Protein Folding- Chance Or 'design'?

[BlackCat]

A guy called 'Evid3nc3' on youtube, did a series of videos that charts his de-conversion from Christianity, and he outlines some major 'pillars' that we tend to base our faith and beliefs on.  My 'pillars' were the same as his: 'prayer', 'morality', 'bible', 'logical arguments' etc. One by one, these 'pillars' have been knocked down leading to my de-conversion which is still on going.  One last 'pillar' that is not unique to Christianity but leads me to still consider the possibility of 'God' or rather some eternal intelligence is the apparent design in nature and the material universe. 

 

Molecular machines within the cell are 'the' pillar to my continued thinking, that design is a part of existence.  Protein folding which is necessary to form these machines blows my mind. 

 

I've tried to copy a you tube link to a short 2 minute film showing amino acids folding to form a protein.  It won't let me copy the link??  If you type in 'Protein Folding' you'll find it.  It's by 'AskaBiologist'.

 

That short film shows how the amino acids have to be in a certain sequence even before they start to fold.  So, by my reasoning, how does nature ensure correct sequences to be maintained EVERY TIME (most times),  and then what causes the folding?  The folding has to occur in a correct order too.  So all the way through the process you have to have what seems to be a pre-determined order (template??) to arrive at the end result. 

 

Is it because I don't understand the biology properly, that this smacks of design?

[BlackCat]

Wow, I've just come across this 'Ted' film on you tube (16 minutes long):

 

'The Protein folding problem: a major conundrum of science: Ken Dill at TEDxSBU'.

 

Thoroughly fascinating. I wish I had my time again, I'd love to have studied this stuff.

[RogueScholar]

This is a God of the gaps argument. Something is not fully understood therefore said process must be the result of an intelligent designer? While it is true that we do not have a completely robust understanding of how proteins fold into their complex secondary, tertiary and quaternary structures, we actually understand a significant amount about this process. However, for us to have a conversation you will need to have a decent grasp of chemistry, particularly when it comes to the concept of intermolecular forces such as Hydrogen bonding. If this is not the case, it will be very difficult to talk about protein folding and protein conformation.

 

Also, these sequences and correct folding most of the time that you cite is incorrect. Misfolding of proteins and a breakdown of this process is what leads to many disease states such as allergies, "mad cow disease" and other neurological diseases.

[BlackCat]

RogueScholar, many thanks for your input.   

 

It is true that I don't have a hope in hell of being able to understand the chemistry/science regarding protein folding.  If I may press you a bit further though: is there no way at all, to convey the gaps in my knowledge, so that I can understand why these machines have not needed to be designed? 

 

And yes, I know that misfolding occurs and leads to the diseases and problems you cite, hence why I said 'most of' the time.  Forgive my sloppy or ignorant remarks.  'A good deal of' the time is maybe better.

 

So, is there a way of explaining the principle behind the ordering of the amino acids, and the fact that they are then folded?  I don't know how a car's engine is made or works but I can appreciate that its construction needs a template and then the parts have to be constructed and calibrated etc.  Parts have to been assembled in a certain order etc.  Am I wrong to transfer my understanding of how man-made machines have to be designed to how molecular machines are assembled? 

[RogueScholar]

Yes and no. Once I begin to distill even basic concepts, huge gaps open up. For example, I would need to describe the kinetics and thermodynamics of chemical bonding and chemical systems in order to explain how protein folding appears to be thermodynamically unfavorable but it is in fact not due to increased entropy of the solvent in the system.

 

Perhaps, leave the protein folding issue on the shelf for a bit and start with a basic concept known as chemical evolution. If we can agree that simple chemical systems can evolve into more complex molecular systems through naturalistic processes, then we will be in a much better position to accept proteins by extension.

 

For that I will turn to the good folks at stated clearly:

 

Pay close attention to how the interaction with water causes these structures to form. This is a key concept when it comes to protein folding.

[BlackCat]

Very interesting.  Thank you for posting that.  I'll need to watch it a few times so it sinks in as a few questions spring to mind but I may be jumping the gun.

[BlackCat]

Have they found fatty acids outside the lab in underground chambers or somewhere suitable, particularly the stable hollow balls they form? 

[Burny]

Thanks for the excellent conversation folks - this is what ex-c is all about. One observation I've made over the years is how quickly a believer will turn from "god of the gaps" to conclude confidently "therefore MY version of god exists and is the designer".

 

All of a sudden all the issues with that particular "god" are forgotten and he definitely exists because something in the natural world can't be explained to a lay person easily?

 

Hmmm.

[BlackCat]

Good points Burny.  Because I can now see how faulty my thinking was when I was a Christian, I am wary of the fact that I 'see' design in molecular machines.  RogueScholar hit the nail on the head when he said:

 

''If we can agree that simple chemical systems can evolve into more complex molecular systems through naturalistic processes,......''  then this last piece of the jigsaw (for me) will slot into place.   

[GraphicsGuy]

It is areas like this where I feel that nature actually disproves God...okay, it disproves the Christian version of God at the minimum.

 

Why?

 

Because nature is far too COMPLEX to have simply been spoken into existence (what really amounts to magic, right? "There's nothing in my hand or up my sleeve, folks." *POOF* "Hey, look! A planet!").

 

The level of genius it would take to even come up with most bio-mechanics is astronomical. How could we, creations of this ultra-mega-super-intelligence, even remotely hope to have some kind of "relationship" with a being like that?

 

No, if "God" does exist and is the creator of all this, he/she is some kind of mad scientist and our universe is sitting in a fish-tank in his laboratory.

[RogueScholar]

BlackCat, I can do even better than naturally occurring macromolecules like fatty acids and amino acids in heated caverns on Earth. How about I give you an example of these complex molecules forming in meteorites from outer space?

 

http://www.ncbi.nlm.nih.gov/m/pubmed/11542462/

[mymistake]

 

 

Is it because I don't understand the biology properly, that this smacks of design?

 

 

It's that you don't understand.  I suck at biology so I can't help you there.  But keep in mind that "design"

 

means "an alien wizard did it".  We shouldn't give design the benefit of the doubt simply because we were

 

indoctrinated as children.  These aliens and the magic they used must be produced before "an alien wizard

 

did it" becomes a reasonable answer.

[rerics]

It's may seem easy to claim "intelligent design" when the so-called design looks too good to be formed by unplanned accumulative processes.  But one can't ignore the poorly designed things in nature, also due to accumulative processes--e.g. the human male urinary tract running straight through the prostate leading to problems as the prostate enlarges with age, respiratory and digestive tracts sharing the same plumbing thereby risking choking, hooved mammals with extra unused toe bones, etc.

[BlackCat]

GraphicsGuy,  good points, although I used to (and many Christians I have spoken to),  have a more pantheistic view of God and the universe. 

 

MyMistake, I take on board what you are saying.  I am certainly coming away from a theistic or even deistic view of 'God'.  That being the case I can now see more clearly how a personal God makes no sense. 

 

Rerics, interesting points.  Thank you.

 

RogueScholar, thank you for posting that link to the complex molecules in meteorites.  That's awesome!  Already you have slotted some of the missing pieces into place.  I'm now beginning to see where my thinking is likely going wrong.  I'll mull all this over.

 

Thanks again everyone. 

[BlackCat]

I clearly see that the building blocks for life occur naturally and due to other naturally occurring things like water, these building blocks start to clump together and form more complex molecules and hence we are surely witnessing the beginning of evolution?

 

So we have the very beginning (as demonstrated in lab experiments) and we ourselves are the 'current' pinnacle of how complex the process can get:

the BEGINNING and the 'END'.

 

This leads me to wonder why we don't have MIDDLE stages.  Now I've surely termed that very crudely.  So I'll explain what I mean and this is something I've been pondering for a long time and is the main obstacle to why I struggle to understand how life could evolve without a designer.

 

When I talk about a 'middle' stage I don't mean a less complex life form.  I'm referring to a multi-part system.  If we take the example of an engine, is it the case that something like an engine HAS to consist of a MINIMUM number of parts in order to have that specific function?  Please guys correct me if I am way off track here.  Here's how I've understood an engine to have evolved: I'll have to use the example of a sewing machine if I may.  You start with a  needle.  You progress to a foot or hand lever system, and finally you have an engine powered sewing machine. The 'jump' from a simple needle to a lever system is surely impossible to achieve BIT BY BIT?  Maybe I'm wrong.  Then a manual lever system to a motor powered system is also impossible IN STAGES.

 

Motors are real machines that exist in molecular form. Our bodies contain billions if not trillions of them.  How did these motors manage to evolve when you need all the parts to be present AT THE SAME TIME?  

 

I read that the fossils found from the Cambrian explosion have systems that are already fully present.  I can't remember if the 'motor' is one of them, but I think it is.  So it's like nature has skipped from the 'needle' straight to the powered motor.  

[mymistake]

I clearly see that the building blocks for life occur naturally and due to other naturally occurring things like water, these building blocks start to clump together and form more complex molecules and hence we are surely witnessing the beginning of evolution?

 

Technically that isn't evolution, it is abiogenesis.  They are completely different fields.

 

 

 

 

This leads me to wonder why we don't have MIDDLE stages.

 

 

I'm referring to a multi-part system.  If we take the example of an engine, is it the case that something like an engine HAS to consist of a MINIMUM number of parts in order to have that specific function?

 

That might be where you are going wrong.  Some parts are useful in themselves.

 

 

 

Here's how I've understood an engine to have evolved: I'll have to use the example of a sewing machine if I may.  You start with a  needle.  You progress to a foot or hand lever system, and finally you have an engine powered sewing machine. The 'jump' from a simple needle to a lever system is surely impossible to achieve BIT BY BIT?  Maybe I'm wrong.  Then a manual lever system to a motor powered system is also impossible IN STAGES.

 

And yet humans invented the sewing machine in stages, bit by bit, exactly the way you assert is impossible.  We started off crafting hooks from fish bones and then it was thousands of years of trial, error and adaptation until we had not-so-intelligently designed sewing machines.  It was the same for all our other inventions.  Why wouldn't the biological world operate much the same way?

 

If you ever get a chance to watch the new Cosmos with Neil Degrasse Tyson I believe episode 2 covers the natural creation of the eye.  Very interesting.

[RogueScholar]

First, I'd be cautious about saying humans are the end of evolution or the apex of this process. With that in mind, what you are asking about does exist. Viruses and prions are key examples of non-living molecular machines. Prions in particular are a very interesting case as they are simply protein molecules and nothing more.

 

http://en.m.wikipedia.org/wiki/Prion

[sdelsolray]

I clearly see that the building blocks for life occur naturally and due to other naturally occurring things like water, these building blocks start to clump together and form more complex molecules and hence we are surely witnessing the beginning of evolution?

 

...

 

Evolution begins once (i) a molecule is subject to mutation, and (ii) that molecule is capable of self-replication.  Once these two requirements are met, natural selection will take effect.  The laws of chemistry and physics are (were) pervasively involved with events before these conditions are (were) met (and they are still involved afterwards).  Two areas of science which deal with events before biological evolution began are cosmology and abiogenesis.

 

...So we have the very beginning (as demonstrated in lab experiments) and we ourselves are the 'current' pinnacle of how complex the process can get:

the BEGINNING and the 'END'.

...

 

 

I fail to see how the single species homo sapiens sapiens, a carbon based lifeform on a planet called Earth, is the "END" of biological evolution. 

 

...

When I talk about a 'middle' stage I don't mean a less complex life form.  I'm referring to a multi-part system.  If we take the example of an engine, is it the case that something like an engine HAS to consist of a MINIMUM number of parts in order to have that specific function?  Please guys correct me if I am way off track here.  Here's how I've understood an engine to have evolved: I'll have to use the example of a sewing machine if I may.  You start with a  needle.  You progress to a foot or hand lever system, and finally you have an engine powered sewing machine. The 'jump' from a simple needle to a lever system is surely impossible to achieve BIT BY BIT?  Maybe I'm wrong.  Then a manual lever system to a motor powered system is also impossible IN STAGES.

...

 

 

You are entering the area of irreducible complexity, a speculation promoted by creationists.  The problem they have (and of which you are experiencing) is that they assume there is a end goal for evolution, e.g., humans are the purpose of evolution.  Now, the invention of a sewing machine is goal oriented, and by analogizing to the sewing machine, the goal of the one is implied in the other.  This is a mistake.  In addition, man-made machines are not organic organisms capable the mutation, self-replecation and subject to natural selection (and other evolutionary forces such as genetic drift, horizontal gene transfer, sexual selection, etc.).  To use your analogy differently, a needle still can do many useful things.  A foot lever can be used in things other than sewing machines (or any machine).  Engines can be functional outside of a sewing machine.  Accordingly, the combination of those three parts into a sewing machine is not irreducibly complex.  Indeed, if the needle breaks, a new one can be inserted.  If the electric motor burns out, a new one can be installed, or the old one repaired.  This could not occur if the sewing machine was irreducibly complex.

 

Creationist have yet to demonstrate any evidence of irreducible complexity.  None.  Each time they have attempted to in the past, others have shown how some or all of the parts have separate function which give (gave) the organism higher survival probability than if the part was not present.

 

...

Motors are real machines that exist in molecular form. Our bodies contain billions if not trillions of them.  How did these motors manage to evolve when you need all the parts to be present AT THE SAME TIME?

...  

 

You are repeating your misunderstandings from above.  The parts had different or similar functions before they changed into something else.  There was no "goal" for the parts to integrate into something different.

 

...

I read that the fossils found from the Cambrian explosion have systems that are already fully present.  I can't remember if the 'motor' is one of them, but I think it is.  So it's like nature has skipped from the 'needle' straight to the powered motor.  

The Cambrian "Explosion" lasted for tens of millions of years.  Life existed before the Cambrian Explosion for billions of years.  It's not surprising that life existing during that time was further evolved than life from billions of years earlier.  According to the current evidence, species before then did not fossilize well, but they had all sorts of things going on inside - metabolism, reproduction, etc.

 

Creationists speculate that the Cambrian Explosion is evidence of Original Divine Creation.  Of course, they leave out the length of that time period, how it fits in the longer time scale of billions of years, and other evidence that renders such a claim silly.

 

[Guest Furball]

It's may seem easy to claim "intelligent design" when the so-called design looks too good to be formed by unplanned accumulative processes.  But one can't ignore the poorly designed things in nature, also due to accumulative processes--e.g. the human male urinary tract running straight through the prostate leading to problems as the prostate enlarges with age, respiratory and digestive tracts sharing the same plumbing thereby risking choking, hooved mammals with extra unused toe bones, etc.

 

So much for psalm 139:14 - I will praise you; for I am fearfully and wonderfully made: marvelous are your works; and that my soul knows right well.

[BlackCat]

Mymistake, if I remember rightly, literature that discusses evolution usually includes the first steps I mentioned above under the term 'evolution'. (I can't quote your replies or copy and paste comments.  Not sure if it's my computer??)  As my questions seem to cross over from chemical evolution (abiogenesis) to evolution, they don't seem to be completely different fields (for the purposes of this discussion). 

 

Regarding your point about parts being useful in themselves:  I'm sure there are valid uses for some or all of the component parts of an engine, but those separate parts can't function as an engine. The Singer foot pedal powered sewing machine we had, could surely have had an electric motor fitted to it, but the jump from pedal powered to electric powered can't be done in stages-  or can it?  I haven't found anything that says it can.  Maybe it can...........

 

I will certainly watch that Neil DeGrasse Tyson film you mention. It sounds very interesting.  I will come back to you when I have watched it.

 

RogueScholar- I thought I was careful in how I described the level at which molecular machines have evolved UP TO NOW.   

 

I have read about prions, as my mum has dementia.  I wasn't making a distinction between 'living' and 'non living' machines. Maybe I've misunderstood your point there.

 

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?

[BlackCat]

Sdelsolray.  Thank you for your many interesting points.  It's nearly my bed time so I 'll come back to you tomorrow.

 

CoolCat- we are fearfully and wonderfully made, only instead of praising a man made 'God' I can 'praise' the universe. (I don't mean 'worship', but rather a sense of connection to all matter that exists and that I was fortunate enough to have come into existence)-  I hope you get what I mean.

[RogueScholar]

Your intuition is not at all correct however and that is not really how "molecular" motors (proteins) work. You seem to believe that a minimal number of components are required for such a "motor" to function. That is simply not the case however. You can have certain proteins perform a similar or identical task with different components. While removing components or adding components may alter function, it may not or the change in function can only be realized under very specific circumstances. Additionally, another thing you do not understand is the concept of conformation. Proteins have a special three dimensional structure that comes from the folding described above.  This structure is held into place through various so called intermolecular forces and on occasion, proper covalent bonds. A protein with a certain conformation may perform a certain job, and then changing its conformation or shape will cause it to perform a different job or lose its ability to function at all.  The easiest way to do this is by heating the protein up until the "vibrational" energy of the molecules overcome the intermolecular forces and cause the protein to lose its conformation and cease to function. This is known is being denatured.  This is what happens when you cook meat. In other situations, conformational changes result in biological activities.  For example, a protein receptor may be acted on by a molecule such as a certain drug.  This will cause molecular changes and a conformational change that will cause the receptor to open and allow ions to flow into a cell, resulting in additional biological actions. This analogy is not at all consistent with your model of a vehicular engine.  

 

Your model may work to help you understand a limited picture but it breaks down when we apply it to biochemical systems and macromolecules.

[bornagainathiest]

That multi-part motor sounds like Behe's Irreducible Complexity argument to me, BC.

 

If it is, then I'm sure that others will quickly link you to sites and articles that debunk that argument.

.

.

.

Btw,  a quick point about the RogueScholar's 'God-of-the-Gaps' observation from yesterday.

 

Q.

What is a skeptic's default position on any topic or argument?

A.

Unbelief. Until sufficient evidence is found.  Then belief becomes an option.  Not before then.

.

.

.

You should therefore be skeptical about intelligent design, irreducible complexity and similar.

These are scientific-sounding arguments crafted by theists to support their supernatural beliefs.  Which is, of course, NOT how science is performed, NOR how scientists should conduct themselves.   No scientist worth their salt ever builds an argument to support their preconceived (and supernatural) notions about reality.

 

Thanks,

 

BAA.

 

 

 

 

 

p.s.

Kudos to you for asking these important questions!  Keep 'em coming!    This is exactly what this forum's all about and exactly why we're here for you. 

 

[bornagainathiest]

Some links for you to follow up in the morning, BC.

 

 

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

 

http://www.millerandlevine.com/km/evol/design2/article.html

 

http://darwin200.christs.cam.ac.uk/pages/index.php?page_id=g2

 

http://www.dnalc.org/view/16982-The-Eye-and-Irreducible-Complexity-Creationism-Debunked.html

 

 

 

 

 

Good night, sleep tight and don't let the bedbugs bite.

 

But DO let RS or the RedNeckProf help you with any technical stuff in these links, ok?

 

 

[bornagainathiest]

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]