This is Science!
I must admit, I find it rather amusing that you decided to link to and quote an article which appears to be written by a scientist, explaining the scientist's perspective, and which corroborates pretty much everything I have said about science and the scientific method. I posted a little while ago about how Marx did not base his socialistic ideas in science, even though he called it "science"--if I had read that article before making that post, I probably could have pointed at quotes in that article that explain the point I was trying to make.
That said, the use of the "historic" vs. "non-historic" terminology as used by that author are different than the way the philosopher used the terms. It is more of a semantic difference than anything else, and approaches into a huge grey area. For example, I may wish to examine the effect of a chemical on gene expression, so I do a series of experiments using successive generations of cells (what I call "passages"). Later, I want to reexamine my experiment, so I repeat it, but I use cells from ten passages later. I find out that my cells have evolved to the extent that they no longer respond to the chemical the way they did during earlier passages. Does this mean my earlier experiments were "historical"? Does it mean my results were invalid (assuming all other components of the experiment were constant)?
I should point out that this situation is not a hypothetical--it really did come up, when I was in graduate school.
Of particular interest is a passage near the end of that same article that you linked:
Evolution is the scientific study of how organisms — bacteria, archaea, protists, fungi, animals and plants — came to be. Evolution relies on the same sort of scientific processes and evidence as do all other fields of science. The methods and processes of evolutionary biology do not differ in any significant way from those used in any other science. Evolutionary biologists use critical thinking, evidential reasoning, judgment of authority, hypotheses development, data gathering, and hypotheses testing just like all other scientists. Evolutionary biologists practice nonhistorical or historical science or both. All biologists contribute to evolution in one way or another. Some use experiments, for example with fruit flies, while others observe the sequence of fossilized organisms in the rock record. Some rely heavily on the other sciences for complementary data, for example the evolutionary paleontologist is beholden to physicists for the understanding of dating by radioactive decay of various rocks.
Darwin (Darwin, 1859) brought together a large number of observations and developed the hypothesis that the environment acted to select individual variants in a population that had particular characteristics. He did not know what caused the variation, such as eye color, growth rates, or height, but he determined that if a particular character were consistently selected by the environment through successful breeding, in the same way that dog breeders selected characters they desired in their dogs, then changes would ensue in future generations. This hypothesis he called "natural selection". As he and others gathered more evidence and added additional hypotheses in the following decades, his hypothesis became strengthened and called a theory. Evolution is a simple elegant theory in its basics, yet it rapidly becomes complex. This complexity leads to other hypotheses to account for aspects of the overall theory. For example, punctuated equilibrium — the idea that species are in some kind of evolutionary stasis for long periods of geologic time and then rapidly evolve into another species — was presented as an alternative to Darwin's idea that evolution was a gradual affair with changes taking place slowly and evenly over a long time. Punctuated equilibrium enhanced Darwin's theory by clarifying how evolution took place through time — it did not disprove the theory as some religious zealots have claimed. Today, many biologists and paleontologists around the world are working to better understand and test Darwin's theory in all its details. Some of these biologists confirm Darwin's ideas, some develop more critical details, and all constantly test the theory, but the theory of evolution has yet to be disproved in spite of all this effort.
As I mentioned earlier at post 509, Henry Gee, Editor of "Nature" was not so kind. He said: [quote not repeated here]
That quote is almost certainly part of a description of something else. While I couldn't find that quote in context, I will say that while such things as the development of language are difficult to reconstruct in controlled-experiment fashion, we can find enough evidence of language evolution to logically conclude that it is an on-going process. That does not mean that careful documentation of language differences over time is not scientific.
Evidently you have no use for Philosophers of Science like Sir Karl Popper and Carol Cleland - both of whom I've linked earlier in this thread.
True. I have little use for philosophers, and little patience for attempts by people untrained in the scientific method at trying to describe it.
Likewise, I have no use for "just so" stories which constitute much of the hypotheses offered by the historical sciences, e.g. anthropology, archeology, Egyptology, evolution biology.
That we are able to observe adaptation of wildlife in the field or evolution of bacteria in the laboratory does not make "just so" stories any less the fabrications that they are.
In my view, the historical record is simply too spotty for historical sciences to be taken as seriously as the hard sciences, e.g. physics.
Apparently, the only evidence you would accept would be a recording made by a time machine that can go back and observe (maybe by time-lapse photography?) the process of evolution as it occurred. That will never exist. Nor will we ever find every single fossil example of every member of a single unbroken lineage stretching back hundreds of millions of years, in which we can see the morphological changes as they occur. That we cannot document every single step along the way does not mean it didn't happen, or that the progression is fundamentally different than what we logically deduce.
To reject the observations that led to the formulation of the theory of evolution, and to its refinements over the years is to essentially reject just about all science--even physics.
Your use of the word "historical sciences" still does not match the usages of that term by either the philosophers or Lipps. Although you apparently reject my specific scientific discipline as "historical" because I make heavy use of evolutionary theory, I have never heard anyone describing biochemistry as "soft", or any science as "historical".
We are polar opposites here as well. For instance, I would say that the geometry (e.g. circle) exists, and the mathematician came along and discovered it.
Physical matter forms geometric shapes. Humans almost certainly observed natural circles, spheres, squares, trapezoids, etc., for millenia before the development of mathematics.
Obviously they cannot test what is not there. It is equally ridiculous to say that there can only be one explanation for evidence in the historical record.
I'll refer you back to the section of the This is Science! article that you linked earlier, and which I quoted above. There may be many explanations, but only those which are borne out in a systematic scientific analysis are accepted. You are perfectly welcome to propose an alternate explanation, test it scientifically, and publish it if it stands up to the scientific scrutiny.
Again, this 'begs the question' by assuming that the 'process of evolution' has occurred even as you admit that you cannot scientifically demonstrate that it has occurred. This is the same philosophy that produced the theory of punctuated equilibrium which 'predicted' that the evidence necessary to support it would not be found. This simply isn't science, it is philosophy.
And, as I pointed out previously, logical deduction is firmly grounded in philosophy; making it no better at explaining reality than the philosophy which underlies it. In order for philosophy not to underly belief in evolution, there must be evidence that uniquely supports evolution without appeal to the 'a priori' philosophical belief of the proponent.
If evolution is so firmly established as science, there should be some unique evidence in evolution that would be impossible for a biology created with a broad ability to adapt.
"Does it mean my results were invalid (assuming all other components of the experiment were constant)?"
Where are the results of the 'historical' experiments documenting 'evolution' that were observed in unobserved time and unobservable assumed events? It is the logical fallacy of equivocation to equate observable experiments with assumed unobservable events. It should be obvious that is a non sequitur.
"To reject the observations that led to the formulation of the theory of evolution, and to its refinements over the years is to essentially reject just about all science--even physics."
Straw man warning. It is not the observations that are at issue. It is the underlying philosophy through which those observations are interpreted that is the issue.
"Although you apparently reject my specific scientific discipline as "historical" because I make heavy use of evolutionary theory, I have never heard anyone describing biochemistry as "soft", or any science as "historical"."
Which brings us back to the question that asked what 'remarkable advance' could only have been made using an evolutionary framework?
"You are perfectly welcome to propose an alternate explanation, test it scientifically, and publish it if it stands up to the scientific scrutiny."
Isn't this more 'question begging' since the issue in question is whether or not 'the explanation' (evolution) is itself subject to scientific testing and scrutiny?
Unfortunately, failing to appreciate philosophers leaves one ignorant of the degree to which philosophy permeates one's 'scientific' worldview. A person could even end up claiming no philosophical influence on worldview which, as philosophy explains, is impossible.
Wouldn't it be funny if avoiding philosophy in the science curriculum has had the 'unintended' (?) consequence of raising up a whole host of philosophical naturalists who deny the influence of philosophy on their worldview?
In most cases, "soft" sciences do not use a historical record for evidence, e.g. psychology. To whatever extent they do, they would be considered "historical" sciences, e.g. anthropology.
In earlier work (Cleland [2001], [2002]), I sketched an account of the structure and justification of ‘prototypical’ historical natural science that distinguishes it from ‘classical’ experimental science. This article expands upon this work, focusing upon the close connection between explanation and justification in the historical natural sciences. I argue that confirmation and disconfirmation in these fields depends primarily upon the explanatory (versus predictive or retrodictive) success or failure of hypotheses vis-à-vis empirical evidence. The account of historical explanation that I develop is a version of common cause explanation. Common cause explanation has long been vindicated by appealing to the principle of the common cause. Many philosophers of science (e.g., Sober and Tucker) find this principle problematic, however, because they believe that it is either purely methodological or strictly metaphysical. I defend a third possibility: the principle of the common cause derives its justification from a physically pervasive time asymmetry of causation (a.k.a. the asymmetry of overdetermination). I argue that explicating the principle of the common cause in terms of the asymmetry of overdetermination illuminates some otherwise puzzling features of the practices of historical natural scientists.
To reject the observations that led to the formulation of the theory of evolution, and to its refinements over the years is to essentially reject just about all science--even physics.
Physics is the epitome of hard science.
Newton's theory has withstood many attempts at falsification and it remains accurate for classical level physics work.
However, to do physics at the quantum level, one needs Quantum Mechanics/Quantum Field Theory. Newtonian physics does not apply to that level. Likewise, to do physics at the astronomical level, one needs General Relativity because Newtonian physics does not apply to that level.
Newtonian physics is not treated as dogma as if it had to explain everything or the entire discipline of Physics would die along with it. Nor was it rewritten or modified to incorporate observations at the quantum and astronomical levels.
Compare the treatment of Newton's theory to the treatment of Darwin's theory at different levels of biological observations.
If a laboratory scientist went to lunch with streptococci in his petri dish and returned to find anthrax bacilli instead - he would not be claiming that he had just witnessed evolution, he'd be calling the FBI because a biological weapons terrorist had evidently gained access to his lab.
He would not however be surprised to see gradual changes in the bacteria over time. That he might attribute to evolution - or perhaps adaptation if the same environmental pressures evoked the same changes in every instance.
At the classical level, the field scientist would not be appealing to evolution if he found a litter of bobcats in a wolf's den. He'd be looking for a behavioral explanation or perhaps a prankster. But if he found the beaks of the local finch population to be longer than before, he might attribute it to evolution - or perhaps adaptation if the same phenomenon occurred every time there was a drought.
At the historical level, the field scientist would not be appealing to evolution if he found a human skull in the same location as a dinosaur's fossil. He'd be looking for a prankster. But if he found a less advanced dinosaur in deeper strata, he would probably attribute it to evolution.
But when he did not observe what the hypothesis called for - gradual change over time - which would have applied in the laboratory and field level, rather than falsifying the theory or coming up with a new theory for that level, he came up with a revision, i.e. punctuated equilibrium.
Thus, the theory of evolution is more like dogma than Newton's theory, i.e. "it must be preserved!"
And punctuated equilibrium is a "just so" amendment to a "just so" story. It cannot be otherwise because the evidence in the historical record is spotty. If we had the complete hard and soft tissue specimen for every organism that ever lived and witnessed its origin and the cumulative evidence did not falsify the theory of evolution, then I would not call it a "just so" story.
But as it sits, the scientist at that level is connecting the dots in a very spotty quantization of the continuum. It requires faith and thus, again, is more like dogma than Newton's theory.
And so, no, I do not find biology comparable to physics.