Comment #34892

Posted by PvM on June 12, 2005 04:20 PM (e) (s)

Great job Nick at exposing the scientific vacuity of Intelligent Design. ID is retreating quickly into its gaps and front loading now that their ‘Icons’ have come crumbling down. No wonder Dembski is ‘returning to theology’, there is no future in science for his arguments.
I can’t wait for Intelligent Design to  be placed on the witness stand. Is Dembski not one of the planned expert witnesses in the Kitzmuller case?
He is becoming a liability I would say…

Comment #34895

Posted by Jon Fleming on June 12, 2005 04:50 PM (e) (s)

Both of these essays are late enough in the history of ID that they have included backup arguments just in case those protein parts are found (many of the homologies are documented in the big flagellum essay, and although I’m pretty well convinced that most of the IDists never read the essay in any detail, perhaps the general idea reached Minnich and Meyer).

This instance of the “big flagellum essay” link is broke.

Comment #34896

Posted by Nick (Matzke) on June 12, 2005 05:01 PM (e) (s)

I fixed the link, thanks.

Comment #34897

Posted by Mike Klymkowsky on June 12, 2005 05:02 PM (e) (s)

Unfortunately, given that ID creationists are not scientists, but rather anti-scientists, it is clear that they feel no allegiance to the standards of honesty, rigor, objectivity, testability or self-criticism to which the scientific community is committed. 

(I reflect with some melancholy at the number of beautiful hypotheses I have had to discard, because of annoying experimental results).

First and foremost, they see no need to be critical of the evidence for their own hypothesis (which is surprising, since they appear to have only one).  They clearly do not feel that they have to make useful predications about the natural world (which is lucky for them, since it might well end up with them espousing atheism). 

Science’s cultural acceptance is due in large measure to its ability to produce tangible, testable, and useful insights and results. 

Perhaps we might suggest that they return to the debate when they have developed a prayer-based antibiotic with a cure rate approaching that of atheistic- (that is science-based) drugs.  Or maybe a race, to see which approach first leads to a reproducible cure for cancer (oops, I believe they may have already lost that one). 

While I firmly believe that arguing with creationists is a futile, I applaud your diligence at not letting such drivel go unanswered.

Comment #34909

Posted by Guts on June 12, 2005 06:28 PM (e) (s)

<quote>
““The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique” was incorrect, and that, in fact, systems homologous to flagellum subsystems (in addition to the T3SS) are known which do have selectable function?”
</quote>

Nick, you are forgetting that your essay is riddled with errors when it comes to homology. For example, you look at similar sequences of E. coli FliH (sequence NP_416450) it looks like there is a sequence that has overlapping hits to both FliH (domain COG1317) and to F0F1-type ATP synthase, subunit b, (domain COG0711). But this is most likely a random occurrence, as the FliH hit has a high evalue of 0.01.

Comment #34910

Posted by PvM on June 12, 2005 06:58 PM (e) (s)

Yawn… Nelson, you’re missing the point. Even if you contest a few of the homologies under the argument ‘your essay is riddled with errors’, Dembski’s retreat is really the topic. See this link for homology data

Comment #34917

Posted by Alex Merz on June 12, 2005 07:57 PM (e) (s)

What’s up with that idiotic flagellum animation? How is it that the motor’s rotor is rotating, but the hook is not?

Comment #34921

Posted by Guts on June 12, 2005 08:22 PM (e) (s)

Pim as usual your comments and link are completely irrelevant.

Comment #34923

Posted by Nick (Matzke) on June 12, 2005 08:25 PM (e) (s)

Actually, Nelson, recent research findings seem to have vindicated my contention that FliH is probably homologous to the F₀-b subunit of the F₁F₀-ATPase.

YscL is a member of the FliH family of proteins. In flagellar systems, FliH binds to and regulates the activity of the ATPase FliI [57], and YscL is also known to bind to YscN [54]. PSI-BLAST searches across the NCBI’s non-redundant database with YscL fail to identify any homologue in the LEE system, because of contamination with low-complexity eukaryotic proteins. However, if the PSI-BLAST search is restricted to bacterial proteins, after one iteration, YscL appears in the results list (15% identity 29/184 residues; e value 0.002). After two iterations, several more FliH homologues are found. Furthermore, consistent with the recent suggestion that the YscL-YscN interaction mirrors similar interactions in other ATPases [54], weak similarity is also reported between Orf5 and several F₀ ATPase b subunits (data not shown). A multiple alignment confirms the presence of conserved residues within FliH, YscL and Orf5 (Figure 5). It thus seems likely that Orf5 is a homologue of YscL and FliH, plays a similar role (Table1, Figure 1) and should be re-named EscL.

[…]

54. Jackson MW, Plano GV: Interactions between type III secretion apparatus components from Yersinia pestis detected using the yeast two-hybrid system. FEMS Microbiol Lett 2000, 186:85-90.

(Pallen et al. 2005, "Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion." BMC Microbiology, 5:9.)

The point goes to Matzke on FliH, it appears. (And I do believe I cited Jackson and Plano (2000) myself, so it wasn’t even a novel idea.)

Like I said in the essay, the case for flagellum-ATPase homology is strongest for FliI and F₁-alpha/beta, then FliH and F₀-b, then FliQ and FliR with F₀-c and F₀-a, respectively.  Mike Gene makes a convincing case that there is no reason to favor homology for F₁-gamma, -delta, and -epsilon, with flagellum proteins, but I made it clear in the essay that homology for these last three proteins was particularly speculative.  Gene’s case against all the others is not convincing, and the unexpected discovery last year that the T3SS uses proton motive force in protein export (!!!) makes the whole question of homology between T3SS and the F₁F₀-ATPase much more interesting. Based on the hypothesis of homology between F₀-c and FliQ, I will stick my neck out and predict that FliQ is the proton channel in the T3SS.  We’ll see how things turn out, I guess.

Here’s a project for you, Nelson: go through the 50 or so flagellum proteins in the “canonical” E. coli flagellum and tell me how many of the proteins are both (a) required for flagellum function in all bacteria, and (b) “unique”, with no evidence of homology to nonflagellar proteins published in the peer-reviewed literature. Hint: it’s a low number.

Comment #34926

Posted by Steve on June 12, 2005 08:44 PM (e) (s)

Here’s a project for you, Nelson….

What?!  Actual research.  What a novel idea.

Comment #34929

Posted by PvM on June 12, 2005 08:57 PM (e) (s)

Nelson without Mike Gene’s “hand holding” seems to be somewhat of a fish out of the water :-)
My links were as relevant as your comments my dear friend and I also addressed your confusion as to the topic of the thread.
Of course, Matzke has shown that his prediction seems to have found supporting evidence. Perhaps you can take up the project Nick has suggested to you?

Comment #34939

Posted by Stuart Weinstein on June 12, 2005 10:29 PM (e) (s)

Alex writes: What’s up with that idiotic flagellum animation? How is it that the motor’s rotor is rotating, but the hook is not?

If what you mean by the “hook” is what I think you mean, the “hook” from which the flagella is extended may be a “protein” sheath or some such thing. It doesn’t have to rotate with the “gears” or the flaglella..

Course, I’m just a geophysicist, and feel free to tell me to mind my own business..

Comment #34940

Posted by Timothy Scriven on June 12, 2005 10:32 PM (e) (s)

I would still maintain that such a discovery would be worth a nobel prize on the grounds that it would perhaps be the most detailed and meticilous model of evolution in action so farproduced. It’s true it would have little practial import on the rest of microbiology but it would have much value as a inspiration for further research.

A detailed explanation of the fallgela would hence be valuable as a archetype, a plan for further plans of a similar sort, I would hold that it would be on those grounds deserving of a nobel prize. I am not a microbiologist, in fact I am a high school student, so please don’t take my comments too seriously.

Comment #34949

Posted by Timothy Scriven on June 13, 2005 12:35 AM (e) (s)

this is probably the closest I’ll ever get to celebrity so I might as well put down my thoughts on my comments. Firstly I’d like to respond to that “Pastor” guy who attacked my spelling. The post was written at 10:30 at night, for the medium of a blog, by a 17 year old whose not even doing biology as a subject, give me a break!

Secondly I’d like to respond to his claim that the problem has already been solved. Yes the basic fragments have been created by they still need to be synthesised. In addition a lot more detail would need to be added.  Mr Pastor also claimed ( to my memory) that such solutions are everyday. They probably are in other areas of biology but I’ve been led to believe by no less a rationalist authority then Daniel Dennet that such explanations are rare in microbiology. I think the good pastor fails to understand what I suggesting, not just a brief basic solution but a meticulously detailed minute step by minute step analysis.

To my very limited knowledge nothing like this exists in the literature. Indeed I’ve heard a lot of you guy’s at panda’s thumb claim that such a thing is impossible and that creationists are unrealistic to demand it, raise the bar for yourselves! I think it could be done. There would be no guarantee that the outlined path was the one the flagella actually took but as a theoretically demonstration of the conceptual failure of “Irreducible complexity” it would be priceless, science education would be saved, at every school board hearing it could be presented in slide show form. As I understand it the rules of the Nobel prize mean that it would not be eligible to actually win ( and besides, as Nick reminded me there is no Nobel prize in biology) but I never said that such a explanation of the flagella would have a chance of winning, only that it would deserve to win.

Comment #34959

Posted by Alex Merz on June 13, 2005 01:49 AM (e) (s)

Stuart, the hook rotates. The first experimental demonstration that the flagellar motor is rotary was obtained when a mutant bacterium with the hook but without the flagellum was attached to a glass slide by anti-hook antibodies. The attached bacteria rotated with respect to the slide.

If the motor is turning, the hook is rotating. The animation is completely wrong.

Comment #34962

Posted by Alex Merz on June 13, 2005 02:42 AM (e) (s)

To be clear: someone clearly put a lot of effort into the flagellum animation, but apparently could not be bothered to take a little time to get the biology consistent with what was known thirty years ago.

Comment #34967

Posted by Pastor Bentonit on June 13, 2005 06:01 AM (e) (s)

TScriven wrote:

this is probably the closest I’ll ever get to celebrity so I might as well put down my thoughts on my comments. Firstly I’d like to respond to that “Pastor” guy who attacked my spelling. The post was written at 10:30 at night, for the medium of a blog, by a 17 year old whose not even doing biology as a subject, give me a break!

Please accept my apologies.

such explanations are rare in microbiology. I think the good pastor fails to understand what I suggesting, not just a brief basic solution but a meticulously detailed minute step by minute step analysis.

To my very limited knowledge nothing like this exists in the literature. Indeed I’ve heard a lot of you guy’s at panda’s thumb claim that such a thing is impossible and that creationists are unrealistic to demand it, raise the bar for yourselves! I think it could be done.

Agreed, the more scientific progress, the more detailed explanations can be expected. However, the “La la la I can´t hear you”-crowd (ID as well as “ordinary” creationists) will likely never be impressionable (see below). Although, I guess there is a real problem “winning” the general public on matters of science. Alas, I´m from Sweden where we have practically no political impact from creationists as school (science) curricula are firmly reality/reason-based over here. I am truly sorry for you in the U.S.A, you have an anti-enlightenment movement on the roll, as is evident from daily perusal of PT comments and news items. I wish you good luck!

There would be no guarantee that the outlined path was the one the flagella actually took but as a theoretically demonstration of the conceptual failure of “Irreducible complexity” it would be priceless, science education would be saved, at every school board hearing it could be presented in slide show form.

Sadly, school board officials touting ID stickers and whatnot, are unlikely to accept neither any current evolutionary explanation of biological observations; nor any future (possibly improved) explanations, that are in conflict with their religious views. In fact, we can be reasonably sure that they would not know a sufficiently detailed “evolutionary path to the flagellum” if it jumped up and bit them on the…nose. This is painfully obvious from numerous posts here on PT.

Comment #34971

Posted by 'Rev Dr' Lenny Flank on June 13, 2005 07:14 AM (e) (s)

Hey Paul, are you ever going to answer my questions?  Why is the ID movement called the ID movement if, as you say, there isn’t any ID theory?

Where can we see a public repudiation by Ahmanson of any of the nutty extremist ideas he’s held for the past 20 years?  What parts has he repudiated, according to you, and why.  More importantly, what parts has he NOT repudiated, according to you, and why NOT?

Comment #34985

Posted by PvM on June 13, 2005 10:29 AM (e) (s)

Lenny: Nelson refers to Nelson Alonso not Paul Nelson

Comment #34991

Posted by Glen Davidson on June 13, 2005 11:41 AM (e) (s)

Dembski (with Nelson) demonstrates his obtuseness and ignorance yet again.  Well gee, “designers” do use “design components” in fairly novel productions.  Of course they do, dim, dim Dembski, which is why we don’t just say that something was “designed by humans”, rather we attempt judicial, psychological, and scientific explanations for “human design”, instead of simply believing that “intelligence” is the cause of “design”. 

Dembski’s mindlessness begins long before his resort to “ID” for biological organisms, in that he has not a clue that “design” is not really a scientific explanation per se, but that “design” is a placeholder for what we don’t yet know about how and “why” certain organisms produce certain things.  That is to say, Dembski’s essentially in the scholastic tradition throughout, who thinks that shortcut words like “intelligence” and “design” are answers to questions, which is why the obtuse fellow doesn’t even have any curiosity about intelligence and its evolution.  To be sure, he might “want” intelligence to be a “Ding an sich” (to use Kant’s phrase), or he might simply not be sophisticated enough to recognize what science and philosophy do.  Either way, though, it’s the same in the end, that he’s too ignorant to ask why humans copy designs.  And evidently he is both too prejudiced and ignorant to ask why God would stupidly co-opt “designs” that are not obviously suited to become the new “design”.  Again, if I were religious I think I’d take his view of God as the most offensive of all his thuddingly idiotic claims.

This is a different sort of projection than the usual psychological projection—Dembski wants to force his lack of understanding onto society.  It is in this way that the mindless one could become the Newton of information science—by dumbing down everything and everyone else to his level.

Of course Dembski’s too dishonest and/or ignorant to consider homologies properly.  Contrasting with homologies found in organisms, intelligent folk know why languages (at least European languages) have a much broader range of sharing of “design traits” than do typically genomes, which is because minds can transfer useful and/or intriguing words between languages.  Horizontal gene flow is much more restricted than is word flow in the typical case.

Something as obtuse as Dembski’s “understanding” of biology is, cannot follow the meaning of homologies, however.  Designers of limited intelligence (like humans) use designs without regard for origin (aside from copyright law, custom, etc.), while evolution is restricted to using inherited information plus a limited amount of variation and horizontal transfer.

How does anyone even as ignorant as Dembski know that anyone quoting or even paraphrasing Isaiah 7:14 is ultimately dependent on the Bible for that string of words?  This is because, in spite of all his prejudice and lack of scientific understanding, Dembski knows that something with as many specific points of correspondence as a Bible verse has derive from the original source.  This is true even of “human designs”, that in fact it requires a sort of “evolution” for there to be even a derivative line of text that shares a considerable correspondence with Isaiah 7:14. 

This is also true of even 10 proteins of the flagellum, as well as the ones that Dembski appears to be ignorant of (why doesn’t anyone ever write of what Dembski shows that he knows?  Surely he must know some things, but clearly he’s mostly blithering in areas where he evidently knows nothing of note).  They must have derived from the apparent source with which they share many specific correspondences (the true story behind “specified complexity”), and this would be so even for a “designer” kludging together a system. 

The trouble is that the appallingly ill-educated Dembski doesn’t have the slightest evidence that some homologies, like those of Death Valley pupfish, are due to evolution, while others are due to some “designer” who is far more limited in scope than are even human designers. 

Of course he needs this idiot savant “designer” to “explain” why the doofus is both so very intelligent as to be able to “design” a working flagellum, while being far too unintelligent and/or perceptive to use new parts and designs, or even to borrow “designs” outside of the bacterial lineage, in order to do so.  Note again the likely projection of Dembski’s very narrow education and intelligence and near-total lack of imagination onto his “God”.  His “God” fits into his almost complete lack of understanding of science, thus he invokes this “God” without any regard for science or for the likelihood that a real God might surpass Dembski’s prejudice and ignorance.

But anyhow, even Dembski probably would admit that pupfish share so much genetic information because of their relatedness to each other.  Dembski turns around and claims that flagella share data with other protein complexes due to a “designer”, without a smidgeon of evidence that the same explanation doesn’t apply across the genomes of organisms. 

That he doesn’t feel the need to validate his different interpretation of data from the same source indicates his utter lack of regard for science and its careful treatment and interpretation of data.  To him, similarities mean one thing in pupfish morphology, quite another thing in the flagellum.  As such he’s pseudoscientist of the first order.

Comment #35028

Posted by Ronald Newland on June 13, 2005 02:22 PM (e) (s)

I am a strong advocate of evolutionary biology and its teaching and consider myself a secular humanist. I say this to assure you that I have a sincere question.

I have been reading Ernst Mayr’s recent book “Toward a New Philosophy of Biology: Observations of an Evolutionist”. Possibly spurred by this a thought occurred to me that was new to me. It concerns the irreducible complexity bogus issue and how to argue against it. 

It occurred to me that evolutionary science readily admits that there are objects in the universe that were not created by the physical evolution of matter initiated by the Big Bang and that were not created by biological evolutionary development either. I refer to human designed and created artifacts. Anthropology uses the regularity of found objects as proof of human, as opposed to natural, origins. For example, is a seeming spear point regular enough to put it outside the possibility of natural, non human, origins? We are, of course surrounded by objects that could not exist without intelligent design by humans and they are all much simpler, less complex, than life, usually by a very wide margin. For example, the comb I carry in my pocket, if found by an anthropologist, would unhesitatingly be attributed to human intelligent design.

All this is by way of preface to the problem that occurred to me. I ask this sincerely as one who is a natural materialist and atheist. How does one counter an argument put forward by intelligent design advocates that goes as follows? 

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

I await your refutation anxiously,

Ronald Newland

Comment #35029

Posted by Wislu Plethora on June 13, 2005 02:37 PM (e) (s)

Ronald wrote:

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

Why would you want to compare living and nonliving things in this regard? Both the brain and the comb give the appearance of having been designed, but no one ever saw a pair of combs reproduce.

Comment #35031

Posted by Glen Davidson on June 13, 2005 03:00 PM (e) (s)

It occurred to me that evolutionary science readily admits that there are objects in the universe that were not created by the physical evolution of matter initiated by the Big Bang and that were not created by biological evolutionary development either. I refer to human designed and created artifacts.

No, that is not right.  Human designed artifacts are indeed considered to be a part of the evolution of matter/energy, as is “biological evolution”.  We split the various areas of study up for our convenience, not because we are not a part of the “evolution of matter”.

Anthropology uses the regularity of found objects as proof of human, as opposed to natural, origins. For example, is a seeming spear point regular enough to put it outside the possibility of natural, non human, origins?

See, this is why I have to at least wonder if you are what you say you are.  How is “regularity” supposed to be evidence for “design”?  Regularity can be the opposite evidence, evidence for nondesign, as we might see in a “perfect crystal”.  Which means that I’m not sure what you’re getting at.

Is a seeming spear point regular enough to put it outside the possibility of natural, non-human origins?  What does that mean?  Archeology often enough has difficulty distinguishing between crude human artifacts and “natural objects”.  In fact there was a cave found in France that was thought to have been the abode of tool-making Homo species, which from various evidences was later discovered almost certainly not to be.  The “tools” were merely broken rocks, having “regularity” for little reason other than the fact that the internal structure of many rocks is fairly uniform, cleaving, or otherwise fracturing along a fairly consistent surface.

We are, of course surrounded by objects that could not exist without intelligent design by humans and they are all much simpler, less complex, than life, usually by a very wide margin. For example, the comb I carry in my pocket, if found by an anthropologist, would unhesitatingly be attributed to human intelligent design.

Yes, generally we make rather simpler artifacts than one would expect of evolution.  And why are you saying that an anthropologist would attribute a comb to “human intelligent design”?  That’s not really the issue (though an anthropologist might indeed say it, since what “intelligence is” does not belong to anthropology) for science has to deal with questions of what “intelligence” is rather than simply crediting “intelligence”.  Btw, I covered enough of that in my own post, which I have to wonder isn’t the source of these “questions”.  I answered some of what you asked, and you responded by using terms and “science” in a manner that simply shows that you don’t understand science.

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

I await your refutation anxiously,

Yeah, sure, what a troll!  Anyway, I did refute it, and though I can see that you didn’t understand a good intelligent refutation, here is part of it again:

Designers of limited intelligence (like humans) use designs without regard for origin (aside from copyright law, custom, etc.), while evolution is restricted to using inherited information plus a limited amount of variation and horizontal transfer.

How does anyone even as ignorant as Dembski know that anyone quoting or even paraphrasing Isaiah 7:14 is ultimately dependent on the Bible for that string of words?  This is because, in spite of all his prejudice and lack of scientific understanding, Dembski knows that something with as many specific points of correspondence as a Bible verse has derive from the original source.  This is true even of “human designs”, that in fact it requires a sort of “evolution” for there to be even a derivative line of text that shares a considerable correspondence with Isaiah 7:14. 

This is also true of even 10 proteins of the flagellum, as well as the ones that Dembski appears to be ignorant of (why doesn’t anyone ever write of what Dembski shows that he knows?  Surely he must know some things, but clearly he’s mostly blithering in areas where he evidently knows nothing of note).  They must have derived from the apparent source with which they share many specific correspondences (the true story behind “specified complexity”), and this would be so even for a “designer” kludging together a system. 

The trouble is that the appallingly ill-educated Dembski doesn’t have the slightest evidence that some homologies, like those of Death Valley pupfish, are due to evolution, while others are due to some “designer” who is far more limited in scope than are even human designers. 

Of course he needs this idiot savant “designer” to “explain” why the doofus is both so very intelligent as to be able to “design” a working flagellum, while being far too unintelligent and/or perceptive to use new parts and designs, or even to borrow “designs” outside of the bacterial lineage, in order to do so.  Note again the likely projection of Dembski’s very narrow education and intelligence and near-total lack of imagination onto his “God”.  His “God” fits into his almost complete lack of understanding of science, thus he invokes this “God” without any regard for science or for the likelihood that a real God might surpass Dembski’s prejudice and ignorance.

But anyhow, even Dembski probably would admit that pupfish share so much genetic information because of their relatedness to each other.  Dembski turns around and claims that flagella share data with other protein complexes due to a “designer”, without a smidgeon of evidence that the same explanation doesn’t apply across the genomes of organisms.

The fact is that there is no single factor distinguishing between designed and evolved objects, rather there is science and getting down to working with the evidence.  The reason you’re so unbelievable as a sock puppet for someone else is that you appear not to know the slightest bit about science and the “natural materialism” you claim.  And that you apparently asked all that stupid uncomprehending nonsense after I had just answered most of it.

Comment #35032

Posted by Flint on June 13, 2005 03:06 PM (e) (s)

I think Ronald Newland asks a good question. So once again, I suggest that if Dembski (or I) were to land on an alien world where we saw nothing familiar, we would have no database of experience against which we could decide if any particular thing we saw were designed, natural, or something else. We might very well not be able to identify the proper boundaries of the thing either. The question of whether we could even identify an alien, much less distinguish one of their artifacts from whatever might be natural on that planet, is probably unanswerwable. We would probably march right up to the nearest zorrgle and try to communicate, while the actual aliens did the equivalent of rolling on the floor laughing.

Even watching zorrgles reproduce might not be sufficient. Plenty of inorganic things reproduce in various ways. And so I would expect we’d need to answer Ronald’s question the hard way: By having thousands of specialists collect millions of data for decades, to build the base of knowledge necessary to generate best-fit explanations with a high likelihood of being correct.

And incidentally, this is why Dembski has never even tried to apply his Explanatory Filter to anything remotely ambiguous, nor has anyone else. Dembski’s Filter works ONLY when the answer is already known (on the basis of substantial evidence if by scientists, on the basis of declared religious doctrine if by Dembski), and not before. Indeed, there are objects archaeologists exhume fairly commonly, which may or may not be artificial. Was this rock a tool? A tool to do what?

So there is no glib answer to Ronald’s question. We know the comb is artificial because of specific knowledge we have about combs. We know the brain evolved because of specific knowledge we have about the evolution of brains. We do NOT know about zorrgles for lack of any specific knowledge about them at all.

Comment #35033

Posted by Steve Reuland on June 13, 2005 03:09 PM (e) (s)

Ronald Newland wrote:

nthropology uses the regularity of found objects as proof of human, as opposed to natural, origins.

I don’t think this is quite the case.  On some occasions, we may use the presence of achaeological artifacts as evidence for the presence of humans, but for the most part, evidence of their human origins is independent.  We know that humans exist and we can discover the precise mechanisms by which they create certain artifacts.  We don’t attribute intelligent design to a spear point because we can’t think of any natural means by which they may have come about (things that look like spear points can be created by natural weathering, afterall) but because we already know how they come about. 

If we were to find some putative “designed” object in a place where we know that humans could never have been (such as in strata that’s a hundred million years old) then we would not immediately jump to the conclusion of “intelligent design”.  We would probably prefer some other hypothesis until such a time as a “design” hypothesis could be substantiated.  There are many examples of things that look designed at first glance but actually aren’t.  We blogged about some of these previously.

The way things work in the real world is that we compare competing hypotheses.  Any design hypothesis must have some sort of evidence in favor of it or else it’s no better than some natural hypothesis that relies on mysterious, hitherto unseen forces.  What it really comes down to is that ID cannot be substantiated by trying (and failing) to rule out natural hypotheses.  In order to be acceptable, ID must present a better hypothesis with its own independent evidence.  Only then can it be compared to competing hypotheses and (possibly) found to be superior.  This is something that ID advocates have been either unwilling or unable to do, preferring instead to use a purely negative approach by which they argue against evolution, and then claim ID true by default. 

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

I wouldn’t maintain that a pencil or a comb are evidence of “intelligent design”.  If I were to find such objects without any prior knowledge of what they were or where they came from, I would consider them an unexplained mystery until such a time as I was able to test hypotheses about their origin.  Knowing that humans use them — and that humans built them — kind of makes it a no-brainer.  But it’s different for something whose origin goes back millions of years and has no identifiable designer.

Here is something that is often overlooked:  We know for a fact that individual brains are not designed.  We know this because we see them develop and arise spontaneously within biological organisms.  Organisms and their components don’t come from a deity’s manufacturing plant, they come from their parents’ genes.  The only way in which we know that biological organisms arise is through birth. 

So what exactly is being “designed”?  It’s never really clear.  I know that I wasn’t personally designed.  But was my species somehow designed?  Some of our ancestral genes?  Maybe a primordial unicellular organism was designed and then everything evolved naturally since then.  All of these notions and more have been put forth by ID advocates, but they are inconsistent. 

Given that we lack anything resembling a coherent theory of ID, there’s just nothing to compare to the already successful and well-evidenced hypotheses that we do have.

Comment #35035

Posted by harold on June 13, 2005 03:17 PM (e) (s)

Ronald -

“How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?”

I don’t understand your logic.  There’s no limit on how simple a human designed object can be.  Are you seriously suggesting that we take the most simple possible human designed objects (which would be far, far less complex than pencils and combs) and conclude that everything more “complex” must have been magically “designed”?

Why do you think that something “complex” had to be “designed” in the first place?  Can’t you think of complex things that clearly arise spontaneously?  Since human designed objects are not necessarily characterized by greater “complexity” than natural objects, why do you use “complexity” as a test for “design” at all?

How do you measure complexity in this regard?  What is the threshold of complexity at which you  conclude that something was “designed”?  Who is the designer?  How does he or she design?  How can we test your answers?  If you use terms like “specificity”, “complexity”, “organized”, or “ordered”, please define these traits and explain how to quantify them.

Comment #35036

Posted by Steve Reuland on June 13, 2005 03:18 PM (e) (s)

Ronald Newland wrote:

nthropology uses the regularity of found objects as proof of human, as opposed to natural, origins.

I don’t think this is quite the case.  On some occasions, we may use the presence of achaeological artifacts as evidence for the presence of humans, but for the most part, evidence of their human origins is independent.  We know that humans exist and we can discover the precise mechanisms by which they create certain artifacts.  We don’t attribute intelligent design to a spear point because we can’t think of any natural means by which they may have come about (things that look like spear points can be created by natural weathering, afterall) but because we already know how they come about. 

If we were to find some putative “designed” object in a place where we know that humans could never have been (such as in strata that’s a hundred million years old) then we would not immediately jump to the conclusion of “intelligent design”.  We would probably prefer some other hypothesis until such a time as a “design” hypothesis could be substantiated.  There are many examples of things that look designed at first glance but actually aren’t.  We blogged about some of these previously.

The way things work in the real world is that we compare competing hypotheses.  Any design hypothesis must have some sort of evidence in favor of it or else it’s no better than some natural hypothesis that relies on mysterious, hitherto unseen forces.  What it really comes down to is that ID cannot be substantiated by trying (and failing) to rule out natural hypotheses.  In order to be acceptable, ID must present a better hypothesis with its own independent evidence.  Only then can it be compared to competing hypotheses and (possibly) found to be superior.  This is something that ID advocates have been either unwilling or unable to do, preferring instead to use a purely negative approach by which they argue against evolution, and then claim ID true by default. 

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

I wouldn’t maintain that a pencil or a comb are evidence of “intelligent design”.  If I were to find such objects without any prior knowledge of what they were or where they came from, I would consider them an unexplained mystery until such a time as I was able to test hypotheses about their origin.  Knowing that humans use them — and that humans built them — kind of makes it a no-brainer.  But it’s different for something whose origin goes back millions of years and has no identifiable designer.

Here is something that is often overlooked:  We know for a fact that individual brains are not designed.  We know this because we see them develop and arise spontaneously within biological organisms.  Organisms and their components don’t come from a deity’s manufacturing plant, they come from their parents’ genes.  Living things are different than human-made objects, and therefore analogies between them don’t work very well. 

So what exactly is being “designed”?  It’s never really clear.  I know that I wasn’t personally designed.  But was my species somehow designed?  Some of our ancestral genes?  Maybe a primordial unicellular organism was designed and then everything evolved naturally since then.  All of these notions and more have been put forth by ID advocates, but they are inconsistent, and never well developed. 

Given that we lack anything resembling a coherent theory of ID, there’s just nothing to compare to the already successful and well-evidenced hypotheses that we do have.

Comment #35037

Posted by Glen Davidson on June 13, 2005 03:26 PM (e) (s)

I tend to believe that many alien objects would be identifiable as “designed”.

There is one very crucial factor in identifying design, however, and it is one that the IDists attempt to obscure.  And this is that we can identify design only where we don’t have a non-design explanation for something.  Take a cube, for instance. 

Suppose we find a nearly perfect cube made out of limestone just sitting in the desert.  I mean a chunk like those  being used in fine Egyptian palaces.  Do we believe that it was designed?  Certainly so, and if it was a large block of genuine limestone found on glorph, we would have good reason to suspect that it was “designed” as well. 

But suppose I find a nearly perfect cube of iron pyrite?  Do I have any reason to suspect that it was designed?  In fact it could have been, and yet if the tool marks have been rubbed off one could not tell the difference. 

With life it’s different, though, because we have the strong genetic evidence for evolution by natural selection (as good as textual evidence between Biblical manuscripts), and we have no evidence that life can be designed.  It’s the method that is known to produce new forms of life that IDists oppose, only hoping to replace it with a “method” not know to be capable of producing life out of other life at all. 

That is to say, we almost certainly could tell if organisms on another planet were indeed organisms which have evolved, or if they were mere machines.  We can distinguish distinct “intelligently made” artifacts from evolution quite readily.  We never look at fish bones from the archeological record that retain cellular level complexity with having been designed.  So our “Newland” troll is misusing his analogy, in that we have no problem differentiating between life and design at the present human level.

Maybe highly advanced aliens could make life indistinguishable from evolved life.  First, I’d like to know why they’d bother, but maybe they would.  Secondly, it would be nothing fundamentally different from our making cubes as good as the cubes sometimes found as “natural crystals”—it would just be much better mimickry than we are now capable of effecting.

Comment #35040

Posted by Ronald Newland on June 13, 2005 03:39 PM (e) (s)

Thanks you both for your replies. I am indeed as I described and am not a troll. I haven’t read any posts by anyone else here and I apologize for that. I know it is proper etiquette to read before posting.
I really meant my question a a simple one and not with hidden traps of any kind.

My comment about anthropologist was not meant to be obtuse. It is a common scientific problem in this field to try to decide if an artifact was created by man or not. Another way of asking that is, “does it exhibit any features that are not likely to have been caused by non human forces?”

I did misspeak at least one place as was pointed out. Of course, science views all matter and objects as ultimately being caused by the Big Bang and subsequent evolution of the cosmos. But, it is common to divide the cosmos into living and non-living, the living being created by organic evolution. I was just pointing out that another way of dividing the matter of the cosmos is into non-human designed, organically evolved and human desiigned. These are three mutually exclusive and exhaustive categories. 

One comment said that we know the comb is artificial. But this is just another word for human designed. I think that supporters of evolution should be a little more precise in their description of the types of “things” in the universe so as not to allow for attacks by IDers such as I tried to describe.

Ron Newland

Comment #35045

Posted by Flint on June 13, 2005 04:19 PM (e) (s)

Glen Davidson:

we almost certainly could tell if organisms on another planet were indeed organisms which have evolved, or if they were mere machines.

Permit me to disagree very strongly. The ONLY basis we have for such identification is our own experience. So you are saying “An alien planet would be sufficiently similar to our own experiences so as to support qualified judgment.” But my point was that this hypothetical alien planet had NO OVERLAP with ANYTHING in our experience.

And I insist that until we accumulated some relevant knowledge, we could do no better than random in guessing which are the aliens, which are the artifacts, and what might be natural.

This is an important point. IF we had intimate knowledge of the Designer and His methods, and if that knowledge indicated that He gets his kicks creating life as we know it, we would surely change our minds and find that we are intelligently designed after all. So if you are arguing that we could reliably identify alien organisms on the basis of no prior experience, I suggest you are simply wrong.

Comment #35046

Posted by Glen Davidson on June 13, 2005 04:40 PM (e) (s)

Well, Ron, I’ll tentatively take you at your word (in spite of the oddly IDist sounding language) and apologize for writing that you’re a troll.  Trouble is, “Simon” has been lurking, and it seemed strange that you’d be leaping from simple regularities to complex brains without any reasonable linkage between the two, much as IDists do.  But hey, can happen.

One comment said that we know the comb is artificial. But this is just another word for human designed. I think that supporters of evolution should be a little more precise in their description of the types of “things” in the universe so as not to allow for attacks by IDers such as I tried to describe.

No, I think the point was that we know that the comb is made by humans.  Where I don’t agree with Flint, for instance is that we can identify artificiality without knowing the source, much as we would probably recognize a trap-door spider’s lair as having been produced by life.  What we would not know is if it was “intelligent” in the sense that we ordinarily mean it, another reason why I thought you sounded IDist.  That is to say, we really don’t know if something as complex as a trap-door spider’s burrow was made by intelligence, but only know that it was made by life (other items could be identified as being made by “intelligent life”, but in many archeological artifacts this would not be so.  Some “tools” are identified as such only because they are smooth stones that fit well into the human hand, and have been transported away from a streambed—which means that we’re identifying “intelligence” which is much less sophisticated than the trap-door spider’s burrow).

With a comb it might be difficult, because if they weren’t associated with dwellings and the like, how would we really know that it wasn’t produced by “non-intelligent” life.  Sure, we’d probably be able to say that it was made by life, but by intelligent life as you wrote?  I’m not so sure, unless of course we could show tool marks, or that the material of the comb was made by nickel catalysts or something of the sort.  A comb is so simple and conceivably of use to some hypothetical organism that we’d just have to work through the problem, and not be certain just on the basis of one comb that it was made by “intelligent life”—unless, again, specific design characteristics could be seen.

One thing we certainly can do on earth is to distinguish between the turtleshell that an antique comb might be made of, and the work that made the comb itself.  The turtleshell has the marks of life in it, including the complexity that goes beyond that of design that we know, while the comb may be made using sophisticated techniques, while not being anywhere near the complexity of life.  While designers might be able to make objects as complex as life someday, it will require a long evolution of “designer knowledge” to get to this point.

Comment #35047

Posted by Henry J on June 13, 2005 04:54 PM (e) (s)

Re “Why is the ID movement called the ID movement if, as you say, there isn’t any ID theory?”

Cause if they called it something else, adding the “-iot” suffix wouldn’t have the same effect?

Comment #35048

Posted by Flint on June 13, 2005 04:55 PM (e) (s)

Well, allow me to reiterate my disagreement with Glen Davidson. We can NOT identify artificiality without a lifetime of experience with our environment, its nature and its constraints. Consider a newborn human child, just old enough to focus its eyes (itself a learned ability). Put something in front of the child, and the child sees it. Move the object to one side, and the child *does not follow it*. Even the recognition that the object is a “separate thing” is learned knowledge.

We recognize that a comb is artificial and man-made for one reason and one reason only: because we know that men make combs, and that no other known process, either organic or inorganic, produces combs of that type. I emphasize: know other KNOWN process.

So what Glen Davidson is talking about is our ability to distinguish natural from designed (in the sense of an intelligent designing agent) within the very well-understood context of our own environment, with which we have all of recorded history to use as a database of comparison. And I agree that backed with this ample body of knowledge, our ability to avoid false positive and false negative identification errors is impressively good. But it’s good ONLY because we know the context so very intimately.

I’m beating away at this dead horse because our knowledge of the nature (supernature?), purposes, methods and techniques, and goals of the “intelligent designer” are as unknown to us as my hypothetical totally alien planet, and perhaps even unknowable to us in principle. And on the basis of ignorance this broad and deep, we can make no statements whatsoever about that that Designer may have done or might be doing.

And it’s this sheer ignorance that permits “theistic evolution” to exist. Anything no conceivable evidence might exist to support or refute, permits any belief about it at all.

Comment #35053

Posted by Glen Davidson on June 13, 2005 05:24 PM (e) (s)

Permit me to disagree very strongly. The ONLY basis we have for such identification is our own experience.

No, it is not, which is one reason for my post.  In fact we are capable of coming to reasonable general conclusions about life and what its effects are by studying life and what it does, and then by extrapolating evolution on earth to understand some of the limits of evolution on other planets.

Even more crucially, if we encounter alien evidence, we will also be able to judge such an experience.  We will try to experience alien traces sufficiently to understand them, and we may very well be able to do so.

You seem to believe that we cannot predict what would occur in evolution.  Yet we can, for we know how information must be conserved, modified, and mixed around in genomes.  That is to say, we can predict from 2LoT and other physical considerations that life will be complex, and, in any reasonably undisturbed environment, that life will become diverse, exhibit “nested hierarchies”, and be very complex due to neutral and near-neutral mutations.  This will not happen in any reasonable design scenario, and this is how we recognize that life has evolved and not been produced by God or aliens (barring Gods or aliens who deliberately mimic evolutionary evidence).

And yes, the alien hunters should be able to identify intelligently-made strings of information, even if they don’t understand the language/code.  As well, if they find pyramid complexes exhibiting copper tool marks and formed sarcophagi on Mars, I’m not going to withhold judgment, I’ll admit that “intelligent life” made these things. 

I’m not going to say much about this “intelligence”, for it may be remarkably unlike our own.  Furthermore, some “intelligent life” may make things that we would never recognize as “designed”.  But obviously I’m only discussing what we’d recognize in life reasonably similar to our own.  I think it would be unwise to suggest that we should not expect any life to be fairly like us, merely to realize that we may not recognize all forms of life, or their productions.

So you are saying “An alien planet would be sufficiently similar to our own experiences so as to support qualified judgment.”

No, I really wasn’t saying that, what I was doing was agreeing with the scenario that Ron brought up, the case where we recognize something as being simple enough yet out of place enough that we’d recognize it as being designed.  I realize that you went for something you said was where “we saw nothing familiar”, but I have no idea what that can mean.  The chemicals aren’t familiar, the rule of 2LoT isn’t familiar?  That’s about what it would take to blur the difference between designed objects and evolved organisms, of course, because evolved beings MUST show many of the same general effects of evolution that we find on this planet.

And I insist that until we accumulated some relevant knowledge, we could do no better than random in guessing which are the aliens, which are the artifacts, and what might be natural.
[quote]But my point was that this hypothetical alien planet had NO OVERLAP with ANYTHING in our experience.

That’s not the same as claiming that we saw nothing familiar, at least without qualification.  Anyway, I don’t know what you mean by “had NO OVERLAP with ANYTHING in our experience”, since of course centuries ago we gave up believing that the “heavens” operated fundamentally different from what happens on earth.  This is why we feel capable of looking for life on Mars, because while we might not recognize ALL life, we should be able to recognize life similar to our own.  Also designs similar to our own should be recognizable in some fashion.

And I insist that until we accumulated some relevant knowledge, we could do no better than random in guessing which are the aliens, which are the artifacts, and what might be natural.

If you move the goalposts to simply insist that nothing at all is recognizable, including evolution, then by definition you are correct.  But I have no idea what evolution that is unrecognizable by us can mean (except for clearly designed evolutions that take place at the hands of intelligent beings, as we are beginning to do—but that’s not what we usually mean in these discussions by “evolution”).  I don’t think that where you are now even allows discussion of real world situations, as opposed to some sci-fi plot.

IF we had intimate knowledge of the Designer and His methods, and if that knowledge indicated that He gets his kicks creating life as we know it, we would surely change our minds and find that we are intelligently designed after all.

So why the odd scenario in which we “recognize nothing” on this “alien planet”?  Is that what you really need to rule out intelligent design?  I can do it with much less strenuous standards, namely via the predictions of evolutionary theory.

We don’t need intimate knowledge of a designer in order to rule it in or out.  We only need to recognize the evidence that points to evolution without intervention in order to realize that we have no evidence of intervention.

So if you are arguing that we could reliably identify alien organisms on the basis of no prior experience, I suggest you are simply wrong.

Here’s the problem for your scenario:  I have learned to identify designing organisms on the basis of no prior experience in my own life.  Of course I had to begin to have experiences with these organisms in order to begin to know what they were, but simply everything we know began without “prior experience”. 

So it will be when we meet aliens, if we ever do.  We will have a head start, however, in that we already know how to identify evolved languages and organisms, and thus we can even study from our own experience whether or not “bacteria” on Mars have evolved, and how.  In fact this is what we would like to be able to do, study Martian life and its evolutions in order to compare it to terrestrial evolution.  Just as we were able to recognize evolution on earth without prior experience of this evolution, we should be capable of recognizing it on Mars. 

Likewise, we will be able to discern whether or not Martian life has made things.  One way that we’ll know if Martian life has made objects of magnetite is that these objects will be lacking in the information which must exist in evolved life (practically it should be simpler than that, but the rule of high complexity in life, and typically low complexity in most of what life “designs”, will still be lurking in the backgraound). 

No, I wouldn’t want to use your criteria for disputing “design”.  This is because if we didn’t have very good methods of detecting evolution we would hardly be anywhere scientifically with evolution, even though we’d still lack a basis for supposing that life was made by design.  We are much more capable than that, and we can definitively distinguish between ‘the evolved’ and ‘the designed’, barring any specific “design” to imitate the evidence of evolution.

Comment #35055

Posted by Glen Davidson on June 13, 2005 05:58 PM (e) (s)

We can NOT identify artificiality without a lifetime of experience with our environment, its nature and its constraints.

The trouble is that you are treating alien environments as if they were not “part of our environment”.  They are, which is why we understand them, why we can land on them and study them using the physics that we presently understand.  2LoT will come into play and make any evolved life very complex indeed, and as such we will be capable of recognizing the difference between life and any sort of machine made similarly to the way we design machines.

Now if you were talking about life on neutron stars, or something as alien as that, I might agree that we could have difficulty knowing what was designed and what was evolved.  I thought of mentioning this way back, but you seemed to be using few enough scientific constraints even with your “planet” that I didn’t get around to it (whatever the causes).  And sure, neutron stars are part of our environment, but they are so very alien compared to planets that studying anything on them would be extremely difficult practically, and the criteria for identifying evolution, while still holding, might not be within our range of perception and thought.

Again, though, we were talking planet, not the extremely alien environment.  I just don’t know how the typical planet could be so difficult to study biologically as Flint proposes it would be.

Move the object to one side, and the child *does not follow it*. Even the recognition that the object is a “separate thing” is learned knowledge.

You were writing this while I was composing my post, and I’ll just repeat what I suggested there, that we have indeed learned to deal with “physical environments”, and it should be rather easier to recognize design and evolution on Mars than it was to initially identify these on earth.

It’s not clear that we really “learn” that an object is a “separate thing”.  I suspect that we more or less inherit these abilities, and are “learned” only through experience (depends on what is meant by “learn”, certainly).  Where we draw the line is learned culturally, at least in part, since there is nothing that inherently “is object”, and nothing that inherently tells us that dreams are “not real” and waking experience is real. (I was just going to repeat and then leave off, but then this “phenomenology” and psychology are right down my lane).

Regardless, we are fortunate that any “normal planet” is unlikely to be beyond our recognition (Venus’ atmosphere’s high refraction will take some getting used to, but that’s about it).  It’s what we inherited from Galileo, and I’m sticking with it.

because we know that men make combs, and that no other known process, either organic or inorganic, produces combs of that type. I emphasize: know other KNOWN process

Sure, we know that.  And how do archeologists know that an abstract symbol “carved in bone” was made by humans?  It’s really more difficult to say, but basically it comes down to facts like that we know what humans are capable of doing, and what animals are capable of doing.  Yet we know humans are really animals, the distinction is artificial, and that we couldn’t say that spider webs and trap-door spider burrows weren’t “intelligently designed” without simply knowing what sorts of objects spiders make (silken, for one criterion) and what sorts of objects humans make.

But we don’t know what “intelligence” is in any non-relative sense.  We know something about what life makes, just not this “intelligence”.  Or do IDists think that an intelligent machine might have made life?  Well, they can’t rule it out from their espoused standpoint.

So what Glen Davidson is talking about is our ability to distinguish natural from designed (in the sense of an intelligent designing agent) within the very well-understood context of our own environment, with which we have all of recorded history to use as a database of comparison.

No, I am not, for I would never understand natural as being different from human. 

Additionally, we can distinguish “designs” that sea creatures make, and what we ourselves make without much difficulty in the majority of cases.  This is part of our “database”, but then so is evolution and physics, and what these entail for any alien evolution similar to our own.

And I agree that backed with this ample body of knowledge, our ability to avoid false positive and false negative identification errors is impressively good. But it’s good ONLY because we know the context so very intimately.

Yes, Flint, we’re studying the planets and stars today.  Or is this beyond our ability to do?

I’m beating away at this dead horse because our knowledge of the nature (supernature?), purposes, methods and techniques, and goals of the “intelligent designer” are as unknown to us as my hypothetical totally alien planet, and perhaps even unknowable to us in principle. And on the basis of ignorance this broad and deep, we can make no statements whatsoever about that that Designer may have done or might be doing.

Well the original question was not about this unknown planet, or even about an unknowable “designer”.  Naturally I’m not interested in discussing anything as meaningless as the “unknown Designer” or “totally alien planet”, rather I was discussing what we know and how we can know it. 

And it’s this sheer ignorance that permits “theistic evolution” to exist. Anything no conceivable evidence might exist to support or refute, permits any belief about it at all.

Well you certainly moved the goalposts beyond anything I was discussing.  I was discussing what we can tell in our environment known through physics and 2LoT, and Flint is discussing something that is by definition unknowable.  It certainly is not going to resolve matters related to the question that Ron asked.

Comment #35056

Posted by Henry J on June 13, 2005 05:59 PM (e) (s)

I wonder if “made by life” might be a more basic concept than “made by an intelligence”? After all, anything made by humans was made by life.

Then again, since an evolving gene pool has some of the attributes of intelligence (it can try different things, react to its environment, and remember results of previous trials), would it be too much of a stretch to say that an evolved species was designed - by the gene pool of its ancestors?

Henry

Comment #35057

Posted by Henry J on June 13, 2005 06:08 PM (e) (s)

Re “2LoT will come into play and make any evolved life very complex indeed,”
Why would 2LoT be a cause of life becoming complex?

Henry

Comment #35058

Posted by Guts on June 13, 2005 06:08 PM (e) (s)

Nic writes:

Actually, Nelson, recent research findings seem to have vindicated my contention that FliH is probably homologous to the F0-b subunit of the F1F0-ATPase.

Huh? That recent research just repeats what I said about weak similarity.

weak similarity is also reported between Orf5 and several F0 ATPase b subunits (data not shown).

The similarity of YscL (Yersinia T3SS homolog of FliH), in the Plano paper to the ATP synthase component was found by a blast search, but was pretty far down the list. The similarity was certainly not high enough to call them homologs.

A blast with E. Coli FliH you’ll see the alignment is less than half the length of the query sequence.  Psi-BLAST brought back only a few apparently ATP-related sequences.  The first round of Psi-BLAST is actually a BLAST search, and is probably less reliable than the next iterations.  The reverse search did not find significant numbers of flagellar proteins but did find many ATP-related proteins, suggesting that the sequence found is not mislabeled.  Thus it is most likely that the similarity here coincidence rather than homology. You could make a case for convergence givent that they both bind an atpase, but event that would be shaky.

[block]
Gene’s case against all the others is not convincing,
[/block]

Well actually I think Gene makes a good case for all the homologs that he discussed, (and he also gives other reasons for thinking that FliH and Fob aren’t homologs that go beyond the weak sequence similarity). But you can discuss that with Gene if you’d like. But I’m not here to defend other people’s statements.
I’m here to remind you that you need to get the homologies right first then accuse other people of being incorrect.

Comment #35063

Posted by Flint on June 13, 2005 06:33 PM (e) (s)

Glen,

We are talking entirely past one another. I don’t know how to get us on the same page. All I can say is, I do not share your optimism that our current general understandings can be accurately extrapolated in detail. I confess that if I were to find Paley’s watch on Pluto, I sincerely would not be able to identify its history. I would guess it was a manufactured item, because on Earth this would be obvious. So I would be extrapolating my Earthly experience and hoping it applied closely enough.

But if I confronted you with a zorrgle and asked you to identify whether it was life, or created by life, or neither, I think you would be mostly guessing, and your probability of guessing correctly wouldn’t be as high as you prefer to think. I may be wrong.

Comment #35064

Posted by Glen Davidson on June 13, 2005 06:42 PM (e) (s)

Why would 2LoT be a cause of life becoming complex?

Technically, 2LoT isn’t a “cause” of anything, being merely a description of what happens.  With that minor caveat gone, 2LoT prevents (or “prevents”) the duplication of long, highly specific genetic sequences through simply random processes (i.e., sans reproduction).  Of course one could simply be appealing to probability theory or some such thing, but either way, life is going to increase in complexity without some major event constricting it, or holding it down to very simple levels.

It was written in a specific context in the first (or nearly first) place:

That is to say, we can predict from 2LoT and other physical considerations that life will be complex, and, in any reasonably undisturbed environment, that life will become diverse, exhibit “nested hierarchies”, and be very complex due to neutral and near-neutral mutations.

I needed to be careful here, for life could conceivably be reduced to a non-complex state by frequent destruction or the like.  One may always increase complexity enough in complex organisms that they cease to live, while the simple survive.  However, in absence of any such scenario, life will become more complex, and it will be explainable via 2LoT (the caveat that 2LoT only applies to energy is moot at any temperature above absolute zero).

I thought about getting into whether or not I meant that organisms would become more complex, or if life as a whole would become more complex, but didn’t know if it would matter.  I meant the latter far more than the former, in fact, though the increase in overall complexity tends to make larger organisms also become more complex over time.  It is in the overall increase in life’s complexity that we really see 2LoT come into play, because 2LoT says that entropy (essentially information) will either be preserved or will increase.  Without extreme extinction, some of this increase in entropy/information will be preserved by the splitting lines of life. 

It’s all context, of course, since life can be reduced down to extreme simplicity (in all probability) or fully destroyed by circumstances.  However, 2LoT predicts that the overall complexity of two splitting lines will increase in the areas of the DNA where neutral mutations may occur, barring any mechanism that prevents this from happening.  While we don’t understand all preserved segments, certainly most obviously randomized sections of evidently unselected DNA are predictable through evolutionary considerations, as are neutral and near-neutral randomization of coding DNA.

Of course I’m not using 2LoT in any hard and fast manner, however the increase in overall complexity of life remains a fulfilled prediction of evolution, while it isn’t a prediction of any sort of design.  In fact of the designs that we know about, the predictions are that such randomization will not occur.  The IDists, however, don’t really have a Designer, but only a word “Designer”, thus they have no predictions, and will not accept falsification based on what we know about tangible “designers”.

Comment #35067

Posted by Glen Davidson on June 13, 2005 06:52 PM (e) (s)

I confess that if I were to find Paley’s watch on Pluto, I sincerely would not be able to identify its history. I would guess it was a manufactured item, because on Earth this would be obvious. So I would be extrapolating my Earthly experience and hoping it applied closely enough.

Certainly we’re talking past each other, but I don’t know how, other than following my own line of reasoning, to discuss how we really can identify designed objects. 

I would expect you to believe that a watch on Pluto was designed and made (if not exactly “manufactured”), because it shows apparent purpose and a lack of a natural means of producing it.

The crux is the predictions that evolution makes.  We best know that life was not designed because it shows only evidence of being evolved, and we lack any means of distinguishing the evidence of evolution from some proposed “design”.  That is to say, we know that life can evolve, at least to some degree, and fully lack any evidence that the genomes that we see are or can be made by any reasonably understandable designer. 

We might have some sympathy for Paley’s nevertheless unsupported assertion if we did not know that life shows evidence of “natural” evolution.  It the evidence of evolution that which moves us beyond mere skepticism to full-blown denial that life was designed.  And it is the predictions of evolution that make it science here or on any other planet that we are capable of investigating.

Comment #35068

Posted by steve on June 13, 2005 07:06 PM (e) (s)

With that minor caveat gone, 2LoT prevents (or “prevents”) the duplication of long, highly specific genetic sequences through simply random processes (i.e., sans reproduction).

No it doesn’t. Such a duplication may be unreasonably unlikely, but 2LoT doesn’t have anything to do with it.

Comment #35071

Posted by 'Rev Dr' Lenny Flank on June 13, 2005 07:25 PM (e) (s)

Lenny: Nelson refers to Nelson Alonso not Paul Nelson

Oh, darn.

Oh well, if Paul is out there, maybe he’d like to answer my questions anyway.  :>

Comment #35072

Posted by Flint on June 13, 2005 07:34 PM (e) (s)

Glen:

You may be right, but I can’t escape the suspicion that There are more things in heaven and earth, Than are dreamt of in your philosophy. You remind me of the proclamation someone once made (which I could remember, I think the president of some university) that science had basically completed the skeleton and fleshed out all there was to be known. All that remained for scientists to do was to grind out the details. Ironically, this speech was made only a year or two before the Year of Einstein, 1905.

Is it necessarily the case that given conditions more or less as we’re familiar with them, natural processes will produce more or less comparable results given enough time? How far can these results vary in the “less” direction before we could not properly identify them without some considerable study? While I don’t wish to denigrate what we have learned with so much effort, I can’t help but consider it local knowledge. The universe presents us with an endless supply of surprises, some quite totally unexpected, and I expect this to continue. I lack your confidence that our local knowledge will be all that portable.

Comment #35073

Posted by 'Rev Dr' Lenny Flank on June 13, 2005 07:35 PM (e) (s)

I am a strong advocate of evolutionary biology and its teaching and consider myself a secular humanist. I say this to assure you that I have a sincere question.

Not sure what difference your beliefs (whatever they are) make.  Science is science.  Makes no differnce if you are atheist or saint, Baptist or Buddhist, Taoist or Tantric, Christian or Quetzalcoatlian.

It occurred to me that evolutionary science readily admits that there are objects in the universe that were not created by the physical evolution of matter initiated by the Big Bang and that were not created by biological evolutionary development either.

Huh? 

I refer to human designed and created artifacts.

Humans are the product of the Big Bang.  Human brains and hands are the product of evolution.  Anything produced by those human brains and hands is, by definition, products of biological evolutionary development.

Anthropology uses the regularity of found objects as proof of human, as opposed to natural, origins. For example, is a seeming spear point regular enough to put it outside the possibility of natural, non human, origins? We are, of course surrounded by objects that could not exist without intelligent design by humans and they are all much simpler, less complex, than life, usually by a very wide margin. For example, the comb I carry in my pocket, if found by an anthropologist, would unhesitatingly be attributed to human intelligent design.

That is only because we see the designer and see it at work.

All this is by way of preface to the problem that occurred to me. I ask this sincerely as one who is a natural materialist and atheist.

I’m not an atheist, and I don’t know what the heck you mean by a “natural materialist”.  But as I said before, I fail utterly to understand why your beliefs (assuming you’re not just bullshitting us) have anything to do with the matter at hand.  Science is science.  No matter WHAT religious beliefs you have or don’t have.

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

Um, combs don’t reproduce, mutate and reproduce their mutations.

The human brain does.

I await your refutation anxiously,

No offense intended, but I’m awfully skeptical of your too-much-vaunted “atheism”.  First, it’s utterly irrelevant to science and the only ones I ever hear bring it up are fundies.  Second, I’ve seen this movie before, ad nauseum.  I wish I had a dollar for everyone who told me “I’m not a creationist IDer, but I have a question to ask”, and then go on to parrot all the standard DI boilerplate —- usually just before they scream “you’re all going to hell !!!!!!” and run away.  apparently, IDers don’t feel themselves bound by that commandment-thingie against “bearing false witness” … . .

Comment #35074

Posted by 'Rev Dr' Lenny Flank on June 13, 2005 07:39 PM (e) (s)

My comment about anthropologist was not meant to be obtuse. It is a common scientific problem in this field to try to decide if an artifact was created by man or not. Another way of asking that is, “does it exhibit any features that are not likely to have been caused by non human forces?”

More the opposite, actually.  In deciding whether a stone flake was the product of human tool-making or natural fracturing, for instance, it is precisely the unmistakable sings of human design that are searched for —— human-produced flakes have distinctive percussion bulbs that natural fractures don’t have.  So the question asked is not “does this have features that couldn’t form naturally?” but “does this have the features that we know are indicative of human activity?”

Comment #35090

Posted by Nick (Matzke) on June 13, 2005 09:50 PM (e) (s)

Nelson/Guts,

Well, I’ll take the published alignment in Figure 5 of Pallen et al.’s article over your unsubstantiated assertions.  Or perhaps Pallen et al. is “riddled with errors” also?

The alignment and BLAST hits, plus the fact that both F0-b and FliH are extended dimers, plus the fact that both are membrane-associated, plus that both associate with homologous ATPase hexamers (a hexameric nature, let us not forget, that you once denied with scorn because it was inferred from homology, until experimental confirming evidence was found, at which point you totally changed your tune and denied your previous scorn), all make for a reasonable case for homology between FliH and F0-b.  The features that Mike Gene points out that distinguish F0-b actually vary among