Origin of Life: Folded Proteins, Twisted Conclusions, Cooked Schemes… It all supports evolution?

FEATURED IMAGE: THE REPLICATION OF DNA.  NOTE THAT EACH DIFFERENT COLORED BLOB IS A THREE DIMENSIONAL PROTEIN MACHINE DESIGNED SPECIFICALLY TO DO A JOB IN THE REPLICATION PROCESS.  EACH PROTEIN THAT BINDS TO THE DNA IS ENCODED BY THE DNA.

 

Dead Sea is dead because of salt.  Only things like bacteria live well in the water.

Dead Sea is dead because of salt. Only things like bacteria can live in the water.

Origin of life researchers generally search for extreme environments that are rare or certainly atypical of the abundant, moderate environments that most life forms thrive in.  The reason for this is the supposed extreme conditions that are postulated for the evolution of the early earth.  Extreme heat, salt, acid or other physical conditions such as lack of oxygen are all important “starting points” for those who claim a materialistic answer to how life began.   If the world was a sewer pit to begin with, the chemical conditions to start life must have existed under those conditions; or so it would seem to some scientists.  If this is the paradigm for evolution then any organism that currently thrives under such drastic conditions may hold answers to how we all got here.  But biologists ignorant of microbiology, molecular biology or chemistry of any kind often proceed on false assumptions like evolution and miss the factors vital to designing useful experiments.

 

A typical example of how this research proceeds was recently published by the Proceedings of the National Academy of Sciences  (1). The research found that proteins made from a handful of amino acids that may have been typical of those deposited on the ancient earth by comets or asteroids, will fold under the extremely salty conditions that may have typified the ancient earth.   These 12 of the 20 amino acids that are considered “essential amino acids”, because they are literally encoded for in the information content of DNA, were chosen for building proteins for the salt experiment since they have been found in some abundance by spectroscopic studies of the night sky.

 

From a specified linear (chain) of amino acids a protein must fold in order to function

From a specified linear (chain) of amino acids a protein must fold in order to function

As the argument for the study goes, it is essential that proteins, when formed, undergo folding to create the 3-D shape of the molecule.  It is understood that the shape of the molecule is what gives it the ability to perform the functions needed for life to occur.  Enzymes all have very specified shapes that impart the ability of the protein to speed metabolic reactions up to a million times faster than would occur without the enzyme.  For instance, it is the fold of the protein called amylase that is secreted in saliva that allows the protein to breakdown potato starch into glucose.  Without this enzyme starch will break down to glucose and a dozen other small chemicals due to heat, radiation and spontaneous chemical degradation.  Enzymes allow for biochemistries to occur in microseconds.  This is one feature that makes life different from non-living things.

Living cells control the folding of proteins using energy and other proteins to "chaperone" the process.

Living cells control the folding of proteins using energy and other proteins to “chaperone” the process.

 

Now, the correct fold for a protein is dependent on a multitude of agencies.  The protein must be made with the correct linear arrangement of amino acids.  The fold must be made while guided by helper proteins and often the attachment of sugar molecules.  However, some proteins because of their specified arrangement of amino acids may fold spontaneously.  This is what has excited Dr. Blaber so much.

 

He has found that some proteins made from a few amino acids can spontaneously fold in the conditions of the supposed primitive earth, in a primitive condition of high salt solution.  He said,

 

“There are numerous niches that life can evolve into,” Blaber said. “For example, extremophiles are organisms that exist in high temperatures, high acidity, extreme cold, extreme pressure and extreme salt and so on. For life to exist in such environments it is essential that proteins are able to adapt in those conditions. In other words, they have to be able to fold.”

 

Salt loving bacterial cells.

Salt loving bacterial cells.

While he is correct that proteins must fold in order to function his experiment adds nothing to the origin of life research.  Why?  Because even bacteria that live in the saltiest lakes on earth do not contain a salt environment inside the cell that is the same as that outside the cell.  This is true of acidophiles as well.  It is inside the cell where proteins are made and function.  All halophilic (salt loving) bacteria have several mechanisms to combat the salt-water environment that they live in.  Many bacteria combat the salty solution outside the cell by creating high concentrations of free amino acids, sugars and even polyols (alcohols and similar chemicals) inside the cell.  They also spend an enormous amount of energy to keep salt out of the cell. A second mechanism bacterial cells use is to preferentially accumulate specific salt ions like potassium and chloride.  In a controlled ionic cytoplasm, proteins rich in negatively charged amino acids can function just fine.   Cells that are acid loving provide neutral conditions inside the cell in order for proteins to function. In the case of salt loving bacteria, this avoids protein aggregation or “salting out” of proteins inside the cell that would kill all life functions.  By creating a chemistry inside the cell that is not detrimental to the precious biochemistry of life, halophilic bacteria survive their harsh conditions.  They make the inside of the cell osmotically the same as  the outside of the cell using biologically safe chemistry and each cell uses safe chemistry to both combat salting out of their proteins and to protect those proteins so they can the do the job they were folded to do.  Life goes on and metabolism proceeds unabated by the harsh conditions outside the cell.

 

Any studies which involve making proteins in salty water or testing their ability to fold under salty conditions is completely irrelevant to the quest for materialistic answers to life’s origin.  Moreover, just because proteins fold without crashing (salting out into aggregates of muck) does not mean anything unless it can be proven that the fold was the correct fold and the protein’s function was preserved.  None of this was part of the interest in the team of scientists who somehow got their work published in a peer-reviewed journal.  No important fold was recognized and no metabolism was provided by the proteins made from these few amino acids.

Three dimensional structure of a calcium binding protein.  Discovered 40 years ago it is still being studied to understand its complexity.  I have spent the past 7 years of my life studying this protein.

Three dimensional structure of a calcium binding protein. Discovered 40 years ago it is still being studied to understand its complexity. I have spent the past 7 years of my life studying this protein.  Gray balls are calcium ions bound to the protein. Without the right folding, calcium is not bound.  The rest of the protein is designed to generate light when the calcium loops bind calcium; this is one form of bioluminescence.

 

In fact, protein folding is one of the greatest mysteries of enzymology.  Folding is rarely predictable and very difficult to engineer into a synthetic protein.   An entire field of biochemical study is trying to decipher this rather ingenious but cryptic mechanism that is inherent in every enzymatic protein produced by a living cell. Even more challenging is how enzymes are able to recognize the chemicals that they bind to and modify.  Still another field of science studies the means by which biochemical molecules attract one another and in just the right configuration in time and in space.  It is this mystery that increases the rate of metabolism millions of times beyond non biological means.  One theory suggests that water is able to transmit specified electrochemical images of one molecule through to another molecule due to its contact with water molecules.  This creates an electromagnetism of sorts that directs the specificity of one molecule’s recognition of another.  Pretty cool huh?

 

I might include a few clues to those researchers looking to find some evidence that life evolved from thermal vents at the bottom of the ocean.  Here, unlike in salt-loving life forms,  protein folding does occur in the cell at the temperature of the surrounding water.   The bacteria and the animals that thrive at temperatures in excess of 400 degrees C and at pressures several hundred times higher than atmospheric pressure also contain proteins that are unique in ways we are only beginning to understand.  Two mechanisms are used by thermophilic (heat loving) cellular life in order to allow metabolism to occur at extremely high temperatures (2).  First, the sequence of amino acids that make the protein is unique at precisely the right regions of the protein so that when the protein folds it does so to create an increase in the strength of the internal contact points that hold the protein in the 3-D shape.  The second trick is similar to the first.  It results in a protein of the same function as bacteria that live in more moderate environments, but there are more contact points within the molecule that tighten the compactness of the protein.  The effect, once again, is to strengthen the protein’s resistance to unfolding even at high temperatures.

Thermohiles live at thermal vents.

Thermophiles live in heated pools.  Evolution at thermal vents is wishful thinking but adds factors that simply complicate the issue.

Good science would recognize that cells must manage their cytoplasmic environment in order for biochemistry to proceed; this is particularly true for the extremophiles.  How could proteins evolve without such controls in place, before they were theoretically made and before they had a function to perform?  Evolution is a non intelligent superstition.  It is not science.

Overall, we are forced to consider the engineering of the DNA molecule that codes for these unique protein structures.  They allow life to proceed unimpeded by the extreme heat but only due to the forethought of the designer that understood how to engineer life for extreme conditions, long before any materialistic mechanism based on chance could have stumbled upon such exquisite knowledge.   We are also forced to consider the design of the halophile and it’s complex sensory knowledge and feedback loops to the DNA molecule.  These biochemical loops are required in order that the cell might “know” what extra amino acids to produce or what kind of polyols and sugars are called for to fight the loss of water from inside the cell to the outside of the cell.

Honestly, I don’t feel much pity on scientist who spend their whole life chasing the shadows of Darwin’s dark nightmare.  These scientists appear to be ill-equipped to critically examine the design of their experiments and are completely lost at interpreting their findings.  Regardless of the results somehow everything that every evolutionary scientists discovers supports evolution.  Somehow each discovery is one “… that could lead scientists a step closer to understanding how life first emerged on Earth billions of years ago.” (Science Daily).

I DON’T THINK SO!

 

[1] L. M. Longo, J. Lee, M. Blaber. Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein. Proceedings of the National Academy of Sciences, 2013; 110 (6): 2135.

[2] Igor N. Berezovsky and Eugene I. Shakhnovich.  Physics and evolution of thermophilic adaptation.  Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138.  2005.

 

Leave a Reply

Your email address will not be published. Required fields are marked *