealing with macromolecular structures. I found this to be especially difficult when Schaffner was discussing ‘essential’ chemical interactions; namely those between enzymes, ribosomes, histones, and DNA. Of these, he states that it’s ‘the nucleotide DNA sequence which is of paramount importance (p. 344).’ Using descriptions such as ‘important,’ or others that imply a sense of value, seem to me like they belong on the level of biology. At the chemical level, the nucleotide sequence of DNA is just one of many factors that play into protein synthesis, and it seems inappropriate to denote one factor as more important than another. However, I believe that after one makes the conversion from proteins to phenotype (or from DNA sequences to genes) you subsequently cross the line between chemistry and biology and allow for the use of comparative terms to arise. Therefore, is it justifiable to use ‘the implications of the Watson-Crick model’ as reason for reducing biology to chemistry? To me it seems that this model, in a traditional sense, has placed value on DNA above other factors, and would thus be a good model for drawing biology out of chemistry rather than the reduction of one to the other.

In Schaffner 1969 he talks about the reduction of biology to chemistry. On pp. 341 Schaffner is narrowed in on the Colinearity Hypothesis. He states that the genetic map, the DNA sequence, and the amino acid polypeptide sequence are all colinear which was established by Kaiser 1962 and Yanofsky 1964. Kaiser concluded from experimental results on phage chromosomes that the 'genetic map sequence and physical sequence of cistrons in the DNA molecule are equivalent...' Yanofsky demonstrated that gene structure and protein structure were associated by a one to one correspondence. AKA genetic map==protein order from polypeptide chain of amino acids.

What I am struggling to understand is the importance of seeing this reduction... I understand that the body of knowledge seems to change and grow but I am lacking clarity in asserting how the change and growth are related. Is human knowledge limited by this reductionistic process? Or does this reduction of one science into another "new" science constitute a small shift towards a more broad scientific paradigm change?

Finally, what are the negative effects associated with reduction? What are your views on reduction within biology? (is it clearly reduction or is it ambiguous)

In Kenneth Schaffner's The Watson-Crick Model and Reductionism, one of Schaffner's main claims is that biology can be reduced to chemistry and physics. I understand the part where biology can be reduced to chemistry by looking at the chemical structure and interactions occurring in DNA. What I don't understand is how biology can be reduced to physics. Is it that biology is reduced directly to physics or does biology reduce to chemistry which is then reduced to physics? When I think of physics, I think about forces, torque, etc and I don't see where any of these concepts are happening in biology.

I think your question is interesting for a couple of reasons. The first is that this was a main topic of discussion today in class and the second is in the reduction of biology to chemistry and chemistry to physics. The latter is where more of my interest layth.
I do not think that biology is being reduced (directly) to physics. The way I see it... The objects being studied in biology are being understood in terms of chemistry and the chemical processes involved with those objects. I think chemistry is often reduced to physics with this being no exception. I have to say that somehow physics or physicists have given biology more than what can be reduced... ie: theoretical contributions, experimental procedure, etc. I hope that makes sense to you.
So, I think you are correct in thinking "Is it that biology is reduced directly to physics or does biology reduce to chemistry which is then reduced to physics?"
I can see what you mean when you talk about physics being about forces and torque. What I do not see is how you do not see those concepts happening in biology... Are there no forces acting within any given biological system of study? Even with my limited knowledge of biology, in general (and specific), I see the concepts in biology through the lens of physics. ie: the words "spindle apparatus" give me a mental scene of an object that torque is acting on.

Anyways, I hope this helps clarify any confusion you may have on this topic, if that was why you posted this question, and iff you are actually reading this. Happy Turkey Day!!

I don't think Schaffner intends for biology to be reduced to chemistry, then from chemistry reduced to physics. I think he intend for there to be a direct reduction of biology to both chemistry and physics. I too, have found it easier to reduce biology to chemistry than physics, but I also recognize that physics applies to everything. Even if you are not using physical theories, you are still using basic physical principals in much of biology. Based on class discussion, I think many of us have struggled with understanding the role physics plays in the reduction of biology.

I find this question interesting. I do agree that it often seem that physisics cannot be applied to biology but the more i think about it, i think that in fact it does tend to apply to biology it just isnt that obvious at times and offten we need to break down the processes into components for the application to become visible.

Though Schaffner’s article doesn’t provide a specific description of how biology could be reduced to physics, many physical concepts can definitely be applied to biology. The physics classes I took during my undergrad tried to apply physics specifically to biology and pre-med students. Though we still studied the basic concepts of physics as you described (force, torque, etc…), many of the problems attempted to tie these examples to biology. For example, in one of my labs we studied pendulums, measuring potential and kinetic energy, angles, velocity, force, and used trigonometric equations to determine the maximum speed in which different mammals can walk. Many of our problems also applied physical concepts to cellular functions. Whether these examples suggest reductionism is still questionable, but we can’t deny that physics can certainly be applied to biology.

Though Shaffner makes a few contradictory statements over the course of his paper, it seems that he would not say that science is simply theory. He agrees with Sellars' statement that "to reduce chemical theory to physical theory is not to reduce chemistry to physics" and says something to the same effect when claiming that one can fruitfully study living organisms from a biological perspective even though it may be reducible to chemical theory. This would seem to indicate that Shaffner will say that science is more than theory: it is also comprised of the techniques and methods used in experiment (among other things, perhaps).

When Schaffner says that biology can be reduced to chemistry and physics, my impression was that he meant a consecutive reduction - that is, from biology to chemistry and from chemistry to physics. While on the biological level it may appear as though physics has no involvement, the interaction of molecules is a physical phenomena, and these interactions make biology possible. There could be many counter arguments to this, but my understanding of Schaffner's text was that he was referring to a consecutive reduction.

I would have to read Donna Haraway's paper myself, but she doesn't seem to be talking about reduction in the same sense that philosophers talk about reduction. "Reducing" biodiversity to genetic diversity is an experimental heuristic, innately fallible and incapable of truly grasping everything there is to express about biodiversity. But, it is fruitful for mathematical formulations in ecology, because genetic diversity is quantifiable in population genetics. I'm not sure many philosophers or scientists for that matter would say that biodiversity is reducible to genetic diversity, in the sense that some philosophers wanted to say that Mendelian genetics is reducible to molecular genetics. Rather, genetic diversity is a tool for estimating biodiversity, and hopefully a good one.

As for your other questions about how to show your classmates that science is not purely objective, I have a few suggestions. First, I think you can make the case for the influence of ideologies, sociology, etc. on science while maintaining its core objectivity. I think many people, except for some skeptics, would see science as the most objective enterprise we have. That's a good starting point. Once, you make that claim, you can introduce scientific biases into the picture before introducing social biases. Take a look at Stephen J. Gould's The Mismeasure of Man for an example how systematic and unconscious social biases creep into science. The important part is the unconscious part. That should be less offensive because the scientists are not culpable for their actions, yet more dangerous to the objectivity of science because it goes unnoticed.

I think it is also important to show how objectivity often sets the limits (no one is claiming any deliberate and acceptable practice of fudging the results). Through my experience in an industry lab, though we had the interests of the company in mind, especially when comparing our instruments to our competitors, we could not fake the results. There were many reasons for this, e.g. repeatability and regulatory oversight by the FDA, Dept. of Agriculture and NIST. Objectivity and reality often had the last say. I hope this helps. I don't claim its entirely correct, I'm just responding on the fly because I think you raise some really interesting points!