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The Evolutionary Origins of Genetic Information, Part 4

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August 6, 2013 Tags: History of Life

Today's entry was written by Stephen Freeland. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

The Evolutionary Origins of Genetic Information, Part 4

Note: This week on the BioLogos Forum, join astrobiologist Stephen Freeland for a look into the nature of information and the origins of life on earth. (These posts were originally published as a paper in the ASA’s academic journal, PSCF, and are reprinted here with permission.)

Stephen was raised in a Christian family, and his father is a Methodist minister in England whose passion for natural history and science provided a rich environment in which to explore the relationship between science and faith. During Stephen’s teenage years, he explored various denominations, from Catholic to charismatic non-denominational churches, and most recently, life in Baltimore has led Stephen to a deep and rewarding connection with St. Bartholemew's Episcopal church, where he enjoys the Christ-centered meeting point of spiritual substance, social justice, inclusive grace, and rich traditions of liturgy and music.

Because of Stephen’s commitment to deepening his faith through conversations with other Christians, which helps to deepen our corporeal understanding of God’s grace and processes—and because the nature of this material being the rather controversial subject of first life and evolution—Stephen will be participating in the online conversation at the bottom of each post in this series. At the end of each post, you’ll find a few discussion questions, which we encourage you to use as starting points for commenting, (but you are of course welcome to ask him questions of your own, and add your own observations to the dialogue).

Note: For more on the topic of genetics and evolution, please see BioLogos Fellow Dennis Venema’s current series.

The deepest origins of genetic information

The observation that RNA sequences can bind amino acids hints at something very important: proteins are not the only type of molecule that can spontaneously fold into shapes with interesting properties. As described in the companion paper by Watts, sequences of RNA can exhibit protein-like behavior. Technologies first developed in the 1980’s and 1990’s have been used to lab-evolve a wide variety of molecules, dubbed ribozymes in deference to the previously known class of protein catalysts known as enzymes. These ribozymes now cover most steps of fundamental biochemistry (such linking together carbon atoms to make important biological molecules.) Proteins are much less necessary for life than they seemed a couple of decades ago. This observation finds unlooked-for synergy with another line of scientific discoveries. In modern living systems, not all RNA performs the simple role of carrying genetic information from DNA to be decoded into proteins. A handful of the genes that are faithfully copied from DNA into RNA fold up into a complex three-dimensional shapes that act as if they were proteins. Interestingly, these natural ribozymes tend to occur in the most ancient metabolic pathways – those shared by bacteria, humans and everything else alive today. Aspects of biology that have not changed much in billions of years of evolution are likely still with us because they have been doing their job very well throughout this period. In other words, this type of RNA behaving like a protein is exactly what one might expect to see if the ribozymes produced by SELEX resemble a stage of our truly ancient evolutionary past when genetic coding of proteins was far less important (if it was present at all.) Oddly enough, Crick (of the Frozen Accident) had suggested something similar to this concept of molecular fossils when he looked at how genetic de-coding works. He noticed that the adaptor molecules responsible for decoding individual genetic code-words into specific amino acids are nothing more than folded-up RNA. He also noticed that the biggest and most complex molecular machine involved with genetic de-coding (the ribosome) seemed to be made of RNA with a few proteins thrown in for good measure. Three decades later, new technology allowed researchers enough precision in their study of the ribosome’s structure to confirm this is correct: although proteins are embedded within the tangled, folded RNA, they appear to offer little more than structural enhancements.1 At its core, the ribosome is a ribozyme. It seems likely that a primitive ribosome could function without any encoded proteins: exactly what we would expect if genetically encoded proteins emerged from a simpler, earlier world in which only RNA existed.

Of equal interest, everything points towards DNA being the last arrival out of the 3 fundamental biomolecules: DNA, RNA and protein.2 DNA is made by complex, genetically encoded protein enzymes without a ribozyme in sight. The individual building-blocks of DNA (deoxynucleotides) are made by taking and modifying a nucleotide of RNA. Again, all this is exactly what we would expect if DNA evolved from RNA, after genetically encoded proteins had already entered the picture. Indeed, DNA is a more chemically inert version of RNA – better for safe storage of genetic information, worse for folding up into a catalyst. This is what you might expect if it emerged after RNA had already handed off the job of catalysis to genetically encoded protein enzymes. The RNA would get left sandwiched in the middle of DNA and proteins, just where we find it today (Box 1).

Observations that expand on all of these themes continue to accumulate and are beginning to sketch a framework that was completely unknown in the mid 1960’s. At its best, this “RNA-world” hypothesis solves much of the puzzle for the origin of living systems. One molecule, RNA, is its own catalyst and information carrier. However, many puzzles remain. For instance, the universe seems quite good at making amino acids without life. They have been found in meteorites, formed in simulations of the conditions of interstellar space and turn up reliably in just about every possible simulation of our planet’s early conditions. For nucleotides, the building-blocks of RNA, the exact reverse is true. It seems relatively simple to make the nucleobases (such as Adenine and Guanine)– but these must be chemically linked to a ribose sugar and a phosphate in order to make a single nucleotide in processes that are antagonistic to those in which the bases form: there are real chemical difficulties in forming the individual nucleotide building blocks, and even bigger difficulties for linking them together into sequences that do not also contain all sorts of unwanted molecular garbage.3 If RNA came first then why is it so much easier to make amino acids than RNA from non-biological scratch?

Scientists are relatively confident that an RNA-protein world preceded ours in which DNA genes are copied into mRNA transcripts en route to protein translation. Every clue that we can find supports this conclusion. What is much less certain is how the RNA-protein world itself emerged. One broad class of ideas asserts that we have simply failed to discover some set of conditions that encourages sequences of RNA to form spontaneously. Mineral surfaces are often mentioned here, as they can catalyze many chemical reactions. For example in 2004, the mineral borate was shown to catalyze the notoriously difficult synthesis of ribose - an essential component of the chemical structure of every single nucleotide.4 Perhaps other minerals will be found to help other steps in nucleotide synthesis, and for linking nucleotides into sequences. Certainly chemists, geologists and biologists are talking more than ever before as they seek to add up their knowledge of the ways in which life, chemistry and the planet interact. Among them, increasing attention is coming to focus on hydrothermal vents as a good place to look next in the search for the origin of life.5 Here, hot water full of interesting chemicals is forced to flow over richly diverse mineral. This can produce a slew of chemical reactions, most of which are still poorly understood.

Another view is that searching for non-biological origins for RNA is looking in the wrong place. Instead, genetic information, at least in the form that we think of it (polymerized nucleotide sequences) was itself an evolutionary invention of an earlier metabolism, a pre-RNA world. Perhaps significantly, proponents here are also drawn to minerals and to hydrothermal vents because the same conditions that might aid nucleotide synthesis produce a slew of interesting and newly discovered chemical reactions.6

It might even be that these two views meet up one day. Since the mid-1960s, a scientist by the name of Grayham Cairns Smith has been proposing that minerals were the original genetic information.7 Crystalline minerals show the interesting property of harnessing energy from the environment to grow by making copies of themselves. As they do this, they are creating chemical order from chaos. That is exactly what a salt crystal is doing as you watch saltwater evaporate in a glass or a rock-pool. They might also catalyze specific chemical reactions on their surface according to their exact atomic composition.8  In effect, they might carry simple genetic information that starts to trap the energy flowing through the system into a chemical reflection of the environment. But by now we are talking about one of the swarm of competing ideas at the edge of Category 2. Here they will compete and rise or fall according to the evidence that can be gathered through careful and ingenious tests.

Summary

Evolutionary theory, like any other branch of science, achieves progress by testing new ideas. Some of these ideas will go on to change what we thought we knew, others will be found incorrect, and some will stagnate as they fail to gather clear evidence, for or against. For evolutionary theory, many suggestions have been made for new causal factors that are required to explain how genetic diversity has arisen. Intelligent Design, for example, proposes that some types of genetic information cannot evolve through natural processes unless we admit a role for an intelligent designer. This proposition claims testability by using a definition of information that usually refers to creation by an intelligent agent. Meanwhile, many biologists perceive that they are able to understand exactly where life’s genetic information comes from (the local environment) by thinking in terms of more fundamental and well-established definitions of information that do not involve Intelligent Design.  A related suggestion is that current evolutionary theory cannot explain how natural processes could produce a genetic information system in the first place. I agree that we are far from a full understanding, but choose to outline some major themes in the scientific progress made since the discovery of life’s Central Dogma in 1966 to provide a context for the reader to judge for themselves whether it is time to conclude that this search has failed.

It would be remiss to finish an article in this journal without some comment on the theology of all this. If we accept the evolutionary explanations sketched above, then science is taking major steps towards understanding the mechanism by which life came into the universe. Some famous advocates of this science claim it presents a logical connection to an atheistic world-view.9 Many others (myself included) perceive that any connection between evolution and spirituality is an act of faith – and faith in atheism is only one of many options.10 For my part, I find excitement and challenge in the search to unravel this marvelous mystery. I choose to associate that inspiration with a loving, creator God whose universe I am exploring. I agree with Dawkins (and Darwin) that from a human standpoint, the suffering and death implicit to natural selection form questions for my faith – and I am grateful that scientists and theologians are able to discuss such issues in forums such as this11, where I can read, learn and grow my relationship with God through an exploration of science.

Box 1.    An Introduction to Biological Coding and the Central Dogma of Molecular Biology

A code is a system of rules for converting information of one representation into another. For example Morse Code describes the conversion of information represented by a simple alphabet of dots and dashes to another, more complex alphabet of letters, numbers and punctuation. The code itself is the system of rules that connects these two representations. Genetic coding involves much the same principles, and it is remarkably uniform throughout life (Figure 2): genetic information is stored in the form of nucleic acid (DNA and RNA), but organisms are built by (and to a large extent from) interacting networks of proteins. Proteins and nucleic acids are utterly different types of molecule; thus it is only by decoding genes into proteins that self-replicating organisms come into being, exposing genetic material to evolution. The decoding process occurs in two distinct stages: during transcription local portions of the DNA double-helix are unwound to expose individual genes as templates from which temporary copies are made (transcribed) in the chemical sister language RNA. These messenger RNA molecules (mRNA’s) are then translated into protein.

The language-based terminology reflects the fact that both genes and proteins are essentially 1-dimensional arrays of chemical letters. However, the nucleic acid alphabet comprises just 4 chemical letters (the 4 nucleotides are often abbreviated to ‘A’, ‘C’, ‘G’ and ‘T’ – but see footnote27), whereas proteins are built from 20 different amino acids. Clearly, no 1:1 mapping can connect nucleotides to amino acids. Instead nucleotides are translated as non-overlapping triplets known as codons. With 4 chemical letters grouped into codons of length 3, there are 4x4x4 = 64 possible codons. Each of these 64 codons is assigned to exactly one of 21 meanings (20 amino acids and a ‘stop translation’ signal found at the end of every gene.) The genetic code is quite simply the mapping of codons to amino acid meanings (Figure 2a). One consequence of this mapping is that most of the amino acids are specified by more than one codon: this is commonly referred to as the redundancy of the code. 

Although the molecular machinery that produces genetic coding is complex (and indeed, less than perfectly understood), the most essential elements for this discussion are the tRNA’s and ribosome. Each organism uses a set of slightly different tRNA’s that each bind a specific amino acid at one end, and recognize a specific codon or subset of codons at the other. As translation of a gene proceeds, appropriate tRNAs bind to successive codons, bringing the desired sequence of amino acids into close, linear proximity where they are chemically linked to form a protein translation product. In this sense, tRNA’s are adaptors and translators – between them, they represent the molecular basis of genetic coding. The ribosome is a much larger molecule, comprising both RNA and various proteins, which supervises the whole process of translation. It contains a tunnel through which the ribbon of messenger RNA feeds; somewhere near to the center of the ribosome, a window exposes just enough genetic material for tRNA’s to compete with each other to bind the exposed codons. 

DISCUSSION QUESTIONS:

Q1: “…the universe seems quite good at making amino acids without life. They have been found in meteorites, formed in simulations of the conditions of interstellar space and turn up reliably in just about every possible simulation of our planet’s early conditions.” If the building blocks of life can, and do, exist outside of earth’s life-filled atmosphere, do you think it’s also possible that life, itself, exists elsewhere in the universe? If so, and if that life is intelligent, how might the discovery of reason-endowed extraterrestrials affect your own beliefs about human exceptionalism? What do you think should be our Christian approach to interacting with extra-terrestrials, should we ever come across any?

Q2: “I agree with Dawkins (and Darwin) that from a human standpoint, the suffering and death implicit to natural selection form questions for my faith…” Many of the criticisms atheists make concerning Christian faith hinge on the idea that no loving creator God would allow—especially plan for—his creatures to suffer as much as they do. Does “the suffering and death implicit in natural selection” create complications for your Christian faith? How about your acceptance of evolution, itself?

Q3: Do you accept evolution and the “RNA-world” hypothesis of the origins of life on earth? Why or why not? We see in our own house pets and in the behavior of various animal species a capacity for problem-solving, for play, and for emotional commitments that resemble love. With this in mind, do you think it’s possible for other animals to evolve to the point where they, too, can have a relationship with God?

Q4: Throughout the four parts of this essay, a consistent theme has highlighted the incompleteness of human scientific knowledge, and the limitations of specific human approaches (e.g. systems of measurement) in representing reality (truth). How do you think these themes of imperfect human understanding translate from science into theology, and what does this concept contribute to the ongoing debate between science and religion?

Notes

1. For an introduction and references to more detailed material, see Cech TR “The ribosome is a ribozyme” Science (2000) 289:878-9

2. A brief review of data here is found in S.J. Freeland, R.D. Knight, L.F. Landweber “Do Proteins Predate DNA?” Science (1999) 286: 690-692.

3. Readers who are interested in this particular sub-topic are encouraged to read Robert Shapiro’s article “A Simpler Origin for Life”, Scientific American, June 2007 pp. 47-53.  Shapiro’s passionate emphasis represents the best traditions of scientific skepticism, ruthlessly pointing out some very real problems with all current attempts to how a non-living universe could have produced RNA. In particular, widespread enthusiasm for the RNA-world has become so fashionable that even high-profile scientific publications which explicitly seek to demonstrate pre-biotic origins for the RNA world continue to ignore well-understood and long-standing criticism of the problems. For example, one recent, high-profile paper claims to demonstrate prebiotic plausibility for synthesis of nucleotides (Powner MW, Gerland B, Sutherland JD. “Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions.” Nature (2009) 459:239-42.) This interesting work shows that exactly the right purified solution of linear organic molecules can cyclize under the right conditions to present activated nucleotides. However, it entirely misses Shapiro’s “garbage bag” point - that one of the biggest challenges for understanding the evolution of an RNA-world is to understand how building blocks form into oligonucleotides when they are coming from any sort of messy molecular organic broth (rather than a purified solution of exactly the right reactants under exactly the right conditions.) There is no chemical reason why nucleotides should form and stick to one another rather than to other chemicals produced in the same broth – such as amino acids, alcohols, esters etc. Of further note, the chemistry reported in this Nature paper bears no resemblance to the reactions by which living organisms have been making nucleotides for more than 3 billion years. Maybe early life changed its metabolic pathways beyond recognition - but as yet we have absolutely no evidence for this whatsoever: Prebiotically possible and prebiotically plausible are subtly different concepts.

4. For example, see the comment by Steve Benner on page 52 of ref. 32. For a more detailed treatment, see  Kim HJ, Ricardo A, Illangkoon HI, Kim MJ, Carrigan MA, Frye F, Benner SA., “Synthesis of carbohydrates in mineral-guided prebiotic cycles.”,  Journal of the American Chemical Society (2011) 133:9457-68.

5. A very readable overview of this topic can be found in the first chapter of Nick Lane’s recent book “Life Ascending: The Ten Great Inventions of Evolution” (2009, W.W. Norton, New York)

6. One recent example is given by Mielke RE, Russell MJ, Wilson PR, McGlynn SE, Coleman M, Kidd R, Kanik I “Design, fabrication, and test of a hydrothermal reactor for origin-of-life experiments.” Astrobiology (2010) 10:799-810.

7. Although Cairns Smith’s ideas date back to the mid 1960’s, they are most accessibly presented in his later book: “Seven Clues to the Origin of Life.” (1985, Cambridge University Press, New York)

8. For a broad introduction to this progress, as of 2001, see “Life’s Rocky Start” by Robert M. Hazen, Scientific American (2001) 284: pp. 77-85

9. For example, see Chapter 4 (“God’s utility function” Pages 95-135) of Richard Dawkins book River out of Eden (Basic Books/Perseus, New York, 1995)

10. For example, see the letter(s) and signatories of the Clergy Letter Project: http://www.theclergyletterproject.org/

11. For example, the excellent pair of articles: Junghyungkim “Naturalistic versus Eschatological Theologies of Evolution” Perspectives and Keith Miller “And God saw that it was good” – both within Perspectives in Science and Christian Faith  (2011)  63(2).

 


Stephen Freeland is currently project manager for the NASA Astrobiology Institute research team based at the University of Hawaii. His academic background (a bachelor’s degree in zoology from Oxford, a master’s in biological computation from York University, and a doctorate in genetics from Cambridge) has led him to spend the past twelve years researching the evolution of genetic coding. Steve’s current research explores the evolution of the amino acid “alphabet”—the set of twenty building blocks with which life has been making the proteins of metabolism for more than three billion years. Underlying this research is a growing interest in the cosmological question, “To what degree is life on Earth (or elsewhere) a result of chance?” As the son of a biology teacher who retrained as a Methodist minister, Steve has been blessed with an encouraging environment with which to explore the interface of science and faith since childhood.

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Andreas Hypki - #82378

August 6th 2013

Hi, Stephen,

thanks a lot for this well-presented information.

I have recently learned about a paper published this year in Icarus. The paper claims to identify artificial signal in the genetic code that cannot be possibly explained by natural selection. However, the authors deny that they are proponents of Intelligent Design, and they give the explanation referring to SETI. What is intriguing, the journal is quite esteemed, and in acknowledgements they mention known researhcers such as Paul Davies and Artem Novozhilov (who is specialized also in genetic coding). Do you know anything about that paper? What is you opinion? Those guys have made up a website, if you didn’t read the paper, there are links provided there: gencodesignal.org.

There was some sceptical reaction in the Internet (like that by PZ Myers), but the authors replied at their website showing the weakness of his critics. It seems that PZ myers is not a specialist in genetic code, after all. It would be intriguing to hear the opinion of someone who deals with the genetic code (by the way, that paper refers also to your works).


Backcreek - #82425

August 12th 2013

My question on these articles is whether the same priciples would not apply to SETI itself.  Why should it be supposed that a pattern detected in radio signals (however cleverly designed the search algorithms) is an indication of intelligent life, rather than a “natural” radio source?  If signs of intelligence can be detected in a radio signal, why is it not possible (theoretically) to detect similar signs in biological systems?  Wouldn’t the Fermi Paradox suggest that the more likely explanation for any pattern found in radio signal would be a non-intelligent process, not currently understood by science?


Roger A. Sawtelle - #82400

August 9th 2013

Question 2:

The fact that humans are physical creatures, as well as intellectual and spiritual, living in a physical world (which is also intellectual and spiritual) means that we are “temporary” and thus subject to death and thus suffering.  We are more than temporary, but only in God’s realm.

If humans were only spiritual, we would not suffer and die, but then we would not be humans.  We would indeed be angels, but since the universe would be superfulous as a home for humanity, so would be the angels as God’s messengers.  

Suffering and death are part of our nature.  We can accept it or not.  The only “realistic” path is to accept who we are ands make the most of it through God’s plan of salvation which leads to Eternal Life with God and victory over sin, fear, pain, suffering, and death.  


Backcreek - #82426

August 12th 2013

I’m neither a proponent of Creationism, Intelligent Design or Theistic Evolution (TE)...I don’t know enough to be able to settle on an approach.  However, it feels at times as though there is a tendancy to resort to a sort of “Science of the gaps” approach, where we don’t know enough now to explain how it was done, but we are sure there must be a scientific answer someday.  If God is in it somewhere, it is all a matter of faith.  “You pays your money and you takes your chances.”  It seems ironic that it took an agnositic Astronomer (Robert Jastrow) to prod this former Atheist down the long road that eventually lead to faith.  Is there no “biological big-bang” (10 amino acids but no less, etc.) beyond which we can get a glimpse of the creator?


Roger A. Sawtelle - #82431

August 12th 2013

Backcreek,

I do not blame you for not choosing a label in this food fight.

I do not know exactly what you are looking for.

Certainly we can see that the Creator not only made possible the physical universe, but also set the perameters to make possible the biological universe.  We know that this cannot be based on chance.

Not only that but God created humans in God’s own Image.  At the risk of being called a Speciesist I would say that this is very special.

It really makes very little difference how God did it, only that it happened.  God does not put the divine logo on Creation to make sure that God gets the credit. 


Backcreek - #82436

August 13th 2013

Thanks for your replay.  I guess my concern is some vague sense of seeing Deism in this, where God is present at the big bang and fine tuning, but otherwise not actively engaged in the process. (Understanding that some concept of “providence” and “in his image” are added to that rather narrow perception of mine.)

 

Perhaps I’m looking for some sort of Heisenberg Confession among scientists who are Christians.  “We believe that God is present in the up and the down, the top and the bottom, the strange and the charm, and therefore there is no uncertainty with God.”, etc.


GJDS - #82445

August 14th 2013

I agree - a Heisenberg confession has been given to us: “In the beginning God created the heavens and the earth”. I cannot detect any uncertainty in this.

I will add to this the following: “Human beings are not in possession of all knowledge, truth and understanding.”

Perhaps a few of us need to restate these obvious insights!


Roger A. Sawtelle - #82437

August 13th 2013

Backcreek,

In other words you, and probably all of us, do not want a Confession of Faith, but a Confession of Certainty. 

However we live by faith and the Spirit, which is known, but unseen and uncertain, rather than by the physical, which is seen and is believed to be certain, but is not.  This is what our friendly atheist pointed out in the essay. 

It is because of our humans that we believe in God as well as despite our humanity that we believe.  God is not the God of the gaps, but faith is an acknowledgement of our human limitations, which we find difficult to make. 

We want to be in control, but we are not.    


GJDS - #82446

August 14th 2013

Steve,

I want to remind you of our brief discussion in your first installment and ask if you would like to discuss the questions I posed.

Thanks.


Roger A. Sawtelle - #82450

August 15th 2013

GJDS,

Gen 1 may be clear, but it is not obvious nor is it certain by many standards.  The point is that God does not give us certainty.  God gives us faith through Jesus Christ.   

Even if humans had all knowledge about life, many would not understand, because understanding takes faith and not all of us are blessed with faith.  


sy - #82493

August 21st 2013

Steve

Thanks for the interesting articles. I do have some questions. You mention that the aptamer SELEX experiements (Yarus and others) are “shaky”. I agree. I was wondering how shaky you think they are? Do you think that the very non specific and weak binding constants found in these experiments would be anywhere near good enough to allow for the degree of error free coding necessary to kick start a replicable system that could allow the required degree of genotype phenotype concordance necessary for heritability of a nascent code? Clearly, I phrased that as a loaded question, since the anwer to me appears to be a definite no.

The problem, as you know is the error catastrophe model, which will not allow a code to develop in slow stages. For general readers, imagine a language where the various words or letters could stand for different meaning. Ths sentnce has fu erors, and cn b undestood. BUT..ts tennce annct.

Cells can survive with low error rate (which are the result of mutations, not of mistakes in the code) but they simply die when the error rate becomes too high.

So it doesnt really work to have a pretty good code, which is the best that can be achieved using aptamers, (recognition between amino acids and RNA anticodon sequences). The error rate would be so high, that no actual evolution by selection would be possible, since such a code would not be inherited by the next generation.


sy - #82494

August 21st 2013

In a more philosophical vein, I would like to comment that it is indeed extremely difficult to envisage the de novo origin of a genetic code, which is not simply information, but symbolic information, an actual language. Yes, other forms of information exist in the universe,but they are not symbolic (like language, where the word tree, neither looks nor sounds like an actual tree). In the same way the codon for Valine has no actual connection to the chemical valine (except in the aptamer experiments referred to above, and very weakly).

That is new in the universe. And, I sometimes wonder if some scientists are so theologically opposed to this idea (being opposed to the possibility of a Creation of life by a Creator) that they might allow their (anti) religious dogma to steer their scientific viewpoints. Which as we all agree, is not a good idea.


Eddie - #82537

August 29th 2013

Excellent points, Sy.  I wish that more biologists exercised your intellectual caution before drawing grand conclusions.

I find it interesting that in the late 19th century and early 20th century, there were physicists who were pretty confident that the universe was well understood in reductionist, materialistic terms, and that all we had to do was fill in a few details, and then we could write God’s epitaph.  Then Einstein and then quantum theory came along and all of sudden the simplistic, reductionistic, materialist-mechanist notion of physics was knocked on its ear.  By the mid-20th century we had even agnostic scientists like Hoyle wondering aloud if there wasn’t some funny finagling of the cosmic constants by an intelligent being, and physicists like Heisenberg were wondering if the reality revealed by physics corresponded with some proposals of Eastern religion.  But even as the most brilliant physicists were becoming less dogmatic, more humble about what they knew, and more inclined to postpone the send-off for God, the biologists, armed with reductionistic neo-Darwinian biology and speculations about the chemical origin of life, seemed to be going in the other direction, seemed to be more and more sure of themselves that total explanation of the evolutionary process, and ultimately even of the origin of life itself, was just around the corner, and that there would be no need to postulate any intelligence to explain any of it, not even the beginning of the process (i.e., origin of life, origin of genetic code).  Darwin (aided and abetted by origin-of-life research) made it possible, as Dawkins said, to be an “intellectually fulfilled atheist.”  The most hard-nosed materialists, reductionists, and militant anti-theists now are more likely to be world leaders in biology than world leaders in physics.

An interesting turn of events, to be sure, especially when we consider that biology is now exploding with new and unanswered questions and that much of what we thought we “knew” about genetics, development, and evolution is daily being called into question.  (Who would have thought, back in the 1950s, that there would be so much new evidence that under some circumstances acquired characteristics *can* be inherited, for example?)  If only the biologists could adopt the broader sensibilities of a Hoyle or a Heisenberg!  But when we look at “official” biology—the pronouncements of Coyne and Dawkins and P. Z. Myers and Larry Moran and their non-biological publicists such as Dennett and Eugenie Scott and Barbara Forrest and Jeffrey Shallit—no evidence of any broader sensibility is to be seen.  A philosophical, reflective biologist, along the lines of a Hoyle or a Heisenberg—where can we find someone like that today?  Has the publish-or-perish, research-factory model of scientific work destroyed the ecological “niche” that such reflective biologists need to survive and thrive?


Roger A. Sawtelle - #82539

August 30th 2013

Eddie,

These are times that when it is not only scientists are caught up on old thinking. 

We all need to reconsider our philosophical assumptions.


Paul Lucas - #82634

September 16th 2013

Origin of life researchers today are really focused not on the origin of life, but on the origin of directed protein synthesis.  However, an entity can be alive without directed protein synthesis. So there is an alternative to the RNA World:  protein first.  It is easy to make proteins from amino acids.  Lots of scenarios, the easiest of which is simply a tidal pool,but they are also made at hydrothermal vents.   The really cool thing (at least to a biochemist like me) is that, once proteins are made they spontaneously make cells.  The proteins also are enzymes, so the abiotically made cells have enzymatic activity.  One of those activities is the ability to catalyze the formation of RNA or DNA if there are nucleotides present.  The RNA, of course, can act as ribozymes and be a “RNA World” inside of existing cells made from protein.

Now, once you have RNA, there is a step-by-step Darwinian path to DNA and directed protein synthesis:

. AM Poole, DC Jeffares, D Penney, The path from the RNA world. J. Molecular Evolution 46: 1-17, 1998. Describes Darwinian step-by-step for evolution from RNA molecules to cells with directed protein synthesis. All intermediate steps are useful.

http://awcmee.massey.ac.nz/people/dpenny/pdf/Poole_et_al_1998.pdf

God created life by chemistry, not by miracle.

 


Paul Lucas - #82637

September 16th 2013

The Icarus paper by shCherbak and Makukov makes a couple of mistakes.  The major one is that it compares the genetic code not to natural selection but to “stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10-13). “  Natural selection is not chance.  Also, the authors claim “The patterns display readily recognizable hallmarks of artificiality, among which are the symbol of zero, the privileged decimal syntax “  There is no “zero” or placeholder and the code is absolutely not decimal.  People have looked at the genetic code and how the 3rd base in the codon is often redundant.  It is easy to trace the evolution of the present genetic code from a 2 base system:

5. David H. Ardell and Guy Sella No accident: genetic codes freeze in error-correcting patterns of the standard genetic code Phil. Trans. R. Soc. Lond. B 2002 357, 1625-1642

www.ncbi.nlm.nih.gov/pubmed/16059752

The final nail in the coffin is that the authors assume that the genetic code is the same for all organisms.  So a great intelligence making a single, best, code.  Unfortunately, it is not universal.  So, did the “intelligence” make several of them?
http://chimerasthebooks.blogspot.com/2012/02/not-so-universal-genetic-code-its.html


Andreas Hypki - #82674

September 22nd 2013

Hi, Paul,

from your post it is just obvious that you actually haven’t read the Icarus paper. But I have read it, and I have also communicated with the authors. So I can object to your points:

The major one is that it compares the genetic code not to natural selection but to “stochastic processes”... Natural selection is not chance.

First of all, it is not generally accepted that the code was shaped by natural selection. Only adaptive model of the code evolution is based on the assumption that main mechanism of the code evolution was selection for error minimization. However, other models (e.g., biosynthetic one) explain error minimization with adaptationally neutral mechanisms, e.g., as a consequence of the evolution of new pathways for amino acid synthesis. Secondly, though natural selection is not chance indeed, it is not deterministic either. And the authors do take it into account in the statistical test, where they filter generated codes to get only those versions which satisfy the error minimization condition (as well as other conditions imposed by other traditional models of the code evolution).

There is no “zero” or placeholder and the code is absolutely not decimal.

There is no such claim whatsoever. The code itself is absolutely not decimal (neither it is binary, or quaternary, or belonging to any other numeral system). The code itself is just a set of assignments between codons and amino acids. But the numerous nucleon equalities in certain logical arrangements of the code are absolutely decimal. And it is strange to deny it, since it is a fact, not assumption - you can write down those equalities yourself and find that they have special notation only in positional decimal system.

People have looked at the genetic code and how the 3rd base in the codon is often redundant.  It is easy to trace the evolution of the present genetic code from a 2 base system

So what? What does this old speculative hypothesis have to do with the decimalism of nucleon equalities?

The final nail in the coffin is that the authors assume that the genetic code is the same for all organisms.

There is a section in Icarus paper discussing known variants of the code. And here is the quote from the authors’ web-site: “Besides, there are several known variations of the standard genetic code in some lineages of microorganisms and organelles. As suggested by comparative genomics, these variations are later modifications of the standard code (no matter how the mapping of the standard code came to be in the first place).”

Please, read carefully before criticizing.


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