Jump to content


Photo

Protein Evolution


  • Please log in to reply
134 replies to this topic

#1 jason777

jason777

    Moderator

  • Moderator Team
  • PipPipPipPip
  • 2670 posts
  • Gender:Male
  • Interests:Machining, Engine Building, Geology, Paleontology, Fishing
  • Age: 40
  • Christian
  • Young Earth Creationist
  • Springdale,AR.

Posted 30 December 2009 - 10:24 PM

Here is a paper I ran across that estimates the "impossibility" of a protein being able to fold properly and fuction by random mutations.



Estimating the prevalence of protein sequences adopting functional enzyme folds.

Axe DD.

The Babraham Institute, Structural Biology Unit, Babraham Research Campus, Cambridge CB2 4AT, UK. doug.axe@bbsrc.ac.uk

Proteins employ a wide variety of folds to perform their biological functions. How are these folds first acquired? An important step toward answering this is to obtain an estimate of the overall prevalence of sequences adopting functional folds. Since tertiary structure is needed for a typical enzyme active site to form, one way to obtain this estimate is to measure the prevalence of sequences supporting a working active site. Although the immense number of sequence combinations makes wholly random sampling unfeasible, two key simplifications may provide a solution. First, given the importance of hydrophobic interactions to protein folding, it seems likely that the sample space can be restricted to sequences carrying the hydropathic signature of a known fold. Second, because folds are stabilized by the cooperative action of many local interactions distributed throughout the structure, the overall problem of fold stabilization may be viewed reasonably as a collection of coupled local problems. This enables the difficulty of the whole problem to be assessed by assessing the difficulty of several smaller problems. Using these simplifications, the difficulty of specifying a working beta-lactamase domain is assessed here. An alignment of homologous domain sequences is used to deduce the pattern of hydropathic constraints along chains that form the domain fold. Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function.The prevalence of low-level function in four such experiments indicates that roughly one in 10(64) signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences.


Source


983lhh20rGY&hl=en_US&fs=1





Enjoy.

#2 Ron

Ron

    Advanced Member

  • Member
  • PipPipPipPipPip
  • 6530 posts
  • Gender:Male
  • Age: 50
  • Christian
  • Creationist
  • Johnstown, PA

Posted 02 January 2010 - 08:26 AM

And, amazingly enough, the protein remains protein. It doesn't evolve into anything else! And yet the evolutheists will attempt to promulgate that assumed time will assume
macroevolution.

Funny isn't it :o

#3 Seth

Seth

    Member

  • Veteran Member
  • PipPipPip
  • 277 posts
  • Age: 36
  • Christian
  • Creationist
  • Chicago

Posted 02 January 2010 - 09:27 AM

I think what is even more amazing is how anyone can look at this and think no intelligent force was behind this process!

#4 Ron

Ron

    Advanced Member

  • Member
  • PipPipPipPipPip
  • 6530 posts
  • Gender:Male
  • Age: 50
  • Christian
  • Creationist
  • Johnstown, PA

Posted 02 January 2010 - 09:33 AM

I think what is even more amazing is how anyone can look at this and think no intelligent force was behind this process!

View Post


Too True!

#5 Guest_tharock220_*

Guest_tharock220_*
  • Guests

Posted 02 January 2010 - 05:18 PM

And, amazingly enough, the protein remains protein. It doesn't evolve into anything else! And yet the evolutheists will attempt to promulgate that assumed time will assume
macroevolution.

Funny isn't it  :o

View Post


If you had any idea what evolution is you wouldn't actually say this sort of thing.

What is the probability of a protein of 20 straight lysines forming???

What is the probability of a protein of a loop of lysine, glutamine, asparagine, and histidine repeating 5 times???

(hint: its sampling with replacement)

As long as we're arguing from incredulity, what was the purpose of having 6 codons code for leucine and 3 codons coding for stop??? Surely one codon would have done for each of the amino acids??

#6 Ron

Ron

    Advanced Member

  • Member
  • PipPipPipPipPip
  • 6530 posts
  • Gender:Male
  • Age: 50
  • Christian
  • Creationist
  • Johnstown, PA

Posted 02 January 2010 - 06:21 PM

If you had any idea what evolution is you wouldn't actually say this sort of thing.

View Post


I know exactly what evolutionist pretend evolution is. And pointing out the flaws at it’s very base is the kind of exposure evolutionists have a hard time dealing with. So they’ll resorts with statements like “you don’t know what evolution is”, or “if you had any idea what evolution is, blah-blah-blah”.

What is the probability of a protein of 20 straight lysines forming???

View Post

What is the probability of a protein remaining protein?

What is the probability of a protein of a loop of lysine, glutamine, asparagine, and histidine repeating 5 times???

View Post


Does the protein remain protein?

(hint: its sampling with replacement)

View Post


(hint: its still protein)


As long as we're arguing from incredulity, what was the purpose of having 6 codons code for leucine and 3 codons coding for stop???  Surely one codon would have done for each of the amino acids??

View Post

Does the protein remain protein?

(pssst, I already gave you a hint)

#7 jason777

jason777

    Moderator

  • Moderator Team
  • PipPipPipPip
  • 2670 posts
  • Gender:Male
  • Interests:Machining, Engine Building, Geology, Paleontology, Fishing
  • Age: 40
  • Christian
  • Young Earth Creationist
  • Springdale,AR.

Posted 02 January 2010 - 07:14 PM

As long as we're arguing from incredulity, what was the purpose of having 6 codons code for leucine and 3 codons coding for stop??? Surely one codon would have done for each of the amino acids??


Adding just 1 amino acid would hinder the fold.

#8 Bruce V.

Bruce V.

    Member

  • Veteran Member
  • PipPipPip
  • 952 posts
  • Age: 54
  • Christian
  • Creationist
  • Northern Califiornia

Posted 02 January 2010 - 08:06 PM

If you had any idea what evolution is you wouldn't actually say this sort of thing.

What is the probability of a protein of 20 straight lysines forming???

What is the probability of a protein of a loop of lysine, glutamine, asparagine, and histidine repeating 5 times???

(hint: its sampling with replacement)

As long as we're arguing from incredulity, what was the purpose of having 6 codons code for leucine and 3 codons coding for stop???  Surely one codon would have done for each of the amino acids??

View Post



I don't get it? Are you saying creation isn't true and evolution is, based on Codons have muliple spellings for the same amino acid and stop?

#9 Ron

Ron

    Advanced Member

  • Member
  • PipPipPipPipPip
  • 6530 posts
  • Gender:Male
  • Age: 50
  • Christian
  • Creationist
  • Johnstown, PA

Posted 02 January 2010 - 08:23 PM

I don't get it?  Are you saying creation isn't true and evolution is, based on Codons have muliple spellings for the same amino acid and stop?

View Post


That is pretty much the evolutheistic stance. Pretending proteins and amino acids somehow prove macroevolution if enough (massive amounts) time can be adduced.

#10 Guest_tharock220_*

Guest_tharock220_*
  • Guests

Posted 03 January 2010 - 03:02 PM

I don't get it?  Are you saying creation isn't true and evolution is, based on Codons have muliple spellings for the same amino acid and stop?

View Post


No, I'm arguing from incredulity as creationists often do.

I know exactly what evolutionist pretend evolution is. And pointing out the flaws at it’s very base is the kind of exposure evolutionists have a hard time dealing with. So they’ll resorts with statements like “you don’t know what evolution is”, or “if you had any idea what evolution is, blah-blah-blah”.


My statements stands.

#11 Ron

Ron

    Advanced Member

  • Member
  • PipPipPipPipPip
  • 6530 posts
  • Gender:Male
  • Age: 50
  • Christian
  • Creationist
  • Johnstown, PA

Posted 03 January 2010 - 04:47 PM

My statements stands.

View Post


It may stand, but it stands incorrect.

#12 Seth

Seth

    Member

  • Veteran Member
  • PipPipPip
  • 277 posts
  • Age: 36
  • Christian
  • Creationist
  • Chicago

Posted 03 January 2010 - 11:17 PM

No, I'm arguing from incredulity as creationists often do.
My statements stands.

View Post


I'd say you were arguing from Credulity as evolutionists often do.

#13 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 04 January 2010 - 05:05 AM

I'd say you were arguing from Credulity as evolutionists often do.

View Post


That´s the reason why we must apply the Universal Plausibility Metric ( UPM ) in science quickly.Otherwise evolutionists will keep wasting reasearch money in ridiculous theories.

#14 Ron

Ron

    Advanced Member

  • Member
  • PipPipPipPipPip
  • 6530 posts
  • Gender:Male
  • Age: 50
  • Christian
  • Creationist
  • Johnstown, PA

Posted 04 January 2010 - 05:32 AM

I'd say you were arguing from Credulity as evolutionists often do.

View Post


In other words he’s using the “argumentum ad ignorantiam” logical fallacy to argue against Credulity!

So, he’s basically using his faith in the religion of evolution to argue against creationism. But, I wonder; doesn’t the "theistic" evolutionist believe God created all of this?

This evolutionary fallacy of divinity, or their argument from incredulity, is a definite type of non sequitur reasoning which follows like this: I can't allow God to be sovereign, therefore I must change the Bible to fit the evolution gospel. And, even though there are many holes in micro evolution and no plausibility for Macro-evolution, for which we have no answer, we must fill the holes (or gaps) with something! Therefore Evolution must have done it. ;)

Note: You can substitute the deity “Nature” for the deity “Evolution” just to add spice to the doctrine.

#15 Bruce V.

Bruce V.

    Member

  • Veteran Member
  • PipPipPip
  • 952 posts
  • Age: 54
  • Christian
  • Creationist
  • Northern Califiornia

Posted 04 January 2010 - 02:46 PM

Found an easy to read article about protein folding you may find interesting.

What is protein folding and why is it important:[SIZE=7]

About page 10

The protein molecule must fold into the shape in which it is active. Folding is a complicated process that requires some steps to occur on the picosecond time scale while others may take milliseconds to seconds.28 Portions of the process are often mediated by chaperone or cofactor29 proteins that are required to guide folding into the proper shape or to prevent misfolding.

The folded shape of a protein is determined by several factors, among them internal covalent bonds (such as disulfide bridges between cysteine units in the chains), hydrogen bonds, and hydrophilic and hydrophobic interactions with the solvent surrounding the protein molecule. Two proteins with very different amino acid sequences can fold into a closely similar shape and have a similar function. The three-dimensional design of the resulting protein is thus more important than the sequence in explaining function. There is much interest in classifying folds of proteins to better understand function and to identify the likely function of newly discovered proteins.30 The shape is also affected by interaction of the protein with the other molecules, large and small, that participate with it in carrying out a particular activity in a cell.

This folding process is possible only because it is guided. A process of folding in which the protein chain bends entirely in random ways could not achieve the functional fold of that protein in any useful period of time. Several models have been developed to describe the folding process.31 “Misfolding” of proteins also is of considerable interest, as it may be a significant factor in the onset of a variety of diseases, such as Alzheimer’s syndrome. Proteins that can pass from one molecule to another through changes in folding conformation from the normal conformation (without involvement of the genome) include the prions, protein molecules implicated in a number of diseases.32

Most cellular functions are carried out by highly organized protein machines that are assembled with what amounts to engineering precision. This was not realized until relatively recently, in part because experimental technologies were inadequate to detect the structure of the machines, but also—in the author’s view—because the Darwinian concept of evolution by random mutation and natural selection encouraged (practically required) treating each protein (gene product) as a distinct unit in the functioning of an organism. For how could a function requiring multiple proteins in a cellular machine ever arise through the required random mutations that developed one protein molecule at a time and in a stepwise manner, and gave no intermediate product with any function that would allow Darwinian natural selection to work?

page 13

Another important category of protein complexes, and one that also has implications for evolutionary theory, comprises the molecular chaperones. These are complexes that contain several proteins and perform a number of cellular functions, such as assisting in the folding of proteins38 and controlling the binding of hormones to hormone receptors.39 The former group of chaperones functions to prevent misfolding or aggregation of a protein as it folds after transcription and appears to be required for proper folding of many proteins. Failure of the system of chaperones to guide folding of a protein properly is implicated in neurodegenerative diseases such as Alzheimer’s and Parkinson’s.40 The latter help stabilize the receptor in a shape that allows access by the appropriate hormone and, following binding of the hormone to the receptor, helping start transcription of the segment of DNA that is controlled by the hormone.



I pulled this out to further emphasize the question.

For how could a function requiring multiple proteins in a cellular machine ever arise through the required random mutations that developed one protein molecule at a time and in a stepwise manner, and gave no intermediate product with any function that would allow Darwinian natural selection to work?



#16 Bruce V.

Bruce V.

    Member

  • Veteran Member
  • PipPipPip
  • 952 posts
  • Age: 54
  • Christian
  • Creationist
  • Northern Califiornia

Posted 04 January 2010 - 02:55 PM

The ribosomes, the molecular machine that folds proteins, is more complicated than we thought.

science daily

Ribosome More Complicated Than Thought

page 12

Many of these machines are extraordinarily complex, including those machines responsible for the essential core functioning of a cell. The ribosome, which is responsible for the synthesis of all cellular proteins, itself is comprised of two distinct subunits that contain in all some 55 proteins and three ribosomal RNAs in the simplest (bacterial) form and about 75 proteins and 4 ribosomal RNAs in the eukaryotic form. Considering the ribosome as the equivalent of an assembly line in a factory makes sense when one describes what it does: bind the messenger RNA (mRNA) that contains the code for the protein to be built; bind a transfer RNA (tRNA) that holds the first amino acid in the protein chain, based on the first three nucleotides of the mRNA (the codon, or “triplet” code specifying which amino acid to select); bind another tRNA carrying the second amino acid in the chain; form the peptide bond between the two amino acids in the proper order; move the peptide chain forward so that the next amino acid can be added; finally, recognize the stop codon on the mRNA that indicates that all the amino acids have been added, and release the completed protein. All this is done with extremely high accuracy.
Imaging the structure of ribosomes has been an extraordinary challenge. At present remarkably good pictures of the three-dimensional structure of a bacterial ribosome have been produced through a combination of technologies, such as neutron scattering, electron microscopy, and x-ray diffraction.35 This structural information shows how tightly interlocked the components of the machine are. No simpler machine is known or even imagined that could carry out all of the steps in protein synthesis with such accuracy and speed. Yet no living cell can exist without the means to rapidly and continually synthesize hundreds of proteins over and over again with high fidelity to the code in its DNA. Even the formation of the ribosome itself requires a large number of synchronized steps and more than 100 proteins and 100 small RNA segments.36 Clearly the traditional idea that organisms evolve from simple to complex does not apply to the protein synthesis machinery.

Much of the functioning of a cell is carried out by similar machines (even if few have as many components as the ribosome). RNA polymerase II, which synthesizes messenger RNA in eukaryotes, is another critical machine. It is a complex of 12 proteins that holds the DNA strand to be transcribed and puts together the mRNA that will guide the ribosome in producing a protein. The mass of the complex is more than 500,000 daltons, involving more than 3500 amino acid residues. The structure of RNA polymerase II from yeast has been solved in an elegant series of experiments. The references describing these experiments should be read if only to see how the complex is put together from its components by the cellular machinery with a precision exceeding that of the most complicated devices designed and engineered by humans.37

Another important category of protein complexes, and one that also has implications for evolutionary theory, comprises the molecular chaperones. These are complexes that contain several proteins and perform a number of cellular functions, such as assisting in the folding of proteins38 and controlling the binding of hormones to hormone receptors.39 The former group of chaperones functions to prevent misfolding or aggregation of a protein as it folds after transcription and appears to be required for proper folding of many proteins. Failure of the system of chaperones to guide folding of a protein properly is implicated in neurodegenerative diseases such as Alzheimer’s and Parkinson’s.40 The latter help stabilize the receptor in a shape that allows access by the appropriate hormone and, following binding of the hormone to the receptor, helping start transcription of the segment of DNA that is controlled by the hormone.

Another category of chaperones helps control the movement of metal ions in cells. Many of the metals (e.g., copper, iron, zinc) are incorporated in key biochemical constituents of cells. Each cell contains a significant number of ions of these metals, yet it appears that all of the atoms of these metals are tightly bound to regulatory and chaperone proteins.41 Breakdown of this metal control system allows abnormal binding of a metal ion to any of a large number of proteins where it normally might not attach, shutting down the function of those proteins and potentially leading to disease. Malfunctions of copper metabolism, for example, are implicated in familial amyotrophic lateral sclerosis and may be involved in several other diseases.42
In this section I have discussed two levels of complexity of cellular chemistry that extend beyond the control of the gene that codes for a protein: post-translational chemical modification and folding of proteins into their active form and the requirement that most proteins be incorporated into large, multi-protein complexes in order to participate in a cellular function. Both of these phenomena were known in 1959, but the extensiveness of each was unexpected. Certainly, evolutionary theory did not alert biologists to the significance of these modifications and the protein machines, given the one-gene/one-protein outlook that random mutation and natural selection strongly encouraged. Can Darwinian evolution really be as fundamental to biology as is claimed by its proponents if it gave no guidance to scientists about the extraordinary complexity and high degree of organization of cellular chemistry that new experimental tools were to discover?



#17 Guest_Tommy_*

Guest_Tommy_*
  • Guests

Posted 05 January 2010 - 08:39 AM

I think what is even more amazing is how anyone can look at this and think no intelligent force was behind this process!

View Post


When looking at the complexity within a cell it's worth keeping in mind the following:
1) single-cell life reproduces quickly and with vast populations,
2) the conventional chronology offers hundreds of millions of years of adaptation before the emergence of multicellular life,
3) the incremental steps of selection serve as a bias towards what works for each generation so the current product is considerably more elaborate than had all components been assembled to fulfill the current function.

#18 Ron

Ron

    Advanced Member

  • Member
  • PipPipPipPipPip
  • 6530 posts
  • Gender:Male
  • Age: 50
  • Christian
  • Creationist
  • Johnstown, PA

Posted 05 January 2010 - 10:33 AM

When looking at the complexity within a cell it's worth keeping in mind the following:
single-cell life reproduces quickly and with vast populations,

View Post

And yet there is absolutely no empirical evidence of one species evolving into another. In other words; no fish to land animal to whale evolution, only speculatory and pre-suppositional modeling.

the conventional chronology offers hundreds of millions of years of adaptation before the emergence of multicellular life,

View Post

More mere speculation, with no empirical scientific evidence (and also equivocation according to the forum rules).

the incremental steps of selection serve as a bias towards what works for each generation so the current product is considerably more elaborate than had all components been assembled to fulfill the current function.

View Post

Who is doing the selecting? From whom is the bias originating? Who is doing the assembling of all of these “elaborate” “components”?

#19 Otto13

Otto13

    Member

  • Banned
  • PipPipPip
  • 223 posts
  • Age: 63
  • no affiliation
  • Theistic Evolutionist
  • Connecticut

Posted 05 January 2010 - 01:16 PM

More mere speculation, with no empirical scientific evidence (and also equivocation according to the forum rules).

View Post

Can you explain the "equivocation according to the forum rules", thanks

#20 Ron

Ron

    Advanced Member

  • Member
  • PipPipPipPipPip
  • 6530 posts
  • Gender:Male
  • Age: 50
  • Christian
  • Creationist
  • Johnstown, PA

Posted 05 January 2010 - 03:50 PM

Can you explain the "equivocation according to the forum rules", thanks

View Post


Absolutely! --> http://www.evolution...forum_rules.htm
See the ninth bullet comment... It's concise and to the point.




0 user(s) are reading this topic

0 members, 0 guests, 0 anonymous users