Hi Reinhard,

this is an interesting question; I think the code could be considered like a phenotypic trait and and I find reasonable the " frozen accident hypothesis", the notion that the standard code might have no special properties but was fixed because all extant life forms share a common ancestor, and subsequent changes regarding the code,in general, are precluded by the deleterious effect of codon reassignment.

Hi Andrea,

thanks for mentioning the "frozen accident hypothesis". However, how can a complete coding system just show up by accident? And how could the complete code for all amino acids evolve, when (as you mentioned) a single change of the code cannot take place, because of the deleterious effect of codon reassignment?

Hi Reinhard,

Thats a very good question. I can suggest you two readings that will not fully answer this questions, but could give you some hints.

1 - This book is amazing, chapter 6 is about origin and early evolution of genetic code, but the whole book is a must-read, if you haven't yet. It also have examples of deviations from the total universality of the code and hypotesis that deal with chemical stability in the origin and maintanence of the code.

http://www.amazon.com/Major-Transitions-Evolution-Maynard-Smith/dp/019850294X

2 - This relatively recent paper also sound interesting, but I haven't read it properly yet.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0072225

Joachim,

in your 4th reference one of the scientists is cited, saying:

"But the universality of the code makes it very hard for researchers to study its formation since there are no organisms using a primitive or intermediate genetic code that we could analyze for comparison,"

Isn't that kind of surprising?

We see all kinds of primitive and advanced creatures on this planet, but just ONE nuclear CODE! (there are mitochondrial variants)

Doesn't that say something about the generation of the code? It implies that it does not and cannot evolve. So how did the DNA "know", how many amino acids are available? Who told the translational machinery what a start and a stop codon look like?

Daniel,

thanks for your links.

I know Maynard-Smith. That's the one, who made this wonderful statement on modern evolutionary theory: “Since that time, the attitude of population geneticists to any paleontologist rash enough to offer a contribution to evolutionary theory has been to tell him to go away and find another fossil, and not to bother the grownups” (Nature 1984)

So it is still a chicken-and-egg problem, right? Living beings need a defined code, but the code can only develop in living beings...and most interestingly the code does not develop anymore.

If I understand the citation of Wilder-Smith correctly, he is an advocate of intelligent design: the genetic code is so complex it could not have originated by chance, therefore it must have been created by a divine being. I won't go into that silly discussion.

As I see it there are two interwoven, main reasons why we hardly observe any variation in the genetic code. 1. It is absolutely fundamental for all living beings. A whole biological machinery is built upon and around it, and all changes (mutations) to the code would be detrimental. 2. The genetic code must have evolved very early in the history life and is for that reason shared by all extant biota.

This pattern, with 'a lot of evolutionary adjustment until it fits', is equivalent to the 'punctuated equilibrium' observable in the fossil record and both exemplify, I think, a general evolutionary principle.

Is not really a chicken egg problem (which, in turn, its not really a problem in a cladistic sense, right?). The origin of the stable code, with DNA and codons, could have proceded a more simple "promiscuous" form of translation, outside membranes. I think that the origin of individuality were crucial to the origin of what life is, and the stable code could only have being selected after it. The book chapter deals with the 2 aproaches of how this could happens, and look also in the chapters of origin of life. The paper show experiamental work that shed some light on the question.

Thomas,

it is not about the complexity of the genetic code. The question is, how the genetic code could evolve, at all. Even very early in the history of life, the code would have needed some kind of "reaction system", right? A code without a reaction system is useless...

As far as I know, Wilder-Smith did not know anything about "Intelligent Design", because this movement was established much later, by US citizens.

Your questions are correct because " frozen accident hypothesis" does not explain how genetic code arised. We can observe incredible adaptations ( for example sensory systems degree of adaptation) in living systems but It's not so difficult to believe these could have emerged just by chance inside current evolutionary biology rules, but if we think of a code, something nearer to informatic and computation than biological tools requested to survive, it's difficult to believe to a stochastic explanation. We still lack an informatic theory of biology and before this we still don't have an informatic theory of evolution for this simple code.

Andrea,

The origin of the code, like in the case of adaptations, has nothing to do with pure chance:

1- Chemical afinities the forms the bonds of molecules that originated the code were not random,

2 - Subsequent selection of stable and viable codes could not have being random, because, by definition and logic, natural selection is a non-random process, of retention and proliferation of fitter emtities/systems in relation to others, less fit.

We should not be too mislead by the metaphor of the genetic code as information per si. Is a good metaphor, but not a reality. Genes are not information beyond their evolved material causality between and within generations.

Daniel you are right, I perfectly know that adaptation is not a stochastic process, I used the word chance in a very broad sense just intending something under natural conditions, It was not a good choice, I agree

Daniel,

how did the triplet code become complete enough, to result in encoded products? After all, you need several triplet codons and a start and stop codon to begin with. Otherwise, there is no code...and it can not be selected for...

Just found this useful overview at Wikipedia:

http://en.wikipedia.org/wiki/Genetic_code#Origin

It still does not answer my question ;-)

Maynard-Smith&Szatmary proposed an answer to it, with a hypotetical scenario. You have access to the book I've suggested you? If not, is even worth buy it.

It seems there is a newer version available:

http://www.amazon.com/Transitions-Evolution-Revisited-Theoretical-Biology/dp/0262015242/ref=sr_1_1?s=books&ie=UTF8&qid=1402250689&sr=1-1&keywords=The+Major+Transitions+in+Evolution+Revisited

Ok, I will order it, but I am not very confident that it contains the solution to my problem. Otherwise, you could have described it in a few sentences... ;-)

The revisited is in fact a collection of papers by biologists and philosophers on the subject, and is not as good as the first one. Is more related to cell=>multicellular, and individual=>group transitions on individuality, and don't touch much on what is this question concerns. If you willing to buy one, get the original first.

Ok, I downloaded the digital version. Could you please tell me, where I find the answers to the questions I posted above?

It is definitely a very interesting book, but I cannot find what I am looking for...

It seems that the online version does not have pages, so I need search terms or chapters.

Thanks

For a fast answer, chapter 6, for a longer one, chapters 4-6.

Thanks Daniel and Simon for the interesting references.

However, my questions are not answered in them.

1. How did the triplet code become complete enough, to result in decoded products? After all, you need several triplet codons and a start and stop codon to begin with. Otherwise, there is no code...and it can not be selected for...

2. How could the genetic code evolve, at all. Even very early in the history of life, the code would have needed some kind of "reaction system". A code without a reaction system is useless...and can therefore not be selected for.

3. We see all kinds of primitive and advanced creatures on this planet, but just one nuclear genetic code! (there are mitochondrial variants) Doesn't that say something about the generation of the code? It implies that it does not or cannot evolve anymore. How does the translational machinery (=decoder) know what a start and a stop codon or any other codon look like? Doesn't a code only make sense when the decoder knows about it? What developed first? The encoder or the decoder?

> chicken-egg problem revisited ;-)

Simon,

the genetic code is not simply a phenotype you can (naturally) select for. The genetic code seems to be the prerequisite for natural selection.

As I said, you need an encoder and a decoder for a code to produce anything useful. I just miss the logic behind these highly speculative models on the origin of the genetic code. They make no sense...

My standard question to Creationists or Intelligent Designers is: Who created/designed the Creator/Designer? Surprisingly, I have not gotten any useful answer from them either.

So, I repeat my first question:

1. How did the triplet code become complete enough, to result in decoded products? After all, you need several triplet codons and a start and stop codon to begin with. Otherwise, there is no code...and it can not be selected for...

Based on natural selection theory, don't you see that there is no solution to the problem? ;-)

Reinhard,

Your questions are debated and at least, partial solutions were proposed in the book I sugested to you. I can't see why you repeat those question like you haven't read anything! The fact that there are exception for the universality of the code (and not only on mitonchondrial genes!), is evidence that it can change!

There's a lot of modern literature as Simon points, to answer your questions, but unfortunetely, I have another priorities to read now, and will not dedicate myself to that subject. If you really wishing to make the statement that there's a problem here, why not do a robust review of the literature first?

But again, i see that your problem is that you *assume* the the current optiamal observed code (or any other adaptation) had to be always like we see today, like in our discussion on migrational patterns, then, you conclude that everything has to arise in magic adaptive jumps.

Daniel,

I read the chapters of the book you suggested, the answers are not there. I would love to hear one...

No, I do not insist in the non-evolvability of the code, but I insist in the problem, how this encoding-decoding-business could start from scratch...based on natural selection theory ;-)

Simon, thanks for pointing that out.

However, the important question is not if a complex system can evolve, but if a very simple coding system can start from scratch.

For a code to have any selective advantage, you need both parties understanding each other, the encoder and the decoder.

I just don't see, how natural selection can interfere at this early stage. So, how did the encoder and the decoder evolve? Seperately or not? What was the selective advantage at this stage, if e.g. the encoder "invented" a new triplet codon, but the decoder didn't know what to do with it and could not translate it into an amino acid?

Forget for a while, what you learned in biology classes...it won't help you ;-)

Reinhard

A model for how a genetic code could form at all (i.e., not a particular code) from scratch in the absence of 'one single intelligent source' is given in my paper:

"Thermosynthesis as energy source for the RNA World: A model for the bioenergetics of the origin of life"

in

Biosystems, Volume 82, Issue 1, October 2005, Pages 93–102

Anthonie Muller

Good luck

Thanks Anthonie, interesting idea...however, I still have this encoder-decoder-connectivity problem.

Interestingly, despite the "extensive literature on these topics", nobody else seems to be worried about it. So according to mainstream science thinking, I must be wrong...because the majority is always right ;-)

Just to summarize my ideas:

In my model life started with unstable membrane vesicles that dissolved at high temperature. These vesicles were stabilized by the the phosphorylation of the constituting lipids by the very first enzyme, what I call the 'First Protein' (FP), which worked on thermal cycling. This vesicle stabilization by the FP is associated with the first selection process. It is assumed that a machinery existed to generate a protein library with randomly sequenced proteins, a few of which could function as the FP. Thermal cycling was the energy source of this random protein sequences generator. Thermal cycling was also the energy source of the RNA world. RNAs, of which some could self-replicate, were selected that enhanced the fraction of the FP in the synthesized protein library. Thus both an RNA and protein libraries evolved, yielding eventually a genome that made use of a genetic code. Coding and decoding RNAs would emerge during a process that selected those RNAs that enhanced the fraction of FPs in the library of at first randomly sequenced proteins.

A progenitor of an RNA set (mRNA, tRNAs) that sustained the genetic code would have been a smaller RNA set that coded only for the main motif of the FP (~an ATP Synthase with promiscuous amino acid and phosphates condensing capabilities during thermal cycling).

There is much more to be said about this all. In addition to the referral to my paper in BioSystems, you can also read:

Life Explained by Heat Engines

in Genesis - In The Beginning

Cellular Origin, Life in Extreme Habitats and Astrobiology

Volume 22, 2012, pp 321-344

Concerning your remarks on 'mainstram science thinking'; the paradoxes of the problem of the origin of life and the genetic code have been discussed by many. I found the papers of the late Leslie Orgel helpful. During a conference I proposed my model in person to him, but he did not seem to get it.

All ideas present in the mainstream science thinking were at first proposed by very small minor minorities, of which some even consisted of a single individual. Some proposals were instantly accepted by the mainstream, the acceptance of others took considerable time. My proposal makes extensive use of concepts from thermodynamics, a discipline that life scientists do not feel comfortable with and try to avoid.

Publicity may help in getting the funding that experimental work requires; competition is fierce and requires much attention and energy. Everybody is screaming for attention, and claims that 'his raven is the blackest'. For theoretical work it is different. The traditional working methods of a scholar: (1) reading a lot, (2) thinking a lot, and (3) writing as concisely as possible, all done in solitude in a quite environment, require comparatively little support, although even that may be hard to get.

Best wishes

Anthonie Muller

Thanks, Anthonie.

I should have written "nobody else at ResearchGate seems to be worried about it..."

These questions have been discussed a lot, I know. However, it has not resulted in any plausible scenarios.

Your model is interesting, but again lacks the explanation, how an encoder-decoder-system could have ever developed, whose proper function is essential for the organism, it is part of.

>chicken-egg problem...extended version ;-)

Hi Reinhard

Are we talking about semantics here? What do you mean with 'explanation' or a 'plausible' scenario ? I describe a theoretical mechanism, based on (1) a random generator of a library of peptide sequences, and (2) a selection mechanism of peptide sequences: phosphorylating lipids, which stabilize lipid vesicles.

Today's encoder-decoder system would have been preceded by a simpler encoder-decoder system that used transfer RNASs to code for a small domain, a catalytic cleft in which during thermal cycling condensation reactions occurred that resembled the ADP + P to ATP condensation reaction still occurring in the beta subunit of today's F1 ATP Synthase. The progenitor of this beta subunit would have been the very first enzyme. It would have made use of a thermal variation of Boyer's well known binding change mechanism.

My background is in the inanimate sciences, where one can use the term explanation in a model such as this. If one restricts oneself in using the word explanation only for mechanisms that have been experimentally verified, then one might call the explanation invalid. In scientific disciplines such as astronomy and geology explanations that have not been experimentally verified but that build upon experimental work are however generally considered scientifically valid.

It can be a matter of subjective judgement to call a scenario plausible. I invite you to explain your objections in further detail.

Anthonie

Anthonie,

an encoder-decoder system cannot develop by chance (ask Edward Snowden or any other computer expert), especially the ones, which contain backdoors for the NSA ;-)

It is not about semantics, it is about the foundations of the modern synthesis. I use the term explanation in a "non-experimentally-verified" sense.

Even if, as you suggested, the current system was preceded by a simpler one, the code of the encoder has to match the code the decoder is using...otherwise you end up in chaos and death!

Natural selection can only select for triplet codons both parties (encoder and decoder) know of and which result in the production of a new protein...which provides some sort of selective advantage to the reaction-system.

How probable is the synchronous appearance of a new triplet codon in the DNA and at the same time an innovation of the translational machinery, which makes it understand that newly generated code?

Reinhard,

"the code of the encoder has to match the code the decoder is using" => Yes, and this is simply due chemichal affinities. More stable and replicatable-prone chemichal systems will be selected and coevolve. Anthonie's model is absolutelly satisfactory on the point you are concerned.

Let's not allow that methaphors rules over our physical reality!!

Reinhard,

You misapply the terms 'chaos' and 'death' to describe a proposed system that is still quite chaotic: intense convection is assumed, and much free energy is dissipated in the present thermal gradient. Moreover, the proposed system can hardly be called alive. It has been found very difficult to define life, but one cannot call a fluid alive that is merely convecting in a thermal gradient.

Note that a convecting system is a self-organizing dissipative structure.

In the proposal, a simple first selection system would work on lipid vesicles and the First Protein, a small fraction of an admittedly still vaguely defined synthesized protein library.

There is no question of ending up in 'chaos and death': on the contrary, the border between death and life would be crossed in the direction of life while the proteins and RNA would be selected that enable a simple genetic system to operate.

Anthonie Muller

Daniel,

you know that the genetic code and the specifity of the translational machinery cannot be explained simply by chemical affinities.

Anthonie,

natural selection can only work on living beings, and living beings need some kind of heritable information (DNA, RNA), which can be translated into proteins. For that purpose the coding language has to be defined. You cannot simply change the code at the encoding site, without confusing the decoder...which in turn will kill the living being and finally terminate the evolving lineage.

Reinhard

Selection can work on inanimate objects: for instance, sand particles with a certain size can be selected by using a filter that permits only particles of a certain size to pass. An iron needle can be selected from a haystack by using a magnet. Are these processes 'selection' or 'natural selection'?

In studies of the origin of the genetic code one should consider mechanisms, and avoid assumptions, preconceptions or circular definitions involving life, as these may not apply to the origin of life.

In my model the first macromolecules were selected by function (phosphorylating lipids) and did not involve heritable information, which emerged later. It is implausible that in a 'big biological bang' multiple biological capabilities emerged simultaneously.

Anthonie

Anthonie,

if, in your model, you have no heritable information, how should organic evolution ever proceed?

No, filtering sand particles is not natural selection!

Living beings are definitely more complicated than inanimate objects, they exist of numerous highly-interconnected and complex biological systems, otherwise they become sand particles again... ;-)

Reinhard

Do you assume that life can only have emerged from inanimate objects by the assistance of an already existing intelligent being?

Anthonie

No, as I mentioned earlier, creationism (intelligent design) does not provide any answers either, since nobody knows who created/designed the creator/designer.

I just want to point out, that despite the "extensive literature on these topics", if you think it through, we have no idea how life started on earth.

"It is better to know less than to know so much that ain't so." Josh Billings

Reinhard,

Evolution requires heritable variation, not heritable information.

Information, in the sense is useful here, is how we name heritable variation the re-instantiate some stable pattern that are being selected "for" its properties that causes those very stable patters.

So, if we wish to understand the transition from non-living to living systems, we should look for molecular interactions that are self-assembled and replicable. The precision of a code, like a genetic code is a late-comer in this process. Your description of encoder-decoder refers to highly specialized physico-chemical systems that have evolved ways of heredity and variation.

Anthonie's model have heredity accounted by RNA-world part (self replicate RNA). You should note that any molecule that could have at least alternative states and replicate, could initiate what we call natural selection. There's a lot of it on the first half of the book I’ve suggested you.

I agree with you that we don't exactly know how life began, but "no idea" is not a good description of current understanding. If one is to succeed in this line of research, it will not by ignoring and misunderstanding our current knowledge. It will be expanding it from what we know now.

Why in every topic you keep insisting that gradual improvements is less plausible than chance adaptive saltation is curious to me, and makes me wonder if there's not a strong ideological and poetical bias against orthodox (and more plausible) explanations.

If I was a psychologist, I would say you have a revolutionary bias =)

Daniel,

you know that heritable variation is based on heritable information.

If there is no blueprint, which is passed from one generation to the next...variation and selection have no target they can act upon.

Since you prefer the multistage model: how did the simple system, based on chemical affinities, suddenly switch to an encoder-decoder system? Hence, any intermediate stage between these two systems would result in chaos and would therefore be inviable...

As a medical doctor I have seen no innovation just suffering caused by the gradual evolutionary mechanisms, you admire so much.

"...by ignoring and misunderstanding our current knowledge..."

Well, this is a very subjective statement! It implies that my knowledge is inferior to yours. ;-)

By the way, it would be better if the anonymous downvoter would participate in this discussion and explain why he thinks that my answers are of poor quality ;-)

Reinhard,

No gene is literally a blueprint or an informational entity by itself. They have material causality on phenotype, and if it's fitness enhancer, it will be selected, and only then we associate it with it's "informative" role. But you are letting the metaphoric "car" lead the ontological "horse". Information in bounded in their functional role, it do not preceded it.

On the early chemical evolution, you are familiar with RNA world hypotesis, in which some molecules (in this case RNA) acts as replicator and catalyzer? That, associated with vesicle and protein self-assembly, is a conceivable way how a rudimentary autopoietic system came to being, with rudimentary replication and metabolism. From this on, selection could shape more efficient, stable and evolvable system. What you calling encoder-decoder is a physico-chemical system, not some computer.

I cannot help you more than the bibliography suggested here. I impressed that you said you read all and yet kept the view that a "simple system, based on chemical affinities, *suddenly* switch to an encoder-decoder system".

As a medical doctor, your understanding of microevolution (and only in this subject I regard your knowledge incomplete for the questions you wish to debate, not as a whole) is not adequate, as I stressed you, you always ignore evidence from ecology and adaptation in nature, which involves “suffering” and innovation, and yes, I admire it.

Daniel,

the blueprint is not in the genes!!!

Genes just code for the building blocks of an organism. The blueprint must be somewhere else...e.g. in the noncoding DNA. There is accumulating evidence that the activity of (retro)transposons is involved in the shaping of the blueprint of an organism.

Otherwise you can hardly explain why the single-celled Trichomonas vaginalis seems to have 60,000 protein coding genes, according to a draft genome sequence published in Science. (26,000 genes had similarities with known proteins or expressed sequence tags in other eukaryotes; however, the function of the majority of the other predicted genes is unknown) (Carlton et al. 2007)

If the human blueprint would be defined by the 20,000 genes or so, a single-celled parasite living in the urogenital tract of humans cannot have 60,000 genes.

That's nonsense...and mainstream molecular geneticists should start realizing these inconsistencies.

Your example of rudimentary replication and metabolism is fine as long as you don't think it through. You cannot gradually change this system, because the organism depends on it. You can only replace a primitive system by an already working advanced system. Intermediates are not possible...

Actually, the biological encoder-decoder system is better than any computer...

I already explained to you, why systems (which are essential for survival) have to change as a whole... ;-)

If you present any convincing evidence from ecology and adaptation in nature, I would really appreciate it.

"...your understanding of microevolution...is not adequate..."

Daniel, I was trained in (medical) genetics for many years at UC-Berkeley and at the University of Vienna...but of course you can say it was in vain...I have no problem with that ;-)

Funny that a young guy like you thinks that the current knowledge on micro- and macroevolution is mostly correct. Whereas, an old guy like me thinks that a large part of it is simply wrong...

Time will tell...

Dear Reinhard,

I guess that will be my last response to you here, and I explain why: None of your statements is logically consistent.

1) - When I talked of "genes", I included any sequence that have causal role on phenotype, so we can include regulatory any sequences on heterochromatin, transposons, but also non-genetic material that acts in transcription/translation/etc., and any other causal influence on phenotype - The argument stands the same - there's no information by itself, those things are informative as long as their function on development is being selected. I guess that the size of genome or number of coding system not being related to complexity is a well know thing to every evolutionary biologist! And surprise: It's also in the book I suggested you!

2) - "You can only replace a primitive system by an already working advanced system. Intermediates are not possible..."

Plain wrong. Look for our your organic systems and take a tour on the phylogeny of Metazoa, to see countless time a system that organisms depended being changed. Otherwise evolution would not be possible. And the change is fairly gradual. You think genomes are much more special, like an essence of what organisms are. The difference is that changed happened early/in beginning of life history and the frozen code we see today is the winner, and you see it as the only possible type of code. And I really can't see why you think a change of RNA to DNA world is something that would lead to "death and chaos".

3) - For evidence on natural selection, I guess you can do your own research and you will find it. My suggestion by now is this book, but don't limit yourself to it, and only after a revision of literature you could make stronger claims that some evidence does not exist, or construct explanations that take its absence for granted. http://books.google.com.br/books/about/Natural_Selection_in_the_Wild.html?hl=pt-BR&id=MYk1XbelDssC.

4) - Surely your medical genetics is part of what I see that takes to understand evolution, but only part, I never said it was in vain, but for what you proposing to debate, it is not enough. Like my knowledge on physiology is not enough to be a doctor. And curiously, the orthodoxy is made by many more "old guys" than the unorthodoxy. On a statistic account in that we don't limit our sample to only two of us, your argument have no meaning, since you're just an outlier. =). That doesn't mean you are wrong BECAUSE of it, just that your argument that I’m "young-ortodhox" and you "old-unorthodox" have any relevance or statistic meaning in reality.

Thanks for the question that reached me only now. Please see the contribution of my group on this topic, available from ResearchGate: Romeu Cardoso Guimarães 2013 Formation of the genetic code – update November 2012.

http://www.icb.ufmg.br/labs/lbem/pdf/GMRTgeneticodeNov12.pdf

In short, the idea that sprung from empirical observations is that the code evolved from RNPs formed from dimers of prototRNAs that started the protein synthesis process. The chronology that emerged from this approach was certified through the prediction, later verified by other groups also, that it started with the encoding of Glycine and Serine, via the Glycine-Serine Cycle of anabolism, involved with the assimilation of C1 units. References are in the review above, also available from ResearchGate.

Daniel,

thanks for the interesting discussion...but we will never agree on this subject.

However, this is not a catastrophe, so just relax ;-)

Romeu,

thanks for the link to your interesting paper and the short description of your idea.

However, I still don't understand how an encoder-decoder system can evolve by chance, if its proper function is essential for the survival of the organism. If "innovations" sporadically happen at the encoder site, how can the decoder (=translational machinery) understand them? So, it seems to me that the same "innovations" would have to happen at both sites, the encoder (=DNA) and the decoder.

It just doesn't make any sense...

The running title in the citation that started the question ‘The natural sciences know nothing of evolution’ is tremendously arrogant; not a good start. The monophyly hypothesis seems to be well supported by the observation of all cells known being constituted by nucleoproteins. I don’t know the cited Kerkut but I also don’t know biologists that support the paraphyly hypothesis. Discussions abound on how many extant phyla there are, on various names and possible constitutions of the ‘Last Common Ancestor Population’, and on how diverse or heterogeneous it might have been etc. The concepts of chance in the natural sciences need careful usage. There are many but I will concentrate on only two: plain probability (as in playing with dice) is applicable without restrictions to the events of ‘meeting or convergence of two independent causal chains’; molecular interactions are essentially biased due to affinities (therefore not probabilistic), and may be subjected to thermal (‘probabilistic’) fluctuations of strength or of ‘fraction of time where the interactants are together or apart’. These two characteristics are combined in the proposition that the prototRNA dimers would have been originated as oligomers synthesized from geochemical monomers on mineral surfaces such as clays, pyrite etc. (that is, common origins) and would be concentrated in the interlayers or porosities, that facilitated the dimerization. (continues)

(cont.) Peptides synthesized by the dimers would form RNPs after rounds of utilization of different substrates, when the peptides were able to bind to the producer prototRNAs. The prototRNAs are stabilized in the RNP and, when these continue functioning in peptide synthesis, a self-stimulating ‘circular’ system is formed, that is, a code is formed from this ‘selfing’ property: the substrate amino acid is polymerized into peptides that bind and stabilize the producers that will produce more of itself; the ingredients that worked well will stay more together, in amounts and time. This embryonic system would evolve into the tRNA-synthetase couples, ribosomes, genes and so forth, all different versions of polytRNAs. These codes are not conventions and did not arise inside an organism but sprung from geochemistry and helped forming organisms, stabilizing them and providing for efficiency. Dear Reinhard, I hope this clarifies some of the doubts. I remain at your disposition for further discussions. I will shortly add to the ResGate files two new contributions I am giving to the ISSOL meetings in Nara – ORIGINS2014 – and Kyoto – OQOL2014 – this July. A prediction of the model has been confirmed, the finding of the metabolic pathways that produced the two first encodings. We are now waiting for experimentation on the dimer mechanism. The process is of sequential addition of pre-encoded couples of tRNA / synthetase, analogous to today’s genetic engineering for new codes.

Dear Romeu,

I know that the title of the citation is arrogant, however the author Wilder-Smith discusses weaknesses of currently accepted biological models, which if true, might justify the title.

Your model is very interesting and sophisticated, still...I cannot understand how a code system can evolve into something like this (see attached link), if the (cell) compartment it codes for, needs a stable code language.

If there is no compartment and the items are just floating around in space and time, so how could you ever select for a living being containing all these essential parts of the whole machinery.

You would need some kind of compartment, which does not rely on the genetic code...but if the code does not code for the compartment, what are the phenotypes natural selection is acting on?

http://en.wikipedia.org/wiki/Genetic_code#mediaviewer/File:GeneticCode21-version-2.svg

The idea is that formation of the code was concomitant with the foundation of the cell, that is, inextricably linked with the origins of the metabolic system, especially the pathways of amino acid biosynthesis: an amino acid needs to be present reliably so that it can be encoded. Its encoding is followed by ligations that produce order in strings, reliable sequences of proteins and their genes. There are many self-referential loops in the network. Initial compartments would be geochemical (porosities, interlayers), then globules of RNPs. Formation of the whole system is stepwise, derived from complementarity of tRNA dimers. Of course, there are many gaps in knowledge to be filled. Yours, Romeu.

Hi Reinhard,

Your question: "how did the simple system, based on chemical affinities, suddenly switch to an encoder-decoder system?" is still one of the greatest scientific puzzles. To even approach the answering of this question one must first ask an even more basic question: What are living beings and why did they even appear on planet Earth? The answer to this question, in my opinion, should be searched in physics (more specifically thermodynamics) not biology, since physical laws underlie everything. The best answer so far to the question "What is Life and why does it exist?" in my opinion has been given by Dr. Karo Michaelian in his papers:

http://www.earth-syst-dynam.net/2/37/2011/esd-2-37-2011.pdf

https://www.researchgate.net/publication/50829197_Biological_catalysis_of_the_hydrological_cycle_life%27s_thermodynamic_function

Recently, I have coauthored a new paper with him, available on RGate, in which we explain how, in essence, life is actually a network of coupled processes for the production and dissemination of pigments throughout Earth's surface. We also theorize how pigments are and have always been central to the existence of life on Earth.

Best regards, Alex

Article HESS Opinions "Biological catalysis of the hydrological cycl...

Hi Alex,

interesting idea, although I do not understand how physics can explain the evolution of higher organisms. However, physics could explain the generation of a code...

Hi Reinhard,

As the most fundamental natural science physics should be able to explain all natural phenomena including living beings, and I think Prof. Michaelian has done a really remarkable job explaining life from a physical viewpoint. All living entities, including higher multicellular organisms, are nothing more than electromagnetic phenomena which persists and proliferate only through interactions with electromagnetic radiation of certain frequencies, reaching us from the sun. You asked a very valid but often overlooked question earlier: How can an encoder-decoder system start from scratch just by chance? The answer is - it can't, unless there is some kind of driving force behind its existence, which is responsible for its birth from the primordial molecular soup. And this driving force is not some mystical, omnipotent creature people refer to as God, but the very same electromagnetic energy flux reaching our planet from the sun we all know as light. Please read Karo Michaelian's work, you will be absolutely fascinated.

Best regards, Alex

Alex,

Some kind of energy input is definitely required for organic evolution to proceed. However, even if energy is an essential ingredient, I think it cannot explain the existence of biological machines...or a genetic code!

Sometimes it's better to know that we don't know ;-)

Hi Reinhard,

Yes, it can explain the existence of complex biological machines if you you think of the machine as a transformer of energy and not some metaphysical form of existence. There is energy input in the biosphere and there is also energy output. The input is in the form of high-frequency visible and ultraviolet photons, and the output is in the form of low-frequency infrared photons. Energy enters our planet in lower entropic form and exists our planet in higher entropic form = second law of thermodynamics. 99% of visible photons absorbed by photosynthetic pigments, chlorophyll and carotene, are dissipated into infrared photons which then enter the water cycle and are ultimately released into space; less than 1% are used for fixing carbon into organic compounds. Living system are processes of energy transformation which obey the second law of thermodynamics and nothing more. Genetics ensures the proliferation of organic material over the entire surface of the planet and most importantly organic pigments which serve this ultimate thermodynamic function.

Regards, Alex

I just noted that the entire discussion starts from what modern biology (excuse an economist for speaking in its name) understands to be a false assumption, and what apparently A. E. Wilder-Smith in 1981 did not (or did not want to?) understand, namely:

Different biological phyla did not originate separately !!! - but the origins of all actually existing forms of life on Earth now appear possible to trace down to a single cell. This is the most natural explanation why all these forms the same genetic code. Perhaps there had first been a competition among different kinds of cells, using different codes, but only this one turned out able to give rise to the four billions years' evolution of the "tree of life" - so that all these form are its more or less distant descendants.

The simple answer to the original question therefore is: NO, A. E. Wilder-Smith's criticism IS NOT valid !

One may suspect him of smuggling in the arbitrary assumption of separate origins of phyla in order to come to what appears to be his desired conclusion: the existence of an "intelligent designer." Beware the eristic dialectics - or the art of winning debates even if you are wrong (cf. Schopenhauer) - of the anti-Darwinian enthusiasts for "intelligent design"!

Pavel

Pavel, the topic of this discussion changed a little. Wilder-Smith's criticism was just the intro...

The discussion is about how a code can evolve at all, if the "carrier" depends on its proper function. If the encoder invents new triplets, the decoder cannot deal with them.

Not every anti-Darwinian is an intelligent designer or creationist. It is simply about logics, and my impression is that the modern Darwinians don't think their numerous models through...

Otherwise, they would realize that they are wrong ;-)

An eukaryotic cell is a complex biological machine, and the code is supposed to code for every part of it. If you change the code at the encoder site, the decoder would be confused and the machine would break down.

See http://www.pearsonhighered.com/mathews/ch01/fi1p11.htm

Reinhard, I am afraid you do not understand what the genetic code really does.  Otherwise you wouldn't write "An eukaryotic cell is a complex biological machine, and the code is supposed to code for every part of it."  Allow me to tell you that the code is only a kind of language that translates sequences of triplets of DNA, via mRNA read by ribosomes, into sequences of amino acides, forming proteins.  The cell is a result of complex chemical self-organizations, of which the proteins are only SOME of the actors, as building blocks or as regulators of processes, including the production and the assembly of the blocks.  True, they are KEY actors, but far from "every part of it."

But you are right that DNA mutations that result in some unusual DNA-triplets are not read, and must therefore fail (to call the genome "the encoder side" is a little unusual, but OK).

The only logical conclusionis appears to be that during the last four billions of years or so, THERE HAS NOT BEEN ANY SUBSTANTIAL EVOLUTION OF THE CODE. It might have been evolving before the appearance of the first primitive cell which started to use it, and of which all actual organisms are more or less distant descendants.  But during the four billions of years, the biological evolution that we know only plays with varieties of DNA sequences, but these are read and expressed only if they make sense in this no longer changing code.

The last question: Reinhard, which anti-Darwinians who are neither creationists nor advocates of intelligent design can you see?  Perhaps Lamackians?  Can you clarify?

In any case, I am afraid that it is you who is wrong, not modern Darwinians (at least some of them).

Pavel

Pavel, self-organizations might work in economies, but not within a cell. The blueprint of an eukaryotic cell must be encoded in the DNA. You are right, there is not just one code. However, the genetic code is the only DNA code we can decode. We don't know nothing about the information stored in the so-called junk DNA. For example, transposons might be involved in the restructuring of the body plan of species.

Anyway, all parts of the cell must be encoded somewhere...

Isn't it interesting that the code (we know of) does not evolve anymore? Why not a quadruplet code? It would protect against reading errors and would therefore be "fitter" in Darwinian terms. Four billion years...and not one primitive cell (successfully) played around with the code...isn't that kind of surprising?

If someone is against a biological theory (=modern synthesis), because it does not comply with the (fossil) evidence, he does not have to be a Lamarckian or a designer. The first step is to realize that we don't know...it is the most important step ;-)

@Reinhard, it's not surprising: tweaking the code would affect too many proteins. There are in fact some atypical codes (e.g. some mitochondria) but they are always in scenarios where low gene number and/or composition bias means that the changed codon was at very low frequency and therefore "safe" to tinker with.

You are right that other codes could be "fitter" (although I don't think a four-letter code would protect against reading errors and it would be a less efficient encoding). The unversality of the genetic code is major evidence against Intelligent Design and other forms of Creationism.

As for "all parts of the cell must be encoded"... that's not strictly true. Only the nucleotides and proteins are explicitly encoded. A lot of the cell is just the product of the chemistry that happens because those encoded things have been made. The environment and learnt behaviour both have an influence on this and are not encoded.

A code with four letters, coding for the same number of amino acids would definitely protect against reading errors. A reading error of one letter would not automatically result in a different amino acid.

During the 10,000 trillion cell divisions in a human lifetime, all cell organelles have to be doubled and distributed equally to the daughter cells.

endoplasmic reticulum, Golgi apparatus, mitochondria, nucleus, etc

Products of the chemistry? Do you really believe in standard biology textbooks? ;-)

Is the fact that the nose sits in the center of the face and not somewhere on the ass...also the result of chemistry? There are no genes coding for the position of the nose...

source: biology.about.com

@Reinhardt, yes. It is all chemistry(, which is all physics.) I'm confused as to what else it could be.

Have you heard of actin? Kinesin? Microtubules? There might be details to work out but I don't think there is an awful lot of mystery left in cell (and organelle) division.

The position of the nose is encoded by transcription factors etc. that control development. There is no "nose in centre of face" gene but the interplay of many genes (and maternal factors) consistently result in a central nose. Read up on HOX genes for good examples of body patterning. (And SOX, FOX etc.) Of course, (chemical!) drugs etc. can mess such things up, e.g. Thalidomide birth defects, as can genetic anomalies.

If you were to activate the appropriate transcription factor(s), I am sure that you could generate a (non-functioning) nose on your ass, just as we can make flies grow legs on their heads or eyes on their legs.

If you have doubts, perhaps you need to read some modern standard biology, biochemistry and genetics textbooks. ;-)

PS. With the present code, you can still have synonymous substitutions. With a four-letter code there would still be non-synonymous substitutions, unless you only used a subset of the code. But how could that possibly evolve unless many codons had no anti-codon? And then what would happen if you accidentally used a codon with no anti-codon? Would evey mutation become effectively a nonsense mutation? A three-letter code encoding 21 states is not obviously worse than a four-letter one.

@Richard

Check this video on cell (chromosome) division.

http://www.youtube.com/watch?v=aDAw2Zg4IgE

It happens 10,000 trillion times in the human body...usually error-free. If this highly complex action does not rely on any kind of instructions (encoded in DNA) and is simply based on physics and chemistry...well, then the earth is flat again ;-)

A non-functioning nose is not what I meant! Of course, mutating around will give you all sorts of non-functional things. That`s actually a major weakness of the modern synthesis. It simply cannot explain, how highly interconnected FUNCTIONAL structures can evolve...

@Reinhard, I did not say there was NO instructions encoded in the DNA! I just said that not everything is encoded. Calcium ions are not encoded. Fats are not encoded, although enzymes for metabolising them are etc. But yes, DNA and proteins only do the things that they do because of physics and chemistry. That's why the study of how these things interact and do stuff is called biochemistry and biophysics. Ultimately, all biology is chemistry and all chemistry is physics. (But practically, it is not helpful to always go back to the underlying physics, hence not all biological science is biochemistry and biophysics.)

The modern synthesis can totally explain how interconnected functional structures evolve. It's just coevolution - all the parts are evolving together from a (usually but not always) simpler ancestral state. In development, cells are always responding to local chemical gradients and cues, not following some encoded blueprint. There are plenty of examples of simple local rule-following producing complex emergent  structures and behaviours. You are inventing problems that simply do not exist.

@Richard, calcium ions are not encoded, but calcium channels (in the cell membrane) are. Fats are not encoded but the assembly of fat molecules (together with proteins) to form the cell membrane  is. Do you agree?

I know what the books say on coevolution. The question is if it makes any sense. How could natural selection drive coevolution of parts of a complex system, if only the whole functional system provides any selective advantage?

To return to our example of the nose on the ass: If a mutation changes the position of the nose, how would the trachea ever find it again?

I am feeling kind of stranger in this discussion. For the question 'How did the genetic code get started or evolved after that', we need biochemistry, geochemistry, some thermodynamics, not statements of principles, possibilities... I dedicated about 15 years to the development of a model based in empirical data which was successful in predicting a biosynthesis pathway that was found. Not experimental yet, but it seems to Be in The right track. See references earliwr in this discussion, original papers also available from it. Thanks to you all. Yours, Romeu

Romeu, I find your model interesting, and did say so...

However, I think principles and probabilities are very important in developing a theory. If in principle there is no solution to the development of a code, if the (primitive) living being depends on its proper function, we should rethink our models...

This is one of the more intelligent questions asked by Intelligent design enthusiasts. I suppose a good answer would be that this was the code used by the last universal common ancestor (LUCA). There are a very minor variation or two known with respect to the stop codons only. If Fred Hoyle was right it would appear to be universal, not only on earth, but throughout the universe. Amazing! 

I see  nothing new here. 

Well, the questions aren't new, but where are the convincing answers? ;-)

If life depends on a (nearly) universal code, how did it evolve? Of course, one explanation could be that the code did not evolve on earth...as Keith (indirectly) suggested.

There is one important restriction in your provided article.

It says:

If all biological phyla evolved seperatly...

Since this is not what we assume that happened during evolution, it is a nice intellectual game to think what would be if ... but usually we take the common code as a very good indication for a shared origin of phyla

You are right, we started the discussion based on this article...

Of course, the mainstream explanation is that the code developed in just one organism...otherwise we lack an explanation, why it is nearly universal. However, how could an organism play around with the encoding and decoding parts of the machinery, if the organism itself depended on the reliable transcription of that code??? So every new code would be dead on arrival ;-)

Reinhard, you jump too far in the history of the evolution of life.  If I understand well the latest theories, life did not start with organisms using this code, but with auto-catalyzing RNA-molecules.  Then, I find it easy to imagine (at least in principle) that selection advantages simply went to those that could, by the standard Darwinian "Blind-Variation-Selective-Retention" process, hit on (1) ways in which some of their segments ("genes") moreover turned out to instruct the synthesis of elements of some protective layers ("proteins"), and (2) ways to secure these RNA-instructions by DNA-back-up-memories - after which the RNA-pioneers were "degraded" to simple "messengers" between the two.  It then suffices that the prevailing genetic code is chemically feasible - it need not be necessary, it may only be one of many equally feasible alternatives.  But its feasibility suffices to make it prevail, thanks to the RNA organism that happened to pick it up first, before any of the alternatives was picked up by any other organism :-)

Pavel, thanks for the interesting comment. A genotype must always beget a phenotype, otherwise "Darwinian selection" cannot act upon it. You need some kind of containment for the encoding and decoding parts of the machinery, to produce a phenotype...whatever it shall be.

I have a problem with the theory of particles floating around in a soup. In this scenario Darwin would be eliminated, because survival of the fittest can only select for encoding-decoding units, which produce something.

Problem is, as long as there is no working encoding-decoding machinery, there is no (phenotypic) product. Say goodbye to Darwin ;-)

Reinhard, if you have "a problem with the theory of particles floating around in a soup," it's your problem.  You must be able to conceive of an initial situation in which genotype=phenotype - as is the case of the auto-catalytic RNA molecules - and to see that the two roles separated later (in about the way I roughly outlined, based on the recent theory of the RNA-origins of life).

Darwin is not eliminated - you are too much in a hurry to get rid of him, it must be emotional !  His principles work very well even at this most elementary level: to be auto-catalytic is the key "fitness" which makes the molecules which by chance appear and happen to have this ability - even if their appearance is a priori only very little probable - to survive and multiply much better than all the other molecules that by chance assemble, and by chance fall apart.  It is in the long run that the category of auto-catalytic RNA molecules is bound to prevail.  Do you know the theory of Markov chains?  E.g., why the fly in a large room with a tiny fly-trap is very unlikely to sit on it in the short run, but sure to end up on it in the long run?  Elementary, Dr. Watson :-)

Feel free to say goodbye to Darwin, if you are unable to understand it, but allow those who do understand it, and are now able to extend it also to include a plausible theory of the origins of life, to keep it as the best hypothesis that works without needing any supernatural interventions (may these be your favorites?).

I speculate that if evolution proceeds mainly by the means of  population genetics, then there does not seem to be any good reason why the code of LUCA (last universal common ancestor) could not have diverged in different lineages, such as different phyla, for example).

However, if TE-Thrust (as per the TE-Thrust hypothesis) is a major cause of evolution, then the whole of life on earth has to have (almost) exactly the  same code, otherwise the essential horizontal transposon transfer (HTT) and endogenisation of viral elements (ERVs & EVEs) could not occur universally, as it appears to do.

I remind you that this is a speculation, and not a hypothesis.

Pavel, the theory of auto-catalytic RNA molecules is similar to the selfish gene story.  Both models are very popular, because they seem to explain the "biological universe". Please think it through...even a RNA molecule already contains a code and a code cannot pop up by chance. A code implies a decoder, otherwise it is no code...just a random chain of molecules...

If the code did not originate on this planet, it does not imply that it is the result of a supernatural intervention.

Keith, very interesting comment! You are right, transposable elements could not have spread over millions of years, if there would have been different code variants.

Reinhard, it is you who must think it through.  An auto-catalytic molecule need no "code"!  Its structure is implied by the selective affinities of its atoms and simpler molecules - this is pure chemistry!  It is not a random chain of molecules - it must be chemically feasible.  True, the same set of atoms and simpler molecules may allow a variety of complex molecules to be feasible, and the choice of which ones of them are actually tried may to a large extent be random.  But: if a small minority of them are auto-catalytic - and this is a property that a large molecule may or may not have - in the long run they will systematically prevail ...

The issue of code appears only much later, when some segments of this molecule (precursors of "genes") appear by chance able to trigger and instruct other chemical reactions that produce some protecting molecules (precursors of "proteins") for the auto-catalytic one.  The code appears as the relation between the segments and the product.  Initially, there might have been a variety of chemically equally feasible codes, but the first one, possibly picked up by chance, got the decisive advantage, and stayed put for the entire tree of life as we know it.

If you do not believe in supernatural interventions, but only think that some of the Darwinian beginnings might have taken place elsewhere in the universe - you cannot say goodby to Darwinism!  You only provide it with a larger theater. :-)

There are a lot of comments now, so I'm sorry whether somebody said this before.

If you want retain your argument of "A code implies a decoder, otherwise it is no code." , So you can do this question more polemic and attack every kind of "biological language" and get to the conclusion that the human language, the bee's communication, the molecular codes as RNA editing process or the protein localization signal and so on; couldn't emerge by biological evolution (or at least by the classic evolutionary mechanism). I think with this strategy (that is a logical extension to many of your critics) you can attract researchers from many different fields that has been permeated by the biological evolution.

My (non) answer to your question is that you can search in the biosemiotics field to find an appropriate answer

Pavel, thanks for the excellent summary of the current dogma ;-) By the way, why is it that in biology (today) there is only one possible choice - with or without Darwin. What about other great biologists, as for example, Otto H Schindewolf, Theodor Eimer or Richard Goldschmidt?

The old and thoughtful theories are not taught to young biology students anymore, so they don't even know about alternatives to Darwin. I think the Danish embryologist Soren Lovtrup perfectly described the problem: “And today the modern synthesis (…) is not a theory, but a range of opinions which, each in its own way, tries to overcome the difficulties presented by the world of facts” (Lovtrup 1987, p. 144).

Aimer, thanks for your interesting comment. I think a language can develop in cognitive animals (=humans) over many generations, because it is just an additional feature which is not required for existence. However, how honey bees developed their language is a complete mystery, they are not regarded as being cognitive. Yet without their complex social interactions, they cannot exist...at all.

So you are right, if somebody could explain how the bee language developed, she/he might also be capable of explaining how the genetic code came into existence...

Reinhardt, a kind of Darwinian selection appears to work also in the evolution of theories.  Why Darwinism is so lastingly appreciated, while all the other biologists you name are more or less forgotten, is simply that to most today's biologists, both theoretical and empirical, it makes much more sense than their theories.  Moreover, genuine natural scientists do not consider any theory a "dogma" - but are ready to revise it in face of new evidence.  Darwinism was thus revised and extended several times - to begin with its nearly a century old synthesis with Mendelism, and more recently with its links to the new developments of molecular biology.  What a certain Lovtrup wrote nearly 30 years ago is hardly relevant today.  What are "the difficulties presented by the world of facts” that he then had in mind?

Pavel, sorry for my late answer. What Lovtrup had in mind (I think), was that Darwinism has been adapted for decades to explain paleontolic and genetic findings. However, the hundreds of single theories (=modern synthesis), if you try to put them together, obviously they do not fit. Todays young biologists do not know the alternative theories anymore, so they can only try to repair the mainstream model...instead of studying the old literature and discovering very thoughtful theories, which mistakenly (and because of politics...mostly Germans) had been dumped after WW II.

Reinhard, I don't know which of the theories that are parts of modern biology do not fit.  I suppose that it depends on for whom - different people may understand different theories differently well, and for those who do not understand them well, many things may not fit.

As far as I know, the last serious challenge of Darwinism by what appeared to be evidence for some Lamarckism was the rapid adaptation of bacterias to changes in their environments - when it seemed that the environments were instructing the bacterias on how to change.  But this was shown not to be so, and Darwinism proved able perfectly to explain even this case.  A clear explanation, with a witty picture that explains it all by itself, is on:

http://www.simonsfoundation.org/quanta/20140115-under-pressure-does-evolution-evolve/

I suppose that all theories are thoughtful, but the problem is that some thoughts are better than others, and it is those that win in the meta-Darwinian evolution of science.  But if you think that some of the no longer seriously considered ideas on the origins and evolution of life are good, you should take them up and try to show their merit.  But I doubt that you will succeed.  You must first understand Darwinism yourself, not to falsely accuse it of being unable to accommodate some empirical facts - as you did several times - while in fact it accommodates them perfectly well.

Pavel, it is not about understanding theories, it is about logical thinking. In todays biological science (molecular genetic) experiments are thought to explain the world, whereas the complete theoretical framework and the observations out in the field are thought to be ancient science. By the way, we are getting off topic here... ;-)

Well, actually I published a paper, which focuses on the merits of old evolutionary models, in the journal Naturwissenschaften several months ago. See the link below.

http://link.springer.com/article/10.1007%2Fs00114-014-1152-8

Pavel, the number of people, who do not understand Darwinism (modern synthesis) very well, is growing. ;-)

Please read this new Nature paper:

http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080

Reinhard, many thanks for references to two interesting papers.  I like your work on telomere erosion as a source of genomic changes, which, if they work, may cause evolutionary jumps and lead to ontogeny of strikingly different phenotypes with non-adaptive features.  I only don't see in what it contradicts properly understood neo-Darwinism, especially when you take into account its relatively recent "evo-devo" version, and understand the collaboration of natural selection with self-organization.

In my view, you do not disturb Darwinism more than Barbara McClintock did with her jumping genes.  You two have simply discovered new ways of contributing to the variety of genomic trials - but, as these ways are not Lamarckian, instructed by the environments "in order" to succeed, they must therefore also be tested, like any other mutations, by Darwinian natural selection for their ability to instruct the forming of some workable phenotype (which certainly far from all can do); and the working of the phenotype must be tested for its fitness in given environments.

But I am much less impressed by the collective article claiming the need to rethink Darwinism.  In principle I agree that all theories all the time need rethinking, but I rapidly concluded that their way of rethinking it is deeply flawed by their ignorance of basic principles of information processing, demonstrated by the following sentence:

"We hold that organisms are constructed in development, not simply ‘programmed’ to develop by genes."

This is capital nonsense.  OK, development is programmed not only by genes, but important instructions may also be contained in other parts of genomes (e.g. DNA coding for regulatory RNA), and moreover many instruction may be blocked by epigenic marks.  But it must be programmed!  Even the inputs through which it can be influenced by environments must be programmed!  And the ways in which its partial results can influence its continuation must also be programmed!  What may seem to be a paradox, but is pure logic of information processing, is that the more extensive influences of environments and preceding steps are to be, the more complex genomic programming must be.

I tried to explain all this in an WP, which I now plan substantially to revise - so if anyone has the patience to read it and send critical comments, they would be most appreciated and fully acknowledged:

http://kie.vse.cz/wp-content/uploads/PP-instruction-centrism-and-multilevel-selection.20131.pdf

Reinhard, one last remark.  If you are so competent molecular biologist, why do you want so much to destroy Darwinism that you even use such incompetent arguments as your initial one, in which you falsely assumed independent origins of fylas, to present their sharing the same genetic code as a quasi-miracle?

Thanks Pavel for your interesting and detailed comment. I did not say that I agree with the Nature article, I just mentioned it to show that other colleagues request an update of evolutionary theory too (in Nature!). So, I am not alone... ;-)

I agree that everything must be programmed somewhere. Evo-devo is just a new name for an old problem, every embryologist was aware of (including Lovtrup): namely that embryonic development is highly regulated (and interconnected) and at these early stages you cannot simply mutate around...and hope that some "fitter adult organism" develops...you would just end up with a bunch of cells.

Lastly, I did not use the argument of independent origins, I just cited an article and asked colleagues here at ResearchGate. ;-)

Dear Andrey,

Unfortunately, ResearchGate only shows you the popular answers regarding the origin of the code. The basic question is how a code can develop without some kind of understanding between the encoder and the decoder. Random mutation cannot create a code, because nobody/nothing can read it. The decoder has to know the encryption rules...if not, life will end before it has started.

There are several examples of capable Russian scientists, who were not mentioned in the anglo-saxon literature for many decades. Alexey Olovnikov is one of them. (end replication problem of linear DNA molecules).

https://www.researchgate.net/profile/Alexey_Olovnikov

So... your father is in good company ;-)

Dear colleagues. Please take a look at the proposal in the self-referential model for the formation of the code. Its basis is the activity of dimer-directed protein synthesis. Dimers are made from RNA-like oligomers that can be spontaneously aminoacylated (e.g. Michael Yarus´s group). The last are already known from  experiments, the dimers have not been tested yet. Formation of codes requires: (1) the protein products are relevant when their constitution is adequate for binding to the oligomers that produced them, therewith stabilizing the nucleoprotein complex. (2) This leads to stimulation of the activity, which means self-feeding. (3) The immediate consequence of the system is growth and cycling with selection for further growth. If this doesn´t happen, the system disappears. This is the plain mechanism of natural selection for stability, applied to the protobiotic realm. The stable association is what we know as code: one member stands for the code to the other in making the association. The ResGate collection has the articles on this. The material is empirically sound, tests for the dimer-directed protein synthesis mechanism in vitro are expected to be conducted soon, that should allow observation of the in vitro evolution of codes. The dimers are analogs to the ribosomes, structures that hold two tRNAs together and propitiate the transferase activity.

Dear Andrey. Yes, I may be one of such bearded and mustached guy (see the pictures in ResGate info and posters). I have the feeling that the hypothesis I developed (the self-referential model for the formation of the genetic code) is testable and I hope it will prove correct through laboratory experimental tests, which are explicited in the published papers and are being put to test by some workers in the community. Then the feeling will become science, as already are the empirical data that support the model and hypothesis.  The question posed by you and Reinhard about laws of nature being of such and such origins is outside science, but metaphysical-ontologic, which is outside my present scope of investigation. Thanks for the kind attention, at your orders I kindly remain, Romeu. 

I'm sorry, but I think my writing was misunderstood. The ORIGINS of the laws of nature are metaphysical-ontologic, not the laws themselves. Please reread. And you introduce another misunderstanding of some other people that may think that the DNA molecule is a 'genetic code'. Of course it is not. The code is the set of correspondences between triplets in protein-coding sequences (codons in mRNAs) and the amino acids that will be enchained into proteins by the ribosomes. This is part of my work. Again, please reread. Thanks again for your kind attention, at yours orders I kindly remain, Romeu.

There is a rich theoretical background to the genetic code but there is much empirical evidence to show that it is true. It is largely natural because the factors that put it in place, be they chemical, physical or metaphysical are not at random. The myth is in the degenerate nature of the code. Why is it that some different combinations code for the same amino acid? In my opinion, though two or more triplet combinations may code for one amino acid, one combination may be more applicable to one protein species, or one organism whereas another triplet becomes the case in another protein species or organism. One thing is that it is real and true, and took millennia to stabilize to the extent it is known in present times, especially since it was discovered. The period from the time it was discovered till now is nearly insignificant compared with the time its evolution may have begun.

It is possible that it may not have evolved like other biological events especially since it does not vary from one organism to the other. Hence it is universal, while most other biological issues evolve in some peculiar way that make them result in the variation between organism and result in biodiversity.

Dear Julian,

if the code has not evolved, where does it come from? Maybe the code evolved in saltatory steps, including the encoder and the decoder. Problem is, we don't know any biological mechanisms, which could do the job. However, we do not know the underlying mechanisms of widespread molecular convergent evolution either.

It seems that many people love mysteries - perhaps Homo sapiens has some genomically encoded predilection for them - and do all to undermine their prosaic, logical, on known natural laws based, explanations.  A popular trick is to start with an advanced, already complex stage of the evolution of life, to claim (out of ignorance or dishonesty???) that this is the starting point, and then show how unlikely it is that all of its many parts would so nicely fit each other without some mysterious organizer or creator.  Until not so long ago, many creationists were claiming that the simplest living thing is a bacteria (!) - which made it easy for them to show how highly unlikely it is that all of its zillions essential parts could appear and so nicely organize all by themselves.  Now the mysteries-lovers seem to retreat from bacterias to the simpler, but still complex enough to make it appear difficult to explain, triplet 'DNA-RNA-proteins.'

Yet all mysteries may disappear by taking one more step back, to auto-catalyzing RNA molecules - as proposed by the most recent theories of the origins of life.  However little probable such molecules might a priori be, if the probability is not strictly zero, they will sooner or later form and then systematically protect their existence and replicate - no mysteries involved (cf. the theory of Markov chains with absorbing states).  Both DNA and proteins could then enter and start evolving later, the former as a back-up memory, and the latter as elements of static or dynamic protection, not all of which may immediately be useful.  Even if many chemical details remain to be clarified, this approach appears logical, fruitful and entirely mystery-free.  NB: the winning code "DNA -> proteins" need not in any sense be optimal, it may only be sufficient.  It would suffice if it allowed its users to win over all the other hypothetical organisms that may have used other codes (cf. the spread of the QWERTY keyboard, arguably not optimal, but workable and sufficient to win over the proposed alternatives).

To accept that we don't know, definitely hurts, but it does not imply a mysterious process. It is not about molecules, it is about a code. A code implies an encoder, for writing, and a decoder, for decoding. Both have to be highly correlated. If the encoder "invents" a new "word", the translational machinery has to "understand" it...and at the same time produce something useful. Such a system can never evolve by the modern synthetic versions of Darwins idea. (just to be correct, it was the Wallace paper, where Darwin read about "his" idea, but nobody seems to care either)

Hi Reinhard,

I an sorry I have been away for awhile. Thanks for your honest views on the subject matter. In my opinion, it is all very simple except we try to make it complex. Thaks for sharing my opinion that its evolution is not like normal biological evolution that causes diversity. Thanks also for feeling with me that there is an encoder, a code and a decoder. Remember that it is al universal. Otherwise there would have been different codes for different orunrelated organisms. I do not believe that convergent evolution could have resulted in the code. Or do you think it is possible for such genomic change could have taken place in the evolution of all life in a convergent form to originate it from a wide array of life forms? It is like a command base that controls every form and function in every organism. It operatsin a unique way that to our understanding does not vary very widely in large detail between organisms. Do you still disagree with me really?