Summing up and evaluating Behe’s arguments
I am getting ready to take my family to a Scottish highland games in central Massachusetts (my two oldest are competing in highland dance), so this will have to be brief. Last night we finished our discussion of Michael Behe’s book, Darwin’s Black Box (DBB). The discussion ran over the end of the class period (it has been doing that pretty consistently), and it seemed that there were a number of points still under dispute, both between the EBers and IDers in the class, and within each group (i.e. we must be going something right, eh?)
Consequently, the following points are basically my own, and do not necessarily represent the concensus of the class.
(1) Behe defines “design” on pg. 194 and provides an algorithm of sorts for its detection:
“…design is evident when a number of separate, interacting components are ordered in such a way as to accomplish a function beyond the original components.
However, as I pointed out, according to this definition a thunderstorm cell (i.e. cumulonimbus cloud) would qualify as designed. We generally agreed that thunderclouds are not designed, but are rather the result of a combination of relatively simple physical (i.e. natural) properties and processes. Ergo, Behe’s definition of design is rejected, as it has a tendency to detect false positives. Furthermore, merely revising it is problematic, as this would tend to bias it toward false negatives.
(2) All of the examples of design Behe provides in pages 194-204 to support his definition and design detection algorithm are clearly and unambiguously designed because they are all designed by humans, and we all agree that humans can indeed design things. However, arguing that this somehow validates his defintion/algorithm is simply an argument by analogy, and we have already concluded that this form of argument alone is logically specious.
(3) In pages 203-205, Behe argues that all of this examples of irreducible complexity (and therefore design - eukaryotic cilia, prokaryotic flagella, mammalian blood clotting, intracellular transport, mammalian immunity, AMP regulation, and biochemical pathways in general) all have functions. But, as Ayala, Mayr, Nagel, Bedau, and others on the EB side have cogently argued, functions per se are fully compatible with evolution by natural selection. In a nutshell, genetic programs are “designers,” but there is no empirical evidence that they are themselves the result of design.
(4) In pages 206-207, Behe argues that not all biochemical systems are designed nor irreducibly complex (and using the phospholipid bilayer “unit membrane” and hemoglobin s examples). This immediately leads to a question Behe does not address: why are only some biochemical systems designed? Therefore, the “Intelligent Designer’s” motives must be an irreducible component of any comprehensive explanation of designed irreducible comlexity (DIC).
(5) From the examples cited through page 230, it is clear that DIC theory is only offered as an explanation for the origin of life from non-living materials, the origin of the genetic code, and the origin of the biochemical systems listed in #3 (above). Therefore, the whole of evolutionary theory as presented by Darwin, plus the overwhelming majority of evolutionary biology that has been investigated since 1859 are entirely unaddressed (and therefore unaffected) by Behe’s arguments.
(6) On page 176, Behe concludes that descent with modification from common ancestors is strongly supported by empirical evidence, most of it from biochemistry (specifically comparative sequence data).
(7) Therefore, since Behe accepts common descent and his arguments do not address the overwhelming majority of observations and generalizations (i.e. theories) in evolutionary biology, the whole of his argument devolves to an attack on the non-designed origin of life and biochemical pathways, which may remain forever beyond empirical verification or falsification.
In conclusion, therefore:
(8) The theory of evolution is essentially unaffected by Behe’s arguments and examples in DBB.
(9) A verifiable explanation of the origins of life, the genetic code, and selected biochemical pathways is still an open question, and may continue to remain so for the indefinite future.
(10) Given #8 and #9, neither DBB nor the components of ID theory that are based upon it will (nor indeed can) have any “revolutionary” (or even significant) effect on the science of evolutionary biology.
Which, given the essentially static, non-empirically-verifiable nature of most if ID theory, it can be concluded that ID is not, and probably will not become integrated into the empirical natural sciences.
I agree with about half of this and disagree with the other half; but since we’ve stated most of our differences in class–and it’s Friday afternoon, and sunny outside–I won’t post a rebuttal right now.
Offtopic as regards all that, but per our discussion of Neurobio and confirmation bias, Telic Thoughts has posted a link to some interesting research findings:
A reminder to not be too political about our science. :)
Comment by Hannah — July 14, 2006 @ 2:23 pm
May one ask whether the focus is solely on Behe’s conception of irreducible complexity, or have you as a class or individually considered Dembski’s new and improved definition? According to Dembski’s revision, one must not only establish that a structure or process meets Behe’s operational definition (loss of function due to knockout of a component), but one must also establish (a) that no simpler structure can perform the function, and (b) that one cannot restore the lost function by rearranging and adapting the remaining parts after successful knockout. I’ve argued elsewhere that Dembsi’s revision is The Death of Irreducible Complexity.
RBH
Comment by Richard B. Hoppe — July 14, 2006 @ 2:29 pm
Allen
This wrongly summarises Behe and does not hold. Behe expressly rebuts this allegation. See Whether Intelligent Design is Science: A Response to the Opinion of the Court in Kitzmiller vs Dover Area School District
Comment by David L. Hagen — July 14, 2006 @ 2:42 pm
I think #1 is your best argument. However, I would point out in the specific example you used I don’t think you have different parts. I could be wrong on this.
However, I would take issue with this statement:
“Ergo, Behe’s definition of design is rejected, as it has a tendency to detect false positives. Furthermore, merely revising it is problematic, as this would tend to bias it toward false negatives.”
ID’ers don’t generally have problems with false negatives. Agents can behave in a number of ways. The fact that we can’t list or distinguish all of them doesn’t mean that it isn’t useful to be able to list or distinguish some of them.
“This immediately leads to a question Behe does not address: why are only some biochemical systems designed?”
He does not say that. He simply says that design cannot be inferred.
“Therefore, the whole of evolutionary theory as presented by Darwin, plus the overwhelming majority of evolutionary biology that has been investigated since 1859 are entirely unaddressed (and therefore unaffected) by Behe’s arguments.”
If this were true, so what? Why do people think that everything must argue entirely for or against an entire set of opinion?
But I do think it does ask the question of whether selection is a primary mover, or if design is a primary mover in organismal systems. We can all agree that the systems Behe names are not shared by all organisms. If Behe’s thesis is correct, _and_ universal ancestry is correct, then these complex systems came to be in their present states either by (a) loss of function by an original, more complex ancestor, or (b) by having internal mechanisms be the primary generator of function, both of which are at odds with the traditional conception of how evolution proceeds.
“the whole of his argument devolves to an attack on the non-designed origin of life and biochemical pathways, which may remain forever beyond empirical verification or falsification.”
Isn’t this true only if you consider his arguments to be invalid? Isn’t he attempting to provide an empirical falsification, or at least the first steps to one?
“The theory of evolution is essentially unaffected by Behe’s arguments and examples in DBB.”
This keeps coming out. Why is this important? At the beginning you gave a list of a huge number of contributors to the development of the theory of evolution, each of which made major modifications in the understanding of evolution. It is tough for me to consider what, precisely, would constitute something that was a _refutation_ of evolution as opposed to a _modification_ or a _better understanding_ of it. Would even YEC be a refutation of evolution? I would think that in its current conception it would not be. Therefore, isn’t the whole question of whether or not ID is going to destroy “evolution” somewhat irrelevant, given that there really isn’t anyone who even wants to do that, given a broad enough definition of evolution? I don’t know anyone who is planning on taking down population genetics, DNA sequence analysis, comparative anatomy and comparative genetics, or any of that. So why is it that ID is treated as needing to either rewrite all of evolutionary theory or just be an irrelevant side-show? Might it not simply be that ID is simply one more enhancement of what we know about evolution?
“A verifiable explanation of the origins of life, the genetic code, and selected biochemical pathways is still an open question, and may continue to remain so for the indefinite future.”
So why has the most consistent explanation in terms of current known causation patterns been removed from consideration until all other attempts are tried?
“given the essentially static, non-empirically-verifiable nature of most if ID theory, it can be concluded that ID is not, and probably will not become integrated into the empirical natural sciences.”
Recently Woese, called for the next generation of biologists to be less reductionist and more holistic. I think you’ll find that, despite the fact that Woese would probably not want it to be so, that ID will be the unifying idea that moves biology from reductionism to a dynamic reductionistic/holistic composite, and will just as importantly provide the philosophical justification for doing so.
Comment by Jonathan Bartlett — July 14, 2006 @ 3:42 pm
Jonathan,
Woese’s essay, while using the “scientific” lingo, has got to be the most hand-waivy paper on molecular biology I’ve read in a while - there isn’t a single example of where reductionist molecular biology has failed in the 20th Century!!!
Woese concludes with:
What, exactly, has reductionist biology failed to teach us or be able to explain?!
Woese points to Horizontal Gene Transfer:
But is utterly incorrect - HGT has only been shown to play a significant role in prokaryotic evolution, which is why describing the universal common ancestor has proven difficult. HGT has not in any way refuted common descent.
Woese is further incorrect when he claims:
This is indeed why Behe and others have been shown to have failed in their refutations of evolution - the “wall of biocomplexity” is more like a few random boulders spread miles and miles apart: quite easy to walk around and still explain the theory of evolution quite easily.
Comment by Dan — July 14, 2006 @ 4:09 pm
Actually, on a hunch, I looked up some other writings of Woese, such as this one:
Could Woese be just thinking in the same line of thinking as Doolittle. Like Doolittle, when read carefully, Woese seems to criticize identification of the universal common ancestor (UCA) and not common ancestry or the tree of life itself. And, like Doolittle, it would seem that Woese has joined the ranks of biologists misinterpretted as supporting ID.
Still, I have no idea what on Earth Woese was talking about with “holistic” biology, or failures of reductionism. As Evo-Devo and Molecular Bio are proving in the last ~20 years, reductionism is proving profoundly successful.
Comment by Dan — July 14, 2006 @ 4:28 pm
Behe:
“Cellular machines and machines in our everyday world share a relevant property — their functional complexity, born of a purposeful arrangement of parts — and so inductive conclusions to design can be drawn on the basis of that shared property. To call an induction into doubt one has to show that dissimilarities make a relevant difference to the property one wishes to explain.”
The dissimilarities between machines and the stuff of life could fill a book, but that won’t stop ID proponents from using this analogy (Behe is wrong, BTW - he is arguing by analogy).
Allen touched on another point that torpedoes Behe’s claims. Allen mentioned thunderstorms; I’ve earlier spoken about tornadoes and hurricanes in the same vein. Consider the hurricane - it is IC (don’t believe me? Remove the eye, eyewall, feeder bands, or other central core parts, and what happens? No storm.), its parts are purposefully arranged, it’s far more complex than, say, a human’s genetic code, atmospheric scientists call them engines (they don’t call them engine-like, but engines). Complex, IC, purposefully-arranged parts, scientists use machine terms to describe them - we’re all there, all of the arguments Behe et al. toss about. The kicker, though, is that hurricanes not the product of design; rather, they form following the rules of chemistry and physics.
This means that this laundry list of features that Behe et al. use to argue design is not a good “tool” for this purpose. One can bicker about the semantics of the logic Behe is using (and, I suspect, many words will be spent doing just this), the more obvious fact is that the reasoning is flawed, refuted by observed reality.
Comment by Art G — July 14, 2006 @ 11:35 pm
Bartlett:
“Ergo, Behe’s definition of design is rejected, as it has a tendency to detect false positives. Furthermore, merely revising it is problematic, as this would tend to bias it toward false negatives.”
ID’ers don’t generally have problems with false negatives. Agents can behave in a number of ways. The fact that we can’t list or distinguish all of them doesn’t mean that it isn’t useful to be able to list or distinguish some of them.
It’s not the false positives that are the real problem, it’s the inevitable false positives which according to Dembski would render the explanatory filter useless which is the real problem of ID. The source of false positives is the lack of any relevant ID hypothesis which can be contrasted with the likelihood of ‘we don’t know’. Only when the likelihood of the design inference can be shown to be higher than that of the null hypothesis can one claim a certain level of reliability.
However since ID refuses to deal with concepts that would constrain the ID hypothesis, their claims will remain unreliable rendering the filter all but useless
Comment by PvM — July 15, 2006 @ 3:29 pm
Re: 1). Allan and Art G assert that a hurricane fits Behe’s definition of “design”.
However, in context, Behe’s “design” is best interpreted by his explicit definition of “Irreducible Complexity” (DBB 1996 p 39)
Behe formulated this to explicitly define a system to fit Darwin’s definition of a biotic system that would invalidate Darwin’s theory. I.e.,
.Allen and Art G give no specification of the “basic function.” No parts were specified. The interaction between the parts was not specified. Nor was “well-matched” specified. The unspecified “function” apparently involves “provide a large system of rotating air.” Thus, they appear to be using a clear “Darwinian” understanding of “design” and the corresponding definition of “function.” i.e., an unspecified description that satisfies the users implied intentions as and when desired.
May I suggest that this is a strawman mischaracterization of Behe’s description of design as exemplified by his definition of irreducible complexity.
Following is an example of a clearly defined function involving fluid pressure and a design specification with interacting parts to provide that function.
Fluid Control Function: Control the fluid pressure in each of two spheres of 1 m radius at separately prescribed values between 10 Mpa and mPa, with a maximum transition time of 100 hours, and then maintain those pressures for 2000 hours with an uncertainty of +/-1%.
Fluid Control System: Provide two spheres each 1 m in radius connected by a duct 100 mm in radius and 500 mm long, the duct containing a flow valve. Connect each sphere to a pressure regulating system via a duct 100 mm in radius and 500 mm long, each duct containing a flow valve. Each flow valve shall be capable of maintaining the full pressure difference across it, with a flow rate not greater than 0.1% per day of the lowest pressure. Be able to separately measure and control the pressure in each sphere as specified in the Fluid Control Function.
(The pressure regulation system could be further specified.)
By reverse engineering, after observing and testing the performance of such a system, suitably skilled engineers could reproduce the above Fluid Control Function and the specification for the Fluid Control System, without previously knowing either definition. The probability of such a system occurring in a closed system of natural causes comprising the four fundamental forces can probably be shown to be less than the Universal Probability Bound of parts per 10^120.
Comment by David L. Hagen — July 15, 2006 @ 5:04 pm
Hannah - perhaps this post over at my blog would be a good point, as it is a direct criticism of claims of biocomplexity as an obstacle for the molecular basis of evolution:
Modeling Evolution of Protein-DNA Interactions.
Or start your own thread if you have another direction in mind for discussion…
Comment by Dan — July 15, 2006 @ 5:08 pm
Moderator
To better keep in spirit of the rules, please change my previous post to delete:
“not a good faith effort to evaluate Behe.”
Thankss
Comment by David L. Hagen — July 15, 2006 @ 5:23 pm
Nice moving of the goalpost David. Of course, whenever people describe clearly Irreducibly Complex systems, IDers are quick to reject them as strawmen. Perhaps the flagellum is equally worthy of the description of a strawman.
When science presents plausible hypotheses, all ID has to offer in defense is that the patwhays are not detailed enough.
Of course, the pathways of ID are totally lacking any detail.
Comment by PvM — July 15, 2006 @ 8:20 pm
David said a couple of things that are a bit mystifying.
“Behe formulated this to explicitly define a system to fit Darwin’s definition of a biotic system that would invalidate Darwin’s theory…”
I am pretty sure that Behe would take issue with the claim that he formulated his concept of IC to explicitly invalidate Darwin. Think about it – if IC is defined as being beyond RM+NS, then it is pretty circular to point to an allegedly IC system and claim it cannot have evolved.
Not to mention that, if this is at least part of the definition of IC, then there exists no such thing as an IC system in all of biology.
Secondly:
“Allen and Art G give no specification of the “basic function.” No parts were specified. The interaction between the parts was not specified. Nor was “well-matched” specified. The unspecified “function” apparently involves “provide a large system of rotating air.” Thus, they appear to be using a clear “Darwinian” understanding of “design” and the corresponding definition of “function.” i.e., an unspecified description that satisfies the users implied intentions as and when desired.”
I don’t know what Allen would say about a thunderstorm. But, for a hurricane, I actually provided most of the items on David’s list. Most, but not all (I teased by leaving unmentioned the matter of function). Parts – eye, eyewall, feeder bands. Interactions – let’s be serious. Are you claiming that these parts do not interact? Or that their interactions are not well-matched? The well-matched interactions and their operation are pretty obvious.
As for function, that’s the fun part. There is the atmospheric/oceanographic one, of energy redistribution. There are numerous theological or philosophical ones (God was sneding a message to PCC, maybe?). The clever mind has no problem with function.
Specification is obvious – look it up on the web (under “hurricane”).
Heck, atmospheric scientists call hurricanes engines. With more force than biochemists call things machines. In most ID circles, that’s the gold standard.
The only “violation” here is that we’ve found examples of clearly IC systems that assemble spontaneously via natural means.
Comment by Art G — July 15, 2006 @ 8:32 pm
While Dembski on Uncommon Descent focused mostly on silly arguments, he seems to have been made aware of the thunderstorm argument and not surprisingly ends up ridiculing the idea.
Of course, in the past, based on the same explanatory filter, the faithful had inferred that the thunder and lightning was caused by deities. A position which was only undermine with the scientific enlightenment which identified the scientific mechanisms.
Of course, using Dembski’s insistence on minute details about the pathways we can reject present day scientific explanations of thunderstorms as ‘just so stories’ and combined with our ignorance and the subjective nature of specification, we can thus conclude that the thunderstorm is designed.
Although Dembski has yet to apply his explanatory filter to any non begging the questions and non trivial problems, one can argue that this application of the explanatory filter is in no way inferior to his own applications of the filter. If Dembski is willing to admit that his explanatory filter has yet to be applied in a non-trivial manner, then fine. Until then he has to deal with the reality that his own arguments that argue for the design of for instance the flagellum are not much different from the thunderstorm argument.
When will ID deal with these questions in a more scientific manner? Or is ID even interested in this? Sometimes I wonder if ambiguity is the true friend of ID.
Comment by PvM — July 15, 2006 @ 10:27 pm
“What, exactly, has reductionist biology failed to teach us or be able to explain?!”
I think that what it has failed to do (generally, there are definitely exceptions) is ask the really, really interesting questions.
For example, let’s look at a recent paper on target-site selection in retroviruses. The big question I have never seen in the retroviral literature (and perhaps I just haven’t looked in the right places) is what is the ecological function of target-site selection in retroviruses? I’ve never seen any evaluation of such beyond just the simple viral function or perhaps viral function in order to not kill the host. But might there be a larger ecological role being played by retroviruses? What might target-site selection tell us about this role? Might there be a purpose to retroviruses beyond just replicating for their own benefit?
I don’t mind keeping a technical paper to technical details, but even the review papers on the subject don’t go much beyond the technical mechanism. Even when beneficial functions of retroviruses are reviewed, the questions about the general role of retroviruses in ecology still aren’t being asked.
In a reductionist framework, it is difficult to go and ask the big questions, which may be even more important.
From an ID perspective, we must take into account the possibility that these may be designed elements, and perhaps the entire ecological system as a whole has a design, in which retroviruses play a part. So rather than just being infectious agents, there may be a real role that these things are playing. And I think that something like target-site selection could be very valuable in determining such a role. But what philosophical justification does one have for asking that question without ID? The Gaia theorists are the only other group I could think of that might ask that question, and a strong Gaia theory (strong than what, for instance, Margulis holds) is actually very close to ID.
Comment by Jonathan Bartlett — July 16, 2006 @ 9:24 am
The ecological function of retroviruses? Clearly the exploit an ecological niche that sustains them with conditions needed to survive and replicate. It seems very likely that they perform no clear benefit to their host organisms, but so what? They don’t have a holistic or beneficial intent for their ecosystem, they’re only function is reproduction without killing off their host - any extreme host pathogenicity exceeds their replication requirements, and therefore is redundant.
So it’s not that these questions aren’t being asked - this question appears irrelevant.
The Design and Gaia implications appear to be just as silly, ignoring that what we’re really talking about is a incidental arrangement of highly-connected ecosystems, making for robust opportunities for the survival groups. Design takes biology’s lingo of structure and function relationships and re-frames the argument, at best; and at worst, posits a wholly unwarranted divine intervention.
Gaia, too, personifies or anthropomorphizes ecosystems in a cute but unwarranted manner. The ecosystem isn’t itself alive, it’s a descriptive explanation of the highly interconnected nature of a community of species, that’s all.
Comment by Dan — July 16, 2006 @ 12:47 pm
Why are you saying that science has not considered the ecological function of the retrovirus? Perhaps it has and found it to be lacking?
While teleological language is still strong in science, especially biological sciences, I still fail to see what ID would have to contribute.
Even the argument that reductionism would not deal with purpose is based upon a flawed premise that purpose and intelligent design are somehow non-reducible.
Perhaps what needs to happen is that ID either supports its claims regarding intelligent design being non-natural or realize that ID is nothing more than methodological naturalism.
Since science has shown to succesfully incorporate design into its methodological framework and since ID has remained scientifically vacuous, I’d say that the latter conclusion seems to make most sense.
Comment by PvM — July 16, 2006 @ 2:20 pm
“Since science has shown to succesfully incorporate design into its methodological framework and since ID has remained scientifically vacuous”
I would say that to the extent that science has successfuly incorporated design into its framework is the extent to which it has included ID into its thinking without the proper recognition of what it is doing. The ID label is making explicit one of the most beneficial implicit assessments in biology.
“Perhaps what needs to happen is that ID either supports its claims regarding intelligent design being non-natural”
For a simple support, here’s a question — is “choice” a valid concept? If it is, then how does “choice” arise from law? How does it arise from a combination of chance and law? If it can, then that means that I cannot help but think the way I think, and you cannot help but think the way you think. Therefore, they must both be equally reasonable (or unreasonable) because they are both unavoidable consequence of law or perhaps just dumb luck (in the case of law+chance). So, the only real way to get rid of “mind” is to get rid of the concept of reasonableness altogether.
There are several other justifications, each made by a number of people. Plantiga has this one. Another good one is Biological function and the genetic code are interdependent. Your friend at good math didn’t seem to understand the paper (if I get time, I’ll write up a response, but until then, just read both writings). I’ll post Voie’s own simpler explanation on the old thread.
Comment by Jonathan Bartlett — July 16, 2006 @ 10:13 pm
Bartlett I would say that to the extent that science has successfuly incorporated design into its framework is the extent to which it has included ID into its thinking without the proper recognition of what it is doing. The ID label is making explicit one of the most beneficial implicit assessments in biology.
Why? In other words, if ID is nothing more than what science has already been doing then it seems that ID may be an extraneous concept and methodological naturalism remains unassailed?
Bartlett
For a simple support, here’s a question — is “choice” a valid concept? If it is, then how does “choice” arise from law? How does it arise from a combination of chance and law? If it can, then that means that I cannot help but think the way I think, and you cannot help but think the way you think. Therefore, they must both be equally reasonable (or unreasonable) because they are both unavoidable consequence of law or perhaps just dumb luck (in the case of law+chance). So, the only real way to get rid of “mind” is to get rid of the concept of reasonableness altogether.
That just does not make sense. Let me explain why I believe the concept of mind is trivially reducible to regularity and chance.
We are presented with a situation and use our knowledge of the past to make an assesment of the future. Given a variety of choices, we make the best choice where best is a combination of regularity and chance processes.
Choice is just reducing a set of possibilities to a single actualization.
In a way you cannot help the way you think as your thought processes are an outcome of probably genetics, your environment, your past experiences. There is an excellent example of research on twins who were separated and science found an interesting level of consistency among the two, suggesting that genetics plays a role in how we think and behave.
While I can appreciate that people do not understand Voie’s arguments (they are rather hard to follow), I find Voie’s claims quite irrelevant. In fact, if regularity and chance can be shown to be Godel complete (see Taner Edis) then these processes are sufficient to explain intelligence, artificial or real.
To suggest that mind is similar to reasonableness merely indicates that the two are related, hardly that the two are somehow irreducible to regularity and chance. In fact, as I keep arguing, regularity seems to capture a signficant part of mind/intelligence.
Comment by PvM — July 16, 2006 @ 11:04 pm
J Bartlett
I would say that to the extent that science has successfuly incorporated design into its framework is the extent to which it has included ID into its thinking without the proper recognition of what it is doing. The ID label is making explicit one of the most beneficial implicit assessments in biology.
Huh? The idea that aliens designed all the life forms that ever lived on earth is one of the most beneficial implicit assessments in biology?
Have you any support for this claim outside of the ID promoting community? I’m sure you must have support or else you wouldn’t be making these bold statements/proclamations.
So let’s see the support. Where are the intelligent aliens who designed life on earth discussed, e.g., in the scientific literature by scientists. Is there a PubMed search that will help me find this information?
Comment by Michael Hubl — July 17, 2006 @ 2:32 am
Umm, if you cannot help the way you think, and you posit it’s purely chance and law that makes you think the way you do- there’s no such thing as choice.
Law and chance are clearly going to MAKE you think a particular way no matter if you posit various “choices.” It’s merely going to be a random outcome from law and chance, and YOU are not doing anything to make the choice. If you posit you ARE making choices, then your mind isn’t just law and chance or a combo of the two.
There’s no way you can even call this “choice” to begin with if it’s simply the result of mindless law and chance that leads to the outcome.
The biggest question of all? Why does Pim spend endless hours attacking ID and using the word “vacuous” every ten seconds? Especially since he thinks the concept of mind is trivially reducible to mindless chance and regularity? I guess chance and law forces him to daily type the same attacks using the same word for hours and hours. Darn you chance and law!
Comment by Ben Katz — July 17, 2006 @ 2:32 am
Michael here- if it’s not a published article found via a pubmed search, it doesn’t count as a benefit to science. Nice.
Funny, I don’t see ANYWHERE in this threat where Jonathan EVER said aliens created all forms of life on earth. I’ve never heard ANY IDer argue that aliens or anything else created all forms of life on earth. That’s strawman definition that just won’t cut it.
Comment by Ben Katz — July 17, 2006 @ 2:35 am
Ben: Law and chance are clearly going to MAKE you think a particular way no matter if you posit various “choices.” It’s merely going to be a random outcome from law and chance, and YOU are not doing anything to make the choice. If you posit you ARE making choices, then your mind isn’t just law and chance or a combo of the two.
Perhaps you are right and choice is an illusion and although I have argued against Allen and ID proponents, they made a pretty compelling case.
I am positing that my ‘choices’ are not dissimilar from the choices made by evolution namely the actualization of one of many possible outcomes. In both cases regularity and chance can be easily observed and if this means that choice is an illusion then perhaps that’s the decision we have to live with. So far I have seen no evidence that choice is non reducible to chance and regularity, in fact I have shown various evidences that regularity and chance can be sufficient, which of course does not mean that it could not involve additional aspects. Think about it though, how does one make a decision/choice? Sometimes its an impulsive decision similar to chance. But there are undoubtably genetic components and environmental components, then there is the past experiences which guide our future behavior. In other words, instincts, cultural influences and a component we tend to call chance because we really cannot put our finger on exactly what caused us to make a particular choice.
In the end choice is simply the actualization of one of many possibilities.
Ben: The biggest question of all? Why does Pim spend endless hours attacking ID and using the word “vacuous” every ten seconds? Especially since he thinks the concept of mind is trivially reducible to mindless chance and regularity? I guess chance and law forces him to daily type the same attacks using the same word for hours and hours. Darn you chance and law!
If the suit fits… In this case it does. Why do I repeat myself? Because my conclusions are reinforced by the statements and claims made.
Why not simply show how ID is scientifically relevant :-)
Why do I ‘attack ID’? Because I believe that ID is scientifically vacuous and theologically risky and hope to share my expertise in exposing ID for what it really is. But to call it attack seems a bit overly dramatic, I merely hold it to task to support its claims and explain why many of its claims are self contradictory, or just irrelevant.
Why do I care? Because I care about science and my Christian faith.
Comment by PvM — July 17, 2006 @ 2:53 am
How can we define “law/regularity/necessity/determinism” and “chance/randomness/contingency/indeterminism” in a way that leaves room for anything else?
If “necessity” describes events that occur with a probability of one, and “chance” describes events that occur with a probability of less than one, then necessity and chance are mathematically exhaustive. Can you provide better definitions, Ben?
Comment by secondclass — July 17, 2006 @ 12:08 pm
Comment by secondclass — July 17, 2006 @ 1:30 pm
Only have a second, but that would be a creationist. No doubt some creationists support ID, or would label themselves IDers, but IDers in general- outside of creationists don’t generally believe that. Behe surely doesn’t, as he thinks common descent from one or a handful of common ancestors fits the evidence.
To Pim- how can you be a Christian if you think that choice is possibly an illusion? Are law and chance forcing some to choose Christ and others to refuse him? Hardly seems fair to me, when the Bible makes it clear that we choose either to follow or not to follow. Your view seemed to be that choice isn’t really choice- that it’s not made by us, but rather by law and properties outside of our control. If that IS the argument you make of mind and choice- then I don’t see how that can, in any manner, fit with Christianity. It’s an aside, but it fits with your mentioning mind, chance, law, regularity, etcetera.
Besides the mind, choice issue, no doubt a blind watchmaker hypothesis doesn’t fit the Biblical worldview, unless you write off the book as nonsense, in which case your Christian faith is based on nothing but a hunch I suppose? Then again, you might disagree with the top names in NDE and say that NDE does NOT mean life has no meaning or purpose, that we’re all the result of a trillion happy accidents, the world doesn’t care about us, we’re not the pinnacle of any process, etcetera. I’d personally say guys like Provine are right if you think NDE suffices.
Comment by Ben — July 17, 2006 @ 3:27 pm
I do not know the percentage but I believe most supporters of ID don’t take Genesis literally though many are Christians. For example, Catholics and many Protestants do not interpret everything in the Old Testament as literal. Michael Behe and Bruce Chapman, the President of the Discovery Institute are Catholics so they would not subscribe to a creationist view. David Berlinski has said he has no religious beliefs.
The implications of ID are often at odds with a young earth creationist belief system and in fact many creationists (Believers in a Literal interpretation of Genesis) have severe disagreements with ID. Supporters of ID will often point to the Cambrian Explosion as undermining a Darwinian mechanism for life’s appearance and transitions and cite the 15 million year period as too short for the disparity of life that first appeared then to be caused by any gradual process.
However, it is imperative that those who want to undermine ID, make the connection of ID with creationism so they can claim a religious connection with ID and thus try to suppress any of its conclusions in educational curriculums.
If anyone is interested in aliens, this is something that ID doesn’t really address since they make no claims about the identity of the designer. But it is covered in some biological journals as a possibility for life’s origins. For example, look at Line, Microbiology (2002), 148, 21–27 for a short review of Origin of Life research. In it he devotes a couple paragraphs to panspermia, or the seeding of life from outside the earth.
Comment by J. Cosgrove — July 17, 2006 @ 3:45 pm
And regarding aliens, I think most IDers consider the designer to be extraterrestial, but I could be wrong.
Comment by secondclass — July 17, 2006 @ 4:08 pm
Comment by secondclass — July 17, 2006 @ 4:14 pm
Sure, and if we define “Russia” as the landmass above the equator and “Australia” as the landmass below it, Russia and Australia are geographically exhaustive.
But really– that is the oddest definition of chance and necessity I’ve ever seen. Whoever made it up?
Comment by Hannah — July 17, 2006 @ 4:36 pm
Hannah, that’s why I’m looking for better definitions. What do those terms mean to you?
Comment by secondclass — July 17, 2006 @ 4:45 pm
Since we’re on the topic of mind, an ID paper that might be of interest to the conversation is Quantum physics in neuroscience and psychology: a neurophysical model of mind-brain interaction (Schwartz JM, Stapp HP, Beauregard M. 2005. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 360(1458):1309-27). I haven’t had the time to read it yet, so I can’t say if there’s anything good in it or not. But I it might be interest to those here who want to persue this topic even more fully than we have done here so far.
Comment by Jonathan Bartlett — July 17, 2006 @ 6:03 pm
“If it can’t be evolution by natural selection then it must be designed.” Sorry if I’m generalizing but it seems like that’s what many IDists say. But to me, that’s a fallacious usage of an if-then statement.
Whether or not evolution by natural selection alone can produce the kind of biodiversity we have today is something this board is meant to discuss. But why don’t I hear more IDers say, “it’s not evolution by natural selection because of x y and z. Hence, right now, we just don’t know yet how it precisely works.” Why is it that they leap from not evolution to intelligent design? What bridges that gap? Why don’t IDsts argue for simply not knowing the mechanism?
Comment by Wondering — July 17, 2006 @ 8:14 pm
At any rate we agree on the ‘regularity/necessity’. Probably the most standard ID treatment of the other two would be Dembski’s, as given in his explanatory filter; there chance is considered to be those explanations which allow contingency and are characterized by probability; those that allow contingency and are not characterized by probability are classified as design. So your
one <1 set is divided in two for us.
I don’t usually think of it in terms of probability theory, so something a bit less mathematical then the above, I guess. But it comes to essentially the same thing: necessity/regularity being the deterministic workings of natural laws; chance being the random workings of contingency. To me the question of design tends to boil down to a question of mind. Is intelligence (consider human intelligence, since that is the sort we have readily available to us to examine) ultimately reducible to the workings of natural law and of chance? If it is I think we’ve a good case for all design being an illusion, a fortuitious mixture, say, of necessity and chance. If not…
It’s a rather bold question we’re asking, and it’s sort of fun to wrap one’s mind around all aspects of it. Are regularity and chance the only causes at work in our world, and can we demonstrate that? Or is there another cause; not reducible to those two– call it ‘design’? Could we demonstrate that?
Comment by Hannah — July 17, 2006 @ 11:00 pm
Wondering,
You misunderstand ID. They simply say that certain features of the universe and of living things are best explained by an intelligent cause rather than an undirected process such as natural selection.
They then go onto discuss some of those aspects of biological life they believe are best explained by design. They certainly don’t say this for everything and for certain aspects of life agree completely that neo Darwinism is a good explanation.
ID is more focused on Origin of Life issues and what some called novo-evolution or the origin of new or complex biological structures or body parts and systems.
They believe in evolution in the sense that life has generally got more complex over time and that there is an apparent progression to these changes.
What they challenge is that Neo-Darwinism can explain all or most of these changes. Thus, a second aspect of their research is to clarify just where Neo Darwinism could work and where it is unlikely to be the explanation for the changes in the fossil record.
They would certainly entertain other explanations and other solutions are occasionally being proffered by members of the scientific community. For example, James Valentine has proposed other possible causes for the Cambrian Explosion and has said that Neo Darwinism cannot explain the fossil evidence.
Not everyone who supports ID agree with each other on how much of life was designed or how it was accomplished. The how or why of the designer is not part of ID. I am also sure that some of the ID supporters here will disagree with some parts of what I am saying.
Comment by J. Cosgrove — July 17, 2006 @ 11:15 pm
Hannah —
I think what we’re going to find is that ID is incredibly naive — not that we are looking in the wrong direction, but that we are classifying “design” or “agency” as one thing. I think as we dive into it, we’re going to find there is a huge amount of “stuff” here that is neither necessity nor chance. Right now, we categorize it as “mind”, but hopefully a further investigation will lead to better, more descriptive categories.
Comment by Jonathan Bartlett — July 17, 2006 @ 11:16 pm
Wondering —
“Why is it that they leap from not evolution to intelligent design? What bridges that gap? Why don’t IDsts argue for simply not knowing the mechanism?”
First of all, there are many arguments _for_ design.
Second of all, many arguments against evolution are arguments against non-telic forms of evolution. That is, there may be a mechanism we don’t know about producing these things, but it is a working out of higher-order mechanisms, not a building-up of higher-order mechanisms from lower-order ones.
Many ID’ers believe in mechanisms behind the evolution of things. If you want to get a taste of them you should listen to these two lectures by Shapiro, discussing evolution as a regulated cell process. I don’t know if Shapiro himself is ID (though he is certainly against Darwinism), but the mechanisms he is explaining are at least of the type which many ID’ers find plausible.
Comment by Jonathan Bartlett — July 17, 2006 @ 11:23 pm
Jonathan, Cosgrove:
Thanks. I will peruse the links you provided but my initial reaction is this:
How can ID prove that for all possible undirected processes it is impossible for these “certain features” or “certain aspects of complex life” to emerge? I mean, even if natural selection is not the mechanism, perhaps some other undirected process is. How can ID nullify all possible undirected processes? To me, unless that is done there’s no reason to even consider “higher dimensional” design.
Comment by Wondering — July 17, 2006 @ 11:36 pm
Cosgrove
If anyone is interested in aliens, this is something that ID doesn’t really address
You misunderstand ID. They simply say that certain features of the universe and of living things are best explained by an intelligent cause
Re the latter: no kidding. We scientists here got the message. Loud and clear. You think “certain features” of living things are “best” explained by an “intelligent cause.”
So who is doing the thinking, Cosgrove, if not aliens? It’s not humans — they weren’t around when those “certain features” first appeared. Or do you think they were?
And if not humans, Cosgrove, then what entities provided the “intelligence”? And exactly which “features” did they design and which “features” did they not design and when did they start and stop designing and what was their motive for designing these things? Why did the entities love microorganisms so much?
These are the elementary questions that any serious 5th grader who learns about your “theory” will want to know the answers to. Why aren’t you willing to answer them? Or even try?
In case you or your peers in the ID movement haven’t figured it out yet, until you express a willingness to answer these questions or propose a research plan for doing so, you’re up a creek without a paddle. Nobody will care about your “theory” except your fellow “promoters,” scientifically ignorant folks who get on board the program simply because they believe it affirms their religious beliefs, and semi-professional gadflies who have nothing better to do except to rock the boat just for the sake of doing so.
Comment by Michael Hubl — July 18, 2006 @ 1:08 am
test
Comment by Michael Hubl — July 18, 2006 @ 1:09 am
My comment got eaten. Argh!
Comment by Michael Hubl — July 18, 2006 @ 1:10 am
Bartlett Many ID’ers believe in mechanisms behind the evolution of things. If you want to get a taste of them you should listen to these two lectures by Shapiro, discussing evolution as a regulated cell process. I don’t know if Shapiro himself is ID (though he is certainly against Darwinism), but the mechanisms he is explaining are at least of the type which many ID’ers find plausible.
That’s hard to believe since anytime science explains mechanisms, ID is effectively blocked. At least the common elimination version of ID. I am sure that Bartlett may have other arguments from/to design in mind but those seem hardly relevant to ID’s position.
We can at least safely state that ID is not about mechanisms and that whenever scientific mechanisms have been identified, ID is effectively blocked.
ID may try to co-opt Shapiro’s research as relevant to ID but such embracing of science is only embarassing to ID as it fully undermines its theses. After all, if natural processes can explain the evolution of life, then why the need for ID?
While Shapiro may use terminology which may excite some IDers, it should be self evident that the use of teleological language nor teleology itself is that unsurprising in evolution and thus, unless ID can explain why such teleology should be seen as evidence for ID, it seems that natural processes may be sufficient after all.
Shapiro shows how evolution has used a toolbox of available mechanisms to shape life. Some me confuse the term toolbox as requiring a person/persons who own the toolbox. Metaphors, as is with analogies, are just very limited arguments.
It should be clear that to most IDers, Shapiro’s solution should be highly objectionable since it provides a natural pathway for the evolution of life. Natural genetic engineering…
If IDers like the sound of science then perhaps it’s time for them to join the hard working group of scientists who are looking for answers rather than looking for things we do not understand?
As to the claim that ID claims that certain aspects are better explained by design than by evolutionary processes, it is an interesting position but ID is not in the business of providing any explanation but rather resorts to eliminative arguments and when pressed for these ever elusive hypotheses, IDers are quick to accuse the requester of equivocation or strawmen.
It seems clear to me, ID is not in the business of describing much of anything relevant to design other than to look for areas which are insufficiently understood by science and then argue that ‘ID explains it better’ yet no attempts are made to even show that ID explains it better. That’s because ID presents no testable hypotheses here, other than negative ones. And no the argument from analogy does not count…
It seems to me that Wondering has understood ID quite well and has rejected its claims as vacuous. Yes, there is that word again which covers such claims by ID as: the explanatory filter is reliable as it suffers from no false positives and that such false positives would render it useless. Later the same person, Dembski admitted that false positives exist and that these are typical problems for science. Ignoring that for eliminative approaches false positives are fundamentally fatal as it cannot even compete with the ‘we don’t know’ hypothesis.
This is simple to understand: in order to compete with the null hypothesis of ‘we don’t know’ it has to present a relevant hypothesis but since ID refuses to constrain its designer(s) it cannot present a scientific hypothesis and thus cannot compete. Now, IDers may argue that they do present hypotheses but these are invariable in the form of a negative argument. Compare this with how science infers design and one quickly realizes how vulnerable the explanatory filter is to false positives rendering it fully unreliable, and how this can be avoided. But that requires side hypotheses about means, motives, opportunities, pathways, capabilities, and physical evidence and hearsay or eyewitness evidence.
ID could learn a lot from science as to how to apply a design inference succesfully.
Comment by PvM — July 18, 2006 @ 1:18 am
Pim
After all, if natural processes can explain the evolution of life, then why the need for ID?
Indeed. Where do the intelligent aliens with powers that we are not supposed to ask questions about come into the picture? I do not remember Shapiro invoking these entities to explain the evolution and diversity of life forms on earth.
ID is not in the business of describing much of anything relevant to design other than to look for areas which are insufficiently understood by science and then argue that ‘ID explains it better’ yet no attempts are made to even show that ID explains it better. That’s because ID presents no testable hypotheses here, other than negative ones.
Pim is correct as usual. This is the opinion of most educated people who have examined ID. Most = the vast majority. I suppose someone here will now describe ID not as a scientific theory but as some sort of “heuristic”.
But that is not a discussion about science as much as it is a discussion about human psychology. Listening to Mozart or Pink Floyd or riding a bike or mountain climbing may help some scientists formulate creative hypotheses which they can test. So what? Surely this is not the “controversy” that ID promoters are trying to promote.
Comment by Michael Hubl — July 18, 2006 @ 1:42 am
You misunderstand ID. They simply say that certain features of the universe and of living things are best explained by an intelligent cause
They simply say that but there is nothing “simple” about invoking intelligent aliens and their purposeful “designs” to explain the “complex features” that are present in every life form that ever lived on earth.
When and how did these entities accomplish the mind-blowing task of designing and creating all these “complex features”??? And where did the entities come from?
Basic questions. Simple questions — the kind that anyone would ask if a genuine scientist presented this “theory” and it was actually taken seriously as a challenge to the idea the life on earth evolved more or less according to the principles which Darwin outlined.
So what are the answers to these questions? And how do scientists begin answering them?
Or is ID vacuous, as Pim and I (and a whole lot of other people) believe it to be?
Comment by Michael Hubl — July 18, 2006 @ 1:48 am
Wonderer How can ID prove that for all possible undirected processes it is impossible for these “certain features” or “certain aspects of complex life” to emerge? I mean, even if natural selection is not the mechanism, perhaps some other undirected process is. How can ID nullify all possible undirected processes? To me, unless that is done there’s no reason to even consider “higher dimensional” design.
The IDer would be ‘quick’ to point out that of course this is a requirement which is untenable but remember that since ID is purely eliminative, it needs to meet these requirements. Otherwise, one runs the risk of false positives and unless one can show that the hypothesis of design is more likely than that hypothesis of ‘we don’t know’, one cannot determine the reliability of the design inference. And history has shown countless examples of design inferences gone awry because of our ignorance.
So on the one hand IDers like Dembski argue that the design inference is reliable because it avoids false positives and on the other hand he accepts false positives as unavoidable. It’s these inherent contradictions which make ID so vulnerable although they are seldomly acknowledged by IDists let alone addressed.
So why should we not conclude ‘we don;t know’ until we have a positive hypothesis of design and/or regularity and chance which sufficiently explains a particular system? Why rush to conclusions ? History has shown that such rush inevitable leads to design having to hide in ever decreasing gaps.
from a scientific and theological perspective I find such a fate unacceptable.
Comment by PvM — July 18, 2006 @ 1:58 am
Ben
Michael here- if it’s not a published article found via a pubmed search, it doesn’t count as a benefit to science. Nice.
Huh? I never said that. What I’m saying is that if “the ID label is making explicit one of the most beneficial implicit assessments in biology” then it would be reasonable to expect scientists to be invoking non-human “intelligent causation” to explain all sorts of biological phenomenon.
I don’t see that in the literature. It’s just a data point, albeit one that is consistent with the vacuity of the ID.
Fact is, when scientists are presented with a biological phenomenon to study, they take stock of what they know and don’t know. When it comes to the features of the phenomenon which are unknown, they ask themselves, “Well, if this thing was beneficial to the organism’s fitness in this way, then we might expect to find X, Y or Z because we know that X, Y, or Z will provide this property.”
But if a scientist finds X, Y, or Z they don’t say, “This is evidence for intelligent design because I predicted it.” They say, “We are beginning to get an understanding of how biology work.”
And if they find that neither X, Y or Z is true, they don’t say the negative finding was “evidence for intelligent design because we can’t explain it.” They say: we need to think harder about this.
That’s how science works. How do I know this?
Guess.
Funny, I don’t see ANYWHERE in this threat where Jonathan EVER said aliens created all forms of life on earth. I’ve never heard ANY IDer argue that aliens or anything else created all forms of life on earth. That’s strawman definition that just won’t cut it.
Comment by Michael Hubl — July 18, 2006 @ 2:08 am
That last paragraph in my previous comment can be deleted.
Comment by Michael Hubl — July 18, 2006 @ 2:09 am
Pim
History has shown that such rush inevitable leads to design having to hide in ever decreasing gaps.
from a scientific and theological perspective I find such a fate unacceptable.
Yes, Pim, but are your fears “logical”? ;)
Comment by Michael Hubl — July 18, 2006 @ 2:11 am
“if x then not y” does not mean “if not x then y”. consider the case where x = evolution by natural selection and y = the existence of a designer. that’s what it seems like is happening here.
my other contention is that if scientific arguments truly existed FOR intelligent design (as was suggested earlier), in my opinion, that would be akin to arguments proving the existence of god/aliens/whatever. so, somehow IDists claim to have provided an answer to one of the world’s biggest questions (”is there anything else out there”?) yet know nothing else about the answer (”who that somebody out there is”,”who created them”,”how”,etc).
hmm… i’m new to ID so please point me towards some of this arguments. i’ll try to keep an open mind.
Comment by Wondering — July 18, 2006 @ 2:24 am
thanks pvm. i had not thought of it that way before.
Comment by Wondering — July 18, 2006 @ 2:24 am
Wondering: ID claims that while it cannot really say much about the designers, it can still infer the imprints of its actions.
For instance ID argues that design is not reducible to chance and/or regularities (such as laws) and thus if we can eliminate all chance and regularity hypotheses, that which remains should be design. As Dembski however also admits, that the step from design to agency (designer) is not a necessary one.
“even though in practice inferring design is the first step in identifying an intelligent agent, taken by itself design does not require that such an agent be posited. The notion of design that emerges from the design inference must not be confused with intelligent agency” (TDI, 227, my emphasis)
Quite an admission I’d say.
In order to claim that ID is not exclusively negative, IDers attempt to argue from analogy that designers are the only known entities that can create something called Complex Specified Information. But since CSI is defined to be zero if science can explain it, it fails to be of much relevance. After all, of design can explain it, the information would similar be reduced to zero as its probability approaches 1 (information is the negative log2 of the probability).
So in other words, that approach does not help either. In fact the whole concept of CSI is mostly an argument from ignorance as specification is trivially supplied by function (and we know how function in evolution is related to variation and selection). In addition, information basically describes our inability to explain how something arose. If we find an explanation, its complexity/information is reduced to zero. But somehow this is only a problem for evolutionary theory and not design. That’s because science provides pathways and mechanisms and ID does not, so ID should not have to worry that it can succesfully explain anything…
ID then argues that while ID should surplant methodological naturalism, since MN rejects ID a-priori, it also argues that MN succesfully applies design inference. Somehow the self-contradiction of the many Id positions are poorly understood or recognized. But when science infers design it does it based not on our ignorance but based on what we don know. Means, motives, opportunities, physical evidence, hearsay, eye witnesses etc all play a role in constraining the ‘designer’. Imagine a supernatural design on trial. Since anything is possible how can we prove his guilt or innocence? After all, could he have been in two places at the same time? Travel fast enough to be in two places almost at the same time? What about motives? How do we establish motives of the supernatural? Can we even venture to try to understand what drives the supernatural? Or more importantly what limits it.
Hope this helps. There is far more and I hope to explain in more detail the approaches of ID and why they are likely to fail.
Needless to say I am quite skeptical of ID’s claims, not a-priori but a-posteriori. This means that I do not reject ID as much before exploring its claims but rather that after exploring its claims and noticing that ID has failed to be scientifically relevant, it has failed a-posteriori (after the fact).
Comment by PvM — July 18, 2006 @ 2:45 am
Wondering —
“How can ID nullify all possible undirected processes”
Four essays to ponder:
Searching Large Spaces
Evolutionary Computation
Evolution and the Second Law of Thermodynamics
Three subsets of sequence complexity and their relevance to biopolymeric information
Comment by Jonathan Bartlett — July 18, 2006 @ 7:32 am
How can ID prove that for all possible undirected processes it is impossible for these “certain features” or “certain aspects of complex life” to emerge? I mean, even if natural selection is not the mechanism, perhaps some other undirected process is. How can ID nullify all possible undirected processes? To me, unless that is done there’s no reason to even consider “higher dimensional” design.
And remember, that’s not just every possible undirected process that’s ever been thought up, it includes possible undirected processes that no one has thought of yet.
Comment by ivy privy — July 18, 2006 @ 10:33 am
The essays are mostly irrelevant. Searching large spaces looks at finding needles in the haystack. As I have discussed elsewhere however under the No Free Lunch Theorems, random search is trivially simple.
Evolution and the Second Law is based on the age old creationist canard.
Evolutionary computation ignores the impact of the environment. In fact, in evolution, information is transferred from the environment into the genome.
I understand that ID is attempting to eliminate any and all pathways here. But extending the logic, they are also eliminating intelligent design as a pathway.
As is the case with the second law, there are no laws prohibiting the local increase in information or the decrease in entropy.
Comment by PvM — July 18, 2006 @ 11:23 am
Hannah:
Comment by secondclass — July 18, 2006 @ 12:13 pm
(Above post reformatted. Sorry.)
Hannah:
Comment by secondclass — July 18, 2006 @ 12:14 pm
(Third time’s the charm…)
Hannah:
I submit that there is no such thing as a contingent (or noncontingent, for that matter) event that is not characterized by probability. Can you give us an example?Comment by secondclass — July 18, 2006 @ 12:15 pm
From Daniel Dennet and Douglas Hofstadter’s book, Mind’s Eye, famous origin of life researcher Harold Morowitz writes:
Thus MIND must be logically prior in physics, it is more primitive than atoms. We know from quantum theory the future can effect the past (experimentally verified by the double-slit-delayed choice experiment). This fact allows MIND to have a non-material component not bound by the necessity of pre-existing atoms.
There is fundamentally a non-physical quality about mind. World class physicists Paul Davies and John Gribbin describe disembodied intelligence in their book, Matter Myth. Considerations for this are derived purely from physical law, not any metaphysical writings!
I think Hannah is has a strong background in mathematical proof. She thus might be familiar with “proof by contradiction”. Wigner made his proof via contradiction.
Here is a related peer-reviewed paper on the topic ID and Neuroscience.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 18, 2006 @ 1:03 pm
There is fundamentally a non-physical quality about mind.
That is an unsupported assertion. Could you demonstrate for us a mind without a material basis? None of this “someone else who is a big shot says it’s so”, give us the actual argument or demonstration.
I’m sure you’re aware that appeal to authority is considered a fallacy when the person appealed to is not actually an authority on the topic under discussion. Therefore I ask you, why would physicists be considered authorities on consciousness? Shouldn’t we rather turn to psychologists and neurobiologists for those questions?
Comment by ivy privy — July 18, 2006 @ 2:55 pm
Comment by secondclass — July 18, 2006 @ 3:30 pm
I provided a link to a peer-reviewed paper by a neuroscientist with an extensive bibliography. The neuroscientist referenced the work of the physicists.
You said my assertion was “unsupported” possibly because you were unwilling to read the referenced papers. I have no desire to cut and paste or otherwise retype all of the arguments from those books and papers on this thread. I have provided enough information for interested readers to independently verify the assertions.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 18, 2006 @ 3:33 pm
PvM:
But, indeed, ID does explain things better. Take, for example, the genetic code. Are we to understood that lengthy, meaningful (i.e., information rich) sequences came about completely by chance? That flies completely in the face of information theory. As Behe and Snoke’s paper illustrate, ‘point-mutations’ take billions of organisms, billions of years, to get 6 nucleotides to come together in a meaningful arrangement. HOW do you then explain billions of nucleotides filled with information? Invoking ‘design’ to explain what is SEEN (!!!!) makes perfectly good sense. Binary code, arranged through intelligent agency, leads to functional, information rich, output.
Now, if you want to say that’s invoking an ‘argument via an analogy’, and thus discredit what is obvious, then that is tantamount to saying that the argument that the complexity of watches implies intelligence is also disallowed. Remember, there is such a thing as “genetic engineering”.
And more and more, scientists are able to control and change nucleotide sequencing. This is proof-positive that human intelligence operates in a way that is analagous to the intelligence that is responsible for DNA design. This is just plain common sense.
Lastly, the actual ‘business’ of ID is not ‘to look for areas which are insufficiently understood by science’, but is just the opposite. That is, it is precisely BECAUSE we know MORE about (i.e., ‘better understand’) biochemistry, and more about information science, and more about nanotechnology, and are able to peer at increasingly smaller and smaller distances, that ID is posited; not the other way around. And that’s why, other than political correctness fighting it tooth and nail, Darwinism will fall, and soon.
Comment by Lino D'Ischia — July 18, 2006 @ 4:42 pm
The paper Sal quotes doesn’t state this. It states that to understand consciousness you need to understand neurological processes at the level of quantum mechanics, rather than classical physics. That’s not exactly a mainstream position, but even if true it says nothing about the mind being non-materialistic.
QM turned our understanding of the physical world on its head in many ways, but doesn’t operate outside the physical world as physicists understand it, at least.
Comment by Don Baccus — July 18, 2006 @ 4:45 pm
I provided a link to a peer-reviewed paper by a neuroscientist with an extensive bibliography. The neuroscientist referenced the work of the physicists.
You said my assertion was “unsupported” possibly because you were unwilling to read the referenced papers. I have no desire to cut and paste or otherwise retype all of the arguments from those books and papers on this thread. I have provided enough information for interested readers to independently verify the assertions.
You don’t have to cut and paste everything. Pick out the single strongest piece of evidence for a non-material mind. Give us that. Just one experimental result or theoretical assertion.
Comment by ivy privy — July 18, 2006 @ 5:28 pm
Are you taking bets? Large ones, preferably? I’m 52, so “soon” probably needs to be no longer than a couple of decades. Also, I assume by “fail” you mean that ID rather than evolution will become the prevailing paradigm in SCIENCE, as we understand science to be today?
And I’m curious about one thing, Lino. Do you really believe, deep in your heart, that scientists are bound by “political correctness”? That it’s only PC that keeps ID from getting the respect you think it deserves?
Comment by Don Baccus — July 18, 2006 @ 5:55 pm
Lino:
“As Behe and Snoke’s paper illustrate, ‘point-mutations’ take billions of organisms, billions of years, to get 6 nucleotides to come together in a meaningful arrangement. HOW do you then explain billions of nucleotides filled with information? Invoking ‘design’ to explain what is SEEN (!!!!) makes perfectly good sense.”
Do you also realize that the population size used in the model is more than 7 magnitudes smaller than what might actually be found in just one ton of soil? Becasue population size and time were the two main factors in determining whether or not these point mutations could occur, the validity of such a model is just preposterous. Furthermore, Behe explicitly admits that his computer model excludes some of the mechanisms by which evolution occurs.
So Lino, according to Behe, just add more time,a more realistic population of prokaryotes, and a few more mechanisms by which evolution is known to occur, and PRESTO!!!! You have a paper that supports biological evolution!
Comment by Mike Hannigan — July 18, 2006 @ 7:37 pm
ivy privy,
This is only a sketch, but follow the links:
Quantum Philosophy
You can look an alternate description of the regress problem ARN: Scientific Necessity of God’s existence
For more info on Barrow and Tipler’s Universal Mind go to:
God in the equations
You don’t have to accept it, but from a scientific perspective, it’s good enough to be a working hypothesis, imho, especially with regard to ID.
Salvador
PS
OK, no more on this topic, if you chose to believe it fine, if not, fine. The books are out there, and this thread isn’t the place for the details.
Comment by Salvador T. Cordova, IDEA GMU — July 18, 2006 @ 9:40 pm
Sal: You don’t have to accept it, but from a scientific perspective, it’s good enough to be a working hypothesis, imho, especially with regard to ID.
I have to agree that it is good enough to be an ID ‘working hypothesis’ and certainly much better than we have seen from Dembski, Behe or Johnson but really… Is this the kind of God you envision? And I thought ID was not about God. Did you not get the talking points :-)
Comment by PvM — July 18, 2006 @ 10:16 pm
Lino But, indeed, ID does explain things better. Take, for example, the genetic code. Are we to understood that lengthy, meaningful (i.e., information rich) sequences came about completely by chance? That flies completely in the face of information theory. As Behe and Snoke’s paper illustrate, ‘point-mutations’ take billions of organisms, billions of years, to get 6 nucleotides to come together in a meaningful arrangement. HOW do you then explain billions of nucleotides filled with information? Invoking ‘design’ to explain what is SEEN (!!!!) makes perfectly good sense. Binary code, arranged through intelligent agency, leads to functional, information rich, output.
Wow, I could not have wished for a better example of how ID when asked to show that it explains something better, it invariably resorts to negative arguments against evolutionary scenarios. Thank you Lino.
In this case Lino is wondering how science explains the genetic code. I have already provided for many links and provided much explanation. Nevertheless, this may be a good place to show 1) how science explains the genetic code 2) how ID has nothing to offer as a scientific explanation.
Before I continue, I would like to point out how Lino seems to have bought into the claims of ID that ID ‘explains’ or ‘explains better’ when in fact all ID does is wonder about things they do not fully understand. In this case, it is clear that it is personal incredulity which leads Lino to conclude design.
And yet, a quick perusal of the internet and the vaste resources it provides would have unearthed a myriad of examples as to how science is resolving the origin and evolution of the genetic code.
There are typically a set of 3-4 (competing and complementary) explanations provided and science has slowly been unraveling which ones seem to be best supported by the data. The explanations invoke stereochemistry, selection, chance and co-evolution.
Stereochemistry is the argument that the original coding arose as a chemical necessity and only later evolved. At least 6 of the 20 amino-acids, and most of them are the ones that are believed to have arisen earliest, show evidence of stereochemistry linkage. That’s quite important as this shows how necessity initiated the genetic coding. In fact, the original genetic code is argued to have contained doublet codes instead of the present day tripet code. In other words, two codons code for the amino-acid rather that the three. Over time, selection played a significant role in the re-assignment of codings to other doublets and later on triplets. Selection comes into play when the code becomes more robust to errors. Then there is the argument that at least some of the genetic code is due to history and chance. Nothing much to say about this than that the code seems to have some aspects that show its relevance to chance.
It should be clear by now that thus Lino’s question is a flawed one since science is not arguing that the code came about by chance. In fact, on the contrary, it argues that necessity was the first step. Behe and Snoke do little to support an origin of life argument, they merely looked at a very limited evolutionary scenario and incorrectly concluded that the scenario showed that it was unlikely to happen. Of course ‘design’ always remains a possibility but sadly enough ID provides no guidance here and certainly no explanations.
Back to the genetic code: Co-evolution argues that coding was extended along biosynthetic pathways
As Bob Knight, graduate student of Laura Landweber shows in The Origin and Evolution of the Genetic Code: Statistical and Experimental Investigations
Science has also shown how evolution of the genetic code can take place as is evidenced by the almost general genetic code. More information on demand.
1. There is strong statistical support for at least two of the three major models of the evolution of the canonical code: the code appears highly resistant to errors relative to random codes, and there is a strong statistical association between at least some codons and the RNA binding sites for their cognate amino acid. I found no support for specific coevolutionary models, although it is likely that the code did evolve from a simpler form.
2. The exact time at which code optimization occurred is unclear: measures that make the code appear highly optimal can be found for the free amino acids, the side-chains in simple peptides, and the side-chains in the context of modern proteins. However, ‘earlier’ measures seem, in general, to make the code appear more optimal. This may indicate that codon assignments were determined early, perhaps in an RNA world. Data from aptamer selections tends to support this idea, though equivocally.
3. Modern variant genetic codes are probably neutral or slightly deleterious mutants of the standard code: all are recently derived. It remains possible that they are adapted to the specific environment of the mitochondria, where most of them occur, although I did not find any evidence for such adaptation. There is no support for the idea that variant codes are optimized for reduced tRNA number, although mitochondrial genomes are so highly optimized for size that each tRNA can lose 20 bases on average in the smallest metazoan mitochondria (nematodes). There is strong statistical support for the idea that code evolution proceeds through an ambiguous intermediate. The molecular basis for certain code changes can be tracked down: in ciliates, the mutations in the release factor eRF1 that prevent stop codon recognition can be recaptured by statistical techniques applied to phylogenies.
4. The genetic code is not just the pattern of codon assignments: it is also the frequency with which each codon is used. Surprisingly, the huge interspecific variation in codon and amino acid usage can largely be recaptured by a neutral model that assumes only purifying selection.
Search google for “evolution genetic code selection stereochemistry” and don’t forget the scholarly links. Enjoy…
Recent research on the origins and evolution of the genetic code have shown how “The standard genetic code enhances adaptive evolution of proteins” in a paper by Wen Zhu, Stephen Freeland, Journal of Theoretical Biology 239 (2006) 63–70
Not only is the genetic code ‘optimal’ in the sense that the effects of point mutations or mistranslations on the phenotype are minimized, a property which seems to argue for stasis, but the genetic code also speeds up the rate of adaptive evolution, a property which seems to argue for rapid change.
Again we see how the concept of robustness and evolvability are intricately linked in the genetic code.
Website: evolvingcodeDOTnet
Check out the reference library for instance… 130 entries on the genetic code and related issues.
Relevant papers
1. Knight, R. and Yarus, M. (2003). “Analyzing partially randomized nucleic acid pools: straight dope on doping.” Nucleic Acids Research 31:e30.
2. Knight, R. and Yarus, M. (2003). “Finding specific RNA motifs: Function in a zeptomole world?” RNA 9:218-230.
3. Yarus, M, and Knight, R. D. (2003). “The Scope of Selection”. To appear in “The Genetic Code and the Origin of Life”, Landes Bioscience 2003.
4. Knight, R. D. and Yarus, M. (2003). “Tests of a Stereochemical Genetic Code “. To appear in “Translation Mechanisms”, Landes Bioscience 2003.
5. Knight, R. D., Freeland, S. J., and L. F. Landweber (2001). “A Simple Model Based On Mutation and Selection Explains Compositional Trends Within and Across Genomes.” GenomeBiology 2(4):research0010.1-0010.13.
6. Knight, R. D., Landweber, L. F., and M. Yarus (2001). “How mitochondria redefine the code.” J. Mol. Evol. 53:299-313.
7. Lozupone, C. A., Knight, R. D., and L. F. Landweber (2001). “The Molecular Basis of Nuclear Genetic Code Changes in Ciliates.” Current Biology 11:65-74.
8. Knight, R. D., S. J. Freeland, and L. F. Landweber (2001). “Rewiring the Keyboard: Evolvability of the Genetic Code” Nat Rev Genet 2:49-58.
9. Knight, R. D. and L. F. Landweber (2000). “The Early Evolution of the Genetic Code” Cell 101(6): 569-572.
10. Knight, R. D. and L. F. Landweber (2000). “Guilt by association: the arginine case revisited.” RNA 6(4): 499-510.
11. Freeland, S. J., R. D. Knight, L. F. Landweber and L.D. Hurst (2000). “Early Fixation of an Optimal Genetic Code.” Mol Biol Evol 17(4): 511-518.
12. Freeland, S. J., R. D. Knight, and L. F. Landweber (2000). “Measuring adaptation within the genetic code [letter].” Trends Biochem Sci 25(2): 44-5.
13. Knight, R. D., S. J. Freeland, and L. F. Landweber (1999). “Selection, history and chemistry: the three faces of the genetic code.” Trends Biochem Sci 24(6):241-7.
14. Freeland, S. J., R. D. Knight, and L. F. Landweber (1999). “Do proteins predate DNA?” Science 286(5440): 690-2.
15. Knight, R. D. and L. F. Landweber (1999). “Is the genetic code really a frozen accident? New evidence from in vitro selection.” Ann N Y Acad Sci 870: 408-10.
16. Knight, R. D. and L. F. Landweber (1998). “Rhyme or reason: RNA-arginine interactions and the genetic code.” Chem Biol 5(9): R215-20.
Could you please explain to me how ID explains the genetic code again?
Thought so.
Comment by PvM — July 18, 2006 @ 10:39 pm
It seems interesting to me though that Sal seems to be abandoning ID’s arguments from elimination such as proposed by Behe and Dembski and is moving the goalposts to yet another attempt to infer design (read God).
Lamoureux observed when Behe mentioned how he can move IC systems to the Big Bang that
Third, note that Behe even speculates that ID could have been implemented in the Big Bang. If this is indeed the case, then he truly betrays the concept of irreducible complexity. By definition, irreducibly complex biomolecular structures cannot be put together one piece at a time through a gradual process. Irreducible complexity can only come about through “one fell swoop” acts during the course of time, and not at the very beginning of time. Behe’s shift in the direction of a full evolutionary theory not requiring interventions during the history of life is characteristic of many who have gone before him in that the gaps they once believed existed in nature are only gaps in their knowledge. Suggesting that intelligent design could have been loaded in the initial conditions of the Big Bang is evidence that the gaps are closing in Behe’s view of origins, and that he is coming to terms with biological evolution.
Seems to me that Sal is going through much a similar evolution with his shifts in direction. Good for you my friend.
Comment by PvM — July 18, 2006 @ 10:41 pm
Lino wrote:
“And that’s why, other than political correctness fighting it tooth and nail, Darwinism will fall, and soon.”
Lino — probably unwittingly — repeats the “longest running falsehood in Creationism.” See:
http://home.entouch.net/dmd/moreandmore.htm
Comment by Kevin Johnston — July 19, 2006 @ 3:49 am
PvM —
Where did Sal say that he was abandoning an argument?
Where are the goalposts moved?
Even if there was, why is updating an argument considered a bad thing? Isn’t this what evolution has done time and time again? It seems that updating an idea based on other, new ideas is a good part of science, not a bad one. You can’t argue both (a) ID is moving goalposts and (b) evolution has been greatly improved since Darwin’s day without imposing a double-standard. Or do you think that science should be a static entity?
As for the early evolution of the genetic code, are you actually familiar with the papers you are citing, or are you just copying someone else’s reference list?
Most of the ones I examined just assumed that it was a naturalistic event, but did not provide any sort of mechanism for it. If you know which one provides the mechanism for the creation of a code (with messages — a code without a message is fairly useless), I would be interested in reading it. The thesis at that site doesn’t add much either in relationship to this discussion. They simply provide a couple of interesting ideas which might be true, but only if the idea that the code formed naturalistically is true. They don’t provide any information on how a code can come to be.
“Science has also shown how evolution of the genetic code can take place as is evidenced by the almost general genetic code.”
No, it hasn’t. Most of those links are simply establishing a chemical relationship between RNA and amino acids. It doesn’t say anything about how a code can come about in the first place. It merely suggests a relationship between the properties of RNA and the properties of amino acids. How is that an explanation for the arising of the code?
Comment by Jonathan Bartlett — July 19, 2006 @ 7:44 am
Kevin wrote:
“Lino — probably unwittingly — repeats the “longest running falsehood in Creationism.” See:”
The link is entitled: “The Eminent Demise of Evolution”. I wrote that “Darwinism will fall.”
This only points out more forcefully the equivocation that Darwinists insist upon. For them there is no distance whatsoever between evolution–which here means simply the increasing complexity of life forms over geologic time, and visible in the fossil record–and Darwinism–which is a ‘theory’ as to how this ‘complexity’ arose. Darwinists seem to refuse to keep these two concepts–one observable, the other theoretical–separate, which only makes any kind of intelligent discussion with them that much harder.
Comment by Lino D'Ischia — July 19, 2006 @ 8:32 am
In comment #72 Lino wrote:
“Darwinists seem to refuse to keep these two concepts–one observable, the other theoretical–separate, which only makes any kind of intelligent discussion with them that much harder.”
What, precisely, is a “Darwinist?” Personally (as an evolutionary biologist), although I know a large number of scientists who investigate natural objects and processes using standard empirical materials and methods, I don’t know any “Darwinists” per se. Clearly, you have a very clear idea of what (or who) a “Darwinist” is, so would you please elucidate?
BTW (and anticipating a “standard” reply), evolutionary biologists are NOT committed to the straw-man “RM+NS” caricature of which creationists are so fond. Indeed, we are not “committed” to anything except the use of time-honored empirical methods of inquiry as a means to a better understanding of nature. More specifically, evolutionary biologists have spent a century and a half collectively investigating the processes Darwin called “descent with modification” and “natural selection” (see my other posts at this website and at The Evolution List for what “natural selection” entails). Both Michael Behe (in Darwin’s Black Box and William Dembski (in The Design Inference and other publications) have agreed that descent with modification from common ancestors is “strongly supported” by the evidence, and both have stated repeatedly that natural selection has an important (albeit not exclusive) role to play in such descent. So, if that’s what you mean by a “Darwinist”, then perhaps you might explain how including people like Michael Behe and William Dembski under that heading implies that “Darwinism” is close to collapse?
And, in the spirit of our rules of engagement, could you please cite some evidence for this collapse (references to peer-reviewed scientific literature preferred, of course…and please, no press releases).
Comment by Allen MacNeill — July 19, 2006 @ 9:14 am
And BTW, the word you are looking for is “imminent” (meaning “impending”), not “eminent” (meaning “important”).
Comment by Allen MacNeill — July 19, 2006 @ 9:15 am
Allen,
The ID people would be happy to take your position. They readily support that many transitions take place with natural selection. Within these transitions that take place with natural selection some can come by the route of mutations and some by no mutations at all or maybe a combination as it may be a lengthy process.
However, they believe that natural selection cannot explain all the transitions and maybe that in some cases there are no transitions at all but the appearance of a new form or function that cannot be explained by an obvious predecessor.
Then there is the origin of life problem which ID claims does not seem to have any transitions.
That is why evolutionary biology should be divided into various problem areas and each approached separately. People have a tendency to conflate them all.
Comment by J. Cosgrove — July 19, 2006 @ 10:25 am
Allen —
“evolutionary biologists are NOT committed to the straw-man “RM+NS” caricature of which creationists are so fond”…”So, if that’s what you mean by a “Darwinist”, then perhaps you might explain how including people like Michael Behe and William Dembski under that heading implies that “Darwinism” is close to collapse?”
RM-NS is not a caricature, but an attempt at precision in detailing a specific problem with specific people. The fact is that there _are_ many people in biology that are stuck in the RM-NS paradigm. _These_ are the people that ID is most adamant against. To say that there exist people (and perhaps many people) in evolutionary biology with whom ID’ers don’t disagree is an obvious point which ID’ers themselves have been long trying to tell people. In fact, the whole point of “teach the controversy” is the fact that RM-NS is the version of evolutionary theory currently taught in many textbooks. If that is incorrect, and it is not where the science currently is, then why aren’t evolutionary biologists _joining_ the ID’ers in fixing the textbooks? This seems to me to be an extremely obvious thing to do. If both ID’ers and evolutionary biologists agree that the current science does not support the views of evolution that is commonly taught in textbooks, then why not say, “on this at least we can agree — let’s update the textbooks to remove the vestiges of the no-longer-supported parts of Darwinism”?
Instead, rather than agreeing with Wells and others that, yes, the textbooks are using outmoded ideas in evolutionary teaching, people have been criticizing anyone who brings up how out-of-sync the textbooks are with current science!
I personally think that the reason for this is that materialism is the first order of business for many. First of all, the idea of agreeing with a non-materialist is nearly blasphemous, so all ideas which come from them must be first poo-pooed away. Second, it is RM-NS which gives a lot of intellectual justification to a lot of people for the materialist worldview, so to downgrade its importance is to remove that justification. As Dawkins said:
“Evolution is very possibly not, in actual fact, always gradual. But it must be gradual when it is being used to explain the coming into existence of complicated, apparently designed objects, like eyes. For if it is not gradual in these cases, it ceases to have any explanatory power at all. Without gradualness in these cases, we are back to miracle, which is simply a synonym for the total absence of explanation.”
“This is another way of saying that objects such as these cannot be explained as coming into existence by chance. As we have seen, to invoke chance, on its own, as an explanation, is equivalent to vaulting from the bottom to the top of Mount Improbable’s steepest cliff in one bound. And what corresponds to inching up the kindly, grassy slopes on the other side of the mountain? It is the slow, cumulative, one-step-at-a-time, non-random survival of random variants that Darwin called natural selection. The metaphor of Mount Improbable dramatizes the mistake of the sceptics quoted at the beginning of this chapter. Where they went wrong was to keep their eyes fixed on the vertical precipice and its dramatic height. They assumed that the sheer cliff was the only way up to the summit on which are perched eyes and protein molecules and other supremely improbable arrangements of parts. It was Darwin’s great achievement to discover the gentle gradients winding up the other side of the mountain.”
Perhaps education has progressed quite a bit since I was there, but my suggestion is simply this — if ID’ers and Evolutionary Biologists are finding so few ways of disagreeing with each other these days, why is it that Evolutionary Biologists are so against ID, and why is it that obvious problems with education about evolutionary biology are being defended simply to spite ID’ers?
Comment by Jonathan Bartlett — July 19, 2006 @ 11:23 am
But, if the state of the system always evolves according to the Schrodinger equation — i.e. continuously and deterministically — how can it discontinuously and probabilistically collapse into an eigenstate on measurement? Especially since, in QM, measurement seems to be a form of interaction
Oddly, I don’t see how that answers my query, since the Schrodinger equation applies to matter and forces, i.e. natural stuff rather than supernatural; but since you wish not to provide a more suitable answer, so be it. I will also reiterate that Wigner is not a psychologist or neurobiologist, and thus I would have trouble accepting him as an authority on the topic of consciousness.
Comment by ivy privy — July 19, 2006 @ 11:39 am
Ok,
I admire and respect Allen very much. And as is the case when one would like to remain on good terms with an acquintance, one tries to avoid as much as possible, discussions about contentious topics (like politics and religion and EB v ID).
However, perhaps being a good friend sometimes means pointing out to someone where you believe they err.
The whole point of Dembski’s work was to point out that evolutionary biology (as it is currently defined by appealing to low information content combinations of stochastic and deterministic processes) might have to be disqualified from empirical science as well.
Ernst Mayr pointed:
IDers are quick to seize upon this, and Dembski (indirectly Yockey and Trevors), have shown mathematically, Mayr’s claims are in fact rigoursly demonstratable. That is evoluionary biology ,as it is currently defined, has no hope of being as rigorous as chemistry or physics.
I have pointed out, however, if ID ever succeeds in it’s grand quest for discovering steganography (like Behe’s hidden codes) in biology, it will be light years ahead of evolutionary biology as it is currently framed.
Why is this? Physics and chemistry are governed by testable laws. A lesser, less immutable idea of “laws” are cybernetic laws (which though breakable, but still have a degree of constancy). For example, a sidewinder missile is governed by cybernetic laws. It has predictable testable behavior within well-approximated statistical parameters. If biotic reality also is governed by cybernetic laws (both it’s day-to-day operation like DNA-translation as well as the lay out of it’s supposed evolutionary history), then ID will be the superior framework for the laws definition.
For example, Kimura was bent on defining the sequence divergences in terms of a stochastic processes (much like diffusions in physics). Denton and especially Hoyle have demonstrated mathematically why that thesis is collapsing, and I can see it playing out in peer-reviewed articles every other month.
The sequence divergences evidence specified complexity, not a random diffusion, and certainly not Blind Watchmaking natural selection, unless somehow Nature were conspiring to make specified complexity across all the DNA of all species!
The hierarchical nested patterning of molecular sequences has been poorly accounted for by common ancestry combined with a kluge known as a molecular clock. But the molecular clock is in defiance of statistical mechanics of physics, and it is being borne out now by the peer-reviewed literature. I could see it coming. We see hints of it in DePristo’s recent paper on Missense Meanderings, and other papers as well….
To illustrate the problem, consider this pattern of coins (H=head, T=tails)
H T H T H T …… H T
Superficially its 1st order statistical moments are consistent with a random pattern (half are heads, half are tails), but upon closer inspection it obeys a cybernetic law inconsistent with a purely stochastic process, and the superficial perception turns out to be glaringly wrong simply by scrutinizing the capability of the presumed stochastic process (random coin flips). It is the same issue that is happening with our interpretation of molecular sequences across taxa and even “junk DNA”. Scrutinizing the capabilities of the supposed stochastic generating mechanism (RMNS) shows RMNS is inconsistent with the patterns! The initial perceptions are turning out to be glaringly wrong!
As it stands, researchers are already unwittingly uncovering the hidden codes, and their inability to characterize various sequence phenomena in terms of low-information content stochastic processes is testament a testable cybernetic law may be at play here, not a low-information content stochastic process (RMNS).
Finally, regarding my post about God being suggested by physics, ID proper does not require His existence, and thus, contrary to PvM’s assertions, I have not abandoned Dembski or Behe. However, the fact physics strongly suggests and Ultimate Intelligence behind all the laws of physics, in the absence of finding another intelligent designer as the author of life (like space aliens), as a last resort, one can fall back on the possible existence of an Ultimate Intelligence. Thus, the objection that “no possible designer exists” is negated. A possible designer exists, but such ideas are only offered by me to pre-empt “no designer” objections, not because ID proper requires a Designer for ID to be formulated as a working scientific hypothesis.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 19, 2006 @ 11:41 am
Finally, regarding my post about God being suggested by physics, ID proper does not require His existence, and thus, contrary to PvM’s assertions, I have not abandoned Dembski or Behe. However, the fact physics strongly suggests and Ultimate Intelligence behind all the laws of physics
I disagree strongly with you about that. Physics does not suggest God, some physicists suggest God, and the physics is not behind them in that suggestion.
Comment by ivy privy — July 19, 2006 @ 12:29 pm
Please, no “cybernetic law” says the perception “turns out to be glaringly wrong”. Probability theory simply says the probability shrinks the longer the sequence becomes.
And, of course, if the probability is low enough, we seek other explanations. In the molecular biology case, we immediately note that the events leading to supposedly improbable results ARE NOT INDEPENDENT as coin flips are. This invalidates your analogy. It’s one of the oldest arguments in the creationist world, the error of which (false premise) has been pointed out endless times, yet here we are, seeing it again.
Why?
And, it’s “kludge” (rhymes with “sludge” in some circles within the UK). “Kluge” was a German General in WW II.
Comment by Don Baccus — July 19, 2006 @ 12:45 pm
Salvador:
If the sequence is long enough, its algorithmic compressibility virtually guarantees that it came from a simple deterministic source rather than a 50/50 random source. That’s the only inference that logic permits.I know you didn’t claim otherwise, but I often see IDers conclude design simply from the elimination of a null hypothesis (in this case a uniform random distribution). In most cases, it’s a non sequitur.
Comment by secondclass — July 19, 2006 @ 1:04 pm
Sal raises an almost random set of objections showing not really problems with evolutionary theory as much as problems with evolutionary concepts. I have to admit that much of science can often be more complex than one may envision. Such is the case with neutrality, common descent, molecular clock.
For instance the term low information content process of RMNS is yet another ad hoc claim which, as I have shown, fails to withstand even the cursory scrutiny.
While Sal objects to my logical conclusions that he is abandoning hope that Behe and Dembski’s arguments will gain a certain level of rigor, it seems clear to me that his random objections are but the last struggles of minor objections which can be easily put to rest by explaining how science deals with concepts of common descent, neutrality etc.
For instance, science has shown that neutrality can improve the “needle in the haystack” search significantly.
To given an example of Sal’s confusion: He argues that a particular sequence of head tails looks random. One can establish the level of randomness by exploring its information content, and just as science has done this for DNA, this requires more than a single sequence.
But I am sure Sal understands how science deals with the concepts of information theory which not only allow science to detect high information content in the genome, detecting for instance binding site, but it also allows science to show how simple processes of variation and selection can in fact explain the information content of the genome.
note that Sal has yet to address this simple fact, in fact, he is addressing it in a somewhat passive agressive manner by calling RMNS a low information process.
Anyone familiar with information theory would just smile at such a claim.
All Sal, Behe and Dembski have shown that ID, by focusing on eliminative approaches, has rendered itself scientifically vacuous. Sal’s random search, aka grasping for aruments, indicates to me that he has not only abandoned the hopes for Dembski and Behe, but also that he is moving his search to even less relevant topics. I have found in the past that Sal is quick to raise quantum theory, Schroedinger equations, when discussing the fallacies of Intelligent Design, and specifically Dembski and Behe’s approaches. It’s an interesting defense mechanism more commonly known as redirection.
To show an example of Sal’s empty claims, look at the following
For example, Kimura was bent on defining the sequence divergences in terms of a stochastic processes (much like diffusions in physics). Denton and especially Hoyle have demonstrated mathematically why that thesis is collapsing, and I can see it playing out in peer-reviewed articles every other month.
Anyone familiar with peer reviewed articles would come to realize that neutrality has been shown to be an essential feature to evolution’s success and would understand that neutrality is a selectable feature.
Thus anyone familiar with science has to reject Sal’s claims that
1. Denton has demonstrated mathematically that Kimura’s thesis is wrong
2. Hoyle has demonstrated mathematically that Kimura’s thesis is wrong
3. That peer reviewed literature supports this thesis.
I challenge Sal to support his claims but i doubt we will hear more on this.
Denton by the way was quite confused about divergence, molecular clock. leading him to misintepret the cytochrome-c data.
Another fallacious claim of Sal’s is
The hierarchical nested patterning of molecular sequences has been poorly accounted for by common ancestry combined with a kluge known as a molecular clock
I am glad that Sal accepts the hierarchical patterns of phylogeny. Seems he accepts common descent after all :-) But his claim that it requires a molecular clock shows another misunderstanding of phylogenetic reconstruction techniques.
I thank Sal for helping us understand how unfamiliarity with evolutionary science seems to underly much of the superficial objections of ID to evolutionary science. This supports my well supported observation that natural selection is rejected not on scientific but rather on religious grounds by many ID proponents.
For those interested in common descent and how ID deals with this, check out Dembski’s latest article in which he misinterprets Woese’s position on the three domains of life. Fascinating how much damage a little knowledge can do.
If anyone is interested in exploring the importance of the consistent phylogenies recovered from a large variety of data, and its relevance to evolutionary theory, I suggest to check out the work by Theobald Douglas on TalkOrigins. He lays out the many evidences supporting the fact of common descent, and in the processes explains why Sal is mostly wrong. In fact, I believe I has mentioned the site to Sal in the past.
I hope that others do not let their philosophical fears lead them to ignore the real evolutionary sciences by creating mostly strawmen versions.
Science and faith deserve better. And science shows a wonderful picture of God’s marvelous Creation.
Needless to say, any interested reader will quickly notice that the concept of neutrality has extended its importance all through evolutionary sciences.
Most importantly science has proposed well supported hypotheses as to how neutrality has arisen through simple processes.
Neutrality, contrary to Sal’s claims, is a hot scientific topic at is brings together such issues as robustness, evolvability, modularity and helps understand why evolution has been so succesful.
But you won;t hear about it form IDers which somehow have managed to ignore most of the (recent) scientific research.
Just ask yourself: If ID is truly about information theory, how come that few if any ID theses discuss the work by Fontana, Schuster, Toussaint, Gavrilets? Or how come that few information theoretical papers discuss intelligent design in any meaningful manner?
Remember; ID is based on an eliminative approach and its usage of the term information is highly equivocating as it shares little relevant to information theoretical concerns.
Remember: Information as defined by ID is merely the negative log(2) of the probability.
Do not confuse this definition with the more common usages of the term or one may make the same mistake as Sal who confused specification with ’specify’.
Comment by PvM — July 19, 2006 @ 1:16 pm
Secondclass, you have hit the nail on its head. When it comes down to applications of the explanatory filter, ID has totally failed to apply it in any non-begging and rigorous manner to support its claims.
Also remember that ID admits that false positives are a real possibility and thus the explanatory filter is unreliable. One could control the level of reliability by actual proposing a scientific hypothesis of ID but that seems implausible to ever happen
Comment by PvM — July 19, 2006 @ 1:23 pm
But he sometimes uses the term “information” to mean CSI, as he does when he refers to the “Law of Conservation of Information.” And in this paper, he uses it as an abbreviation for “added information,” which is a term he invented to describe subtracted information. (Don’t believe me? Read the paper.)
Why do IDers play so fast and loose with this term if a clear information theoretic explanation of ID is supposedly in their best interest?
Comment by secondclass — July 19, 2006 @ 2:19 pm
I plead you reconsider your statement. We’re talking physical coins, NOT bit strings output by a computer.
The bolded portion of your comment is therfore inaccurate. The proper conclusion is design.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 19, 2006 @ 3:12 pm
Analogy, Induction, and Specious Arguments
I submit that this charge is itself specious; that the design hypothesis, while based on analogies in the same way all non-deductive reasoning must necessarily be, is nevertheless a valid inductive argument; fraught with the same pitfalls as other non…
Trackback by Evolution and Design — July 19, 2006 @ 3:47 pm
Last time I looked, I wasn’t made of coins…
Coin tosses represent independent events. Again, I don’t understand why you insist upon arguing upon this false premise, that you can compute the probability of a chain of linked events as though they’re independent events.
Comment by Don Baccus — July 19, 2006 @ 4:17 pm
We can actually try an empircal experiment. Have 500 coins uniquely marked (via a light-weight ink).
If one, upon finding such coins in a room and going from coin #1 to #500, and finds the pattern
H T H T H T….H T
One will conclude this pattern could not possibly be the result of a deterministic process (law) or a stochastic process (chance), or any combination thereof, but only design.
That should addres Don’s absolute obfuscation and confusion of the spirit of my argument.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 19, 2006 @ 4:26 pm
Salvador:
I reconsidered, but I’m pretty hopeless.
I assume that your design conclusion stems from an unstated premise that a human is flipping the coin, and your background knowledge informs you that humans are intelligent and capable of cheating. If, on the other hand, the coin is tumbling down an incline which causes it to flip over periodically, we see the same pattern but we don’t infer design.
In either case, if the sequence is long enough, it’s obvious that the state of the coin is fully determined by its previous state, which makes the coin-flipping a deterministic process. The question of whether the pattern was chosen intentionally or whether it occurred naturally can be determined only by looking at who or what generated the pattern. It’s that “who or what” question that ID refuses to address WRT biology.
Comment by secondclass — July 19, 2006 @ 4:31 pm
Salvador, I’ve been discussing the “necessity&chance vs. design” dichotomy with Hannah, and I’m waiting for her to get back to me, but maybe you can answer a question in the meantime: How do you define necessity and chance in a way that isn’t collectively exhaustive?
Comment by secondclass — July 19, 2006 @ 4:39 pm
Perhaps you meant to ask, how do you define necessity and chance exhaustively?
1. necessity (deterministic process)
2. chance (stochastic process)
One can in principle quantify the information content in a stochastic process. For example the distributions could be simple (50/50 coin is head), or slightly more sophisticated like Normal distribution with a mean and variance, or some of the more fancy distributions like Chi-Squared, etc….whatever.
Dembski DEFINES designed objects as objects which lie outside those generated by:
1. purely deterministic,
2. purely stochastic,
3. or combinations of deterministic and stochastic processes
#3 was only recently dealt with rigorously in the Displacement theorem.
That is the formal DEFINITION of design, it does not automatically mean intelligence was involved, this is only a formal definition of what it means for an object to look designed.
Now, does the appearance of design necessarily mean an intelligence must always create designs? Not necessarily, only reasonably when the design has many bits of CSI.
However, what Dembski demonstrated was that Dawkin’s claims were square circles, that Dawkins mechanisms were inconsisten with the claimed outcomes. That is what is mathematically sound.
However, the question of the involvement of intelligence in the creation of design is separate, and that is the ID-hypothesis not the D-definition (Design definition). So when you ask, “how can Dembski be so sure something is designed?” you might have to consider that a definition is only being offered, not an argument automatically for intelligent agency.
Defining design is not the same as inferring an intelligent agency. Formally speaking Design is merely a definition, it is not making claim of intelligence. Informally, however, I and others may mean ID when we merely use the word Design. So please be careful to note when the mode of discussion is formal versus informal. If in doubt, ask….
Formally speaking ID is offered as a falsifiable hypothesis like any other scientific theory, IDers therefore do not officially demand it be accepted as an absolute truth, but rather offer it as a falsifiable hypothesis in various specific instances (i.e., spontaneous abiogenesis in the lab, growing a flagellum in the lab via RMNS, etc. ).
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 19, 2006 @ 5:16 pm
No, it is Dembski’s definition of design, which is not (be gentle, Don) widely accepted.
Right. If you do the impossible, then that would falsify ID. Except the backup position is well-known, Sal: falsify ID by doing what you believe to be impossible, then ID will just claim that the experiment was designed. Which is, in essence, what you do with Avida …
Comment by Don Baccus — July 19, 2006 @ 5:23 pm
Salvador:
You seem to be implying that design events cannot be quantified probabilistically. Please correct me if I’m misreading you.
I submit that there is no such thing as an event that can’t be quantified probabilistically. An event is either constrained by causal antecedents (including material and immaterial laws and state variables) or it isn’t. If it is, then those constraints confer a quantifiable probability on the event. If, on the other hand, an event is completely unconstrained, then literally anything can happen, with nothing to favor one outcome over another. In other words, the outcome is chosen from a uniform, infinite distribution, which confers a probability of zero.
I therefore conclude that design, as Dembski defines it, describes events that mathematically can’t exist.
Comment by secondclass — July 19, 2006 @ 5:42 pm
Salvador:
You seem to be implying that design events cannot be quantified probabilistically. Please correct me if I’m misreading you.
I submit that there is no such thing as an event that can’t be quantified probabilistically. An event is either constrained by causal antecedents (including material and immaterial laws and state variables) or it isn’t. If it is, then those constraints confer a quantifiable probability on the event. If, on the other hand, an event is completely unconstrained, then literally anything can happen, with nothing to favor one outcome over another. In other words, the outcome is chosen from a uniform, infinite distribution, which confers a probability of zero.
I therefore conclude that design, as Dembski defines it, describes events that mathematically can’t exist.
Comment by secondclass — July 19, 2006 @ 5:43 pm
How in the world can you characterize my response as a ‘negative argument against evolutionary scenarios’? I propose two explanations for the genetic code: chance, and design. And, from an ‘information theory’ basis, and from the work of Behe and Snoke, I demonstrate that design is the better explanation.
This response is no more than hubris on a monumental scale. Why don’t you try this language: “In this case, Lino is wondering how science proposes to explain the genetic code.”
More hubris. Instead of telling people what I think, why don’t you begin by asking me what I think. On the basis of INFORMATION THEORY (are you paying attention yet?), the explanation that RM+NS can, by itself, give rise to all the INFORMATION contained in the genome is just simply absurd. Behe and Snoke’s paper clearly demonstrate that. (Now before you refer me to the thread at PT, note this: I’ve already looked at their criticism. Here are my reactions: First, they don’t fully understand Behe’s rationale for ‘rho’. Second, they completely overlook the fact that Behe and Snoke point out that the MOST critical factor in their calculations is ‘lambda’, since that enters into the exponential part of the equation. Third, even when they take liberties and crunch numbers, they still come up with a time to fixation of 100 million years. That’s for a “di-sulfide’ bond. It represents 6 nucleotides of information. Fourth, they take no note that Behe and Snoke’s model assumes that anytime a ‘null allele’ occurs, that a new ‘duplicated gene’ replaces it—having the effect of making their calculations more conservative; i.e., tending toward shorter time requirements.) The analogy of DNA’s coding system to the binary coding systems used by computers makes it an easy step in logic to conclude that the genome has been designed. Thus, one negative reason: RM+NS, discredited by Behe and Snoke’s paper, and a completely counter-intuitive idea when it comes to an information system as rich and robust as the genome; and one positive reason: our only experience with such information rich coding systems comes from our knowledge of how the binary code works in computers. Hence, my opposition to Darwinian notions as to how the genome came about has everything to do with ‘information theory.’ We are living in an ‘Information Age’, you know.
But I thought you said science ‘explained’ it. What, exactly, needs to be ‘resolved’ if it’s already been ‘explained’?
But there’s no mention of ‘information theory’ in all of this. Is the information stored in the genome the simply the result of chance chemical events? Is it completely reducible to chemistry? I think not. Otherwise, that would be like saying that computer systems are completely reducible to electricity, which, of course, indubitably, we know NOT to be the case.
This is simply an opinion, isn’t it?
This isn’t more than just speculation. Need I go on?
Just one more:
So, with time, the genetic code either stays the same, or gets worse. That’s what the statement says. So how did the “optimal” code come about? From the penultimate quote: “The exact time at which code optimization occurred is unclear:” So, we have no idea as to when or how this optimal code came about. Is this the ‘explanation’ that ‘science’ has given for the genome?
If the ‘optimal code’ exhibits ‘stasis’, then how did it become ‘static’? If it is both ‘static’ and able to ‘speed up the rate of adaptive evolution’, then this argues for the genome having some kind of ‘decision point’ built within it so that it can switch from one to the other. This sounds like ‘programming’ to me. This is an observation that favors ‘design’, not random mutation.
That’s one way of describing it. Another way is: the genetic code contains contrary elements within it. Does random mutation and natural selection contradict itself?
Comment by Lino D'Ischia — July 19, 2006 @ 7:53 pm
If true then ‘information theory’ also proves that the designer was designed, and the designer of the designer, recursively without limit.
That alone should tell you there’s a problem with this misuse of ‘information theory’ which no real information theorist buys into for a minute.
I just have to say that as a CS guy who’s worked in industry for 35 years, I am absolutely appalled at the continued effort to apply this analogy.
“It looks like a computer program to me, therefore it must’ve been designed!” is nothing more than the usual argument from ignorance, I’m afraid.
Lino, can you tell us how your designer programmed the biological computer? Which tools were used? Why do we not find traces of the tools (if not the tools themselves) here on earth? How did the designer debug this program?
Let us get specific, here. We want some real, hard, evidence of who this designer is and how this designer goes about writing the “software” that makes life what it is.
Comment by Don Baccus — July 19, 2006 @ 8:41 pm
Don Baccus:
And of course, “for every action there is an equal and opposite reaction.” Thus we recursively go back without limit. But wait, there HAS TO BE a ‘first cause’, because if there wasn’t a ‘first cause’, then there wouldn’t be a ’second cause’, nor a ‘third cause’, etc, etc. So, just as this recursive loop can’t go backwards forever, neither can that of intelligent designers. But why this distraction?
Don again:.
From Wikipedia:“The argument from ignorance, also known as argumentum ad ignorantiam or argument by lack of imagination, is a logical fallacy in which it is claimed that a premise is true only because it has not been proven false, or that a premise is false only because it has not been proven true.”
From the above description, you can see that I’m not arguing from ignorance. But here’s one:
Comment by Lino D'Ischia — July 20, 2006 @ 1:08 am
Lino asks
Indeed it does, because it is only seemingly contradictory.
Let me explain. And this is the real fascinating part of all this namely that both evolvability and robustness can co-exist and be explained by a single mechanism. Robustness arises because degeneracy reduces the likelihood that a change will change the aminoacid involved. Evolvability arises because neutrality allows the genome to explore sequence space while remaining at a single point in structure space. Let me explain: the sequence (the DNA) can vary while the structure (RNA or proteins) remain the same. Since the srtucture space is scale free, structures can be found all throughout space and any given structure is close to any other given structure in the numbers of selective mutations needed to go from one to the other.
Some beautiful examples exist of this concept.
So yes, natural processes do explain this apparant contradiction. Hope this helps. if not let me know what still confuses you and I will do my best to explain. These concepts, none of which are discussed in any relevant form in ID literature, are instrumental to evolutionary theory.
Why is it that ID ignores it, I wonder? Is it ignorance?
Comment by PvM — July 20, 2006 @ 1:13 am
Allen wrote:
Has the discussion devolved down to semantics? A “Darwinist” is someone who considers Natural Selection to be so powerful a force as to be able to explain the panoply of biological diversity one encounters in Nature. Neither Behe, nor Dembski, falls into this category; but Darwin does.
Allen:
Here’s my theory. The surest sign in 2000 that the stock market was about to crash was the buying hysteria exhibited by ordinary folk.
Now, if you consider Pandas Thumb, the apoplexy that is shared by so many at that blog, it is a sure indicator that their pet theory–which they have all so heavily invested in–is about to collapse. Just a theory; not a fact!
“And BTW, the word you are looking for is “imminent” (meaning “impending”), not “eminent” (meaning “important”).”
I wasn’t looking for any word. But I did find the word “eminent” on the Darwinian website to which I was directed. Do you think it was a Freudian slip?
Comment by Lino D'Ischia — July 20, 2006 @ 1:33 am
The surest sign in 2000 that the stock market was about to crash was the buying hysteria exhibited by ordinary folk.
Did you sell your stock at that time, Lino?
Comment by Michael Hubl — July 20, 2006 @ 2:37 am
So Lino:
When people talk a lot and get worked up about a particular topic that means it is on the verge of collapse?
Ok . . . I could think of about a million reasons why that argument is totally bogus. Is this all you have is bluster?
Comment by Mike Hannigan — July 20, 2006 @ 11:21 am
Since we’re spending a lot of time here talking about Intelligent Design, I do hope he’s right :)
Comment by Don Baccus — July 20, 2006 @ 12:16 pm
Alan Greenspan kept talking about ‘irrational exuberance’, his way of saying the market was over-bought. I’m talking about ‘irrational vehemence’, where spit is flying out of people’s mouths in their effort to condemn anything non-Darwinian. In both cases, something is/was wrong.
Personally, I don’t find the arguments persuasive.
Here’s something from Wikipedia:
“These scale-free networks do not arise by chance alone. Erdős and Renyi (1960) studied a model of growth for graphs in which, at each step, two nodes are chosen uniformly at random and a link is inserted between them. The properties of these random graphs are not consistent with the properties observed in scale-free networks, and therefore a model for this growth process is needed.” Seems like there’s a non-random element involved in scaled networks–could that needed element be intelligent input?
Comment by Lino D'Ischia — July 20, 2006 @ 1:43 pm
I am grateful to Lino’s response which shows a level of personal disbelief as evidence.
Of course ‘design’ is always a logical possibility and an uninformed reading of scale free networks may lead one to ignore that scale free networks have well described mechanisms which do not require design input.
A common confusion of Lino seems to be that he believes that evolution is fully random, when in fact it involves processes of chance and regularity.
But Lino has not answered the question
Why does ID literature ignore these contributions? Especially, if as Lino suggests that Scale Free networks somehow show the required involvement of design?
How can ID claim to be relevant in evolution and information theory when it ignores most any relevant mechanism and knowledge in this area to throw up its arms and proclaim
“thus designed”?
Why is it that when ID reviews the Cambrian it omits the crucial research and evidence which would help explain the Cambrian in natural terms and instead invokes poorly defined concepts of ‘information and complexity’?
Why is it that ID appears to be so ignorant of the relevant sciences it opposes?
Should that not be a concern to those who hold hope in ID being able to present its arguments in a robust and scientific manner?
Comment by PvM — July 20, 2006 @ 2:22 pm
PvM:
Just because I don’t agree with your conclusions, doesn’t mean I don’t understand it–which is the strawman argument you love to use over and over again.
Secondly, along these lines, why is it that Darwinists don’t want to take seriously the very well-thought out, realistic, model of evolution that Behe and Snoke present?
But, let me go further. Let me point out that there’s no wiggle-room in Behe and Snoke’s model, while there is a serious lacuna in what is known about scale-free networks; and not only that, there’s the suggestion that certain added information is needed in such networks–which is, of course, the kind of argument that ID marshals against the Darwinian paradigm.
Comment by Lino D\'Ischia — July 21, 2006 @ 1:12 am
It has been taken seriously. After all, they showed that what they imagined they proved to be very improbable actually is extremely probable.
Behe was forced to admit so under cross-examination in Kitzmiller, after all.
Comment by Don Baccus — July 21, 2006 @ 10:48 am
Secondly, along these lines, why is it that Darwinists don’t want to take seriously the very well-thought out, realistic, model of evolution that Behe and Snoke present?
But, let me go further. Let me point out that there’s no wiggle-room in Behe and Snoke’s model, while there is a serious lacuna in what is known about scale-free networks; and not only that, there’s the suggestion that certain added information is needed in such networks–which is, of course, the kind of argument that ID marshals against the Darwinian paradigm.
Maybe it’s because “Darwinists” are aware of the many weaknesses of Behe and Snoke, some of which were pointed out by Michael Lynch in “Simple evolutionary pathways to complex proteins”, Protein Science, (2005), 14: 2217-2225.
For example:
1) Although Behe and Snoke claimed to be evaluating “Darwinian” evolution, their model was not Darwinian. Since they included no selection of intermediates, their model was of neutral drift, not natural selection.
2) Behe and Snoke ran on at length about the inability of protein function to survive mutation, and yet anyone capable of doing a BLAST search can verify the incredible number and variety of sequence mutations which can be sucessfully accomodated in an enzyme without destroying its overall structure or function.
Comment by ivy privy — July 21, 2006 @ 11:09 am
I’m looking over the Detailed Syllabus for the course now, and I see that Behe & Snoke, and the response by Micahel Lynch will not be covered. Schade.
‘
Comment by ivy privy — July 21, 2006 @ 11:12 am
Jonathan Bartlett:
Jonathan, have you read and do you agree with those essays?
Comment by secondclass — July 21, 2006 @ 1:23 pm
Lino,Secondly, along these lines, why is it that Darwinists don’t want to take seriously the very well-thought out, realistic, model of evolution that Behe and Snoke present?
Two problems: 1) Evolutionary scientists have taken Behe and Snoke’s claims seriously 2) Evolutionary scientists have shown a) that their model is limited and b) that a more realistic model provides better answers.
But, let me go further. Let me point out that there’s no wiggle-room in Behe and Snoke’s model, while there is a serious lacuna in what is known about scale-free networks; and not only that, there’s the suggestion that certain added information is needed in such networks–which is, of course, the kind of argument that ID marshals against the Darwinian paradigm.
Seems you have to do a lot of reading up to do on the topic of scale free networks. Try starting with Barbasi. Even a cursory search of the terms show how the simple processes of gene duplication and preferential attachment (both observed processes) are sufficient to explain scale free networks.
As to the ‘no wiggle room’ for Behe and Snokes, you are wrong as well.
Too bad that ID has oversold the work of Behe and Snokes… It seems to be a trend and Del Ratzsch warned against this to no avail it seems.
Imagine the crisis of faith (not to mention of science) when the well intentioned Christian who convinced by the veracity of ID’s claims insists that science has shown that there exists evidence of design, only to find out that ID’s claims were vacuous? By presenting ID as a falsifiable position, ID has forced an unnecessary crisis of faith. After all, the falsification of ID’s claims should have some impact on ID, should it not?
Imagine the crisis of faith I went through when I found out that the claims of YEC were scientifically flawed, showing how cherry picking of data and other tricks were used to maintain the unscientific position of a young earth?
Comment by PvM — July 21, 2006 @ 2:10 pm
Lino D’Ischia: Please comment on why you don’t think the criticisms of Behe and Snoke in Michael Lynch’s response effectly rebut their findings. Once again, that reference is: Michael Lynch, “Simple evolutionary pathways to complex proteins”, Protein Science, (2005), 14: 2217-2225. Also, do you consider the “improved” model in Lynch’s paper to be better than Behe and Snoke’s or not? Why?
You may also want to read Behe and Snoke’s short rejoinder, “A response to Michael Lynch”
Michael J. Behe and David W. Snoke, Protein Science (2005), 14:2226-2227
Comment by ivy privy — July 21, 2006 @ 5:58 pm
Judge Jones on the trial…
In this case, however, it wasn’t simply a matter of everyone just doing their jobs. In Jones’ view, the lawyers performed exceedingly well.
“I think that some of the cross-examination was absolutely fabulous,” said Jones. “It will endure, and I think it will be excerpted for advocacy classes…. I would say, in particular, Eric Rothschild’s cross-examination of Professor [Michael] Behe — the intelligent design proponent — that might be as good a cross-examination of an expert witness as I have ever seen. It was textbook.
PandasThumb Link
Ed Brayton observes
Aside from the testimony of Barbara Forrest, I thought that the Behe cross was the single most important turning point in the trial. It was during that cross that it was established, beyond a doubt, that ID is primarily an argument from ignorance. Behe continuing to assist that the scientific literature contains nothing to explain the evolution of the immune system even after admitting that he had not read an enormous portion of that literature could not have looked worse.
Judge Jones seems to agree.
Remember the claims by ID proponents on this group about the relevance of the Behe Stokes paper?
Brayton:And his admission that the paper he authored with Snoke was essentially rigged against evolution by the application of wildly unreallistic paramaters for the simulation and still concluded that the allegedly IC binding site could have evolved in a relatively short period of time was probably even more devastating. I also thought his comment about the interaction with his fellow judges on the circuit was fascinating:
Wow I bet you don’t get that news from ID sites…
Comment by PvM — July 22, 2006 @ 4:06 am
Lino, could you explain the relevance of Behe’s testimony in Kitzmiller regarding his Behe and Snokes paper?
Q. And one last other question on your paper. You concluded, it would take a population size of 10 to the 9th, I think we said that was a billion, 10 to the 8th generations to evolve this new disulfide bond, that was your conclusion?
A. That was the calculation based on the assumptions in the paper, yes.
and
Q. In that first paragraph, he says, There are more than 10 to the 16 prokaryotes in a ton of soil. Is that correct, in that first paragraph?
A. Yes, that’s right.
Q. In one ton of soil?
A. That’s correct.
Q. And we have a lot more than one ton of soil on Earth, correct?
A. Yes, we do.
Q. And have for some time, correct?
A. That’s correct, yes.
Q. And, in fact, he gives us a good way of comparing it. It says, as compared to a mere 10 to the 11th stars in our galaxy?
A. Yes, that’s what he writes, uh-huh.
Q. And 10 to the 16th prokaryotes is 7 orders of magnitude higher than the population you included in your calculations, correct?
A. No. We considered a wide range of populations, and we considered a wide range of number of substitutions that would be — or point mutations that would be necessary. You’re focusing on two, but perhaps I can direct your attention again to that figure from the paper — excuse me. Let me find it.
The best place I think to look is figure 6, which is on page 10 of the document. Up in the upper right-hand corner, that figure there.
Q. Sure.
A. If you look on the bottom, the x axis there, the bottom of the figure that’s labeled lambda, it has the numbers 2, 4, 6, 8, 10, and so on, those are the number of point mutations that we consider perhaps some multi-residue feature might entail. As we said in the paper, forming a new disulfide bond might require as few as two point mutations.
But forming other multi-residue features such as protein, protein binding sites might require more. And so the number on the X axis lambda 2, 4, 6, 8, those are the number of point mutations that we entertained or we calculated numbers for to see how long such things would be expected to take under our model.
And if you look up at the top axis, the top x axis labeled N, at the top of the figure. N stands for population size. Okay. So if you look at the figures there on the left, it’s slanted, and it’s not enlarged yet, so it’s hard to see. It says, 10 to the 6th. That’s a million. And then skip a line. These are in every 10 to the 3rd increments of population size. That would be 10 to the 9th.
The next label is 10 to the 12th, which is a trillion. The next label is 10 to the 18th, which is much more. The next label is 10 to the 24th, which is much, much, much more. The next label, 10 to the 30th, which, again, is very much more.
So, in fact, we considered population sizes from 1000 all the way up to 10 to the 30th, and multi-residue features from 2, which might involve disulfide bonds, up to many more, which might be involved in protein, protein binding sites.
Q. 10 to the 30th, that is quite a lot, right?
A. Yes. That’s roughly what is calculated to be the bacterial population of the Earth in any one year. And so over the course of the billion year, 4 billion year history of the Earth, there would probably be a total of roughly 10 to the 40th.
Q. And so in the case of prokaryotes, which you said was a good example of what you were studying, 10 to the 16th in one ton of soil?
A. Yes.
Q. So a few tons of soil, and we’ve gone past that 10 to the 30th?
A. Well, no. In the 10 to the 14th tons of soil. 10 to the 30th is the number that’s in the entire world, according to the best estimates, including the ocean as well as soil. So — but I agree with your point, that there’s a lot of bacteria around and certainly more than 10 to the 9th.
Q. So just with the prokaryotes, 10 to the 16th, 7 orders of magnitude higher than what you were calculating here?
A. That’s certainly true, but in our paper, we had our eye not only on prokaryotes, but also on eukaryotes as well, which, if you leave out recombination, one can — they certainly undergo point mutations. They certainly have genes and so on. So much of this is also applicable to eukaryotes.
And the populations of eukaryotes and certainly larger plants and animals are much, much smaller than populations of bacteria. So we view our results not just as supplying that, but to giving us some feel for what can happen in more complex organisms as well.
Q. Well, you’re not talking about more complex organisms here, are you?
Behe then continues to argue that sulfide bond claims also extended to more complex organisms. At least the argument seems irrelevant to evolution as it pertains to bacteria etc
. I think we do. I think at the end, if I’m not mistaken, if I remember correctly — okay, yes. On page 11, the second full paragraph, on page 11. It begins on the right-hand column, the second full paragraph. It says, The lack of recombination in our model means it is most directly applicable to haploid, asexual organisms. Nonetheless, the results also impinge on the evolution of diploid sexual organisms.
The fact that very large population sizes, 10 to 9th or greater, are required to build even a minimal MR feature requiring two nucleotide alterations within 10 to the 8th generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.
Thus, mechanisms in addition to gene duplication and point mutation may be necessary to explain the development of MR features in multicellular organisms.
So here we were trying to point out that, because of the results of the calculation, it seems that, when we’re trying to explain MR features in multicelled organisms, then we’re going to have to look to other processes for that.
Q. Okay. So if we exclude some of the processes by which we understand evolution to occur, it’s hard to get there for multicellular organisms?
A. I’m sorry.
Q. If we exclude some of the mechanisms by which we understand evolution to occur, like recombination, it’s hard to get there?
A. Yes.
Q. And bringing it back to the prokaryotes. We’re in agreement here, the number of prokaryotes in 1 ton of soil are 7 orders of magnitude higher than the population, you said it would take 10 to the 8th generations to produce the disulfide bond?
A. Yeah, certainly. Yeah, the bacteria are — can grow to very large population sizes.
Q. So the time would be?
A. Much shorter.
Q. Much shorter?
A. Absolutely.
Devastating absolutely devastating. I bet you won’t hear about this from ID sources.
Comment by PvM — July 22, 2006 @ 3:22 pm
PvM:
What’s devastating about Behe’s testimony, or his paper. According to his model, if we assumed that for the last 100 million years there have been 100 million elephants who have reproduced and died every year (which isn’t anywhere near their total number nor their actual reproductive rate), according to Behe and Snoke’s paper, they would have produced ONE ‘di-sulfide’ bond. Is that what you call evolution? And Behe did attempt an answer. He said there was likely 10^40 bacteria in all the world. And he admitted that this “total” population could bring about a ‘di-sulfide’ bond in less than 10^8 generations. But if you look at Behe’s Figure 6, you’ll see that even with a population of 10^40 bacteria, if there were 8 amino acids that had to be placed in order, they couldn’t have accomplished it even in the 3.5 billion years they’ve been on this planet. Now THAT is DEVASTATING!!!
Comment by Lino D\'Ischia — July 22, 2006 @ 7:59 pm
ivyprivy:
As to Lynch’s first concern, my reaction is that he must not understand the paper. The only ‘intermediates’ that the model COULD have considered would be those who had two amino acid substitutions, not the minimum of three that Behe was considering. You can consider that “neutral”, but Behe had selection built into his model, but ’selection’ did not begin until once the minimum three amino acids first appeared. He’s just quibbling. How in the world could ‘nature’ select from a two amino acid substitution on a protein molecule?
As to his second objection, there might be some merit to it. I’m not familiar enough with the literature to make an intelligent assessment of the values Behe included. But Behe does stress that he is using values that he has found in the literature. But, note this, as I stated elsewhere, the value of “lambda” is more critical than “rho”; meaning that the frequency with which ‘null alleles’ arise does not affect the numbers as much as how many amino acid substitutions (”lambda”) are required. Behe says that the literature says ‘rho’ should be 2400. He used 1000. The model isn’t much affected by ‘rho’ unless it drops well below 100. And, finally, even when, whoever it was over on PT, revised the numbers, they still calculated it would take a 100 million years for a MR to come about in a non-bacteria.
Comment by Lino D'Ischia — July 22, 2006 @ 8:16 pm
Lino, how are you dealing with Behe’s admission that using his numbers evolution of the disulfide binding sites would be quite possible given the amount of bacteria in a ton of soil?
So now Lino is moving the goalposts, what about 4 or 8 such binding sites.
Facinating how quickly IDers are to move the goalposts when original arguments fail.
Thanks Lino, I hope that the readers of this forum understand and appreciate how ID once again is shown to be vacuous….
So how does ID again explain the origin of disulfide bonds?….
Poof… How long does it take for poof to happen?
Comment by PvM — July 22, 2006 @ 10:13 pm
I am not sure why a calculation for asexual organisms is relevant to elephants though although I am sure Lino is going to explain to us this little detail…
Comment by PvM — July 22, 2006 @ 10:15 pm
Some interesting science
In a paper published Feb. 20 in the journal Science, a joint research team at the University of Michigan and the University of Texas describes how a resourceful bacterium was able to develop an entirely new way to make disulfide bonds. This restarted its motor and enabled it to move toward food before it starved to death.
The laboratory of George Georgiou, a professor of chemical and biomedical engineering at UT Austin, used a strain of mutant bacteria developed by Bardwell that had lost their ability to make disulfide bonds. These disulfides are critical for the ability of the bacteria’s propeller-like swimming motor, the flagellum, to work. The researchers then put these non-swimming bugs to the test by placing them on a dish of food where, once they had exhausted the food they could reach, they either had to repair that broken motor or starve to death on the spot.
The bacteria used in the experiment were forced to use a protein called thioredoxin—which normally destroys disulfide bonds—to make the bonds instead. In a process similar to natural selection, UT graduate student Lluis Masip made random alterations in the DNA encoding thioredoxin and then subjected thousands of bacteria to the swim-or-starve test. He wanted to see if an altered version of thioredoxin could be coerced to make disulfides for other proteins in the bacteria.
To the researchers’ surprise, a mutant carrying only two amino acid changes, amounting to less than 2 percent of the total number of amino acids in thioredoxin, restored the ability of the bacteria to move. The altered thioredoxin was able to carry out disulfide bond formation in numerous other bacterial proteins all by itself, without relying on any of the components of the natural disulfide bond pathway. The mutant bug managed to solve the problem in time and swim away from starvation and multiply.
Wow
Comment by PvM — July 22, 2006 @ 10:16 pm
96. … And, from an ‘information theory’ basis, and from the work of Behe and Snoke, I demonstrate that design is the better explanation.
…
the explanation that RM+NS can, by itself, give rise to all the INFORMATION contained in the genome is just simply absurd. Behe and Snoke’s paper clearly demonstrate that…
116. …As to his second objection, there might be some merit to it. I’m not familiar enough with the literature to make an intelligent assessment of the values Behe included…
Your other arguments are founded on Behe & Snoke, but you don’t have what it takes to evaluate its validity and relevance?
Also, are you aware that there are other mechanisms of evolution other than natural selection (e.g. neutral drift, recombination, gene duplication, polyploidy)? So that, even if Behe & Snoke’s calculation was accurate and relevant, extrapolating your argument to all of evolution would be wrong?
BTW, I encourage you to read Michael Lynch’s paper, to get a more complete and accurate view of his criticisms than I relayed here.
Comment by ivy privy — July 22, 2006 @ 10:54 pm
As to Lynch’s first concern, my reaction is that he must not understand the paper. The only ‘intermediates’ that the model COULD have considered would be those who had two amino acid substitutions, not the minimum of three that Behe was considering. You can consider that “neutral”, but Behe had selection built into his model, but ’selection’ did not begin until once the minimum three amino acids first appeared. He’s just quibbling. How in the world could ‘nature’ select from a two amino acid substitution on a protein molecule?
I gather from your response that, like Behe & Snoke, you do not understand the distinction between “natural selection” and “neutral drift”. In this context the distinction is certainly not just a “quibble”. I believe that Michael Lynch understood the Behe & Snoke paper very well, and I think you should refrain from making further comments of that nature until you have read his paper and have obtained the background to understand it.
Here’s a quibble: the Behe and Snoke model considered three nucleotide positions, not three protein residues.
Comment by ivy privy — July 22, 2006 @ 11:07 pm
But if you look at Behe’s Figure 6, you’ll see that even with a population of 10^40 bacteria, if there were 8 amino acids that had to be placed in order, they couldn’t have accomplished it even in the 3.5 billion years they’ve been on this planet. Now THAT is DEVASTATING!!!
Could you explain why that is DEVASTATING?
1) As I’ve already said, there are mechanisms other than natural selection (or in fact, neutral drift) known to be at work in evolution.
2) Natural selection presumes small steps, so showing the unlikelihood of 8 specific substitutions at once doesn’t seem to be relevant to the claims made by modern biology; i.e. evolutionary biology.
Comment by ivy privy — July 22, 2006 @ 11:11 pm
More recent research showing how Behe and Snoke underestimate the probabilities
In summary, not only is cryptic genetic variation not significantly eroded by the accumulation of deleterious mutations, but instead it is positively enriched for potential adaptations. The minimum condition for enrichment is that selection on hidden lethals is appreciable, and the optimal condition is when selection on unhidden potentially adaptive alleles is highly effective. Enrichment is weak with respect to potential adaptations resulting from a single mutation, but is dramatic for potential adaptations based on a combination of mutations. This provides a powerful mechanism for achieving an adaptation involving multiple mutations when each mutation, taken by itself, is deleterious. This gives a rigorous basis to previous speculations that adaptive combinations of mutations may appear more readily when variation is subject to weakened selection (KOCH 1972; TRUE and LINDQUIST 2000; HARRISON and GERSTEIN 2002). Recent models of the rate of obtaining an adaptive combination of mutations (BEHE and SNOKE 2004; LYNCH 2005) are therefore substantial underestimates, since they do not take this enrichment into account.
Joanna Masel Cryptic Genetic Variation Is Enriched for Potential AdaptationsGenetics, Vol. 172, 1985-1991, March 2006
Cool stuff
Comment by PvM — July 22, 2006 @ 11:41 pm
One more point on Behe & Snoke; their model is a targeted one. They (attempt to) model the probability of a specific set of mutations to introduce a particular structural feature, a disulfide bond, in a particular place. I see no reason the same benefit could not be acheived through other possibilities, such as a metal binding site, hydrogen bonds, backbone constraints (e.g. proline) or ion pairs. B & S discuss this slightly, so I gather they got some criticism from reviewers, but they don’t take it into account in any way in their calculations. In short, their model is very limited, but the conclusions drawn by Behe and Snoke, and by uncritical readers such as D’Ischia, exceed the scope of the model.
Since I mentioned reviewers, I will bring up another point: what was this paper doing in Protein Science? The choice of journal is clearly not appropriate. The model is one of population genetics, whereas the usual subject matter for Protein Science is protein chemistry and structure. The editors of Protein Science should have rejected the manuscript simply on the grounds that it is out of area covered by their journal. Maybe this explains how the paper could have gotten through the review process with the glaring errors pointed out later by Lynch.
Comment by ivy privy — July 24, 2006 @ 10:52 am
As I’ve already said, there are mechanisms other than natural selection (or in fact, neutral drift) known to be at work in evolution.
After thinking about this for a day or two, I probably should have said there are other methods of genetic change other than multiple serial point mutations. There are alternatives to natural selection as well (neutral drift, sexual selection).
Comment by ivy privy — July 25, 2006 @ 8:13 pm
As I have said before, it’s child’s play to inflate probabilities to make something improbable (check out Dembski’s calculations of the flagella for instance, the one with P_local etc). What is much harder, is providing a likely scenario, either via intelligent design or natural pathways to explain a particular feature.
Science involves a lot of hard work. And so far I have yet to see any supporting evidence that ID is even involved in ID relevant science. I fully appreciate that absence of evidence is not evidence of absence, but even the much touted Biologic Institute seems to be dormant.
Comment by PvM — July 26, 2006 @ 1:04 pm