PRO

Where Your Ideas can change Minds

Please visit our new forum at

http://www.4forums.com

CON


YouDebate.com Forum
» back to YouDebate.com
Register | Profile | Log In | Lost Password | Active Users | Help | Board Rules | Search | FAQ |
Custom Search
» You are not logged in.   log in | register

  YouDebate.com Forum
   Creationism vs Evolution Debates
     Protein translation
       Is it chemistry or not?

Topic Jump
« Back | Next »
Multiple pages for this topic [ 1 2 ]
Forum moderated by: admin
    

    
AFJ

|     |       Report Post



Member
Post Score
Adjustment:
n/a

Rate this post:

Quote from Apoapsis at 12:55 PM on September 17, 2009 :
Quote from AFJ at 10:09 PM on September 16, 2009 :
Bottom line, unless you can give me a chemical process that causes the tRNA to deliver the amino acids in in an order corresponding to the mRNA sequence, chemical evolution fails to account for this process.


Here ya go:

During ribosomal protein synthesis, aminoacyl-tRNA (aa-tRNA) is delivered to the ribosome in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Subsequent GTPase activation constitutes a critical step that determines the fidelity of aa-tRNA selection1. When the anticodon matches the mRNA codon displayed in the A-site (cognate anticodon), rapid GTP hydrolysis is triggered, at which point EF-Tu changes its conformation from the GTP- to the GDP-bound form and releases aa-tRNA. The aa-tRNA is accommodated in the peptidyl transferase center and takes part in peptide bond formation. An incorrect codon−anticodon interaction leads to rejection of the ternary complex (noncognate anticodon) or slow GTP hydrolysis (near-cognate anticodon)2, 3, 4, indicating that the strength of the interactions at the decoding site on the 30S subunit controls the reaction that takes place on the 50S subunit. Kinetic and structural work has shown that GTPase activation is coupled to codon recognition by induced fit involving a conformational change in the decoding center of 16S rRNA that is induced by codon recognition1, 2, 5. How the conformational state of the decoding site on the 30S subunit modulates the GTPase activity of EF-Tu bound to the 50S subunit is not known in detail, although codon recognition has been shown to induce coupled conformational changes of both aa-tRNA (ref. 6) and EF-Tu (ref. 7). The conformational signal may be transmitted from the 30S to the 50S subunit by changing the structure and/or contacts of intersubunit bridges connecting the two subunits8 and/or through the aa-tRNA, because intact tRNA is required for GTPase activation9. Ribosomal residues involved in GTPase activation of EF-Tu include protein L7/12, as well as other structural elements of the 50S subunit10.

Nature Structural Biology  9, 849 - 854 (2002)
Published online: 15 October 2002; | doi:10.1038/nsb859
Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex
Holger Stark1, Marina V. Rodnina2, Hans-Joachim Wieden2, Friedrich Zemlin3, Wolfgang Wintermeyer4 & Marin van Heel5


These are MY questions, not regurgitated by someone else.  Please put down your stereotypes.

Thank you, Apoasis.  This is a very detailed explanation of translation.  However I am speaking of the transport and delivery,  not translation processes inside the ribosome. We understand this process.

No 1. Transport Initiation--The tRNA does not go to the ribosome UNTIL --UNTIL it has bonded with an amino acid.  Is there a yet undiscovered chemical trigger which programs the tRNA to go to the ribosome?  

Why do they not go "emptyhanded?"  How does that hypothetical program work--is there a language that we do not see--does it have a directional guidance system--why can we not detect it?

No.2. Discriminating Delivery-- Upon arrival the nucleotide chain is mostly outside the ribosome.  Only two nucleotides are inside the two subunits (P & A) of the ribosome.

Some people on this forum seem to be inferring that the nucleotide bases are attracting the tRNA into the ribosome.

Three arguments are against this hypothesis.

a. If this were the case and van der wells forces or some kind of polar attraction or "electrostatic"  fit were at play--NOTE again that MOST of the mRNA chain is OUTSIDE the ribosome--if only simple chemical attractions were involved,  then the tRNA anticodons would begin be drawn to complimentary codons of the mRNA chain and chaos would result.

b. This attraction of the chain would slow down the process, which is two a second in eukaryotes and much faster in prokaryotes.

c.  The tRNA is transporting and in control of the amino acids. The tRNA waits until the proper complimentary codon has arrived in the A unit of the ribosome--not before.


Therefore there is empirical discrimination with the tRNA.  It is not a victim of random chemical reactions, but it part of and a participant in a highly advanced mechanism that man does not completely understand.




(Edited by AFJ 9/19/2009 at 10:27 AM).

(Edited by AFJ 9/19/2009 at 10:32 AM).

(Edited by AFJ 9/19/2009 at 11:53 AM).
 


Posts: 86 | Posted: 10:18 AM on September 19, 2009 | IP
derwood

|      |       Report Post




Fanatic
Post Score
Adjustment:
n/a

Rate this post:

Quote from AFJ at 10:18 AM on September 19, 2009 :

No 1. Transport Initiation--The tRNA does not go to the ribosome UNTIL --UNTIL it has bonded with an amino acid.  Is there a yet undiscovered chemical trigger which programs the tRNA to go to the ribosome?  


After a tRNA has had its amino acid removed, its shape changes.  I don't know, but I assume that this altered shape interferes with it binding to its appropriate codon.


No.2. Discriminating Delivery-- Upon arrival the nucleotide chain is mostly outside the ribosome.  Only two nucleotides are inside the two subunits (P & A) of the ribosome.

P and A are not subunits of the ribosome, they are catalytic sites on the ribosome.  

Some people on this forum seem to be inferring that the nucleotide bases are attracting the tRNA into the ribosome.

I've not written so or read it.  


Three arguments are against this hypothesis.

a. If this were the case and van der wells forces or some kind of polar attraction or "electrostatic"  fit were at play--NOTE again that MOST of the mRNA chain is OUTSIDE the ribosome--

Yes, of course it is. A codon is 'exposed' in the catalytic site.  This is irrelevant.

if only simple chemical attractions were involved,  then the tRNA anticodons would begin be drawn to complimentary codons of the mRNA chain and chaos would result.



I suppose that a mRNA transcript, 'free floating', has all sorts of secondary structure that prevents this 'chaos.'  Of course, ribosomes speed up reactions that would likely occur on their own anyway.

b. This attraction of the chain would slow down the process, which is two a second in eukaryotes and much faster in prokaryotes.

All events at the molecular level proceed much faster than we envision them.  

c.  The tRNA is transporting and in control of the amino acids. The tRNA waits until the proper complimentary codon has arrived in the A unit of the ribosome--not before.

It 'waits' because the codon is not exposed until it is in the appropriate active site (not subunit).


Therefore there is empirical discrimination with the tRNA.

Physical/chemical, you mean.

 It is not a victim of random chemical reactions,

Nobody said such reactions are random.  Chemical reactions are in fact not random at all.

but it part of and a participant in a highly advanced mechanism that man does not completely understand.

Or, more likely, the entire operation which is, I assure you, very complicated, while not completely understood 'by man' isd nevertheless not the handiwork of any of the deities as depicted in ancient Holy Books.  Rather, the act of protein synthesis, form beginning to end, is a series of chemcial reactions that can be understood using basic physics and chemistry.

Lets not try to make "mysteries" out of everything that we cannot see on TV.



-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 3:38 PM on September 19, 2009 | IP
derwood

|      |       Report Post




Fanatic
Post Score
Adjustment:
n/a

Rate this post:

Guess not...


This is going to be fun...

Quote from AFJ at 10:09 PM on September 16, 2009 :
Quote from derwood at 11:10 AM on September 16, 2009 :

What do you mean by "cause"?  The cause of complementary binding is an elctrostatic 'fit' between molecules.  If your tRNA arrangment of 'exposed' nucleotides does not 'fit' with the 'exposed' nucleotides of the mRNA, binding will not normally take place, just as your car key will not unlock the door of another car.



First, It is "bonding," not "binding."  Molecules bond.

You say tomahto...

Second, perhaps instead of "electrostactic fit" you mean the peptide bond between the amino acids, or perhaps vander waals force or London forces.

Um, no, I meant what I said.

You asked about tRNA and mRNA interaction.  tRNA and mRNA interact via complementary bonding.  What is complementary?  Their ability to form hydrogen bonds .


 Electrostatic is not usually associated with molecular bonding.  

Molecules that form hydrogen bonds between each other do not actually chemically bond.  I used the term electrostatic to refer to the basic premise behind hydrogen bonding.

TO get to my point, unless I bring a key in close proximity to the lock and make a successful insertion, the door will remain locked.  Molecules are the same way, they have to be in close proximity in order for van der waals forces to pull them together and make a bond.

Cells are pretty small.

Bottom line, unless you can give me a chemical process that causes the tRNA to deliver the amino acids in in an order corresponding to the mRNA sequence, chemical evolution fails to account for this process.

Well, I'm not a physical chemist or a biochemist (are you?) and I am not going to do a bunch of research on this to satisfy your idiosyncratic demand.  
So, I guess since the exact specific answer your demand is not forthcomiong, Creation must be true.  I do have to ask, however - if I make a similar demand that you cannot answer to my satisfaction, do I get to declare that creationism cannot explain it?


Note that they are coming from other parts of the cell to the ribosome.  Van der waals forces or polar attraction can not account for this behavior.

Never heard of
Brownian motion , I suppose.






-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 3:41 PM on September 19, 2009 | IP
AFJ

|     |       Report Post



Member
Post Score
Adjustment:
n/a

Rate this post:

Derwood,

Thank you.  I would rather just answer than spend all day cutting and pasting.

First of all, I stand corrected on the subunits.  P and A sites are contained in the large subunit.  This helps me to understand more thoroughly what is going on.  

The A site stands for  aminoacyl tRNA  binding site--the P-site which is peptidyl tRNA binding site. If you go to this-- I can't get the link to work--you'll have to type this manually.

http://phschool.com/science/biology_place/biocoach/translation/init.html

It shows the tRNA in the p and a sites, the anticodons bonding with the codons on the bottom of the tRNA and the amino acids on top of the the tRNA making the peptide bond. 

As far as your comments suggesting that the secondary (or tertiary) structure of the tRNA would prevent any attraction to the outside chain, this is a possibility.  However, about the "exposure" of the codons inside the ribosome--I don't think there is anything "covering" them outside of the ribosome.

My question was what attracts or guides them inside the ribosome?  Point being it is more than simply being pulled in by polar attraction.

The ribosome, as you stated contains rRNA and other protein enzymes that do a speedy reaction but I still maintain that delivery of the acids to the ribosome requires a very advanced (as yet undiscovered) guidance system.

I'm not sure if Brownian motion is a dynamic for tRNA  though tRNA do wobble.  Please note that as in the post from Apoasis GTP (in prokaryotes ATP in eukaryotes) is bonded onto the tRNA --obviously for energy.  So I would lean toward self propulsion of some type, though I would not rule out Brownian or a combination of both.  Or perhaps the energy is used solely in catalytic actions.

As to your final comments on a deity--this  is a personal conviction.  We have the same science.  You say it happened by unguided mutation in the DNA and natural selection.  I agree with selection, but the term "unguided" is directly philosophical and indirectly metaphysical.

In light of the fact that all the enzymes involved in protein synthesis are also proteins themselves they had to be synthesized also. The process would not take place without them. A hard circle to explain.  
It is not therefore illogical to assume a higher power simply because you can not see the higher power.

You will simply say this process evolved from a simpler process like RNA world or something.  Note that
cyanobacteria (blue green algae) are supposedly 3.5 billion years old and exist today with DNA.  I can not offer complete exact evidence from the past, but neither can you--we have the same science--and it is not operational science (though operational science is involved) it is historical science.  Because of this some parts are simply untestable--and so the debate goes on.

I don't think the existence of God is irrelevant if it can be included as a POSSIBILITY.  This is inductive reasoning.  Logically this does not exclude evolution.  I believe there is a difference between empirical science and personal conviction about God either way--atheist or believer.  But since science people or scientists are people it is difficult to separate the subject of our origin from our personal beliefs, whether we be atheist, deist, theistic evolutionist, Christian or Muslim.  










(Edited by AFJ 9/19/2009 at 7:58 PM).
 


Posts: 86 | Posted: 5:19 PM on September 19, 2009 | IP
Demon38

|      |       Report Post




Fanatic
Post Score
Adjustment:
n/a

Rate this post:

I don't think the existence of God is irrelevant if it can be included as a POSSIBILITY.

Occam's Razor, we can see how these processes could have arisen through natural causes, we have evidence that they did arise through natural causes, not conclusive evidence yet, but evidence nonetheless.  There is still no evidence that a supernatural being exists, let alone created anything.  The existance of god is as relevant as pink unicorns creating everything, and according to you, you can't exclude them as a possiblity either.
 


Posts: 1664 | Posted: 9:14 PM on September 19, 2009 | IP
AFJ

|     |       Report Post



Member
Post Score
Adjustment:
n/a

Rate this post:

First of all, there is evidence that God exist.  You just choose to explain away everything a Christian might tell you as coincidence, or a figment of their imagination, or subjective and not provable, and so on.

What would be evidence that God exist? I can't use the universe or life, because you  choose to attribute that to natural causes.  I  can't use the Bible, because you choose to believe it is historically inaccurate and full of metaphors and fictional stories.  I can't make God come to speak to you, because even if he did , you would probably ask him for his ID

So what about unexplained healing in correspondence to prayer.  For instance, I knew a lady in my church who was diagnosed with ovarian cancer.  We prayed for her for several weeks.  The doctor one day simply could no longer find the cancer.  

What about my oldest son who at that time was 9 years old, when we were in Ivory Coast Africa.  They have meningitis over there and lots of other things--you learn to diagnose things and self medicate over there (with the help of books and other mission workers).  My son had a fever all night of 105 which as you know is dangerous.  One of the African  pastors came over at 1 AM with another missionary and prayed for him.  God is my witness, in 90 minutes his temp was 98.6.  What's more is my son told me when they prayed he kept feeling heat in his body. THe fever was causing chills, so the fever does not account for the sensation of heat.  If it is capillary dilation why did it only happen during the prayer, and what would be another reason for a "hot flash" in a 9 year old boy?  He was yet 2 years from puberty.

This happened to another man I went to church with who was being prayed for (he was sick) one Sunday--he was sitting right beside me.  He was amazed that he had felt it.

14 Is anyone among you sick? Let him call for the elders of the church, and let them pray over him, anointing him with oil in the name of the Lord.  15 And the prayer of faith will save the sick, and the Lord will raise him up. And if he has committed sins, he will be forgiven.  James 5:14,15

These are just two things.  I could tell you more from myself and people that I've known or know now, as I have been a Christian since 1974.

Now, you can deny or scoff at what I said, but there is really nothing you can do to explain away these occurrences--because they don't just come from me but tons of people who serve God.
 


Posts: 86 | Posted: 07:36 AM on September 20, 2009 | IP
Apoapsis

|     |       Report Post



Fanatic
Post Score
Adjustment:
n/a

Rate this post:

Quote from Apoapsis at 9:03 PM on September 13, 2009 :
Quote from AFJ at 6:05 PM on September 13, 2009 :

Science can't "account" for alot of things.  How many times do you read "...for reasons scientists don't completly understand..."?  

Not being able to account for something is no justification for denial of it's existence.



There is no denial of the existence of God,  there is the inability to assess.  If you want science to include God, produce a test, repeatable by anyone, that will provide a result that is yes/no on the existence of God.  Provide the test and results for peer review and duplication.







-------
Pogge:” This is the volume of a sphere with a 62 kilometer (about 39 miles) radius, which is considerably smaller than the 2,000 mile radius of the Earth.”
Wikipedia:” For Earth, the mean radius is 6,371.009 km(≈3,958.761 mi; ≈3,440.069 nmi).”
Wisp to Lester (on Pogge): Do you admit he was wrong about the basics?
Lester: No

 


Posts: 1747 | Posted: 11:19 AM on September 20, 2009 | IP
derwood

|      |       Report Post




Fanatic
Post Score
Adjustment:
n/a

Rate this post:

Quote from AFJ at 5:19 PM on September 19, 2009 :
As far as your comments suggesting that the secondary (or tertiary) structure of the tRNA would prevent any attraction to the outside chain, this is a possibility.  However, about the "exposure" of the codons inside the ribosome--I don't think there is anything "covering" them outside of the ribosome.

mRNA would/could also assume secondary and/or tertiary structure, which would in effect 'cover' the codons.


My question was what attracts or guides them inside the ribosome?  Point being it is more than simply being pulled in by polar attraction.


tRNAs do not go 'into' the ribosome.  When the mRNA binds the ribosomal subunits, it is 'exosed' on the ribosomes surface.


The ribosome, as you stated contains rRNA and other protein enzymes that do a speedy reaction but I still maintain that delivery of the acids to the ribosome requires a very advanced (as yet undiscovered) guidance system.

If you maintain that, then it seems that it is up to you to provide the actual evidence for this.  Thus far, all I have seen is 'disbelief' that fairly well understood issues such as polar/electrostatic attractions cupled with things like Brownianmotion cannot do it.  But that is not evidence supportive ogf some sort of guidance system.


I'm not sure if Brownian motion is a dynamic for tRNA  though tRNA do wobble.  Please note that as in the post from Apoasis GTP (in prokaryotes ATP in eukaryotes) is bonded onto the tRNA --obviously for energy.  So I would lean toward self propulsion of some type, though I would not rule out Brownian or a combination of both.

You may want to brush up on what phosphorylation actually accomplishes.  


 Or perhaps the energy is used solely in catalytic actions.

As to your final comments on a deity--this  is a personal conviction.  We have the same science.  You say it happened by unguided mutation in the DNA and natural selection.  I agree with selection, but the term "unguided" is directly philosophical and indirectly metaphysical.


Actually, the randomness of mutation can be indirectly observed.  Philosophy/metaphysics plays precious little role in such observations.


In light of the fact that all the enzymes involved in protein synthesis are also proteins themselves they had to be synthesized also. The process would not take place without them. A hard circle to explain.  

Yes, it is, but this subsumes that the current system is and has always been THE system that accomplishes these acts.  There is evidence for autocatalytic molecules, and molecules that catalyze synthesis reactions of other molecules.  Not the whole answer, for sure, but not having an explanation right now is not, to me, a rational impetus for conclusing that a god/designer was behind it all.



It is not therefore illogical to assume a higher power simply because you can not see the higher power.

Nor is it illogical to reserve such judgement considering the track record of science versus religion/philosophy on such matters.  It was not prayer or divine intervention that allowed us to find out what crazy sorts of things go on inside our cells.


You will simply say this process evolved from a simpler process like RNA world or something.


I personally will say this is likely, but I do not have an opinion on it one way or another.


 Note that
cyanobacteria (blue green algae) are supposedly 3.5 billion years old and exist today with DNA.  I can not offer complete exact evidence from the past, but neither can you--we have the same science--and it is not operational science (though operational science is involved) it is historical science.  Because of this some parts are simply untestable--and so the debate goes on.


Historical science is still science.  We can infer based on the evidence that exists.  


I don't think the existence of God is irrelevant if it can be included as a POSSIBILITY.  This is inductive reasoning.  Logically this does not exclude evolution.  I believe there is a difference between empirical science and personal conviction about God either way--atheist or believer.  But since science people or scientists are people it is difficult to separate the subject of our origin from our personal beliefs, whether we be atheist, deist, theistic evolutionist, Christian or Muslim.  


This is true.  However, I would argue that 'evolution' scientists in general have had a much better track record of keeping their personal beliefs apart from their science, for I have docuemtned how creaton scientists use their beliefs to DICTATE their science - both its practice and the acceptance of their results.  And I think you would agree that this is unsatisfactory.


-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 12:34 PM on September 21, 2009 | IP
orion

|      |       Report Post




Fanatic
Post Score
Adjustment:
n/a

Rate this post:

Derwood -

who was the author you recommended reading for 'Origins of Life' research?  Robert Hazen?
 


Posts: 1460 | Posted: 3:40 PM on September 21, 2009 | IP
derwood

|      |       Report Post




Fanatic
Post Score
Adjustment:
n/a

Rate this post:

Quote from orion at 3:40 PM on September 21, 2009 :
Derwood -

who was the author you recommended reading for 'Origins of Life' research?  Robert Hazen?



Yes, but he's more of a pre-biotic chemical evolution kind of guy.  He gave a talk at my school last year and presented some really fascinating research.  His team has been able to synthesize lipids, peptides and all sorts of other organic compounds, including homochiral (or mostly homochiral) mixtures, all in simulated early earth environments.  And not just one environemnt, but many.  An interesting one was where they just put some common organic compounds into a gold tube and put it in a chamber that put it under pressure, and voila - aromatic organic compounds formed...






-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 4:13 PM on September 21, 2009 | IP
Demon38

|      |       Report Post




Fanatic
Post Score
Adjustment:
n/a

Rate this post:

First of all, there is evidence that God exist.  You just choose to explain away everything a Christian might tell you as coincidence, or a figment of their imagination, or subjective and not provable, and so on.

There is NO evidence of any supernatural being.  All you present is coincidence and figments of the imagination for evidence.  You can't present any verifiable, testable e vidence for god.
 


Posts: 1664 | Posted: 5:15 PM on September 21, 2009 | IP
orion

|      |       Report Post




Fanatic
Post Score
Adjustment:
n/a

Rate this post:

Derwood -

I see Robert Hazen has a book out 'Genesis: The Scientific Quest for Life's Origin' - seems to be a non-technical book for the layperson.  Just the thing I'm looking for.  

Genesis: the scientific quest for life's origin

Thanks.
 


Posts: 1460 | Posted: 5:55 PM on September 21, 2009 | IP
derwood

|      |       Report Post




Fanatic
Post Score
Adjustment:
n/a

Rate this post:

Quote from orion at 5:55 PM on September 21, 2009 :
Derwood -

I see Robert Hazen has a book out 'Genesis: The Scientific Quest for Life's Origin' - seems to be a non-technical book for the layperson.  Just the thing I'm looking for.  

Genesis: the scientific quest for life's origin

Thanks.



I've not read it, but if it reads as well as he speaks, it should be a good one.  His talks (he actually gave 2, a 'technical' one and a more general one) were interesting and entertaining.



-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 12:12 PM on September 22, 2009 | IP
    
Multiple pages for this topic [ 1 2 ]

Topic Jump
« Back | Next »
Multiple pages for this topic [ 1 2 ]
Forum moderated by: admin
    

Topic options: Lock topic | Unlock topic | Make Topic Sticky | Remove Sticky | Delete thread | Move thread | Merge thread

 

© YouDebate.com
Powered by: ScareCrow version 2.12
© 2001 Jonathan Bravata. All rights reserved.