I am creating this topic for a new discussion emerging from Is there really information being conveyed within a cell?
What might have been a flame war is touching on questions which are intended to be the heart of this forum. I will offer my opinion on that after I move those comments here. I urge viewers to read all the comments at least as far as my next highlighted comment before replying tit-for-tat to any of them.
I note that. I also note that it was in response to Dan pointing out the massive lack of admissions in the ID literature. Do you agree?
Yet I clarified what I wrote, as it was completely dependent on one’s use of “made of.” Do you disagree?
We definitely agree on that!
As an example, here is a statement of fact that is highly relevant to @theaz101’s focus, translation:
“A protein within the ribosome known as a peptidyl transferase then catalyzes a polymerization (linking) reaction…”
Do you agree with it?
I’m interested in your response to:
It is not clear to me how systems theory or biology is (or can be) in any way an alternative to (or in opposition to) evolutionary theory or biology. I’m all but certain that none of the systems biologists whom I know, or the even larger number I have met, would see that either. Can you elaborate? What is the meaning of “neutral” there?
Heartfelt thanks for that.
That’s fair. In fact I did notice where John made a correction and I probably should have mentioned it. I suppose it was the best immediate example I could find of the problem I was trying to address, and it seemed all the more relevant since I was addressing him specifically.
I would like to think that if John knew what people like me really thought of him he would soften his rhetoric a bit. My wife asked me why I get so nervous posting here and responding to people like John (or you and others here), and I told her, “These guys are not just exceptionally intelligent, they know so much more than I do that a lot of times it’s downright intimidating.” And of course reading insulting rhetoric, likening me to a third-grader for example, only makes that feeling worse.
I can’t verify one way or the other, but suppose you’re right and they don’t own up to errors the way they should. I think it’s possible such failure is a symptom of the very problem under discussion; that is, maybe they think that if they do acknowledge errors (especially errors affecting their central argument) a sizeable segment of the scientific community, here and elsewhere, will ridicule them and show them no mercy. I honestly don’t know. From what I understand, though, the whole idea of Peaceful Science was to have a place where that would not happen.
But I agree that examples of them publicly self-correcting would be helpful, and in fact I hope some of them are following this conversation. If I may: Scripture says “Confess your sins to one another…that you may be healed.” Maybe acknowledging error, or even explaining why it’s so difficult to do so in the context of public evolution debates, would help heal the breach. In any case, I personally would love to see some of the more familiar ID people come back to the forum and participate the way they once did.
I would say that’s great advice, and well stated.
It’s worth plenty, thank you. And you’ll notice I’m not exactly averse to long responses. 
Presuming that by systems theory you are meaning a top down, holistic, approach to energy flow, ecology, morphology, and physiology; that is not an alternative to evolution. The biological systems we see before us in the present are a snapshot of evolution, and evolution is biological systems over time. As in all the sciences, understanding a present state requires understanding of process and change.
And to be even more fair, maybe mentioned it directly to me, instead of third parties?
Wow, Don. Have you never considered the impression YOU have made?
Let’s go back to your first appearance here:
Continuing the discussion from Is Evolutionary Theory a Fallacy?:
You never replied to Michael’s polite, respectful question! Your dodging spoke volumes.
You told us clearly what you thought of us right off the bat. And there’s the revealing bit where you obviously derived your judgment of a whole field of biology (not just theory) on a single book written by a single, very arrogant guy.
Do you not see your book, which you started here by touting, as an explicit claim to understand biology and biology education better than the experts do? Do you not think that if you had approached this forum pseudonymously and asked questions, that we would have interacted with you very differently?
Golden Rule, man.
But would any of us have responded in an intimidating way if you softened your rhetoric, not just a little bit, but a whole lot? Why write a whole book claiming that we don’t know what we’re doing, on a subject you admit you know so little about?
Don, if you think that your accusing me of:
made any sense at all, wasn’t incredibly rude to me, or should have been handled more respectfully by me, please explain it to me in detail. I was responding directly to the attitude you expressed.
If you want to start again, please excise the insults and respond directly to my substantive response:
Do you disagree with any of that?
No, I don’t. In my book I explain why that is not actually the case.
Yes, I think so, and if I were to go back and do it again I would do it differently. If I offended you or anyone else, I can honestly say that was not my intention. Also let me add that not everyone here responded to me the same way. Some were more friendly and cordial, others less.
I am not claiming that you don’t know what you’re doing. I am, however, claiming to have reasons to suspect that evolution is not quite the “phenomenon” you think it is – whether you know what you’re doing or not. My book explains those reasons. Think of the history of science. Lots of brilliant scientists have been proven wrong, even “spectacularly wrong,” about any number of theories. So even if you turn out to be spectacularly wrong you’re still in pretty good company.
Perhaps more importantly, I am claiming freedom – to think for myself, to write books if I feel inspired to do so, and to express my opinions here, again if I feel so inspired, in keeping with the open invitation to participate in the Peaceful Science forum: “Science can certainly be wrong. At times it is. Even when it is right, science’s certainty and scope are sharply limited. If you feel the need, go ahead and disagree with science. You might even be right….” Remember that there is a chair saved here for me.
Anyway, this will be my last reply to you. There aren’t a lot of people I simply can’t get along with, but admittedly there are a few and you are one of them.
That’s not too far off the mark. The only thing you get wrong is the sequence of events.
ID proponent makes an error or false statement, often one that would be easily evident to a person familiar with the relative scientific topic.
The ID proponent’s error is pointed out and corrected in good faith.
Rather than gratefully accept this assitance, the ID proponent refuses to acknowledge his error and, instead, engages in vitriolic attacks against those who corrected him and claims to be a victim of oppression.
After over twenty years of such behaviour by ID proponents, with nary a single exception, they increasingly become the targets of ridicule, although at the same time the careful corrections of their many errors continue to be made.
In that case, does it surprise you that ID proponents are treated the way they are?
For those of us (all of us, I suspect) who have no interest in reading your book, could you present these reasons? I would also like to know what explanation you have for the history of life, if evolution isn’t it. I’ve asked before, and you have consistently ignored such requests, which strikes me as rude.
Exactly what I’ve always thought.
Yes, that’s pretty much what I mean by systems theory. And I think you’re right that understanding present states in terms of process and change is one of the distinguishing characteristics of science. But I don’t think analysis of the dynamic causal interactions that occur within and among biological systems and subsystems, or of their characteristics – functional integration, nestedness and so forth – requires understanding how those systems came to exist in the first place.
In my vision of a systems-centered approach, the origins of many of those systems would remain mostly unaddressed (hence unexplained). Evolution and possibly other theories addressing origins would be set aside as a branch of biology dedicated to those questions, but would no longer be the central organizing principle. Such an arrangement might be very roughly like the relationship of cosmology to the standard model of physics.
I like the idea of systems theory just because systems appear to be a ubiquitous feature of the entire biosphere and there is much to discover from that perspective. Also it would have the added benefit of being religiously-philosophically neutral in a way that evolution and ID evidently are not.
There is indeed a place for you. The @moderators here are among the most patient people I’ve ever encountered, graced with abilities I simply don’t have. They can’t do miracles (nor can the gods that at least two of them confess) but I think they can help if you want to try a topical discussion of an idea or two. It doesn’t have to be a crapfest.
However, you might not fully understand the expectations that many of us bring, unapologetically, to such discussions. Speaking just for myself but likely for most others here, we don’t care much about “opinions” about science. What I mean is that, for example, it simply doesn’t matter what one’s “opinion” of the C-value paradox is. What matters is 1) whether they tell the truth about it (I know of zero ID proponents who do) and then 2) how they think it might be explained. Now, #2 involves “opinion,” great, let’s discuss. But #1 is not actually about opinion, and when I see organized misinformation about it, couched as “disagreement,” I recognize plain old dishonesty. I sense from your writing so far that this is an important distinction to make, because I am a bit concerned that you use terms like “opinion” and “disagreement” in ways that can be misleading. Unintentionally so, I am fairly certain, but… potentially problematic.
So. What shall we disagree about?
Well for starters, universal common ancestry, the evolution of new phyla in the Cambrian, the evolution of irreducible structural adaptations, etc., cannot really be one big “phenomenon,” because a phenomenon is observable by definition and to witness all that would in principle require observation of virtually the entire history of life on earth (the vast majority of it undocumented). Evidence, inferences, and arguments are another matter, of course. But as I argue at some length in the book, at the core of what Darwin called “one long argument” appears to be a fallacy of composition, which remains (at least implicitly) at the core of most evolutionary explanations for functionally complex systems to this day.
One reason I wrote my book was to air my thoughts on what has always been for me an important but vastly wide-ranging subject without having to debate on a forum like this ad infinitum. Another reason, which may surprise you, was to learn more about the subject myself. For me there’s really no better way to learn more about something than to write a book about it. In a lot of respects what I set out to write scarcely resembled what I wound up putting to paper.
As for my explanation for the history of life: it won’t surprise you to hear that I think the creative activity of God best explains the origins of the universe, of life, of eukaryotes, of new body plans in the Cambrian, of chordates, of vertebrates, of irreducibly complex biological systems, and especially of remarkably intelligent, morally aware beings like you and the other scientists here. But I will emphasize again that my explanation is not supposed to be scientific.
Now if I didn’t answer you previously, it may be that I didn’t actually have an answer at the time. Or that I didn’t have the time. Or even that I didn’t think what you said was particularly interesting or relevant. Usually when that’s the case I have tried to remember to “like” such posts to acknowledge that I appreciate the question even if I can’t or won’t answer. But please don’t take it as rude.
Suppose I posted something and a day later saw that twelve people had responded to me or asked me questions. Do you really think I would be obligated to abandon all my other personal pursuits and responsibilities, and answer each of them? I mean, it’s an informal discussion forum, not a congressional hearing. On that note, I plan to stay away from the forum for a while and get caught up on other things (though I hope to return). But be of good cheer: I was working on something else when I saw your post today and dropped it just to answer you.
While that may sound reasonable, it really does not work, because among other reasons, the present is not static. Systems are dynamic in real time, and that reality is why creationist allow limited concepts such as microevolution, baraminology, and plate tectonics, all the while attempting to locate some sort of fence around the extent of change possible. This exercise invariably is beset by arbitrary fiat proclamations driven by dogma.
Understanding the dynamics of biological systems naturally sheds light on their development. Observing how endogenous retrovirus insertion happens in present systems sheds light on the genetic sequences handed down from the past. Observing the generational rate of mutation leads to genetic clocks. Measuring half lives allows for radiometric dating. And given that nature is all of a cloth, the systems come together. Radiometric dating of the Hawaiian chain matches with the measured rate of tectonic drift, and record of magnetic reversals, and that fits well with the erosion observed in the sequence of islands, which fits with the isolated ecology. Name any process, and those gears will interlock with others which validate an old and dynamic planet. Systems imply consilience.
A few hundred years ago, it was possible to believe that the world was created, and from then on nothing changed. Because nothing appeared to. There was no GPS to measure plate tectonics, no DNA testing to detect the generation rate of mutation, no view of deep space, and no mass spectroscopy of radiometric decay products. There is not any returning to such an oblivious and naive worldview. The precision of modern instrumentation divides time into nanoseconds and distance into femtometers, and nothing stands still anymore. It is inescapable that an dynamic understanding of nature extends explanatory power further into the past.
That is not correct. Science can, and has, examined the supernatural. For instance:
Intercessory Prayer for the alleviation of ill health | Cochrane
Please elaborate on what you believe is the fallacy of composition committed by Darwin and every other evolutionary biologist that has come after him for the past century and a half. TBH, I am highly skeptical that such an error could have been committed for that long with no one but you noticing.
This seems to be something of a strawman. I don’t think anyone thinks that those are directly observable as you imply. At best we have another serious misunderstanding - which really does not bode well for your argument.
Ah, Stephen Meyer and Darwin’s Doubt. Rumraket may have thoughts on that.
http://theskepticalzone.com/wp/beating-a-dead-horse-darwins-doubt/
Ok. Explain it then. All the relevant data.
Thanks for the reply, though I undertand that you won’t be continuing. Sadly, it has problems. The above, for example, is the same basic misunderstanding of science that Ken Ham makes with his artificial distinction between “operational” and “historical” science. Presumably you believe that protons exist, despite the fact that you have never observed one. All you can see are effects that are most reasonably explained by their existence. It’s the same with everything you mention above. All science is inference from observation, nothing more.
Have you forgotten how easily your claim was refuted when you presented it here? If every step of a 100-mile journey is doable, isn’t the journey doable? So much for fallacies of composition.
A better way to learn is to pay attention to what people say to you.
That’s not a satisfying answer because it’s so vague. How is this creative activity manifested? Fiat creation, ex nihilo, of “kinds”? Macromutations? Lots of micromutations? The “cosmic billiard shot”? I especially wonder to what extent you allow for common descent. But you probably aren’t reading this. Too bad.
I considered NOT approving John’s comment (which I am replying to), because going back to Don’s first visit here and dredging up that old argument seems unfair. At the same time I think John has a legitimate complaint; it is unfair to make claims that a working scientist, or indeed ALL scientists, are ignoring something to basic as a Fallacy of Composition. @misterme987 approved the comment while I was pondering, and I would have too given a bit more time. The discussion since has not turned this thread into a game of Brockian Ultracricket, for which I thank all involved.
It does warrant a thread split, which I will do presently.
No one is denying your freedom of thought or expression. I think the trouble starts at the good old Demarcation Problem.
Demarcation again, mixed in with something else. The something else runs the gamut from mild misunderstanding to outright lies.
I think I can speak for everyone here, that we appreciate this understanding. Thank you.
We try, and I think we do far better than the typical FB group featuring arguments about Science and Religion.
Indeed.
From the scientific perspective, very few claims from Intelligent Design or Young Earth Creationism warrant any discussion at all, except to explain the scientific thought to the inquisitive. For example the YEC claim that the Second Law of Thermodynamics prohibits evolution has long been debunked; it is even on a “list of arguments that Creationists should not use”. BUT an equivalent claim, that “Evolution cannot create new Information”, remains common in ID arguments. Should we discuss such questions?
ID frequently makes claims about the improbability of “something” evolving, and this invariable depends on math that is flawed in calculation or interpretation, or both. When someone who has the education to correctly understand that math but makes these claims anyway (like William Dembski), do we really want to take them seriously?
If we restricted discussion only to topics that have scientific or educational merit, there would be less to discuss, and very little to argue about. Yet here we are arguing about it. 
Much of the argument is our own damned fault. Too many are eager to prove the other wrong before establishing the basis of the original claim. Faulty claims fade away under careful examination, but that is rarely what happens. Instead, someone jumps in to argue against the claim, tacitly accepting the claim has merit, and setting off a long and often pointless argument based on a false premise. We really should not allow ourselves to be goaded into pointless arguments.
We create these arguments in part to resolve disagreement, and in part because we enjoy arguing. It’s a hard habit to break, and I have to count myself among the offenders, but I’m trying to be better about it.
Material evidence of the immaterial is unlikely. However, I don’t think questions on the edge of the Demarcation problem will ever go away.
This might require another thread split. 