Chemical evolution / selection
“The basic idea is that simple principles of chemical interactions allow for a kind of natural selection on a micro scale: enzymes can cooperate and compete with each other in simple ways, leading to arrangements that can become stable, or “locked in,” says Ken Dill, PhD, senior author of the paper and professor of pharmaceutical chemistry at UCSF.”
Comment: Even if accepting natural selection just for the sake of argument, this principle cannot be applied in the same way on both living and non-living things because of their huge difference. The article explained: “the chemical interactions in the model involve competition, cooperation, innovation and a preference for consistency.” However, these functions are always directed by genetic code that are only present in living cells and not in non-living chemicals. Thus, already the phrase “chemical evolution” or “chemical selection” is rather just an oxymoron. Competition, cooperation, innovation and preferences can hardly be attributed to molecules.
Trying to explain away the contradiction Justin Bradford and Ken Dill continued:
“The word “complex” is key because it shows how simple chemical interactions, with few players, and following basic chemical laws, can lead to a novel combination of molecules of greater complexity.“
Comment: This sounds quite like teleology or the doctrine explaining phenomena by their ends or purposes. But, do molecules really understand they should improve and so get desire to interact? And even if we would accept their argument as good, how did these molecules became programed to search for improvement and higher complexity? In the continuation of their paper they try to prove their points rather with an analogy than a lab experiment.
Here the analogy of human beings is given for a comparison to the activity of non-living molecules. However this sounds very obscure. Being not even sure whether chemical and biochemical reactions could chain together in complex and innovative ways, driven only by simple physicochemical search and processes, the researchers were already mentioning the benefit: “If so, it may be useful, not only as a tool in chemistry and biochemistry, but also for giving insights into the processes of chemical organization that may have occurred during prebiotic evolution.”
One can just wonder how long will scientists come up with newer and newer “perhaps happened like this” theories. For them imagination in scientific research might be important however, that doesn’t necessarily describe the scenario what actually happened, especially, because their hypothesis was not tested by mere observation. In other words, even controlled laboratory experiment would be a fallacious proof and so not a disproof of intelligent design, the intention of this whole theory. The only proof was computer simulation.
Let’s here briefly summarize the steps the theory proposes and see the problems of each step.
1. Catalysts A and B interact according to simple rules.
Problem: a) where did the rules came from, b) A and B are imaginary computer molecules not real chemicals mixed in the test tubes. Although they said: “It has been seen in computer simulations that stochastic innovation works differently: evolution doesn’t “know” the final end-goal in advance, but finds it through a random search in indirect, incremental steps.” Proof of evolution by computer simulation is fallacious because the computers have to be programmed. But according to standard evolution theory, was the whole evolutionary development programmed? No.
2. The next step was the emergence of: cooperation, competition, consistency, and innovation forming an AB complexes.
Problem: Again, this is noting else than teleology. Without function or goal, AB complexes would be mere lumps of inert chemicals.
3. The next step was appereance of more catalytic pairs resulting in “functional hierarchies.” They wrote: “Thus, multiple catalysts can be driven together, potentially into a variety of topological arrangements, including metabolic chains, networks, and cycles.”
Problem: How suddenly without any explanation, just like out of the blue sky, metabolism got sneak into the scene? Metabolism presupposes the harnessing of energy for function.
In their paper Justin Bradford and Ken Dill use phrases like: ‘stronger evolutionary forces’, ‘different purpose’, ‘the protein does not know’, ‘headed toward’, ‘seeking a situation’ etc. all indicating teleology and personification what is contradictory to their main tenet that irreducible systems has emerged “by blind physicochemical forces.” Thus, their theory does not really disprove that complex systems were intelligently designed, what was one of the goals of their paper as seen from the following paragraph that offers a mechanistic answer to the intelligent design.
A key distinction between stochastic innovation, explored here, and design-based innovation, in which a complex system is engineered and constructed by a designer, is that stochastic innovation involves no implicit “goals” and no guidance toward a particular purpose. The Darwinian paradigm shows how increasing complexity and order can arise from processes that do not involve guidance through intelligence or design.
Giving a proposal how to test their theory in the lab it was not clear whether anything would happen without an intelligent lab worker whose presence is important to select the catalysts and control the concentrations.
At the end, explaining the weak points of previous self-organization models, they praised their model that requires no genetics and no designer. The only reqirement is the laws of thermodynamics and chemical attraction.
A well known process in chemistry is the binding and association of molecules, driven by thermodynamic forces. Here, we consider whether catalyst molecules might be driven to associate with each other, through typical binding forces, but based on their molecular functions. Functional driving forces are well-known in biology, through the principles of evolution, but are not yet much studied in chemistry. We propose a model for how different Michaelis-Menten enzymes or catalysts might tend to associate, driven by the production or depletion of common resources. The agents do not associate if the common resource is plentiful. We call this the shielding principle. In this way, agents organize adaptively, and complexity can form from simpler systems. In our model, “function dictates structure,” a reversal of the paradigm in which “structure dictates function.”
As obvious, the proposed model relies very much on function. But this begs the question, can function exist without biology? If chemical function is meaningless, then they have assumed a biological concept that they needed to prove.
Reference:
1. Stochastic innovation as a mechanism by which catalysts might self-assemble into chemical reaction networks by Justin A. Bradford and Ken A. Dill from Graduate Group in Biophysics and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
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Update: Can life arise from basic molecules?
“SAN DIEGO: Can life arise from nothing but a chaotic assortment of basic molecules? The answer is a lot closer following a series of ingenious experiments that have shown evolution at work in non-living molecules. For the first time, scientists have synthesized RNA enzymes – ribonucleic acid enzymes also known as ribozymes – that can replicate themselves without the help of any proteins or other cellular components. What’s more, these simple nucleic acids can act as catalysts and continue the process indefinitely. “There’s nothing in biology in this system: no proteins, no cells, no biological matter. We just provide them with the building blocks,” said molecular biologist Gerald Joyce of the Scripps Research Institute in San Diego.
The researchers began with ribozymes known to occur naturally, and put these in a growth medium, heated them and allowed the ribozymes to replicate.”
Dr. Robert Shapiro, a self-declared agnostic and opponent of ID theories, wrote the following in his book Planetary Dreams (page 102) in 1999 regarding the future engineering of self sustained RNA systems:
“When that event takes place, the media probably will announce it as the demonstration of a crucial step in the origin of life. I would agree with one modification. The concept that the scientists are illustrating is one of Intelligent Design. No better term can be applied to a quest in which chemists are attempting to prepare a living system in the laboratory, using all the ingenuity and technical resources at their disposal…the search for ribozymes invokes the same feeling of achievement and beauty in me that I get when I see a skilled golfer playing a difficult course at well under par. To imagine that related events could take place on their own appears as likely as the idea that the golf ball could play its own way around the course without the golfer.”
On 1/26/2010, Dr. Shapiro posted the following comment to an article by Carl Zimmer on the SCIENCE Magazine website under the heading “Origins, a history of beginnings”. “Despite the clarity of his prose, Carl Zimmer has fallen into a trap that has impeded progress in the origin of life field for the last half century. He has confused the process of total organic synthesis with the abiotic chemical reactions that may have taken place on the early Earth. Total synthesis involves the preparation by skilled chemists in laboratories of substances that we isolate from biology. The late Nobel Laureate Robert Burns Woodward was a master of this endeavor… On the early earth, however, there were neither chemists nor laboratories. No driving force has been demonstrated that would direct complex mixtures of organic chemicals of modest size to assemble themselves into a functional RNA. According to Gerald Joyce and the late Leslie Orgel, such an event would constitute a near miracle…
Reference
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Evidence for early locomotion
“Evidence for locomotion in the Precambrian fossil record isscant. Reliable Ediacaran trace fossils are all younger than560 Ma, and consist of relatively simple horizontal burrowsand trails from shallow-water deposits. Here we describe anassemblage of macroscopic locomotory traces from deep-waterenvironments at Mistaken Point, southeastern Newfoundland, Canada,dated to ca. 565 Ma. These trails extend the record of complextrace fossils back into the earliest Avalonian biota. Our newevidence for large motile organisms on the seafloor at thistime suggests that at least some of these early Ediacaran organisms,whose biological affinities are widely debated, could have beenmuscular and of metazoan grade.”[1]
Comment: The newly discovered fossil markings of the see-dwelling animals on the rocks of Newfoundland poseanother challenge to the officially established Darwin theory. Having had great similarity with modern anemones – a marine invertebrate that still lives attached to rocks, and is related to corals and jellyfish – one of the paleontologists remarked: “Anemones are capable of crawling across sediment and can exhibit swimming and burrowing behavior.”[1] In other words, muscular animal locomotion is now pushed back “five million years earlier,” which means that already in that time, for the ability of locomotion, precisely specified muscle proteins, including actin, myosin, and a host of supporting enzymes for construction and operation had to be developed. Moreover, according to the new evidence, Cnidarians did not evolve much in the past “565 million years.”
Reference:
1. Geological Society of America, Alexander G. Liu1, Duncan Mcllroy2 and Martin D. Brasier1,2
1 Department of Earth Sciences, University of Oxford, Parks Road, Oxford OX1 3PR, UK
2 Department of Earth Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X5, Canada
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Ribosomes
With the enhanced instruments for observing the nano-world, namely by nanoscopes, scientists are now able to peer at the amazing complexity of ribosomes.
In Aug. 23, 2009 ScienceDaily reported: “Ribosomes, which number in the millions in a single human cell, have long been considered the “black boxes” in molecular biology. “We know what goes in and what comes out of ribosomes, but we’re only beginning to learn about what is going on in between” said the study’s principal investigator, Jamie Cate, UC Berkeley associate professor in chemistry and molecular and cell biology, and a faculty scientist at Lawrence Berkeley National Laboratory.”[1]
Ribosomes are cell organelles present in all cells; involved in the production of proteins by translating messenger RNA. In this process, hundreds of components like proteins, cofactors and RNA take part, precisely translating the genetic code coming from the DNA in the nucleus.
“The mRNA dutifully delivers the code to the ribosome, which somehow reads the instructions, or “data tape,” as each amino acid is added to a growing protein chain.”
At the same time, other RNA molecules, called transfer RNA (tRNA), bring amino acids to the ribosome, the raw building blocks needed for protein construction.[1]
Considering again the hundreds of components envolved in this process of bringing in raw materials, catalyzing reactions and checking for errors, the speed of “adding 20 new amino acids to a protein chain every second,” is amazingly high.
Moreover, if Jamie Cate says “We know what goes in and what comes out of ribosomes, but we’re only beginning to learn about what is going on in between”, that certainly includes more future discoveries about the complex biochemical network system. With the discoveries of many details in molecular biology, biologists should come to the point of rejecting their prejudiced opinion that nothing in biology makes sense except in the light of evolution. Actually, already now, the available information on complex cellular life, strongly undermines the popular theory of evolution.
One of the descriptions of the ribosome that describes its irreducible, specified complexity, thus undermining the concept of evolution, was given by Robert F. Service: “Since then, the three groups and others have begun to combine these atomic snapshots, and others like them, into a jerky movie of the atomic dance ribosomes perform to translate genetic information into proteins. Structural biologists have captured dances of complex molecules before. The ribosome’s dance, however, is more like a grand ballet, with dozens of ribosomal proteins and subunits pirouetting with every step while other key biomolecules leap in, carrying other dancers needed to complete the act.”[2] Thus, if even one dancer would fail, the ballet would become a grand failure. What has caused the choreography needed to make the ballet a grand success? How can this be the result of a gradual process of random change and natural selection?
References:
1. ScienceDaily: New Images Capture Cell’s Ribosomes At Work based on the article of Zhang, Dunkle and Cate, “Structures of the Ribosome in Intermediate States of Ratcheting,” Science, 21 August 2009: Vol. 325. no. 5943, pp. 1014-1017, DOI: 10.1126/science.1175275.
2. Robert F. Service, “Honors to Researchers Who Probed Atomic Structure of Ribosomes,” Science 16 October 2009: Vol. 326. no. 5951, pp. 346-347, DOI: 10.1126/science.326_346.
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DNA-Repair Proteins
Recently, closer observations of the DNA strands in the E-coli revealed that small molecular machines jumpfrom one strand to another, fixing any suspicious errors. Illustrating this scenario, Dr. Bennett Van Houten of the Pittsburgh University said: “How this system works is an important unanswered question in this field…It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.”
The E-coli genome sequencing that was completed in 1997 counted over 4.64 x 10^6 bp (base pairs) or 4,408 genes. The in toto 40 repairing molecular machines, sometimes moving slowly, sometimes quickly or even jumping randomly, can scan the whole genome of the E-coli in about 20 minutes, cooperating occasionally with other repairing machines when they cannot fix the problem on the spot.
This whole news is just another good example from genetics that questions the popularly accepted axiom that nothing makes sense in biology except in the light of evolution. Strangely, the discoverers of these repairing molecular machines did not give any explanation of how these machines evolved, not to say anything about whether the E-coli could survive without the existence of these repairing machines from the very beginning.
Reference:
1. Quantum Dots Spotlight DNA-Repiar Proteins in Motion, ScienceDaily (Mar. 14, 2010)
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The supporters of intelligent design (ID) camp is increasing.
Already more than 800 PhD scientists from the world’s top universities, signed a paper declaring:“We are sceptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.” Here you can download the complete list of supporters, last updated in August 2008.