As Stephen Jay Gould describes it, there is an apparent inconsistency between the fossil record and the theory of evolution:
I do not know in what context the quotes (which I have omitted for space) were made. However, there are a few considerations here. Fossils are only formed under fairly unusual conditions. So, out of the vast numbers of various organisms, only a minuscule number became fossilized. Furthermore, since a "transitional form" could be taken to be any individual of a species, it is impossible to have an example of every single "transitional form." Perhaps if conditions are favorable for fossilization to occur, an unusual number of organisms from a single species might be preserved, which could have the appearance of a species springing up "fully formed", but that just isn't the case. The mechanisms of evolution are well-characterized; we can see those mechanisms occurring in modern living species.
exDemMom, you wrote that "I've never started off with making observations; I need to have a hypothesis in place first, or I won't even know what observations to make." But where does the hypothesis come from? If you don't make observations first, how can you tell whether the hypothesis is suitable to your investigation? If hypotheses are something you can just pick up, ready-made, off the shelf — presumably because they have been blessed by one's peers as acceptably orthodox — then is this even science?
I guess I wasn't quite clear above on the process I use to formulate a hypothesis. I was about to say that in no case is a hypothesis picked up ready-made--but that's not true, since during the entire period of my graduate studies, I used a single "big" hypothesis to guide my research, and I believe the hypothesis is still being used. But "small" hypotheses guide specific sets of experiments, and undergo frequent revision as the experimental results are gathered.
Getting back to where I said that I don't make an observation and then make a hypothesis, that's because research (observations) is hypothesis driven. I formulate the hypothesis based on where gaps in the current knowledge are, which does not require observation, but requires a very detailed knowledge of the subject at hand. I consider different possibilities about what knowledge might fill the gap--those are my hypotheses--and then I make my observations. I rarely find that the observations fit the hypothesis exactly, but they inform me as to how I should revise my hypothesis. For example: I know that exposure to a poison causes symptoms after a week, with death occurring in two weeks (on average). The symptoms might include thymic damage. So I hypothesize that the poison attacks thymus cells and kills them. I put thymus cells into several flasks, and expose some to the poison. I see no difference between the flasks; all cells remain healthy. So, I can reject the hypothesis that the poison attacks thymus cells, and develop a new hypothesis. And so on.
BTW, you do not say where the "signals" emanate from; nor do you indicate how the myriads of reactions are coordinated, dynamically, instantaneously, simultaneously utterly collaboratively from moment-to-moment for the purpose of maintaining the life of the organism.
That's because there are so many signals, from so many sources, that it is impossible to state where they all come from, or what all the feedback mechanisms are. Signals can be passed between components of a single cells; they can be secreted into the bloodstream by glands and picked up by target cells; they can come from externally; they can be chemical, light, or heat. A typical pathway might consist of a cell encountering a sugar, and activating a pathway to metabolize the sugar, possibly through the sugar binding an enzyme necessary to the pathway and "turning on" the enzyme. The metabolism continues until the sugar concentration is so low that it doesn't bind the activating enzyme any more; that feedback shuts down the pathway. Each pathway, taken alone, is fairly straightforward and amenable to understanding; the thousands of pathways all competing with each other and yet enabling life to continue is really where the wonder is.
Sorry, exDemMom. I should have provided the cites: The Darwin quote was from The Origin of Species, New York: Oxford University Press (1998), pp. 140, 141, 146, 227. The Gould quote was from the transcript of a Lecture he gave at Hobart and William Smith College in 1980.
Thank you for the plausible explanation of why transitional forms are scarce in the fossil record, and the problems of interpreting what is found — or not found as the case may be. However, it seems to me that a "plausible explanation" is not necessarily the same thing as what actually occurred. Your explanation is further freighted (it seems to me) with the problem of how to prove "absence," of how to prove a negative....
You wrote: "The mechanisms of evolution are well-characterized; we can see those mechanisms occurring in modern living species." This may be a stupid question, but are you here suggesting that evolution is entirely "mechanistic?" That biological organisms — thus modern living species — are essentially "machines?" Well, if so, how does a machine become a living being? Yet Darwinism can't tell you what life is.... So why are we justified in concluding life forms are "machine-like?"
All these arguments we've been having regarding the definition of a species to me basically boil down to what taxonomic category we want to sort a particular specimen into. While taxonomy is a wonderfully useful thing, what it is not is the natural world itself. That is, it is an abstraction from, and a formalization of the natural world. Which is fine — unless one commits A. N. Whitehead's famous fallacy of misplaced concreteness, which consists in taking the human-created formalism for "the real world," eclipsing the natural world altogether. The problem is this falsifies reality, for the natural world is ever so much "messier" than can be fully captured in any neat, well-defined formalism. I cite Kurt Gödel's Incompleteness Principle in support of this statement.
Another way to describe the situation would be to say that any formalism stands in the same relation to the real world as Kant's phenomenon — knowledge of reality based on sense perception — stands vis-á-vis the noumenon — the "thing" as it is "in itself," i.e., in its full existential completeness.
As Heraclitus said, "Nature loves to hide."
But I digress.
exDemoMom, you wrote:
....I don't make an observation and then make a hypothesis, that's because research (observations) is hypothesis driven. I formulate the hypothesis based on where gaps in the current knowledge are, which does not require observation, but requires a very detailed knowledge of the subject at hand. I consider different possibilities about what knowledge might fill the gap —those are my hypotheses — and then I make my observations. I rarely find that the observations fit the hypothesis exactly, but they inform me as to how I should revise my hypothesis.Sounds like a good working model to me! Yet I guess everything depends on the soundness of the hypotheses, which will depend on the soundness of the initial hypothesis or premise that generates the following hypotheses sequentially in time.
Here's where things get dicey. It is so obvious to me that you have great love for your work, are scrupulous about its proper conduct, are most likely highly successful at it, and have zero doubt about its, shall we say, epistemological foundations. That is, you exhibit all the qualities of fides in action. Fides being the Latin word for "faith" and "trust." In this you are like any Christian, any "person of faith." Hold that thought.
It seems to me the reigning fallacy of our time, which has perverted so much of human experience and understanding (i.e., the cultural evolution of the human race), can be stated thusly: Faith and Reason are necessarily mutually-exclusive entities.
To me, such a notion is nonsense — and I cite you as evidence!
The problem is that the Faith vs. Reason problem gets further reduced to a conflict between "science" and "religion." "Reasonable" people [e.g., scientists] are not supposed to be "religious" people [e.g., Christians]: Faith and reason cannot be combined without tainting "science." Or vice versa. They must stand apart forevermore!
Arrgghhh! At this point I recall Bacon's observation, "[W]hat a man had rather be true he more readily believes." Every man believes in something. The propensity to faith is in-built in the human character, if I might put it that way.
Even an atheist believes in something: The soundness of his atheism. Whether that is reasonable is another matter.
But the two — faith and reason — are designed to be in synergetic relation, not in a relation of mutual exclusivity. Or so it seems to me.
You wrote, "there are so many signals, from so many sources, that it is impossible to state where they all come from, or what all the feedback mechanisms are." So is the task impossible?
I suppose the first point that needs to be considered is the nature of a signal. By definition, a signal is "…a gesture, action, or sound that is used to convey information or instructions, typically by prearrangement between the parties concerned…." [Oxford English Dictionary On-line]
Thus, signals presuppose some sort of intelligent communications between intelligent agents or actors.
Does Darwin's theory have anything to say about that?
Thanks for putting up with me, a person coming from the epistemological and mathematical side, more than the biological side for sure.
Thanks for your excellent essay/post, exDemMom! Good to speak with you!