The Making of a Protein

[lucaspa]

Of course the wave expands. That is what causes the Red Shift.

The wave doesn't "expand". Instead, the wavelength lengthens.

Nope. The CMB is a measure of the amount of expansion, not the rate at which the expansion occurred.

Sorry, but the CMBR is the light emitted when the universe cooled enough so that light could shine thru. The stretch of the wavelength shows expansion AFTER that point. You are having all expansion of the universe come BEFORE that point. Therefore the CMBR disproves your hypothesis because it comes AFTER you say the second inflationary expansion stopped the expansion of the universe.

BTW, this explanation doesn't explain how we can see galaxies 10 billion light years away. If the universe were young, as you say, the light could not have reached us yet.

Search on "stretched out the heavens".

Isaiah 45:12 "I have made the earth, and created man upon it: I, [even] my hands, have stretched out the heavens, and all their host have I commanded."

The heavens have "hosts"? It's apparent that this isn't referring to inflation.

Jer 10:11-12 "Thus shall ye say unto them, The gods that have not made the heavens and the earth, [even] they shall perish from the earth, and from under these heavens. He hath made the earth by his power, he hath established the world by his wisdom, and hath stretched out the heavens by his discretion."

Again, not talking about inflation, but about the power of God. This statement is simply another way of saying God created the heavens.

BTW, your link had nothing to do with protein folding.

Yes, it did. I even quoted the relevant passage to you! Here it is again:

"Structural predictions - Proteins are complex molecules and can fold and bend into different planar and three-dimensional structures. Bioinformatics enables scientists to predict the structure a given protein sequence may form " http://www.csrees.usda.gov/ProgViewOverview.cfm?prnum=6252

Apparently you didn't realize that "structure" is the result of folding and that, therefore, to predict the structure means to predict the folding.

No wonder you claim don't "find" the evidence in the article. You either don't read the article or your reading comprehension is so poor that you don't understand the evidence and relevance when it is right in front of your eyes.

OR, this is a convenient way for you to try to deny data that disproves your position. That last sounds like a very likely hypothesis.

 

[lucaspa]

Found this paper:

Biopolymers. 2002 Aug 5;64(4):210-20. Importance of mutant position in Ramachandran plot for predicting protein stability of surface mutations.Gromiha MM, Oobatake M, Kono H, Uedaira H, Sarai A.
RIKEN Tsukuba Institute, Institute of Physical and Chemical Research, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.

Understanding the mechanisms by which mutations affect protein stability is one of the most important problems in molecular biology. In this work, we analyzed the relationship between changes in protein stability caused by surface mutations and changes in 49 physicochemical, energetic, and conformational properties of amino acid residues. We found that the hydration entropy was the major contributor to the stability of surface mutations in helical segments; other properties responsible for size and volume of molecule also correlated significantly with stability. Classification of coil mutations based on their locations in the (phi-psi) map improved the correlation significantly, demonstrating the existence of a relationship between stability and strain energy, which indicates that the role of strain energy is very important for the stability of surface mutations. We observed that the inclusion of sequence and structural information raised the correlation, indicating the influence of surrounding residues on the stability of surface mutations. Further, we examined the previously reported "inverse relationship" between stability and hydrophobicity, and observed that the inverse hydrophobic effect was generally applicable only to coil mutations. The present study leads to a simple method for predicting protein stability changes caused by amino acid substitutions, which will be useful for protein engineering in designing novel proteins with increased stability and altered function. Copyright 2002 Wiley Periodicals, Inc. Biopolymers 64: 210-220, 2002

 

[bob b]

The wave doesn't "expand". Instead, the wavelength lengthens.

The coordinates of space expand, which causes the wavelength to lengthen.

Sorry, but the CMBR is the light emitted when the universe cooled enough so that light could shine thru. The stretch of the wavelength shows expansion AFTER that point. You are having all expansion of the universe come BEFORE that point. Therefore the CMBR disproves your hypothesis because it comes AFTER you say the second inflationary expansion stopped the expansion of the universe.

The 2nd inflationary expansion was merely a continuation of the first. Actually there was only one inflationary expansion which lasted twice as long as typically assumed. The expansion only stopped when the universe had reached its current size.

BTW, this explanation doesn't explain how we can see galaxies 10 billion light years away. If the universe were young, as you say, the light could not have reached us yet.

The light wave expanded due to the coordinates of space being expanded. The light could not have failed to have reached us because it was expanded along with everything else in the universe. Of course any light emitted from a star after the coordinate expansion had ceased would take its normal amount of time to reach us.

Isaiah 45:12 "I have made the earth, and created man upon it: I, [even] my hands, have stretched out the heavens, and all their host have I commanded."

The heavens have "hosts"? It's apparent that this isn't referring to inflation.

It is obvious that "stretched out the heavens" is referring to the expansion of the coordinates of space and the "hosts" are of course the stars.

צְבָאָה צָבָא

tsâbâ’ tsebâ’âh

tsaw-baw', tseb-aw-aw'

From H6633; a mass of persons (or figurative things), especially regularly organized for war (an army); by implication a campaign, literally or figuratively (specifically hardship, worship):—appointed time, (+) army, (+) battle, company, host, service, soldiers, waiting upon, war (-fare).

Jer 10:11-12 "Thus shall ye say unto them, The gods that have not made the heavens and the earth, [even] they shall perish from the earth, and from under these heavens. He hath made the earth by his power, he hath established the world by his wisdom, and hath stretched out the heavens by his discretion."

Again, not talking about inflation, but about the power of God. This statement is simply another way of saying God created the heavens.

Of course it would take great power to stretch out the heavens (expand space to its present size).

Yes, it did. I even quoted the relevant passage to you! Here it is again:

"Structural predictions - Proteins are complex molecules and can fold and bend into different planar and three-dimensional structures. Bioinformatics enables scientists to predict the structure a given protein sequence may form " [/quote] Again, the progress in being able to do this is exaggerated.

 

[bob b]

Protein design
From Wikipedia, the free encyclopedia

Protein design is the design of new protein molecules from scratch. The number of possible amino acid sequences is infinite, but only a subset of these sequences will fold reliably and quickly to a single native state. Protein design involves identifying such sequences, in particular those with a physiologically active native state. Protein design is a rational design technique used in protein engineering.

Protein design requires an understanding of the process by which proteins fold. In a sense it is the reverse of structure prediction: a tertiary structure is specified, and a primary sequence is identified which will fold to it.

Protein design is also refered to as inverse folding. From a physical point of view, the native state conformation of a protein is the free energy minimum for the protein chain, at least at biological temperatures (i.e. at temperatures between zero and a hundred degrees Celsius). Hence, designing a new protein involves the identification of the sequences which have the chosen structure as free energy minimum. This can be done by use of computer models, which, while simplifing the problem, are able to generate sequences to fold on the desired structure.

The design of minimalist computer models of proteins (lattice proteins), and the secondary structural modification of real proteins, began in the mid-1990s. The de novo design of real proteins became possible shortly afterwards, and the 21st century has seen the creation of small proteins with real biological function including catalysis and antiviral behaviour. There is great hope that the design of these and larger proteins will have application in medicine and bioengineering.

Computational protein design algorithms seek to identify amino acid sequences that have low energies for target structures. While the sequence-conformation space that needs to be searched is large, the most challenging requirement for computational protein design is a fast, yet accurate, energy function that can distinguish optimal sequences from similar suboptimal ones. Using computational methods, a protein with a novel fold has been designed[1], as well as sensors for un-natural molecules[2].

On the other hand, it is widely believed that not all possible protein structures are designable, which means that there are compact configurations of the chain on which no sequences can fold to. In particular, conformations which are poor in secondary structures are unlikely to be designable. The designability of given structures is still an issue poorly understood.

Software
EGAD: A Genetic Algorithm for protein Design[3]. A free, open-source software package for protein design and prediction of mutation effects on protein folding stabilities and binding affinities. EGAD can also consider multiple structures simultaneously for designing specific binding proteins or locking proteins into specific conformational states. In addition to natural protein residues, EGAD can also consider free-moving ligands with or without rotatable bonds. EGAD can be used with single or multiple processors.


References
Jin et al, Structure, 11, 581 (2003).
Nagai et al, Proc. Natl. Acad. Sci. USA, 98, 3197 (2001).
Saghatelian et al, Nature, 409, 797 (2001).
Kuhlman et al "Science", 302:1364 (2003)[4]
Looger et al "Nature", 423:185 (2003)[5]
Pokala and Handel "J Mol Biol", 347:203 (2005)[6]
Retrieved from "http://en.wikipedia.org/wiki/Protein_design"

 

[JustinFoldsFive]

The coordinates of space expand, which causes the wavelength to lengthen.

The lengthening of a wavelength does not increase the speed of light. The speed of light is a constant. Are you unfamiliar with general relativity?

 

[bob b]

The lengthening of a wavelength does not increase the speed of light. The speed of light is a constant. Are you unfamiliar with general relativity?

The people who promote the inflationary period of the Big Bang (Guth and others) claim that the expansion of the coordinates of space does not violate the laws of nature, yet the effective speed of light during such rapid expansion would be millions of times greater than its normal speed due to the expansion of the wavelengths (Red Shift).

So no, the speed of light in one sense is not greater than its normal value, but because the wavelengths of light are expanded the effective speed as far as light from stars reaching us is much greater.

The inflationary hypothesis was advanced to solve the horizon and flatness problems, but it also inadvertantly solved the starlight travel time problem as well.

 

[bob b]

Metric expansion of space
From Wikipedia, the free encyclopedia
The metric expansion of space is a key part of science's current understanding of the universe, whereby spacetime itself is described by a metric which changes over time in such a way that the spatial dimensions appear to grow or stretch as the universe gets older. It explains how the universe expands in the Big Bang model, a feature of our universe supported by all cosmological experiments, astrophysics calculations, and measurements to date.

The expansion of space is conceptually different from other kinds of expansions and explosions that are seen in nature. Our understanding of the "fabric of the universe" (spacetime) requires that what we see normally as "space", "time", and "distance" are not absolutes, but are determined by a metric that can change. In the metric expansion of space, rather than objects in a fixed "space" moving apart into "emptiness", it is the space that contains the objects which is itself changing. It is as if without objects themselves moving, space is somehow "growing" in between them.

Because it is the metric defining distance that is changing rather than objects moving in space, this expansion (and the resultant movement apart of objects) is not restricted by the speed of light upper bound that results from special relativity.

 

[JustinFoldsFive]

Hasn't Guth's inflationary model been replaced by Linde's chaotic inflationary model?

 

[bob b]

Hasn't Guth's inflationary model been replaced by Linde's chaotic inflationary model?

Yes, but this doesn't change the metric expansion of space situation, which is the main factor which solves the starlight travel time problem.

Basically, a universe created by rapid expansion would have meant that if Adam had a powerful enough telescope he could have seen all the way back to the beginning of the creation (expansion), but because all lightwaves had been expanded equally, everything he saw would transpire in ultraslow motion, the exact opposite of what an astronaut falling into a black hole would see behind him happening among the galaxies and stars (ultrafast motion).

Neat. God has provided us a ringside seat to his great and glorious creative act.

 

[lee_merrill]

Life has formed from non-life by simple chemical reactions. This is a website to start but you won't even go there:
http://www.theharbinger.org/articles/rel_sci/fox.html

"Figure 1. Cells from thermal protein."

Well, what are they, though? Certainly not cells, or we'd have been hearing about this on every street corner. So this is deliberate deception? I'm not sure but proteiniods is about the best I know of, which are little bubbles, but that's all, they are not cells.

"One thing that will make tonight so exciting is a video tape ... in which you will see the phenomenon of living cells forming before your eyes."

No way!

"The expectation of protein chemists, which we shared, is that thermal protein, then called proteinoid, would be randomly disordered."

Right, it's a proteinoid, these are not cells!

"Since when is a videotape "handwaving"? "

When the author is waving his or her hands?

"What emerges is a set of 153 molecules that include the 11 members of the reductive citric acid cycle, as well as some other molecules from the metabolic chart. We argue that there is an enormous simplification as well as indication that the chemistry at the core of the metabolic chart is necessary and deterministic and would likely characterize any aqueous carbon-based life anywhere it is found in this universe."

Please! Let's simplify some more, there are only about 20 standard amino acids, or we can make this even simpler, most biochemical molecules are combinations of C-O-H-N atoms, but that proves no more than an assertion that posts here are written with 26 letters.

That explains nothing about their origin...

 

[seer]

3. Life has formed from non-life by simple chemical reactions. This is a website to start but you won't even go there:
http://www.theharbinger.org/articles/rel_sci/fox.html

You want demonstration?
"One thing that will make tonight so exciting is a video tape ... in which you will see the phenomenon of living cells forming before your eyes."

First, lucaspa, as Lee pointed out this is a falsehood - they don't show living cells forming before your eyes. Second, even if you could tweak inorganic compounds and make organic compounds how do you know that was how organic life was created on earth? The fact is you can't - nor could you ever...