Protein Folding- Chance Or 'design'?

[sdelsolray]

...

I think we need to nail this issue with the motor.  A multi-part system (machine) like a motor has a specialised function.  That function will cease if the motor's sub parts are reduced to beyond the minimum parts required.  This is the case for a molecular motor and a man made motor.  A non functioning motor will then affect the system it is a part of, maybe in some cases rendering that whole system as 'broken' or unworkable. Can you see what I'm driving at?

As applied to living organisms, you are describing disease, not evolution.

[sdelsolray]

 

Michael Behe's testimony in the 2004 Dover vs. Kitzmiller case.

 

http://en.wikipedia.org/wiki/Michael_Behe#Dover_testimony

 

Dover testimony[edit]

Main article: Kitzmiller v. Dover Area School District

In Kitzmiller v. Dover Area School District, the first direct challenge brought in United States federal courts to an attempt to mandate the teaching of intelligent design on First Amendment grounds, Behe was called as a primary witness for the defense and asked to support the idea that intelligent design was legitimate science. Some of the most crucial exchanges in the trial occurred during Behe's cross-examination, where his testimony would prove devastating to the defense. Behe was forced to concede that "there are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred"^[42] and that his definition of 'theory' as applied to intelligent design was so loose that astrology would also qualify.^[43] Earlier during his direct testimony, Behe had argued that a computer simulation of evolution he performed with Snoke shows that evolution is not likely to produce certain complex biochemical systems. Under cross examination however, Behe was forced to agree that "the number of prokaryotes in 1 ton of soil are 7 orders of magnitude higher than the population [it would take] to produce the disulfide bond" and that "it's entirely possible that something that couldn't be produced in the lab in two years... could be produced over three and half billion years."^[42][44][45]

Many of Behe's critics have pointed to these exchanges as examples they believe further undermine Behe's statements about irreducible complexity and intelligent design. John E. Jones III, the judge in the case, would ultimately rule that intelligent design is not scientific in his 139-page decision, citing Behe's testimony extensively as the basis for his findings:

• "Consider, to illustrate, that Professor Behe remarkably and unmistakably claims that the plausibility of the argument for ID depends upon the extent to which one believes in the existence of God."^[46]
• "As no evidence in the record indicates that any other scientific proposition's validity rests on belief in God, nor is the Court aware of any such scientific propositions, Professor Behe's assertion constitutes substantial evidence that in his view, as is commensurate with other prominent ID leaders, ID is a religious and not a scientific proposition."^[46]
• "First, defense expert Professor Fuller agreed that ID aspires to 'change the ground rules' of science and lead defense expert Professor Behe admitted that his broadened definition of science, which encompasses ID, would also embrace astrology. Moreover, defense expert Professor Minnich acknowledged that for ID to be considered science, the ground rules of science have to be broadened to allow consideration of supernatural forces."^[47]
• "What is more, defense experts concede that ID is not a theory as that term is defined by the NAS and admit that ID is at best 'fringe science' which has achieved no acceptance in the scientific community."^[48]
• "We therefore find that Professor Behe's claim for irreducible complexity has been refuted in peer-reviewed research papers and has been rejected by the scientific community at large."^[49]
• "ID proponents primarily argue for design through negative arguments against evolution, as illustrated by Professor Behe's argument that 'irreducibly complex' systems cannot be produced through Darwinian, or any natural, mechanisms. However, … arguments against evolution are not arguments for design. Expert testimony revealed that just because scientists cannot explain today how biological systems evolved does not mean that they cannot, and will not, be able to explain them tomorrow. As Dr. Padian aptly noted, 'absence of evidence is not evidence of absence.'… Irreducible complexity is a negative argument against evolution, not proof of design, a point conceded by defense expert Professor Minnich."^[50]

 

 

• "Professor Behe's concept of irreducible complexity depends on ignoring ways in which evolution is known to occur. Although Professor Behe is adamant in his definition of irreducible complexity when he says a precursor 'missing a part is by definition nonfunctional,' what he obviously means is that it will not function in the same way the system functions when all the parts are present. For example in the case of the bacterial flagellum, removal of a part may prevent it from acting as a rotary motor. However, Professor Behe excludes, by definition, the possibility that a precursor to the bacterial flagellum functioned not as a rotary motor, but in some other way, for example as a secretory system."^[51]

 

 

• "Professor Behe has applied the concept of irreducible complexity to only a few select systems: (1) the bacterial flagellum; (2) the blood-clotting cascade; and (3) the immune system. Contrary to Professor Behe's assertions with respect to these few biochemical systems among the myriad existing in nature, however, Dr. Miller presented evidence, based upon peer-reviewed studies, that they are not in fact irreducibly complex."^[52]
• "In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty-eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not "good enough."^[53]
• "With ID, proponents assert that they refuse to propose hypotheses on the designer's identity, do not propose a mechanism, and the designer, he/she/it/they, has never been seen. ... In addition, Professor Behe agreed that for the design of human artifacts, we know the designer and its attributes and we have a baseline for human design that does not exist for design of biological systems. Professor Behe's only response to these seemingly insurmountable points of disanalogy was that the inference still works in science fiction movies."^[54]

 

Behe has been, and remains, a creationist whore.

[sdelsolray]

BlackCat,

 

Take a look at this 2 minute video.  Dr. Kenneth Miller actually made a similar demonstration at the Dover trial by appearing on the witness stand using the mousetrap for a tie clip.  It garnered laughs from those present, including Judge Jones.  There's a video somewhere with the actual event (Miller getting on the witness stand with a partial mousetrap as a tie clip) but I couldn't find it.

 

The video demonstrates that a device with fewer parts can have an alternative function.

 

https://www.youtube.com/watch?v=rW_2lLG9EZM

[bornagainathiest]

Here's another link for you to follow up, BC.

 

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

 

Please compare this...

 

"Among some creationists, the cave tetra is evidence 'against' evolution.  One argument claims this is an instance of 'devolution' - showing an evolutionary trend of decreasing complexity.  But evolution is a non-directional process, and while increased complexity is a common effect, there is no reason why evolution cannot trend towards simplicity if that makes an organism better suited to it's environment."

 

To this...

 

"In fact, on cross-examination Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system.  He was presented with fifty-eight peer-reviewed publications, nine books, and several immunology textbooks about the evolution of the immune system; however he simply insisted that this was not sufficient evidence of evolution, and that it was not "good enough."

.

.

.

See the pattern?

Creationists like Behe have pre-decided the issue of evolution's viability by religious faith, not scientific evidence.  (See Hebrews 11 : 1 - 3)  So no amount of scientific evidence that conflicts with their faith will ever be 'good enough' for them. 

 

And this is why Behe is held in such low regard by his peers, BC.

He begins from a pre-decided, faith-based position on the issue of evolution and then rejects any evidence which conflicts with it.  Which is about as unprofessional as a scientist can get, short of outright fraud.

 

As per the Hebrews quote, Behe doesn't see that which he believes by faith to be real.

 

Yet the evidence he does see (58 publications, 9 books, etc.) he dismisses.

 

'nuff said? 

 

 

 

Thanks,

 

BAA.

 

 

 

 

 

[BlackCat]

Hey guys, great replies.   Much food for thought.  I had a terrible night's sleep last night, as all this stuff was going round in my head, so my brain is a bit slow today, so may take me a day or two to read through those links BAA.    

 

Sdelsolray, I have watched the Miller videos on You tube a few years back.  I've emailed Kenneth Miller in the past and have read his book 'Finding Darwin's God' but thank you for reminding me of it.

 

RogueScholar, I don't think I've conveyed to you the points that I am struggling with, although it may be that I am not grasping your answers, which is the likeliest cause.  

 

Three key points have been highlighted by you guys:

 

Sdelsolray: you mentioned 'goal'.   I wasn't implying that humans are the 'end goal' but rather certain machines like a motor imply a prior template or prior intention or design.

 

BAA: you said I should be sceptical about intelligent design and scientific sounding arguments.  This is what I am being, I hope.

 

RougeScholar: you hit the nail on the head when you mentioned my 'intuition'. 

 

I think it's clear that the driving force behind my thinking on this matter is my intuition.  I may not understand how or why a protein folds and so by focusing on the end result e.g. a molecular machine, I apply a certain reasoning- like seeing a 'goal' or a pre-intended function and all this kills any scepticism that should arise maybe??  Now I know my intuition was wrong about a 'heavenly Father' and yet I trusted it for most of my life,  and so I am forced to be suspicious of it now as regards intelligent design.  Molecular machines look intelligently designed.  Why do they look intelligently designed?  That is what I am trying to get to the bottom of.

[RogueScholar]

What makes them look intelligently designed? Evolution has shaped how organisms have developed. The proteins that animals have are evolved to work in a certain environment under certain selection pressures. if they don't work well enough to compete the animal dies off. This is why the basic components of cell respiration are nearly universal among animals. It just works and allows animals to live long enough to breed and pass said mechanisms along to their off spring.

[BlackCat]

BAA, I've started looking through those links.  The second one from Ken Miller's Home Page is very interesting.  I've been checking some things he raises and which I have found strange in the past so hopefully we can put the issue of IC to bed once and for all. 

 

I need us all to agree on what irreducible complexity means because it certainly doesn't seem to mean what Ken Miller is saying it means in that article.  

 

My understanding of an irreducibly complex system, is that it is comprised of a minimum number of parts which are ALL needed in order for a system with a specific function to function.  If we use that worn out ridiculed example of a mouse trap as it is nice and simple and the one Miller MISUSES, then by removing a couple of parts of the mouse trap to form a tie clip, this renders the mousetrap inoperable.   Who is saying that each component part of a system cannot function elsewhere?  If Behe or his buddies are saying this, then they are wrong of course, but I don't think they are saying this.  The same argument applies to Ken Miller's use of the Type III SS.  If you take away the parts of the flagellar motor that leave you with another machine: the Type III SS, then you no longer have the motor.  

 

I contend that systems can be irreducibly complex and the mousetrap is a simple example of IC, and a motor (molecular or man-made) is a more complex example of IC. 

 

Do you agree? 

[bornagainathiest]

BAA, I've started looking through those links.  The second one from Ken Miller's Home Page is very interesting.  I've been checking some things he raises and which I have found strange in the past so hopefully we can put the issue of IC to bed once and for all. 

 

I need us all to agree on what irreducible complexity means because it certainly doesn't seem to mean what Ken Miller is saying it means in that article.

 

My understanding of an irreducibly complex system, is that it is comprised of a minimum number of parts which are ALL needed in order for a system with a specific function to function.  If we use that worn out ridiculed example of a mouse trap as it is nice and simple and the one Miller MISUSES, then by removing a couple of parts of the mouse trap to form a tie clip, this renders the mousetrap inoperable.   Who is saying that each component part of a system cannot function elsewhere?  If Behe or his buddies are saying this, then they are wrong of course, but I don't think they are saying this.  The same argument applies to Ken Miller's use of the Type III SS.  If you take away the parts of the flagellar motor that leave you with another machine: the Type III SS, then you no longer have the motor.  

 

I contend that systems can be irreducibly complex and the mousetrap is a simple example of IC, and a motor (molecular or man-made) is a more complex example of IC. 

 

Do you agree? 

 

Before I answer that question BC, there's something I'd like to draw your attention to, concerning your previous post.

 

Please compare and contrast these two extracts from it.

 

"BAA: you said I should be sceptical about intelligent design and scientific sounding arguments.  This is what I am being, I hope."

 

"I think it's clear that the driving force behind my thinking on this matter is my intuition.  I may not understand how or why a protein folds and so by focusing on the end result e.g. a molecular machine, I apply a certain reasoning- like seeing a 'goal' or a pre-intended function and all this kills any scepticism that should arise maybe??  Now I know my intuition was wrong about a 'heavenly Father' and yet I trusted it for most of my life,  and so I am forced to be suspicious of it now as regards intelligent design.  Molecular machines look intelligently designed.  Why do they look intelligently designed?  That is what I am trying to get to the bottom of."

 

Skepticism and intuition are rather strange bedfellows, wouldn't you say, BC?

 

The first takes nothing that isn't evidence-based for granted and relies on reason to guide it.

The second doesn't rely on evidence at all and draws conclusions without the use of reason.

 

Mutually incompatible, wouldn't you say?

 

So what should be the driving force behind your thinking on ID and IC?  Intuition?  Or skepticism?  

What is the default position for a skeptic on ID and IC?  An intuited belief or beliefs about them?  Or the blank page of disbelief?

 

Please consider these questions carefully, BC.

 

Thanks,

 

BAA.

[bornagainathiest]

I hope this helps highlight the problem, BC.

Please don't get upset!  This isn't personal or a cheap shot at you.  I'm just trying to illustrate something.

 

Here's a sentence that I wrote about Michael Behe in post # 29.

 

"Creationists like Behe have pre-decided the issue of evolution's viability by religious faith, not scientific evidence."

 

Now I'm going to change a few words.

 

"BlackCat has pre-decided that molecular machines look designed by intuition, not scientific evidence."

 

See the problem?

 

Neither Behe nor BlackCat are beginning from a position of skepticism on the issues in question.  

Neither of them are using methods (faith or intuition) that are compatible with skepticism.  

Faith doesn't require evidence to draw conclusions.  

Intuition doesn't require evidence to draw conclusions.  

 

But skepticism uses ONLY evidence to draw conclusions. 

 

Oil and water don't mix!

 

Thanks,

 

BAA.

[sdelsolray]

BAA, I've started looking through those links.  The second one from Ken Miller's Home Page is very interesting.  I've been checking some things he raises and which I have found strange in the past so hopefully we can put the issue of IC to bed once and for all. 

 

I need us all to agree on what irreducible complexity means because it certainly doesn't seem to mean what Ken Miller is saying it means in that article.

 

My understanding of an irreducibly complex system, is that it is comprised of a minimum number of parts which are ALL needed in order for a system with a specific function to function.  If we use that worn out ridiculed example of a mouse trap as it is nice and simple and the one Miller MISUSES, then by removing a couple of parts of the mouse trap to form a tie clip, this renders the mousetrap inoperable.   Who is saying that each component part of a system cannot function elsewhere?  If Behe or his buddies are saying this, then they are wrong of course, but I don't think they are saying this.  The same argument applies to Ken Miller's use of the Type III SS.  If you take away the parts of the flagellar motor that leave you with another machine: the Type III SS, then you no longer have the motor.  

 

I contend that systems can be irreducibly complex and the mousetrap is a simple example of IC, and a motor (molecular or man-made) is a more complex example of IC. 

 

Do you agree? 

 

Behe provided his own definition of IC:

 

 

An irreducibly complex structure is defined as " ... a single system composed of several well matched,

interacting parts that contribute to the basic function, wherein the removal of anyone of the parts causes the system to effectively cease functioning." (Behe 1996a, 39):

 

"An irreducibly complex system cannot be produced directly by numerous, successive, slight modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. .... Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on." (Behe 1996b)

 

As Behe (2002) wrote: " ... natural selection can only choose among systems that are already

working," and an irreducibly complex system does not work unless all of its parts are in place.

The flagellum is irreducibly complex, and therefore, it must have been designed.

 

Source (Expert Statement of Kenneth R. Miller pp 13-14 of the .pdf, entered into evidence in the Dover trial):

 

http://ncse.com/files/pub/legal/kitzmiller/expert_reports/2005-03-30_Miller_expert_report_P.pdf

 

Then he applies it to biological evolution claiming natural selection cannot be responsible for the formation of a particular IC item because the precursor lacks the final function of the final IC item.  He conveniently leaves out and ignores the possible functionality of the precursors.  This is fatal to his argument.  Moreover, under Behe's definition (which, by the way, has not been adopted by science - only by the Discovery Institute Mafia), an H2O water molecule is irreducibly complex.  Remove a hydrogen atom and form an OH molecule, and, voila, it no longer functions as water.  Remove a proton from an Argon atom (an inert gas with no functionality) and you end up with a Chlorine atom (which has all kinds of functionality).  Behe's definition is so insightful and helpful.

 

Yes, a mousetrap with two of the five components removed no longer functions as a mousetrap, but it functions as a tie clip, or a paper clip, or a great spitball launcher.  That is all that is required for natural selection to operate.

 

Again, you are goal-minded, just as Behe is.  For example, you (and Behe) assume the biochemical flagellum motor in certain bacteria was the ultimate direction/purpose/end-game for evolution, and, since the end result is IC (according to Behe's faulty definition), then it could not have evolved.  That's simply wrong.  The biological theory of evolution makes no such claim or prediction.  You are chasing a strawman argument.  Behe's intentional avoidance of precursor functionality demonstrates a rather narrow and myopic intellect or, more likely, a duplicitous and intentional motive to deceive the gullible with his brand of pseudoscience.

[BlackCat]

This is so annoying that I can't quote replies or cut and paste replies......

 

BAA- you haven't offended me or upset me at all.  You know I value your opinions and everyone else's  and I am learning to not be so sensitive to criticism that I know is intended for good.

 

I now see that I have long misunderstood what 'intuition' actually is.  I  thought intuition was where you sense something but don't know why, or your mind is telling you something but it's coming from the sub-conscious and so it seems like this 'knowledge' has popped out of no where but in fact you are reacting to something that you do have some knowledge of but maybe the knowledge is fragmented too much and so your mind puts them together to give you that 'instinct' about something.  So apologies for misunderstanding and misapplying the word 'intuition'.  Sh*t!  Maybe I've used 'instinct' wrong as well.................................................    

 

So,  I am being sceptical about how evolution can produce living things that SEEM to be irreducibly complex and because of my limited knowledge of chemistry etc, I am relying on other kinds of reasoning  that  I do understand e.g spotting a design.  I am putting faith in my ability to reason because my reasoning in matters like spotting a sandcastle from a lump of muddy sand caused by pebbles, drift wood and the waves, has not let me down.  But I am aware that the brain can fill in gaps and cause something to seem to be there, in order to make sense and hence I am sceptical about irreducible complexity. 

 

You mentioned Behe and me as being guilty of not starting from a position of scepticism.  That may be the case, but Ken Miller's article you linked to (the second link) in post 24, addresses that concern, or rather he seems to allow for ID/IC to be understood to be coming from a scientific foundation and not a faith based or religiously motivated one.  I'll pause for now as my son needs the laptop, and I will re-read Miller's article later to make sure I've understood what he is saying.   Speak later.

 

Edit: 

 

Sdelsolray, thank you for your very interesting post.  I'll come back to you later.

 

RogueScholar, thank you for your reply regarding why things look like they've been designed.  No doubt we can pursue that some more once we sort out IC. Cheers.

[bornagainathiest]

This is so annoying that I can't quote replies or cut and paste replies......

 

BAA- you haven't offended me or upset me at all.  You know I value your opinions and everyone else's  and I am learning to not be so sensitive to criticism that I know is intended for good.

 

I now see that I have long misunderstood what 'intuition' actually is.  I  thought intuition was where you sense something but don't know why, or your mind is telling you something but it's coming from the sub-conscious and so it seems like this 'knowledge' has popped out of no where but in fact you are reacting to something that you do have some knowledge of but maybe the knowledge is fragmented too much and so your mind puts them together to give you that 'instinct' about something.  So apologies for misunderstanding and misapplying the word 'intuition'.  Sh*t!  Maybe I've used 'instinct' wrong as well.................................................    

 

So,  I am being sceptical about how evolution can produce living things that SEEM to be irreducibly complex and because of my limited knowledge of chemistry etc, I am relying on other kinds of reasoning  that  I do understand e.g spotting a design.  I am putting faith in my ability to reason because my reasoning in matters like spotting a sandcastle from a lump of muddy sand caused by pebbles, drift wood and the waves, has not let me down.  But I am aware that the brain can fill in gaps and cause something to seem to be there, in order to make sense and hence I am sceptical about irreducible complexity. 

 

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

Spotting a design is not the default position for skepticism.  The choice to 'spot' depends on having a predetermined idea of what a design is and what something 'designed' should look like.  The default position for a skeptic is not to go out looking for a design but to look at the evidence first and see what it tells you.

 

Assuming the conclusion (what a design should look like) is not what skeptics do.  

 

You mentioned Behe and me as being guilty of not starting from a position of scepticism.  That may be the case, but Ken Miller's article you linked to (the second link) in post 24, addresses that concern, or rather he seems to allow for ID/IC to be understood to be coming from a scientific foundation and not a faith based or religiously motivated one.  I'll pause for now as my son needs the laptop, and I will re-read Miller's article later to make sure I've understood what he is saying.   Speak later.

 

But look at the Wiki court transcript of what the judge had to say about Behe's motivation, BC.

Miller (quite properly) confines himself to the science involved and says little about why Behe does what he does.  Whereas the judge's summary is damning!  Please read what judge Jones' has to say about why Behe needed to 'redefine' what science is.

 

Because Behe is working from a creationist script he necessarily has to redefine what science is to include the supernatural.  

If he stuck with the proper definition of science from get go then he wouldn't be able to that.  His religious faith doesn't allow him to begin from the blank page of skepticism - which is what all trustworthy and professional scientists do.

 

Here's a worked example of what I mean.

 

http://en.wikipedia.org/wiki/Abdus_Salam (a devout Muslim) 

http://en.wikipedia.org/wiki/Steven_Weinberg (an atheist) 

http://en.wikipedia.org/wiki/Sheldon_Lee_Glashow (a humanist, from an orthodox Jewish background)

 

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

 

These three men did not bring their personal beliefs, religion or philosophies into their scientific work. They did not need to redefine the meaning and workings of science to conform to their faith.  Instead they did the right and proper and professional thing and put their beliefs to one side.  Something which Behe refuses to do.  Instead, he forces science to be redefined to suit his faith.

 

Not skeptical!  Not scientific!  

 

Edit: 

 

Sdelsolray, thank you for your very interesting post.  I'll come back to you later.

 

RogueScholar, thank you for your reply regarding why things look like they've been designed.  No doubt we can pursue that some more once we sort out IC. Cheers.

[BlackCat]

BAA, I can't speak for Behe, but I DID NOT go out looking for a design.  When I first saw pictures of a molecular machine I was instantly blown away.  In a split second my brain had computed from information it had garnered throughout my life, that I was looking at a designed thing.  Now it's true that because I am not scientifically trained in any way and my critical thinking skills have been f***ed  up by religion, I am guilty of easily accepting that it's a design i.e. I have failed to be sceptical or no alarm bells have gone off in order for me to know to be sceptical.  But, over time, along with the realisation I had been so egregiously wrong about God etc, I started to ponder on why only religious people champion intelligent design?  Also, the fact that the scientists who support ID are very few indeed and are usually religious.  And so a healthy scepticism has started to grow I hope.    

 

So, as we explore IC, no doubt you guys will remind me and help me with any errors I make in terms of my thinking/reasoning, hopefully bringing out biases that are down to prior religious beliefs or lack of scientific knowledge.  Are we ready to proceed? 

[RogueScholar]

Again, your intuition is creating significant bias. Your mind was blown by looking at one of these proteins. That is okay. However, this idea that you can break a molecule down into easily identified components is simply not correct.

 

I want to take you down another path if I may. Are you familiar with the concept of a chemical bond? Do you believe that a chemical bond is one of the components that make up these "machines?"

[Burny]

BAA, I can't speak for Behe, but I DID NOT go out looking for a design.  When I first saw pictures of a molecular machine I was instantly blown away.  In a split second my brain had computed from information it had garnered throughout my life, that I was looking at a designed thing.  

 

But this shouldn't surprise you? Humans invented gods and religions for a reason. Every time they looked at the world around them, it was a scary, beautiful, designed place - how could it be anything else? Than Darwin came along and stood everything on it's head.

 

A snowflake HAS to be designed right? But it's not. It can be explained and replicated quite easily.

 

The human brain is an amazing organ. It leaps to conclusions really fast, because 100,000 years ago it had to make judgments about reality really quick or it would be a lion's snack. We still make the mistake of leaping to conclusions because we think they make sense, when in reality that is an illusion.

 

You should read up on how much of a liar your brain really is. It's a fascinating (and disturbing) subject.

[bornagainathiest]

BlackCat,

 

You say that you didn't go out looking for a design.  Ok, I shouldn't have written that about you.  My bad for not wording my message correctly.  Sorry about that.  What I should have written was something along these lines.

 

At the time that you first saw an image of a molecular machine, there were things happening in your mind that you weren't aware of.  

You weren't aware that evolution has wired your brain to see patterns and designs where none exist.  You also weren't aware that you do this subconsciously, without applying any kind of critical thinking to the conclusions your brain has come to.  You weren't aware of your pareidolia, your confirmation bias and your motivated reasoning.

 

This list isn't a personal criticism of you BC.

ALL of the above happens to ALL of us - because that's the way the human brain has evolved.  But thru training and self-awareness we can become aware of the tricks our brains play on us. Skepticism and critical thinking are major tools in this process.  So perhaps it's best if I draw your attention to what an arch-skeptic has to say about the snares our brains set for us.  Over to Michael Shermer.  (This is the kind of reading Burny has suggested, btw.  Thanks, Burny!)

 

 http://www.scientificamerican.com/article/patternicity-finding-meaningful-patterns/

 

http://www.scientificamerican.com/article/skeptic-agenticity/

 

As I understand it, what happens is this.

Our brains are built to see patterns, but we're apt to see patterns where none actually exist.  This is pareidolia at work.

http://en.wikipedia.org/wiki/Pareidolia  Once we've convinced ourselves that this pattern is real, our brains then take the self- delusion a step further, using confirmation bias. http://skepdic.com/confirmbias.html Now we see confirmation of our original (and false) conclusion because our brains preferentially filter what we see, emphasizing the pattern we thought we saw and de-emphasizing everything else.  When our emotions become involved, this leads to motivated reasoning.  http://en.wikipedia.org/wiki/Motivated_reasoning And many, if not most people are totally unaware that these three, linked processes are happening in their brains.

 

So I'm not selecting you out for unwarranted criticism, BC.

We ALL suffer from these glitches in our thinking and it's only thru recognizing them and knowing how they subtly influence us that we can cope with and compensate for them.  However, I'm quite confident that when you first saw an image of a molecular machine, these mechanisms swung into action in your brain without you even knowing it.  

 

Thanks,

 

BAA.

 

 

[BlackCat]

RogueScholar, to quote Richard Feynman: ''everything is made of atoms'' and having just had a cursory glance at what a chemical bond is, then yes, chemical bonding must occur with molecular machines at the atomic level.   Now I don't think I said you can break a MOLECULE down into easily identified compounds.  I said you can break a 'machine' down into 'parts'.  When I say 'molecular machine' I'm not referring to individual molecules but the mass collection of proteins that form the machine'.

 

I don't think it's necessary to understand the chemical composition of a machine, in order to understand that a collection of molecules or rather proteins are arranged in such a way that a REAL MACHINE is formed and not something that seems to resemble a machine by its 'appearance'. 

 

 

Burny, thank you for your response.   Yes, it is very interesting to discover all the ways our brains can trick us.

 

BAA, no need to apologise.    I've checked those links.  Thank you.  About a year ago I got wise to how my brain has been tricking me all these years.  I had a major operation beginning of 2014.  I had some very strong pain killers which I didn't really bother with.  One day though I was struggling so I took two and gave it no more thought.  About half an hour or an hour later I was praying and I had this wonderful feeling come over me. It didn't last long but I assumed it was spiritual and me connecting with God in some way.  Then those painkillers popped into my head.  Hang on.  I'd not long taken two very strong co-codamol and I suddenly realised that I'd had a mild 'high' off them.  It just so happened that the timing of the prayers with this 'high' coincided. I'd falsely connected the two things.  It hit me very forcefully the realisation that I'd been doing this all my life: associating God with coincidences, feelings caused by hormone fluctuations, all manner of ways of falsely connecting the spiritual with perfectly natural things.   Yesterday I was walking through the woods and in the distance I could see a 'person'.  As I got nearer I could see it was a tree with a sign near it.  The light and shade and distant view etc had all come together to make the shape of a person, just like the 'faces on Mars'.  But................

 

I'm struggling to follow how this applies to molecular machines.   That maybe because there are TWO parts to this mystery.  Unlike the faces on Mars, or the 'person' in the distance, molecular machines can be studied up close and taken apart and put back together etc.  We're not dealing with half the facts (as far as determing what it is).  We are dealing with a REAL MACHINE.  The second part to this is (if I can put it crudely)  what is a machine doing being found under a microscope?  It's not the case that scientists having found these machines then discovered that they only look like machines (i.e the face on Mars). 

 

The big question is:

 

If we are dealing with a REAL MACHINE (which we are) then how did it manage to assemble without any element of design? 

 

Please watch that Ted video I mentioned.  It's called ''The Protein folding problem: a major conundrum of science: Ken Dill'' to get an appreciation for these real machines.

 

Edit:

 

I understand that  'design' seems an impossible consideration when discussing evolution/molecular machines and this is where the accusation of the brain arriving at a wrong conclusion comes about.  I don't see any way out of avoiding the 'design' conclusion that my mind is making.  A 'machine' always means design surely? Please help me to see where I am going wrong.

[bornagainathiest]

 

 

BAA, no need to apologise.    I've checked those links.  Thank you.  About a year ago I got wise to how my brain has been tricking me all these years.  I had a major operation beginning of 2014.  I had some very strong pain killers which I didn't really bother with.  One day though I was struggling so I took two and gave it no more thought.  About half an hour or an hour later I was praying and I had this wonderful feeling come over me. It didn't last long but I assumed it was spiritual and me connecting with God in some way.  Then those painkillers popped into my head.  Hang on.  I'd not long taken two very strong co-codamol and I suddenly realised that I'd had a mild 'high' off them.  It just so happened that the timing of the prayers with this 'high' coincided. I'd falsely connected the two things.  It hit me very forcefully the realisation that I'd been doing this all my life: associating God with coincidences, feelings caused by hormone fluctuations, all manner of ways of falsely connecting the spiritual with perfectly natural things.   Yesterday I was walking through the woods and in the distance I could see a 'person'.  As I got nearer I could see it was a tree with a sign near it.  The light and shade and distant view etc had all come together to make the shape of a person, just like the 'faces on Mars'.  But................

 

I'm struggling to follow how this applies to molecular machines.   That maybe because there are TWO parts to this mystery.  Unlike the faces on Mars, or the 'person' in the distance, molecular machines can be studied up close and taken apart and put back together etc.  We're not dealing with half the facts (as far as determing what it is).  We are dealing with a REAL MACHINE.  The second part to this is (if I can put it crudely)  what is a machine doing being found under a microscope?  It's not the case that scientists having found these machines then discovered that they only look like machines (i.e the face on Mars). 

 

BlackCat,

 

Just think for a moment about the process that goes on when your brain tells you you're seeing something in a random pattern that's not really there.  Does your brain tell you that this random pattern looks like something you're unfamiliar with or does it tell you that it looks like something you're familiar with?  The answer is, of course, that your brain will always do the second.  It searches thru what you've already experienced and what you already know and tries to find a 'best fit' with what you're familiar with.  

 

That which you don't know and haven't experienced can't, by definition, be available to your brain to make a best fit out of the random pattern you're seeing.  Nobody can recall or remember that which isn't already stored in their memory.  So when you see something new and unfamiliar, your brain automatically tries to make sense of it out with what you are familiar with.  Do you see where I'm going with this?  Up until the moment you first saw an image of a molecular machine, your brain had nothing to go to make sense of what you were seeing.  

 

Now let's try a test, BC.  Is this an image of something 'designed' by an intelligent mind?

 

 

 

 

 

It certainly looks as if it's designed by an intelligence.  

It's symmetrical from every p.o.v.  It's regular in shape.  Every sphere links up to the same number (3) of rods.  The angle between each rod is always 120^o.  The hexagons and pentagons meet each other precisely, without any overlap or distortion.  On a humanocentric level it resembles the geodetic domes that house radars at airports.  Or perhaps a climbing frame for kids.  It also looks a bit like a soccer ball. Surely this must be an artifact designed by a mind to perform a special function or purpose!

 

But it isn't.    

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

"Buckminsterfullerene is the most common naturally occurring fullerene molecule, as it can be found in small quantities in soot.^[3][4] Solid and gaseous forms of the molecule have been detected in deep space.^[5]"

 

It's a naturally-occurring molecule, BC.

It's not artificial.  It's natural.  It's not designed.  It just happens to be formed in this way by the laws of nature, acting blindly and without purpose or design.  We only think that it's been designed because our brains are fooling us again.  Whenever we see something like this molecule our brains trick us into thinking that this couldn't possibly have come about by purely natural means.  But the evidence says otherwise.

 

And this is why you mustn't heed what your brain tells you BC, but you must always look at the evidence before drawing a conclusion.

 

The big question is:

 

If we are dealing with a REAL MACHINE (which we are) then how did it manage to assemble without any element of design? 

 

Please watch that Ted video I mentioned.  It's called ''The Protein folding problem: a major conundrum of science: Ken Dill'' to get an appreciation for these real machines.

 

Edit:

 

I understand that  'design' seems an impossible consideration when discussing evolution/molecular machines and this is where the accusation of the brain arriving at a wrong conclusion comes about.  I don't see any way out of avoiding the 'design' conclusion that my mind is making.  A 'machine' always means design surely? Please help me to see where I am going wrong.

 

You are going wrong BC, because when you think about evolution, you must first check your preconceptions in at the door.  Evolution is a branch of the life sciences and no branch of science is ever permitted to introduce supernatural explanations into what is being studied, investigated and observed.

 

Science is agnostic, not theistic.

It studies only natural phenomenon.  By definition, the supernatural is always excluded from science.  It's not within the remit of science to acknowledge the existence of the supernatural, let alone study it or offer it up as an explanation for what is being observed.

 

This explains why Behe seeks to redefine science and allow the supernatural into it.

He knows full well that if he were to conduct himself properly, as a bona fide scientist, there would be no place for ID or IC in his scientific work.  Once again BC, please go back to the court proceedings of Dover vs. Kitzmiller and see how Behe violated the ground rules of science in the name of his particular preconception - Christianity.

 

You too are bringing your preconceptions into the mix if you allow your judgement to be swayed by anything other than the scientific evidence, seen only within the context of science.  If the evidence is scientific, then any conclusion you draw from it MUST be agnostic, not theistic.  Even if scientists call these things REAL machines and they look like REAL machines - scientists should not and must not attribute their existence to a supernatural designer.  That is not permitted within science!  Once they do that they've ceased to be professional scientists, just as Behe has ceased to be one.

 

If you want to stay within science, then you must stay within the rules of science, BC.

 

So the big question should be re-worded like this.

 

Q.

If we are dealing with REAL MACHINES, is it scientific to invoke an unscientific explanation (a supernatural designer) to explain them?

 

A.

No.  A scientific understanding of molecular machines must stay strictly within the context of science.  Anything else simply isn't science.  Therefore science can only conclude that these things are the products of natural processes, not the products of supernatural design.

 

Thanks,

 

BAA.

[EyesOpened]

RogueScholar, to quote Richard Feynman: ''everything is made of atoms'' and having just had a cursory glance at what a chemical bond is, then yes, chemical bonding must occur with molecular machines at the atomic level.   Now I don't think I said you can break a MOLECULE down into easily identified compounds.  I said you can break a 'machine' down into 'parts'.  When I say 'molecular machine' I'm not referring to individual molecules but the mass collection of proteins that form the machine'.

 

I don't think it's necessary to understand the chemical composition of a machine, in order to understand that a collection of molecules or rather proteins are arranged in such a way that a REAL MACHINE is formed and not something that seems to resemble a machine by its 'appearance'. 

 

 

Burny, thank you for your response.   Yes, it is very interesting to discover all the ways our brains can trick us.

 

BAA, no need to apologise.    I've checked those links.  Thank you.  About a year ago I got wise to how my brain has been tricking me all these years.  I had a major operation beginning of 2014.  I had some very strong pain killers which I didn't really bother with.  One day though I was struggling so I took two and gave it no more thought.  About half an hour or an hour later I was praying and I had this wonderful feeling come over me. It didn't last long but I assumed it was spiritual and me connecting with God in some way.  Then those painkillers popped into my head.  Hang on.  I'd not long taken two very strong co-codamol and I suddenly realised that I'd had a mild 'high' off them.  It just so happened that the timing of the prayers with this 'high' coincided. I'd falsely connected the two things.  It hit me very forcefully the realisation that I'd been doing this all my life: associating God with coincidences, feelings caused by hormone fluctuations, all manner of ways of falsely connecting the spiritual with perfectly natural things.   Yesterday I was walking through the woods and in the distance I could see a 'person'.  As I got nearer I could see it was a tree with a sign near it.  The light and shade and distant view etc had all come together to make the shape of a person, just like the 'faces on Mars'.  But................

 

I'm struggling to follow how this applies to molecular machines.   That maybe because there are TWO parts to this mystery.  Unlike the faces on Mars, or the 'person' in the distance, molecular machines can be studied up close and taken apart and put back together etc.  We're not dealing with half the facts (as far as determing what it is).  We are dealing with a REAL MACHINE.  The second part to this is (if I can put it crudely)  what is a machine doing being found under a microscope?  It's not the case that scientists having found these machines then discovered that they only look like machines (i.e the face on Mars). 

 

The big question is:

 

If we are dealing with a REAL MACHINE (which we are) then how did it manage to assemble without any element of design? 

 

Please watch that Ted video I mentioned.  It's called ''The Protein folding problem: a major conundrum of science: Ken Dill'' to get an appreciation for these real machines.

 

Edit:

 

I understand that  'design' seems an impossible consideration when discussing evolution/molecular machines and this is where the accusation of the brain arriving at a wrong conclusion comes about.  I don't see any way out of avoiding the 'design' conclusion that my mind is making.  A 'machine' always means design surely? Please help me to see where I am going wrong.

I can not speak for BAA but i think i understand what he is saying to you. He isnt applying his response to you about molecular machine. His response to you is to show you how YOU ARE APPROACHING THE PROCESS of putting a MM together. I think i could be wrong but it is kind of like looking at it in hind sight. Do you think when the wheel was invented that the inventor had a car in mind for the final result or was it more simple than that?

[RogueScholar]

How are these molecules arranged? Is it not the result of chemical bonding and intermolecular forces? You seem to have developed an arbitrary set of rules. We agreed earlier that chemical evolution can give rise to complex molecules and that chemistry underpins the process. Why would you now ignore this? Chemistry is a direct extension of physics and physics explains natural processes.

[BlackCat]

Agghhhhhh........just lost my reply that took me half an hour to type. You basket! 

 

In a nut shell guys, I've got it.  Really. 

 

RogueScholar, you started the process by introducing chemical evolution.  For some reason what the fatty acids didn't do, BAA's beautiful molecule did. (I'm sure fatty acids are beautiful too).  I'm rather slow at grasping things. 

 

BAA, I applied the same logic to that molecule as I had done to the 'motor'.  I can't deny that natural processes formed that molecule.  Why should I then suppose that a more complex structure of molecules, needs any other kind of help?  See, I certainly wasn't trying to attribute a theistic God to this 'other kind of help'.  I didn't even want to think of this help (design) as supernatural. So I don't know what it could have been, other than the natural processes it is.  Your molecule has helped me to see this now. 

 

It is no coincidence that the timing of this breakthrough has happened since I have been free of Christianity and the associated beliefs.  As you know BAA, we tried to thrash this same topic out a couple of years back but I wasn't free of the God virus then and so I wasn't able to get to first base with really understanding this stuff.

 

Thank you thank you guys for all your help.  Please continue to sow your seeds of truth.  If you see me slipping into wrong thinking, please tell me. 

[bornagainathiest]

Well done, BC!  

 

You've just climbed Mt. Improbable.  http://en.wikipedia.org/wiki/Climbing_Mount_Improbable

 

The gist of Dawkin's argument is that even highly-improbable looking things (like flagellum motors) can be constructed blindly by natural processes in a long series of incremental steps.  Things that look as if they were designed can be gradually formed in this way too.

 

Mount Improbable cannot be climbed in one go.

That's like assaulting the mountain's vertical face.  But if you go around to the other side of the mountain, you'll find that the route to the summit can be made in a series of small, easy steps.  And nature has had ample time and ample opportunity to ascend the mountain and place improbable-looking things on the summit.

 

Theists see only the vertical face of improbability, throw up their hands and say, "God must have done it!"

"There's no way atoms and molecules can come together blindly to make something as improbable as a duck-billed platypus, a human eye or molecular machine. These things can only have been the product of an intelligent designer."

 

​They refuse to compromise and go around to the other side of the mountain to see that the fossil record shows us these small, incremental steps. Which explains why the most vocal anti-evolutionists are the Young Earth Creationist Christians, who read the Bible literally and believe that the universe is only about 6,000 years old.  And, of course, ID and IC are just tools used by the YEC's to further their long-term plan, the Wedge Strategy.  http://en.wikipedia.org/wiki/Wedge_strategy 

 

Again, BC well done!  

 

Thanks,

 

BAA.

[Brother Jeff]

Well done, BC!  

 

You've just climbed Mt. Improbable.  http://en.wikipedia.org/wiki/Climbing_Mount_Improbable

 

The gist of Dawkin's argument is that even highly-improbable looking things (like flagellum motors) can be constructed blindly by natural processes in a long series of incremental steps.  Things that look as if they were designed can be gradually formed in this way too.

 

Mount Improbable cannot be climbed in one go.

That's like assaulting the mountain's vertical face.  But if you go around to the other side of the mountain, you'll find that the route to the summit can be made in a series of small, easy steps.  And nature has had ample time and ample opportunity to ascend the mountain and place improbable-looking things on the summit.

 

Theists see only the vertical face of improbability, throw up their hands and say, "God must have done it!"

"There's no way atoms and molecules can come together blindly to make something as improbable as a duck-billed platypus, a human eye or molecular machine. These things can only have been the product of an intelligent designer."

 

​They refuse to compromise and go around to the other side of the mountain to see that the fossil record shows us these small, incremental steps. Which explains why the most vocal anti-evolutionists are the Young Earth Creationist Christians, who read the Bible literally and believe that the universe is only about 6,000 years old.  And, of course, ID and IC are just tools used by the YEC's to further their long-term plan, the Wedge Strategy.  http://en.wikipedia.org/wiki/Wedge_strategy 

 

Again, BC well done!  

 

Thanks,

 

BAA.

 

BAA, let's make sure we have our facts straight. Jesus magically created our small, three-tiered universe (Sky Kingdom, flat earth, flaming torment chamber of divine love) 10,000 years ago by speaking a powerful magical spell from Nowhere. He magically created our flat world 6000 years ago after He got lonely and decided He needed creatures to worship Him. 

 

I love it how in Genesis 1:2 the Holy Spook flies over the newly created flat world in His Bird Form to check out the Kryasst Version of Himself's handiwork. And, of course, He approved of what He had magically accomplished! Glory!

[BlackCat]

Thanks BAA.  Mount improbable indeed!    What a perfect analogy.  That Wedge Strategy sounds really dodgy.  Thankfully it doesn't stand a cat in hells chance (I hope).

 

Brother Jeff, you make me smile.   

[sdelsolray]

Thanks BAA.  Mount improbable indeed!    What a perfect analogy.  That Wedge Strategy sounds really dodgy.  Thankfully it doesn't stand a cat in hells chance (I hope).

 

Brother Jeff, you make me smile. 

The Discovery Institute is a den of disingenuous pseudoscience aimed at gullible theists.  They lie, cheat, employ common logical fallacies and collect money.  For example, when criticized for not having produced any peer reviewed science papers, the DI formed their own shell (and hidden) "peer review" society, populated by (guess who?) members or the DI Mafia.  Now, the DI proudly displays a page on their website showing all the "peer reviewed" papers concerning Intelligent Design.  It's quite Orwellian.