Does ribozyme research prove Darwinian evolution?
5 August 2006
This feedback comes from DB of California, a 16-year-old agnostic with a great interest in chemical evolutionary theories. While agreeing that creationist criticisms are factually accurate, he disagrees with the conclusion. Thus a particular experiment with ribozymes is discussed in some detail, as well as a number of other issues in the origin of first life, but it was also necessary to address a few of DB’s claims about the problem of evil, human evolution and philosophy of science. Dr Jonathan Sarfati responds to the points.
First, I will introduce myself as an inquisitive sixteen year old who has a profound interest in biochemistry. Another relevant fact about myself is that I am an agnostic (I am an atheist concerning the existence of the Judeo-Christian God) who was considering becoming a catechumen in the Roman Catholic Church later last year.
Origin of life (OOL) skeptic
I must add that the literature of Professor Robert Shapiro of NYU (mainly his book Origins) and Professor Gerald Joyce of the Scripps Research Institute has profoundly influenced my views.
Naturally I am very familiar with their work, and have analyzed their views in previous articles, as is easily verifiable (e.g. see Origin of life: instability of building blocks). I read Origins: A Skeptic’s Guide to the Origin of Life well before I joined CMI, and it supported my skepticism about chemical evolution. In this book, he supported a protein-first scenario rather than an RNA-first one. And in the work cited in the previous link, and as you would know from your own reading, he was still skeptical of the RNA-first idea:
‘the evidence that is available at the present time does not support the idea that RNA, or an alternative replicator that uses the current set of RNA bases, was present at the start of life.’
And in case you haven’t read the links (given that there are many others you have overlooked when writing this email), I will remind you of Shapiro’s dogmatism in Origins, in a striking admission that no amount of evidence would upset his faith:
‘some future day may yet arrive when all reasonable chemical experiments run to discover a probable origin of life have failed unequivocally. Further, new geological evidence may yet indicate a sudden appearance of life on the earth. Finally, we may have explored the universe and found no trace of life, or processes leading to life, elsewhere. Some scientists might choose to turn to religion for an answer. Others, however, myself included, would attempt to sort out the surviving less probable scientific explanations in the hope of selecting one that was still more likely than the remainder.’
Origins has transformed me into a skeptic as I remember the Skeptic in his book constantly questions every proposed hypothesis regarding the origin of life. Also Shapiro portrayed science not as a body of information, but as a method of inquiry. In the case of science, knowledge is derived from empirical evidence usually by observations or by controlled repeatable experimentation. Furthermore, scientific theories, unlikely religious dogmas, are tentative as they are subject to change when new information is obtained.
Unfortunately, the actual dogma lies with the worshipers of the church of evolution, ‘Darwiniacs’ as Ann Coulter called them in her new book Godless: The Church of Liberalism, who refuse to acknowledge any information that does not conform to their beliefs and demand complete and total indoctrination of every child who attends the public education system. As Miss Coulter correctly pointed out:
‘They cling to Darwinism even as the contrary evidence accumulates, because it allows them to ignore God … [and they] will not admit evolution is a crock until they have concocted a new creation myth that also excludes God.’
In the correct definition of the word, it is a religion; a religion funded by taxpayer dollars.
One should always scrutinize the evidence critically and not follow popular opinion blindly, which is encouraged in the sciences. An example of this is Robert Shapiro’s views on the origin of life, which are diametrically opposite the established paradigm, as he is a critic of the vogue RNA World hypothesis. Shapiro’s emphasis on critical thinking had a profound impact on my life. After reading Origins, a valuable lesson I learned is that one should apply critical thinking in all aspects in life and not restrict it in a few areas such as the sciences.
But evidently not enough to make you skeptical of materialism.
Problem of evil
This lesson made me examine my nascent faith, and I found that the concept of a benevolent God is not congruent with reality, thus making me reject Catholicism.
Here is an example of a throwaway line, which does you no credit. You have made not the slightest attempt to demonstrate a contradiction between a benevolent God and reality. Mind you, a philosophy prof. was not much better: see the answer to him on the problem of evil; see also Answering angry anti-Christianity, especially on the point that evil is not a ‘thing’ but a privation of good, and the links therein.
Also, C.S. Lewis pointed out decades ago that your idea of benevolence in the first place is incongruent with reality if we are just rearranged pond scum with no absolute moral lawgiver. So you have no basis under your belief system for making this argument in the first place.
I’m not sure how you could even make a case for incongruence with reality. Here is the usual attempt:
- An all-powerful God could get rid of evil
- A perfect God would want to get rid of evil
- Evil exists
The first two are held to be the judeo-Christian premises, while #3 is indisputable, so antitheists draw the conclusion that no perfect and all powerful God exists. Others resort to schemes where God is not all-powerful, e.g. ‘open theism’ and ‘process theology’. However, Christian philosophers have long argued that Premise 2 should be extended to:
2′. A perfect God would want to get rid of evil unless He has a good reason for allowing it.
Then there is no incompatibility with #3. Since no antitheist can show that there is no possible good reason for allowing evil, since that would be a universal negative, the argument collapses as logical disproof of theism. We have argued that one good reason for God’s allowing evil in the world today is a judgment resulting from the Fall.
Apologists have also long pointed out that #2 is not
2″. A perfect God would want to get rid of evil immediately (otherwise he would have to destroy all of us)
While premise 3 would be better stated as:
3′. Evil exists for now but will one day be destroyed (as the Bible says)
1, 2/2‛ and 3‛ are certainly compatible.
Science v religion?
The irony of this is that the critics of various origins of life hypotheses (like Shapiro and Professor Leslie Orgel) initially made me consider the existence of God even though they do not believe in God, (Shapiro is an agnostic/Orgel is probably an atheist) but ultimately helped me reject the existence of a benevolent God. In addition, I realized that science and religion do not mix well.
Pity that Newton, Boyle, Pascal, Faraday, Pasteur, Maxwell, Joule and many others weren’t around to benefit from your wisdom. However, you are around to benefit from the wisdom of those who can document that science first flourished in a biblical judeo-Christian milieu, for example Stanley Jaki and Loren Eiseley and most recently Rodney Stark. I explained the reasons in Creationist contributions to science. (See also Newton was a creationist only because there was no alternative?.)
Science relies on objective evidence,
This would be news to prominent philosophers and historians of science. ‘Facts do not “speak for themselves”; they are read in the light of theory,’ as the late Marxist paleontologist Stephen Jay Gould pointed out [Ever Since Darwin, 1978]. Gould also said:
‘Our ways of learning about the world are strongly influenced by the social preconceptions and biased modes of thinking that each scientist must apply to any problem. The stereotype of a fully rational and objective “scientific method”, with individual scientists as logical (and interchangeable) robots is self-serving mythology.’
‘At this point, it is necessary to reveal a little inside information about how scientists work, something the textbooks don’t usually tell you. The fact is that scientists are not really as objective and dispassionate in their work as they would like you to think. Most scientists first get their ideas about how the world works not through rigorously logical processes but through hunches and wild guesses. As individuals, they often come to believe something to be true long before they assemble the hard evidence that will convince somebody else that it is. Motivated by faith in his own ideas and a desire for acceptance by his peers, a scientist will labor for years knowing in his heart that his theory is correct but devising experiment after experiment whose results he hopes will support his position.’
while religion relies on faith and dogmatism and its evidence is often subjective, usually in the manifestation of personal experiences, which evade controlled experimentation.
On what do you base this categorical claim? You won’t find this in my explanation to an agnostic why it is rational to trust the axioms of Christianity. What about the 50 Ph.D. scientists who contributed to In Six Days? Leading apologist William Lane Craig defends the faith with the Kalām Cosmological Argument and explains that the Resurrection of Jesus Christ is the best explanation for a number of historical facts. Craig lists four: The burial, empty tomb, post-mortem appearances, and the origin of the disciples’ belief (see his debate with apostate Bart Ehrman (PDF)). James Patrick Holding, founder of Tekton Apologetics Ministries, explains 17 factors that meant Christianity could not have succeeded in the ancient world, unless it was backed up with irrefutable proof of the Resurrection (The Impossible Faith: Or, How Not to Start an Ancient Religion).
I also noticed that Shapiro was free of any dogmatic influences when interpreting the experimental data (this is evident in his cytosine, adenine, ribose papers and his analysis of Professor James Ferris’ montmorillonite model in his latest origin of life paper) so he is able to perform an objective assessment of the evidence.
How is it the epitome of objectivity to reject theistic explanations a priori while it is mere religious bias to accept them (cf. The religion of scientism)?
Surely, one could argue that a God exists (usually from the argument from design), but does it logically follow that such a God is benevolent, especially when exposed to the various cases of human suffering in the world.
Never claimed it did, and we have made that point before, in relation to ID theorist Wm. Dembski and ex-atheist philosopher Antony Flew.
Of course, Shapiro not only influenced me in this respect, as I also share his views about certain origin of life hypotheses.
Such as that life did not start with RNA.
As I mentioned before, another person who has influenced me is Professor Joyce, even though we do not agree with one another regarding the complex topic of the origin of life.
Does this include:
‘The most reasonable assumption is that life did not start with RNA…. The transition to an RNA world, like the origins of life in general, is fraught with uncertainty and is plagued by a lack of experimental data.’ [RNA evolution and the origins of life. Nature 338:217–224, 1989]
In his literature, Joyce advocates the definition of life as a self-sustaining system capable of undergoing Darwinian evolution. In other words, life is evolution! Thus, it would not be prudent to omit the teaching of evolution in high school biology class.
I agree. In fact, we would like to see students taught more about evolution than the evolutionists want them to know. Conversely, many evolutionists don’t want students to learn the problems with evolution in case they end up disbelieving it, as Eugenie Scott admitted. And are you happy when the Miller–Urey experiments are presented to students almost as if life itself had formed spontaneously, or if the RNA world was presented as fact?
‘The worlds of prebiotic chemistry and primitive biology lie on opposite sides of the defining moment for life, when darwinian evolution first began to operate ... Once a general mechanism existed for self-replication, allowing the introduction of variation and the ability to replicate those variants, darwinian evolution began to operate. This marked the beginning of life.’ — Joyce, Gerald F. (2002). The antiquity of RNA-based evolution. Nature 418:214-221; pp. 214–215.
If we accept Joyce’s definition of life, one must what is the position of the species Homo sapiens in the universe. Are humans just another branch on the tree of life, descended from primates, which in turn are descended from a primitive common ancestor whose lineage is characterized by unbroken continuity spanning 3.8 billion years?
That indeed is a problem for theistic evolutionists. But since I try not to hold mutually contradictory ideas (like theism and evolution) in the same skull, I don’t have that worry.
I have accepted that humans are nothing more than units of hereditary material,
So why are you bothering to tell me this instead of making sure your material is inherited (cf. some implications of this philosophy)?
which are capable of being influenced by the processes of Darwinian evolution, but we have the power to add subjective purpose to our own lives unlike other animals. Could Joyce’s definition of life be reconciled with Christian theology, which proposes that the purpose of human life is to have eternal fellowship with God, not simply vectors for genes whose purpose is to simply multiply? If so, one has to demonstrate that humanity is the exception to the inherent disteleology [sic] of Darwinian evolution.
Dysteleology is essentially a theological argument, not a scientific one, as pointed out before. In any case, why should I demonstrate that humanity is an exception to evolution when I don’t believe in evolution?
But the evidence speaks against such a supposition. We could be influenced by the forces of nature in detrimental way like all other organisms on Earth.
Of course, because all of us live in a fallen world.
For example, humanity is not exempt from the malady of the bubonic plague, nor where the thousands of people who died in the calamity of the Indian Ocean tsunami where spared from that force of nature. Is this the testimony of a God of loves each one of us on a personal level?
Yes, but also of a God who is holy enough to punish Adam’s sin with a judgment on the whole creation of which he was head. As all of us are sinners, we are not exempt from the consequences, which is not to say that the worst sinners suffer the worst consequences in this life. We have already explained this in Waves of sadness: Tsunami terror raises age-old questions.
I might have stumbled upon the reason why some Christians think that young-Earth creationism is a necessity for their faith as opposed to theistic evolution. Under this framework, the Fall is a justification for the suffering of humanity, but unfortunately there is ample evidence supporting human evolution (I will not elaborate as I do not claim to be an expert in this field).
It is also interesting that with such ‘ample evidence’ you couldn’t elaborate enough to provide even one example. You appear to be adhering to a belief of human evolution that you are unable to substantiate with fact, and your inability to elaborate could indicate ‘blind faith’.
The message above is far from conveying the optimistic tone of the Gospel, which states that one could be endowed salvation through faith in Jesus Christ, but it is consistent with empirical reality especially in the light of human suffering.
Faith in Jesus Christ is compatible with the historical evidence that could have been examined empirically by His contemporaries. Chemical evolution that you now believe in has no such evidence. It would actually be a good exercise to follow Dr Craig’s explanation of the probability of Jesus’ resurrection (using Bayes’ theorem), and then plug in the data for origin of life research, and compare the probabilities. It might just indicate that you have put your faith in the wrong place.
I do believe that creationists are afraid of dealing with reality, thus they dogmatically adhere to doctrines such young-Earth creationism to palliate the pain of human suffering.
Conversely, you should examine why you are dogmatically adhering to a doctrine of Darwinian evolution that you cannot support by fact. Who's really ignoring reality here?
However, Professor Joyce does not elaborate on the moral implications of his definition of life nor I do I think he completely agrees with me, and he certainly is not an ethicist, but I respect him as a competent scientist.
So do I. So I tend to trust his data, disagree with the materialistic paradigm under which he interprets the data, but take any ethical pronouncement with a grain of sugar.
I will start off by mentioning that I used to be somewhat sympathetic towards the notion of so-called ‘Intelligent Design’.
This whole hype on hydrothermal systems and everything is just bogus.
But falling into the evidentialist roller coaster.
Such evidence is found here [link deleted as per feedback rules] when I was rebutting a ‘critique’ by Dr Gary Hurd regarding Dr Sarfati’s analysis of hydrothermal polypeptide synthesis.
Thank you for that. Yes, it’s amazing what happens when people like Hurd, whose main qualification is in social science, decide to become atheist apologists and start writing for gutter sites taking on chemists in their own field. It’s really bizarre that he accused me of ignorance of Wächterhäuser’s work when my second footnote linked to the more detailed article Origin of life: the polymerization problem which critiques his theory in detail. Anyway, leading OOL researcher Jeffrey Bada scathingly denounced this idea:
‘This whole hype on hydrothermal systems and everything is just bogus.’
I must add that I have written it when I was sympathetic to Catholicism, but currently I do not retain those sentiments. I still retain most of my technical criticism from that post even though I am not skeptical of abiogenesis anymore. This was also written at I time when I did not have access to that many online journals (hence why I referred some creationist resources), but I have access to computers from a university library now, which would grant me such access.
Yes, very handy. It is useful to see how even chemical evolutionists knock gaping holes in the theories of other chemical evolutionists. Even without the online access, it is not too hard to find, e.g. Cairns-Smith’s devastating criticisms of RNA-first and general Miller–Urey scenarios.
I will then discuss the topic of the origin of life, a topic that I pursue on my own free time as a hobby.
Personally, I find it quite sad that my fellow skeptics do not express any skepticism towards origin of life research.
I must agree. In many cases, it is an unhealthy combination of an atheistic belief system and ignorance of the chemistry involved.
Even though I immensely disagree with young-Earth creationism, I must say that most of the technical materials regarding the origin of life on CMI’s website, depict the facts quite accurately,
Thanks, we try. It helps to have chemistry specialists on staff.
even though I obviously disagree with the creationist conclusion. This is in stark contrast to Ian Musgrave’s hilariously atrocious article about abiogenesis. Does he really believe or expects us to believe that peptides are capable of self-replication and the prebiotic ocean could form 1049 oligonucleotides up to 200 nucleotides long!!??
Who knows what Musgrave believes? Like Hurd, his purpose in life is apparently to show there is no purpose. He should stick to neurology because his chemistry is abysmal, and his article is deceitful. For example, his diagram (right, with that red ‘negation’ graphic in front to show that it is not a true representation) is a complete distortion of what creationists believe. As you have verified, we understand perfectly that chemical evolution is proposed as per the ‘real theory’, precisely because we address the proposed stages in detail. Indeed, long ago, Ph.D. biochemist Duane Gish wrote a three part critique of chemical evolution (linked here), dealing with simple chemicals, theories of polymerization, and the development of complexity and protobiont models.
Musgrave is also besotted with the Ghadiri peptide that I showed in detail was irrelevant for chemical evolution (see Self-replicating Peptides?).
For probabilities, see Probabilities of randomly assembling a primitive cell on Earth.
Where’s the evidence for profound claims of this nature?? The origin of life is certainly a complex topic and by no means our scientific understanding is even complete.
Indeed not. This year, an article sympathetic to chemical evolution had to admit:
‘[The Origin of Life] is full of unknowns and uncertainties, of raging controversies, of passions and prejudices. Of all the great unknowns, the origin of life is particularly daunting. Direct evidence of the origin is essentially nonexistent: It happened too long ago, in too subtle a way. There’s no fossil of the First Microbe … In the words of George Cody, an origin-of-life researcher, “No one knows anything about the origin of life.” …
‘Hazen [another OOL researcher] writes that the origin-of-life field is “at times tarnished by questionable data, contentious debates, or even outright quackery.”‘
Non-creationist information theorist Hubert Yockey also argued that Chemical evolution is based on (blind) faith not fact
I admire the efforts of various origins of life researchers such as Gerald Joyce and Leslie Orgel who are working to improve our understanding on the origin of life through laboratory experimentation, even though I disagree with them.
Although as a physical/inorganic chemist, I think Orgel, famous for ‘Orgel diagrams’ in ligand field theory of metal complexes, was a great loss to my field and at best a draw for biochemistry. For example, Orgel’s First Rule:
‘Whenever a spontaneous process is too slow or too inefficient, a protein will evolve to speed it up or make it more efficient.’
But consider the problems with this, because without a protein efficient enough for some processes, there could be no life, therefore no Darwinian evolution. See World record enzymes.
However, Orgel did make it clear how living organisms could be distinguished from non-living things:
‘Living things are distinguished by their specified complexity. Crystals such as granite fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity.’
That is, specified complexity is not some illegitimate invention of the intelligent design movement, but really is something different from both order and randomness.
At least they are doing something!!
Reminds me of the brilliant British television political satire, Yes, Minister. In one episode (‘Party Games’), two head civil servants (Sir Arnold Robinson and Sir Humphrey Appleby) illustrated ‘politician’s logic’:
1) Something must be done;
2) This is something;
∴ We must do it.
As pointed out in the program (see clip below), this is just as invalid as:
1) All cats have four legs;
2) My dog has four legs;
∴ My dog is a cat.
In the case of your heroes, they are merely doing something materialistic. But real science, the science of Newton et al., should be about finding logical explanations, not necessarily materialistic ones.
I also think Shapiro’s proposal in ‘Small Molecule Interactions were Central to the Origin of Life’ might lead to a solution to this perplexing problem (Shapiro 2006).
You ‘think’ it ‘might’? At least you’re honest.
To conclude, I will say that I disagree with Dr Richard Dawkins’ remark:
‘Darwin made it possible to be an intellectually fulfilled atheist.’
Abiogenesis is not evolution as evolution starts when life begins, thus they are two discrete theories.
Actually, another name for abiogenesis is ‘chemical evolution’, and still another is ‘prebiotic evolution’. Scientific American 239(3), September 1978 was a special issue devoted to evolution, and pp. 62–83 was ‘Chemical Evolution and the Origin of Life’ by Richard Dickerson. He cited one of the pioneers as follows (emphasis added):
‘J.B.S. Haldane, the British biochemist, seems to have been the first to appreciate that a reducing atmosphere, one with no free oxygen, was a requirement for the evolution of life from non-living organic matter.’
Also, ‘General Theory of Evolution’ (GTE) was defined by the evolutionist Kerkut as:
‘the theory that all the living forms in the world have arisen from a single source which itself came from an inorganic form.’
Note that all Dawkins’ books have verbose handwaving attempts to explain the origin of life, as do most biology textbooks. So it is revisionism to claim that origin of life is not part of evolution.
I will concede, however, that naturalistic evolution requires abiogenesis, but any scientific explanation of the origin of life will require some form of abiogenesis even if the details are not known.
Except that you are baiting-and-switching from ‘scientific’ to ‘naturalistic’.
Origins v operational science
An often touted canard posted on this website is the claim that evolution is not ‘operational science’.
I discussed this fully in Who’s really pushing bad science?, especially the section regarding Naturalism, Origin and Operation Science (and in Refuting Compromise, chapter 1). It’s interesting that you refer to this as an ‘often touted canard’ but then demonstrate by your next words that you fail to understand the point.
Presumably this delineation is made so young-Earth creationists are not perceived as the enemies of science as science is usually characterized by controlled repeatable experimentation.
Our ministry is not concerned with the perception of the ‘world’ (cf. John 15:19), but rather our concern is with providing the truth to those who honestly seek it.
Also, as many of our writers are scientists, the perception that we hate science or are enemies of science, is faulty. Our love for science is one of the reasons we were led to make sure that others properly understand it. See also The Genesis Files for many other examples.
Of course, a majority of evolutionary biology is an ‘origins science’, but in my opinion ‘historical science’ would be an apt description of a majority of evolutionary biology.
And we would agree, as we’ve repeatedly pointed out, e.g. ‘It’s not science’.
Evolutionary biologists cannot create a so-called ‘Jurassic park’
and explain exactly how the dinosaurs became extinct.
Of course, historical sciences rely on evidence. For example, analyzing some archeological evidence and various historical documents would allow historians to elucidate the fall of the Roman Empire.
And it is unfortunate that the Bible, a tremendous source of historical data, is ignored a priori because they ‘cannot allow a Divine Foot in the door’. The evidence for Jesus’ Resurrection is equally good, rejected only because of anti-supernaturalistic dogma.
But evolutionary biology draws conclusions from similar inferences such as fossil evidence, phylogenetic trees, biogeography, the sequences of certain proteins, etc.
Yes, they ‘draw conclusions’ from ‘inferences’, i.e., they interpret the evidence.
Creationists would often retort that it is the way we interpret the evidence,
Not just creationists, as pointed out above.
but I prefer to let the evidence speak for itself instead of adhering to an a priori truth such a belief in a literal Genesis.
Do you often find fossils with tags attached stating they are millions of years old? All science is based on interpretation of evidence, and formulation of theories. If you were to honestly allow the evidence to speak for itself, you would sadly find it completely silent. A recent feedback explained how age is not something that can be measured, and still more recent feedbacks apply this to radiometric dating as well as dating methods consistent with a younger age.
If it often stated on this website that a priori axioms influence the way we interpret evidence, but there are few axioms in science; one that I could recall are that the laws of nature are immutable.
It would be better to study than to rely on your recall, which in turn not only presupposes a good memory but also that you memorized the points in question. In fact, there are a number of premises required for science to work, as explained. They would have to be axioms for an atheist, since they are not provable under their system—indeed some are inconsistent with it—but are theorems for Christians since they follow from the propositions of Scripture.
There might be some weird exceptions to this as I recall in loop quantum gravity (a rather controversial topic that I have little insight about), gravity could become a repulsive force. This axiom renders the results from controlled experiments reliable and repeatable.
Note also, this ‘axiom’ misunderstands ‘laws of nature’. In reality, they are descriptive, not prescriptive. Scientific laws do not cause or forbid anything any more than the outline of a map causes the shape of the coastline. For a Christian, the laws are our description of the way God now sustains His creation in an orderly way.
However, I believe evolution is confirmed by the so-called ‘operational sciences’. The effects of evolution are subject to controlled, repeatable experiments.
What does this mean? There is a far greater case that the effects of a Designer are observable and repeatable, in producing objects of specified complexity. See also Is the design explanation legitimate? and a recent feedback response.
While I was reading various papers about the origin of life, I came across Professor David Bartel (I am confident that he will soon be a member of the National Academy of Sciences because he is a promising young scientist) and Professor Gerald Joyce’s research. These scientists have conducted various in vitro evolution experiments on catalytic nucleic acid molecules (especially ribozymes), and I believe their work satisfies the criterion of ‘operational science’.
In one sense. The trouble is when they try to apply their results to origins; then it becomes fuzzier, as will be shown and as even you have partly acknowledged.
These experiments are excellent models of Darwinian evolution, as they involve changes of real nucleotides in a real nucleic acid molecule, which the phenotypic consequences of these changes could be observed and studied, unlike computer simulations of evolution. Let’s take a look at my favorite example, an RNA-directed RNA polymerase ribozyme, which is the cornerstone of evolution in the putative RNA World. This example is a 189 nucleotide ribozyme derived from a multi-year effort that is able to catalyze the template-directed extension of an RNA primer up to fourteen nucleotides in a twenty-four hour incubation (Johnston et al. 2001). Johnston et al. (2001) attached a sequence of 76 random nucleotides to the 3′ end of the ‘Class I’ ligase, which was the product of previous work with in vitro evolution experiments (Bartel and Szostak 1993; Ekland, Szostak, and Bartel 1995), along with replacing two loops within the ligase domain with eight random nucleotides for each loop, and attaching primer binding sites for reverse transcription and PCR (see figure 1B in Johnston et al. 2001).
They began with the ‘catalytic core of the ligase ribozyme’.
The resulting pool of RNA molecules (a starting population of 1015 RNA molecules) would be subject to selection, as the resulting population was pressured to extend a covalently-linked RNA primer tethered to the 5′; end of the ribozyme with tagged nucleotides with decreasing incubation times and tagged NTP concentrations as the rounds progressed along with competitor NTPs (to select against improper nucleotide incorportation) in the latter rounds for a total of 18 rounds.
Notice though that the actual reproduction of the RNA strands had a number of differences with Darwinian selection. It had more in common with Dawkins’ Weasel program and B-cell hypermutation in our immune system. That is, the Darwinian idea of mutation and selection ultimately applies to real self-reproducing organisms, so the entity selected had within itself the capacity to reproduce. The mutation/selection of RNA strands, letters in the Weasel program, and the antibodies produced by the immunoglobulin genes are reproduced by a much more complex system from outside. That is, polymerase enzymes, the computer program and the genome respectively. Thus they are reproduced at much higher rates, have higher selection coefficients and can stand high mutation rates that would result in error catastrophe for whole genomes.
Argument creationists should NOT use
Note that some creationists use a fallacious argument about this sort of thing: that the randomness generators of the Weasel program and RNA were themselves designed, therefore they are not valid simulations of Darwinism. In reality, it is legitimate to use such simulations to show what genuinely undirected randomness can achieve. My main objection to the simulation is based on the difference between reproducing sequences and reproducing whole genomes. Certainly iterative processes may find solutions to problems (they have been used in mathematical modeling for many years), but are the parameters used realistic biologically, for even a minimal organism? No, they are not, and when realistic parameters (genome size, mutation rate and selection coefficient) are used, the simulations and experiments show that evolution is an impossible process, even given billions of years of time (again, see the explanation about the Weasel program).
Not a support for RNA world ideas
Variation was added when a new population (mutagenized at 20% per residue with the exception of the ligase domain) based on an isolate from round 10 of selection was constructed for the eleventh round of selection and by mutagenic PCR in the latter rounds (15th–17th rounds) of selection. This is truly an example of Darwinian principles at work in an observable laboratory setting.
Debatable, as shown above.
Yes, I will admit on closer inspection of that paper and the other work by Bartel’s group will reveal that his work DOESN’T support the RNA World hypothesis, contrary to Bartel’s opinion.
To my mind, these experiments allow one to see the improbability/impossibility of such a molecule forming outside a laboratory and without the influence trained biochemists.
That was the conclusion of Cairns-Smith, as linked above.
For example, the template-directed condensation (these assays allowed the polymerase to extend a primer up to fourteen nucleotides in 24 hours without the primer being covalently-linked to the catalyst) was conducted with a high concentration of nucleoside 5’-triphosphates (4 mM of each: ATP, GTP, CTP, UTP) without other things that would pollute the prebiotic soup.
And note that such reactive compounds would not last long in a primordial soup, and have never been found in Miller–Urey experiments. It is no accident that one of them, ATP, is The Perfect Energy Currency for the Cell. Now we know it is produced by the ‘world’s tiniest motor’, one of the many machines necessary for life to function.
In addition, the buffer and ionic conditions (pH 8.5, 200 mM Mg++ at 22°C) favorable to polymerization quickly degrade the ribozyme as Bartel’s group directly admits (Johnston et al. 2001; pg. 1323).
That is a problem with a lot of OOL simulations: the conditions are mutually incompatible. One well known one is the impossibility of sugars and amino acids existing together because of Maillard reactions (between the amino groups (–NH2) of the amino acid and carbonyl groups (>C=O) in the sugars) that would destroy both.
There are other reasons why Bartel’s ribozyme would not be satisfactory for the RNA World such as its low accuracy (approximately 97% in an equimolar concentration of the four NTPs so it is unable to support a Darwinian system),
Yes, error catastrophe would result. Real organisms have sophisticated error-checking mechanisms.
but the main point is that the ribozyme was a product of evolution and it is a testimony to the power of Darwinian evolution.
Is that so? But if the ribozomes themselves can’t reproduce, and needed a more complex system for their ‘evolution’, then what was the original self-reproducing system that could have generated such a ribozyme on the primordial earth?
Although the research did not demonstrate natural selection as they often used protein enzymes (Taq DNA polymerase, reverse transcriptase, RNA polymerase) in the selection protocols, it nevertheless illuminates the efficacy of evolution despite the assiduous amount of investigator interference involved.
Actually, what you said (and the points I made above) show that the analogy with evolution is seriously flawed.
Indeed, one might say that 14 nucleotides in 24 hours is feeble,
Yes, how could living things subsist with only 14 nucleotides worth of information (equivalent to <5 amino acid residues in a protein)?
especially when compared to protein polymerase, but one should remember that RNA has four chemically similar aromatic subunits and that the polymerase reaction is not an easy reaction to catalyze. Their ribozyme is truly an impressive feat, especially because it was created only from random sequences, which were under the influence of Darwinian evolution, without the addition of information from biological nucleotide sequences being incorporated in the ribozyme (except, of course, for the primer binding sites):
‘General template-directed RNA polymerization requires recognition of the generic features of a primer-template complex in addition to ever-changing NTP specificity, as dictated by the next template residue. It is a complex reaction—one of the more sophisticated reactions catalyzed by single polypeptides. The demonstration that such an activity can be generated de novo, without reference to any biological ribozyme or structure, is a testament both to the catalytic abilities of RNA, as well as to modern combinatorial and engineering methodology.’ - (Johnston, W.K., Unrau, P.J, Lawrence, M.S., Glasner, M.E., and Bartel, D.P. (2001). RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension. Science 292:1319–1325; p. 1324)
Just imagine what an organism, which has access to a diverse array of catalytic subunits, such as various aromatic (e.g. histidine, tryptophan, tyrosine, phenylalanine), basic (e.g. histidine, arginine, lysine), acidic (e.g glutamic acid, asparatic acid), polar (e.g. serine, threonine, cysteine), and hydrophobic (e.g. alanine, valine, leucine, isoleucine, methionine) subunits could accomplish with evolution, in contrast to using a polymer with limited chemical diversity such as RNA!!!
|… until you have the capacity for self-reproduction, you have no Darwinian evolution at all!|
Furthermore, such an organism could co-opt parts from existing metabolic pathways to create new pathways,
If there are already metabolic pathways, then it is already living. Thus you can’t use this to explain where life came from in the first place.
and unlike the laboratory conditions, it would undergo perpetually evolution without the need of someone adding enzymes from an external source to amplify any successful products.
That’s the problem—such a system would already be living, which is what you need to explain. It would take a great deal of complexity to have a system that could generate the very reactive activated monomers and reproduce the genome. It is no accident that even the minimal genome is estimated to be 387 protein-coding and 43 RNA-coding genes.
Nucleotides are sufficient for Darwinian evolution as in the case of Bartel’s ribozyme. Furthermore, four different nucleotides need not be necessary, as a binary ribozyme (composed only of 2,6-diaminopurine and uracil) suffices for Darwinian evolution even though it is substantially weaker in terms of catalytic ability than its counterparts with four nucleotides (Reader and Joyce 2002).
So it has minimal catalytic activity! Really, it is even less of a candidate for the beginnings of first life, quite aside from all the problems of forming any sort of nucleotides prebiotically, let alone polymerizing them.
Another important lesson is that evolution does not only apply to a system utilizing protein catalysts and DNA genomes, but it could also be applied to a system that is not utilizing the ubiquitous attributes of terran biochemistry, for example, a population of RNA molecules.
Still doesn’t explain the origin of self-reproduction in the first place.
Contributions of creationist thought to science
But how does young-Earth creationism contribute to ‘operational science’? Does young-Earth creationism use flood geology to find oil. I am no expert in geology, but it seems that flood geology is a pragmatic failure.
Once again, it’s nice of you to give us the benefits of your self-confessed lack of expertise. In fact, there are Flood geologists in the oil industry (and the mining industry for that matter). But geologists look for geological features that are likely to have oil, and other practical things like hardness, all in the realm of operational science. However, Flood geologists are less likely to be surprised to hear that oil can be formed rapidly, e.g. by thermodepolymerization. Other researchers have argued that crude oil may be a natural non-biological product and therefore ‘not a stepchild of unfathomable time and organic degradation’, which could open up more possibilities for exploration.
In contrast, there is abundant evidence for evolution; for example, as discussed above, Bartel’s ribozyme is an example of Darwinian evolution at the molecular level.
As discussed above, there are serious problems using this as an analogy for Darwinian selection of real organisms.
But what has young-Earth creationism contributed to the science?
Already explained above how the source of YEC provides the metascientific framework, without which science can’t be justified coherently. You might like to consider some of the contributions of the creationist scientists listed on our website. You might also like to ask why it is that the most Christian country on earth (the USA) leads the world in scientific output by such a large margin—and did so, even in biology well before evolution was imposed into the school classrooms.
For a start, I would suggest that you provide some suggestions about how the concepts of young-Earth creationism could help Joyce and Bartel’s research as a response.
The main feature of their research is that they have already assumed the conclusion, something you profess to be against. That is, they assume a materialistic origin of life by faith, and are merely trying to work out some remotely feasible scenario to make their faith seem reasonable. I’ve also pointed out before:
Real scientists actually make no use of evolution in their research, because they are concerned with operational science not origins. The leading chemist Philip Skell, a member of the National Academy of Sciences, blew the whistle on the overrating of evolution in a famous column in The Scientist, Why Do We Invoke Darwin? Evolutionary theory contributes little to experimental biology. In this, he took up a point made in a BioEssays special issue on evolution in 2000, that ‘most [biologists] conduct their work quite happily without particular reference to evolutionary ideas’ so evolution is a ‘highly superfluous’ idea. How much less relevant is evolution to other major fields of science such as physics or chemistry?
And you should realize how vacuous evolution is in this case. That is, one evidence for the alleged common ancestry of all life is the common genetic code (overlooking exceptions for now) involving DNA, RNA and proteins. Yet now Joyce is proposing a first living thing that contained none of these supposedly homologous features that are allegedly explained only by evolution from a common ancestor!
I am sure they would be glad to receive any helpful suggestions as long is it is not inane. But I doubt scientists of their caliber (Joyce is a member of the National Academy of Sciences) would take this seriously.
Make up your mind: would they be glad to receive suggestions, or would they not take them seriously? But since you have affirmed that YEC criticisms of chemical evolution are often sound, if Joyce didn’t take them seriously it would be due to the grip of the paradigm on his thinking rather than the cogency of the criticisms.
I would certainly appreciate any feedback! Thank you for reading this.
It took a while ;)
Jonathan Sarfati, Ph.D.