Talk:Irreducible complexity/Archive 2

message: __TOC__
Let's try to contain this to a single discussion. -- Ec5618 21:01, 31 January 2006 (UTC)

message: My intention was to clarify, not to make a stronger or weaker argument for either side of this controversy. Scientists dismiss Behe's notion as pseudoscientific hogwash, right? If so, the intro should clarly state this. --Uncle Ed 23:38, 22 February 2006 (UTC)
replies: text: Well, it does, it's just a bit more subtle than saying, "IC is hogwash".  No offense, but the current intro seems pretty clear -- that's not to say it's perfect, but it's pretty much on the mark. Jim62sch 01:15, 23 February 2006 (UTC)
thread_title: New intro

message: How does the concept of functionality creep apply here? DS 23:00, 3 March 2006 (UTC)
replies: text: Interesting correlation, although I usually think of "feature creep" from a programming standpoint where the customer keeps changing their mind about what they want. Has either Behe or his critics used "functionality creep" as part of their arguments? BradC 06:23, 4 March 2006 (UTC)
replies: text: Ugh, you just had to mention "feature creep".  I'm surprised more programmers don't jump off of bridges. Jim62sch 18:38, 4 March 2006 (UTC)
thread_title:  A thought 

message: I don't think it was based on my most recent edit, but the endnote numbering seems out of whack. And when should we use endnotes vs simply putting the link straight into the text? (which oddly also generates a number) It seems like both techniques are used in this article, somewhat randomly. Then we have this unexplained bulleted list at the end. Can someone help straighten it out? BradC 05:57, 5 March 2006 (UTC)
replies: text: Changed format; this format isn't quite as nice looking but it is consistent, and has the advantage of the endnotes never getting out of order. If someone wants to change it to another format it won't bother me. KillerChihuahua?!? 12:24, 6 March 2006 (UTC)
replies: text: That silly arrow drives me nuts, but, I guess it'll work (and no, it doesn't look as nice). Jim62sch 14:17, 6 March 2006 (UTC)
replies: text: The 'arrow' is a result of a recent vote, of sorts, at Wikipedia talk:Manual of Style#Changes to Cite.. It was decided that the ^ was confusing, whereas an arrow is not. Personally, I find the arrow anything but an improvement, and I'm considering bringing the issue up for a proper vote. -- Ec5618 14:27, 6 March 2006 (UTC)

text: Please do! Jim62sch 00:29, 7 March 2006 (UTC)

text: I'm sorry? What are you saying? The ref tag was specifically developed for Wikipedia, specifically to replace the ref/note templates. How could it possibly not be used on the project? If you have an issue with the appearance of the references, please take it up elsewhere, but the tag is clearly 'used on the project'. See also Wikipedia:Footnotes. -- Ec5618 09:17, 8 March 2006 (UTC)
replies: text: Ref templates, yes. Ref tags, no. There's a difference. FeloniousMonk 00:57, 10 March 2006 (UTC)
replies: text: As of late December 2005, tags also. Follow Ec5618's link. KillerChihuahua?!? 01:43, 10 March 2006 (UTC)
thread_title:  End note help 

message: "In the 2005 Kitzmiller v. Dover Area School District trial Behe testified under oath that irreducible complexity did not rule out known evolutionary mechanisms and that there are no peer-reviewed articles supporting his argument that certain complex molecular structures are "irreducibly complex." [2] that intelligent design is not science and is essentially religious in nature."  Is this sentance meant to say what it does?  I would think it would be more accurate to say "In the 2005 Kitzmiller v. Dover Area School District trial Behe testified under oath that irreducible complexity did not rule out known evolutionary mechanisms and that there are no peer-reviewed articles supporting his argument that certain complex molecular structures are "irreducibly complex." [2] The Judge ruled in that case that intelligent design is not science and is essentially religious in nature."
Or if you think it should remain as is, can you give a citation for his position on "not science"?  It just seems a bit contrary to what I heard him say in that trial. --AlsatianRain 12:23, 6 March 2006 (UTC)
replies: text: Never mind, it appears the text was in fact there, just not visible because of a broken reference tag.  I've fixed the tag.  --AlsatianRain 14:06, 6 March 2006 (UTC)
thread_title:  Not Science 

message: "It is illustrative to compare a mousetrap with a cat, in this context. Both normally function so as to control the mouse population. The cat has many parts that can be removed leaving it still functional; for example, its tail can be bobbed or it can be spayed. Evolution has endowed it with redundant eyes, so if one eye goes blind, the cat can still catch mice. Comparing the cat and the mousetrap, then, one sees that the mousetrap (which is not alive) offers better evidence, in terms of irreducible complexity, for intelligent design than the cat."
The above paragraph compares a mousetrap (small, specific system) to a complete organism (many small, specific system_s_). The comparison itself is overly flawed, as well, giving the impression that the vision system is redundant (overlooking depth perception) and using cherry-picked examples (eyes vs heart, brain, stomach/intestines/etc.). I suggest that better analogy should be picked, or IMO, the paragraph should be removed altogether to better allow the reader to draw his/her own conclusions. 
For clarification, the mousetrap argument is oft used in comparison with a single system within a complete organism - the eye or the bacterial flagellum being the most common example. WeedWhacker 09:58, 4 April 2006 (UTC)
replies: text: Both the eye and flagellum contain components which can be removed and still leave a functioning unit. Jefffire 10:55, 4 April 2006 (UTC)
replies: text: Uh, the mousetrap was Behe's choice.  Send him an e-mail.  •Jim62sch• 21:38, 5 April 2006 (UTC)
thread_title:  Removal of bad analogy? 

message: I don't know enough about the topic of this article to edit it myself, but this (#2) says 2. MISSING GENES: FINDING THE KEY THAT OPENS DARWIN'S BLACK BOX. 
It was a lousy day for intelligent design, which has had a lot of bad days lately. Even as a missing link showed up on the pages of Nature, a report in Science from the University of Oregon showed how a new hormone-receptor pair evolved. An existing molecule, created for a different role, was recruited to do the new job. The lead author, Joseph Thornton, believes this may be common in the evolution of complex systems. Hormone-receptor pairs would seem to be an example of what intelligent-design guru Michael Behe calls "irreducible complexity" (ID). One without the other would be useless. However, Behe scoffed to the NY Times that Hormone-receptor pairs aren't really ID. Either he's still a little cranky from the Dover trial, or he just prefers miracles (WN 21 Oct 05) .   It might be worthy of inclusion in the article.  (When he says "ID", does he mean "IC"?) Bubba73 (talk), 02:31, 8 April 2006 (UTC)
thread_title:  new data 

message: re evolution 
Ties in well with the above. •Jim62sch• 22:22, 12 April 2006 (UTC)
thread_title: Interesting news article

message: The first appearance of the term (and probably the modern concept) of IC is claimed to be the book Templets and the explanation of complex patterns by Michael J. Katz. This should be mentioned in the article, and it would be interesting to know more about it, if someone can check the book. --Tgr 20:59, 10 May 2006 (UTC)
replies: text: Why should we add that Casey Luskin stated in a post made on November 4, 2005 10:31 AM, that "My understanding is that the first usage of the term “irreducible complexity” comes from a 1986 Cambridge University Press book entitled “Templets and the explanation of complex patterns” by theoretical biologist Michael J. Katz."? I fail to see the notability of Casey Luskin, and how his understanding somehow is relevant. KillerChihuahua?!? 21:04, 10 May 2006 (UTC)
replies: text: Luskin appears to be one of the ID crew, and it's very questionable if evolutionnews is a reliable source. From the linked blog it seems that Katz has used the two words together in a different context, and the DI has put together an elaborate argument claiming that he's on their side. Not very convincing. ..dave souza, talk 00:05, 12 May 2006 (UTC)
replies: text: Luskin is one of the founders of the IDEA network. Reliability is not an issue with quotations (unless you suggest he made them up), and the quotes show that Katz used the term before Behe, and in a similar meaning (complex systems that "cannot effectively be reduced to smaller or less intricate predecessor components"). Of course, it would be better if someone could actually read the book, but the quotes do support mentioning Katz in the article. --Tgr 19:00, 12 May 2006 (UTC)
replies: text: Made them up? That's always a concern when dealing with the Discovery Institute's statements. Luskin's statements are appropriate for examples of what Luskin says and/or the Discovery Institute party line, but little else. FeloniousMonk 19:07, 12 May 2006 (UTC)

text: For clarification, Wikipedia:Reliable sources sets the standard, which Casey's blog pretty obviously doesn't meet. Quotations directly from the original in the original context and without the DI's spin could be considered, but beware of assuming a similar meaning without careful impartial analysis. ..dave souza, talk 22:53, 12 May 2006 (UTC)
thread_title:  Origin of the term 

message: I think there's an awful lot of confusion over what IC is.  All complex systems are, by definition, irreducible in the sense that they possess emergent properties which cannot be traced to individual subcomponents.  The goal of architecture is to design systems which have such properties.
However, such properties can also grow on their own.  Mousetraps are a piss poor example obvious to anyone who has two brain cells to rub together (since they don't build themselves, they can't evolve on their own - to discuss mousetraps in the context one would have to include the systems which build them and, by doing so, one has to look at the entire history of snare building since pre-history which would include natural holes, then man made pits, then perhaps trip lines then snares etc. etc.).  Business enterprise systems are not such a poor example (because they do incorporate the means by which they are built into themselves).  Enterprises can have incredibly complex means of managing (or mismanaging) their intellectual capital which are a result how technology, policy, history, resources, vision, etc. work together.  A website such as Amazon which starts in a garage can grow in such a way that it ends up with a knowledge management system which is irreducibly complex (such a term is redundant and demonstrates ignorance of complex systems, but I'm using it here since that's the term used to identify this concept in this article).
I'd like for this article to point out in no uncertain terms that "irreducible complexity", just the term itself, makes one look like an idiot by using it since it is redundant (which would be obvious to anyone who knows what "complex" means).  Those who use the term, presumably, don't know what "complex" means and, therefore, eliminate themselves from any serious discussion on the very topic they are trying to discuss.198.97.67.56 17:14, 14 June 2006 (UTC)
thread_title: What is IC?

message: Adami C.: Evolution. Reducible complexity. Science 312:5770 (2006), 61–63 comments on Bridgham JT, Carroll SM, Thornton JW: Evolution of hormone-receptor complexity by molecular exploitation. Science 312:5770 (2006), 97–101 as being in opposition of irreducible complexity. --Rtc 05:28, 16 June 2006 (UTC)
thread_title:  ''Science'' article 

message: This article's actual list of structures that IDers have claimed are irreducibly complex is pitifully small: only two examples are given, one of them (Blood clotting cascade) only one line long. Why aren't some of the more famous examples of "irreducibly complex" organs listed, like the evolution of the eye? -Silence 04:15, 22 June 2006 (UTC)
replies: text: You've added evolution of the eye, but from my limited knowledge the ID proponents who've produced this "concept" accept the evolution of the eye, and so this properly belongs in the Forerunners section under Darwin. However others using the term may still use the example: a citation would be appropriate. ..dave souza, talk 08:10, 22 June 2006 (UTC)
replies: text: The eye is becoming a major subsection: do any "irreducible complexity" proponents actually use this example? ...dave souza, talk 08:01, 23 June 2006 (UTC)
replies: text: Every ID supporter and creationist I've ever met has used the eye as the main example of claimed "irreducible complexity" and design. I don't know of any reliable way to test how common it is on Google or anything (though "intelligent design" + "eye" gets around 750 times more Google hits than "intelligent design" + "flagella"), but it seems to be that the eye is the most common example of "irreducible complexity" cited by laypeople. It's noted by Answers in Genesis as a prominent IC argument (alongside the flagellum and the "complex cell"), and numerous book-reviews of Darwin's Black Box (both positive and negative) quote Behe discussing the eye. Even if it wasn't one of his more prominent examples, it's clearly an immensely noteworthy and common example within the movement in general. -Silence 08:31, 23 June 2006 (UTC)

text: Thanks, I've answered my own question and amended the article to suit, though you may wish to reposition the reference to their arguments or add a refutation. The IC argument is evidently propagated by YECs and OECs as well as by the IDers themselves, and I've added creationism to the intro to make this clearer. Apologies, but I'd picked up the idea that the eye was too well explained and ID made more of flagella and blood clotting. ..dave souza, talk 10:06, 23 June 2006 (UTC)

text: Thought you might move things around! That's looking a lot better, just had two links to the same reference which I've unified. It's also in the external links section, which seems good to me as it covers several topics. ..dave souza, talk 10:23, 23 June 2006 (UTC)
thread_title: Examples of irreducibly complex structures?

message: Bahe's claim is very hard to test directly, as it requires knowledge of past protein-protein interactions.  However, a 2006 paper in Science (Volume:312, Page:97-101) uses evolutionary theory coupled with bioinformatics to physically reconstruct ancient proteins and test their interactions.  These experiments directly address the concept of irreducible complexity and show that slow gradual changes in pre-existing protein systems can generate more complex interactions.  Here is the abstract from the paper entitles Evolution of Hormone-Receptor Complexity by Molecular Exploitation:
:According to Darwinian theory, complexity evolves by a stepwise process of elaboration and optimization under natural selection. Biological systems composed of tightly integrated parts seem to challenge this view, because it is not obvious how any element’s function can be selected for unless the partners with which it interacts are already present. Here we demonstrate how an integrated molecular system—the specific functional interaction between the steroid hormone aldosterone and its partner the mineralocorticoid receptor—evolved by a stepwise Darwinian process. Using ancestral gene resurrection, we show that, long before the hormone evolved, the receptor’s affinity for aldosterone was present as a structural by-product of its partnership with chemically similar, more ancient ligands. Introducing two amino acid changes into the ancestral sequence recapitulates the evolution of present-day receptor specificity. Our results indicate that tight interactions can evolve by molecular exploitation—recruitment of an older molecule, previously constrained for a different role, into a new functional complex.
I think this finding should be included in the Irreducible Complexity section.  For one, it addresses the fact that apparent irreducible protein-protein interactions can be explained by gradual amino acid changes, but, more importantly, it shows that scientific work is being done investigating the issues in evolution that Bahe has brought up. --Roland Deschain 04:17, 26 July 2006 (UTC)
thread_title:  Experimental evidence concerning irreducible complexity 

message: I added a link to Mark Perakh's essay, "Does irreducible complexity imply Intelligent Design?"
The article is decidedly non-mainstream, but I decided to add the link because of its unique perspective on the discussion.
Typically, ID proponents argue that there is IC, and therefore ID, while opponents of the argument attack it by arguing that there is no IC.  Perakh, in contrast to either of these two camps, argues that IC does not imply ID.  I felt this "third camp" merits a link, despite not being mainstream.  I hope I have acted correctly. Capedia 05:32, 22 August 2006 (UTC)
replies: text: Thanks for the link to an interesting and informative essay. In my opinion it's well worthwhile, despite a plague of pop-ups and intrusive ads - turn off sound before viewing! ..dave souza, talk 08:59, 22 August 2006 (UTC)
thread_title:  Mark Perakh's argument