Doing Biology

Important words and concepts supplemental to Chapter 1, Campbell et al., 1999 (1/10/03):

by Stephen T. Abedon (abedon.1@osu.edu) for Biology 113 at the Ohio State University

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(1) Chapter title: Doing Biology

(a) Some quotes:

(i) "...science is simply common sense at its best; that is, rigidly accurate in observation and merciless to fallacy in logic." Thomas Henry Huxley, 1880

· from The Crayfish as quoted by Stephen Jay Gould, p. 2, Full House, 1996

(ii) “Scientists are critical realists.”

· John Polkinghorne (from a letter published in The Sciences 39(4):3)

(iii) “Anyone going into biology expecting to find the sorts of exceptionless laws that characterize physics will be sorely disappointed.”

· Ernst Mayr (1999, Structure for theories of biology, a book review published in Science 285:1856-1857)

(iv) “…scientists are not a select few intelligent enough to think in terms of ‘broad sweeping theoretical laws and principles.’ Instead, scientists are people specifically trained to build models that incorporate theoretical assumptions and empirical evidence. Working with models is essential to the performance of their daily work; it allows them to construct arguments and to collect data.”

· Peter Imhof (2000, Tools for Thinking, a book review published in Science 287:1935-1936)

(v) “Success in science is rewarded with attention. You gain full membership in the scientific community only by receiving the attention of your fellow scientists. Earning this attention ‘income’ is a prime motive for becoming a scientist and for practicing science. In order to maximize this income, you have to employ your own attention in the most productive way. It does not pay to find things out anew that have been discovered already. Nor is reinvention rewarding in terms of the attention paid. It pays to pay attention to the work done by others.”

· Georg Franck (1999, Scientific communication—a vanity fair? Science 286:53-55)

(vi) “Science is properly described as ‘organized skepticism,’ a realm in which nothing is to be accepted without question.”

· Philip W. Anderson (from a letter published in The Sciences 39(4):3)…

(vii) …nevertheless, and probably quite accurately, Margaret Wertheim replies with: “Science has always had a huge component of faith.”

· (same issue though continued on p. 46)

· This latter statement simply reflects the idea that ultimately not everything (nothing?) can be proven to 100% confidence. A good scientist nevertheless allows that even those things she accepts on faith could very well be incorrect

· (e.g., an agnostic accepts that God could exist but nevertheless accepts as faith that she probably doesn’t).

(viii) "Science is better understood by observing it than by trying to create a precise definition. The word science is derived from a Latin verb meaning "to know." Science is a way of knowing. It emerges from our curiosity about ourselves, the world, and the universe. Striving to understand seems to be one of our basic drives. At the heart of science are people asking questions about nature and believing that those questions are answerable."

· (p. 15, Campbell, 1996)

(b) It is "important for you to learn, by example and by practice, how the process of science works." (p. 20, Campbell, 1996)

(i) asking good questions;

(ii) coming up with good, plausible answers (hypotheses); and then

(iii) testing these hypotheses robustly, unambiguously, and honestly (from the point of view of both oneself and that of others).

(2) Wasting time

(a) The price one pays for failing to work diligently at these strategies for doing science well is wasting everybody's time.

(b) The cost of wasting one's own time is the failure to efficiently answer one's own questions (or even answer them at all)

(c) The cost of wasting the time of others can be ostracism by scientific colleagues. Above all, in science you want to avoid wasting time.

(d) On the other hand, there often is a fine line between following a difficult lead and wasting your time or the time of others. The perception that scientists are conservative comes, at least in part, from an acute sense among scientists that hard or impossible problems aren't worth wasting one's time on.

(e) The "open-mindedness" that a non-scientists may feel often comes simply from their lacking a well-developed compunction to answer hard questions robustly, unambiguously, and honestly (i.e., rigorously).

(f) Just because one or many individuals pronounce that a question is not worth addressing, however, does not mean that it either cannot be addressed nor that successfully addressing it will not be fruitful. More often than not it is instead a statement that the effort necessary to address the question is more than many would prefer to employ. Therefore it may be considered to be a question that should not be addressed, at least given limited resources (the most precious of which, of course, is time) or different interests.

(g) Thus, for some questions, science is willing to invest enormous amounts of resources to answer (curing cancer, creating weapons of mass destruction during national military emergencies, etc.), while for many other questions science is unwilling to invest many if any resources. The basic questions thus come down to:

(i) Is the end point worthwhile (i.e., if the question is answered correctly, will anyone care)?

(ii) Are the resources, suspected to be necessary to reach the end point, in excess of the perceived worth of the end point?

(iii) Is the evidence for the potential existence of both the path and the end point sufficiently robust that one trusts ones own (or others) estimates?

(iv) Finally the wild card: is the question and means to answering the question interesting, scientifically, in its own right?

(h) One finds that for conservative, applied research, using established techniques, the answers generally are yes, yes, and yes, even when questions aren't terribly interesting. On the other hand, for speculative, basic, or extremely difficult research, the answers can be no, no, no. Ultimately, however, whether or not a question is pursued is fundamentally a function of the amount of resources a society is (or individuals are) willing to devote to science, in general, or to specific questions, in particular.

(i) Thus, whether or not an attempt is made to answer a scientific question often is based as much on scientific concerns as it is on societal concerns, with the consequence that science does not always work toward its own goals with the efficiency it would prefer.

(j) ["wasting time" science research -political (Google Search)] [index]

(3) Good questions

(a) A good scientific question is one that may be answered through experiment, observation, or logical inference that is built upon previous experimentation or observation.

(b) Questions are also judged on the worth one or many perceive to be associated with successfully answering that question.

(c) In addition, questions are often distinguished simply in terms of the perceived degree of effort necessary to answer the question.

(i) For example, even successfully establishing correlation between two variables does not imply causation. Sometimes it is very easy to establish that two things happen together, but at the same time it may be very difficult to show that one causes the other (indeed, one may not cause the other but, instead, both may be caused by a third variable).

(d) "Items investigated must be well defined, measurable, and controllable. The questions should be reasonable and consistent with existing bodies of knowledge. (Individuals) have a variety of ways to exclude wild speculations."

(i) (from p. 1-2, Morgan & Carter, 1996)

(e) ["good scientific questions" (Google Search)] [index]

(4) Examples of good and bad scientific questions

(a) Examples of good and bad scientific questions (from pp. 1-2, Morgan & Carter, 1996) include:

(i) Does exposure to ultraviolet radiation cause increased risk of skin cancer?

· Good question, but not necessarily easy to answer, though finding correlations may be relatively easy.

(ii) Was Lee Harvey Oswald possessed by demons?

· Bad question. Why? Well, first you must start with a definition of demon, and then come up with some objective means of measuring possessed-by-demons-ness.

(iii) Does good nutrition lead to increased intelligence?

· Good question, but not necessarily easy to answer: (a) There are too many confounding variables that can't be well-controlled, (b) human life spans are very long, and (c) there probably does not exist a good (and inexpensive) model system for satisfyingly answering this question (i.e., if nutrient impacts on rat "intelligence," can we thereby infer that it must impact on human intelligence?).

(iv) Why do cacti have spines?

· Good question and relatively straightforward to answer, especially operationally (i.e., if herbivores eat more of plants lacking spines than those possessing spines, all else controlled for, then perhaps spines exist to prevent or at least impede herbivore browsing).

· However, note that there are two additional ways of looking at this question. One is the proximal approach, i.e., what developmental mechanisms are involved in cacti having spines? Two is the question of ultimate causes, i.e., what combination of events resulted in cacti having spines? Both of these latter questions are good ones, but ones that are much more difficult to answer than the simple, operational question.

(v) Was the malignant tumor found in the lungs of a 70-year-old man caused by his 45-year habit of smoking cigarettes?

· Good question but not necessarily easy to answer. At best, one is likely to find correlations and probabilities with no clear certainty that smoking did cause the cancer (after all, non-smokers also get lung cancers).

(b) ["bad science" (Google Search)] [index]

(5) Hypotheses [hypothesis]

(a) A hypothesis is a proposed answer to a scientific question.

(b) A hypothesis is "a proposition tentatively assumed in order to draw out its logical or empirical consequences and test its consistency with facts that are known or may be determined (Webster's, 1985)."

(i) it supplies a testable mechanism

(ii) it is not unnecessarily complicated

(iii) it conforms with existing knowledge

(d) When one speaks of testable, one implicitly implies falsifiable. That is, there should exist, either actually or hypothetically, a means by which the hypothesis may be demonstrated to be incorrect. A hypothesis that cannot be demonstrated to be incorrect cannot be demonstrated to be correct (e.g., if the negative control produces a positive result, you can't trust that the experimental procedure could have produced a negative result).

(e) Note, however, that the converse is not required of a hypothesis: A hypothesis need not be provably correct. Thus, hypotheses tend to gather favor not because they have been demonstrated to be correct, but because they have not been demonstrated to be incorrect.

(f) "The test of a hypothesis may include experimentation, additional observations, or the synthesis of information from a variety of sources."

(i) (from p. 1-3, Morgan & Carter, 1996)

(g) When employing hypotheses, one should always keep in mind the following (p. 16, Campbell, 1996):

(i) hypotheses are possible causes

(ii) hypotheses reflect past experience with similar questions

(iii) multiple (i.e., alternative) hypotheses should be proposed whenever possible

(iv) hypotheses should be testable via the hypothetico-deductive approach

(v) hypotheses can be eliminated but not confirmed with absolute certainty

(h) Note that in practice hypotheses are a dime a dozen. Very few are sufficiently comprehensive nor stand up sufficiently, to the test of time and experimentation, to achieve the status of a theory.

(i) For example, the hypotheses of scientific creationism attempt to reconcile modern observations of the universe (facts) with modern interpretation of bronze-age observations (mythologies, but arguably facts, though suffering from documentation and repeatability problems).

(ii) However, these hypotheses have poor predictive power and consequently are not considered theories, much less laws (and, in fact, by and large they do not even constitute successful hypotheses).

(i) [hypothesis and (science or scientific) (Google Search)] [index]

(6) Bad questions and bad hypotheses

(a) Questions can be scientifically not good (i.e., not useful).

(b) The problem with bad hypotheses typically is a high likelihood that they will never lead to or achieve a useful answer.

(7) Theory

(a) A hypothesis becomes a theory following lots of testing (i.e., attempted falsifications), all of which fail to disprove the hypothesis. An important aspect of this testing is that it is done by more than one (ideally by many) groups using more than one (ideally many) independent techniques. In other words, a theory is a very robust hypothesis.

(b) Webster's (1985) defines theory as:

(i) "The general or abstract principles of a body of fact, a science, or an art,"

(ii) "a plausible or scientifically acceptable (i.e., see first paragraph of this section) general principle or body of principles offered to explain a natural phenomena,"

(iii) "a working hypothesis that is considered probable based on experimental evidence or factual or conceptual analysis and is accepted as a basis of experimentation (ditto)."

(iv) "Because theories are comprehensive, they only become widely accepted if they are supported by a large body of evidence." (p. 20, Campbell, 1996)

(c) Since, by definition, a theory has gone through considerable criticism and attempted falsifications, it is very unlikely that you or me or anyone we know or admire is going to successfully demonstrate that a well-established theory is false. However, to all of you would-be Einsteins out there, please don't take that as a discouragement.

(d) ["scientific theory" (Google Search)] [index]

(8) Law

(a) A law is "a statement of order or relation holding for certain phenomena that so far as is known is invariable under the given conditions (Webster's, 1985)."

(b) In other words, a law, as far as we can tell, is an infallibly robust hypothesis.

(d) ["scientific law" (Google Search)] [index]

(9) Fact (scientific fact)

(a) A fact is what is witnessed upon observation.

(b) A fact is only as good as the observer, method of observation, and degree to which the environment is sufficiently controlled during the observation. Thus, facts are very fallible and must always be considered suspect especially if they are contrary to established theory and are not repeatable under well-controlled conditions (in other words, extraordinary claims require extraordinary proof!).

(c) In the semantics of science, a fact does not have explanatory or predictive power. Instead one speaks of hypotheses, theories, and laws as ways of organizing, explaining, and extrapolating from facts.

(d) ["scientific fact" (Google Search)] [index]

(10) Scientific reasoning

(a) The testing of hypotheses involves far more than the carrying out of experiments. Instead, a key aspect of doing science is the reasoning that goes into the designing experiments, something that I'm designating here as scientific reasoning.

(b) There are two general categories of scientific reasoning

(i) inductive reasoning

(ii) deductive reasoning

(d) ["scientific reasoning" (Google Search)] [index]

(11) Inductive reasoning [synthesis, unification of facts]

(a) unification of facts:

(i) Inductive reasoning is associated with great ideas but not necessarily very good experimental design.

(ii) Inductive reasoning involves the gathering of observations and hypotheses into a unifying whole.

· For example, Darwin's theory of evolution by natural selection was achieved via inductive reasoning: A great many observations were gathered and a unifying theme was discovered.

(iii) While inductive reasoning does not make for good hypothesis testing, the results of inductive reasoning can typically supply fertile ground for hypothesis making.

(b) synthesis:

(i) Another word for inductive reasoning is synthesis. Synthesis, in general, is analogous to the more specific synthesis observed in chemistry laboratories. That is, synthesis is the build-up of a different whole from smaller parts.

(ii) An example of a synthesis is the "Evolutionary Synthesis" from the middle of the twentieth century, which involved the building up, by inductive reasoning, of a theory of evolution that combined both Darwinian evolution and Mendelian genetics.

(i) "Many people associate the word discovery with science. Often, what they have in mind is the discovery of new facts. But accumulating facts is not really what science is about; a telephone book is a catalog of facts, but it has little to do with science. It is true that facts, in the form of observations and experimental results, are the prerequisites of science. What really advances science, however, is a new idea that collectively explains a number of observations that previously seemed to be unrelated. The most exciting ideas are those that explain the greatest variety of phenomenon. People like Newton, Darwin, and Einstein stand out in the history of science not because they discovered a great many facts but because they synthesized ideas with great explanatory power." (p. 20, Campbell, 1996)

(d) ["inductive reasoning" (Google Search)] [index]

(12) Deductive reasoning [assumption of consistency, what biology is all about]

(a) assumption of consistency:

(i) Deductive reasoning is the converse of inductive reasoning.

(ii) Deductive reasoning is the application of generalizations to specific circumstances.

(iii) This is hardly a profound statement. It simply means the application of what we generally know to specific things that we don't yet fully understand.

(b) what biology is all about:

(i) More than anything else, introductory biology introduces students to a sampling of the general themes of biology. With time you will learn to apply these themes to novel situations to deduce explanations for observations.

(ii) For example, once you understand why lipids tend to not dissolve in water, but that carbohydrates do, then you will be able to look at organic compounds that are new to you and make specific predictions as to their water solubility.

(13) Hypothetico-deductive thinking [doing science as triage]

(a) The process by which science typically progresses is employing a mechanism known as hypothetico-deductive thinking.

(b) This is a fancy phrase that basically means that one understands new observations in light of previously learned or subsequently looked up general knowledge, and that one phrases that understanding as testable predictions, i.e., deductive reasoning followed by hypothesis making.

(c) The catch, of course, is that not all knowledge is correct, knowable, or even necessarily applicable to the new observation. Furthermore, it isn't always obvious how to apply general knowledge to new observations.

(d) When you have an interesting or important (and repeatable) observation that cannot be explained in detail by current scientific knowledge, what you have is the core of what I would call an interesting scientific question.

(e) doing science as triage:

(i) Doing science often is a triage where:

· the first questions considered are those that are the most interesting or important

· the less-easily-solved or less-interesting problems are considered second (i.e., when you get around to it or have nothing of greater import or ease to work on)

· the least interesting or least-easily solved problems are considered last, if ever.

(ii) This is why questions that many consider important (Why do we exist?) are typically never considered by scientists. In a world of interesting, solvable problems, no rational individual commits enormous quantities of time and energy to questions that are not readily solved, no matter how interesting they may appear.

(iii) Think about your own life. When was the last time you elected to attain world peace and prosperity before dealing with more mundane concerns such as eating lunch or voiding your bladder?

(f) [hypothetico deductive (Google Search)] [index]

(14) Skepticism [avoidance of wasting time, extraordinary claims require extraordinary proof, predicting the future]

(a) Avoidance of wasting time:

(i) Attitudes of skepticism derive from desires to avoid wasting one's time on questions perceived to be without significant usefulness.

(ii) Typically the burden to answer questions (failure to falsify the hypothesis) is placed on the proponents of a particular hypothesis rather than the observer or the detractor.

(b) Extraordinary claims requiring extraordinary proof:

(i) Extraordinary claims, one's not consistent with an existing base of knowledge which so far has stood the test of time, typically demand extraordinary proof to be persuasive. Such proof is found in rigorous, robust, and honest attempts at falsifying the hypothesis in an unambiguous manner.

(ii) For many hypotheses, of course, existing technology and understanding is not sufficient to supply such proof, regardless of the efforts of proponents, and such hypotheses are generally discarded by other scientists.

(iii) In other words, scientists are typically skeptical of claims that "fly in the face of reason," i.e., that are inconsistent with what is already known.

(c) Predicting the future (and a buck and a quarter) will buy you a cup of coffee:

(i) Sometimes, when technologies and understanding do catch up with speculations, the hypotheses speculated turn out to be correct.

(ii) Proposed future utility of a given hypothesis, however, is no guarantee of present usefulness.

(iii) An otherwise empty promise of future utility should never be accepted in the stead of a demonstrated usefulness of a hypothesis in the present.

· (that is why science fiction can be very cool but is nevertheless still fiction)

(d) [skepticism, "extraordinary claims" and "extraordinary proof" (Google Search)] [index]

(15) Self correction

(a) "Another key feature of science is its progressive, self-correcting quality. A succession of scientists working on the same problem build on what has been learned earlier. It is also common for scientists to check