Changing the way we look at the world
The origin of life
In this blog post I want to review an article recently posted by Science Daily about the origin of life.
The sub-title is:
“An experiment in recreating primordial proteins solves
a long-standing riddle”. Click here for the paper.
The riddle is the origin of positively charged
amino acids, like arginine and lysine, which are
part of almost all proteins found in living things.
But before looking at the solution to this problem,
consider the whole notion of primordial proteins
arising spontaneously in a primordial soup.
This whole scenario is completely hypothetical!
After a summary which gives the background to the problem of how the first proteins appeared spontaneously, without the necessary cellular equipment or an external intelligent agent, the article states that:
“Scientists believe that the very first true proteins materialized from shorter protein segments called peptides.”
They should have qualified “scientists” by writing “some scientists” or “evolutionist scientists”, or “scientists who believe in evolution” because not all scientists share this belief in the miraculous “materialisation” of proteins from peptides which it is claimed,
“would have been sticky assemblies of the amino acids that were spontaneously created in the primeval chemical soup”.
The origin of this “primeval chemical soup” has never been explained because it cannot be explained. It is simply assumed to have existed even though no-one can provide a rational explanation. Or even a definitive list of ingredients for this “soup”.
Instead there is a rather disingenuous attempt to provide a credible argument by referring to “the famous experiment by Miller and Urey” who by using carefully arranged laboratory apparatus and carefully selecting the starting ingredients and carefully excluding oxygen, were able to manufacture a mixture of amino acids. The idea that this replicated conditions on earth prior to life is completely incorrect, unless there were retort stands, glass flasks and other laboratory equipment used by Miller and Urey on the "early" earth!
Neither do they mention that the amino acids formed in this experiment were a racemic mixture of L and D amino acids (two different optical isomers of each amino acid). Proteins are made up of only L amino acids. A protein or peptide made up of an equal mixture of L and D amino acids is non-functional.
Another problem it that if you put amino acids in water, they will not spontaneously form chains of amino acids known as peptides. So the peptides have to form in some non-aqueous solution. The origin and nature of this non-aqueous solution is a mystery. Not to the mention that peptide synthesis is a very complicated process and requires carefully controlled conditions and precisely timed introduction of highly purified reagents or a living cell. To anyone with a basic understanding of the chemistry of peptide synthesis, this hypothetical primeval chemical soup appears to be somewhat magical!
All of these problems makes the problem of the missing positively charged amino acids like arginine and lysine which this article claims has been solved, rather less of a triumph than the authors suggest.
In the next post I will look at why, even though on the face of it the scientists’ solution to this problem is ingenious, this does not really make origin of life theories any more credible.
In this 2nd blog post on this subject I want to look at the solution to the riddle which the Science Daily article mentions.
As I wrote earlier the solution to this problem is ingenious, but this does not really make origin of life theories any more credible?
They started with the fact that one positively-charged amino acid did form in the Miller-Urey type experiments, an amino acid called ornithine. This amino acid is an intermediate step in arginine production in living cells.
They then designed an experiment based on proteins which contains arginine and lysine and binds to DNA (e.g. histones). This required the manufacture of similar, but smaller proteins, of about 60 amino acids of which about one sixth were ornithine instead of arginine and lysine. This protein also bound to DNA, but not very well. By converting more and more of the ornithine to arginine they were able to show that the protein bound more strongly to DNA.
They stated that ornithine can be converted to arginine under “those conditions assumed to have prevailed on Earth at the time the first proteins would have appeared”. What they mean is the absence of oxygen. However, that is not enough because other chemicals which they introduced in carefully control conditions were required to convert ornithine to arginine. Furthermore, they did not provide a plausible mechanism which works without the intervention of a chemist.
Just because a reaction can occur under certain conditions if the right chemicals are brought together at the right time, does not make that a plausible route for abiogenesis, in a hypothetical primeval chemical soup. There also has to be a mechanism to assemble the amino acids into a peptide chain. This is not straight forward, because a random mixture of amino acids will not produce a linear sequence of a peptide since there are reactive side groups. So even if somehow the right amino acids were produced in the right proportions and somehow brought together, they are very unlikely to have formed the peptide constructed by the scientists who carried out the experiment.
Have look here to see what is involved in real peptide synthesis!
Then the researchers went on to show that, in the presence of RNA, phase separation took place which is analogous to the formation of isolated droplets. From there they make another leap to proto-cells from which true living cells might have evolved.
Let’s look at what they are suggesting:
All that we know about chemistry makes this impossible.
There is no abiotic pathway to pure optical isomers of amino acids.
There is no known route to form a peptide of more than a few amino acids from a random solution of amino acids. Even though one experimenter showed that heating a mixture of carefully selected amino acids produce short peptides of a few amino acids. The problem was that these were cross-linked and therefore not the linear peptide chains that are required (see here for more information )
What we are talking about here is the abiotic generation of a peptide more than 60 amino acids long.
And what about the RNA that suddenly becomes available in this primeval chemical soup.
There is no known abiotic route to RNA, not even the production of all four nucleotide bases, in some primeval chemical soup. Not to mention that these too would all have to be the same optical isomer.
All of these things have to occur without anyone controlling the process. The hypothetical conditions would have to produce amino acids, peptides and RNA at the right time and in the same place in high enough concentrations to interact.
The best that can be said for this scenario is that some of components can be manufactured under what is believed to have been the atmosphere of the early earth.
But there is another problem for abiogenesis. This all has to start in an atmosphere without oxygen. Evolutionists say that there was plenty of time for these improbable events to take place, but the best evidence we have suggests that oxygen was present in the atmosphere very soon after the formation of the Earth as shown here. So even if you believe that the Earth is billions of years old, you still only have a few 100 million years to overcome the improbability of life appearing.
In conclusion the claim that this experiment solves a riddle and somehow makes the theory of abiogenesis more of a possibility is hardly a valid statement.
The whole process from chemical soup to chemical engineer is so improbable that we really should examine the alternative of an intelligent designer.
In this blog post I want to review an article recently posted by Science Daily about the origin of life.
The sub-title is:
“An experiment in recreating primordial proteins solves
a long-standing riddle”. Click here for the paper.
The riddle is the origin of positively charged
amino acids, like arginine and lysine, which are
part of almost all proteins found in living things.
But before looking at the solution to this problem,
consider the whole notion of primordial proteins
arising spontaneously in a primordial soup.
This whole scenario is completely hypothetical!
After a summary which gives the background to the problem of how the first proteins appeared spontaneously, without the necessary cellular equipment or an external intelligent agent, the article states that:
“Scientists believe that the very first true proteins materialized from shorter protein segments called peptides.”
They should have qualified “scientists” by writing “some scientists” or “evolutionist scientists”, or “scientists who believe in evolution” because not all scientists share this belief in the miraculous “materialisation” of proteins from peptides which it is claimed,
“would have been sticky assemblies of the amino acids that were spontaneously created in the primeval chemical soup”.
The origin of this “primeval chemical soup” has never been explained because it cannot be explained. It is simply assumed to have existed even though no-one can provide a rational explanation. Or even a definitive list of ingredients for this “soup”.
Instead there is a rather disingenuous attempt to provide a credible argument by referring to “the famous experiment by Miller and Urey” who by using carefully arranged laboratory apparatus and carefully selecting the starting ingredients and carefully excluding oxygen, were able to manufacture a mixture of amino acids. The idea that this replicated conditions on earth prior to life is completely incorrect, unless there were retort stands, glass flasks and other laboratory equipment used by Miller and Urey on the "early" earth!
Neither do they mention that the amino acids formed in this experiment were a racemic mixture of L and D amino acids (two different optical isomers of each amino acid). Proteins are made up of only L amino acids. A protein or peptide made up of an equal mixture of L and D amino acids is non-functional.
Another problem it that if you put amino acids in water, they will not spontaneously form chains of amino acids known as peptides. So the peptides have to form in some non-aqueous solution. The origin and nature of this non-aqueous solution is a mystery. Not to the mention that peptide synthesis is a very complicated process and requires carefully controlled conditions and precisely timed introduction of highly purified reagents or a living cell. To anyone with a basic understanding of the chemistry of peptide synthesis, this hypothetical primeval chemical soup appears to be somewhat magical!
All of these problems makes the problem of the missing positively charged amino acids like arginine and lysine which this article claims has been solved, rather less of a triumph than the authors suggest.
In the next post I will look at why, even though on the face of it the scientists’ solution to this problem is ingenious, this does not really make origin of life theories any more credible.
In this 2nd blog post on this subject I want to look at the solution to the riddle which the Science Daily article mentions.
As I wrote earlier the solution to this problem is ingenious, but this does not really make origin of life theories any more credible?
They started with the fact that one positively-charged amino acid did form in the Miller-Urey type experiments, an amino acid called ornithine. This amino acid is an intermediate step in arginine production in living cells.
They then designed an experiment based on proteins which contains arginine and lysine and binds to DNA (e.g. histones). This required the manufacture of similar, but smaller proteins, of about 60 amino acids of which about one sixth were ornithine instead of arginine and lysine. This protein also bound to DNA, but not very well. By converting more and more of the ornithine to arginine they were able to show that the protein bound more strongly to DNA.
They stated that ornithine can be converted to arginine under “those conditions assumed to have prevailed on Earth at the time the first proteins would have appeared”. What they mean is the absence of oxygen. However, that is not enough because other chemicals which they introduced in carefully control conditions were required to convert ornithine to arginine. Furthermore, they did not provide a plausible mechanism which works without the intervention of a chemist.
Just because a reaction can occur under certain conditions if the right chemicals are brought together at the right time, does not make that a plausible route for abiogenesis, in a hypothetical primeval chemical soup. There also has to be a mechanism to assemble the amino acids into a peptide chain. This is not straight forward, because a random mixture of amino acids will not produce a linear sequence of a peptide since there are reactive side groups. So even if somehow the right amino acids were produced in the right proportions and somehow brought together, they are very unlikely to have formed the peptide constructed by the scientists who carried out the experiment.
Have look here to see what is involved in real peptide synthesis!
Then the researchers went on to show that, in the presence of RNA, phase separation took place which is analogous to the formation of isolated droplets. From there they make another leap to proto-cells from which true living cells might have evolved.
Let’s look at what they are suggesting:
- First: amino acids have to appear, and in the right proportions.
- Second: these all have to be the same optical isomer.
- Third: the conditions have to change to cause the amino acids to form peptides with the right proportions of each to make the proto-histone.
- Fourth: the ornithine has to be converted to arginine.
- Fifth: Then RNA has to appear (where did that come from!)
- Then the droplets of RNA and histone like protein form and these somehow develop into proto-cells.
- Last but not least the proto-cells evolve into cells with all the machinery needed to maintain metabolism, manufacture proteins, RNA and DNA. A cell capable of life.
All that we know about chemistry makes this impossible.
There is no abiotic pathway to pure optical isomers of amino acids.
There is no known route to form a peptide of more than a few amino acids from a random solution of amino acids. Even though one experimenter showed that heating a mixture of carefully selected amino acids produce short peptides of a few amino acids. The problem was that these were cross-linked and therefore not the linear peptide chains that are required (see here for more information )
What we are talking about here is the abiotic generation of a peptide more than 60 amino acids long.
And what about the RNA that suddenly becomes available in this primeval chemical soup.
There is no known abiotic route to RNA, not even the production of all four nucleotide bases, in some primeval chemical soup. Not to mention that these too would all have to be the same optical isomer.
All of these things have to occur without anyone controlling the process. The hypothetical conditions would have to produce amino acids, peptides and RNA at the right time and in the same place in high enough concentrations to interact.
The best that can be said for this scenario is that some of components can be manufactured under what is believed to have been the atmosphere of the early earth.
But there is another problem for abiogenesis. This all has to start in an atmosphere without oxygen. Evolutionists say that there was plenty of time for these improbable events to take place, but the best evidence we have suggests that oxygen was present in the atmosphere very soon after the formation of the Earth as shown here. So even if you believe that the Earth is billions of years old, you still only have a few 100 million years to overcome the improbability of life appearing.
In conclusion the claim that this experiment solves a riddle and somehow makes the theory of abiogenesis more of a possibility is hardly a valid statement.
The whole process from chemical soup to chemical engineer is so improbable that we really should examine the alternative of an intelligent designer.
