Jim And Penny Caldwell's Archaeological Findings:

[ExCBooster]

Hmm... I've never thought of living things of any kind as machines at all. Precisely because, as stated above, machines have a purpose.

The intelligent design theory and other flavours of creationism stands on the same grounds as the "watchmaker" vision of deism, that the universe was created, like a finely tuned watch, by something for a purpose (whatever that is). The problem, in my view, is that, while it's a philosophical stance, it's not science. Science doesn't assume anything, by definition, or it's simply not science. Note that the watchmaker analogy is considered an informal fallacy (fallacies in an argument are like fouls in sports, and the presence of fallacies in an argument negate the fair play of the side using them). Here's why: one of the cornerstones of science, engineering, and other logic is Occam's Razor. Occam's Razor, in a nutshell, is that in the case of two equally valid explanations for the same thing, the one that is least complicated is to be preferred. If you take ID at it's word, you now have to add the interference of a creator, the designer, and that creator's intentions, and a "meaning of life" in the literal sense. None of which can be explained, but rather must be taken as a literal article of faith (this is what brings up the sticky question of parasites, and apparently malign flaws in said design). These complex factors, the creator, or designer, violate Occam's Razor. Evolution by natural selection, on the other hand, covers all the available evidence, and eliminates the need to consider complex forces beyond our understanding. That's why natural selection is a scientific theory: by using Occam's Razor, it's simple, intuitive explanation that covers the evidence, and doesn't require articles of faith to explain complex mysterious forces beyond our comprehension.

One example that may help show how this issue works, is Sickle Cell Anemia. In this disease, the red blood cells that carry oxygen through your body are misshapen, preventing them from doing their job well. This is horrible. The degree to which someone is afflicted by this disease depends on how many copies of the sickle cell form of the gene they have. If they have none, their red blood cells are normally shaped, and they're healthy. If you have two copies, your cells can't carry oxygen well, and you've got a potentially life-threatening illness. If you have just one copy, however, something interesting happens: you may not have symptoms of Sickle Cell Anemia, but you DO get the nifty bonus of being resistant to malaria. That's interesting. And handy. Now, if you had to explain these facts with ID, you'd have to come up with WHY in Heaven a Creator of any kind would make innocent people sick, by designing our blood cells that way. This opens a whole lot of icky moral questions, that you have to tapdance around without actually answering (at least, not in any way that's going to come up comfortably, in a non-Lovecraftian sense). Either a benevolent creator has "mysterious ways" he's incompetently torturing innocent children with, or we live in a universe designed by a starkly, inhumanly disinterested, and utterly incomprehensible alien mind that wouldn't care. Not a good choice.

Natural selection, however, explains it tidily: you're more likely to die of malaria than Sickle Cell Anemia, and having just one copy protects you to some degree from the malaria parasite. The odds of survival favour this random mutation (people with just one copy could live to have kids), so it spread, where malaria was common. The mutation for sickle cells may have happened in other areas that didn't have malaria, but then it did more harm than good, so it didn't make it to the extent that it lived on in malarial environments. That's it. Covers the evidence, no complex creator to remain unexplained, no awkward mysterious ways, no hideous moral questions, no complications. Sickle Cell Anemia is just one of countless examples - the principle of Occam's Razor applied to explanations by Intelligent Design vs Evolution by Natural Selection favours Natural Selection, by definition, every time.

 

I'm not telling you this to tell you what to think, by any means. The issue here, in my mind, is that science has certain rules, just like formal argument, and ID violates quite a heck of a lot of them. So, I choose to side with evolution: it explains things efficiently and the evidence supports it. Evolution is the cornerstone of modern biology. Science is a tool for understanding our world, not an ideology. The results, I think (vaccinations, modern medicine, space program stuff, among other things) show how effective and powerful it is, as a tool. I just love science, I discuss stuff for fun, honestly, and I'm always curious as to how people think - in this case, it's the idea that people are comfortable with the idea of a creator behind nature, instead of terrified by it, that I find pretty intriguing. (I removed a bit about horrible parasites on that note. Don't want to upset people, or any stomachs.)

 

(P.S. I don't think the auto spell-check likes American spelling (Curse you, Daniel Webster!). I've been adding "U" to things to make it happy, But it doesn't like anemia at all. It should have another a, I think... Anemia, Anaemia... BINGO!)

[bornagainathiest]

Oh yes of course, BAA. I thought that I was open enough in the post to get the point across that I was simply throwing something out there off the top of my head just for the sake of conversation. And I drew from some pantheistic eastern mystical thinking too, which is why I see it as rejectable for most western monotheists.

 

But you read my over all point well. The main point is to look at nature, not the supernatural for the simplest explanation. And by intention I did mean something more along the lines of the primal urge or natural tendency that I had posted about previously. The tendency towards the evolution of life and eventually intelligence where conditions are favorable to permit that possibility. And natural selection and gradual evolution is the means by which you get from point A to point B, how else? That's why I threw in there that if some one really put their mind to it they could come up with a nice naturalist alternative to ID and IC which is perfectly in line with established science by staying with natural selection and gradual evolution.

 

The only reason for this "NT" venture is to perhaps help along people like BC and those who are raising similar questions due to the very obvious fact that nature looks very mechanical. You watch the video she posted and it looks like a nice and neat little factory production at work. And indeed some of our man made machines are more or less based on natural systems we've observed in nature which in some cases we have intentionally sought to duplicate in a round about sense.

 

The flagellum motor is more or less duplicated by man in some of our own machine making efforts, however coincidental that may be. But in any case Nature did it first. Technically the word "machine" may not apply to the flagellum motor but it's something that propels the bacteria through fluid in the way that a motor propels a boat through fluid. I think we all understand that. And I can see why BC would be frustrated by you suggesting that it's just a metaphor. Even if you let it slide and call it a machine just for the heck of it, we're still faced with how it came to be.

 

But how did nature do it first?

 

I see that none of the newest posts have acknowledged in any way the quotation I posted at the top of the page (post #181) or the links to how science supposes that the flagellum motor (whether conceived of as a machine literally or metaphorically) could have evolved in stages via natural selection and gradual evolution, which is the very point of this entire inquiry. Isn't that what we ought to be focusing in on now?

 

http://www.talkorigins.org/faqs/comdesc/ICsilly.html

 

The issue isn't nearly as simplistic as Behe would have it (see the IC refutation link now post above^). And it's entirely possible for the flagellum motor to have evolved in gradual stages contrary to how Behe would have it. The naturalistic theory for gradual evolution is by far a much simpler explanation than the seemingly magical instant appearence of a flagellum motor fully intact. There's a wealth of revelant info in that post.

 

The reason I threw out NI - which is more along the lines of NT as you point out - is to let BC know that she's not crazy, there's reason to feel amazed at the complexity and seemingly designed structures of nature. She doesn't necessarily have to loose that feeling of awe even if ID and IC completely unravel before her eyes. This isn't very different from the first problem we faced with the Caldwell's and Mt. Sinai. These two religious based camps are preying on innocent peoples emotions and they have it set up to where people are afraid that if their pseudo-archaeology or pseudo-biological science falls apart, then life is devoid of all meaning or any other such fallacy that isn't actually true. It keeps people in fear of fully looking into the alternatives whether they mean to do that to people or not. I want BC to know that there's no real danger in ID and IC falling apart, because, from where I sit I see it all coming unglued and she ought to be prepared for it...

 

Ah thanks Josh!

 

I was a little wary of treading on your toes.  So thanks for your reply.

 

How did nature do these complex things first?  I dunno!

 

But I do know two things.

 

First, there's a curious paradox associated with the birth of the universe - which I'll go into at the end of this message. 

 

Second, from the cosmological p.o.v. at least, the universe's NT towards complexity has had to take it's cue from the available materials. 

 

These earliest chemical elements to emerge from the heat of the Big Bang are also the lightest (in terms of their atomic weight) and also the ones least able to form complex structures.  So, the universe was obliged to start out simple and then work it's way slowly and tentatively towards complexity, using only what was around.

 

http://en.wikipedia.org/wiki/Chronology_of_the_universe ...Here we see that no kind of material structure was possible until between 3 and 20 minutes after the Big Bang event, when certain isotopes of Hydrogen, Helium and Lithium were able to form. (See,  2 Early Universe 2.5.1. Nucleosynthesis)  Even then the temperatures were much too high to permit anything other than hot gases and plasmas to exist.  Not much scope for complexity there!

 

Then we have to wait more than a billion years (almost 14% of the universe's age) before the very first material objects can form - these being the first stars. (See, 3 Structure Formation 3.2 Formation of Stars) As I mentioned to BC, the cores of the stars are where these heavier elements are made. 

 

http://en.wikipedia.org/wiki/Stellar_nucleosynthesis  This page shows how Hydrogen and Helium are 'cooked up' into Carbon, Neon, Oxygen, Silicon, etc.  These heavier elements are the key players in the universe's NT towards complexity.  Without them, anything but the lowest levels of complexity is impossible.  Why so?  Heavy elements have more protons and neutrons in their nuclei.  Putting it simply, this means that there are many more ways other elements can 'bond' with them to form complex compounds.  Here I'm talking about interesting stuff like this... http://en.wikipedia.org/wiki/List_of_molecules_in_interstellar_space

 

So, it's only after the first generations of stars exploded and died that these elements were strewn across the universe, to be swept up into clouds of dust and then to accrete and accumulate into the earliest solar systems.  Even then, the levels of anything 'heavier' than Lithium were exceeding low and stayed that way for billions of years. 

 

This page... http://en.wikipedia.org/wiki/Metallicity ...gives the lowdown on the gradual increase in complexity-friendly elements in the universe.  Our Sun is considered to be a second or third generation, metal-rich star.  It owes it's abundance of heavy elements to the earlier generations of lighter, metal-poor stars that preceded it. 

 

So the message is quite clear.  Early epochs of the universe's history would also have been less complex ones.  There simply weren't enough complexity-friendly elements like carbon, oxygen, calcium and silicon to support the wonderful complexity we see around us today.  It's possible that the universe had to wait for up to a third of his history (4.5 billion years) before there was sufficient abundance of heavy elements for truly complex structures to naturally arise.

 

Which now brings me back to my first point, that curious paradox.

 

For all of the above to happen, look what HAD to take place, Has taken place and what MIGHT take place.

 

1. (The Paradox)

The universe had to emerge from the domain of the pure SuperForce in the Big Bang event, shattering itself in the process.  This initial 'breakage' continued as the fireball cooled and expanded, with Gravity, the Nuclear forces and Electromagnetism splintering into the various forms we see them in today.  Therefore, for there to be any kind of complexity at all, reality had to be 'broken'.  Now, if there were an Intelligent Designer, this early 'breakage' suggests to me that God was stupidly clumsy, dropping his flawless and perfect, brand-new Creation from a great height and damaging it horribly in it's first microseconds. (Yes, this is tongue-in-cheek.  But I write it to stimulate thought!)

 

2. Complexity is a Recent Thing.

The universe's NT towards complexity began very slowly and feebly at first.  If this were represented in a graph, the line would barely rise above the horizontal for billions of years.  So, we musn't fool ourselves into thinking that everything's always been as complex as we see it now.  Quite the reverse!

 

3. Complexity need Not Increase.

http://en.wikipedia.org/wiki/Ultimate_fate_of_the_universe

This page outlines the range of possible endings that might befall our universe.  You'll note that in the Big Freeze, the Big Rip, the Big Crunch, the Big Bounce and the False Vacuum scenarios, complexity is NOT preserved - it is destroyed!  The only one that offers escape is the Multiverse scenario.  Only in a Multiversal reality is there the hope that complexity will survive, thrive and go on.

 

Food for thought!

 

Thanks,

 

BAA.

[Ravenstar]

Wow BAA.. good stuff

[Joshpantera]

Nice post BAA. 

 

Special creation of fully intact complex organisms is just plain out as far as possibility's go. It just doesn't gel with what we know of the universe at all. But gradual evolution certainly does. The only alternative I can see for those who insist on a theistic God but are willing to accept science is to go in the direction of guided evolution, accepting natural selection as God's way of creating. I've run into a few people who have felt that way. But even that is largely problematic because it's contrary to what is presented in Genesis in terms of a special creation of fully intact creatures. They're really parting ways with theism at that point and are probably viewed as heretical by others. 

 

One thing I've faced over and over again - and BC might relate to this - is that I've gone between seeing life and existence as purpose driven over to seeing it completely accidental with no purpose and back and forth between those options several times. Just when I start thinking that it's all a freak accident I'll second guess myself because of one thing or another. But if I start exploring the purpose driven way I'll second guess myself again. Eventually I started exploring the middle ground in case both sides of the coin are only partially correct. The purpose thing is difficult, but so is the freak accident way.

 

I think the main reason the freak accident thing is so difficult is because I see no alternative to existence extending on forever in some way. If that's the case then life must be more common than we understand at this point, especially as concerns repeating factors when confronting infinity.

 

But I also fully understand there can be no one fixed meaning or reason for that which exists eternally, it simply is without any specific explanation for why it is. What is the meaning of the existence of an eternal God, for a theist? What is the purpose of something with no beginning or end? It too is more or less left alone as something that simply is, something to just accept as a mystery in their thinking. It extends beyond the categories of purpose and non purpose. 

 

Even what I'm talking about in terms of NT doesn't really address the question of meaning because it's a question that can elude us forever as infinitely out of reach. Especially as concerns an infinite cosmos extending forever. What meaning or purpose could there be for that which has always existed and extends forever without end, whether or not it has a Natural Tendency towards the possibility of life and intelligence?

 

So I've made peace with the deep mystery at the base of it all that must be faced head on no matter which path I choose. I've found that it's ok to have no one 'fixed grand meaning or purpose' to turn to through either theism or non theism deep down at the very base of either path. And so I've made friends with the great unknown, so to speak. 

[♦ ficino ♦]

good posts, BAA, ExC, Josh.  I like your sickle-cell anemia point, ExC.

 

On the Bible Study thread in the Lions' Den, Ordinary Clay has resurfaced to demand an answer to the question, what is the scientific explanation for the origin of life? 

[bornagainathiest]

Thanks guys! 

 

Josh,

 

Could it be that the destination isn't the ultimate goal?  (Grand meaning or purpose or whatever we call it.)  Maybe it's how you get there that's just as important?  The act of seeking becomes an end, in of itself, changing the seeker from what they were into something new.  This, in itself, can be seen as a kind of evolution, wouldn't you say?

 

Btw, there's a fabulous diagram on the third page down (p.599) of the pdf article I'm linking to below.

http://www.Iapetus.uchile.d/Iapetus/archivos/1339604923linandcho12.pdf

It neatly sums up what I was getting at in my rather lengthy post, yesterday.

.

.

 

 

The Big Bang ---> 

                             Hydrogen (H) & Helium (He) --->

                                                                                Stars ---> 

                                                                                               Oxygen (02), Iron (Fe), etc. ---> 

                                                                                                                                                 the Earth ---> 

 

the first Life (Archaea, etc.) --->

                                                   Eukaryota ---> 

                                                                          Animalia --->

                                                                                               Humans--->

                                                                                                                  the next phase of Evolution...?

.

.

.

As Ravenstar quite correctly pointed out - we aren't at the top of a hierarchy. This is just a timeline.  We can't presume to be the pinnacle of everything (which ID assumes from get go!), nor can we presume that we are in any way 'complete' or 'finished'.  We can't be sure if that next phase will bypass us completely, leaving us as an evolutionary dead-end.  Nothing is certain.

 

Anyway, I heartily recommend Lineweaver & Chopra's work to you all. 

 

Please enjoy! 

 

Thanks,

 

BAA.

[bornagainathiest]

Oh shuggles! 

 

Can't get the link to work properly.

 

Please Google, "Charles Lineweaver + galactic habitable zone"

 

...then click on the link,

[pdf] The Habitability of Our Earth and Other Earths - Universidad de Chile.

 

That should work.

 

Thanks,

 

BAA.

[bornagainathiest]

On the Bible Study thread in the Lions' Den, Ordinary Clay has resurfaced to demand an answer to the question, what is the scientific explanation for the origin of life? 

 

Oh, you mean this guy?

 

http://images.fanpop.com/images/image_uploads/The-Black-Night-monty-python-and-the-holy-grail-591464_800_441.jpg

 

The Christian apologist who can never be defeated, who never gives up, who never admits when his arguments have been refuted and who just keeps coming back for more?

 

Him?

 

BAA

[BlackCat]

1. All machines are designed by designers.

2. The flagellum is a machine.

3. Therefore the flagellum is designed by a designer.

 

For this argument to go through, "machine" has to have the same value in 2 as it has in 1.  If "machine" has a different sense in 1. from the sense it has in 2., the argument will be invalid due to an equivocation fallacy.

 

I gather that BAA would say that "machine" is used metaphorically in 2. and that there is indeed an equivocation in this argument.  BC, I gather that you would deny that "machine" in 2. is a metaphor.

 

In that case, be careful that you are not falling into a different fallacy, i.e. begging the question.  If you are defining the flagellum in advance as a literal machine, not as a metaphorical one, then, if you conceive of machines in general as systems that are designed, your definition of flagellum will include already the property of its being designed.  But that is the very proposition that needs to be proved.  So your conclusion, under this conception, will be already entailed by your premises, thus making the argument question-begging.

 

It is very tricky to tease out suppressed premises.  I am suspecting that there are suppressed premises like the above in your thinking.

 

So, am I saying that any argument for ID in the case of the flagellum will be doomed from the start?  No.  I can't construct a valid one for it right now, though - have to get ready to leave the house!

 

Cheers, F

 

Good points.

[BlackCat]

Hi BlackCat, I think you are still analyzing the traits of earlier organisms by subtraction from the traits possessed by modern organisms.  An example of what seems to me to be analysis by subtraction is this in your reply above:  "If we take the flagellum and tinker with its dna so that one of it's core parts doesn't get produced, then the effect is that the whole thing doesn't get produced or you don't have a functioning motor."  I know that you mean this "tinkering" in a virtual sense, i.e. if we imagine a flagellum without one of the parts that are found in modern flagella.  This model slips in the notion of defect without admitting it;  you are thinking of a defective modern flagellum and saying that no cell could function with that.  The people who propound this sort of IC argument seem to me to commit a kind of ignoratio elenchi fallacy, i.e. they misconceive what the argument is about.  I don't know enough to lay out the intermediate stages between a very early cell that had some means of locomotion and the earliest cell that moved itself with a flagellum as we know flagella today.  My guess is that an evolutionary cell biologist, if there is such a discipline, needs to form a hypothesis about how the flagellum developed by stages.  It doesn't seem impossible in principle to do this.  The IC position, that either the flagellum arose all at once as a complex system fully formed OR it could not have arisen at all, seems to create a false dichotomy.  Since I gather the IC people are dropping the eye as their paradigmatic example and are focusing on the flagellum, I'm thinking that the problems with their earlier eye example will come up with their flagellum example, too.

 

There's another problem along the lines of what other folks mentioned above, i.e. how do we imagine the cause of the postulated, sudden genesis of the flagellum fully formed as we know it today?  Does the flagellum IC scenario imply a special creative act by a creator outside nature?

 

Edited to add:  I wonder whether Behe is misled by thinking too much of biological systems by analogy with machines.  He is a biochemist, not a biologist.  Since a machine is a human artifact to begin with, one's thinking will be skewed by comparing it too closely with a system in a living organism.  Calling a system in a cell "irreducibly complex" is to commit a question-begging fallacy, because it imposes a model derived from a modern organism as a standard for what traits should be possessed by a hypothetical earlier organism.  But that the earlier organism could not function at all with different traits from the modern one is just the claim that needs to be proved.

 

These guys point out problems with Behe better than I can:

 

http://www.talkorigins.org/faqs/behe.html

I missed this post.  Sorry. 

I meant a literal tinkering in the lab.  When I've listened to the ID guys talking about this (Scott Minnich) , I assume they've done experiments in the lab, where they knock out some of the proteins, or whatever it is they do, and their experiments show how ALL the parts are needed for the assembly to take place, or certain tinkerings may allow the assembly but then no function. 

 

I'll check out the link.  I've had a quick look and there are some interesting articles. 

[BlackCat]

Okay.. I'm no biologist... and I probably understood about 4% of this paper, but it's interesting to see that at least 2 of three components of the proto-flagellum could have other functions

 

"It was recently discovered (Cascales et al., 2001; Kojima and Blair, 2001) that the flagellar motor proteins MotAB have nonflagellar homologs: ExbBD and TolQR (Figure 4c).  These proteins share significant sequence similarity and all form ion channels that energize work at a distance by a third protein; ExbBD and TolQR energize outer membrane transport via action on TonB and TolA, respectively, while MotAB energize flagellar motion via action on FliG."

 

and at least one is also found in some archaea. (which is cool because archaea are a different line from us)

 

Those here may get more out of the info than I could...

 

http://www.talkdesign.org/faqs/flagellum.html

Thanks for this link.  I doubt whether I'll fare any better in understanding it, but I'll give it a go. 

[Joshpantera]

good posts, BAA, ExC, Josh.  I like your sickle-cell anemia point, ExC.

 

On the Bible Study thread in the Lions' Den, Ordinary Clay has resurfaced to demand an answer to the question, what is the scientific explanation for the origin of life? 

I entered the arena, guns blazing...

 

http://www.ex-christian.net/topic/54831-theistic-satanism-age-of-aquarius-discussion-continued/page-4#entry838688

[bornagainathiest]

 

good posts, BAA, ExC, Josh.  I like your sickle-cell anemia point, ExC.

 

On the Bible Study thread in the Lions' Den, Ordinary Clay has resurfaced to demand an answer to the question, what is the scientific explanation for the origin of life? 

I entered the arena, guns blazing...

 

http://www.ex-christian.net/topic/54831-theistic-satanism-age-of-aquarius-discussion-continued/page-4#entry838688

 

So I see! 

 

[Joshpantera]

 

Okay.. I'm no biologist... and I probably understood about 4% of this paper, but it's interesting to see that at least 2 of three components of the proto-flagellum could have other functions

 

"It was recently discovered (Cascales et al., 2001; Kojima and Blair, 2001) that the flagellar motor proteins MotAB have nonflagellar homologs: ExbBD and TolQR (Figure 4c).  These proteins share significant sequence similarity and all form ion channels that energize work at a distance by a third protein; ExbBD and TolQR energize outer membrane transport via action on TonB and TolA, respectively, while MotAB energize flagellar motion via action on FliG."

 

and at least one is also found in some archaea. (which is cool because archaea are a different line from us)

 

Those here may get more out of the info than I could...

 

http://www.talkdesign.org/faqs/flagellum.html

Thanks for this link.  I doubt whether I'll fare any better in understanding it, but I'll give it a go. 

Here's a very simple article which I think you'll understand quite well:

http://www.talkorigins.org/faqs/comdesc/ICsilly.html

 

 

Introduction

 

 

Michael Behe's term "irreducible complexity" is, to be frank, plainly silly — and here's why.

 

 

"Irreducible complexity" is a simple concept. According to Behe, a system is irreducibly complex if its function is lost when a part is removed¹. Behe believes that irreducibly complex systems cannot evolve by direct, gradual evolutionary mechanisms. However, standard genetic processes easily produce these structures. Nearly a century ago, these exact systems were predicted, described, and explained by the Nobel prize-winning geneticist H. J. Muller using evolutionary theory². Thus, as explained below, so-called "irreducibly complex" structures are in fact evolvable and reducible. Behe gave irreducible complexity the wrong name.

 

 

Behe's flawed argument

 

 

Behe claims that irreducibly complex systems cannot be produced directly by gradual evolution³. But why not? Behe's reckoning goes like this:

 

 

• (P1) Direct, gradual evolution proceeds only by stepwise addition of parts.
• (P2) By definition, an irreducibly complex system lacking a part is nonfunctional.
• © Therefore, all possible direct gradual evolutionary precursors to an irreducibly complex system must be nonfunctional.

 

 

Of course, Behe's argument is invalid since the first premise is false: gradual evolution can do much more than just add parts. For instance, evolution can also change or remove parts (pretty simple, eh?). In contrast, Behe's irreducible complexity is restricted to only reversing the addition of parts. This is why irreducible complexity cannot tell us anything useful about how a structure did or did not evolve.

 

 

Example 1: The stone bridge

 

 

A clear example of the Mullerian two-step is given by a stone bridge. Consider a crude "precursor bridge" made of three stones. This bridge spans the area needed to be crossed and is thus functional. For step one of the Mullerian two-step, a part is added: a flat stone on top, covering all precursor stones. Whether this improves the functionality of the bridge is irrelevant — it may or may not, the bridge still functions. For step two of the Mullerian two-step, the middle stone is removed. Voilá, we have an irreducibly complex bridge, since the last step made the top-stone necessary for the function.

 

 

The precursor bridge: three stones.

 

Step #1, add a part: the top-stone.

 

Step #2, make it necessary: remove the middle stone. As promised, we now have an irreducibly complex stone bridge. None of the three stones can be removed without destroying the bridge's function.

[BlackCat]

Thanks for the link: http://www.talkdesign.org/faqs/flagellum.html

 

Abstract: The bacterial flagellum is a complex molecular system with multiple components required for functional motility.  Such systems are sometimes proposed as puzzles for evolutionary theory on the assumption that selection would have no function to act on until all components are in place.  Previous work (Thornhill and Ussery, 2000, A classification of possible routes of Darwinian evolution. J Theor Biol. 203 (2), 111-116) has outlined the general pathways by which Darwinian mechanisms can produce multi-component systems. However, published attempts to explain flagellar origins suffer from vagueness and are inconsistent with recent discoveries and the constraints imposed by Brownian motion.  A new model is proposed based on two major arguments. First, analysis of dispersal at low Reynolds numbers indicates that even very crude motility can be beneficial for large bacteria.  Second, homologies between flagellar and nonflagellar proteins suggest ancestral systems with functions other than motility.  The model consists of six major stages: export apparatus, secretion system, adhesion system, pilus, undirected motility, and taxis-enabled motility.  The selectability of each stage is documented using analogies with present-day systems. 

 

Conclusions include: (1) There is a strong possibility, previously unrecognized, of further homologies between the type III export apparatus and F₁F₀-ATP synthetase. (2) Much of the flagellum’s complexity evolved after crude motility was in place, via internal gene duplications and subfunctionalization.  (3) Only one major system-level change of function, and four minor shifts of function, need be invoked to explain the origin of the flagellum; this involves five subsystem-level cooption events.  (4) The transition between each stage is bridgeable by the evolution of a single new binding site, coupling two pre-existing subsystems, followed by coevolutionary optimization of components.  Therefore, like the eye contemplated by Darwin, careful analysis shows that there are no major obstacles to gradual evolution of the flagellum. 

 

 

 

Table 6: Functions and analogs at each stage of the presented model.  See Figure 7 and text for further details. 

 

 

Once again, what's the alternative to gradual evolution BC and everybody following along? 

 

Isn't it either gradual evolution or special creation with entire life forms coming into being ex nihilo as in Genesis 1?

 

What other option is on the table? 

 

One of the links specific to refuting IC is interesting as well: http://www.talkorigins.org/faqs/comdesc/ICsilly.html

 

The more I am looking into this and considering all the points everyone is making, the more I can see the problems with rejecting 'gradual evolution'.  All the evidence is overwhelming in favour of gradual evolution.  So, how can I hold on to that, AND consider 'design' which seems to infer 'prior intent'?  If something is irreducibly complex, then that suggests that its blueprint was in existence 'somewhere' and was made available.  Can we really have strands of dna popping into existence and being rained down onto this planet to seed it with all the life forms?  That is as far fetched as the biblical account.  Another possibility is that the natural 'urge' for molecules to lump together (acting like a magnet), and life forms gradually forming are the inevitable outcomes of the matter and energy available to them.  Obviously our reality of matter and energy can and does produce complex life, and just as I can't comprehend how the energy/matter could have always been in existence, so too it's hard to comprehend how it can give rise to such complex life forms. 

[bornagainathiest]

BlackCat!

 

Just a word of warning, if I may.

 

Please beware of this OrdinaryClay.  He's just as dangerous as Thumbelina and way, way cleverer.  Unlike Thumbelina, OC's been 'clever' enough not to fall foul of the Mods - so he's got complete freedom of this entire forum.  Therefore, he can enter into any thread he wants to.

 

Please DO NOT engage in dialog with him. 

Please DO NOT divulge any personal information to him.

Please report it to the Mods if he begins harrassing you via Private Messaging.

 

This Christian fanatic is not to be trusted, heeded or even acknowledged.

 

Thanks,

 

BAA.

[Joshpantera]

The more I am looking into this and considering all the points everyone is making, the more I can see the problems with rejecting 'gradual evolution'. All the evidence is overwhelming in favour of gradual evolution. So, how can I hold on to that, AND consider 'design' which seems to infer 'prior intent'? If something is irreducibly complex, then that suggests that its blueprint was in existence 'somewhere' and was made available. Can we really have strands of dna popping into existence and being rained down onto this planet to seed it with all the life forms? That is as far fetched as the biblical account.

You see, I too was interested in ID when it was all the rage for a while. And upon much contemplation I realized that it was mainly wishful thinking and didn't really negate Darwinian Evolution as a valid alternative.

Another possibility is that the natural 'urge' for molecules to lump together (acting like a magnet), and life forms gradually forming are the inevitable outcomes of the matter and energy available to them. Obviously our reality of matter and energy can and does produce complex life, and just as I can't comprehend how the energy/matter could have always been in existence, so too it's hard to comprehend how it can give rise to such complex life forms.

Yeah, the main thing is that regardless of the mystery factors involved everything has unfolded this way and here we are now trying hard to figure out how and why. Not yet knowing the specifics is ok.

 

I guess we've been through most of the videos posted here recently and you don't have too much on your plate at the moment. So I'll go ahead and tip you off on another path of investigation that you may really enjoy, like the deconversion video series:

 

 

The problem of consciousness is far from settled. There may be a paradigm shift ahead for all we know. I post this because it seems to accord with the notion of NT and other factors that could be involved in gradual evolution and natural selection that may not be fully realized yet and which science may catch up to at some point.

[ExCBooster]

I don't think Ordinary Clay's going to be convinced, just annoyed... if that. He's got his bible blinkers on, just like a nervous racehorse. But, the explanation there is abiogenesis - that conditions in Earth's early seas and atmosphere, as the planet cooled off, were just right actually for precursor molecules to stick together, and begin replicating. We know this because a famous experiment showed that amino acids could be created from chemicals in the early seas (they weren't much like our seas now, being a seething brew of ammonia, among other things), just by adding electricity (lightning strikes on oceans). A recent re-analysis, showed that even more amino acids were produced than the original authors could tell were there. And that's just in a small flask, over a preposterously short amount of time (see previous post on geologic time scale in 24 hours), compared to literal oceans, and skies, and lightning on the surface of the seas. Over a literal geological aeon... The early seas would have been swimming with precursors to life under these conditions. Actually, lots of things, which aren't technically even alive, do replicate, from prions (contagious misshapen proteins) to viruses (a RNA warhead in a protein jacket). Rather than a miracle, the rise of life from sterile conditions in these circumstances becomes pretty darn likely. Life as we know it is just one part of a continuum. Even the skies swarm with life. Our oceans of water, the oxygen in our atmosphere, our Earth itself is shaped by the processes of life. And it wasn't pretty. Oxygen was a poison to early life - there's quite some evidence showing that it was a pollution catastrophe that trashed the climate. Whoops. But, fortunately, life's tough stuff, once it gets going. It's not really a hierarchy, as pointed out above: we're all winners, here.

 

[Akheia]

Saw this on Friendly Atheist and thought of this thread. BC, just so you know, Friendly Atheist does stuff about how stupid ID/Creationism is all the time; it's written by a math teacher and his guest writers include people with actual degrees in biology and whatnot (so in other words, making them far more knowledgeable on the subject than most of the big name creationists!).

 

I feel so bad for the South... like their educational systems aren't fucked enough as it is.

[BlackCat]

Great replies guys and thanks for the links.  I shall work my way through them.

 

Thought2Much- I'm not having much luck with your challenge.  It doesn't appear that many scientists in the fields of biology or molecular biology are persuaded or interested by the challenge of ID/IC, and so that list I posted which I think only had 2 non theists in it, is the best I can find.  It seems that the appearance of design doesn't arouse much interest and so because it's mainly theists who are making all this fuss, it's viewed as suspect.  I did find an atheist who's written a book about ID: 

 

http://www.amazon.com/Seeking-God-Science-Atheist-Intelligent/dp/1551118637/

 

The purpose of the book seems to be more about giving credence to ID as a legitimate theory/proposal  rather than the author accepting the theory.

 

I shall no doubt continue to take a keen interest in ID/IC.  I've emailed the Discovery Institute to ask if any scientists have refuted the proposed models for gradual step by step evolution of the 'systems' claimed by the ID crowd, to be irreducibly complex.  I'll let you know if they reply.  The Mullerian two-step example of a stone bridge, explained in an earlier link of Josh's, seems to refute IC, but I suspect it may not disprove  ALL examples of IC.   Each individual 'stone' is a bridge. At every stage of the bridge's evolution, it was still a bridge.  The same logic wouldn't apply to an outboard motor surely? 

[Thought2Much]

Thought2Much- I'm not having much luck with your challenge.  It doesn't appear that many scientists in the fields of biology or molecular biology are persuaded or interested by the challenge of ID/IC, and so that list I posted which I think only had 2 non theists in it, is the best I can find.

 

Yes, I pretty much knew that when I issued the challenge, but I wanted you to find this out for yourself. And why do you think that the scientists who should be the most intrigued by this theory are not doing any work regarding it? It's not because of silly reasons like they're all "closed-minded" or they would be ostracized by other scientists if they pursued it. It is entirely because they see nothing in the theory that is worthy of pursuit. If it were worthy of study, someone would be trying to be the first to win a Nobel prize by studying it.

 

And regarding the flagellum/outboard motor comparison: No one is saying that a flagellum would work if you started stripping pieces out of it; what is being said is that all of its components have independently served different functions in other organisms prior to the development of flagellates, and that these components have all happened to come together in flagellate organisms. They all evolved on their own, and were later combined into one unit in flagellates, probably over the span of many millions of years. To call in some completely unprovable outside force that has been "designing" things for Earth's 4.6 billion year history to explain these things is totally unnecessary.

[Akheia]

BC - oh, I can't blame you. The story of creationism and how it morphed into ID, how it wedged into schools, how it gained political power, how it is being used by fundie groups to push their feet in the door of non-Christians, and how it's being combated by various legitimate scientific groups and educational groups, is simply fascinating. I find the whole movement absolutely fascinating too. Nothing wrong with that. It's like being fascinated with the Tea Party (another movement whose sociology I also find fascinating).

 

Do I think anything they say has actual credence? Oh hell no. But I think that legitimate science can learn from how it's wormed its way into classrooms. Creationism's spokespeople definitely know how to speak to the unwashed, ignorant masses, whereas scientists, real ones, often have a lot of trouble articulating their findings and their revelations (there is no question in my mind why creationism's speakers are generally very eloquent and well-spoken, whereas the few eloquent scientists end up becoming rock stars because they're so damned rare). And I think that by examining the claims of creationism, namely the numerous fallacies and pseudo-science they routinely employ to demonstrate their ideas, non-scientists (meaning normal folks like me and you) end up learning a shitload about real science. Nothing teaches you better than learning enough about it to discover it's bullshit. So go ahead, be fascinated! Explore everything. There is nothing wrong with questioning and exploring.

 

ETA Oh wow I used the word fascinating a lot. Nothing was meant by it. I promise.

[BlackCat]

 

Thought2Much- I'm not having much luck with your challenge.  It doesn't appear that many scientists in the fields of biology or molecular biology are persuaded or interested by the challenge of ID/IC, and so that list I posted which I think only had 2 non theists in it, is the best I can find.

 

Yes, I pretty much knew that when I issued the challenge, but I wanted you to find this out for yourself. And why do you think that the scientists who should be the most intrigued by this theory are not doing any work regarding it? It's not because of silly reasons like they're all "closed-minded" or they would be ostracized by other scientists if they pursued it. It is entirely because they see nothing in the theory that is worthy of pursuit. If it were worthy of study, someone would be trying to be the first to win a Nobel prize by studying it.

Good points.  I don't understand why more scientists (especially molecular biologists) aren't intrigued by this, but I assume they have every 'faith' that evolution will be shown to have produced these systems gradually, bit by bit, and so they don't get excited (like I do) by the (premature?) assumption that molecular systems demonstrate design and ic. 

 

 

And regarding the flagellum/outboard motor comparison: No one is saying that a flagellum would work if you started stripping pieces out of it; what is being said is that all of its components have independently served different functions in other organisms prior to the development of flagellates, and that these components have all happened to come together in flagellate organisms. They all evolved on their own, and were later combined into one unit in flagellates, probably over the span of many millions of years.  This isn't the case.  Of the flagellum's 40 or so 'parts', only 10 (which are similar to the type III SS), are found in other molecular machines.  The other 30 are unique to the flagellum.  This is the point that is brought out in the short video I posted back on page 5 if I remember rightly.  Scott Minnich, professor of microbiology has been studying the flagellum for many years and he talks about how the majority of its parts are unique.  The co-option theory where 'parts' are used by different systems (e.g borrowed) can't apply to the flagellum.  So how did all the unique parts get produced gradually, when you need ALL these unique parts to be in place in order for the whole system (a motor) to function?  Check that video out, as it  poses some difficult questions that evolution is yet to answer fully.   

 

To call in some completely unprovable outside force that has been "designing" things for Earth's 4.6 billion year history to explain these things is totally unnecessary.

Umm, I'm being open minded about this.  This 'force' needn't be viewed as 'outside'.  If there is SOMETHING that is having an influence on how life is evolving it may well be woven into every particle or into all energy.  We don't need to jump to biblical type gods.  I want to try and stay within the material realm whilst exploring this inferred design.  We have such a limited view of the material universe and what may lie beyond our universe that 'forces' of energy and matter may well resemble 'mind' or may well cause realities that defy logic. What I'm struggling to say, is that we don't know enough to rule out other forces that may effect our reality.   

[Joshpantera]

BC, did you see the 2nd example after the irreducibly complex bridge? 

 

 

 http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html#how2eatpcp

 

 

Swimming Systems

We come now to what have become the very most important purported examples of IC in nature: swimming systems. These are flexible projections that microbes use to move themselves through fluids. The three main types of microbes, bacteria, archaea, and single celled eukaryotes, use different swimming structures, and there are major differences between species of each type. Some bacteria even manage to swim without flagella, including little understood Synechococcus (17) and much better understood Spiroplasma melliferum (18). Of course microbial motion is not limited to swimming. They also have ways to move along surfaces and maneuver in sand and ooze. Bardy et al. review almost all of the known ways bacteria and archaea move (19).

Swimming systems depend on what are called molecular motors, a favorite topic of molecular biologists. Those who are curious about molecular motors may start here (20). Brownian ratchets, fascinating in their own right (21), are one of the energy sources for these tiny motors.

From a biological perspective, the function of an organism is to live and grow enough to reproduce. The function of any part of the organism is to contribute to this in any ways whatsoever. Appendages can help a cell in various ways such as sensing the environment, finding food or mates or communicating with other cells. It helps if the appendage can move about. This in turn will move the cell a little. (Think of waving your arm under water). In an environment where swimming is advantageous, it is not surprising that the ability to swim would evolve. Never the less, as the evolution of vertebrate systems like the clotting cascade and the immune system has become better understood, ID proponents have come to rely more and more on swimming systems, especially the bacterial flagellum, as the real evidence for Design in nature.

 

The Bacterial Flagellum

Here it is -- the number one argument for design in nature. ID advocates have even made a movie called Bacterial Flagella: A Paradigm for Design. It is on sale at the ARN web site (30) and briefly discussed in talk.origins (31). Behe said recently:

Bacterial flagella are many, diverse, and complicated. Behe concludes that any bacterial flagellum is composed of at least three parts: a paddle, a rotor, and a motor, and so with swimming as the specified function must be IC (page 72). Even at this crude level, the ICness of a flagellum is not so clear. The problem is that there are additional parts to a complete flagellum. For instance, there are proteins at the base that react to external stimuli and turn the motor on and off, and in some flagella cause it to change directions. And there are other proteins that are arranged in rings where the flagellum passes through the cell membrane."If [biologist Jerry] Coyne demonstrated that the [bacterial] flagellum, (which requires approximately forty gene products) could be produced by selection, I would be rather foolish to then assert that the blood clotting system (which consists of about twenty proteins) required intelligent design". (32)

But the more interesting question is: could a flagellum be IC with proteins, not paddles etc. as parts? Remember, IC is supposed to be the biochemical challenge to evolution. We've already seen that it isn't such a challenge after all, but so much has been made of the purported ICness of the flagellum that one should be well informed on the subject just to be more interesting at parties . In order to decide, one must first choose a flagellum. Even within a single bacteria species, different strains may have different proteins and different numbers of proteins in their flagella. Even a single rod-shaped bacterium may have quite different flagella at its ends and around its sides. Next, discover and list all the proteins in that particular flagellum. This requires deciding just where it begins, and one's decision about this may depend on the exact function one has in mind for 'the' flagellum. Then comes the hard part: proving that every last protein is required for the function. Oddly, ID proponents show no interest in doing any of this work, not even picking a particular flagellum of a particular bacterium to start on. It is as if just asserting the ICness of 'the' flagellum gives them full satisfaction.

What's the answer? Is any flagellum IC with proteins as parts or not? As this would depend on arbitrary criteria, scientists have not pursued this question as such. But quite a bit has been learned about various flagella. It is clear that all of them absolutely require a good many of their proteins in order to function as swimming systems. But not one is yet known to require every last protein, and some are known not to (19, 33, 34). Could a flagellum be IC with proteins as parts? Sure. As we have seen in the much simpler case of hemoglobin, proteins can evolve to become codependent. There may be a perfectly IC flagellum out there just waiting to be discovered.

Even so, it wouldn't be the simplest swimming system. As the diagram shows, a bacterial flagellum is much more complex than an archaeal one. This is in part because it is built from, in fact secreted by what is called a type three secretion system (TTSS). This is a complicated thing in itself. It is a tiny tube which starts below the cell wall and sticks out through it, and serves as a conduit for protein export. The flagellar TTSS (there are other kinds) specializes in secreting the rest of a flagellum. The TTSS base counts as part of the flagellum, and is itself about as complex as an archaeal flagellum.

Since it is more complicated than is required for swimming alone, you might suspect that a bacterial flagellum has other functions. You would be right. These other functions vary from bacterium to bacterium and from situation to situation, and scientists have only recently been able to observe them. First, some flagella also export proteins, including ones that cause sickness (35). This is not too surprising since that's what the other TTSS's are known for.

But spirochetes, the spiral shaped bacteria, use flagella in a way one wouldn't expect. Their flagella don't stick out, yet are used for swimming, burrowing, and maintaining the cell's shape. Flagella are grown at both ends and extend toward the middle under the outer membrane. The flagella maintain the cell's spiral shape, and by rotating can create a moving wave along the cell, causing the cell to move in the opposite direction (19).

It is not easy to observe the behavior of individual bacteria in the wild. Just recently though, Danish researchers noticed some unusual behavior by bacteria living on low oxygen marine sediments. To see exactly what the bacteria were doing, they recreated the ecosystem in the laboratory. Who would have thought that some bacteria, shaped like slightly bowed rods, would tether themselves to the sediment with a mucus stalk secreted from the center and then use flagella at both ends to move like a propeller? But that's what these bacteria do. They create a tiny current, refreshing the water around them much faster than diffusion alone could do it (36).

Bacteria can move across surfaces in organized swarms, and quickly colonize a new food source such as your own much larger cells. When swarming, they often grow more flagella than usual and make cell-to-cell contacts with these flagella (37). Some bacteria also use their flagella to hang on to our cells as they try to break in and eat the cell contents (38).

This brings us to the dark side of design. Flagella participate in the cause of quite a few bacterial diseases, including diarrhea (38), ulcers and urinary tract infections (39). If the Designer is directly responsible for flagella then he is implicated as a cause of human diseases. Diarrhea is no joke; it is a leading cause of infant death in some parts of the world. To make matters worse, one can hardly give the Designer credit for flagella without also crediting him with TTSS's in general (40). This puts the Designer solidly behind Bubonic plague (41, 42) and many other diseases (43). Happily, science makes such beliefs unnecessary.

Swimming systems provide a good illustration of how (not) to think about evolution. Behe argues that evolution can't produce them because they are IC (a dubious claim and not an obstacle to evolution as we have seen). He buttresses this by arguing that is quite improbable that a swimming system good enough to be useful would appear all at once. And it wouldn't evolve slowly, he supposes, because until it became an effective swimming system, there would be nothing for natural selection to select. However, he envisions a part that sticks out, but that has no use at all other than swimming - and at first it can't even do that. But parts that stick out can have a number of functions, and bacterial flagella clearly have several. If there is another reason for it to be there, the sticking out part can gradually evolve more abilities. This involves change of function, or indirect evolution as Behe calls it. He dismisses this possibility, calling it improbable. A closer look shows the opposite.

 

The whole article is a good read, but I just zeroed in on the parts specific to the flagellum motor argument. 

 

Even if there is awareness in the micro world, that only seems to point towards a means by which gradual evolution works. The natural selection would be tied into awareness on micro levels. It might explain why everything looks so much like a nice little factory and so on on these micro levels. But what it doesn't seem to do is lend a hand to special creation. There's no evidence of special creation, not even the flagellum motor. All of the evidence keeps pointing back to gradual evolution.

 

That doesn't knock consciousness out of the picture entirely, it just shows how consciousness would have to operate through trial and error to make ever increasing better use of things. And since it's in everything (presumably), it then applies even to the dark side such as disease. The disease problem doesn't make any sense with respect to an advanced designing intelligence like God. That isn't how nature seems to work. God - or something like it which is a fully developed consciousness - is supposed to distinguish good from bad while consciousness ingrained into nature itself doesn't do that at all. It's in everything. Nothing is good or bad for that type of consciousness. It's just a driving force towards the perpetuation of all varieties of existence. There's no reason to assume that it wouldn't work through disease any more than anything else in existence. It's just this bubbling urge towards the perpetuation of existence and the ability for existence to experience itself on various levels, including from the subatomic to the very macro (refer back to the primacy of consciousness argument for details). 

 

None of this deeper mystical and metaphysical thinking on consciousness as more fundamental than space and matter seems to detract from or counter biological evolution as science has come to understand it. There's really no reason to take off trying to refute science unless you already have the preconceived idea that an external God created all living things via special creation fully functional in present form. And this is something that ought to be made known throughout the spiritual community for those who do not view God as something external and "other." Darwinian evolution is not a threat to the deeper seated mystical views. It need not be treated as one either. Because in the process of trying to refute graduation evolution and natural selection we find all variety of error and a path essentially leading further and further away from truth, rather than closer to it. I think the driving force behind all of this ID and IC is the wrongly supposed idea that it takes away from consciousness and awareness when it really doesn't. It just shows that whatever consciousness may turn out to be, it doesn't start out extremely "intelligent." Rather it has to struggle and work hard to achieve greater levels of intelligence. 

[BlackCat]

BC - oh, I can't blame you. The story of creationism and how it morphed into ID, how it wedged into schools, how it gained political power, how it is being used by fundie groups to push their feet in the door of non-Christians, and how it's being combated by various legitimate scientific groups and educational groups, is simply fascinating. I find the whole movement absolutely fascinating too. Nothing wrong with that. It's like being fascinated with the Tea Party (another movement whose sociology I also find fascinating).

 

Do I think anything they say has actual credence? Oh hell no. But I think that legitimate science can learn from how it's wormed its way into classrooms. Creationism's spokespeople definitely know how to speak to the unwashed, ignorant masses, whereas scientists, real ones, often have a lot of trouble articulating their findings and their revelations (there is no question in my mind why creationism's speakers are generally very eloquent and well-spoken, whereas the few eloquent scientists end up becoming rock stars because they're so damned rare)  .

 

Ahhhhh, Brian.........  (he's on the telly tonight- good ol' BBC)

 

I think that by examining the claims of creationism, namely the numerous fallacies and pseudo-science they routinely employ to demonstrate their ideas, non-scientists (meaning normal folks like me and you) end up learning a shitload about real science. Nothing teaches you better than learning enough about it to discover it's bullshit. So go ahead, be fascinated! Explore everything. There is nothing wrong with questioning and exploring.

 

ETA Oh wow I used the word fascinating a lot. Nothing was meant by it. I promise.

I'm always fascinated by something......it's good.  Life is certainly interesting...........