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Intelligent Design, the best explanation of Origins » Intelligent Design » Biologic Institute's Groundbreaking Peer-Reviewed Science Has Now Demonstrated the Implausibility of Evolving New Proteins

Biologic Institute's Groundbreaking Peer-Reviewed Science Has Now Demonstrated the Implausibility of Evolving New Proteins

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Biologic Institute's Groundbreaking Peer-Reviewed Science Has Now Demonstrated the Implausibility of Evolving New Proteins…/bi…/

In 2011, Ann Gauger and Douglas Axe published a paper in BIO-Complexity, "The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway." They reported results of their laboratory experiments trying to convert one enzyme (Kbl2) to perform the function of a very similar enzyme (BioF2), thought to be very closely related to Kbl2. Because these proteins are both members of the GABA-aminotransferase-like (GAT) family, and are believed to be very closely related, this is the sort of evolutionary conversion that evolutionists say ought to be easily accomplished under the standard co-option model. However, after trying multiple combinations of different mutations, they found otherwise:

We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions.
2010 paper by Axe
Evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl2 and BioF2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution.
Now in their new study, "Enzyme Families-Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase [GAT] Family," Reeves, Gauger, and Axe examine nine other enzymes from the same GAT family. Once again, the idea was to see if it is possible to convert them to perform the function of BioF2. They tested proteins that are closer to BioF2, or more distant from BioF2, than the enzyme they tested in their prior study (Kbl2). But all of the proteins studied are in the same family, and are thought to be closely related.
First, they sought to determine if the enzymes could be converted to perform the function of BioF2 through a single mutation. They created mutation libraries with every single possible mutation in those nine enzymes. No BioF2 function was ever detected. As they explain:
The present study has added to our previous examination of these problems in several respects. We have shown, based on sequence alignment of α-oxoamine synthases (a subset of the GAT family), that our previous use of rational design did indeed target regions of Kbl2 that are likely to be functionally significant. Furthermore we have now shown that the lack of a simple evolutionary transition to BioF2 function is not at all unique to our initial choice of Kbl2 as the starting point. Single mutations cannot convert any of eight other members of the GAT family to that function, despite the fact that all of these enzymes are regarded as close evolutionary relatives.

Last edited by Admin on Thu May 07, 2015 11:47 am; edited 1 time in total

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The arrangement of amino acids determines the enzyme's function

Each enzyme has it own unique three-dimensional structure that determines the function of the enzyme. The three-dimensional structure of enzymes is determined by the order of the amino acids in the coiled string. Even slight changes in the sequence of the amino acids on the string have a huge impact on the structure of the protein. With just one or perhaps a few amino acids replaced or switched, an enzyme may not only look different, but also act different. With only a slight change in the sequence of the amino acids, an enzyme may be converted into working on other biological molecules or treating them differently.

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Getting function in the first place is tough going. Szostak did an experiment with Anthony Keefe in 2001. They tested 6 trillion peptides, each with 80 randomly selected amino acids, for ATP binding. “We were able to select out small, single-domain proteins that did bind ATP. But they were rare, on the order of one in 10^11 sequences,” says Szostak. “Getting function from randomness is hard.” For selection to start happening to peptides, there has to be that spark of function. How that spark appears remains the big, elusive question in the field of protein origin.

under normal circumstances, about one-third of a modern cell’s resources is devoted to protein quality control and turnover. “We’re not talking about a few proteases here and there. We’re talking about substantial resources of the cell just for this routine maintenance,”

Szostak says that the origin of protein function also brings up the question of how many amino acids were around for making the first proteins. “There is pretty good evidence that at least some of the standard 20 amino acids came in late” in evolution, says Szostak. “Some of the simple, easy-to-make ones, like glycine and aspartate, were probably there right from the beginning.” The reduced number of amino acids plays into the folding issue, because there may be constraints in folding peptides made from a smaller number of amino acids.

Overall, what the field of protein evolution needs are some plausible, solid hypotheses to explain how random sequences of amino acids turned into the sophisticated entities that we recognize today as proteins. Until that happens, the phenomenon of the rise of proteins will remain, as Tawfik says, “something like close to a miracle.”

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The problem of building a protein

We can see that the process of chemical evolution has failed at the first hurdle. But, in order to get a complete picture, let’s assume the problem can be solved (and no-one has done that yet!). We now need the amino acids to join together (polymerise) to form proteins.
Figure 3. Primary, secondary, tertiary and quaternary protein structure

Here again we have a string of problems. Let’s start with the basic chemical one. To link the small molecules together, we need to remove water molecules between adjacent amino acid molecules. In the case of two amino acid units, it looks like this:

HOOC - CHR1 – NH2 + HOOC – CHR2 - NH2

↔ HOOC - CH R1 – NH- OC - CHR2 - NH2 + H2O

This is an equilibrium reaction, which does not occur spontaneously, and the yield of protein depends on removing the water. But, the scenario pictured by evolutionary scientists is one that occurs in a pool of water! Not a promising start!

Since it is an equilibrium system, we can apply equilibrium calculations to it. Consider a protein of just 100 amino acids (rather a small one in terms of naturally occurring materials),
K = [protein] = 10-36

If all the atmospheric nitrogen was used to produce the maximum amount of protein, the concentration of protein would be about 10-106 And that is for just one protein – we need hundreds of different ones!

Miller and his colleague Orgel, summed up the position themselves: “Another way of examining this problem is by asking whether there are places on the earth today where we could drop, say, 10 grams of a mixture of amino acids and obtain a significant yield of polypeptides … We cannot think of a single such place.” (Polypeptides are small proteins).

To form these proteins so quickly in the cell, we need accelerators, called enzymes, to enable the reactions to occur rapidly (before the cell dies through lack of a protein!). These enzymes enable reactions to occur in milliseconds. Without them, the reactions can take millions, even trillions, of years. The problem is that enzymes are proteins themselves, and they need enzymes to form themselves!

Consider a cell containing just 124 proteins. Professor Morowitz has calculated that the chance of all these forming without information input is 1 in 10100,000,000. One of the smallest known genomes is that of Mycoplasma genitalium which manufactures about 600 proteins, so what are the chances of that happening without intelligent input? Humans have about 100,000 proteins.

But the problems are only just beginning!

Another big hurdle lies in the structure of the protein molecule. We have seen that it has to be formed by the joining together of these twenty amino acids. For example, the sequence might begin something like this:

Lys – Ala – His – Gly – Lys –Lys – Val – Leu – Gly – Ala -

where the three letters are shorthand for specific amino acids. “Gly” stands for glycine, the simplest amino acid. This chain then twists into a helix. The sequence is called the primary structure and the helix is the secondary structure. Other than the fact that the helical structure can twist in one of two directions (“clockwise” or “anticlockwise”) and it only takes one of these forms in nature, there is no real problem in this second step.

The helix then folds over on itself to give a more complex structure (tertiary structure). This can be imagined most easily by thinking of a floppy spring. If it is released, it will fold over on itself. With the protein chain, there are estimated to be some 100 million different ways it can fold. BUT, only one of these is biologically active. How does it achieve the correct conformation?

The correct tertiary structure for each protein is, in turn, dependent on the primary structure: if the amino acid sequence is changed, the structure will fold incorrectly and lose some or all of its activity. An example of this is in haemoglobin. This is a large molecule with protein side chains. It occurs in our red blood cells and transports oxygen around the body. In one example of the effect of a change in the amino acid sequence, just one change can convert the cell from the very efficient structure we have to a very fragile cell which results in sickle cell anaemia. A person suffering from this deficiency will die young unless they get regular blood transfusions.

A super-computer (“Blue Gene”) is being constructed in order for it to work out what is the best conformation of the protein chain in such structures. When it is complete, it will take a year to do all the calculations. The cell does this in less than a second!

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How Did Protein Synthesis Evolve?

The molecular processes underlying protein synthesis in present-day cells seem inextricably complex. Although we understand most of them, they do not make conceptual sense in the way that DNA transcription, DNA repair, and DNA replication do. It is especially difficult to imagine how protein synthesis evolved because it is now performed by a complex interlocking system of protein and RNA molecules; obviously the proteins could not have existed until an early version of the translation apparatus was already in place.

From our knowledge of present-day organisms and the molecules they contain, it
seems likely that the development of the directly autocatalytic mechanisms fundamental
to living systems began with the evolution of families of molecules that could
catalyze their own replication.With time, a family of cooperating RNA catalysts probably
developed the ability to direct the synthesis of polypeptides. DNA is likely to have
been a late addition: as the accumulation of additional protein catalysts allowed
more efficient and complex cells to evolve, the DNA double helix replaced RNA as a
more stable molecule for storing the increased amounts of genetic information
required by such cells.

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