falsifying Natural Selection

[spinoza99]

They cannot be obeying laws of their properties because it is not a property of an object[/color][/i][/b]: ok, when this amino acid gets in this location and that amino acid gets in that location, I will get in this location.

Let me explain. The amino acid Leucine is written: C6H13NO2. It's the property of Carbon Hydrogen Nitrogen and Oxygen to bond with each other. But once you get one Leucine it has to coordinate with another 120 amino acids to get certain protein. Different Leucines have to be placed in a different order in the sequence. One Leucine might have to occupy place 47, another place 63. It cannot be a property of Leucine that it knows in what sequence to get in, because two Leucine have the same composition and yet they move to different locations.

Do you believe that Beethoven's 9th is the result of biochemical processes?

[GenesForLife]

The precise location you speak of exists throughout the cytoplasm in prokaryotes and throughout the endoplasmic reticulum, which occupies a very large part of the Eukaryotic cell, in Eukaryotes, drop that canard immediately.

Look, during transcription all these GTF have to work in coordination with each other and they have to know where they're going. What you just said is similar to saying that they have to go to a baseball stadium but if you would watch the video carefully they have to go to a precise location in the baseball stadium, it's as if they have to find the right seat in the stadium. How do they know how to do this?

I also never got answers about what you think the basic building blocks are for the construction of the first cell.

Transcription happens within the nucleus, and involves transcription factors and RNA polymerase, which are also present in the nucleus, diffusion again, the reaction works by maximizing the probability of an interaction between RNA Polymerase, Transcription factors and the promoter TATA binding box, which is specific.

[spinoza99]

Spinoza, here is the Biochemistry textbook.

http://www.4shared.com/document/11OhNS0 ... ioche.html

Thanks, Genes, I really appreciate it. It's amazing how real you are.

[spinoza99]

Are you saying that anything we don't have an answer for Proves god ?

Feck, one, do you agree that coordination exists in the real world?

Either that coordination is the result of dumb luck, or it's the result of intelligence. I see no evidence that coordination can arise out of randomness.

[GenesForLife]

They cannot be obeying laws of their properties because it is not a property of an object[/color][/i][/b]: ok, when this amino acid gets in this location and that amino acid gets in that location, I will get in this location.

Let me explain. The amino acid Leucine is written: C6H13NO2. It's the property of Carbon Hydrogen Nitrogen and Oxygen to bond with each other. But once you get one Leucine it has to coordinate with another 120 amino acids to get certain protein. Different Leucines have to be placed in a different order in the sequence. One Leucine might have to occupy place 47, another place 63. It cannot be a property of Leucine that it knows in what sequence to get in, because two Leucine have the same composition and yet they move to different locations.

Do you believe that Beethoven's 9th is the result of biochemical processes?

It is the property of the mRNA to hold the tRNA containing leucine when the corresponding codon is obtained.

the property of a U on mRNA is to bind with an A on other RNA.
the property of a tRNA carrying AAU on it's anticodon arm (the shape of this is again determined by base pairing) is to carry leucine with it, this again comes from the property of the aminoacyl tRNA synthetase that fixes a particular amino acid to a particular tRNA.

When mRNA is undergoing translation, when the ribosome meets finds UUA on the mRNA, only the tRNA carrying AAU is able to bind to the UUA on mRNA, then the ribosome catalyzes a peptide bond between leucine and the next.

The sequence of nucleotides in the mRNA, through it's properties of base pairing, governs what amino acid is incorporated into a protein at what position.

[GenesForLife]

and the reason UUA should hold AAU is that U binds to A, which again is the fundamental property of nucleic acid strands.

[JimC]

... what evidence can you present for that?

The evidence lies in the odds. The general transcription factors are moving in precise locations. They are not moving like Brownian Motion. They cannot be obeying laws of their properties because it is not a property of an object: ok, when this amino acid gets in this location and that amino acid gets in that location, I will get in this location. We know this because although that happens the same amino acid that has that composition will act in a different way.

Could you please clarify the statement/claim that is bolded and colored in the quote? Especially the word "it" throws me off - what does that "it" reference to / signify?

Ronja, I suspect that what spinoza99 is puzzling over is the information content embedded in a given sequence of amino acids, and how the sequence seems to "miraculously" produce a perfect function for that given protein. Until one has thought hard about the immensity of geological time and the vast number of self-replicating molecules, the ability of selection to blindly fashion such intracacies must seem like an affront to reason. Dan Dennet's "Darwin's Dangerous Idea" deals very nicely with the philosophical questions which arise in this area.

[Feck]

Do you believe that Beethoven's 9th is the result of biochemical processes?


Well yes, ultimately, especially as the western idea of music is based on a set of note values that are arbitrary . A Chinese person would not recognise the chords or the tones as signifying the same emotions as a western person would . BuT MEH

Bored with losing the game over biology and now we are onto music and art and beauty ?


You do know that the fuse on that Petard you are carrying is awful short don't you Spinoza !

Fuck at this rate you will be down to proofs for god as inane as Mandleson our Muslame member ,whose proof was that Allah made Cheryl Cole beautiful therefore there is a god Innit .

[GenesForLife]

In fact, it now appears that the binding of the right amino acid to the right tRNA through aminoacyl tRNA is governed by other equations that govern any chemical reaction, those familiar with enzymology should have heard about Km and Vmax and so on. Here is one abstract.

http://www.sciencedirect.com/science?_o ... archtype=a

It is generally believed that the specificity of tRNA aminoacylation results solely from a specific recognition between the aminoacyl-tRNA synthetase and the cognate tRNA. In fact, this specificity is not absolute: this is supported by the following observations (1) the existence of tRNA mischarging in homologous systems under usual aminoacylation conditions, (2) the existence of inhibitions produced by « non-cognatetRNA species in correct aminoacylation reactions, (3) the lack of specificity of AMP- and PPi- independent aminoacyl-tRNA synthetase catalysed deacylation of aminoacyl-tRNA species, (4) the isolation of complexes between aminoacyl-tRNA synthetases and non-cognate tRNA species.

The affinities between aminoacyl-tRNA synthetases and non-cognate tRNA species, estimated by the Km measurements in mischarging reactions, have been found only diminished by 1 or 2 orders of magnitude as compared to the values found in specific systems, whereas the Vmax values for mischarging have been found diminished by 3 or 4 orders of magnitude. This suggests that tRNA aminoacylation depends more upon the maximal velocity of the reaction than upon the recognition between aminoacyl-tRNA synthetase and tRNA.

Furthermore, we found that the recognition of a tRNA by an aminoacyl-tRNA synthetase does not seem to require the 3′ terminal part of the amino acid acceptor stem. As the importance of this part of the tRNA molecule during the aminoacylation process has been well established, it is possible that it is involved in determining the Vmax of the aminoacylation reaction, probably by positioning the 3′ terminal adenosine in the catalytic site of the enzyme.

In conclusion, it appears that the specificity of the tRNA aminoacylation reaction proceeds through two discrimination mechanisms: the first one, measured by the Km, acts at the recognition level; the second one, which is more effective, is measured by the Vmax values.

Competition phenomena have been observed between cognate and non-cognate tRNA species. They enhance the specificity of the tRNA aminoacylation, but their contribution to the specificity is low compared to that brought by Km and Vmax.

Finally we found that a more rapid enzymatic deacylation of mischarged tRNA species (as compared to correctly charged ones) cannot be considered as a general mechanism for correction of misaminoacylation.

That explains why it is the property of certain tRNAs to carry certain amino acids, this combined with why tRNAs bind specifically to mRNA by base pairing explains how DNA, through mRNA, can "tell" amino acids to be incorporated in a specific order in a protein.

[GenesForLife]

And on that note, someone came up with this back in 1987.

Abstract

Single-stranded RNA viruses often have 3'-terminal tRNA-like structures that serve as substrates for the enzymes of tRNA metabolism, including the tRNA synthases and the CCA-adding enzyme. We propose that such 3'-terminal tRNA-like structures are in fact molecular fossils of the original RNA world, where they tagged genomic RNA molecules for replication and also functioned as primitive telomeres to ensure that 3'-terminal nucleotides were not lost during replication. This picture suggests that the CCA-adding activity was originally an RNA enzyme, that modern DNA telomeres with the repetitive structure CmAn are the direct descendants of the CCA terminus of tRNA, and that the precursor of the modern enzyme RNase P evolved to convert genomic into functional RNA molecules by removing this 3'-terminal tRNA-like tag. Because early RNA replicases would have been catalytic RNA molecules that used the 3'-terminal tRNA-like tag as a template for the initiation of RNA synthesis, these tRNA-like structures could have been specifically aminoacylated with an amino acid by an aberrant activity of the replicase. We show that it is mechanistically reasonable to suppose that this aminoacylation occurred by the same sequence of reactions found in protein synthesis today. The advent of such tRNA synthases would thus have provided a pathway for the evolution of modern protein synthesis.

http://www.pnas.org/content/84/21/7383.abstract

They argue that RNA viruses carry molecular fossils that may enable the reconstruction of the evolution of modern protein synthesis.

[GenesForLife]

If one is wondering about the three dimensional structure of proteins, it boils down to some complicated chemistry, and that is that, including hydrogen bonding, hydrophobic and hydrophilic interactions, and substrate binding. This is the reason we can use nothing more than the sequence of a protein to predict its structure and function, there are tools such as I-TASSER which involve what we call ab-initio or "from scratch" modelling

[Ronja]

... coordination exists in the real world?

Either that coordination is the result of dumb luck, or it's the result of intelligence. I see no evidence that coordination can arise out of randomness.

That either - or statement is a just one variation of false dichotomy (false dilemma) http://www.nizkor.org/features/fallacie ... lemma.html , which is a well-known non sequitur = failure of logic. You would do well to learn a bit about those: http://www.nizkor.org/features/fallacies/ or http://www.csun.edu/~dgw61315/fallacies.html or http://www.infidels.org/library/modern/ ... logic.html

You cannot possibly know for certain that there exists only two alternative explanations for coordination. For example, I coordinate my activities with many other human beings daily. Much of that coordination is the result of neither dumb luck nor intelligence, but instinctive-based and deeply routine reactions to automatic observations of other people's movements, postures, trajectories and speeds of movement, tone and loudness of voice, etc, etc.

[JimC]

If one is wondering about the three dimensional structure of proteins, it boils down to some complicated chemistry, and that is that, including hydrogen bonding, hydrophobic and hydrophilic interactions, and substrate binding. This is the reason we can use nothing more than the sequence of a protein to predict its structure and function, there are tools such as I-TASSER which involve what we call ab-initio or "from scratch" modelling

GFL, I heard somewhere that some proteins have more than one possible structure after folding. Can you illuninate this, just out of interest?

[GenesForLife]

Spotted another fallacy, peptide bond catalyzing ribozymes are different from peptide bond catalyzing ribosomes.

[spinoza99]

mRNA = to hold the tRNA containing leucine when the corresponding codon is obtained.
U = on mRNA is to bind with an A on other RNA.
tRNA = carrying AAU on it's anticodon arm (the shape of this is again determined by base pairing) is to carry leucine with it,
ribosome = catalyzes a peptide bond between leucine and the next.

This is what you don't understand. The fact that objects have properties is just like a language. According to the American Chemical Society there are some 52 million substances, 50 thousand being added each week, all of them having different properties. In a random universe without intelligence you cannot expect objects to coordinate their properties, no more that you can expect randomness to coordinate a set of 26 letters to form words. mRNA, U, tRNA and ribosomes as well as the other General Transcription Factors they all have to be present at a specific point in a specific time. Basically what it comes down to is

if
mRNA and TRNA and U and Ribosomes
then
cell replication

albeit it is much more complicated than that.

Just to give you an idea of how hard it is for randomness to coordinate between even very small finite sets, let's imagine that there were only 120 substances in our universe and at one point in time in order to solve a problem only two substance were needed but they needed to be in the right order, even though this series is only two long. That's 120^120, which comes to 10^258 possibilities. To put that in perspective, there are 10^80 atoms, 10^26 nanoseconds in our universe and if we lived in a multiverse where there are as many universes as there are stars in our Universe that would be 10^22, which brings that to a sum total of 10^128. So even if every atom in our universe tried to utter the correct two word combination every nanosecond in every universe in our hypothetical multiverse, the odds of them hitting on the right combination would still one in 10^130.