Posted on 02/14/2002 3:30:12 PM PST by jennyp
This quote from the link you gave is very revealing to me.
In terms of a 21st Century view of evolution, the major importance of natural genetic engineering is that this capability removes the process of genome restructuring from the stochastic realm of physical-chemical insults to DNA and replication accidents. Instead, cellular systems for DNA change, place the genetic basis for long-term evolutionary adaptation in the context of cell biology where it is subject to cellular control regimes and their computational capabilities (9-11).
Did you read my #123? How about this from that post:
I've seen some hypotheses offered by various camps: "all replicative biological systems will involve proofreading", or "bacteria will perform terraforming function for future evolution", or other such things.
The hypotheses may have to await technology for testability, but they are both clearly testable.
1) Knock-out proofreading systems from cellular replicative, translation, and transcription machinery. The ID hypothesis would be that evolvability will be lost, i.e. this altered population will shortly yield its existence to error catastrophe.
2) Identify the biological features important for the terraforming function. The ID hypothesis would be that these features are more important as role in future evolution than they are in whatever role they serve for the organism. Julie Thomas has an essay expounding upon this very hypothesis. It’s currently off-line, but I’m trying to locate it for you.
This seems to be equivalent to untestable. There's no indication that the technology will become available (nor indication that it will not.)
How does this distinguish ID from other other evolutionary theories?
What features are these? What is terraforming? The ability to kill everyone with bombs or poison gas or biological organisms? Beavers change the landscape (and atmosphere) as much as most creatures.
If there are no such features, does this refute ID? If these features exist but are not important (and how is importance measured?), would this be a refutation? There doesn't seem to be much testable here.
Perhaps. But it's not unusual in the Sciences for an experiment to be conceived of well in advance of the technological availability allowing execution.
You wrote: How does this distinguish ID from other other evolutionary theories?
I wrote this to Nebullis on another thread:
ID is not a theory, and ID is not a hypothesis. ID is often put in contradistinction with evolution by those who do not understand it. You made that error earlier. ID should be put in contradistinction with MN as practiced by evolutionary biologists. It is an epistemological challenge to the philosophical underpinnings of the field.Every field of Science has slightly different epistemology. Archaeologists, for instance, don’t exclude teleology in their science. (That would be silly, hmm?) Yet evolutionary biologists clearly do. As Christian De Duve says: "Any hint of teleology must be avoided."
So the listed hypothesis that begins this thread is not THE ID hypothesis; it is one possible hypothesis that is consistent with ID and inconsistent with MN.
Why is it inconsistent with MN? Because the MN assumption requires the conclusion that life came about by abiogenesis. If self-replicators require proofreading to be evolvable, then abiogenesis within the biochemical platform is impossible.
If there are no such features, does this refute ID? If these features exist but are not important (and how is importance measured?), would this be a refutation? There doesn't seem to be much testable here.
You ask all of these questions, indicating that you know not of what you speak, and then you finish your post by concluding that there's "not much testable here".
This is indicative of a closemindedness. I'm therefore not sure you're worth the effort. A friend e-mailed me the Julie Thomas essay outlining the terraforming hypothesis. It's over 20 pages, without abstract. I would make the effort to summarize the document if I had any thought that I might not be wasting my time.
What say you?
If "...ID is not a theory, and ID is not a hypothesis..." what is it's point? Under these conditions, it's not even useless.
I've been reading this link & your other recent posts, and I have to say that although the possibility of these other functions is very intriguing, you guys are making quite a leap when you think they help ID in any way. Or even that they hurt the Modern Synthesis, unless you define "Modern Synthesis" very narrowly.
I can see how "junk DNA" could actually be useful for several reasons, and the explanation that there just aren't any mechanisms to edit out junk DNA & that's why they keep piling up in the genome never sat well with me. The heirarchical nature of the genes is not surprising, and the regulatory nature of the promoter regions makes lots of sense. And the fact that introns can be spliced together in more than one configuration per gene - depending on the circumstances & cell type - introduces a whole new level of complexity & subtlety to the resulting structures. And if it turns out that the rates of certain kinds of mutations really do increase when the host organism is stressed, that would be Nobel material.
But. Still. None of this helps ID any! It actually helps Nebullis' prediction in #107 that "if [ID] looks at life, it will find more evidence of evolutionary processes." Evolution is more complex & hierarchical than had been assumed. OK. But there's nothing there that opens the way for a mind to enter into the process - just more complex evolution!
Deny, Deny, Deny. I suppose "A Tale of Two Cities" is merely a very complex arrangement of one type of chemicals atop another type....
removes the process of genome restructuring from the stochastic realm of physical-chemical insults to DNA and replication accidents
Obviously it does, and any unbiased observer would recognize as much. You assume that all of these complex systems arose via Natural Selection. But Shapiro is finding these complex systems in the simplest life of which we know. There are two reasons why this helps ID.
1) Their origin is currently unaccounted for. Attribution to NS is purely speculative.
2) The complexity of these unaccounted for systems helps account for future evolution. You attribute this future evolution to Natural Selection. But if these systems were indeed designed, which you cannot exclude as a possibility (except by philosophical assumption), proper attribution for future evolution should go to frontloading.
I’ve been re-reading the Julie Thomas essay. Though there is no abstract, there is a summary which may not be too long to post:
SummarySo I ask you: Is ID fundamentally religious, or fundamentally scientific?We began by considering the origin of life in terms of design and employed the objective of terraforming to bring focus to our approach. Immediately, a design problem emerges, namely, how would our designed cells obtain biologically useful nitrogen necessary for the synthesis of their amino acids and nucleotides? Without a solution to this problem, the goal of generating a sufficient biomass to terraform the planet would appear unreachable. This then led me to the enzyme complex, nitrogenase, as this molecular machine nicely solves this design problem. Thus, I ran nitrogenase through the SIBO screen and found it to be a good candidate for design. Finally, I considered other biochemical aspects of nitrogenase from the perspectives of evolution and design and attempted to show how, at the very least, all such aspects can be coherently interpreted with the concept of design.
But the most encouraging thing about this whole analysis is just how easy it is to employ the concept of design to study the biological world from a novel perspective. Problems for SIBO and design really become opportunities to address issues through the use of research. That is, once one is able to find a plausible design objective, using simple analogy and extrapolation of human-like purposes [which is something science unconsciously does in biology), "design problems" emerge that beg for more information and more research. In my previous discussions of other IC systems, I have outlined several areas of potential research and have used design to generate testable predictions (which is some cases, turned out to be supported by evidence). In this case, the potential research opportunities are many. Imagine a design institute focused only on this problem. What would its labs be doing?
1. What is the minimally complex state of nitrogenase and how much evolutionary noise is involved?
To answer this question more fully than I have proposed, we would need to sequence several genomes of distantly related nitrogen fixers and further characterize these complexes at a detailed biochemical level. Put simply, SIBO and design are sufficient motivation for doing basic scientific research on this level.
2. How do we explain the similarities that are part of the FeMo protein in engineering terms?
Here we might begin looking for ways to reinterpret evidence of "gene duplication" (similarities) in purely functional terms. The concept of NAIGS is simply a vague beginning. This approach would strongly encourage the redesign of molecular machines to tease out these design principles. It should also be remembered that if life was designed around such principles, it would not be surprising to see standard evolution and gene duplication exploit these pre-existing strategies through natural selection. Thus, even the study the products of evolution-by-gene- duplication may indirectly shed light on these design principles integrated into life.
3. If nitrogenase was designed, what was the source of its electrons and ATP?
SIBO had to begin somewhere. Prior to nitrogenase, I have discussed five systems. I first discussed DNA replication as a test case to determine how robust IC was as a criterion. This system was chosen because so many of its components were vulnerable to the standard criticisms leveled against Behe's thesis. I used this system to introduce concepts that better refined IC and the type of phenomena that is invoked to discredit the design inference (see the introduction to my original posting on DNA replication and IC). Then, flagella and the F-ATPases were chosen largely because of subjective appeal (basically, I think they are neat). Next, I chose the synthesis of the bacterial cell wall as the origin of this system would seem crucial to the origin of cellular life and it was a system that strongly implied the design of the cell. Finally, I considered the Kreb's Cycle as I was challenged to do so. I found that I could not score this as a design candidate as it failed to pass several criteria outlined in my original posting on DNA replication.
But now that some of the "data points" have been filled in, focus is beginning to emerge. The choice to analyze nitrogenase followed from the speculation involved in the hypothesis of terraforming that emerged from my consideration of the five IC systems. And now we can see that nitrogenase as a designed system points to something else, namely, what was its source of electrons and ATP? It is worth noting that the F-ATPase as a designed entity nicely fits into this scheme and this was an unanticipated realization. Now both the design of the F-ATPase and nitrogenase are converging on the electron transport chain as something that was designed. Thus, a design lab might attempt to gather all information about this particular system, and generate needed new information in order to put an electron transport chain through SIBOS.
4. Why design nitrogenase so that it is oxygen sensitive? This feature doesn't seem to fit nicely into the hypothesis of terraforming. Yet this problem led to the following hypothesis:
H: The oxygen-sensitive aspect of nitrogenase is a necessary byproduct to carry out efficient nitrogen fixation.
Design research would thus seek to understand exactly why nitrogenase is oxygen sensitive. As in #2, this would eventually entail attempts to design alternative nitrogenase activities to determine if oxygen-sensitivity is inherently coupled.
5. Were cells originally designed with mechanisms to protect nitrogenase from oxygen? If so, why? If so, how? Does the hydrogen produced by nitrogenase actually play a role in oxygen protection?
6. Can any of the mechanisms of nitrogen fixation regulation be scored as the product of design? Do any current mechanisms reflect this state? Was the original state a mosaic of current mechanisms?
7. Is it possible to design new bacterial cells, by recombining and modifying different metabolic modules, so that N2 fixation is not as costly as it is in the cells we observe today? If such a cell could be designed, how likely is it that is reflects originally designed cells and what are the reasons for thinking so?
8. Is there evidence that the mechanism of horizontal transfer was designed? Are there any clear examples where nitrogen fixation has been passed on by horizontal transfer?
While some of these questions can be approached today, most of them require much more knowledge and advanced techniques to offer meaningful answers. Nevertheless, I am optimistic that as our knowledge and abilities improve over the next few decades, such a design approach will be viable and fruitful. Add this to the various lines of inquiry I have proposed for the OriC, the bacterial flagellum, and the F-ATPase and I remain perplexed as to why anyone would think a design hypothesis was incapable of guiding a coherent and systematic research program.
With random mutation also being eliminated from the evolution equation, per my previous citation, not much is left for the pure Darwinian explanation, if this analysis is correct. That seems to leave any argument for a purely Darwinian explanation in the area proximal to the formation of the complex cell. This lies outside the presently observable and lies close to the question Darwinists studiously avoid, abiogenesis.
4. Why design nitrogenase so that it is oxygen sensitive? This feature doesn't seem to fit nicely into the hypothesis of terraforming. Yet this problem led to the following hypothesis:
H: The oxygen-sensitive aspect of nitrogenase is a necessary byproduct to carry out efficient nitrogen fixation.
Design research would thus seek to understand exactly why nitrogenase is oxygen sensitive.
I'm sorry Jazz, this is pure foolishness.
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