There is no inherent conflict of interest in citing one’s colleagues or collaborators, even if their lab adjoins yours. Perhaps you are thinking of peer review, where it is a huge COI to review a colleague’s paper; doing that is no mere faux pas – it’s misconduct.
@John_Harshman is right to label the whole thing “incestuous,” and everyone should know by now that an explicit strategy of the DI is to create illusory scientific controversies and then to portray DI affiliates as heroic combatants in fictitious scholarly disputes. In that context, it is definitely unethical (and can amount to misconduct) to selectively cite colleagues or allies (regardless of their affiliation or proximity) to distort the nature of (or even the existence of) scientific uncertainty or disagreement. I don’t think that has happened here but it’s pretty close.
CORRECTION: what I wrote below is wrong. The Burgess paper is published in a journal that does in fact offer double-anonymous peer review, subject to author choice. And Burgess chose double-anonymous, meaning that neither he nor the reviewers could see each other’s identities. This is all revealed under “Article and author information” on the paper. I’m sorry about that! My inaccurate statement is left below so that my shame can be as complete as possible.
Quick note, not super important but: double-blind peer review is very rare in science and is not practiced (as far as I know) at this or any of the IOP journals.
Allow me to second this question. After a first pass of this paper all I see are qualitative assessments of representative/idealized/averaged (?) versions of classes of objects like bird wings. Is this typical for demonstration of optimality in engineering? It reads more like assessment of satisfying requirements (with the choice of requirements raising another set of questions).
These questions are seem very salient, and the paper makes no mention of these other wings or shark fins. It does make this observation:
Optimal hydrofoil shape. Whales have a flipper with a low-drag planform shape [34] and hydrodynamically efficient cross-section [35] that gives a high lift-to-drag ratio. Humpback whales also have tubercles (bumps) on the leading edge that can improve lift-to-drag ratio by producing vortices on the surface of the fin that energize flow [36].
So is the humpback whale flipper more optimal than other whale flippers? On the one hand, I appreciate that here this is some acknowledgement of biological diversity which in general seems lacking from the paper, but there seems to be no engagement with the implications of this diversity.
Finally, even if this paper weakens the argument for historical contingency (and it would seem to need to address shark fins, bat wings and possibly even insect wings to actually do so), it would seem to support the plausibility of the evolvability of these limbs from a common ancestor, in contrast to Miller’s conclusion. Again, from the paper:
The vertebrate limb pattern is a remarkably versatile design solution that can be fine-tuned to produce a vast range of shapes and motions as well as perform structural functions. The segmented design of wrist/ankle/phalanges is particularly effective at enabling morphing of shapes whilst maintaining smooth curvatures.
I read that to mean that (1) a given instantiation of a vertebrate limb can be manipulated to achieve multiple conformations and thus functions, providing a plasticity that enables exploration of niches without genotype change and (2) adapting the limb to specific niches only requires the kind of small or incremental adjustments in size, shape and number of existing bones that are consistent with observed variation within populations rather than wholesale innovation of new skeletal arrangements.
Except that Miller provides no evidence of this, he merely assumes it:
The extent to which a population can traverse a landscape depends on whether the landscape is smooth or rugged. A smooth landscape contains relatively few peaks with gently rising paths connecting the base of one peak to the summit of another (Figures 1 and 4d). An organism could potentially traverse significant distances along such a landscape, resulting in large evolutionary change. In contrast, a rugged landscape contains a multitude of sharp peaks (Figure 4f). Populations will tend to spend most of their time trapped on a local peak, so evolutionary change will be largely confined to minor modifications to existing traits.
Therefore this:
… is merely you building your own wishful thinking on top of Miller’s unsubstantiated assumption.
You have no more evidence that antibody landscapes are smooth than Miller has that rugged landscapes preclude evolution. This is on top of your and Miller’s simplistic treatment of rugged versus smooth as a binary, rather than a continuous measure (as others have pointed out). Also (as others have pointed out) fitness is multidimensional – meaning that it is perfectly conceivable that fitness may be more rugged against some dimensions and simultaneously less rugged against others.
Given Miller’s lack of evidence and lack of any expertise relevant to evolutionary biology, and EN’s lack of any credibility whatsoever, I’m curious as to why you thought presenting it on this forum was a good idea.
It is apologetics not science Gil. It is “designed” to impress the gullible and/or ignorant – not the skeptical and/or expert (which would be the majority of active members of this forum). And, like most of apologetics, it is very superficial.
I see no more reason to treat “as Miller said” with any more credibility than Ray Comfort’s banana claims, Kent Hovind’s dinosaur claims, or the “according to Dembski” claims you asserted in a recent thread.
Populations occupy a region in a fitness landscape, NOT a single point, and the size of this region depends on the variability of the population genome.
Every point of a fitness landscape offer some level of fitness, and is “optimal” for the population at that region. The population might be prevented from moving to relatively higher fitness if some OTHER population already occupies that ecological niche. In other words, competition alters the fitness landscape. A species might get stuck at a local peak, but some other species (or sub-population) may be forced to avoid that peak as a result.
Practically speaking, this means any given species might be sub-optimal in a non-competitive fitness landscape, but optimal given competitive pressures. Some species are “Generalists”, which may have advantages over “Specialist” species occupying a local fitness peak.
As an addition to the point about wings I wonder how many of the flightless terrestrial birds are really better off with vestigial wings rather than arms.
What is remarkable is that (according to Burgess source paper), the vertebrate limb pattern is so versatile that it is actually highly optimal not just for arms and legs but also for flippers and wings. If true, under the common descent paradigm, this would certainly suggest that foresight, ie., intelligence, has been involved when the vertebrate layout first appeared in the history of life.
One might ask you the same question. If you think that having both arms and wings would be beneficial, why evolution neither produced animals having both of these structures ?
In the article below, the authors draw the conclusion that according to their data, RM+NS only cannot find the wild type optimal function, unless a starting library of 10^70 sequences could be provided, which is far beyond the reach of nature itself. And the reason for the failure to recover the wild type function is because it is associated with a rugged landscape.
Burgess has published in AiG, which screens it authors pretty hard for any deviation from YEC. I assume his history of life extends 6,000 years.
The relation of limb optimization to environment is central to physical anthropology and primatology, as the transition from arboreal to ground based lifestyle is strikingly reflected in the humanoid fossil record. I did not notice Burgess discussing this.
Evolution, as ID proponents are ever ready to point out, is constrained. There is an edge to evolution, and nature as it exists in all its variety is the product of constraint and possibility. Design, on the other hand, is not constrained by ancestry, and is characterized by innovation, abrupt departures, and mix and match transfers of technology from unrelated sectors.
Altering proportions for limb bones does not require different proteins, and given that there is always existing variation for size and proportion, the landscape appears to be smooth.
By “random mutation” they imply only substitutions and have no way of estimating the effects of indels in their adaptive walk, just to pick one enormously obvious shortcoming of their vacuous extrapolation. They of course correctly conclude the WT sequence didn’t climb to the global peak by substitutions alone (and suggest for example that recombination could have made a big difference too).
Incidentally the D2 domain of the g3p protein evolved by an internal duplication and divergence of another domain in the same protein. Simple, really.
I just read that 2006 paper and in absolutely SHOCKING news, Gil has misrepresented its claims while ignoring far more recent papers that have been posted in this very thread. It’s weird. It’s almost as if he wants to hide something from us.
I think it’s entirely possible that Gil was himself deceived about that paper and the state of the field by the DI and similar organizations, than that he’s intentionally trying to hide something from us. If he is trying to hide it from us, that’s doubly foolish since he should know that almost everyone here is going to fact-check his claim.
Yes, there may well be a form of ‘information attenuation’ here. The DI, being apologists, will only cite papers that either support, or can be misrepresented as supporting, their case. If Gil exclusively, or even mainly, bases his understanding on DI (and similar) content, this would lead to a profound misunderstanding of the state of play in such fields.
This in turn would lead to Gil’s claims resulting in immediate, and complete, car-wrecks when he presents them here – as has been observed.
The question is why, after a number of such car-wrecks, he hasn’t learned from his mistake and either (i) started reading more widely on a topics before posting about them, or (ii) avoid making them on knowledgeable and/or skeptical forums such as this one?
I agree. It is more or less the same ideas (except, I can imagine, my point regarding foresight) that I tried to convey to @RonSewell at 30 with the following: What is remarkable is that (according to Burgess source paper), the vertebrate limb pattern is so versatile that it is actually highly optimal not just for arms and legs but also for flippers and wings . If true, under the common descent paradigm, this would certainly suggest that foresight, ie., intelligence, has been involved when the vertebrate layout first appeared in the history of life.
Ignoring evolutionary constraints for the moment, having wings OR arms may represent a “fork” in evolutionary paths, with one feature existing at the expense of the other. Flight requires minimizing weight, and an extra set of limbs that do not assist in flight make flight more difficult.
Flight is a sort of fitness peak (maybe fitness highlands plateau). It offers some big advantages, but flight capable species will indeed have difficulty escaping that local maxima to evolve into a species that uses wings for something other than flight. That transition is especially unlikely when existing species already occupy the ecological niches necessary to make such a transition. I think it would require a mass extinction of everything except birds - a MAJOR rearrangement of the fitness landscape - for such a transition to be possible.
Foresight for these features, but ignorance and historical constraint for so many others (like the difficulties of upright posture in humans). There’s a few descriptive terms we might apply here; one is cherry picking, the other is named after a marksman in a southern US state.
Taking this back to fitness landscapes, I have a prediction: There should exist fitness peaks that are undiscovered by evolution. These will be rare, and might enable new kinds of traits not existing in nature. Such searches are already ongoing for new drug discovery, among other application.
Once we have identified a sufficient number of these peaks, then we will have some actual data about what is and is-not discoverable by evolution.