Following is a series of discussion points and replies. The Italic quotes are arguing the case to leave biology alone, while mine are toward its liberation and reform.

“….That reliance on rational evidence is also why you can’t take evolution (even Gould’s ‘fact and theory’) out of biology. Internal consistency is required in science, as are the rules of logic (and again, not to be inflammatory; I refer to logic in the formal, rules-of-evidence-and-argument sense)….”

I agree that “rational evidence” and plain logic in light of rational, empirical, in implied, evidence provides a framework for science that facilitates discovery. In biology it is currently “the fact and theory of evolution”, but I don’t think it will always be; in any case, I do agree with the concept.

(Note: “fact and theory of evolution” was a term coined by Stephen Jay Gould in a 1981 article to describe the complex system of facts and theories encompassed in the scientific “theory of evolution”.)

….” “adaptation happens in populations, and species change over time,” in the neoDarwininan sense, those processes can explain extant biodiversity and processes going all the way back to the base of the tree of life….”

For perhaps half of the people in any region that is the logical conclusion. I think it is because of this belief that the word evolution is often used in place of adaptation where the words would otherwise seem interchangeable. Certainly, as you say, the prevailing thesis in biology is not that we simply adapt to fit our environment, but that by some mechanisms of adaptation, radical improvement repeatedly happened, taking us from non-living inorganic molecules into life like DNA or RNA onward through the eons to the super beings we are perhaps destined to become. More rationally speaking, the most basic “fact of evolution” remains that “adaptation happens in populations, and species change over time in relation to their environmental and other influences. The rational facts end there and so starts the series of theories that add up to the above conclusion as an interpretation of “teh data set.”

“…To suddenly change the rules of the argument and say, at that point, “well, divine influence is required here,” is inconsistent in logical process. Brady, you’re right to note that we’re assuming that the observable part is the whole, but logically, that’s all we can assume without allowing for sudden, dramatic change in the nature of the formal evidence we accept and admit into the argument….”

I did not hear anyone say or imply that “divine influence” is required here. If you got that, you mistook me for a creationist. No, I am specifically talking about the logical “agnostic”process needed to draw unbiased conclusions from all that is known and most logically perceived.

Note: the next quote refers to this statement: “Finally, it should be accepted that the core disprovable tenant of the ‘the fact and theory of evolution’ is a presumption that life as we see it in 2014 can be explained by mapping a series of mechanical and electro-chemical processes, while attributing original cause to the power of random-over-time-infinity resulting in a spontaneous generation of increasingly reliable reproducibility. In other words the hypothesis now “fact and theory” is an effect, without a cause—apart form sufficient time—governed by mechanical and electrochemical processes eventually resulting in the earth’s entire living ecology from prion and virus to all the mammals including humans.

“…That’s as keen a turn of phrase as I’ve ever seen, and you’re right. Popper would encourage us to keep that hypothesis (I’ll call it that, rather than a core tenet)… If better, more robust, durable, empirical evidence comes along, then we’re forced to falsify this core hypothesis, but the data MUST meet those criteria. Bring a better data set, and you win!”

I believe that is an example of the overshoot. Biology is not Math. Biology exists in the realm of the complex phenomenon of life. To hold dear the current ideas, because they are‘currently held’ while demanding Math’s equivalent of empirical evidence is lopsided since the current theory itself never reached that standard. As you suggest later, this is a tightrope walk between the material and the sub-material reality, which, by the way, the other sciences acknowledge. Biology excludes the sub-material as “religious”. It is not religious; it is reality of which denial perverts perspective on the whole. Biologist will interpret sub-material paradoxically, as microscopic material, electricity, or energy, none of which match the data set we have to work with.

For as you say:

“…My experience, though, and that of most openly atheistic proponents of science (Dawkins and his crowd, Sagan and the more thoughtful) is that the evidence simply isn’t there. Part of it is that belief is inherently not falsifiable — rendering it, in Gould’s words, one of two, “non-overlapping magisteria.” One doesn’t, and can’t, falsify the other, because the evidence is simply too different. I’m not impeaching anyone of faith; all I’m saying is that one camp is using radically different notions of evidence than the other….”

Translates to: Anyone challenging the “fact and theory of evolution” will run into a ‘catch 22′which renders the task essentially impossible within the artificially imposed constraints of biological science even if the challenges represent obvious reality.

“…These differences persist even in the academic pursuit of each discipline: science relies on evidence and is (arguably) agnostic about the practitioner (even Einstein could be disproven). Theology relies on argument from history and authority (St. Augustine is a commonly cited source). They’re just not comparable lines of evidence. Science gets into this trouble in courtrooms, too. …”

“…But as an atheist, I would counter that including the spiritual dimension privileges a particular school of thought….”

If your ‘bent‘ cannot deal with the word spiritual as a reference to that particular reality, substitute the word of your choice, say:“sub-material”. Science is not inherently, this constrained. Science deals with reality “agnostically”, whatever it may be.

If observing and noting a “spiritual” or sub-material dimension “privileges a particular school of thought”, refusing to observe and note in the discussion that same sub-material reality equally “privileges a particular school of thought”. Yes, Biology currently “privileges a particular school of thought”, exactly the point! Thus, biology is inbred with a dangerously narrow gene pool of prejudice which perverts the science toward a skewed reality and a self deceiving belief that it is impartial.

“…Back to the core of the discussion: how can we get as many voices to the sustainability table as possible? Must science simply “shrug” and say, “OK, we’ll admit all comers, even if it means abandoning the rules?” Do we then admit that we’ll do,“sustainability by committee?” That, I think, doesn’t work well in science. I’m not trying to be exclusionary, but a commitment to objectivity has served science well….”

Yes, science must admit “all comers” that is open source relevant to the mass infusion of ecology. No the rules must not be abandoned, but they must be “reformed”. The budding knowledge and conscience revolution must enlighten, and open the avenues of knowledge acquisition to transparent total access of all interested parties abandoning exclusionary forinclusionary. Science club and class, meet grassroots populous!

Conclusion:

Let me give a parallel example. Leaders of states in the Soviet Union were members of the communist party. Upon independence, the leaders of the eastern ‘Stans’ all denounced communism and were sworn in as the democratic leaders until an organized vote could be accomplished. When the organized vote occurred they were voted in as the democratic leaders because no other serious candidates were allowed standing, while inconsequential ones were. Many years later after a continual re-election of “the peoples’ choice”, the same men continued to “faithfully serve the people”. At some point in the country of Kyrgyzstan, an alternative method of voting was exercised in millions rallying—in a country of 5 million—demanding the resignation of the “peoples’ choice”. Their voice contrasted with the egalitarian claims that to step down would ‘disserve the faithful voting majority who had elected them’. It all culminated in the overrunning of the government buildings supported by the refusal of the military to counter their own people. The democratically elected government, having existed on an exclusionary platform, fled in dishonor and disrepute. Meanwhile, a form of soft-sanctions was imposed over coming years on Kyrgyzstan by the nervous neighboring governments while the same democratic oligarchs have yet to lose an election 24 years and running!

Sure, all the rational seems to build a case that “biology is the fact and theory of evolution”, but the exclusionary realities and delimitations that have “served biology so well”, have in effect, turned biology into another allegorical “Stan” of untouchable theories privileging a particular school of thought and insulating the “bent” from the broader scientific critique. Even the alienation of alternative agnostic ideas and hypotheses as “religious” or “creationist” mirrors the “Stan effect” of big power in governance excluding all but the most ridiculous of candidates to stand against them, essentially creating a one party system. On a level playing field with all naturally inclined scientists on deck acting agnostically by the true and full data set of biology, with all other disciplines of science; “the fact and theory of evolution” would be trumped and prefaced by the yet stable but wholly testable theory that “life cannot spontaneously generate, but rather, life comes from life.” I believe this would open the floodgates of knowledge and acceptance of biology and revolutionize our world.