Predictions of the Theory of Evolution that did not concretize
DNA predictions : The DNA structure gave rise to first life
Despite the fact that the origin of life belongs to abiogenesis, many propose evolution as the driving force to produce the first living cell, despite the fact that evolution only works after replication begins. The following article deals with the proposal that evolution could be the driving force for the arise of the first life.
http://web.archive.org/web/20090126042355/http://darwinspredictions.com/#_4._L._E.
The DNA structure gave rise to first life
Introduction
DNA is a double helix. As Fig. 1 illustrates, it contains two strands that are twisted about each other, just as a rope might consist of two smaller ropes wrapped around each other. Both DNA strands consist of a series of molecules bonded together in sequence. The molecules are called nucleotides and if you stretched out the strand the nucleotides would line up in a row, like beads on a string. These nucleotides are the DNA’s information which encodes the genes in the DNA. If each nucleotide represents a letter, then a gene is similar to a paragraph in a book. DNA strands use four different kinds of nucleotides, so in this language there are only four letters.
A tremendous amount of effort has been spent on understanding how these molecular letters are read. In 1953, before the DNA structure was deciphered using X-ray photographs, the great American chemist Linus Pauling predicted that the nucleotides pointed outwards from a helix. A few years earlier Pauling had successfully predicted the helix structure of proteins. Now he would try to do the same for the DNA structure. If the nucleotides pointed outwards, Pauling reasoned, they could be read without having to pull apart the DNA. But this time Pauling’s intuition failed him.
Not long after that Francis Crick and James Watson, working in Cambridge, England, solved the puzzle. Using Rosalind Franklin’s X-ray measurements they determined not only that DNA normally is a double helix, but that the nucleotides are pointed inwards, toward the center of the helix. [1] “We have discovered the secret of life,” proclaimed Crick at a nearby Cambridge pub.
Watson and Crick’s new DNA model was a great breakthrough and soon DNA was viewed as the blueprint that was modified over the course of evolution to create new species.
Prediction
Most proponents of evolution believe that the first life arose from non-living chemicals. In a letter Darwin speculated of a warm little pond with a protein compound ready to undergo more complex changes. [2] After Darwin evolutionists attempted to flesh out this story.
It was not easy to explain how something as complicated as a living cell could emerge on its own. Proponents of evolution needed to start with something far simpler than an entire cell. If some fundamental component of the cell could arise on its own, perhaps then the other cellular components would gradually aggregate and eventually build up to a complete cell. The research was driven not by positive scientific findings so much as the acceptance of Darwin’s theory.
Before Watson and Crick discovered the DNA structure, some proponents of evolution felt that life began with a single gene. With the gene’s molecular structure explained by Watson and Crick, this genes-came-first view began to take shape. That first gene, it was then understood, would have been a segment of DNA.
Nobel Laureate H. J. Muller had promoted the genes-came-first idea, and the DNA structure did nothing to detract from his convictions. He continued to advocate for the primacy of genes. After all, DNA coded for proteins, not vice-versa. A segment of DNA contained the sequence information for a protein, but a protein did not contain the DNA sequence information.
The great popularizer (and scientist) Carl Sagan also held to this idea that life must have come from non-life via the spontaneous assembly of DNA. Sagan used the term “naked gene” to convey the idea that life began with DNA, absent the other cellular components and environment. [3]
Falsification
The prediction that the DNA molecule formed on its own, and then led to the formation of the first life, we now know is problematic for many reasons. For instance, each nucleotide, consisting of its nitrogenous base, ribose sugar and phosphate group, is a fairly large organic molecule. These do not spontaneously form, even when the right ingredients are coaxed together in experiments mimicking some hypothetical primitive, early Earth condition. “There is at present,” concluded one senior researcher recently, “no convincing, pre-biotic total synthesis of any of the nucleotides.” [4]
Beyond this there remain several more problems. For instance, even if nucleotides could somehow form on their own, they would likely be at low concentrations because there are many alternate conformations they could assume. Also a great many other organic molecules could form in the brew. What is needed is a particular type of molecule, not a menagerie.
And even if the right type of building block molecule could somehow be created at reasonable concentrations, these molecules would have to polymerize (i.e., chemically bond to form a sequence, like beads on a string). This requires energy and precision. Nonetheless, what is needed are long DNA polymers (thousands or at the very least hundreds of nucleotides long).
Next the nucleotides must encode information. Even if DNA polymers could form on their own, they cannot be just any polymer. Long DNA polymers that are functional are rare. One experiment, dealing with randomized protein sequences, showed that about one hundred trillion such sequences are needed before even a simple binding function is obtained. [5] This result is optimistic because the protein was relatively unstable and short. Most proteins are several times longer, and longer sequences would likely have even lower rates of functionality. Also the function was elementary. Proteins that do something useful do far more than merely bind to a chemical.
Finally, even if long, functional DNA polymers could form on their own, they would need helper molecules (such as today’s proteins) to perform the copying, translating and replicating tasks. This chicken-or-the-egg problem arises because DNA alone cannot perform the various tasks needed to form a living entity, no matter how simple.
The theory of evolution motivated the idea that a lone DNA molecule was the starting point for the history of life on Earth, but we now know of several substantial problems with this hypothesis. Alternative theories have not fared well either.
Reaction
To address these many failures of earlier expectations, proponents of evolution have continued to speculate about how first life could have arisen, constructing a variety of complicated hypotheses. For instance, one idea is that evolution formed information bearing, functional sequences via natural selection. The appeal to natural selection certainly fits well within the theory of evolution, but is rather heroic in this case because selection requires that many test trials can be run with a mechanism for selection. In Darwin’s theory that mechanism is reproductive success, but that requires elaborate mechanisms to be in place . The selection of functional DNA polymers requires more than merely some trial sequences. New DNA sequences can be selected in the laboratory, such as in directed evolution experiments, but this requires an elaborate apparatus. [6,7]
Another hypothesis proponents of evolution constructed in recent decades is that life began not with DNA but with its cousin molecule, RNA. There is no trace of this today, but proponents of evolution hypothesized that first life was RNA-based, and then at some point it switched to DNA. This more complicated hypothesis takes advantage of the fact that RNA not only can store information like DNA, but also can accomplish some of the copying tasks by itself, without the help of proteins. Soon the DNA-first hypothesis was replaced with the idea of an “RNA world,” which gave proponents of evolution substantially more room to speculate. [8,9]
The new RNA world hypothesis was often interpreted as more or less solving the problem of how the first replicating molecule arose. Yet even if this hypothesis completely resolves the chicken-or-the-egg problem, there still remain the other problems, including nucleotide synthesis and low concentration, polymerization and information. As one paper put it, the RNA world is a “prebiotic chemist’s nightmare.” For as Leslie Orgel explained, “The prebiotic synthesis of nucleotides in a sufficiently pure state to support RNA synthesis cannot be achieved using presently known chemistry.” [4] This has led to the search for substitutes for DNA and RNA which perhaps could do the job initially, and then be replaced by today’s genetic system at some later time. But DNA and RNA have excellent properties and substitutes do not come close to fulfilling their roles. As Robert Shapiro writes:
Gerald F. Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute concluded that the spontaneous appearance of RNA chains on the lifeless Earth “would have been a near miracle.” I would extend this conclusion to all of the proposed RNA substitutes that I mentioned above. [10]
No one can say what future research will tell us, but the evolutionary hypotheses from the early and mid 20th century about how life initially arose have led research down long, circuitous, trails. Consequently evolutionary ideas of how life arose are highly complex, consisting of low-probability events and substantial serendipity.
References
1. Horace F. Judson, The Eighth Day of Creation: The Makers of the Revolution in Biology (New York: Simon and Schuster, 1979), 147ff.
2. C. Darwin The Life and Letters of Charles Darwin, ed. Francis Darwin (London: John Murray 1887, Vol. III), 18.
3. Robert Shapiro, Origins: A Skeptic’s Guide to the Creation of Life on Earth (New York: Bantam Books, 1986), 136.
4. L. E. Orgel, “Prebiotic chemistry and the origin of the RNA world,” Critical Reviews in Biochemistry and Molecular Biology, 39 (2004): 99-123.
5. A. D. Keefe, J. W. Szostak, “Functional proteins from a random-sequence library,” Nature 410 (2001): 715-718.
6. Y. Hayashi, H. Sakata, Y. Makino, I. Urabe, T. Yomo, “Can an arbitrary sequence evolve towards acquiring a biological function?,” J Molecular Evolution 56 (2003):162-168.
7. G. F. Joyce, “Directed evolution of nucleic acid enzymes,” Annual Review of Biochemistry 73 (2004): 791-836.
8. T. A. Lincoln, G. F. Joyce, “Self-sustained replication of an RNA enzyme,” Science (2009).
9. S. Pino, F. Ciciriello, G. Costanzo, E. Di Mauro, “Nonenzymatic RNA ligation in water,” J Biological Chemistry, 283 (2008): 36494-36503.
10. R. Shapiro, “A simpler origin for life,” Scientific American, February 12, 2007.
DNA predictions : The DNA structure gave rise to first life
Despite the fact that the origin of life belongs to abiogenesis, many propose evolution as the driving force to produce the first living cell, despite the fact that evolution only works after replication begins. The following article deals with the proposal that evolution could be the driving force for the arise of the first life.
http://web.archive.org/web/20090126042355/http://darwinspredictions.com/#_4._L._E.
The DNA structure gave rise to first life
Introduction
DNA is a double helix. As Fig. 1 illustrates, it contains two strands that are twisted about each other, just as a rope might consist of two smaller ropes wrapped around each other. Both DNA strands consist of a series of molecules bonded together in sequence. The molecules are called nucleotides and if you stretched out the strand the nucleotides would line up in a row, like beads on a string. These nucleotides are the DNA’s information which encodes the genes in the DNA. If each nucleotide represents a letter, then a gene is similar to a paragraph in a book. DNA strands use four different kinds of nucleotides, so in this language there are only four letters.
A tremendous amount of effort has been spent on understanding how these molecular letters are read. In 1953, before the DNA structure was deciphered using X-ray photographs, the great American chemist Linus Pauling predicted that the nucleotides pointed outwards from a helix. A few years earlier Pauling had successfully predicted the helix structure of proteins. Now he would try to do the same for the DNA structure. If the nucleotides pointed outwards, Pauling reasoned, they could be read without having to pull apart the DNA. But this time Pauling’s intuition failed him.
Not long after that Francis Crick and James Watson, working in Cambridge, England, solved the puzzle. Using Rosalind Franklin’s X-ray measurements they determined not only that DNA normally is a double helix, but that the nucleotides are pointed inwards, toward the center of the helix. [1] “We have discovered the secret of life,” proclaimed Crick at a nearby Cambridge pub.
Watson and Crick’s new DNA model was a great breakthrough and soon DNA was viewed as the blueprint that was modified over the course of evolution to create new species.
Prediction
Most proponents of evolution believe that the first life arose from non-living chemicals. In a letter Darwin speculated of a warm little pond with a protein compound ready to undergo more complex changes. [2] After Darwin evolutionists attempted to flesh out this story.
It was not easy to explain how something as complicated as a living cell could emerge on its own. Proponents of evolution needed to start with something far simpler than an entire cell. If some fundamental component of the cell could arise on its own, perhaps then the other cellular components would gradually aggregate and eventually build up to a complete cell. The research was driven not by positive scientific findings so much as the acceptance of Darwin’s theory.
Before Watson and Crick discovered the DNA structure, some proponents of evolution felt that life began with a single gene. With the gene’s molecular structure explained by Watson and Crick, this genes-came-first view began to take shape. That first gene, it was then understood, would have been a segment of DNA.
Nobel Laureate H. J. Muller had promoted the genes-came-first idea, and the DNA structure did nothing to detract from his convictions. He continued to advocate for the primacy of genes. After all, DNA coded for proteins, not vice-versa. A segment of DNA contained the sequence information for a protein, but a protein did not contain the DNA sequence information.
The great popularizer (and scientist) Carl Sagan also held to this idea that life must have come from non-life via the spontaneous assembly of DNA. Sagan used the term “naked gene” to convey the idea that life began with DNA, absent the other cellular components and environment. [3]
Falsification
The prediction that the DNA molecule formed on its own, and then led to the formation of the first life, we now know is problematic for many reasons. For instance, each nucleotide, consisting of its nitrogenous base, ribose sugar and phosphate group, is a fairly large organic molecule. These do not spontaneously form, even when the right ingredients are coaxed together in experiments mimicking some hypothetical primitive, early Earth condition. “There is at present,” concluded one senior researcher recently, “no convincing, pre-biotic total synthesis of any of the nucleotides.” [4]
Beyond this there remain several more problems. For instance, even if nucleotides could somehow form on their own, they would likely be at low concentrations because there are many alternate conformations they could assume. Also a great many other organic molecules could form in the brew. What is needed is a particular type of molecule, not a menagerie.
And even if the right type of building block molecule could somehow be created at reasonable concentrations, these molecules would have to polymerize (i.e., chemically bond to form a sequence, like beads on a string). This requires energy and precision. Nonetheless, what is needed are long DNA polymers (thousands or at the very least hundreds of nucleotides long).
Next the nucleotides must encode information. Even if DNA polymers could form on their own, they cannot be just any polymer. Long DNA polymers that are functional are rare. One experiment, dealing with randomized protein sequences, showed that about one hundred trillion such sequences are needed before even a simple binding function is obtained. [5] This result is optimistic because the protein was relatively unstable and short. Most proteins are several times longer, and longer sequences would likely have even lower rates of functionality. Also the function was elementary. Proteins that do something useful do far more than merely bind to a chemical.
Finally, even if long, functional DNA polymers could form on their own, they would need helper molecules (such as today’s proteins) to perform the copying, translating and replicating tasks. This chicken-or-the-egg problem arises because DNA alone cannot perform the various tasks needed to form a living entity, no matter how simple.
The theory of evolution motivated the idea that a lone DNA molecule was the starting point for the history of life on Earth, but we now know of several substantial problems with this hypothesis. Alternative theories have not fared well either.
Reaction
To address these many failures of earlier expectations, proponents of evolution have continued to speculate about how first life could have arisen, constructing a variety of complicated hypotheses. For instance, one idea is that evolution formed information bearing, functional sequences via natural selection. The appeal to natural selection certainly fits well within the theory of evolution, but is rather heroic in this case because selection requires that many test trials can be run with a mechanism for selection. In Darwin’s theory that mechanism is reproductive success, but that requires elaborate mechanisms to be in place . The selection of functional DNA polymers requires more than merely some trial sequences. New DNA sequences can be selected in the laboratory, such as in directed evolution experiments, but this requires an elaborate apparatus. [6,7]
Another hypothesis proponents of evolution constructed in recent decades is that life began not with DNA but with its cousin molecule, RNA. There is no trace of this today, but proponents of evolution hypothesized that first life was RNA-based, and then at some point it switched to DNA. This more complicated hypothesis takes advantage of the fact that RNA not only can store information like DNA, but also can accomplish some of the copying tasks by itself, without the help of proteins. Soon the DNA-first hypothesis was replaced with the idea of an “RNA world,” which gave proponents of evolution substantially more room to speculate. [8,9]
The new RNA world hypothesis was often interpreted as more or less solving the problem of how the first replicating molecule arose. Yet even if this hypothesis completely resolves the chicken-or-the-egg problem, there still remain the other problems, including nucleotide synthesis and low concentration, polymerization and information. As one paper put it, the RNA world is a “prebiotic chemist’s nightmare.” For as Leslie Orgel explained, “The prebiotic synthesis of nucleotides in a sufficiently pure state to support RNA synthesis cannot be achieved using presently known chemistry.” [4] This has led to the search for substitutes for DNA and RNA which perhaps could do the job initially, and then be replaced by today’s genetic system at some later time. But DNA and RNA have excellent properties and substitutes do not come close to fulfilling their roles. As Robert Shapiro writes:
Gerald F. Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute concluded that the spontaneous appearance of RNA chains on the lifeless Earth “would have been a near miracle.” I would extend this conclusion to all of the proposed RNA substitutes that I mentioned above. [10]
No one can say what future research will tell us, but the evolutionary hypotheses from the early and mid 20th century about how life initially arose have led research down long, circuitous, trails. Consequently evolutionary ideas of how life arose are highly complex, consisting of low-probability events and substantial serendipity.
References
1. Horace F. Judson, The Eighth Day of Creation: The Makers of the Revolution in Biology (New York: Simon and Schuster, 1979), 147ff.
2. C. Darwin The Life and Letters of Charles Darwin, ed. Francis Darwin (London: John Murray 1887, Vol. III), 18.
3. Robert Shapiro, Origins: A Skeptic’s Guide to the Creation of Life on Earth (New York: Bantam Books, 1986), 136.
4. L. E. Orgel, “Prebiotic chemistry and the origin of the RNA world,” Critical Reviews in Biochemistry and Molecular Biology, 39 (2004): 99-123.
5. A. D. Keefe, J. W. Szostak, “Functional proteins from a random-sequence library,” Nature 410 (2001): 715-718.
6. Y. Hayashi, H. Sakata, Y. Makino, I. Urabe, T. Yomo, “Can an arbitrary sequence evolve towards acquiring a biological function?,” J Molecular Evolution 56 (2003):162-168.
7. G. F. Joyce, “Directed evolution of nucleic acid enzymes,” Annual Review of Biochemistry 73 (2004): 791-836.
8. T. A. Lincoln, G. F. Joyce, “Self-sustained replication of an RNA enzyme,” Science (2009).
9. S. Pino, F. Ciciriello, G. Costanzo, E. Di Mauro, “Nonenzymatic RNA ligation in water,” J Biological Chemistry, 283 (2008): 36494-36503.
10. R. Shapiro, “A simpler origin for life,” Scientific American, February 12, 2007.
