|
Author
|
Topic: Organisms using GAs vs. Organisms being built by GAs
|
Janitor@MIT
Member
Member # 125
|
posted 21. September 2002 13:38
Re: Dr. Taylor’s demand for an “ID” explanation.
Every design is an experiment; an experiment in the process of discovery/innovation. Design isn’t merely the rigorous and detailed planning and implementation of intents and purposes with well-defined explicit objectives and goals. Such a conception of design eliminates even the possibility of discovery. Design is highly contingent, extemporaneous, ad hoc, filled with unknowns and uncertainties, it is developmental and evolutionary, and obviously, this is where the possibility of discovery enters the whole process. Design is experimental in exactly the same way as the natural sciences are experimental, except often the experiments are considerably more elaborate than those in natural science. It is in the elaboration and complexity that discovery is made.
(This debate appears to be informed by some rigid preconceptions of both what design is and what evolution is (or must be). A broader conception of both may be necessary.)
One thing is clear, this peculiar network topology, discovered originally by linguists, then rediscovered by economists, then rediscovered again by sociologists, then rediscovered yet again by physicists, and then once more by the engineers, then finally by the biologists, can and does emerge by a process of design that does not have as its objective scale-invariance .*
Now, to my mind this represents quite a paradox, because, as we are always reminded, evolution is a “mindless” process, with no objectives, goals, or purposes, etc. And even though evolution may in its process and products resemble design, we usually discriminate between the two on this very basis: evolution has no objectives, etc., while designers do.
Yet here we have two systems (e.g., the Internet and the proteome), isomorphic in a definitive global property, but one basis for the usual distinction we make between the origins of these two systems has evaporated! A network designer can design and build a network with the identical generic properties but with no explicitly formulated plan or intention of doing so.
Now, there are some technical points of issue: Dr. Taylor’s “expectation” appears to me to ex post facto. Biologists have typically been modeling proteomic networks per Poisson for the last thirty years, following the tradition explored originally by Kauffman, if I recall correctly. (Now, if Dr. Taylor did anticipate the discovery I applaud her prescience.)
Preferential attachment is problematic on both design and evolutionary theoretic terms, as has been noted by many researchers, including Alberts and Barabasi themselves. They have attempted to give it a “fit-get-fitter” spin, but this is a simplism, and is to be rejected on both evolutionary and design theoretic terms. W/o explanation or PubMeds (!); I’ll simply refer the reader to the already unmanageably voluminous research on the subject. There are many ways to reproduce scale-invariance.
Just very generally, the arrival at and persistence of any global, time-independent state via the usual evolutionary dynamics is difficult to account for. These dynamics should significantly modify such a global state even over very brief evolutionary time scales. My “expectation” was that genomes shaped by chance and contingency should have resembled the antlers of the Irish elk, the elephant’s proboscis, the fish’s gills, and the cat’s pajamas. Was I wrong here?
As is even implicit in the PA rule, the impression is that genomes are largely shaped by purely intrinsic factors. This would explain the fine-tuning that effectively renders as a constant parameter what should be a stochastic variable and relation in a truly evolutionary model. But I don’t think that biologists generally are prepared for or anticipating a possible paradigm shift that this implies. Not meaning to be intentionally provocative, but I anticipate that resistance to the very idea will be shaped by more “metaphysical” considerations, than by the science. Tradition is a powerfully enervating force, even in science.
Dr. Dembski’s criticism is well taken, if I’ve understood him correctly. We have formed a bad habit of calling a description plus some traditional “formula” an explanation. But I am far more demanding than he is: “just so-just happened” narratives are to be tested experimentally. Until they are tested such hypothetical scenarios are just tales that we tell and not science.
*I forgot the ecologists and planetologists!
IP: Logged
|
|
Frances
Member
Member # 169
|
posted 21. September 2002 14:00
I disagree. "Just so stories" are an intricate part of scientific progress. When confronted with an unknown situation science progresses through the formulation of hypotheses followed by attempts to support or more importantly disprove the hypotheses. Of course such ideas need to be tested. And yes they are explanations, perhaps bad ones but they are an attempt to incorporate our present knowledge with the facts. Which is why using elimination to ´prove´ design seems ultimately doomed to be a failure. This is why I have been asking for design to be given the same requirements as regularity-chance hypotheses.
IP: Logged
|
|
yersinia
Member
Member # 324
|
posted 21. September 2002 15:09
This is another topic, but I think that the term "just-so story" is much abused, and has shifted considerably from its original meaning. Gould & Lewontin's paper "The Spandrels of San Marco" (read the actual article online at AAAS), usually cited as the origin of the term, does not even contain it. What Gould & Lewontin were arguing, however, was that some features of organisms have dubious functions, and might therefor have "accidental" origins, being the by-products of other processes (human sacrifice and T. Rex limbs were two of his examples); and this was the logic behind the original point of labelling something a "just-so story".
This is all well and good, but the one thing this critique does not apply to is organismal features that *clearly* have an important function and are clearly highly refined and adapted to perform that function. This includes, by the way, all of the IC systems favored by Behe et al.
As Maynard Smith wrote:
quote:
Confronted with feathers, or eyes, or ribosomes, we cannot not ask what they are for. It would be no more plausible to suppose that they are accidental and non-selected byproducts of something else than it would be to suppose that the gyroscope in the V2 rocket was connected as it was because some German fitter made a mistake.
Now it may be that Gould (or others) expanded the term to include "weakly-supported origins scenarios" in general, but it is at least worth acknowledging that this is different from original usage.
If we do move to the broader usage, however, it surely should be noticed that "IDdidit" is a much more flagrant just-so-story than any of the evolutionary hypotheses for the origin of the immune system advanced here.
nic
[ 21 September 2002, 15:11: Message edited by: yersinia ]
IP: Logged
|
|
Deanne M. Taylor
Member
Member # 274
|
posted 21. September 2002 15:35
Janitor@MIT is quoted down the following:
quote:
Re: Dr. Taylor’s demand for an “ID” explanation.
Every design is an experiment; an experiment in the process of discovery/innovation.
So, here, you are defining "design" as a process of experimentation/innovation in stepwise fashion (process, you said above), which must be optimized as it was once imperfect, instead of created whole and perfect with aforethought and deliberate planning.
In that sense, then, the "irreducibly complex", intelligently designed systems posited by people like Mr. Dembski were once more imperfect and seperable than they are now? Are you saying the Designer needed to experiment to get his/her design to work?
Despite your objections, I believe that ID posits deliberate, intelligent design that produces complex irreducible systems that cannot be seperable or evolvable. That is, ID posits that the Designer was competently able to design a system from the start.
That is, the design was never haphazardly created to later evolve into a better form. It was not a "process". Conversely, evolution claims a process. I, personally, am arguing for a process of "design" by natural causes.
I believe that ID insinuates that the design was perfect from the get-go. Perhaps you'd like to speak to Mr. Dembski on this.
I am addressing this claim of "designed from the get-go" in the previous messages on this thread.
quote:
Design isn’t merely the rigorous and detailed planning and implementation of intents and purposes with well-defined explicit objectives and goals.
So, you are saying the Designer was goal-less, and didn't have an idea what he/she was trying to accomplish when he/she started the design? That the Designer set out to experiment from simple forms up through more complex forms? That would work if the Designer was evolutionary process.
quote:
Such a conception of design eliminates even the possibility of discovery.
Conception of design, if wide-reaching, negates any possibility of discovery, as you can posit the whole shebang was designed to be random and associative, and designed to evolve according to the mechanisms proposed by evolutionary theory. So, yes, you could say "design did it, but evolution is the result", which wouldn't do much for the current theories in Intelligent Design.
quote:
Design is highly contingent, extemporaneous, ad hoc, filled with unknowns and uncertainties, it is developmental and evolutionary, and obviously, this is where the possibility of discovery enters the whole process.
Design done by optimization, perhaps.
Design done with acceptance of mistakes, perhaps.
I don't think "Intelligent Design" wants to see their "intelligent design" fall into the category of "intelligently designed to evolve exactly as the evolutionists are saying it all happens"
Design by random, natural causes are highly contingent, extemporaneous, ad hoc, filled with unknowns, etc. That's my point. I am saying that the "design" we see in biological networks can be explained by all of the above with the processes we have observed or have found proof of.
Do you have an alternative to the mechanisms I've named in previous posts to create a network with the same qualities we see in the protein-protein interaction network? Is design then to accomplish its objectives in the same way evolution does, or is it an event with a point of creation and no science involved?
Was the design of these irreducibly complex systems placed into being as a whole and total, irreducibly complex part, or did it evolve by often random process and sequential addition? You cannot defend intelligent design of irreducibly complex systems AND suggest that the irreducibly complex systems evolved through a process of optimization or discovery, &tc. That means that the system was once not irreducibly complex. Do you see the conundrum, there?
quote:
Design is experimental in exactly the same way as the natural sciences are experimental, except often the experiments are considerably more elaborate than those in natural science.
That's a whopper of an assumption. And completely contradictory to what you're saying. If design is ad-hoc in its experimentation, it's not planned. The "design experiments" as unplanned cannot be as elaborately planned, therefore, as most scientific experiments already are.
quote:
It is in the elaboration and complexity that discovery is made.
Discovery of what, the elaboration and complexity of random design? I still don't see how that supports an instantaneous creation of irreducibly complex systems by an intelligent designer.
Unless that intelligent designer was just like evolution is, without any of the science attached to back up proof of intelligent design. Then, I guess you could posit "intelligent design" except that you'd have to defend it using nothing but your gut instinct for what "Design" means. Not quite enough to justify teaching it in schools.
quote:
(This debate appears to be informed by some rigid preconceptions of both what design is and what evolution is (or must be). A broader conception of both may be necessary.)
You'd like to suggest a broader interpretation of Intelligent Design? Be my guest.
Evolution is already pretty broad. It posits everything you've been saying, except the "intelligent agent" are natural processes that follow certain rules of assembly, innovation and selection.
As for ID becoming more liberal in its definition, I'm not so sure that'd go over really well. Intelligent Design posits an intelligent Designer. Irreducibly complex systems are offered as PROOF for an Intelligent Designer. I would like to point out that what you're doing is removing the ability of the "IC" argument to defend ID. You're neutering it, essentially, and saying that an evolutionary process could be undertaken by an intelligent agent. Evolution is evolution. If you claim that irreducibly complex systems can evolve through experimentation, then that takes down Mr. Dembski's argument, and might also offend some people who might think that any powerful Designer was well-equipped to create perfection the first time around.
quote:
One thing is clear, this peculiar network topology, discovered originally by linguists, then rediscovered by economists, then rediscovered again by sociologists, then rediscovered yet again by physicists, and then once more by the engineers, then finally by the biologists, can and does emerge by a process of design that does not have as its objective scale-invariance .*
You know, removing the word "Design" up above describes evolution: "...can and does emerge by a process that does not have as its objective scale-invariance"
Of course, UNLESS you want to say that evolution is a process of design.
I have a feeling you are confusing the meaning behind "Intelligent Design". I have not read (yet, anyway) anyone purporting that Intelligent Design happened with random, imperfect processes to yield a final result! That's what evolution posits! Conflating the two removes the problem, but not, I think, for people like Mr. Dembski who may take exception.
I hope this does NOT evolve into a pedantic argument about what "design" means.
By the way, it was physicists who discovered scale invariance is pervasive through most networks that grow by random association and preferential attachment. Look up A.L. Barabasi at Notre Dame, and his papers over the past few years. If you know of earlier papers that he doesn't cite, please share them, so I can add the references to my collection.
quote:
Now, to my mind this represents quite a paradox, because, as we are always reminded, evolution is a “mindless” process, with no objectives, goals, or purposes, etc.
Ask yourself: Does consequence need purpose or goals?
If you make a decision in a completely random way you still have to take the consequences of your decision.
How are the consequences of a mindless decision any less important than the consequences of a mindful decision, if both decisions yield the same exact consequences?
quote:
And even though evolution may in its process and products resemble design, we usually discriminate between the two on this very basis: evolution has no objectives, etc., while designers do.
quote:
Yet here we have two systems (e.g., the Internet and the proteome), isomorphic in a definitive global property, but one basis for the usual distinction we make between the origins of these two systems has evaporated!
Yes, they both share a similar quality in that both were created by random processes. However, the Internet had a bit of designing here and there. The Internet, for the vast majority of it, is randomly "designed" and often at the mercy of selective processes. See Barabasi's papers on the WWW in the links I gave in earlier posts.
quote:
A network designer can design and build a network with the identical generic properties but with no explicitly formulated plan or intention of doing so.
The internet wasn't designed. But let's assume another network, say, in a University.
You're saying that a network designer is going to create a network that looks as if it was haphazardly designed on purpose. I seem to remember some papers on network design. They don't suggest scale-invariance as a good design principle. For instance, see Cisco.com's Campus network design white paper
In fact, I believe that a lot of "best practices" network design principles in IT these days seem to fall into the category of "bipartite graph", but someone out there who does that for a living should correct me if I'm wrong.
Anyway, good design principles of any network should NOT include hubs that can be hit and cause the network to break down completely. That's not a good network design, hence the bipartite graph structure, from what I remember.
As far as a designer designing a network to look as if it was randomly assembled, ID says that the Designer had a plan, and many of the components thus built must have been planned to be interlocking BECAUSE they are irreducibly complex. Yes, Irreducible Complexity says a designer must have planned these systems to be indivisible and perfect on design.
quote:
Now, there are some technical points of issue: Dr. Taylor’s “expectation” appears to me to ex post facto.
What, that I expect ID to explain why the concept of "irreducibly complex" design can explain the observed quality of scale invariance in biological networks?
Science provides proof and data on scale-invariance, gene duplication and retrotransposons which supports evolutionary theory. I'm waiting to see how this data supports ID while also supporting irreducibly complex systems.
quote:
Biologists have typically been modeling proteomic networks per Poisson for the last thirty years, following the tradition explored originally by Kauffman, if I recall correctly. (Now, if Dr. Taylor did anticipate the discovery I applaud her prescience.)
You recall incorrectly. Biologists were rarely modeling proteomic networks per Poisson for the last thirty years as there was precious little data to prove or disprove the models they generated.
I have a graph I made, about three months ago, of every "network" paper out there, on biological networks. Until the 1990s and the emergence of data from the Human Genome Project, there were very few papers, relative to papers in other subfields of biology. I have that graph, if you'd like it, and all my network/system biology references (all 800 of them...the graph is exponential!).
Additionally, I find it VERY interesting that you invoke Poisson models, which have been shown as inadequate to model biological networks. Poisson models are shown to be "old news", not sufficient, by several research groups, including Barabasi's papers, which I assumed you read, as you invoked him here.
Kauffman's work, which was indeed seminal, was established to study the distribution of connections, modeling gene networks as random boolean networks and was an early result in estimating their behavior.
HOWEVER, the scale-invariant property of protein-protein interaction networks does NOT fit Kauffman's model. The Kauffman model does not fit reality.
Scale invariance is an observed quality.
I quote an excellent short explanation of this for you, from this link
If you read Barabasi's papers you'll notice that he compares the Poisson distribution to the actual observed distribution, and it was clearly not a Poisson distribution. It is a power law.
See various papers on Poisson modeling of biological networks. For instance, here's an abstract at Cornell that says,
"Using three different measures, namely types of attractors, fraction of elements that are active, and length of period, we show that finite, scale- free networks are more ordered than either the Poisson or delta function networks below the critical point. Thus the topology of scale-free biochemical networks, characterized by a wide distribution in the number of inputs per element, may provide a source of order in living cells."
Other work has shown that Poisson models are not good approximations, first off. They've failed for modeling the internet which is scale invariant. See for instance this paper at citeseer.
Poisson models are not good enough. That's because the network is already scale invariant, and Kauffman's work was not based on the kind of data that Barabasi's group had access to.
quote:
Preferential attachment is problematic on both design and evolutionary theoretic terms, as has been noted by many researchers, including Alberts and Barabasi themselves.
I don't recall them ever saying it was problematical to the point of being impossible, which is what you're implying. Can you give me a direct reference and the context in which they're saying it, and then scan later papers to see what they say, later on, as more data came to light? Citing an earlier paper when they say "we haven't figured it out yet" is not acceptable as "problematical". It's "lack of data".
But before you bother, consider this. Preferential attachment in biological terms is perfectly reasonable because the hubs which are preferred are already, by definition, more ripe for gene duplications than their less-connected peers. A hub protein that has the most interaction partners will have a greater chance of receiving a gene duplication as a new partner since duplication events are generally random, and these hub proteins have more protein interaction parterns TO duplicate. That's not problematical. Were you reading my posts?
quote:
They have attempted to give it a “fit-get-fitter” spin, but this is a simplism, and is to be rejected on both evolutionary and design theoretic terms.
Um, by who, and by what? What's your measure? Simple disbelief is not allowed, here. You're invoking ignorance to explain away something you can't understand.
quote:
W/o explanation or PubMeds (!); I’ll simply refer the reader to the already unmanageably voluminous research on the subject.
You don't have to cite PubMed. Give us a name and a quote, at least, that says that biological networks can't evolve by gene duplication and attachment. I'll supply my own in kind that says they can. You'll have to start by negating Eichler's work (Case Western) or Gerstein's work (Yale). No, actually, you'll have to begin by negating gene duplication in the first place, which means negating the data coming out of the human genome project, as it provides the proof.
Start with Eichler's work. Maybe you can explain why gene duplication and rapid Darwinian selection cannot explain gene duplication and innovation. It's been observed, so why not begin by criticizing the experimental data.
quote:
There are many ways to reproduce scale-invariance.
Key word there: Reproduce. So?
There are many ways to reproduce a truly random number, too, and they involve writing a computer program and hoping your algorithim is sufficient (I remember the saying: rand() is NOT.)
quote:
Just very generally, the arrival at and persistence of any global, time-independent state via the usual evolutionary dynamics is difficult to account for.
Again, what do you base that conjecture on?
There's plenty of evidence that a complex network can have "attractors" that create a stable state out of apparent nonlinear behavior. Are you saying attractors cannot exist?
Biological networks, however, are feedback control networks, for all their complexity. Are you saying feedback control cannot stabilize a steady-state solution? Argue with the engineers.
If the state is to time-independent as a requirement for survival, why wouldn't regulatory control systems establish as neccesary dynamic-range tolerance over physiological states, and steady-state solutions of functional parameters?
In terms of systems, that's what evolution claims happens, essentially: survival of a lineage by a system's adaptation to changes that perturb the system from stasis. Sometimes that adaptation causes phenotypic change that reproductively isolates the descendents from the ancestral lineage.
Do you have any evidence that a feedback control network, created under selective pressure, can not become a more complex network by all the mechanisms I've been naming, and maintain a steady-state solution by selection?
There are papers on evolution of complex networks, including a model of the evolution by gene duplication, one out of the Santa Fe Institute:
http://www.santafe.edu/sfi/publications/wpabstract/200202008
quote:
These dynamics should significantly modify such a global state even over very brief evolutionary time scales.]
So what you're saying is that you believe that an evolutionary network cannot evolve as steady-state and therefore any impetus in this non-steady-state solution will modify the global state over brief evolutionary time?
Besides the fact that you're basing YOUR argument on "it can't happen because I said so", this is (almost) exactly what I said in a previous post.
If a system is perturbed with a gene duplication that becomes necessary and that evolves away from its duplicate, it would be expected the system will undergo a pendulum swing of evolutionary change to accomodate the duplication's drift and change.
And that's what we see.
See human chorionic gonadatropin as one example. If you want me to get more specific on this, just ask. It was a recent duplication in the primate lineage and there's a rapid (and traceable) positive Darwinian evolutionary change in the receptor-substrate systems up through the primates.
These changes are not expected to be found if a system is in evolutionary stasis.
Perturb the stasis and you see change.
Let things continue on in happy continuity and any impetus for change does not exist. Genes that could get fixed into that scale-invariant network do not need to get fixed. That's the general idea behind punctuated equilibrium: evolution happens not by gradualism but by fast spurts.
I might mention that drug companies use this principle -- that essential proteins are evolutionarily static -- and therefore do not evolve quickly in relation to their lineage. Those essential proteins are then studied in that context as targets (or dangerous targets). I know this, because I do that regularly at work. It's homology modeling. In fact, UCSC's genome browser has a whole track of human/mouse similarity for that very purpose...find the proteins that are conserved through evolution...those will likely be the hub proteins.
And to make matters even nicer, Barabasi's gone and done a study on yeast to show that the hub proteins are indeed important for cellular function. See the links in previous posts, under "cellular networks"...there's a very fine knockout paper in there.
quote:
My “expectation” was that genomes shaped by chance and contingency should have resembled the antlers of the Irish elk, the elephant’s proboscis, the fish’s gills, and the cat’s pajamas. Was I wrong here?
Um, they do. That's why we talk about PROTEIN FAMILIES. That's basic undergraduate protein structure, there. Go look up protein families.
quote:
As is even implicit in the PA rule, the impression is that genomes are largely shaped by purely intrinsic factors. This would explain the fine-tuning that effectively renders as a constant parameter what should be a stochastic variable and relation in a truly evolutionary model.
What parameter? What variable? What fine-tuning? Genomes are full of crap, generally. The human genome even more so. Which supports, by the way, swaths of segmental duplication. But we'll leave that alone for now.
Please explain the above paragraph, it's very...fuzzy.
quote:
But I don’t think that biologists generally are prepared for or anticipating a possible paradigm shift that this implies.
I could figure out what you were implying if you'd come out, directly, and say what "this" is that is being implied.
quote:
Not meaning to be intentionally provocative, but I anticipate that resistance to the very idea will be shaped by more “metaphysical” considerations, than by the science. Tradition is a powerfully enervating force, even in science.
I'm still looking to see what the "very idea" is that biologists would resist. Please try to be more explicit for people like me, who cannot read minds.
quote:
Dr. Dembski’s criticism is well taken, if I’ve understood him correctly. We have formed a bad habit of calling a description plus some traditional “formula” an explanation. But I am far more demanding than he is: “just so-just happened” narratives are to be tested experimentally. Until they are tested such hypothetical scenarios are just tales that we tell and not science.
Exactly my point. I've pointed out evidence for all of the things I am talking about. ID and IC does not have any data that provides evidence that supports intelligent design and excludes evolution (can you name some that I'm not aware of?). However, evolution has plenty of data that is evidence to exclude intelligent design. When you suggest that science provide proof, perhaps you'd like to demand it of evolution AND intelligent design, simultaneously. Evolution will present you with thousands of tests of evolutionary theory. The person who can prove that evolutionary theory is wrong, using ordinary scientific means, will get famous and also rich. That nobody has been able to do that thus far should say something to you.
You make some grand pronouncements on what is or what is not possible, but you do not present explicit examples or name specific scientific findings. If you feel the need to debate with me again on widely-published results, please name your sources, and I will (again, as I have been doing), reply with mine.
Deanne
[ 21 September 2002, 16:53: Message edited by: Deanne M. Taylor ]
IP: Logged
|
|
William A. Dembski
Member
Member # 7
|
posted 22. September 2002 08:23
I'm directing these remarks to Deanne Taylor's most recent posts. I had expected to have more time this weekend, but I don't, so I'm going to have to make it short.
It seems that Deanne works with a very limited conception of design and how it would play itself in natural history. For her, design creates things from scratch. Otherwise, it's evolution, and naturalistic evolution at that. Thus she will claim that the Internet was not designed. True, there was no micromanaged design in the sense that some one designer or central committee planned it out down to the last details. But the broad contours were designed and then subsequently intelligent agents acted within those contours. So, to claim that the Internet was designed is misleading. The Internet is chock-full of design.
With regard to biology, ID is certainly compatible with a nonnaturalistic form of evolution. The model I'm working with these days is that of technological evolution as advanced by TRIZ (see http://www.ideationtriz.com/). This nonnaturalistic evolution works by naturalistic processes solving "routine problems" and design solving "inventive problems" (this is a standard distinction within the TRIZ literature -- the one is solvable by trial and error, the other requires a conceptual breakthrough). This form of evolution therefore will have many of the features that Deanne cites (like scale invariance) but also exhibit clear marks of intelligence. At any rate, the design possibilities for how life emerged and developed are much richer than Deanne indicates or seems to grasp (she might have a look at chapter 6 of my book No Free Lunch).
One final remark: when I said that scale invariance "disappears" in Deanne's account of how IC systems arise when she lays out bridge principles to connect her scale invariance to actual biological systems, I didn't mean that scale invariance ceases to exist. I was simply saying that scale invariance did not figure in substantively or even appear in her account of those bridge principles. Indeed, she merely reverted to the standard coevolution/cooption explanation. I therefore continue to maintain that scale invariance has very little empirical content but merely serves as a convenient framework for organizing certain facts.
IP: Logged
|
|
Deanne M. Taylor
Member
Member # 274
|
posted 22. September 2002 10:02
Mr. Dembski writes: quote:
It seems that Deanne works with a very limited conception of design and how it would play itself in natural history. For her, design creates things from scratch. Otherwise, it's evolution, and natural evolution at that.
Please keep my statements in context. I was discussing the general definition of "design" vs. "naturalistic evolution" and drawing a line between the two in that one supposes a deliberate design, while the other supposes that natural process over extended time produces the patterns as seen in nature.
If you call my conversations on "design", as supposing a designer, as NOT the idea behind Intelligent Design, then I was perhaps being too narrow in my assumptions. Are you telling me that "Intelligent Design" does not need to suppose an intelligence behind the design?
If not, then how do you seperate a design with no intelligence behind it, from natural unintelligent process?
Mr. Dembski writes:
quote:
Thus she will claim that the Internet was not designed. True, there was no micromanaged design in the sense that some one designer or central committee planned it out down to the last details.
I don't have to "claim" that. It's not even in question. Why are you setting up this strawman?
Mr. Dembski writes:
quote:
But the broad contours were designed and then subsequently intelligent agents acted within those contours. So, to claim that the Internet was designed is misleading. The Internet is chock-full of design.
To claim the contrary is actually what is misleading. If you check your history of the Internet, it was NOT created as a large superstructure that was later filled in. It was a simple network connecting Universities and government labs, only 30 of them, from my memory, not the thousands it does, now. It was ARPNet, I believe, that connected Universities who already had the infrastructure in place internally and the internal support hook in. Thus, it was preferentially created at first to link together nodes that were ready. This was not "design", this was "let's hook up whomever is ready and we can try this out".
And it just got more haphazard from there. Do you remember the early days of the internet when one router going down could wipe out half the country? I do. I was using the Internet during its tender years.
I remember we used to curse Sprint for effectively knocking out half the entire US network with their crappy routers and service. That's because the early internet was poor in design -- it wasn't designed at all. It was slapped together in stages of adaptation and cooptation. That was my point. Not designed as a complete whole with an objective in mind.
One router, one hub, would take down the entire network. That's not intelligently designed Internet, there. That's haphazardly slapped together early infrastructure, and that's the way it was.
If you are saying, now, that ID accepts that things can be slapdashed together as design principle, then as I'll point out in several places in this post ![[Smile]](smile.gif) that you cannot use IC as an argument for intelligent design, since intelligent design would never create IC from the get-go. IC would have once had to have been reducible complexity.
I expect you set up the strawman to knock it over with the fact that the Internet had to have people to fill in the connections in between the loose "design" of the Internet.
That's a weak argument. The Internet structure sprang up out of necessity and underwent a lot of pruning and ...well, pardon the expression, evolution. The backbones followed where the Universities had already established data-sharing strategies.
The ironic thing behind your statement is that the basic layout of the Internet was based on necessity, on a layout of what Universities and hubs were already established and had been added to through ARPAnet.
In other words, this "basic design" of the first Internet was based on cooptation of early architectures that already existed and were subsequently added to through necessity and opportunity.
See, for example, Walt Howe's "History of the Internet".
http://www.walthowe.com/navnet/history.html
or the PBS timeline on the Internet:
http://www.pbs.org/internet/timeline/
So, if in the light of that, if you want to claim that the Internet was "designed", by cooptation and constant adaptation and re-deployment, I certainly do not object. You are saying design requires constant adaptation and addition from simple systems to more complex, "irreducibly complex" in some cases, systems.
Therefore, are you admitting that at a certain points in these "adapted designs" with or without intelligent agents, "irreducibly complex" systems were not once NOT irreducibly complex? That the intelligent agents BUILT UP the irreducibly complex systems from simpler systems?
This kind of architecture-building requires that once simple systems can become complex. Even in systems like the Internet. Simply saying "See, the Internet IS designed" does not support the claim that "irreducibly complex" systems prove designers, if the designers themselves had to build up these "irreducibly complex" systems from simpler systems. This means you allow that simpler systems yield more complex systems, that fully "irreducibly complex systems" are able to be built out of smaller components.
I imagine you can see the contradiction, here. You cannot claim intelligent design on the basis of irreducible complexity if you say that design must admit an evolutionary change, since you therefore must acknowkedge that irreducible complexity is incompatible with this alternative idea of gradualist design!
Unless, of course, you claim that design is full of slow gradualist evolution intespersed with sudden appearence of IC design as soon as the designer thinks the system is "ready" for it, like modular plug-ins on occasion.
In that case, how can you tell which systems are IC and which are not, as there seems to be a nice blend of "IC" to "not IC" along the power-law spectrum that scale-invariance observes. See the Barabasi paper on yeast knockouts, I believe they cover that in there.
Life seems very willing and able to adapt to perturbation, as knock-out studies show.
How would you seperate out such an approach from punc eek, which posits the same exact thing,except punctuated equilibrium holds that natural processes, such as bottlenecking of populations, causes these rapid and sudden changes in system architectures?
So, design must hold that:
- Design springs forth in the instantaneous, complete and limited sense (the "limited view" you were accusing me of), or
- Design proceeds by processes that go from simpler to more complex as we observe, and "irreducible complexity" cannot prove design in and of itself, thus removing IC from your stable of "proof" for ID, or
- you (colloq.) assume that design proceeds by gradual adaptation and "filling in" (evolution) of networks in early life forms to gradually build up a more complex life form but you assume it does not do so by random natural process. You assume that occasionally in that gradual process an "intelligent agent" inserts something that is so amazingly unadaptable that you view it as proof for intelligent design.
The only problem with the last point, of these sudden insertions of IC, is that if they are sudden insertions into a network, they must be seperable by measure from a hub or IC system that was evolved by natural processes. For instance, do you see any hubs that lay in illogical places according to the random model of gene insertion, drift, innovation? Thus far, that has not been observed.
In biological systems, such definition of "design" by incremental change is what is posited by evolutionary theory in the first place, only evolution requires on natural causes, not specific design.
In the case of evolutionary theory, we have evidence for what those processes originate from.
We have evidence or have observed the mechanisms in action, as I have posted previously.
In the case of that new idea of 'design', you have no evidence that biological networks have an intelligent agent behind them, nor that "design" excludes evolution from explaining the same processes. Both theories on that level ONLY are indistinguishable.
Mr. Dembski writes:
quote:
With regard to biology, ID is certainly compatible with a nonnaturalistic form of evolution.
Then you are saying that "irreducible complexity" can be generated from reducible complexity and ID is okay with that?
Mr. Dembski writes:
quote:
The model I'm working with these days is that of technological evolution as advanced by TRIZ (see http://www.ideationtriz.com/). This nonnaturalistic evolution works by naturalistic processes solving "routine problems" and design solving "inventive problems" (this is a standard distinction within the TRIZ literature -- the one is solvable by trial and error, the other requires a conceptual breakthrough). This form of evolution therefore will have many of the features that Deanne cites (like scale invariance) but also exhibit clear marks of intelligence.
You will have to establish how "inventive problem solving" through naturalistic process will be discernable from "inventive problem solving" by an intelligent agency. Do you have any details on how you'll go about trying to tell the difference between the two cases as to exclude one over the other with a scientific method?
Mr. Dembski writes:
quote:
At any rate, the design possibilities for how life emerged and developed are much richer than Deanne indicates or seems to grasp (she might have a look at chapter 6 of my book No Free Lunch).
Please be attentive to the fact that here, you are thinly veiling an insult established by assuming that I can indicate the entire sum of my knowledge and expectations in ISCID posts on one subject. I was attending, in earlier posts, to the fact that IC, in support of ID, does not tolerate the idea of gradual addition. That was your entire thesis in the first place. Are you saying you are now not requiring systems to be always irreducibly complex in their entire histories? If you are requiring that, then your accusations of my limited view are groundless, since that was directly what I was addressing. I would expect you know that.
As to what we were discussing in other posts, I asked you about mathematical properties of observed networks, and the mechanisms that have been studied and have generated data in terms of how this observed data fits into ID and IC systems.
You have, thus far, given me a thinly veiled insult, a wave of a hand back to your book, and a reference to a theory of problem-solving. None of them really address how ID and IC fit into the observed characteristics of the natural world that I have cited, including gene duplication, scale invariance, retrotransposons, segmental duplications, and the like
I'm willing to wait for ID to catch up to recent events in genomics. I might mention, aside, that evolutionary theory hasn't worked very hard to catch up...the observations were unexpected but not unpleasantly surprising.
I'm willing to wait to hear an explanation for all these events on solid mathematical terms from the ID side, how any ID theory can be supported by mathematics intimately tied with observation of the natural world.
Mr. Dembski writes:
quote:
One final remark: when I said that scale invariance "disappears" in Deanne's account of how IC systems arise when she lays out bridge principles to connect her scale invariance to actual biological systems, I didn't mean that scale invariance ceases to exist. I was simply saying that scale invariance did not figure in substantively or even appear in her account of those bridge principles. Indeed, she merely reverted to the standard coevolution/cooption explanation.
You didn't read carefully enough, then, or you missed the point entirely. I linked my explanation TO an example of how a HUB protein, an "irreducibly complex" system, can change and indeed confer a new pathway into a system without ever needing to change in a discontinuous way, and how the mechanism of gradual change can add to the qualities of a scale-free network. I used observed natural processes to explain this.
ISCID cites the Santa Fe Institute on its website when it talks about complex systems. Perhaps you'd like to read the working paper on gene duplication creating complexity in biological systems at that very same site...
http://www.santafe.edu/sfi/publications/wpabstract/200202008
Abstract of the Santa Fe Working Paper,
"Evolving Protein Interaction Networks through Gene Duplication"
quote:
The topology of the proteome map revealed by recent large-scale hybridization methods has shown that the distribution of protein-protein interactions is highly heterogeneous, with many proteins having few links while a few of them are heavily connected. This particular topology is shared by other cellular networks, such as metabolic pathways, and it has been suggested to be responsible for the high mutational homeostasis displayed by the genome of some organisms. In this paper we explore a recent model of proteome evolution that has been shown to reproduce many of the features displayed by its real counterparts. The model is based on gene duplication plus re-wiring of the newly created genes. The statistical features displayed by the proteome of well-known organisms are reproduced, suggesting that the overall topology of the protein maps naturally emerges from the two leading mechanisms considered by the model.
That is, a mutation in the system will NOT kill the system, especially if the mutation is necessary. You will notice I termed everything in the context of irreducibly complex systems.
As an aside, it's nice to see Kauffmann will be talking at ISCID's chat room on the 25th of November. The kind of adjacency he discusses in his new book supports the gradual adaptation of complex networks through adjacent states...something you dismiss as "the usual" up above.
Mr Dembski writes:
quote:
I therefore continue to maintain that scale invariance has very little empirical content but merely serves as a convenient framework for organizing certain facts.
Am I correct in assuming you think that protein-protein interaction networks, real physical quantities, operate in a framework that is mere organizational convenience? That's like claiming that the US highway system is mere organizational convenience, instead of being an entity unto itself.
Again, I'm a patient person. I can wait until ID publishes something that can provide mathematical, discerning analysis that will be able to seperate out the conditions for the emergence of these scale-invariant networks between Intelligent Design and evolutionary theory.
Several people I know, however, call that patient part of me an "idealist". Being the cynic I am, I take exception to that.
[ 22 September 2002, 11:53: Message edited by: Deanne M. Taylor ]
IP: Logged
|
|
Frances
Member
Member # 169
|
posted 22. September 2002 10:31
Dr Dembski,
I find it interesting to hear you propose a more detailed idea of ID. With TRIZ you seem to be suggesting that naturalistic processes will solve routine problems and that design solves "inventive problems". Does this include the possibility that design can involve naturalistic processes as well? But more interestingly you seem to be proposing a design in which the designer(s) intervened and various intervals.
I would like to hear more about the detailed pathways to support such a design hypothesis that surely must exist for it to be more than a 'just-so' story.
I do agree with your statement that design possibilities may be ´rich´ in the sense that design can explain anything and thus nothing as long as it relies on elimination rather than on a positive approach.
Perhaps we can learn from nature how it ´designed´ and apply this in useful manners to improve our own capabilities of design. Looking through the TRIZ website I am not too surprised to see that creative techniques include
2. Randomization
6. Evolutionary directed techniques
An example of an innovative-creative step found in nature would for instance be gene duplication which now expands the dimensions of the original search space. Or HOX genes which seem to have been instrumental in the Cambrian explosion.
Another creative step involves the reuse of available materials in the jawbone of reptiles to form the inner ear bones of the mammal.
We may find evidence of creative or innovative solutions but are such evidence supportive of design and not evolution? Or do we need detailed pathways for either to assign probabilities allowing us to determine which of these hypotheses is most likely?
IP: Logged
|
|
William A. Dembski
Member
Member # 7
|
posted 22. September 2002 20:52
Briefly Deane,
**You write explicitly "The internet wasn't designed." Granted, you probably meant that there was no grand top-down design architecture, and that is true. But with the internet there are elements of real design through and through (not random design, natural design, or some other reductionist conception of design). For instance, the transfer protocols had to be designed, promulgated, and rendered conventional. The point at issue is whether such real design pervades biology.
**As for your bridge principles, I looked at them again, and scale invariance in your account ends up dispensable as an analytic tool in accounting for the origin of IC systems. You are telling a standard coevolution-cooption story. You then try to make it still more plausible by pointing to scale invariance, as though this will further enhance natural selection's ability to suitably channel the evolution of biological systems. But that added plausibility depends on having accepted the standard evolutionary story in the first place. I see no causal power in scale invariance. I still see only a framework for rendering plausible what you already believe according to general evolutionary theory, and not a means of independent verification. Your point #7 is unanchored speculation.
**I looked at the Santa Fe Institute article you cited in the last post. I don't think the mileage you are trying to get from it is warranted. Protein-protein interaction maps are fine and well -- they describe a biological reality. But then, in standard Santa Fe fashion, we go to a mathematical model, and suddenly everything we want to be true about evolution is confirmed (with considerable fine-tuning of the mathematical model, I might add; though you, no doubt, will justify such fine-tuning by a programmer as mirroring fine-tuning due to natural selection). This is a toy model, as the authors themselves admit: "The model is a simple approximation to the evolution of the real proteome map, and no functionality is considered (i.e. no dynamics is explicitly introduced)." Note well: "No functionality is considered."
**As for TRIZ, I take it that IC provides the analytic cut between routine and inventive problems in biology. This requires justification and I'm working on it.
IP: Logged
|
|
Janitor@MIT
Member
Member # 125
|
posted 23. September 2002 11:33
No, Dr. Taylor, I’ll decline your invitation to debate. You’re quite a formidable debater!
As you’ve indicated, a “war of authorities” would appear to be pointless. And some of the participants have indicated that it’s tiresome. I will however add to the ISCID Bibliography the references that support the statements of fact that I made, and I will include comments as indicators.
Just a few observations: Obviously, the IDers conception of design is far broader than mine. My ideas about design, such as they are, are informed by own limited and mundane experience. But they are also informed by what little I know of biology. It seems to me that biologists’ understanding is similarly informed, as biologists seem to be quite familiar with engineering design methods, concepts, and theories: codes, programs, networks, communications, control, regulation, strategies, optimization, robustness, etc. I find it ironic that biologists’ understanding of life has been so profoundly shaped by design, even since antiquity, and never more than now, but they feel compelled to deny the obvious: Life is design.
It’s not difficult to trace the source of this denial, because it wasn’t always true that biologists were so insistent that life is not designed. But then when one refers to the source one finds something very interesting: Charles Darwin cannot be the source of the “anti-design” notion, because he makes of his theory an argument from design : “I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection, in order to mark its relation to man's power of selection.” (He even closes his opus with a “god-of-the-gaps” argument!)
Here, Darwin has had the perfectly naïve insight, which he can’t make explicit, because it never appears to rise to the level of consciousness, that the intentions, designs, actions, and productions of mundane intelligent agents are ultimately explicable in terms of a principle of variation and selection. (I had a college instructor who made the very point: All mathematics, e.g., is “combinatorics.” I had another instructor concur when he informed us that all engineering is “optimization.”)
Darwin’s motives, as revealed in his Autobiography, are quite plain, but also quite confused, even on his own admission. He’s plainly identified traditional, “revealed” religion with the natural theology that was so influential of his scientific contemporaries. But Darwin was a little myopic. His target was revealed religion, he took aim at natural theology, but his dart struck at the very heart of biological science . Darwin’s poorly conceived and executed attack upon religion has misfired disastrously. The IDers are quite correct to point this out. Among other things, what has suffered is the science, because the biologists cannot fully explore and exploit their own design paradigm as long as they are influenced by Darwin’s “muddled” theology.
To an outsider such as myself, this confused and contradictory etiology of ideas is quite evident and paradoxical: Biologists often invoke design and occasionally argue it with some sophistication and in detail, all the while denying that it is, indeed, what they are talking about! In my own round about way, what I’ve suggested to the IDers is that the biologists might be led to a less “muddled” conception of the design of life via baby steps; via the very design “metaphors” they routinely employ—beginning with natural selection, e.g.
Now, none of this addresses Dr. Dembski’s topical question. But no, GA’s do not explain the origin of anything. If we say that they do, we beg the next embarrassing question that he no doubt already has in mind. If science must assume an agnostic position wrt to origins, well fine. Let’s not compound embarrassment with absurdity. Scientifically, we can only treat life as a found object and as found, it is an intelligent design indeed. Darwin’s emphasis upon the chance, contingency, and necessity as eliminative of design is nothing more than an argument from ignorance. And I have repeatedly and rather pointedly criticized it: the most persistent argument from ignorance made in this “debate,” Dr. Taylor, is an argument from ignorance of design.
IP: Logged
|
|
Deanne M. Taylor
Member
Member # 274
|
posted 29. September 2002 09:16
I was away at a conference all week, so I'm back to continue.
Mr. Dembski writes:
quote:
**You write explicitly "The internet wasn't designed." Granted, you probably meant that there was no grand top-down design architecture, and that is true. But with the internet there are elements of real design through and through (not random design, natural design, or some other reductionist conception of design). For instance, the transfer protocols had to be designed, promulgated, and rendered conventional. The point at issue is whether such real design pervades biology.
I wasn't talking about the specifics of network component protocols in earlier posts (in the context of specific interactions between network components). I was talking about the entire network's observed architecture, and the need to develop theories based on what is observed.
However, if you say transfer protocols had to be designed (and might I add, optimized!) during the maturation of the current state of the Internet, that is very true. But moving into this new analogy, let's examine the parallels in evolutionary biology to TCP/IP and other protocols. Transfer protocols in protein-protein interaction networks need no such special creation design: "communication protocols" in biological networks are simple physical interactions: negative charges are attracted by positive charges, hydrophobic surfaces attract through Van der Waals forces, proteins interact by simple physical interactions. Ab initio, the "protocols" already exist in nature in the very descriptors of physical interactions and behave in the same way that interactions between inorganic molecules behave. That is, the physical laws apply to proteins as well as chemicals as well as, well, rocks.
Using the protocol analogy, if you want to argue that the entire Universe was designed before it sprang into being to specifically allow proteins to interact through intermolecular forces that act as "interaction protocols", that's a design argument that can never enter the realm of science, as it can never be isolated from the naturalistic origin theories of the Universe nor independently studied and compared to "another" Universe.
Mr. Dembski writes:
quote:
**As for your bridge principles, I looked at them again, and scale invariance in your account ends up dispensable as an analytic tool in accounting for the origin of IC systems.
Except that scale invariance in networks has been mathematically shown to occur in those systems that are randomly assembled with preferential attachment. Translating that into evolutionary theory, that means gene duplication on well-populated nodes and then mutational drift, to follow the example you were talking about.
Mr. Dembski writes:
quote:
You are telling a standard coevolution-cooption story. You then try to make it still more plausible by pointing to scale invariance, as though this will further enhance natural selection's ability to suitably channel the evolution of biological systems. But that added plausibility depends on having accepted the standard evolutionary story in the first place.
Can you come up with an alternative explanation that would fit the observed data? Can you give another line of plausible reasoning that can link together "genetic fossils" which are evidence of gene duplication, junk DNA, scale-invariant networks that assemble by preferential attachment, and mutational drift, also specific conservations of proteins in special hub-positions of that interaction network?
Mr. Dembski writes:
quote:
I see no causal power in scale invariance. I still see only a framework for rendering plausible what you already believe according to general evolutionary theory, and not a means of independent verification. Your point #7 is unanchored speculation.
Scale invariance in biological networks has an immediate causal power in the requirement that it arise from random processes with preferential attachment, which is anchored quite firmly to the mathematics. And gene duplication is anchored quite firmly in mathematical analysis of the human genome. And those are just two examples, not to say that everything else I've discussed isn't also experimentally verified. I just don't feel like repeating myself, see previous posts for references.
If you want to label the linking together of several observed phenomena with a system that has an observed architecture that is best FIT by those observed phenomena as "unanchored speculation", then I would ask what you call "Irreducible complexity" in that light? It's certainly much weaker in position by its lack of supporting evidence in the first place, especially since the same characteristics of "irreducible complexity" arise from a natural model that includes protein-protein network scale invariance.
Mr. Dembski writes:
quote:
**I looked at the Santa Fe Institute article you cited in the last post. I don't think the mileage you are trying to get from it is warranted. Protein-protein interaction maps are fine and well -- they describe a biological reality. But then, in standard Santa Fe fashion, we go to a mathematical model, and suddenly everything we want to be true about evolution is confirmed (with considerable fine-tuning of the mathematical model, I might add; though you, no doubt, will justify such fine-tuning by a programmer as mirroring fine-tuning due to natural selection).
To say that the researchers had to do "considerable fine-tuning of the mathematical model" is disingenuous.
For those who want the reference, here's the paper and abstract again:
http://www.santafe.edu/sfi/publications/wpabstract/200202008
Let's examine their assumptions in detail:
That correlation of gene duplication events to re-wiring events have to do with the assumption of evolutionary significance and an examination of how uncorrelated rewiring has no support in observed network structure:
From the paper:
quote:
"The reason to consider correlations has to do with the assumption that the evolutionary significance of gene duplication lies in the fact that changes in the newly created genes can lead to the emergence of novelty (Patthy, 1999). After gene duplication, one of the two copies becomes redundant and either one of them becomes non-functional (i.e. a pseudogene) or accumulates molecular changes that provide a new function. The new function might be very different. An example is provided by mouse lysozyme genes. One of them has a digestive function in the intestine and the second has a bactericide action in myeolid tissues. Strong divergences from the original function displayed by the ancestor can develop. Moreover, from a numerical point of view, the analysis of the models in which creation or deletion of links is uncorrelated yield results which are in disagreement with the experimental observations in real proteome maps."
So their first assumption is based on observation: that correlated addition and loss of links is supported by the observation, the alternative is NOT supported.
The article also says (page 9):
quote:
Two essential components define the model: growth by single gene duplication plus correlated re-wiring. Unequal cross-over is actually known to be the dominant contribution to genome growth and dynamics (Ohno, 1970). The second rule is inspired in the assumption that
novelties derived from changes in regulation patterns will be constrained by the functional properties present in already established interacting networks or subnetworks. Such constraints are likely to be relaxed when new genes are created through duplication.
The authors assume that the rate of gene duplication and re-wiring is not important -- it is time independent. (ie, you can model the current state of the protein-protein interaction network by sequential events with no assumed rate.) This "collapses time". Time is not important to this model.
The authors assume:
- Gene duplication occurs among the members of a protein-protein interaction network.
- Areas of gene duplications in a network are re-wired, preferentially, over areas that were not duplicated because of the implied freedom that area of the network now has to move away from its initial function. That is, the correlation exists between adding a duplicate and then re-wiring the local network, versus adding a duplicate and re-wiring another part of the network. This is also borne up by observation.
As a programmer, I do not argue here that fine-tuning a model is akin to evolution fine-tuning a model. Besides, the researchers here did not fine tune as much as compare their model to the data.
They then go on to say they derived the rate constants in this model from real data:
From the article:
quote:
We derived the rate equations for the evolution of the degree distribution nk(t) and its stationary states under some constraints imposed by available data from the analysis of yeast proteome.
I find it interesting that you suggest they "fine-tuned" the model, when their only assumptions were gene duplication (preferential attachment) and mutational drift and comparison then to the real data.
The "fine tuning" you might be referring to is their test of the assumption that there's a correlation between attachment and reordering, which isn't a fine-tuning, it's a test of the model against the real data. They assumed several models, ran them, and compared them to the data.
They tested their very simple "toy model" against reality and got a good match using known mechanisms of gene duplication and innovation.
There was no big black box with a dozen dials and arbitrary tweaking to get the results they were looking for. These are good scientists, and they're not going to waste time. As any physicist is taught early on, "Five arbitrary parameters can fit an elephant." But that's not the case, here, and they explicitly address that fact.
Mr. Dembski writes:
quote:
This is a toy model, as the authors themselves admit: "The model is a simple approximation to the evolution of the real proteome map, and no functionality is considered (i.e. no dynamics is explicitly introduced)." Note well: "No functionality is considered."
My goodness, you truncated that quote and insinuated a different meaning than what the authors intended. Here's the real version:
From the paper (page 9):
quote:
"The model is a simple approximation to the evolution of the real proteome map, and no functionality is considered (i.e. no dynamics is explicitly introduced). "
Read further, and they explain WHAT they mean by dynamics:
From the article:
quote:
Further developments of this model should consider different components of proteome structure and the underlying dynamics of protein-protein interactions.
To say they're somehow limited in that they're not examining the underlying dynamics of protein-protein interactions or time-dependent behavior of the gene duplication networks says nothing about their success in modeling the observed architecture from a simple model that went very far in its simulation based on two tightly constrained assumptions.
In other words, no functionality OF the network is presented. That little "i.e." at the end gives what they really meant. They're saying they're not modeling the dynamics, just the method of generating the scale invariance through gene duplication events. If they considered dynamics, it would strengthen their argument, not weaken it.
And it goes both ways. That a simple approximation can work so well with a minimum number of parameters is startling. That functionality didn't have to be considered in developing this model should tell you that the architecture is easily generated from a minimum of assumptions. That makes the model more robust than if they had to assume a dozen parameters and fine-tuned each of them, as I said above.
Mr. Dembski writes:
quote:
**As for TRIZ, I take it that IC provides the analytic cut between routine and inventive problems in biology. This requires justification and I'm working on it.
I would be careful in pointing fingers at scientists who make assumptions to generate their data, when you are, out loud, musing on doing exactly the same thing with much less supporting evidence...arbitrary assumptions that IC is true in the first place and can provide any kind of "analytic cut".
[ 29. September 2002, 10:21: Message edited by: Deanne M. Taylor ]
IP: Logged
|
|
Deanne M. Taylor
Member
Member # 274
|
posted 29. September 2002 11:11
Janitor@MIT writes:
quote:
Just a few observations: Obviously, the IDers conception of design is far broader than mine. My ideas about design, such as they are, are informed by own limited and mundane experience. But they are also informed by what little I know of biology. It seems to me that biologists’ understanding is similarly informed, as biologists seem to be quite familiar with engineering design methods, concepts, and theories: codes, programs, networks, communications, control, regulation, strategies, optimization, robustness, etc. I find it ironic that biologists’ understanding of life has been so profoundly shaped by design, even since antiquity, and never more than now, but they feel compelled to deny the obvious: Life is design.
Look, as I said in the previous post, I was talking about "design" from the ID perspective, design was a catch-all I was using to indicate design by intelligent agency. NOT design by naturalistic process. Life is design in the general term, yes, if you want to go OUTSIDE my clearly-stated definition of the same in the earlier post.
So, here, in this post, you conflate my stated definition of "design" (which was CLEARLY STATED as being limited to Intelligent design). Can I make that very clear to you?
In Previous Posts I Indicated that "DESIGN" meant "DESIGN BY SPECIAL AGENCY". Let's re-read that.
In previous posts I indicated that design meant "design by special agency", de novo design, springing forth outside the agency of evolutionary process.
Now that we have that clear, let me make this next point clear:
You're arguing that "Life is Design". Nobody is questioning that. You're basing some wide pronouncements on a section of the argument that I had never addressed. I never said that life did not show an architecture of some kind. That architecture, I argued, showed RANDOM process "designing" it by some kind of self-organizational principle (as Kauffmann might say, I think) rather than some intelligent agency appearing and saying "voila".
That I'm making such a clear point on all of this is because, reading through your letter, I can see that I have to explain this once again.
EVOLUTIONISTS DO NOT argue that life does not have *A* design in terms of "an architecture". Of course life has an architecture of some kind, besides the architectures we've explicitly observed, including Davidson's work on regulatory networks in sea urchin, how else could life function and behave in all the ways we observe?
But by re-stating that "life shows design" you're implicitly arguing semantics, here.
I am asking if life has a special creation kind of design. Was it DESIGNED by an external agency outside of naturalistic process? That's the question. That's the point of "intelligent design". If you ask an IDer if "design" was naturally evolved or specially created, they'd say life has a creation point, a designer of some kind. An intelligent agent in the sense that there's an intelligence behind the design.
To say that a piece of pure crystalline rock salt shows "a design" would get you agreement from crystallographers who can point out the regularities of spacing in the crystal among the atoms. Would they say that the crystalline solid shows "design" in the sense that it infers intelligence? Would you say that an invisible intelligent agent had to design that crystal to crystallize, or would you say that natural processes caused the crystal to assume its natural shape? That's the kind of questions we're talking about, here.
As I indicated previously, I do NOT want this to become some kind of debate on the definition of "design" and I clearly stated what I meant by design. But I've felt it is necessary to exhibit that the two meanings of "design" meaning some kind of ordered architecture vs. "design" in the idea of an intelligent agent creating that ordered architecture are conflated in your description, and that is a misleading conflation.
quote:
It’s not difficult to trace the source of this denial, because it wasn’t always true that biologists were so insistent that life is not designed.
You're switching definitions again.
Are you saying that life has some kind of A DESIGN, or are you saying LIFE IS DESIGNED? I don't think this is getting through to you, here, and it's worrisome.
Life can show a specific "design" without an intelligent entity designing it. Life can show "a design" from naturalistic processes, like a crystal can. It does not have to be DESIGNED by an outside entity, outside of natural processes.
There is no contradiction to evolutionary theory to say that life shows "design by natural processes". NOT by intelligent agents. Most biologists (note "most", there) would disagree with your assumptions.
And it wasn't so long ago that we thought the earth was flat, that the sun went around the earth, and big sky-turtles held up the world.
Doesn't mean we should go back to those erstwhile time-honored traditions, no matter how insistent the learned heads of Europe were on those issues at the time.
quote:
But then when one refers to the source one finds something very interesting: Charles Darwin cannot be the source of the “anti-design” notion, because he makes of his theory an argument from design : “I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection, in order to mark its relation to man's power of selection.” (He even closes his opus with a “god-of-the-gaps” argument!)
Yes, and you must get out of your self-referential illogic, here. First, evolutionary biology has come quite a long way since Darwin. Gould's book "The Structure of Evolutionary Theory" does a nice job in showing how it's changed.
Second, neo-Darwinian evolutionary theory does posit the idea of general design arising from natural selection. The argument is where that "biological design" originates from. Darwin cited design by Natural Selection.
Evolution does not posit a design that springs forth outside of the agency of evolution or natural selection. Evolution does not accept a designer who creates biological systems entire by special agency. That is outside the realm of observation and of science.
You are conflating the issue of "observed design" which is a completely different issue than the AGENCY of design.
Design is either brought about by intelligent agency outside of the natural process of evolution and natural selection, or it's a natural process called Darwinian evolution.
quote:
Here, Darwin has had the perfectly naïve insight, which he can’t make explicit, because it never appears to rise to the level of consciousness, that the intentions, designs, actions, and productions of mundane intelligent agents are ultimately explicable in terms of a principle of variation and selection.
In which way are you using "intelligent agents", here?
quote:
(I had a college instructor who made the very point: All mathematics, e.g., is “combinatorics.” I had another instructor concur when he informed us that all engineering is “optimization.”)
And all evolved life forms show "design" by th unintelligent agents of random process and selection as suggested by the data.
quote:
Darwin’s motives, as revealed in his Autobiography, are quite plain, but also quite confused, even on his own admission. He’s plainly identified traditional, “revealed” religion with the natural theology that was so influential of his scientific contemporaries. But Darwin was a little myopic. His target was revealed religion, he took aim at natural theology, but his dart struck at the very heart of biological science . Darwin’s poorly conceived and executed attack upon religion has misfired disastrously. The IDers are quite correct to point this out. Among other things, what has suffered is the science, because the biologists cannot fully explore and exploit their own design paradigm as long as they are influenced by Darwin’s “muddled” theology.
Besides the fact that that is a muddled bit of rhetoric, above, making more assumptions than I think the gentle reader will care that I dissect, I'd like to politely ask that you cite your reference where ANY biologist is constrained by the simple premise that life evolves. In fact, I'd like you to show me some data (and feel free to use the ID'ers data) to somehow "prove" that biologists are constrained in interpreting the data based on evolutionary theory, because I all I hear from ID proponents is how widely accomodating evolutionary theory IS, in that it seems to fit data so well. You can't have it both ways. Either evolutionary theory is constraining and prevents biologists from interpreting data or it's so widely adaptable that it can fit any data.
Or are you suggesting, in the alternative, that evolutionary theory is constraining in that it is so adapatable to observation, that evolutionary theory is constraining to the point where we can't accept "Intelligent Design" where we're not looking? Find us some actual data on "intelligent design" and someone will pay money to study it and publish it in peer-reviewed journals. Until then, you're pointing at nothing.
What you're saying, is comparable in my mind to saying that Gravitational Theory is constraining to the point where we can't accept frogs fly when we're not looking. Sure, we might be missing the fact that frogs fly. Want to pay some scientist a research budget to spend all their time monitoring frogs for flight? There's no EVIDENCE for flying frogs. Find us evidence for flying frogs and we'll pay to study them. Until then, stop warning us that we might be missing the flying frogs. You're pointing at nothing.
quote:
To an outsider such as myself, this confused and contradictory etiology of ideas is quite evident and paradoxical: Biologists often invoke design and occasionally argue it with some sophistication and in detail, all the while denying that it is, indeed, what they are talking about!
Sigh. Again, you're conflating "design arising from natural process" to "design because someone put down the blueprints and manufactured it"
quote:
In my own round about way, what I’ve suggested to the IDers is that the biologists might be led to a less “muddled” conception of the design of life via baby steps; via the very design “metaphors” they routinely employ—beginning with natural selection, e.g.
And, in your own round-about way, you're conflating design arising from naturalistic process from design arising from intelligent, outside agencies. Again, the "design from naturalistic process" is what we observe. We have a lot of data on that. As you've admitted that you're an outsider, perhaps you should find out why all these biologists are mysteriously saying they see no evidence for design. It's not because Darwinism has some kind of mythical spell over the minds of thousands of highly intelligent individuals. It's because there's a host of observations which leave it little in doubt, except, perhaps, to people who haven't studied the evidence.
quote:
Now, none of this addresses Dr. Dembski’s topical question. But no, GA’s do not explain the origin of anything. If we say that they do, we beg the next embarrassing question that he no doubt already has in mind. If science must assume an agnostic position wrt to origins, well fine. Let’s not compound embarrassment with absurdity. Scientifically, we can only treat life as a found object and as found, it is an intelligent design indeed. Darwin’s emphasis upon the chance, contingency, and necessity as eliminative of design is nothing more than an argument from ignorance. And I have repeatedly and rather pointedly criticized it: the most persistent argument from ignorance made in this “debate,” Dr. Taylor, is an argument from ignorance of design.
The only ignorance of design I see, here, is the conflation of "design from natural agents" with the "design from intelligent agents".
To clarify:
1) ID "design" claims "design from intelligent agency." All evidence for ID thus far presented to me can be explained by evolutionary theory. I showed that in previous posts, "irreducible complexity" comes about naturally from observation of protein-protein interaction networks. ID supposes an outside agency, outside of natural process, must have come up with the apparent design in living beings, from viruses up through ecosystems.
2) Evolution claims 'mutation and natural selection' can give rise to the architecture we see on every level of life, from viruses up to ecosystems. As any cellular automata researcher can tell you, even the simplest models can lead to regularities and strategies that appear "designed" ab initio. Evolution does not contradict apparent design from self-organizational principles in natural processes. That "life is design" does not suppose an intelligent designer.
I suggest you focus, intead, on the differences in #1 and #2, and the science that's been performed in the over 100 years since Darwin first published his ideas. NO biologist ever claims that life has no design. They do, however, claim that life does NOT show directed design from outside agencies.
Does that design arise from self-organizational principles in nature (evolution) or from an outside organizational source (ID)? That's the question, here.
Arguing about amorphous ideas of design does nothing to address #1 and #2, and conflating the two ideas of design obviously muddies the problem.
While design existing as an architecture, as a strategy, is shared by #1 AND #2, the origin of the strategy of design as an organizational AGENCY is NOT shared between #1 and #2. My arguments in previous posts addressed design as AGENCY, as clearly stated.
The fact that you and Mr. Dembski claim I am ignorant or have a limited view of "design" comes from the fact that I have little problem discerning the difference between 1) design as architecture and 2) the origin of design by an organizational agency.
When I claim there is no apparent design in previous posts I was doing so in a stated context, saying that there is no need to posit a top-down organizating agency to produce the architecture we observe in biological systems. In fact, the observed architecture is quite well suited to production by preferential attachment (gene duplication) and random process (mutation, drift), real observeations which are, currently, best explained by evolutionary theory.
[ 29. September 2002, 11:28: Message edited by: Deanne M. Taylor ]
IP: Logged
|
|
jasonyoung
Member
Member # 432
|
posted 29. September 2002 18:59
quote:
Was it DESIGNED by an external agency outside of naturalistic process? That's the question.
No, it isn't, and any "ID theorist" conflating 'design by God the benevolent entity external to reality' and 'design by a seemingly intelligent agency embedded in nature/reality' needs to hastily extricate themselves from the debate for the sake of their cause.
Eg. Life as an expression of fundamental symmetry bifurcations would be an example of a non-Darwinian account of how life arose, for instance. No one worth listening to is denying that a naturalistic explanation of evolution will inevitably be found.
Neo-Darwinism, aka. "Modern Evolutionary Theory", presupposes nature's 'blind, pitiless indifference' when 'creating' life, expressed through the random mutations that are seemingly done without rhyme nor reason. Dembski et al. are arguing that this is false; that, a) it's not mathematically plausible; b) it doesn't match the empirical evidence: phyla demarcation observed in Cambrian period alone is counterfactual to what would be expected if Darwinism was true; c) Darwinism does NOT predict the emergence of irreducibly complex systems. Again, 'Intelligent Design' theorists are not debating whether or not irreducibly complex systems can be explained using naturalism - they're debating whether or not the fundamental assumptions of neo-Darwinism are true, which they obviously are not.
quote:
Look, as I said in the previous post, I was talking about "design" from the ID perspective, design was a catch-all I was using to indicate design by intelligent agency. NOT design by naturalistic process
What you're talking about isn't what Dembski/Janitor are talking about.
quote:
springing forth outside the agency of evolutionary process.
There is no 'agency' in the current account of the evolutionary process."Blind, pitiless indifference", remember, precludes "intelligent agency". Unintelligent agency isn't agency at all.
quote:
That architecture, I argued, showed RANDOM process "designing" it by some kind of self-organizational principle (as Kauffmann might say, I think) rather than some intelligent agency appearing and saying "voila".
Self-organizational principle, eh? That's not neo-Darwinism.
quote:
Was it DESIGNED by an external agency outside of naturalistic process?
See above. External agency isn't even possible. Anything outside of reality real enough to effect reality would be real; reality is self-contained and self-configuring - reality is, for all intents and purposes, currently "the universe" and everything that 'it' entails, including the fabric of 'space-time. This should be emphasized ad nauseam until neo-Darwinists get the picture: Intelligent Design is not a challenge to NATURALISM, it is a challenge to NEO-DARWINISM/WASM.
quote:
"design" in the sense that it infers intelligence?
It does infer a kind of intelligence, and that intelligence comes in the form of a variety of fundamental syntactical rules governing reality, which we HAVE ALREADY 'FOUND'. No rules, no rock. Rules, such as a natural 'self-organizational principles', are akin to 'intelligence' - quit anthropomorphizing the term, transmuting it into recognizably obsolescent theological notions. Human intelligence is analogous to the 'intelligence' ID theorists are speaking of, but it is NOT the same, and it does NOT imply that 'God' waving around his finger for his own 'personal' amusement can/will explain our existence.
Point: neo-Darwinism, as a 'pseudo-rule', lacks adequate explanatory power to account for complex animate systems in nature. Blind, pitiless indifference doesn't 'work'; there's something fundamental about 'life' that'll likely be explained as we learn more about reality through further observation. It'll likely come from physics, but hey... that's tangential.
quote:
I clearly stated what I meant by design.
You're distorting the idea in order to make it easily confutable.
quote:
Second, neo-Darwinian evolutionary theory does posit the idea of general design arising from natural selection.
It's the random mutations that most have a problem with. -Random- mutations + natural selection does not = irreducibly complex systems. Hell, it's improbably that 'random mutations' could give rise to anything useful unless there was a 'self-organizational principle' embedded in nature. But, as I said earlier, that's not neo-Darwinism.
quote:
Design is either brought about by intelligent agency outside of the natural process of evolution and natural selection, or it's a natural process called Darwinian evolution.
Intelligent agency outside of the natural processes is a non-starter - you're right. That being said, your dichotomy doesn't even exist: option #2 isn't limited to Darwinian explanations. Neo-Darwinism is not Naturalism.
quote:
And all evolved life forms show "design" by th unintelligent agents of random process and selection as suggested by the data.
Wrong, and this has been pointed out by Dembski.
quote:
biologist are constrained by the simple premise that life evolves
Let me correct my janitorial friend: ethicists, not biologists, are constrained by the simple premise that life evolved from natural, deterministic, indifferent processes.
quote:
Either evolutionary theory is constraining and prevents biologists from interpreting data or it's so widely adaptable that it can fit any data.
It's so widely adaptable that it can fit any data. Ever heard of memes?
Because its so adaptable, scientists are limiting discovery by restricting possible interpretations of data (because they have 'the easy way'). Biologists aren't constrained by Darwinism, but science is, and that's the problem.
quote:
It's not because Darwinism has some kind of mythical spell over the minds of thousands of highly intelligent individuals
Recommended reading: Thomas Kuhn, "The Structure of Scientific Revolutions"
quote:
ID supposes an outside agency, outside of natural process
Again, no it doesn't.
Further reading: http://www.scitec.auckland.ac.nz/~king/Preprints/bchtm/biocos.htm
Something tells me that it may be in the best interest of genuine, scholarly intelligent design theorists to find a new label for themselves so as to avoid being mistinterpreted by a school of thought that assumes all anti-Darwinist arguments are endorsing a parochial attitude towards scientific investigation. The ironic part of this is, of course, that Darwinists themselves are limiting scientific discovery with their insular outlook, perversely preferring the sanctity of ego-stroking rectitude over Truth (scientific). Paradigmatic inertia is the enemy of Thought.
-jason
IP: Logged
|
|
Deanne M. Taylor
Member
Member # 274
|
posted 30. September 2002 00:00
Jason writes:
quote:
Deanne writes:
--------------------------------------------
Was it DESIGNED by an external agency outside of naturalistic process? That's the question.
--------------------------------------------
No, it isn't, and any "ID theorist" conflating 'design by God the benevolent entity external to reality' and 'design by a seemingly intelligent agency embedded in nature/reality' needs to hastily extricate themselves from the debate for the sake of their cause.
So, you believe intelligent design is best served by those who already assume an intelligent agency embedded in nature/reality, that evolves creatures towards some kind of end result? If so, then perhaps you can tell me what you consider to be hallmarks of "design" that can be differentiated from "evolution". Wait, let's examine the writings of Mr. Dembski, below...probably a good source.
Jason writes:
quote:
Eg. Life as an expression of fundamental symmetry bifurcations would be an example of a non-Darwinian account of how life arose, for instance. No one worth listening to is denying that a naturalistic explanation of evolution will inevitably be found.
Let's go to Dembski's quote, here...
http://www.origins.org/ftissues/ft9810/articles/dembski.html
(I'm sure there are more like this)
Dembski says:
quote:
The irreducible complexity of such biochemical systems cannot be explained by the Darwinian mechanism, nor indeed by any naturalistic evolutionary mechanism proposed to date. Moreover, because irreducible complexity occurs at the biochemical level, there is no more fundamental level of biological analysis to which the irreducible complexity of biochemical systems can be referred, and at which a Darwinian analysis in terms of selection and mutation can still hope for success. Undergirding biochemistry is ordinary chemistry and physics, neither of which can account for biological information. Also, whether a biochemical system is irreducibly complex is a fully empirical question: Individually knock out each protein constituting a biochemical system to determine whether function is lost. If so, we are dealing with an irreducibly complex system. Experiments of this sort are routine in biology.
Okay, so, you're telling me here, after reading the Dembski quote, when you say
Jason writes:
quote:
No one worth listening to is denying that a naturalistic explanation of evolution will inevitably be found.
that Dembski isn't worth listening to?
In case there's some confusion as to what "Intelligent Design" MEANS, and let's not dodge any bullets, here, let's go to another site, who isn't Mr. Dembski:
This one is from IDEA
http://www-acs.ucsd.edu/~idea/idintro.htm
IDEA (website) says:
quote:
What is Intelligent Design?
Something has been intelligently designed when it is the end product of a thoughtful process that had that product in mind. In other words, intelligent design originates in a mind.
The 'intelligence' in Intelligent Design is an awareness, or consciousness, that is purposeful, that conceives of something it wants to see actualized and directs whatever activities are necessary to achieve that end. It doesn't have to be smart, and we might not understand its purpose. For example, the Smithsonian has presented intelligently-designed objects whose function, or intended function, is unknown to us. I say intended, because an object may have been a failure in the sense that it did not perform as its designer wanted it to. It could have been badly designed. These objects, however, are nonetheless artifactual, not products of the mindless interplay of wind, rain, gravity, etc (see Figure 1).
So, the "intelligence" might not be "smart", meaning, it could be physical law? Or is IDEA saying it's not physical law that's the intelligent agent, but some kind of underlying myterious force? I hope they're not positing some kind of selection of hidden variables that DIRECT natural law. That's something for Bell's Inequality.
(For those outside physics, there's a certain test called Bell's Inequality, that deals with the non-existence of hidden variables in quantum mechanics. I wish more people were aware of Bell's Inequality -- go looking through google for some treatments of it).
I believe that Bell's could be applied to the notion that there are no such "hidden" design processes in nature. It's either natural law and stochastic process, or it's nothing. That would be an interesting approach.
Jason writes:
quote:
Neo-Darwinism, aka. "Modern Evolutionary Theory", presupposes nature's 'blind, pitiless indifference' when 'creating' life, expressed through the random mutations that are seemingly done without rhyme nor reason.
Except here, you seem to have no clue at all what modern genomics & evolutionary theory is saying from what you're saying about "random mutations" that occur without rhyme or reason being unable to generate the systems we see now. There's a wealth of modern and recent theory and evidence and study out there, and to claim "random mutations" without "rhyme or reason" simplifies the theory to the point of, well, a strawman, and there you have your argument of incredulity again. Maybe you want to look into most of the new literature over the past 3 years on evolution, including evo-devo (evolutionary development), and data coming out of the Human Genome Project.
I suspect that the proponents of ID haven't kept up on recent developments in biological data too closely. It's my feeling from having discussions and reading output on various boards at ISCID. Some of the beliefs are woefully out of date. But I'll leave that for another thread.
Jason writes:
quote:
Dembski et al. are arguing that this is false; that, a) it's not mathematically plausible; b) it doesn't match the empirical evidence: phyla demarcation observed in Cambrian period alone is counterfactual to what would be expected if Darwinism was true; c) Darwinism does NOT predict the emergence of irreducibly complex systems.
Okay, point by point:
a) Wrong. Evolution is certainly mathematically plausible. All anti-Evolution arguments to that fact that I've seen have been merely arguments from ignorance, and arguments from lack of data, misunderstanding of probability, incredulity, and not from established fact. Got something spectacular that isn't one of the above?
b) You're making an assumption here based on less data than biologists allow themselves in making assumptions. No matter how much you'd like to point out that the Cambrian diversification is not borne up by current neo-Darwinian theory, the fact is that new research into HOX control of body plan and the possible emergence of HOX genes during the Cambrian period would have given life a great deal more plasticity for diversification and evolution.
Again, you guys have to keep up with recent research before you toss out little nuggets like that one. That isn't even new!
The impact of small tiny one-nucleotide changes in HOX genes leading to body-plan changes is already known. In body plans, SINGLE MUTATIONS MAKE A DIFFERENCE. That is borne up by current data, I'll slip and include a reference for a VERY readable review, here:
http://www.sigmaxi.org/amsci/articles/97articles/Erwin.html
Scientific journal articles are cited at the end of the review.
c) Wrong. As far as IC systems go as they're defined by Behe, Darwinism DOES predict the emergence of IC systems in the context of scale-free network hubs. See my earlier posts about scale-free networks and the necessity for conserved (IC) hub systems within the biological network. This is borne up by data, including data on gene duplication (first proposed by Ohno back in 1970ish) and seen many times. Here's one of many recent publications on such dupliciations.
Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey", J Zhang, Y-P Zhang, HF Rosenberg, Nature (Genetics) 30:April 2002, pg 411-415 - ONLY the Colombine monkeys have RNAse1B and RNAse1; all other primates only have RNAse1. This gene duplication has advantage for the Columbine monkey's digestive strategy.
All you need to generate a biological network with IC hubs the way we've measured it from real data, is to suppose gene duplications happen, and mutation happens. The rest is simple assembly and mathematics. The network self-assembles -- the Santa Fe paper, which was the subject of one my last posts, deals with that.
Jason says:
quote:
Again, 'Intelligent Design' theorists are not debating whether or not irreducibly complex systems can be explained using naturalism - they're debating whether or not the fundamental assumptions of neo-Darwinism are true, which they obviously are not.
They certainly do not think that IC systems arose from naturalistic processes.
And obviously are not true? Obviously, to whom? Thousands of scientists around the world are laboring under a mass delusion and finding evidence when there is none? Using it in biotechs to find drug targets? Establishing more evidence from disparate sources?
And IDers are not trying to establish non-naturalistic sources of design? Perhaps I should find another quote from Mr. Dembski, Here's one...
http://www.origins.org/offices/dembski/docs/bd-theologn.html
Mr Dembski writes:
quote:
The design theorists' beef is not with evolutionary change per se, but with the claim by Darwinists that all such change is driven by purely naturalistic processes which are devoid of purpose.
That looks FRIGHTFULLY as if Mr. Dembski is saying that ID has " a beef" with the Darwinist claim that all such change is driven by purely naturalistic processes which are devoid of purpose.
In other words, no, it's not naturalistic processes that guide the change of organisms, but of some underlying design which has nothing to do with random naturalistic process. So you'll have to make a decision, here. Either Dembski is denying Darwinian evolution and saying it can't possibly happen with the naturalistic processes put forth by Darwinism, or he's saying that naturalistic process is okay, but as long as it's not random or anything like that.
I suspect the latter, and that's ignores how random process can create self-assemblies and complexities with simple rules. Heck, look at Wolfram's book, that's a major part of its thesis: self-assembly rules can create complexity even with stochastic process.
Jason says:
quote:
Deanne said:
-------------------------------------------------Look, as I said in the previous post, I was talking about "design" from the ID perspective, design was a catch-all I was using to indicate design by intelligent agency. NOT design by naturalistic process
-------------------------------------------------
What you're talking about isn't what Dembski/Janitor are talking about.
No, they're not talking about what *I* was talking about in the first place. You've got your order mixed up. Consider that they were replying to ME. Not the other way around. I later had to reply to their replies, and that's what you're replying to. Crystal clear, I hope.
You will notice that I had to call their attention to the fact that they were replying to what I had said in the wrong context. I said time and time again that what I was trying to say is that directed design, or design by an intelligent agency, is what ID says happens. Why this is up for argument is beyond me. ID is not supposing "intelligent design" outside the pale of random, naturalistic process? I'll add "random" there to clarify what I mean, since you seem to conflate my assignment of "naturalistic process" with anything that is NOT Darwinism despite every effort I took in the past post to draw the line between what I was referring to as "intelligent design" and the converse "naturalistic process" of Darwinian selection.
Jason writes:
quote:
Deanne writes:
-----------------------------------------
springing forth outside the agency of evolutionary process.
-------------------------------
There is no 'agency' in the current account of the evolutionary process."Blind, pitiless indifference", remember, precludes "intelligent agency". Unintelligent agency isn't agency at all.
Unintelligent agency is AGENCY, my dear sir.
Sigh. I hate to do this. I really do. But I like to get the record straight. "Evolutionary agency" is certainly correct.
American Heritage Dictionary says:
quote:
a·gen·cy n. pl. a·gen·cies
1. The condition of being in action; operation.
2. The means or mode of acting; instrumentality.
3. A business or service authorized to act for others: an employment agency.
4. An administrative division of a government or international body.
[Medieval Latin agentia, from Latin agns, agent- present participle of agere, to do. See agent.]
Source: The American Heritage® Dictionary of the English Language, Fourth Edition. Copyright © 2000 by Houghton Mifflin Company.
Jason writes:
quote:
Deanne writes:
-------------------------------
That architecture, I argued, showed RANDOM process "designing" it by some kind of self-organizational principle (as Kauffmann might say, I think) rather than some intelligent agency appearing and saying "voila".
----------------------------------
Self-organizational principle, eh? That's not neo-Darwinism.
It certainly is congruent with neo-Darwinism. Neo-Darwinism simply says that the self-organizational principles should be based on natural princples including random (stochastic) events, not on some intelligent agency.
Neo-Darwinism doesn't go against self-organization. Heck, protein folding is self-organization. Crystals self-organize. Polymerization is self-organization.
You have a very strange idea of what neo-Darwinism says or does not say.
Water can self-assemble into snowflakes with no other self-assembly agency than intermolecular forces -- hydrogen bonding....and the unique pattern of every snowflake shows the random, stochastic process that must go into every self-assembling drop of water to produce a unique crystal pattern. Simple processes, repeated over time, can produce complexity from random process and natural forces. That's neo-Darwinism in a nutshell.
Jason writes:
quote:
Deanne writes:
quote:
---------------------------------------
Was it DESIGNED by an external agency outside of naturalistic process?
--------------------------------------
See above. External agency isn't even possible. Anything outside of reality real enough to effect reality would be real; reality is self-contained and self-configuring - reality is, for all intents and purposes, currently "the universe" and everything that 'it' entails, including the fabric of 'space-time. This should be emphasized ad nauseam until neo-Darwinists get the picture: Intelligent Design is not a challenge to NATURALISM, it is a challenge to NEO-DARWINISM/WASM.
Except when Intelligent Design goes against naturalism in the form of, well, naturalism. Against random stochastic processes, against statistical mechanics, against probability, against all the evidence for those processes operating to produce complexity. It's pure denial, and I would politely like you to consider that your opinions on this matter can only be brought into agreement with the above quotes by Mr. Dembski and IDEA (just three of several I've found) that explicitly SAY that naturalism is in question. STOCHASTIC PROCESS IS NATURAL. Randomness is NATURAL. Natural agency is NATURAL. Design is unnnatural and supposes a designer or intelligent agent. See above.
Jason writes:
quote:
Deanne writes:
----------------------------------
"design" in the sense that it infers intelligence?
----------------------------------
It does infer a kind of intelligence, and that intelligence comes in the form of a variety of fundamental syntactical rules governing reality, which we HAVE ALREADY 'FOUND'. No rules, no rock. Rules, such as a natural 'self-organizational principles', are akin to 'intelligence' - quit anthropomorphizing the term, transmuting it into recognizably obsolescent theological notions. Human intelligence is analogous to the 'intelligence' ID theorists are speaking of, but it is NOT the same, and it does NOT imply that 'God' waving around his finger for his own 'personal' amusement can/will explain our existence.
You're basically then, agreeing with neo-Darwinism except for one basic point: You deny the power of randomness, directed by these "organizational principles", to produce complexity.
You say (repeat of above):
quote:
It does infer a kind of intelligence, and that intelligence comes in the form of a variety of fundamental syntactical rules governing reality, which we HAVE ALREADY 'FOUND'. Rules, such as a natural 'self-organizational principles', are akin to 'intelligence'
If you're re-defining natural law as "intelligence", I do take issue with that. Natural laws as self-organizational principles do not demand a designer.They're merely natural laws that follow a fairly simple (in reductionist terms) pattern of behavior that can lead to complex structures WHEN YOU ADD STOCHASTIC PROCESS. Snowflakes, again, are a simple example of self-organization through a natural and simple phenomenon that, when combined with stochastic process, yields a complexity that is not easily predicted from the point of nucleation.
By positing "intelligence" behind physical law, you're re-inventing hundreds of years of secular science. That's nothing but new-ageism, thinly cloaked, to make an argument for "design" from existing science that works JUST fine in predictive power with no such assumption.
Or -- and I always like to give the benefit of the doubt -- are you saying instead that natural law is NOT "intelligence" and you're assuming, what, that some other kind of hidden "design" occurs through something other than physical law? That there's some kind of force we can't measure, can't see, can't consider, that somehow governs the behavior of matter, a force that is not a physical law? That's purely imaginary, in that sense. I doubt you mean that.
Well, you know, I'm supposed to NOT anthropomorphize intelligence in terms of ID, but when you offer to include physical reality as some kind of "intelligent' design, whether or not your views hook up with the REAL ID, who can resist noticing that you're guilty of the same thing? Turning physical law into ANY kind of "intelligence" smacks of the anthropomorphic by the very constrast between the two positions: naturalistic random process and directed "intelligent design". I'm merely restating for you what ID says. Maybe you should journey a-reading and come back and tell me what ID REALLY says, because I just don't buy your "rules" (natural laws) as "intelligent agents" when they work just fine as "unintelligent agents" (sic).
Jason writes:
quote:
Point: neo-Darwinism, as a 'pseudo-rule', lacks adequate explanatory power to account for complex animate systems in nature.
No, the point is that you cannot conceive of neo-Darwinism being able to explain complex animate systems because you've not kept up with recent events, studies, data, etc. The data is huge, overwhelming, almost a tidal wave these days, and it's all evidence for evolution. I challenge you to go read Eichler, Davidson, Gerstein, Barabasi, to go examine the mouse/human DNA homology maps, to examine the HOX evo-devo discussion. Go do searches for "evolution" on PubMed, examine data, analyse databases, do directed experiments. Play with carbon dating, mutate Drosophila flies in your laboratory, study nylon-eating bacteria. Examine yeast-human homologies, align mitochondria in the interest of molecular clocks, examine the VAST amount of mutational data arising from an examination of a few individuals representing the human genome.
I could go on, and on, and those are RECENT developments. GO read, read, and read. Study and read, and do experiments, and stop saying "It can't happen because I said so!" when so many people are quietly (and not so quietly) doing this kind of work and coming up with vast results that allow biotechnology companies to use evolution to make predictions about the human animal.
quote:
Blind, pitiless indifference doesn't 'work'; there's something fundamental about 'life' that'll likely be explained as we learn more about reality through further observation. It'll likely come from physics, but hey... that's tangential.
Oh, don't hold back with physics -- it's near and dear to my heart; my dissertation was in the subject.
By the way, I work for a biotech. Evolution works for us. We assume evolution is true and do cross-species comparisons to assume gene duplication, drift, and ancestral states. And that actually gets us success in drug and target development. Maybe you can argue about evolution from a philosophical point of view, but you'll have to come up with a good reason why biotech companies are making progress by assuming neo-Darwinism is true.
And on a side note, if it's said that naturalistic "design", as you decide it stands, is responsible for evolution by gradualism, then irreducible complexity cannot stand, which is one of the cornerstones, at least one of the first cornerstones, of the whole ID argument.
Jason writes:
quote:
Deanne writes:
--------------------------
I clearly stated what I meant by design.
--------------------------------------------------------------------------------
You're distorting the idea in order to make it easily confutable.
Except that I plainly said what it was, before they replied. You were reading my reply TO their reply. But I think I already covered that.
Jason writes:
quote:
Deanne writes:
------------------------------
Second, neo-Darwinian evolutionary theory does posit the idea of general design arising from natural selection.
------------------------------------
It's the random mutations that most have a problem with. -Random- mutations + natural selection does not = irreducibly complex systems.
Have you been following the mathematical treatment of scale-invariant networks at all? My last posts covered them in detail.
Jason writes:
quote:
Hell, it's improbably that 'random mutations' could give rise to anything useful unless there was a 'self-organizational principle' embedded in nature. But, as I said earlier, that's not neo-Darwinism.
Natural law IS imbedded in Darwinism. To suppose that it's not is a vast denial or simply ignorance to the facts. Darwinism is scientific. IT believes in electromagnetism (which can allow things to self-organize). It believes in quantum theory (ditto). It believes in hydrogen bonds (ditto, ditto). Etc. To suppose that neo-Darwinism cannot assume that natural process gives rise to self-organization is a complete distortion of what neo-Darwinism IS. Neo-Darwinism at its best is scientific literacy and awareness of the power and the impact of stochastic (random) fluctuations within the bounds of NATURAL LAW. I cannot, for a moment, see how you can avoid the appreciation of that fact.
Jason writes:
quote:
Deanne writes:
----------------------------
Design is either brought about by intelligent agency outside of the natural process of evolution and natural selection, or it's a natural process called Darwinian evolution.
-------------------------------
Intelligent agency outside of the natural processes is a non-starter - you're right. That being said, your dichotomy doesn't even exist: option #2 isn't limited to Darwinian explanations. Neo-Darwinism is not Naturalism.
Well, here we go again. Let's define Neo-Darwinism!
quote:
Ne·o-Dar·win·ism n.
Darwinism as modified by the findings of modern genetics.
-----------------------------------------
Neo-Dar·wini·an (-där-wn-n) adj.
Neo-Darwin·ist n.
Source: The American Heritage® Dictionary of the English Language, Fourth Edition
Copyright © 2000 by Houghton Mifflin Company.
Published by Houghton Mifflin Company. All rights reserved.
---------------------------------
neo-Darwinism
\Ne`o-Dar"win*ism\, n. The theory which holds natural selection, as explained by Darwin, to be the chief factor in the evolution of plants and animals, and denies the inheritance of acquired characters; -- esp. opposed to Neo-Lamarckism. Weismannism is an example of extreme Neo-Darwinism. -- Ne`o-Dar*win\"i*an, a. & n.
Source: Webster's Revised Unabridged Dictionary, © 1996, 1998 MICRA, Inc.
------------------------------
Weismannism \Weis"mann*ism\, n. (Biol.) The theories and teachings in regard to heredity propounded by the German biologist August Weismann, esp. in regard to germ plasm as the basis of heredity and the impossibility of transmitting acquired characteristics; -- often called neo-Darwinism.
Source: Webster's Revised Unabridged Dictionary, © 1996, 1998 MICRA, Inc.
------------------
neo-Darwinism
n : a modern Darwinian theory that explains new species in terms of genetic mutations [syn: Neo-Darwinism]
Source: WordNet ® 1.6, © 1997 Princeton University
That being said, let's focus in on exactly what neo-Darwinism must say. Neo-Darwinism must say that the Darwinist proposition, we'll call it all "evolution" under the agreement of the Darwinist perspective, occurs through genetic change through natural processes at the genetic level. Right? Are we in agreement, here?
So self-organizational principles are PERFECTLY in line with neo-Darwinism, since genetics RELIES on self-organizaional principles in the first place.
Jason writes:
quote:
Deanne writes:
-----------------------------
And all evolved life forms show "design" by th unintelligent agents of random process and selection as suggested by the data.
------------------------------------------
Wrong, and this has been pointed out by Dembski.
Sorry, but I presented data and evidence. Dembski calling it "wrong" doesn't erase the data, especially since all he did is wave his hands at the evidence and the mathematics and argue from incredulity.
Care to go into the math with me? We can start a thread on that, keep me updated.
Jason writes:
quote:
Janitor@MIT wrote:
---------------------------------
biologist are constrained by the simple premise that life evolves
----------------------------------
Let me correct my janitorial friend: ethicists, not biologists, are constrained by the simple premise that life evolved from natural, deterministic, indifferent processes.
Deanne writes:
----------------------------------------
Either evolutionary theory is constraining and prevents biologists from interpreting data or it's so widely adaptable that it can fit any data.
----------------------------------------------
It's so widely adaptable that it can fit any data. Ever heard of memes?
Because its so adaptable, scientists are limiting discovery by restricting possible interpretations of data (because they have 'the easy way'). Biologists aren't constrained by Darwinism, but science is, and that's the problem.
I believe my flying frog analogy holds. Despite the search for "meaning" that ID seems to have taken on (and you speak of memes, that's a big one), science is not as limited in its examination of reality as you suppose.
You cannot convince me that I, in the daily execution of my work, will be so blinded by "evolution" that a contradiction will go unnoticed. You seem to forget that most scientists spend all their time refuting one another, getting famous by climbing on one another's shoulders and never offering a hand-up. As I said in other places, it's a dog-eat-dog world in science, where competition is fierce and if you can one-upmanship the other guy, more power to you. If you could come up with a valid proof that evolution is false, if you could find some data disproving evolution that would hold up under scrutiny and review, you'd have not only a slew of papers, but a guaranteed place in the history books.
It's in science's best interest to challenge theories. That's what every experiment testing evolutionary theory DOES. It challenges the theory.
Faulting evolutionary theory for being "highly adaptable" is interesting, when exactly the opposite could help disprove evolution. Prove that any system is not highly adaptable. But don't bother using IC protein-protein "machines" if you want to argue that gradual evolutionary process produced them, because the data shows that the protein-protein interaction networks were likely assembled piecewise from simpler components. Mr. Dembski can deny the data, but it's NOT going to go away because he doesn't like it.
Jason writes:
quote:
Deanne writes:
-----------------------------------
It's not because Darwinism has some kind of mythical spell over the minds of thousands of highly intelligent individuals
------------------------------------
Recommended reading: Thomas Kuhn, "The Structure of Scientific Revolutions"
Funny that you should mention Kuhn's book.
That book helped shape SJ Gould, who took it to heart early in his career.
And it speaks exactly to what I was saying, above. The rule-breakers get famous. Not the people who toe the line. That's known, that's discussed, that's what every scientist out there wants to do (except the shy or aesthetic ones). Get famous, make a dent, make a revolution. If you think that every scientist out there is somehow brainwashed into believing evolution, I'd hazard that you don't know a thing about how competitive science really is.
Jason writes:
quote:
Deanne wrote:
------------------------------------------
ID supposes an outside agency, outside of natural process
---------------------------------------
Again, no it doesn't.
Further reading: http://www.scitec.auckland.ac.nz/~king/Preprints/bchtm/biocos.htm
Oh, except when Dembski is quoted, or IDEA is quoted, above. We can go into a quote war, here?
Just ask, I've got plenty of quotes of what ID'ers beleive, and none of them assume naturalistic process.
quote:
Something tells me that it may be in the best interest of genuine, scholarly intelligent design theorists to find a new label for themselves so as to avoid being mistinterpreted by a school of thought that assumes all anti-Darwinist arguments are endorsing a parochial attitude towards scientific investigation.
Except when they do? I know that's so terribly unconstructive, but it's not merely anti-Darwinian, but it's pro-intelligent-agent and exactly as it was defined, above.
quote:
The ironic part of this is, of course, that Darwinists themselves are limiting scientific discovery with their insular outlook, perversely preferring the sanctity of ego-stroking rectitude over Truth (scientific). Paradigmatic inertia is the enemy of Thought.
My goodness, the pot is calling the kettle burned, here.
Tell me, instead, how your amorphous "design" can make a biotech some money. I can counter with how evolutionary theory is already doing that. Let's get down to the bottom line, here.
Evolutionary theory works, and [moderated, see private messages for explanation]
So, Jason, as you decided to jump in, I offer you these challenges:
- Show me, with one example, and have data to back it up, a unique prediction that intelligent design can make for biological systems that evolutionary theory cannot make in kind. I have several of the converse to offer.
- Make a prediction for the behavior or characteristics of any genome we will observe that is currently in sequencing, with ideas behind "intelligent design". Feel free to add mathematical equations if necessary.
- Make a prediction on human mutational patterns based on "intelligent design" that evolutionary theory does not also independently predict. That is, is there anything that "intelligent design" can predict on the variation in human alleles as we see them today?
- Make a prediction on the arrangement of the genomes of bonobo, gorrilla, orang, etc. etc. in terms of their similarities to the human genome. se intelligent design to argue why these genomes must or must not be highly similar. Cite why differences in these genomes must or must not be dependent or interdependent. Use computer analysis to back up your claims.
I can come up with more, because these are studies that if they're not completed or being done now, will be done eventually. If you expect "intelligent design" is such a whiz-bang theory, then I expect you will have NO trouble in attacking any of those problems with mathematical rigour and gusto, like evolutionists have, can, and will. Enjoy.
[ 30. September 2002, 00:37: Message edited by: Moderator ]
IP: Logged
|
|
Janitor@MIT
Member
Member # 125
|
posted 01. October 2002 16:43
Pretty much signals closure if I can only discuss in terms and categories as defined by the IDers or Dr. Taylor.
Most of what I’ve had to say on this board is based on a simple predicate that there is no “hard” distinction between “natural” evolution and evolution as applied science. Even though traditional evolutionary biology relies on that very lack of “hard” distinction, the distinction is insisted upon for “metaphysical” reasons—none of which, as near as I can tell, have much to do with science.
In any case, I do have some questions (with Mr. Moderator’s indulgence if he pleases):
1) I noted above that this scaling exponent is interesting for many reasons, but I was wondering if anyone knew anything about parameter bounding or fixed parameter problem solving techniques? Specifically wrt to this class of graph problems?
2) Many of the early researchers on the subject of scale-free networks (all the way back to Mandelbrot), used the term “fractal” or “fractal-like.” For some reason that made me think of holograms and associative memory. (Don't ask me why.) That this topology reduces network latencies has been reported by many of the researchers. But relating it further, aside from “user-induced latencies” (keyboarding), the significant network delays/CPU-router-transit times are due to accessing, searching, and retrieving from memory. Anyone know of anything good on “fractal memory”?
3) When I did a little reading on gene duplication/multiplication the first thing that occurred to me is that this is not a “Darwinian” search at all, but a tabu-like search (and you can see how that relates to the previous question). Usually tabu isn’t even included in the reviews of EC I’ve read. (Except those written by engineers for engineers.) Does anyone know of any researcher who has modeled biological evolution as tabu search?
Just “brainstorming.” Any help would be greatly appreciated. Thank you.
IP: Logged
|
|
RBH
Member
Member # 380
|
posted 02. October 2002 00:24
Janitor wrote quote:
2) Many of the early researchers on the subject of scale-free networks (all the way back to Mandelbrot), used the term "fractal" or "fractal-like." For some reason that made me think of holograms and associative memory. (Don't ask me why.) That this topology reduces network latencies has been reported by many of the researchers. But relating it further, aside from "user-induced latencies" (keyboarding), the significant network delays/CPU-router-transit times are due to accessing, searching, and retrieving from memory. Anyone know of anything good on "fractal memory"?
3) When I did a little reading on gene duplication/multiplication the first thing that occurred to me is that this is not a ?Darwinian? search at all, but a tabu-like search (and you can see how that relates to the previous question). Usually tabu isn?t even included in the reviews of EC I?ve read. (Except those written by engineers for engineers.) Does anyone know of any researcher who has modeled biological evolution as tabu search?
I don't know where the associative memory association (!) came from, though the hologram reference goes as far back as the 1960s when Karl Pribram was arguing that interference patterns in DC microcurrents in layer VI of cortex formed 2-D holographic patterns that supported (were identified with? instantiated?) working memory. Or something like that - the 1960s were a long time ago!
I don't know of anyone modeling biological evolution as tabu search. There's a fair amount in the EC stuff published in the operations research, optimization, and engineering lit, as you note. That's an interesting notion, though. Real interesting, in fact. I'm going to have to think about it a bit. Just what I need: Something more to noodle on!
RBH
IP: Logged
|
|
|
Topic Closed
Printer-friendly view of this topic
