Topic: Distinguishing Mechanisms of Co-option
Member # 169
posted 29. March 2003 14:22
You seem to be confusing natural pathways with Darwinian pathways. But I am not talking about Darwinian pathways versus ID pathways but about the inference of ID from the existence of a gap as suggested by John.
quote:Until ID can be infered through a positive means, increased knowledge would seem to be reducing the gaps. Thus my proposal for John to elaborate on
If "little is known about the mecahnisms by which co-option of gene function takes place," there seems to be plenty of room for an intelligent or teleological mechanism to be involved in this transition. The question is, how do we distinguish the different mechanisms of co-option?
quote:Indeed one may be able to form a hypothesis that Darwinian pathways may have been responsible for co-option and formulate perhaps tests. Darwinian pathways restrict the possibilities. Can John formulate an ID hypothesis which similarly limits the possibilities?
What is the ID mechanism and pathway that is being proposed here? That seems to be the crux of the matter. But I thought that according to Dembski ID does not deal in mechanisms and pathways hence its focus on rejecting scientific pathways. John seems to be suggesting that there may be ID mechanisms of co-option.
For an example of proposed Darwinian pathways see "GENE CO-OPTION IN PHYSIOLOGICAL AND
MORPHOLOGICAL EVOLUTION" by True and Carroll
If however the argument is that "My point is that a design-driven co-option event would look exactly the same from our vantage point and hence the Darwinian comparison-of-similarity approach doesn't really test different mechanisms that might have been responsible for a given system. " then all John has pointed out that co-option by itself is unable to distinguish perhaps between ID and natural pathways. But what is that supposed to prove?
If John is so concerned about the truth then perhaps he will help us move forward this discussion in a more fruitful manner by proposing mechanisms and pathways for ID co-option which would help us to distinguish between ID pathways and Darwinian pathways. Claims that ID co-option would be identical to Darwinian co-option from our perspective are not very useful in furthering an ID perspective.
John then asks "Francis, show us how to test the Darwinian explanations."
Since the original question also included "And, as a corollary, how might we independently test design-based co-option scenarios?"
I would like to hear from John what are design-based co-option scenarios?
Others have already addressed the conflation of function and purpose wrt transistors, capacitors etc.
But I would like to repeat my statement which John may not have noticed but which I believe may be a very good way to differentiate between technological design and naturalistic design namely redundancy versus degeneracy. While redundancy is a typical engineering approach, degeneracy seems to prevail in biological systems and seems to be best understood from an evolutionary perspective.
To come back to the question "How do we independently test Darwinian vs. intelligent co-option mechanisms?"
I would like to see John or others propose intelligent co-option mechanisms. Does John propose that every co-option event in biology required intelligence, or may have required intelligence? Could John help us understand if he approaches ID from the eliminative perspective of Dembski's which would reject evidence for ID if there can be shown regularity or chance pathways? Also if John argues that ID cannot be distinguished from non-ID in the case of co-option, how does John deal with the objections raised by Murray in "NATURAL PROVIDENCE (OR DESIGN TROUBLE" ?
I am looking forward to seeing some intelligent design pathways and mechanisms defined before we set out to actually test for them.
Is ther anyone who proposes ID co-option mechanisms/pathways? That ID always remains a possibility for any scenario does not mean that ID should be considered as a serious alternative.
Good article on regulatory genes and co-option
As far as degeneracy and redundancy is concerned see for instance 'Degeneracy, Redundancy & Complexity in Biological Systems & Their Measures"
by Qing-jun Wang
In engineering, redundancy refers to duplication of elements within electric or mechanical components to provide additional power for protection from failure or the repetition of messages sending to decrease transmission error. Despite the commonness of redundancy in engineering, true redundancy in biological system is rarely seen due to the rareness of the presence of identical elements.
quote:The interesting question
On the contrast, examples of degeneracy exist in all fields and all levels of biology, which were discounted as redundancy
quote:Edelman in "Degeneracy and complexity in biological systems" similarly addresses these concepts:
With the widespread of degeneracy in biological system, a question has to be asked is why. It is argued that “degeneracy is a necessary accompaniment of natural selection”. However, it is “not a property simply selected by evolution, but rather is a prerequisite for and an inescapable product of the process of natural selection” because in an evolution system there is no a priori design on how to survive and any change, such as mutation or interaction with the environment, is possible to lead to strong selection. In the absence of degeneracy, there are not many chances for changes to be beneficial since there is only one correct way which not many may be lucky enough to find.
quote:Also from the True and Carrol paper referenced by John I quote:
Degeneracy, the ability of elements that are structurally different to perform the same function or yield the same output, is a well known characteristic of the genetic code and immune systems.
Here, we point out that degeneracy is a ubiquitous biological property and argue that it is a feature of complexity at genetic, cellular, system, and population levels. Furthermore, it is both necessary for, and an inevitable outcome of, natural selection.
"Analyses of crystallins found in the lenses of particular vertebrate lineages have revealed that co-option has not only marked the ancient history of eye evolution, but has also been a frequent and ongoing process within lineages. "
Does John's proposal for ID pathways and mechanisms take into consideration the frequent and ongoing nature of co-option?
[ 29. March 2003, 14:37: Message edited by: Frances ]
Member # 324
posted 29. March 2003 18:42
quote:This is the problem with the "vague designer" hypothesis -- an uncharacterized designer could, for all we know, do things however the heck he wants. The "vague designer" hypothesis can "explain" not only observations supporting standard evolutionary biology but also any other set of observations.
This is the question I am trying to get at in this thread: how do we know that Darwinian co-option events really occurred by a non-intelligent mechanism? My experience is that there is no "test" that Darwinian thinkers apply to co-option events; rather they simply look at protein similarities and use that as "evidence" for their view. My point is that a design-driven co-option event would look exactly the same from our vantage point and hence the Darwinian comparison-of-similarity approach doesn't really test different mechanisms that might have been responsible for a given system.
Darwin had a similar problem: once he had convinced someone that the special creation "poof" model was untenable, a common response was to retreat to a vaguer position such as "the plan of Creation" or whatnot. There are some great Darwin quotes somewhere on just how scientifically useless such statements are, unfortunately I can only find one at the moment:
quote:To get a little more specific, consider one major difference between human intelligent design and "design" as seen in biology. Human designs -- such as transistors, computers, radios, plastics, GPS systems, etc., etc., -- get invented in one place and then transplanted wholesale into a multiude of other "lineages" -- cars, boats, planes, rockets, etc. In biology, on the other hand, the transmittance of designs through lineages appears to be strictly limited to that allowed by known processes of heredity, namely:
It is so easy to hide our ignorance under such expressions as the “plan of creation,” “unity of design,” &c., and to think that we give an explanation when we only restate a fact. (OoS)
1) Lineal descent (parents to children, species to descendent species). This is the major one.
2) or, sometimes, lateral gene transfer (although this seems to be limited to fairly simple systems that can fit on plasmids and subject to a number of other constraints, e.g. rare in things like metazoans with protected germline cells).
In other words, in human design you see an invention originate and then get basically simultaneously integrated across a wide range of "lineages". In biological design the invention sits in whatever lineage it originated in (small groups of genes on mobile genetic elements being the exception, with a known and observed natural mechanism).
The fact that putative instances of cooption (the "same" structure being used for different functions) appear to follow the above pattern to a tee seems to me to be a perfect example of John's request regarding:
quote:There is no reason for us to expect a designer to constrain design-transmittance to the processes of heredity; and yet we see such constraints, as we would expect based on common descent (= the continous operation of everday heredity).
how do we know that Darwinian co-option events really occurred by a non-intelligent mechanism?
However, a typical response that I've seen is to invoke front-loading, or "maybe the designer constrained himself to work within lineages for some reason", or "the designer might work in mysterious ways", or some other backup defense in order to save design from the falsification given in the above argument. And this gets us back to Darwin's point about how vague designer-talk is scientifically vacuous and actually does no explaining at all.
In summary, you need at least a somewhat specific model of the designer (this does *not* require foreknowledge, just like any proposed hypothesis does not require foreknowledge) in order to have something with scientific tractability. If ID stays in the "vague" category -- then it will never rise above the level of other such vague ideas ("an immaterial innate force causes design").
PS: Another similar test is that:
1) Evolved cooptions will always have the "purpose" of increasing the reproduction of the genes of the organism carrying the new adaptation, but
2) There is no reason to expect such from IDed cooptions, indeed in human designs the designs are always meant to serve the purposes of the designer.
This is also, IMO, a good test, but again the IDist can escape by post-hoc appeals to a designer that mimics evolution for some reason. In doing so they escape the frying pan of falsification but fall into the fire of scientific vacuousness.
[ 29. March 2003, 18:48: Message edited by: yersinia ]
Member # 149
posted 07. August 2004 00:46
I just discovered this thread. Most of the arguments centered around a specific example – crystallins. Concerning that issue, I think Charlie made the most significant point:
quote:Nevertheless, I think the larger issue raised by John remains:
Now, let's look back at the crystallins: different lineages use entirely different proteins for the same purpose. Why? Sure, as John mentions in the beginning post, some of these proteins actually have apparent good engineering reasons to be utilized, but that raises the question of why didn't all crystallins use the same solution. For instance, if the epsilon and tao crystallins are particulary well engineered, as John argues, because of their double duty as metabolic enzymes, then why didn't the designer utilize them in most, maybe all crystallins? What good engineer would reinvent the wheel every time?
I propose the following: if multiple components of a system are required for function and hence were coopted at the same time, then we ought to infer design. If only a single cooption event was sufficient to confer selectable advantage, we ought to infer Darwinian process (for example, the nylon-digesting bacteria are a good example of this single-component functional system).