hear me out # 1

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Sheldon's picture
1. Complexity does not donate

1. Complexity does not donate design, you're claiming we live in a universe where everything is designed, by a deity that is more complex than anything else, it's such an obvious contradiction it's asinine. We know when something is designed only when there is sufficient objective evidence for design, and in every instance where this is the case we we also know those things evidenced as designed do not occur in nature.
2. How many universes did you use in your test group to establish this one is fine tuned? How do you even know any other type of universe is possible? This is a very tired religious canard. However even were true this demonstrates no objective for a designer, or a cause, and certainly none for any deity.
3. Utter gobbledegook, and please do link the breaking news that any branch of science demonstrates any evidence for any deity, as the entire scientific world seems to have missed this.
4. Irreducible complexity is creationist pseudoscience, again the entire scientific world knows this. All living things evolved, and this is an objective fact established beyond any reasonable doubt.
5. Again you are misrepresenting science as supporting your superstitious belief in a deity, just turn on any news channel to see this is a risible nonsense.
6. Nothing in science evidences a deity, or anything supernatural, you're simply lying, and it is as tedious as it is dishonest.
7. If pixies were a programmer it would easier for them to hack the programme and perform miracles, are you saying this is evidence for pixies? If not then your risible claim to be open minded is exposed as a lie, since you are biased in favour of your belief in a deity without any objective evidence to support it.
8. The creation myth in the bible is demonstrably false, making wild assertions based on subjective conjecture evidences nothing.

With all that said, I believe the chances that we wer created are very likely. It may be harder to fathom but none the less it is no longer an obscene idea based solely on a book."

Human beings evolved slowly over billions of years, as did all living things, this is an objective fact supported by an overwhelming amount of scientific evidence from multiple and converging fields of science. There is no evidence that anything in nature was created. The main religious creation myths are demonstrably false.

Jordan's picture
@sheldon

@sheldon

there is zero proof that life can ever start from
Non life. There is zero proof that a self replicating organisms can evolve into two sexes. There is no proof that macroevolutiom is possible. The fossil record, with few obscure exception, shows fully developed species rather than all the supposed intermediary species.

And who is to say God is complex? And just because something is asinine doesn’t mean it’s not true. Also define pixie.

Talyyn's picture
@Jordan

@Jordan

And who is to say God is complex?

The christian definition of God is that is is all-powerful, all-knowing, all-loving and ahem... infinite, whatever this last term may means in the religious mind. On top of that, there is the topic of Trinity, stating that he can be divided in three entities, that are both completely unique in themselves, but can each be identified for the two others.

And just because something is asinine doesn’t mean it’s not true.

You clearly think evolution of organisms and abiogenesis are asinine. Why couldn't it be true?

Calilasseia's picture
Oh, dear, more canards in

Oh, dear, more canards in need of the relevant ordnance.

Let's take a look at this shall we?

there is zero proof that life can ever start from Non life.

Actually, if you bother to survey the relevant literature, scientists have established that all the chemical reactions thus far postulated to be implicated in the origin of life work. There's a large body of experimental evidence to this effect. Everything from the synthesis of amino acids and nucleotides upwards has been investigated in the laboratory by people such as Jack Szostak and Leslie Orgel, and the relevant chemical reactions all work under prebiotic conditions.

The Emergence Of Life On Earth

In the earliest period of the history of the planet, it was a body devoid of life, and conditions on the planet were far from conducive to the appearance of life, particularly during the episode termed "The Late Heavy Bombardment" [1] by scientists, which saw intense bolide impact activity taking place on the planet's surface. Once this episode, and subsequent episodes postulated to have taken place, were complete, the Earth cooled, a solid crust formed, and liquid water in quantity began to appear. Thus, the stage was set for the processes that were to result in the emergence of life.

It was Darwin himself who first speculated about the origins of life, with his short remarks about a "warm little pond" [2], but, in the middle of the 19th century, this would remain speculation, as the means to determine the mechanisms that might apply had not yet been developed. However, it made eminent sense to scientists following Darwin, to hypothesise that any natural mechanisms responsible for the origin of life would be based upon organic chemistry, since life itself is manifestly based thereupon - millions of organic reactions are taking place within your body as you read this, and indeed, the cessation of some of those reactions constitutes the end of life for any organisms affected. Alexander Oparin, the Soviet biochemist, was the first to publish hypotheses about the chemical basis of the origin of life [3], and based his own hypotheses on the notion that a reducing atmosphere existed on the primordial Earth, facilitating the production of various organic compounds that would then react further, producing a cascade of escalating complexity that would ultimately result in self-replicating entities. Back in 1924, his hypotheses remained beyond the remit of scientists to test, but that would soon change.

The first indications that Oparin had alighted upon workable ideas came in 1953, with the celebrated Miller-Urey Experiment [4], in which electrical discharges in a reducing atmosphere composed of simple molecules produced measurable quantities of amino acids. Miller himself only cited the presence of five amino acids, as he was reliant at the time upon paper chromatography as his primary analytical tool, which was only sensitive enough to detect those five amino acids cited. However, Miller had been more successful than he originally claimed: after his death, preserved samples of his original reaction mixtures were subject to state-of-the-art analysis, using gas chromatograph mass spectrometry, a technique millions of times more sensitive, and regarded as the 'gold standard' in modern organic analysis. That subsequent analysis yielded not five, but twenty-two amino acids [5].

Early criticism of Miller's work in the scientific community focused upon the requirement for a reducing atmosphere in accordance with the Oparin model. However, subsequent workers determined by repeat experimentation, that a range of atmospheric constitutions would be suitable for a Miller-Urey type synthesis on a prebiotic Earth [6], several of those constitutions being only mildly reducing, expanding the range of conditions for which the Oparin model would be viable. More recently, work has suggested that the prebiotic Earth could have developed an atmosphere containing considerably more hydrogen than originally thought [7], making the Oparin reducing atmosphere once again more plausible. Indeed, the range of conditions under which amino acids could be synthesised has since been expanded to include interstellar ice clouds, courtesy of more recent research [8 - 14], and the Murchison meteorite was found to contain no less than ninety amino acids, nineteen of which are found on Earth, which were obviously synthesised whilst that meteorite was still in space. Other data from meteorites adds to this body of evidence [10, 15, 16].

The formation of amino acids itself, whilst an important step in any naturalistic origin of life, would need to be accompanied by some means of linking those amino acids into peptide molecules [17] - the process by which proteins are formed. A significant step forward with respect to this, arose when researchers alighted upon the fact that carbonyl sulphide, a gas that is produced in quantity naturally by volcanoes, acts as a catalyst for the formation of peptides, increasing yields dramatically [18]. This would facilitate peptide formation not only in the vicinity of hydrothermal vents, but in the vicinity of terrestrial volcanoes close to bodies of open water. Indeed, Miller had produced the 22 amino acids found in some of his reaction mixtures by extending the synthesis to include volcanic input, though not carbonyl sulphide - the addition of carbonyl sulphide would, however, facilitate peptide formation rapidly once the amino acids themselves were formed.

One additional problem to be overcome was the 'chirality problem'. Amino acids, with the exception of glycine, are chiral molecules, existing in two forms that are mirror images of each other in space (stereoisomers). Initially, methods for producing one form preferentially over another were something of a puzzle, but chemists working in an entirely different field established that a process called 'chiral catalysis' exists, indeed, this work led to a Nobel Prize for the researchers in question [19]. The demonstrated existence of working chiral catalysts [20] led abiogenesis researchers to seek such catalytic processes in their own field, and, in due course, these were alighted upon [15, 21- 24].

However, amino acids are not the only molecules required for life, important though they are. Some form of self-replicating molecule, providing the basis of an inheritance mechanism, is required. Given the difficulties involved in synthesising DNA as a total synthesis, researchers turned to RNA instead, a molecule that still forms the basis of the genomes of numerous extant taxonomic Families of viruses today. RNA, being easier to synthesise, was considered a natural first choice for the basis of primordial genomes, and thus, attention turned to the synthesis of RNA under prebiotic conditions. This was soon found not only to be possible, but to be readily achievable in the laboratory, and indeed, catalysis plays a role in these experiments. Natural clays formed from a mineral called montmorillonite provide a ready natural catalyst that would have been present in quantity on a prebiotic Earth, and the catalytic chemistry of RNA formation whilst adsorbed to such clays is now a standard part of the scientific literature [22- 42].

Having established that RNA was synthesisable under prebiotic conditions, researchers then turned to the matter of establishing the existence of self-replicating species of RNA molecules. This was duly successful [30, 43, 45 - 47], establishing that such species could have arisen among the extant RNA molecules being synthesised on a prebiotic Earth, and of course, once one self-replicating species exists, the process of evolution can begin, which has also since been demonstrated to apply to replicating RNAs in appropriate laboratory experiments [48].

Once a self-replicating molecule that can form the basis of an inheritance mechanism exists, the next stage scientists postulate to be required is encapsulation within some sort of selectively permeable membrane. The molecules of choice for these membrane are lipids, which have been demonstrated repeatedly in the laboratory to undergo spontaneous self-organisation into various structures, such as bilayer sheets, micelles and liposomes. Indeed, in the case of phospholipids, they can be stimulated to self-organise by the simple process of agitating the solution within which they are suspended - literally, shake the bottle [49 - 53]. Moreover, research has established that these lipids can encapsulate RNA molecules, and selectively admit the passage of base and sugar molecules to facilitate RNA replication [54, 55]. With the advent of this discovery in appropriate laboratory research, protocell formation is but a short step away, and indeed, the latest research is now actively concentrating upon the minimum components required in order for a viable, self-replicating protocell to exist. Prebiotic lipid formation is also a part of the repertoire of the literature in the field, and some papers now extant document the first experiments aimed at producing viable self-replicating protocells [55 - 70].

Whilst scientists naturally accept that 'joining the dots' between these individual steps is entirely proper, particularly on a body the size of a planet over a 100 million year period, the absence of experiments actively coupling these stages is a matter remaining to be addressed, though such experiments will be ambitious in scope indeed if they are to produce complete working protocells at the end of a long production line starting with a Miller-Urey synthesis. A 'grand synthesis' of this sort in the laboratory is not high on the scientific agenda at the moment, which is more concerned with validating the individual hypothesised steps, but once those steps are accepted as valid in the field, doubtless one day a 'grand synthesis' will be attempted, and the success thereof will establish beyond serious doubt that our pale blue dot became our home courtesy of well-defined and testable chemical reactions. Even so, no one conversant with the literature seriously considers any more that magical forces are required to produce life: just as vitalism was refuted by Wöhler's classic experiment, that gave rise to organic chemistry as an empirical science in the first place, so it is likely to be rendered ever more irrelevant in abiogenesis research, as the steps leading to life's blossoming on our planet are traversed and studied in ever greater detail.

References:

[1] An apposite paper (among many) covering the Late Heavy Bombardment is:

Origin Of The Cataclysmic Late Heavy Bombardment Period Of The Terrestrial Planets by R. Gomes, H. F. Levison, K. Tsiganis and A. Morbidelli, Nature, 435: 466-469 (26th May 2005)

[2] Cited in The Life And Letters Of Charles Darwin, Including An Autobiographical Chapter, edited by Francis Darwin, 1887

[3] The Origin And Development Of Life by Alexander Oparin, 1924 (English translation: NASA TTF-488)

[4] A Production Of Amino Acids Under Possible Primitive Earth Conditions by Stanley L. Miller, Science, 117: 528-529 (15th May 1953)

[5] The Miller Volcanic Discharge Spark Experiment by Adam P. Johnson, H. James Cleaves, Jason P. Dworkin, Daniel P. Glavin, Antonio Lazcano and Jeffrey L. Bada, Science, 322:404 (17th Ocotber 2008)

[6] Amino Acid Synthesis From Hydrogen Cyanide Under Possible Primitive Earth Conditions by J. Oró and S. S.Kamat, Nature, 190: 442-443 (1961)

[7] A Hydrogen Rich Early Earth Atmosphere by Feng Tian, Owen B. Toon, Alexander A. Pavlov and H. de Sterck, Science, 308: 1014-1017 (13th May 2005)

[8] A Rigorous Attempt To Verify Interstellar Glycine by I. E. Snyder, F. J. Lovas, J. M. Hollis, D. N. Friedel, P. R. Jewell, A. Remijan, V. V. Ilyushin, E. A. Alekseev and S. F. Dyubko, The Astrophysical Journal, 619(2): 914-930 (1st February 2005)

[9] Interstellar Glycine by Yi-Jehng Kuan, Steven B. Charnley, Hui-Chun Huang, Wei-Ling Tseng, and Zbigniew Kisiel, The Astrophysical Journal, 593: 848-867 (20th August 2003)

[10] Prebiotic Materials From On And Off The Early Earth by Max Bernstein, Philosophical Transactions of the Royal Society Part B, 361: 1689-1702 (11th September 2006)

[11] Racemic Amino Acids From The Ultraviolet Photolysis Of Interstellar Ice Analogues by Max P. Bernstein, Jason P. Dworkin, Scott A. Sandford, George W. Copoper and Louis J. Allamandola, Nature, 416: 401-403

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[17] Peptides By Activation Of Amino Acids With CO On (Ni,Fe)S Surfaces: Implications For The Origin Of Life by Claudia Huber and Günter Wächtershäuser, Science, 281: 670-672 (31st July 1998)

[18] Carbonyl Sulphide-Mediated Prebiotic Formation Of Peptides by Luke Leman, Leslie Orgel and M. Reza Ghadiri, Science, 306: 283-286 (8th October 2004)

[19] Nobel Prize for Chemistry, 2001, was awarded to William S. Knowles, Ryoji Noyori and K. Barry Sharpless, for their work establishing the existence of asymmetric catalysts and chiral catalysis - see the Nobel Lecture by William S. Knowles here

[20] Homogeneous Catalysis In The Decomposition Of Diazo Compounds By Copper Chelates: Asymmetric Carbenoid Reactions by H. Nozaki, H. Takaya, S. Moriuti and R. Noyori, Tetrahedron, 24(9): 3655-2669 (1968)

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[26] Ligation Of The Hairpin Ribozyme In cis Induced By Freezing And Dehydration by Sergei A. Kazakov, Svetlana V. Balatskaya and Brian H. Johnston, The RNA Journal, 12: 446-456 (2006)

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[30] Nucelotide Synthetase Ribozymes May Have Emerged First In The RNA World by Wentao Ma, Chunwu Yu, Wentao Zhang and Jiming Hu, The RNA Journal, 13: 2012-2019, 18th September 2007

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[33] RNA Catalysis In Model Protocell Vesicles by Irene A Chen, Kourosh Salehi-Ashtiani and Jack W Szostak, Journal of the American Chemical Society, 127: 13213-13219 (2005)

[34] RNA-Catalysed Nucleotide Synthesis by Peter J. Unrau and David P. Bartel, Nature, 395: 260-263 (17th September 1998)

[35] RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension by Wendy K. Johnston, Peter J. Unrau, Michael S. Lawrence, Margaret E. Glasner and David P. Bartel, Science, 292: 1319-1325, 18th May 2001

[36] RNA-Directed Amino Acid Homochirality by J. Martyn Bailey, FASEB Journal (Federation of American Societies for Experimental Biology), 12: 503-507 (1998)

[37] RNA Evolution And The Origin Of Life by Gerald F. Joyce, Nature, 338: 217-224 (16th March 1989)

[38] Sequence- And Regio-Selectivity In The Montmorillonite-Catalysed Synthesis Of RNA by Gözen Ertem and James P. Ferris, Origins of Life and Evolution of the Biosphere, 30: 411-422 (2000)

[39] Synthesis Of 35-40 Mers Of RNA Oligomers From Unblocked Monomers. A Simple Approach To The RNA World by Wenhua Huang and James P. Ferris, Chemical Communications of the Royal Society of Chemistry, 1458-1459 (2003)

[40] Synthesis Of Long Prebiotic Oligomers On Mineral Surfaces by James P. Ferris, Aubrey R. Hill Jr, Rihe Liu and Leslie E. Orgel, Nature, 381: 59-61 (2nd May 1996)

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[44] Emergence Of A Replicating Species From An In Vitro RNA Evolution Reaction by Ronald R. Breaker and Gerald F. Joyce, Proceedings of the National Academy of Sciences of the USA, 91: 6093-6097 (June 1994)

[45] Ribozymes: Building The RNA World by Gerald F. Joyce, Current Biology, 6(8): 965-967, 1996

[46] Self-Sustained Replication Of An RNA Enzyme by Tracey A. Lincoln and Gerald F. Joyce, ScienceExpress, DOI: 10.1126/science.1167856 (8th January 2009)

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[49] Formation Of Bimolecular Membranes From Lipid Monolayers And A Study Of Their Electrical Properties by M. Montal and P. Mueller, Proceedings of the National Academy of Sciences of the USA, 69(12): 3561-3566 (December 1972)

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[52] Simulation Of The Spontaneous Aggregation Of Phospholipids Into Bilayers by Siewert J. Marrink, Eric Lindahl, Olle Edholm and Alan E. Mark, Journal of the American Chemical Society, 123: 8638-8639 (2001)

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[60] Formation Of Protocell-Like Structures From Glycine And Formaldehyde In A Modified Sea Medium by Hiroshi Yanagawa and Fujio Egami, Proceedings of the Japan Academy, 53: 42-45 (12th January 1977)

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Moving on ...

There is zero proof that a self replicating organisms can evolve into two sexes.

Oh, by the way, other forms of sexual differentiation exist in present day living organisms that point to the likely origin of sexual differentiation in the past. You are now going to learn everything you never wanted to know about yeast sex, but were forced to find out. :mrgreen:

Yeast mating is actually rather interesting. To cover this, we need to go over some background information first.

Yeast cells can exist in two major forms, a haploid form (which can undergo mitosis and produce two daughter cells), and a diploid form (which can undergo meiosis during times of stress, and produce four haploid daughter cells). The haploid cells are the ones that can mate, and when haploid mating occurs, the participant mating cells fuse to form a stable diploid cell. Diploid cells can also undergo mitosis, producing two diploid daughters.

Now, in order to understand haploid mating, we need to look at the genes and how they affect the process. First, we need to locate a special locus on chromosome 3 called MAT. There are two alleles present on this locus, called MATa and MATα, for reasons I don't understand. These loci differentiate the cells into two types, a cells and α cells. Next, we need to locate two other loci on the same chromosome, called HML (Hidden MAT Left) and HMR (Hidden Mat Right). HML contains a silenced copy of the MATα allele, and HMR contains a silenced copy of the MATa allele. The names refer to their position relative to the MAT locus itself. Laying chromosome 3 out so that its short arms are to the left of the centromere, and the long arms to the right, HML is on the short arm, then MAT is on the long arm relatively close to the centromere, and HMR is on the long arm further away from the centromere. So, in effect, both a and α cells contain a copy of the MATa and MATα allele, but these copies are silenced. These come into play later. The active locus is the MAT locus itself, and this locus contains one of the two alleles, MATa or MATα.

Additionally, there is a separate gene called HO, which is activated specifically only in haploid cells, and which only then during the G1 phase of the cell cycle (the phase during which the cell absorbs nutrients and grows). It affects the identity of the cells, though the precise mechanism has yet to be fully elucidated. More on this later.

Now, let's return to the MAT locus. This contains either a MATa allele, or a MATα allele. These alleles contain two genes, viz:

MATa : contains genes a1 and a2

MATα : contains genes α1 and α2

These genes are the master control genes for a transcription sequence, involving some downstream regulation, whose ultimate products are a cell surface receptor and a substance released into the environment that can be thought of as a 'pheromone' of sorts. As you might guess at this stage, the 'pheromone' associated with the MATa genes is called a-factor, whilst that associated with the MATα genes is called α-factor. The cell receptors are named according to a different convention though - the cell surface receptor generated by the MATa genes is called the ste2 receptor, and the receptor generated by the MATα genes is called the ste3 receptor.

Basically, what happens is this. An a cell and an α cell, in close proximity and in condition for mating, release their respective 'pheromones'. When the ste2 receptor of the a cell detects the presence of α-factor, the a cell grows a projection in the direction of highest concentration of α-factor. Likewise, when the ste3 receptor of the α cell detects a-factor, the α cell grows a projection in the direction of highest concentration of a-factor. These two projections eventually meet, whereupon the two cells undergo fusion and become a diploid cell. This diploid cell has two sets of the 16 chromosomes of a haploid yeast cell, one with the MATa genes on its copy of chromosome 3, the other with the MATα genes on its copy of chromosome 3.

Now here's the clever bit. A cell that only has one copy of the MAT genes allows the HO gene to be active in those cells, whilst a cell with two copies (a diploid cell) suppresses the HO gene. The reverse is true for genes that are activated by diploid cells, such as IME1, but this is irrelevant here: it's included simply in order to alert the reader wishing to pursue yeast genetics further that some genes are haploid-active only, and some diploid-active only. Suppression of HO allows both diploid mitosis to take place, or meiosis to produce four haploid daughters under conditions of stress.

So, what happens to haploid cells between mitotic divisions? This is where HO, and those two silenced loci HML and HMR, come into their own. During the G1 phase of the cell cycle, HO becomes active, generates a DNA endonuclease that cleaves the DNA at the MAT locus, wherupon exonuclease enzymes are attracted to the site and degrade the DNA there. Now here's the crunch: having effectively deleted its active MAT genes, the haploid cell now copies one of the silent copies back into the MAT locus. The clever part is this: if the cell began as an a cell, it copies the silenced copy from the HML locus, and in doing so switches identity to that of an α cell. Likewise, an α cell, when it deletes its MAT genes, copies the contents of the HMR locus to the MAT locus, and thus undergoes an identity switch to an a cell. Why this happens is a part of the mating system that isn't fully understood, but it happens, and so, in between mitotic divisions, an a cell switches to become an α cell and vice versa. Thus, even if a yeast population is founded in a new location entirely from haploid cells of one type, that population can generate cells of the other type, and the now mixed population of cells can mate, produce diploid cells, and set about increasing the genetic variation within the new founder population via meiosis. Very clever, is it not?

Now it turns out that scientists can manipulate this system. Deletion of one of the copies of the MAT locus in a diploid cell will cause that cell to exhibit haploid behaviour, and the HO gene will be activated, resulting in type switching of the remaining undeleted MAT locus after each diploid mitosis. Addition of an extra active MAT locus to a haploid cell results in the cell exhibiting diploid behaviour, and suppressing the HO gene. This will prove fatal in times of stress, because the haploid cell will attempt to undergo meiosis, resulting in destruction of the cell.

In order to make the study of yeast genetics easier, scientists work with haploid strains that have had the HO gene knocked out, so that type switching never occurs, and such yeast cells cannot therefore produce the mixed populations required for mating and diploid formation.

Note that this form of sexual differentiation relies upon a small set of genes all lying on one chromosome, and does not rely upon separate sex chromosomes. These were a later development.

So, yeast cells acquired the ability to engage in sexual reproduction, using a simple antecedent system to the one seen in later organisms, and which is a candidate for a stepping stone to the later variations of sexual reproduction that emerged. The fun part being, of course, that yeasts only activate this sexual reproductive system when the HO gene is active - a gene whose activity differs between haploid and diploid life stages. Otherwise, yeasts reproduce asexually.

So yeasts acquired a facultative sexual reproduction mechanism, which is a candidate for the foundation upon which later, obligate sexual reproduction mechanisms were constructed. Indeed, the emergence of facultative sexual reproduction systems in various unicellular organisms occurred more than once - there are numerous unicellular organisms in existence, that reproduce asexually for the most part, but which can switch to a sexual reproduction mode in a manner akin to yeast cells. Diatoms are a classic example, and an example in which sexual reproduction emerged as a solution to the offspring size problem inherent in these organisms, courtesy of the asymmetrical outer integument and the differential inheritance thereof by offspring during mitosis. Another collection of organisms under investigation with respect to their interesting switch between asexual and sexual reproduction are the Choanoflagellates, though research into their reproductive biology is still somewhat in its infancy. A small number of Dinoflagellate species also exhibit a switch between asexual and sexual reproduction.

However, among the more interesting finds, is this one, covering a multicellular eukaryote:

PFRU, A Single Dominant Locus Regulates The Balance Between Sexual And Asexual Plant Reproduction In Cultivated Strawberry by Amèlia Gaston, Justine Perrotte, Estelle Lerceteau-Köhler, Mathieu Rousseau-Gueutin, Aurélie Petit, Michel Hernould, Christophe Rothan & Béatrice Denoyes, Journal of Experimental Botany, Volume 64, Issue 7, April 2013, Pages 1837–1848, https://doi.org/10.1093/jxb/ert047 [Full paper downloadable from here

In this paper, the authors establish experimentally that the switch between sexual and asexual reproduction in cultivated Strawberry plants is controlled by a single gene. Viz:

Abstract

Strawberry (Fragaria sp.) stands as an interesting model for studying flowering behaviour and its relationship with asexual plant reproduction in polycarpic perennial plants. Strawberry produces both inflorescences and stolons (also called runners), which are lateral stems growing at the soil surface and producing new clone plants. In this study, the flowering and runnering behaviour of two cultivated octoploid strawberry (Fragaria×ananassa Duch., 2n=8×=56) genotypes, a seasonal flowering genotype CF1116 and a perpetual flowering genotype Capitola, were studied along the growing season. The genetic bases of the perpetual flowering and runnering traits were investigated further using a pseudo full-sibling F1 population issued from a cross between these two genotypes. The results showed that a single major quantitative trait locus (QTL) named FaPFRU controlled both traits in the cultivated octoploid strawberry. This locus was not orthologous to the loci affecting perpetual flowering (SFL) and runnering (R) in Fragaria vesca, therefore suggesting different genetic control of perpetual flowering and runnering in the diploid and octoploid Fragaria spp. Furthermore, the FaPFRU QTL displayed opposite effects on flowering (positive effect) and on runnering (negative effect), indicating that both traits share common physiological control. These results suggest that this locus plays a major role in strawberry plant fitness by controlling the balance between sexual and asexual plant reproduction.

Oh look. Strawberry plants have a system switching between sexual and asexual reproduction, controlled by a single gene. And that is in a multicellular eukaryote to boot.

Moving on ...

There is no proof that macroevolutiom is possible.

This is complete poppycock. Speciation has not only been observed and documented on multiple occasions, but has been the subject of laboratory experiments. Perhaps the best example I can provide comes courtesy of this paper:

Speciation By Hybridisation In Heliconius Butterflies by Jesús Mavárez, Camilo A. Salazar, Eldredge Bermingham, Christian Salcedo, Chris D. Jiggins and Mauricio Linares, Nature, 441: 868-871 (15th June 2006) [Full paper downloadable from [url=http://si-pddr.si.edu/dspace/bitstream/10088/4131/1/Mavarez_Salazar_Berm...

Speciation is generally regarded to result from the splitting of a single lineage. An alternative is hybrid speciation, considered to be extremely rare, in which two distinct lineages contribute genes to a daughter species. Here we show that a hybrid trait in an animal species can directly cause reproductive isolation. The butterfly species Heliconius heurippa is known to have an intermediate morphology and a hybrid genome [1], and we have recreated its intermediate wing colour and pattern through laboratory crosses between H. melpomene, H. cydno and their F1 hybrids. We then used mate preference experiments to show that the phenotype of H. heurippa reproductively isolates it from both parental species. There is strong assortative mating between all three species, and in H. heurippa the wing pattern and colour elements derived from H. melpomene and H. cydno are both critical for mate recognition by males.

The authors continue with:

Homoploid hybrid speciation—hybridization without change in chromosome number—is considered very rare [2–4]. This has been explained by the theoretical prediction that reproductive isolation between hybrids and their parents is difficult to achieve [3,5,6]. However, if a hybrid phenotype directly causes reproductive isolation from parental taxa, this difficulty can be overcome. Such a role for a hybrid phenotype has been convincingly demonstrated only in Helianthus sunflowers [7]. In animals, the evidence for homoploid hybrid speciation is less convincing. Putative hybrid species are known with mixed genomes [8–11], but in these examples shared genetic variation could also be a result of introgression subsequent to a bifurcating speciation event.

Heliconius cydno and H. melpomene are two closely related species that overlap extensively in lower Mesoamerica and the Andes [12]. Speciation in these butterflies has not involved any change in chromosome number [13] but is instead associated with shifts in colour patterns that generate both assortative mating and postzygotic isolation due to predator-mediated selection [14–17]. Heliconius cydno is black with white and yellow marks, whereas H. melpomene is black with red, yellow and orange marks. Both species exhibit strong positive assortative mating based on their wing colour patterns and also differ in habitat use [18] and host plant preference [19], but interspecific hybrids do occur at low frequency in the wild [15]. Heliconius heurippa has an intermediate wing pattern, which has led to the suggestion that this is a hybrid species [1,20]. Its hindwing is indistinguishable from that of sympatric H. m. melpomene, whereas the yellow band on its forewing is similar to that of parapatric H. cydno cordula. Ecologically, H. heurippa is most similar to H. cydno, which it replaces geographically in the eastern Andes of Colombia. Here we first establish that H. heurippa is currently genetically isolated from its putative parents and provide evidence that its genome is of hybrid origin. A Bayesian assignment analysis using 12 microsatellite loci scored in populations from Panama, Colombia and Venezuela divides H. cydno (n = 175), H. melpomene (n = 167) and H. heurippa (n = 46) individuals into three distinct clusters (Fig. 1). Hence, H. heurippa is genetically more differentiated than any geographic race sampled of either species. Moreover, analyses of polymorphism at two nuclear genes (Invected and Distal-less) show no allele sharing between H. cydno and H. melpomene, whereas the H. heurippa genome appears as an admixture, sharing allelic variation with both putative parental species (Supplementary Fig. 2, and C.S., C.D.J. and M.L., unpublished observations).

So, the authors begin by noting that the wing pattern of Heliconius heurippa is intermediate between that of local races of Heliconius melpomene and Heliconius cydno, and ask the question whether or not this is because Heliconius heurippa is a hybrid between individuals from those two races of Heliconius melpomene and Heliconius cydno. Suspicions that this might be the case were reinforced, when a genetic analysis demonstrated that certain genes present in Heliconius heurippa were admixtures of those found in Heliconius melpomene and Heliconius cydno, whilst the genes in question show NO such admixture in the other two species.

[SPECIAL NOTE: I alighted upon papers after writing the original version of this article, covering the intricacies of the invected and distal-less genes in butterfly wing pattern formation, and how these genes produce a Turing-type morphogenetic system. But I digress. Back to the Heliconius speciation paper!]

Moving on ...

To test the hypothesis of a hybrid origin for the H. heurippa colour pattern, we performed inter-specific crosses between H. cydno cordula and H. m. melpomene to reconstruct the steps of introgressive hybridization that could have given rise to H. heurippa. The colour pattern differences between H. m. melpomene and H. cydno cordula are determined largely by three co-dominant loci controlling the red and yellow bands on the forewing and the brown pincer-shaped mark on the ventral hindwing (see Fig. 2a) [21,22]. Most H. cydno × H. melpomene F1 hybrids seem intermediate to both parents (Fig. 2a), with both a yellow (cydno) and a red (melpomene) band in the median section of the forewing, whereas the ventral side of the hindwing shows a reduced brown mark intermediate between the parental species.

So, the authors produced some experimental crosses, and noticed that those experimental crosses produced individuals possessing wing pattern intermediate between those of the parents. However, they didn't just produce single-generation crosses, instead, they tested the effects that would arise from multiple crossings across several generations, and the results were extremely illuminating to put it mildly! But I'm jumping the gun here a little ... let's see what the authors have to reveal to us, shall we?

Female F1 hybrids resulting from crosses between H. melpomene and H. cydno are sterile in accordance with Haldane’s rule [1,23], and thus only male F1 hybrids backcrossed to either H. cydno cordula or H. m. melpomene females resulted in offspring. Backcrosses to H. melpomene produced offspring very similar to pure H. m. melpomene, and further backcross generations never produced individuals with forewing phenotypes similar to H. heurippa (Fig. 2a). However, after only two generations a phenotype virtually identical to H. heurippa (Supplementary Fig. 3) was produced by backcrossing an F1 male to an H. cydno cordula female and then mating selected offspring of this cross (Fig. 2b). In offspring of crosses between these H. heurippa-like individuals the pattern breeds true, showing that they are homozygous for the red forewing band (BB) and the absence of brown hindwing marks (brbr) characteristic of H. melpomene, and similarly homozygous for the yellow forewing band (N-N N-N) derived from H. cydno. The pattern of these H. heurippa-like individuals also breeds true when crossed to wild H. heurippa (Fig. 2b), implying that pattern genes segregating in our crosses are homologous with those in wild H. heurippa.

Oh, now look at that for a spectacular set of results!

First of all, the authors crossed Heliconius melpomene with Heliconius cydno to produce F1 hybrids, then back-crossed the fertile males with females of each species. Back-crossing with Heliconius melpomene resulted in melpomene wing patterns reappearing, but back-crossing the F1 hybrids with Heliconius cydno to produce the F2 generation, then mating selected offspring of the F2 generation, produced individuals that were virtually identical to Heliconius heurippa!

But it gets even better. When the laboratory produced Heliconius heurippa analogues were mated to wild type Heliconius heurippa, they produced fertile offspring and the wing patterns bred true!.

These crossing experiments, as a consequence, constitute compellingly strong evidence that Heliconius heurippa resulted from a similar process occurring among hybrid butterflies in the wild. Not only did the authors reproduce the likely crossing sequence that produced Heliconius heurippa in the wild, thus providing a repeatable test of the relevant speciation mechanism, but the laboratory crosses were interfertile with the wild type Heliconius heurippa, further strengthening the hypothesis advanced by the authors.

Moving on ...

Furthermore, in a wild population of sympatric H. m. melpomene and H. cydno cordula in San Cristóbal, Venezuela, we observed natural hybrids at an unusually high frequency (8%), including some individuals very similar to our laboratory-produced H. heurippa-like butterflies (Fig. 2b). Microsatellite data show that these individuals have genotypes indistinguishable from that of H. cydno and must therefore be at least fifth-generation backcrosses (Supplementary Fig. 4). This shows that multiple generations of backcrossing can occur in the wild and that female hybrid sterility is not a complete barrier to introgressive hybridization. The fact that the H. heurippa pattern can be generated by laboratory crosses between H. melpomene and H. cydno, and is also observed in wild hybrids between the two species, establishes a probable natural route for the hybrid origin of H. heurippa.

Well, at this point, one is tempted to say, QED. The authors could hardly have asked for better, could they? Not only did their laboratory crosses reproduce virtually identical Heliconius heurippa analogues, that were furthermore interfertile with wild Heliconius heurippa, but they observed hybrids in the wild that included individuals matching both the wild type Heliconius heurippa and the authors' laboratory analogues!

Not satisfied with this, however, the authors then turned their attention to the next part of the speciation process, and performed some experiments to determine if an isolating mechanism was in place, which would reinforce speciation. Let's take a look at those experiments, shall we?

The next step in species formation is reproductive isolation. We therefore tested the degree to which H. heurippa is isolated from H. melpomene and H. cydno by assortative mating. No-choice mating experiments showed a reduced probability of mating in all interspecific comparisons, with H. heurippa females particularly unlikely to mate with either H. cydno or H. melpomene (Table 1). When a male of each species was presented with a single female, H. heurippa males were tenfold more likely to court their own females than the other species (Supplementary Fig. 5). In mating experiments with choice, there was similarly strong assortative mating, although occasional matings between H. cydno and H. heurippa were observed (Table 2). Isolation due to assortative mating, on average more than 90% between H. heurippa and H. melpomene and more than 75% between H. heurippa and H. cydno, is therefore considerably greater than that caused by hybrid sterility (about 25% isolation between H. heurippa and H. melpomene, and zero between H. heurippa and H. cydno) [1] or predator selection against hybrids (about 50%) [24]. Therefore, strong assortative mating, in combination with geographic isolation from H. cydno and postzygotic isolation from H. melpomene has contributed to the speciation of H. heurippa.

So, the females of the new species, Heliconius heurippa, exhibited strong preference for other male Heliconius heurippa, with probabilities of out-crossing being 0.073 with Heliconius melpomene males and 0.022 with Heliconius cydno males. Male Heliconius heurippa again exhibited strong preference for female Heliconius heurippa, with probabilities of outcrossing being 0.1 with Heliconius melponeme and 0.44 with Heliconius cydno females. The table in the paper also demonstrates that the parent species also show strong assortative mating, though exhibit enough tendency to hybridise with each other to produce the offspring needed to generate Heliconius heurippa in the first place (hybridisation rate approximately 8%).

However, apart from mating experiments, the authors conducted some other experiments too. Let's take a look at these shall we?

We next investigated the role of colour pattern in mate choice. Experiments with dissected wings showed that both elements of the forewing colour pattern of H. heurippa were necessary for the stimulation of courtship (Fig. 3). H. heurippa males were less than half as likely to approach and court the H. m. melpomene or the H. cydno cordula pattern than their own (Fig. 3).When either the red or yellow bands were experimentally removed from the H. heurippa pattern, this led to a similar reduction in its attractiveness, demonstrating that both hybrid elements are necessary for mate recognition by male H. heurippa (Fig. 3).

So in this experiment, the authors demonstrated that visual cues are important to Heliconius heurippa, and that experimental manipulation of the wing pattern to mask certain features reduces their attractiveness as visual stimuli to mating.

Similar results were obtained when these experiments were replicated with printed-paper models (Fig. 3), showing that the colour pattern itself was the cue rather than pheromones associated with the dissected wings. Additional experiments showed that males of both H. m. melpomene and H. cydno cordula showed a greatly reduced probability of approaching and courting the H. heurippa pattern than their own (Supplementary Figs 6 and 7). Given the incomplete postzygotic reproductive isolation between all three species [1], this pattern-based assortative mating must have a continuing role in generating reproductive isolation between H. heurippa and its relatives.

Nice. The above experiments established that visual stimuli reproduce the same pattern of assortative mating behaviour even in the absence of pheromones, demonstrating that visual cues are the primary means of stimulating courtship behaviour in these butterflies, and that those visual cues exert strong effects upon mate preference, leading to the assortative mating patterns seen above.

Novel patterns in Heliconius probably become established through a combination of genetic drift and subsequent fixation of the novel pattern driven by frequency-dependent selection [25]. Such an event could have established the hybrid H. heurippa pattern as a geographic isolate of H. cydno. Subsequently, the pattern was sufficiently distinct from both H. melpomene and H. cydno that mate-finding behaviour also diverged in parapatry, generating assortative mating between all three species (Supplementary Fig. 8). This two-stage process indicates a possible route by which the theoretical difficulty of a rapid establishment of reproductive isolation between the hybrid and the parental taxa could have been overcome [5,6]. Furthermore, because we are proposing divergence in mate behaviour in a geographically isolated population, reinforcement or some other form of sympatric divergence is not required for speciation to occur.

Our study provides the first experimental demonstration of a hybrid trait generating reproductive isolation between animal species, and the first example of a hybrid trait causing pre-mating isolation through assortative mating. None of the theoretical treatments of homoploid hybrid speciation have considered the effects of assortative mating[5,6]. If variation for mate preference were incorporated, the theoretical conditions favouring hybrid speciation might not be as stringent as has been supposed. Finally, two other species, H. pachinus [20] and H. timareta [26], have also been proposed as having H. cydno/H. melpomene hybrid patterns, indicating that this process might have occurred more than once. However, whether these cases represent a particularity of Heliconius or a common natural process that has been undetected in other animal groups studied less intensively remains a matter of further study. Suggestively, other proposed cases of homoploid hybrid speciation in animals occur in well-studied groups such as African cichlids [8–10] and Rhagoletis flies [11.

So, the authors were able to reproduce a wild speciation event in the laboratory, produce laboratory analogues of the new species that were interfertile with wild type members of that species, and demonstrate the existence of assortative mating preferences producing a reproductive isolation barrier between the new species and the parents once the new species existed. Furthermore, this mechanism of speciation has been erected as a probable model in other well-studied groups of organisms, including those particular favourites of mine among the vertebrates, African Cichlid fishes.

Game over for your assertion. That's before we take into account the literature covering speciation genes and observed instances of speciation. The following is a small sample of the available literature:

A Model For Divergent Allopatric Speciation Of Polyploid Pteridophytes Resulting From Silencing Of Duplicate-Gene Expression by Charles R.E. Werth and Michael D. Windham, American Naturalist, 137(4): 515-526 (April 1991) - DEVELOPMENT OF A MODEL TO MATCH OBSERVED SPECIATION IN NATURE

A Molecular Reexamination Of Diploid Hybrid Speciation Of Solanum raphanifolium by David M. Spooner, Kenneth. J. Sytsma and James F. Smith, Evolution, 45(3): 757-764 - DOCUMENTATION OF AN OBSERVED SPECIATION EVENT

A Mouse Speciation Gene Encodes A Meiotic Histone H3 Methyltransferase by Ondrej mihola, Zdenek Trachtulec, Cestmir Vlcek, John C. Scimenti and Jiri Forejt, Science, 323: 350-351 (16th January 2009) - DETERMINING THE FUNCTION OF A GENE DIRECTLY IMPLICATED IN SPECIATION AND FAILURE OF INTERFERTILITY BETWEEN DIVERGING POPULATIONS

A Rapidly Evolving MYB-Related Protein Causes Species Isolation In Drosophila by Daniel A. Barbash, Dominic F. Siino, Arron M. Tarone and John Roote, Proceedings of the National Academy of Sciences of the USA, 110(9): 5302-5307 (29th April 2003) - DETERMINING THE BEHAVIOUR OF A GENE DIRECTLY IMPLICATED IN SPECIATION AND FAILURE OF INTERFERTILITY BETWEEN DIVERGING POPULATIONS

A Screen For Recessive Speciation Genes Expressed In The Gametes Of F1 Hybrid Yeast by Duncan Greig, Public Library of Science Genetics, 3(2): e21 (February 2007) - Determining the presence of speciation genes in a primitive eukaryote, and the roles of any genes thus located

Adaptive Divergence And The Evolution Of Reproductive Isolation In The Wild: An Empirical Demonstration Using Introduced Sockeye Salmon by Andrew P. Hendry, Genetics, 112-113: 515-534 (2001) - DIRECT EXPERIMENTAL TEST OF REPRODUCTIVE ISOLATION AND ITS ROLE IN SPECIATION EVENTS

Adaptive Evolution And Explosive Speciation: The Cichlid Fish Model by Thomas D. Kocher, Nature Reviews Genetics, 5: 288-298 (April 2004) - DISCUSSION OF METHODS OF EMPIRICAL DEMONSTRATION OF SPECIATION INCLUDING MOLECULAR ANALYSES

Chromosomal Rearrangements And Speciation by Loren H. Rieseberg, TRENDS In Ecology & Evolution, 16(7): 351-358 (July 2001) - determination of the input that chromosomal rearrangements may have upon speciation evnets

Chromosome Evolution, Phylogeny, And Speciation Of Rock Wallabies by G. B. Sharman, R. L. Close and G. M. Maynes, Australian Journal of Zoology, 37(2-4): 351-363 (1991) - DOCUMENTATION OF OBSERVED SPECIATION IN NATURE

Evidence For Rapid Speciation Following A Founder Event In The Laboratory by James R. Weinberg Victoria R. Starczak and Danielle Jörg, Evolution 46: 1214-1220 (15th January 1992) - EXPERIMENTAL GENERATION OF A SPECIATION EVENT IN THE LABORATORY

Evolutionary Theory And Process Of Active Speciation And Adaptive Radiation In Subterranean Mole Rats, Spalax ehrenbergi Superspecies, In Israel by E. Nevo, Evolutionary Biology, 25: 1-125 - DOCUMENTATION OF OBSERVED SPECIATION IN NATURE

Experimentally Created Incipient Species Of Drosophila by Theodosius Dobzhansky & Olga Pavlovsky, Nature 230: 289 - 292 (2nd April 1971) - EXPERIMENTAL GENERATION OF A SPECIATION EVENT IN THE LABORATORY

Founder-Flush Speciation On Drosophila pseudoobscura: A Large Scale Experiment by Agustí Galiana, Andrés Moya and Francisco J. Alaya, Evolution 47: 432-444 (1993) EXPERIMENTAL GENERATION OF A SPECIATION EVENT IN THE LABORATORY

Gene Duplication And Speciation In Drosophila: Evidence From The Odysseus Locus by Chau-Ti Ting, Shun-Chern Tsaur, Sha Sun, William E. Browne, Yung-Chia Chen, Nipam H. Patel and Chung-I Wu, Proceedings of the National Academy of Sciences of the USA, 101(33): 12232-12235 (17th August 2004) - EMPIRICAL ANALYSIS OF THE ROLE OF A DEFINED SPECIATION GENE AND DUPLICATION THEREOF IN SPECIATION EVENTS

Gene Transfer, Speciation, And The Evolution Of Bacterial Genomes by Jeffrey G. Lawrence, Current Opinion in Microbiology, 2(5): 519-523 (October 1999) - determining the role of horizontal gene transfer in the development of new bacterial serotypes

Genes And Speciation by Chung-I Wu, Journal of Evolutionary Biology, 14: 889-891 (2001) - development of a rigorous theory of reproductive isolation taking into account incomplete interfertility failure events

Hybrid Lethal Systems In The Drosophila melanogaster Species Complex. II. The Zygotic Hybrid Rescue (Zhr) Gene Of Drosophila melanogaster by Kyoichi Sawamura, Masa-Toshi Yamamoto and Takao K. Watanabe, Genetics, 133: 307-313 (February 1993) - EMPIRICAL DETERMINATION OF THE ROLE OF A NAMED SPECIATION GENE IN SPECIFIC LIVING ORGANISMS

Hybridisation And Adaptive Radiation by Ole Seehausen, TRENDS In Ecology & Evolution, 19(4): 198-207 (April 2004) - development of a rigorous theory underpinning hybrid speciation and SPECIFICATION OF EMPIRICAL TESTS OF THAT THEORY

Incipient Speciation By Sexual Isolation in Drosophila: Concurrent Evolution At Multiple Loci by Chau-Ti Ting, Aya Takahashi and Chung-I Wu, Proceedings of the National Academy of Sciences of the USA, 98(12): 6709-6713 (5th June 2001) - EMPIRICAL DEMONSTRATION OF THE EXISTENCE OF GENES GOVERNING MALE MATING SUCCESS AND FEMALE MATING PREFERENCE LEADING TO SEXUAL SELECTION AND SPECIATION

Laboratory Experiments On Speciation: What Have We Learned In 40 Years? by William R. Rice and Ellen E. Hostert, Evolution, 47(6):1637-1653 (December 1993) - review of speciation literature and determination of the validity of reproductive isolation as a speciation mechanism

Models Of Evolution Of Rperoductive Isolation by Masatoshi Nei, Takeo Maruyama and Chung-I Wu, Genetics, 103: 557-559 (March 1983) - DIRECT EMPIRICAL TEST OF MODELS OF REPRODUCTIVE ISOLATION, AND ESTABLISHMENT OF CORRELATION WITH REAL WORLD DATA

Phylogenetics And Speciation by Timothy G. Barraclough and Sean Nee, TRENDS in Ecology & Evolution, 16(7): 391-399 (July 2001) - Determination of rigorous methods for using phylogenetic analyses to establish speciation events

Pollen-Mediated Introgression And Hybrid Speciation In Louisiana Irises by Michael L. Arnold, Cindy M. Buckner and Jonathan J. Robinson, Proceedings of the National Academy of Sciences of the USA, 88(4): 1398-1402 (February 1991) - OBSERVATION OF A SPECIATION EVENT IN NATURE

Premating Isolation Is Determined by Larval Rearing Substrates in Cactophilic Drosophila mojavensis. IV. Correlated Responses In Behavioral Isolation To Artificial Selection On A Life-History Trait by William J. Etges, The American Naturalist, 152(1): 129-144 (July 1998) - DIRECT EMPIRICAL TEST OF BEHAVIOURAL ISOLATION AS A MECHANISM DRIVING SPECIATION

Rapid Evolution Of Postzygotic Reproductive Isolation In Stalk-Eyed Flies by Sarah J. Christianson, John G. Swallow and Gerald S. Wilkinson, Evolution, 59(4): 849-857 (12th January 2005) - DIRECT EMPIRICAL TEST AND MOLECULAR ANALYSIS OF SEXUAL SELECTION AND HYBRID STERILITY AS MECHANISMS DRIVING SPECIATION

Role Of Gene Interactions In Hybrid Speciation: Evidence From Ancient And Experimental Hybrids by Loren H. Rieseberg, Barry Sinervo, C. Randall Linder, Mark C. Ungerer and Dulce M. Arias, Science, 272: 741-745 (3rd May 1996) - DIRECT EXPERIMENTAL TESTS OF HYPOTHESES REGARDING HYBRID SPECIATION

Searching For Speciation Genes by Roger Butlin and Michael G. Ritchie, Nature, 412: 31-33 (5th July 2001) - DIRECT EMPIRICAL SEARCH FOR GENES IMPLICATED IN SPECIATION EVENTS

Selfish Operons And Speciation By Gene Transfer by Jeffrey G. Lawrence, Trends in Microbiology, 5(9): 355-359 (September 1997) - EMPIRICAL DETERMINATION OF MECHANISMS FOR DEVELOPMENT OF NEW BACTERIAL SEROTYPES

Sex-Related Genes, Directional Sexual Selection, And Speciation by Alberto Civetta and Rama S. Singh, Molecular & Biological Evolution, 15(7): 901-909 (1998) - EMPIRICAL DETERMINATION OF THE SHAPING OF GENES IMPLICATED IN SPECIATION VIA SEXUAL SELECTION

Sexual Selection, Reproductive Isolation And The Genic View Of Speciation by J. J. M. Van Alphen and Ole Seehausen, Journal of Evolutionary Biology, 14: 874-875 (2001) - application of known speciation mechanisms to the Lake Victoria superflock of Cichlid fishes

Speciation Along Environmental Gradients by Michael Doebeli and Ulf Dieckmann, Nature, 421: 259-264 (16th January 2003) - determination of the effects of environmental pressures upon the outcome of speciation events

Speciation And The Evolution Of Gamete Recognition Genes: Pattern And Process by S. R. Palumbi, Heredity, 102: 66-76 (2009) - determination of the role of gamete recognition genes in speciation events, and their rapid evolution in segregated populations

Speciation By Hybridisation In Heliconius Butterflies by Jesús Mavárez, Camilo A. Salazar, Eldredge Bermingham, Christian Salcedo, Chris D. Jiggins and Mauricio Linares, Nature, 441: 868-871 (15th June 2006) - DETERMINATION OF A SPECIATION EVENT IN NATURE, FOLLOWED BY LABOARTORY REPRODUCTION OF THAT SPECIATION EVENT, AND CONFIRMATION THAT THE LABORATORY INDIVIDUALS ARE INTERFERTILE WITH THE WILD TYPE INDIVIDUALS (already expounded in detail above)

Speciation By Hybridization In Phasmids And Other Insects By Luciano Bullini and Guiseppe Nascetti, Canadian Journal of Zoology 68(8): 1747-1760 (1990) - OBSERVATION OF A SPECIATION EVENT IN NATURE

Speciation By Postzygotic Isolation: Forces, Genes And Molecules by H. Allen Orr and Daven C. Presgraves, Bioessays, 22(12): 1085-1094 (2000) - EMPIRICAL DETERMINATION OF THE EXISTENCE OF SPECIATION GENES AND THEIR ROLE IN INTERFERTILITY FAILURE BETWEEN SEGREGATED POPULATIONS

Speciation Genes by H. Allen Orr, John P. Masly and Daven C. Presgraves, Current Opinion in Genetics & Development, 14: 675-679 (2004) - DETERMINATION OF THE EXISTENCE OF SPECIATION GENES AND THEIR SUSCEPTIBILITY TO DARWINIAN SELECTION

Speciation, Hybrid Zones And Phylogeography - Or Seeing Genes In Space And Time by Godfrey M. Hewitt, Molecular Ecology, 10: 537-549 (2001) - review of origins of speciation theory, current developments, and application to past and present speciation events

Speciation By Habitat Specialisation: The Evolution Of Reproductive Isolation As A Correlated Character by William R. Rice, Evolutionary Ecology, 1: 301-314 (1987) - LINKING OF SPECIATION EVENTS TO NICHE MOBILITY AND ADAPTATION FOR NEW NICHES

The Evolution Of Asymmetry In Sexual Isolation: A Model And Test Case by Stevan J. Arnold, Paul A. Verrell and Stephen G. Tilley, Evolution, 50(3): 1024-1033 (June 1996) - DEVELOPMENT OF AN EXTENDED MODEL OF SEXUAL SELECTION FOLLOWED BY EMPIRICAL TEST OF THAT MODEL AND DETERMINATION OF CORRELATION WITH A REAL WORLD POPULATION DIVERGENCE EVENT

The Evolution Of Reproductive Isolation Through Sexual Conflict by Oliver Y. Martin and David J. Hosken, Nature,423: 979-982 (26th June 2003) - DIRECT EXPERIMENTAL TEST OF SEXUAL CONFLICT AS A DRIVER OF SPECIATION

The Evolutionary Genetics Of Speciation by Jerry A. Coyne and H. Allen Orr, Philosophical Transactions of the Royal Society of London Part B, 353: 287-305 (1998) review of recent advances in speciation theory and empirical results

The Genetic Basis Of Reproductive Isolation: Insights From Drosophila by H. Allen Orr, Proceedings of the National Academy of Sciences of the USA, 102 supplement 1: 6522-6526 (3rd May 2005) - review of work on speciation genes and the empirical determination of their roles

The Genic View Of The Process Of Speciation by Chung-I Wu, Journal of Evolutionary Biology, 14: 851-865 (2001) - review of theory of speciation including renewed insights into Darwin's own early view of the topic, and how this correlates to a hitherto unforeseen extent with modern genetic results

The Gibbons Speciation Mechanism by S. Ramadevon and M. A. B. Deaken, Journal of Theoretical Biology, 145(4): 447-456 (1991) - DEVELOPMENT OF A MODEL ACCOUNTING FOR OBSERVED INSTANCES OF SPECIATION

The Phylogeny Of Closely Related Species As Revealed By The Genealogy Of A Speciation Gene, Odysseus by Chau-Ti Ting, Shun-Chern Tsaur and Chung-I Wu, Proceedings of the National Academy of Sciences of the USA, 97(10): 5313-5316 (9th May 2000) - EXPERIMENTAL VERIFICATION OF A PREDICTION ABOUT SPECIATION MECHANISMS AT THE MOLECULAR LEVEL

The Population Genetics Of Speciation: The Evolution Of Hybrid Incompatibilities by H. Allen Orr, Genetics, 139: 1805-1813 (April 1995) - development of a gene-based model for speciation and the implications of the results obtained from that model for speciation research

The Theory Of Speciation Via The Founder Principle by Alan R. Templeton, Genetics, 94:1011-1038 (April 1980) - development of a model for founder speciation, and DIRECT EXPERIMENTAL TEST of that model by applying it to a real world organism

What Does Drosophila Genetics Tell Us About Speciation? by James Mallet, TRENDS in Ecology & Evolution, 21(7): 386-393 (July 2006) - Comparison of Drosophila data with data from other organisms to produce a more complete picture of speciation mechanics

I think this is pretty much Game Over for your assertion. But, there's more. I'm also aware of a paper describing an experiment, simple to conduct (it can be conducted in a high school laboratory), which will, when run to completion, generate a speciation event in the laboratory. Yes, an experiment that everyone here can conduct in their kitchens, and in doing so, generate their own speciation events if run to completion. The paper in question is this one:

Reproductive Isolation As A Consequence Of Adaptive Divergence In Drosophila pseudoobscura by Diane M. B. Dodd, Evolution, 43(6): 1308-1311 (September 1989) [Full paper downloadable from here]

According to the biological species concept, speciation is basically a problem of reproductive isolation. Of the many ways to classify isolating mechanisms, the two main divisions are premating isolation, in which mating is prevented from occurring, and postmating isolation, in which mating takes place but viable, fertile offspring are not produced. There is much debate over which type of mechanism, premating or postmating, is most likely to develop first and how the isolation comes about (e.g., see Dobzhansky, 1970; Mayr, 1963; and Muller, 1949).

In an attempt to gain insight into the process of the development of reproductive isolation, eight populations of Drosophila pseudoobscura were studied. These were first used by Powell and Andjelkovič (1983) in a study of the alpha-amylase (Amy) locus. Four were reared on a starch-based medium, and four were reared on a maltose-based medium. These two media are both quite stressful; it initially took several months for the populations to become fully established and healthy. Considering the pressure placed on the populations by the media, one would expect to see some kind of adaptive divergence between the starch-reared and maltose-reared flies.

Several changes were in fact observed in the eight populations. Powell and Andjelkovič noted an increase in the "fast" allele of Amy in the starch populations as well as an increase in one of the patterns of amylase activity in the midgut. However, no corresponding changes were seen in the maltose populations. Elsewhere (Dodd, 1984), I have presented evidence that the populations have become differentially adapted to the two media. In this study, it is shown that the populations have also developed behavioral isolation as a pleiotropic by-product of this adaptive divergence.

Basically, Dodd's experiment consisted of maintaining populations of flies, subjecting them to different dietary régimes in a manner that would result in adaptations to those régimes appearing, then demonstrating that assortative mating took place amongst the flies - in other words, members of each population exhibited a strong preference for members of their own population as mate choices.

Assortative mating is regarded as a major sign of incipient speciation, because it eliminates gene flow between the populations, thus ensuring that those populations will diverge. Eventually, said divergence will result in a fertility gap arising between the two populations. If we have two such populations, A and B, then individuals from population A can be trial mated to individuals from population B, to determine if interfertility failure has taken place. If it has, then you have a bona fide speciation event. Prior to such tests indicating interfertility failure, what you have, from a rigorous standpoint, is an incipient speciation event - the potential is there, but it hasn't actually been put to the test fully. Dodd only claimed in her paper that assortative mating was observed, but of course, assortative mating is a significant indicator that speciation is taking place, because of its effects upon gene flow. Continue the experiment for sufficient time, and interfertility failure between the divergent populations will emerge (as indeed Dobzhansky demonstrated in separate, earlier experiments with other fruit flies), at which point, we have a bona fide speciation event.

Let's delve into the paper in more detail, shall we?

Materials And Methods

All eight D. pseudoobscura populations were derived from a single population collected at Bryce Canyon, Utah (see Powell and Andjelkovič [1983] for details on the media and the generation of the populations). The four starch-reared populations were designated Ist- IVst; the maltose-reared populations were designated Ima-IVma. The flies were maintained in population cages at 25°C. The present investigation was begun approximately one year after the populations were started.

Starch-adapted populations were tested against maltose-adapted populations in every possible combination to determine whether adaptation to the two new regimes could have induced the development of ethological isolation. Multiple-choice tests were performed using mating chambers modeled on those described by Elens and Wattiaux (1964). All flies used in the mating-preference tests were reared for one generation on standard cornmeal-molasses-agar medium. Virgin males and females were anesthetized with CO2, isolated from the opposite sex, and aged on standard medium for 3-6 days. Twelve females from each of the populations to be tested were placed in the chamber. Twelve males from the two populations were then introduced as nearly simultaneously as possible. The flies were not anesthetized for this procedure. The tests were performed at room temperature (no higher than 25°C), under bright (but not direct) lighting. The chambers were observed for 60-90 minutes.

Individuals of one population had the tips of their right wings clipped to allow identification. At least two replicates of each test were performed, with the wing clipping alternated between populations. Wing clipping has not been found to interfere with mating success in Drosophila (Ehrman, 1966; Ehrman and Petit, 1968; Powell, 1978; Robertson, 1982; Knoppien, 1984; van den Berg et al., 1984; Dodd and Powell, 1985; Spiess, 1986), and once again in the present tests, wing clipping had no effect on mating propensity in either sex. Of the 1,558 matings scored, 778 were with nonclipped males, and 780 were with clipped males; 793 non-clipped females mated, while 765 clipped females mated. These differences are not statistically significant.

An isolation index (I) was calculated for each mating test. The index used follows Stalker (1942), Bateman (1949), and Merrell (1950), with the standard error derived following Malogolowkin-Cohen et al. (1965):

I = (homogamic matings - heterogamic matings) ÷ total matings(N)

Standard Error (SE) of I = [(1-I^2)/N]^½

I ranges from -1 to 1; a value of zero indicates random mating; I > 0 indicates positive assortative mating; and I < 0 indicates negative assortative mating. Contingency chi-square tests were also performed to check for deviations from random mating.

Basically, the procedure consisted of the following:

[1] Set up several populations of Drosophila pseudoobscura, divided into two groups. One group of populations is raised on a starch-rich medium (these populations are designated in her paper with the postfix "st"), and the other group is raised on a maltose-rich medium (these populations are designated with the postfix "ma").

[2] Keep these populations separate from each other for a number of generations. In Dodd's experiment, approximately 1 year elapsed before the assortative mating tests took place. For this species, 1 year equates to 8 new generations, which might seem to be a surprisingly small number of generations for any such effect to become noticeable: more usually, one would expect something like 30 or 40 generations to be required. One of the interesting features of Dodd's research, which has since been replicated with essentially the same results, is that the experimental results were obtained after just 8 generations of separation.

Oh look, an experiment in speciation that can be performed by a reasonably astute high school student in his kitchen or greenhouse, one whose results have been demonstrated repeatedly to work.

Meanwhile, there's also two species of tree frogs in the USA to consider, namely Hyla chrysocelis and Hyla versicolor. Now these two species are interesting, because, wait for it, the Hyla versicolor genome is virtually an exact copy of the Hyla chrysocelis genome, but with one important difference - the Hyla versicolor genome is duplicated wholesale. So while Hyla chrysocelis is an entirely typical diploid vertebrate (chromosomes in pairs), Hyla versicolor has two complete copies of the Hyla chrysocelis genome, with its chromosomes arranged in groups of four (tetraploid). As a corollary of this wholesale genome duplication that took place in the ancestors of Hyla versicolor, individuals of that species can no longer mate successfully with individuals of Hyla chrysocelis, despite the genetic evidence pointing conclusively to an ancestral population of Hyla chrysocelis being the ancestors of Hyla versicolor. In short, a speciation event of a particularly unusual nature took place - speciation via polyploidy. Now this mechanism has been observed occurring with some frequency in plants (Primula kewensis being perhaps the canonical example in the scientific literature to date), but observing this in vertebrates is very unusual indeed.

Again, Game Over for your assertion.

The fossil record, with few obscure exception, shows fully developed species rather than all the supposed intermediary species.

What ignorant drivel.

Oh wait, even before we consider the fact that many of these fossils constitute developmental series over time (see, for example, the tetrapod sequence from Eusthenopteron to Ichthyostega), there's another elementary concept to consider here, that destroys wholesale the "fully developed species" creationist bullshit you're peddling here. that elementary concept centres upon one readily demonstrable fact, namely, you are not identical to either of your parents, and for that matter, none of your offspring will be identical to you. In short, every population of living organisms is a dynamic entity, with the collective genomic status of that population changing with every new generation, even before mutations are factored in. Meiosis - the process by which sperm and egg cells are formed - guarantees this. As a corollary, you are a transitional form between your parents and your offspring. The same is true for every sexually reproducing eukaryote organism on the planet.

The moment mutations are introduced into the mix, matters become even more interesting, because the moment these occur, the potential for those mutations to spread to future generations and proliferate becomes open. The moment this happens (and, yes, documented instances of this happening in humans as well as other organisms exist in the literature), you have the genetic basis upon which morphological change and speciation can take place. Even in the absence of a genetic audit trail, the emergence of a systematic pattern or morphological changes (see those tetrapods again) constitutes evidence that the organisms in question were members of a clade.

Oh, and if you don't think morphological change can occur, I've known this to be a fact, courtesy of my being a tropical fishkeeper for over 35 years. Back in the 1970s, a new mutation appeared in aquarium bred populations of Betta splendens, the Siamese Fighting Fish, known as the Double Tail mutation, which results in the fish inheriting this mutation having two tail fins instead of one. Furthermore, subsequent scientific research has shown this mutation to be centred upon a single gene, exhibiting single-factor Mendelian recessive inheritance of the exact same sort that is seen in, for example, Factor VIII Haemophilia in humans. Furthermore, in the aquarium environment, the Double Tail mutation makes males more attractive as mates to females, because the finnage is expanded, and female Betta splendens prefer males with the largest fins. Therefore, if females Betta splendens are given a choice of mates, they routinely, in appropriate experiments, prefer the Double Tail males to the single tail males, which means that in that scenario, the trait is positively selectable.

I think that covers all the bases here.

Cognostic's picture
You are using the word "proof

You are using the word "proof" as a synonym for "evidence." I already posted the video indicating how sex evolved. The fact that you did not understand it is not a reflection on what actually occurred but rather on your ability to understand.

Macroevolution?? Do you mean Evolution? Perhaps you are referring to speciation? Here is a little cartoon to help you understand Speciation: https://www.youtube.com/watch?v=udZUaNKXbJA

There is just EVOLUTION. Dividing it into micro and macro is a Creationist "Straw Man" ploy.

Sheldon's picture
"there is zero proof that

"there is zero proof that life can ever start from Non life."

Straw man fallacy, as I never made any such claim, I never even mentioned abiogenesis as this has nothing to do with evolution, which explains and evidences the origin of species, not life.

You mean other then the overwhelming amount of objective evidence for the fact all living things evolved, and the indisputable fact many of those species consist of two sexes? Dear oh dear that was dumb.

"There is no proof that macroevolutiom is possible."

Macro and micro evolution are the same thing on different timescales, this is a very tired and moronic creationist canard. And again the evidence for species evolution establishes it as a scientific fact beyond any reasonable doubt.

The fossil record only show intermediary species, as all species are intermediary, again this is one of the dumbest canards creatards espouse.

"And who is to say God is complex? And just because something is asinine doesn’t mean it’s not true. Also define pixie."

Theists say it, both directly, and of course it must be inferred from their unevidenced claim the deity they believe in created everything, that this deity is more complex than it's creation. The argument you use is as valid for pixies as it is for deities, and you can define pixies in the same way as deities are defined, if theists can make things up and claim it represents sound argument then it must be valid for anything, otherwise it's selection bias as I said.

You've also ignored several rebuttals to your claims:

1. Complexity does not donate design,We know when something is designed only when there is sufficient objective evidence for design, and in every instance where this is the case we we also know those things evidenced as designed do not occur in nature.
2. How many universes did you use in your test group to establish this one is fine tuned? How do you even know any other type of universe is possible? This is a very tired religious canard. However even were true this demonstrates no objective for a designer, or a cause, and certainly none for any deity.
3. Utter gobbledegook, and please do link the breaking news that any branch of science demonstrates any evidence for any deity, as the entire scientific world seems to have missed this.
4. Irreducible complexity is creationist pseudoscience, again the entire scientific world knows this. All living things evolved, and this is an objective fact established beyond any reasonable doubt.
5. Again you are misrepresenting science as supporting your superstitious belief in a deity, just turn on any news channel to see this is a risible nonsense.
6. Nothing in science evidences a deity, or anything supernatural, you're simply lying, and it is as tedious as it is dishonest.
7. If pixies were a programmer it would easier for them to hack the programme and perform miracles, are you saying this is evidence for pixies? If not then your risible claim to be open minded is exposed as a lie, since you are biased in favour of your belief in a deity without any objective evidence to support it.
8. The creation myth in the bible is demonstrably false, making wild assertions based on subjective conjecture evidences nothing.

Did you think I wouldn't notice your evasion?

Sheldon's picture
Jordan

Jordan

@sheldon

"there is zero proof that life can ever start from
Non life."

Like clay you mean? Which is what the risible biblical creation myth claims humans were created from, using magic.

Your claim is something of an own goal.

Calilasseia's picture
Oh look. More tiresome

Oh look. More tiresome incredulity. Let's take a look at this shall we?

1. The complexity of DNA.

Yawn. What part of "DNA is a chemical molecule with well understood synthesis paths" do you not understand?

If you took all the DNA in your body and uncoiled and stretched it out, it would be 2 times the length of the solar system.

So what? This doesn't validate an imaginary magic man.

DNA is an actual LANGUAGE

Poppycock.

It's time to unleash this again ...

[22] The infamous canards surrounding "information".

Now this is a particularly insidious brand of canard, because it relies upon the fact that the topic of information, and its rigorous analysis, is replete with misunderstanding. However, instead of seeking to clarify the misconceptions, creationist canards about information perpetuate those misconceptions for duplicitous apologetic purposes. A classic one being the misuse of the extant rigorous treatments of information, and the misapplication of different information treatments to different situations, either through ignorance, or wilful mendacity. For example, Claude Shannon provided a rigorous treatment of information, but a treatment that was strictly applicable to information transmission, and NOT applicable to information storage. Therefore, application of Shannon information to information storage in the genome is a misuse of Shannon's work. The correct information analysis to apply to storage is Kolmogorov's analysis, which erects an entirely different measure of information content that is intended strictly to be applicable to storage. Mixing and matching the two is a familiar bait-and-switch operation that propagandists for creationist doctrine are fond of.

However, the ultimate reason why creationist canards about information are canards, is simply this. Information is NOT a magic entity. It doesn't require magic to produce it. Ultimately, "information" is nothing more than the observational data that is extant about the current state of a system. That is IT. No magic needed. All that happens, in real world physical systems, is that different system states lead to different outcomes when the interactions within the system take place. Turing alighted upon this notion when he wrote his landmark paper on computable numbers, and used the resulting theory to establish that Hilbert's conjecture upon decidability in formal axiomatic systems was false. Of course, it's far easier to visualise the process at work, when one has an entity such as a Turing machine to analyse this - a Turing machine has precise, well-defined states, and precise, well-defined interactions that take place when the machine occupies a given state. But this is precisely what we have with DNA - a system that can exist in a number of well-defined states, whose states determine the nature of the interactions that occur during translation, and which result in different outcomes for different states. indeed, the DNA molecule plays a passive role in this: its function is simply to store the sequence of states that will result, ultimately, in the synthesis of a given protein, and is akin to the tape running through a Turing machine. The real hard work is actually performed by the ribosomes, which take that state data and use it to bolt together amino acids into chains to form proteins, which can be thought of as individual biological 'Turing machines' whose job is to perform, mechanically and mindlessly in accordance with the electrostatic and chemical interactions permitting this, the construction of a protein using the information arising from DNA as the template. Anyone who thinks magic is needed in all of this, once again, is in need of an education.

As for the canard that "mutations cannot produce new information", this is manifestly false. Not only does the above analysis explicitly permit this, the production of new information (in the form of new states occupied by DNA molecules) has been observed taking place in the real world and documented in the relevant scientific literature. If you can't be bothered reading any of this voluminous array of scientific papers, and understanding the contents thereof, before erecting this particularly moronic canard, then don't bother erecting the canard in the first place, because it will simply demonstrate that you are scientifically ignorant. Indeed, the extant literature not only covers scientific papers explicitly dealing with information content in the genome, such as Thomas D. Schneider's paper handily entitled Evolution And Biological Information to make your life that bit easier, but also papers on de novo gene origination, of which there are a good number, several of which I have presented in the past in threads on other forums. The mere existence of these scientific papers, and the data that they document, blows tiresome canards about "information" out of the water with a nuclear depth charge. Post information canards at your peril after reading this.

Whilst dwelling on information, another creationist canard also needs to be dealt with here, namely the false conflation of information with ascribed meaning. Which can be demonstrated to be entirely false by reference to the following sequence of hexadecimal bytes in a computer's memory:

81 16 00 2A FF 00

To a computer with an 8086 processor, those bytes correspond to the following single machine language instruction:

ADC [2A00H], 00FFH

To a computer with a 6502 processor, those bytes correspond to the following machine language instruction sequence:

CLC
ASL ($00,X)
LDX #$FF
BRK

To a computer with a 6809 processor, those bytes correspond to the following machine language instruction sequence:

CMPA #$16
NEG $2AFF
NEG ??

the ?? denoting the fact that for this processor, the byte sequence is incomplete, and two more bytes are needed to supply the address operand for the NEG instruction.

Now, we have three different ascribed meanings to one stream of bytes. Yet, none of these ascribed meanings influences either the Shannon information content, when that stream is transmitted from one computer to another, or the Kolmogorov information content when those bytes are stored in memory. Ascribed meaning is irrelevant to both rigorous information measures. As is to be expected, when one regards information content simply as observational data about the state of the system (in this case, the values of the stored bytes in memory). Indeed, it is entirely possible to regard ascribed meaning as nothing other than the particular interactions driven by the underlying data, once that data is being processed, which of course will differ from processor to processor. Which means that under such an analysis, even ascribed meaning, which creationists fallaciously conflate with information content, also requires no magical input. All that is required is the existence of a set of interactions that will produce different outcomes from the different observed states of the system (with the term 'observation' being used here sensu lato to mean any interaction that is capable of differentiating between the states of the system of interest).

Moving on ...

with such precision iT has been compared to a work of Shakespeare.

See the above. The moment one has any set of entities that can exist in multiple states, and interactions moving them from state to state, it becomes representable in Turing-type terms. But it doesn't mean for one moment that those entities or interactions needed a magic man to bring them about.

Bill gates said “DNA is like a computer program but far far more advanced than any software ever created”.

Bill Gates isn't a molecular biologist. Also, learn the difference between analogy and actuality.

Without guidance, evolution alone would have to produce a novel like instruction code through trial and error.

Guess what? IT DID.

There's a wealth of scientific literature on the evolvability of the "genetic code". I have 22 papers devoted to this topic on my hard drive. Let's start with these:

A Coevolution Theory Of The Genetic Code by J. Tze-Fei Wong, Proceedings of the National Academy of Sciences of the USA, 72(5): 1909-1912 (May 1975)

A Mechanism For The Association Of Amino Acids With Their Codons And The Origin Of The Genetic Code by Shelley D. Copley, Eric Smith and Harold J. Morowitz, Proceedings of the National Academy of Sciences of the USA, 102(12): 4442-4447 (22nd March 2005)

Collective Evolution And The Genetic Code by Kalin Vetsigian, Carl Woese and Nigel Goldenfeld, Proceedings of the National Academy of Sciences of the USA, 103(28): 10696-10701 (11th July 2006)

Emergence Of A Code In The Polymerisation Of Amino Acids Along RNA Templates by Jean Lehmann, Michel Ciblis and Albert Libchaber, PLoS One, 4(6): e5773 (June 2009)

Evolution Of Amino Acid Frequencies In Proteins Over Deep Time: Inferred Order Of Introduction Of Amino Acids Into The Genetic Code by Dawn J. Brooks, Jacques R. Fresco, Arthru M. Lesk and Mona Singh, Molecular & Biological Evolution, 19(10): 1645-1655 (2000)

Evolution Of The Genetic Code: Partial Optimization Of A Random Code For Robustness To Translation Error In A Rugged Fitness Landscape by Artem S. Novozhilov, Yuri I Wolf and Eugene V. Koonin, Biology Direct, 2(4): doi:10.1186/1745-6150-2-24 (23rd October 2007)

Exceptional Error Minimisation In Putative Primordial Genetic Codes by Artem S. Novozhilov & Eugene V. Koonin, arXiv (25th August 2009)

Importance Of Compartment Formation For A Self-Encoding System by Tomoaki Matsuura, Muneyoshi Yamaguchi, Elizabeth P. Ko-Mitamura, Yasufumi Shima, Itaru Urabe and Tetsuya Yomo, Proceedings of the National Academy of Sciences of the USA, 99(11): 7514-7517 (28th May 2002)

On The Origin Of The Genetic Code: Signatures Of Its Primordial Complementarity In tRNAs And Aminoacyl-tRNA Synthetases by S. N. Rodin and A. S. Rodin, Heredity, 100: 341-355 (5th March 2008)

Origin And Evolution Of The Genetic Code: The Universal Enigma by Eugene V. Koonin and Artem S. Novozhilov, arXiv (10th September 2008)

Recent Evidence For Evolution Of The Genetic Code by Syozo Osawa, Thomas H. Jukes, Kimitsuna Watanabe and Akira Muto, Microbiological Reviews, 56(1): 229-264 (March 1992)

Rewiring The Keyboard: Evolvability Of The Genetic Code by Robin D. Knight, Stephen J. Freeland and Laura F. Landweber, Nature Reviews Genetics, 2: 49-58 (January 2001)

A Simple Model Based On Mutation And Selection Explains Trends In Codon And Amino-Acid Usage And GC Composition Within And Across Genomes by Robin D. Knight, Stephen J. Freeland and Laura F. Landweber, Genome Biology, 2(4): research0010.1–0010.13 (22nd March 2001)

Let's take a look at some of these papers in more detail, shall we? First, the PNAS paper by Wong:

ABSTRACT The theory is proposed that the structure of the genetic code was determined by the sequence of evolutionary emergence of new amino acids within the primordial biochemical system.

In more detail, the author opens with the following:

The genetic code for protein molecules is a triplet code, consisting of the 64 triplets of the four bases adenine, guanine, cytosine and uracil (1, 2). The cracking of the code was a monumental achievement, but it posed in turn what Monod (3) regards as one of the challenges of biology, namely the "riddle of the code's origin." Crick (4) has discussed two different theories which have been proposed regarding this origin. The Stereochemical Theory postulates that each amino acid became linked to its triplet codons on account of stereochemical reasons, whereas the Frozen Accident Theory postulates that the linkage arose purely by chance. Since neither theory has given a systematic solution to the riddle, the present purpose is to explore a third hypothesis, which postulates that:

The structure of the codon system is primarily an imprint of the prebiotic pathways of amino-acid formation, which remain recognizable in the enzymic pathways of amino-acid biosynthesis. Consequently the evolution of the genetic code can be elucidated on the basis of the precursor-product relationships between amino acids in their biosynthesis. The codon domains of most pairs of precursor-product amino acids should be contiguous, i.e., separated by only the minimum separation of a single base change.

This theory, which may be called a Co-evolution Theory, is readily tested. If many pairs of amino acids which bear a nearest (in terms of the number of enzymic steps) precursor product relationship to each other in a biosynthetic pathway fail to occupy contiguous codon domains, the theory would be untenable. The known precursor-product conversions between amino acids are (5-7):

Glu -> Gln
Glu -> Pro
Glu -> Arg
Asp -> Asn
Asp -> Thr
Asp -> Lys
Gln -> His
Thr -> Ile
Thr -> Met
Set -> Trp
Ser -> Cys
Val -> Leu
Phe -> Tyr

Of these, only the relationships of Asp to Lys and Thr to Met require some comment. Lys can be synthesized either from Asp via the diaminopimelate pathway (8), or from Glu via the a-aminoadipate pathway (9). Since the former pathway operates in prokaryotes and the latter in eukaryotes, an Asp-Lys pairing has greater prebiotic significance than a Glu-Lys pairing. The biosynthesis of Met can proceed best from Asp, but Thr is nearer to Met in terms of the number of enzymic steps involved (homoserine, which might represent a more primitive form of Thr, is even nearer still to Met). Although Ser and Cys can enter into the Met-biosynthetic pathway subsequent to the entry of Thr, neither Ser nor Cys is a straightforward precursor of Met. Ser is not the only possible contributor of a one-carbon group to -Met, and Cys is not the only possible contributor of sulfur (10). a-Transaminations, because of their relative nonspecificity, are not regarded as useful criteria for the tracing of precursor-product relationships. Aside from the above precursor-product relationships, Glu, Asp, and Ala are known to be interconvertible via the tricarboxylate cycle, and Ala, Ser, and Gly via the metabolism of pyruvate, glycerate, and glyoxylate (6).

Evolutionary map of the genetic code

When the codons for various precursor-product amino acids (Table 1) are examined, many of the codon domains of product amino acids are found to be contiguous with those of their respective precursors. The only noncontiguities are those of the Glu-Pro, Glu-Arg, Asp-Thr, and Asp-Lys pairs. If the prebiotic derivations of Gln from Glu, and Asn from Asp, had not occurred at the earliest stages of codon distribution, CAA and CAG could be expected to form part of the early Glu codons, and AAU and AAC part of the early Asp codons. This simple secondary postulate regarding the dicarboxylic amino acids and their amides suffices to remove all noncontiguities between precursors and products. It becomes possible to construct in Fig. 1 a map of the genetic code in which the codon domains of every precursor-product pair of amino acids (connected by single-headed arrows), as well as those of other interconvertible pairs (connected by double-headed arrows) are separated by only a single base change. This confirms the prediction by the Co-evolution Theory that codon distribution is closely related to amino-acid biosynthesis. Furthermore, since the theory suggests that the enzymic pathways of amino-acid biosynthesis largely stemmed from the prebiotic pathways of amino-acid formation, the pathways of this map are regarded as co-evolutionary pathways through which new amino acids were generated within the primordial system, and through which the triplet codons became distributed to finally the 20 amino acids.

Tests for randomness

The correlation between codon distribution and amino-acid biosynthesis indicated in Fig. 1 could arise not only from coevolution, but also in principle from chance. However, the unlikelihood of the latter explanation can be demonstrated in two different ways. First, consider the widespread contiguities between the codons of precursor and product amino acids. For any precursor codon triplets, there will be a other triplets in the genetic code which are contiguous with the group, and b other triplets which are noncontiguous. If a product of this amino acid has n codons, the random probability P that as many as x of these n codons turn out to be contiguous with some precursor codon is determined by the hypergeometric distribution.

The calculated values of P for eight precursor-product pairs are shown in Table 2. Using the method of Fisher (11), the eight corresponding -2 1n P values can be summed to give a χ^2 value of 45.01 with 16 degrees of freedom; this indicates an aggregate probability of less than 0.0002 that these eight sets of contiguities could have become so numerous by chance. Amongst the eight amino-acid pairs, either Phe-Tyr or Val-Leu may represent sibling products of a common biosynthetic pathway rather than true precursor and product. Their deletion from calculation leaves a χ^]2 value of 27.10 with 12 degrees of freedom, which still points to an aggregate probability of only 0.0075. The potential Glu-Pro, Glu-Arg, Asp-Thr, Asp-Lys, Thr-Met, Ala-Ser-Gly and Glu-Asp-Ala contiguities, plausible but less certain, have not been included in these calculations; their inclusion would lower the aggregate probability even further. Also, there are other ways to perform the statistical analysis, e.g., by taking a pair of codons such as UGU and UGC as one rather than two units in the hypergeometric distribution, but the nonrandom character of the precursor-product contiguities is far too striking to be fundamentally circumventable by statistical methodology.

Secondly, Gln, Pro, and Arg are biosynthetic siblings of the Glu family, and Asn, Thr, and Lys are siblings of the Asp family. Likewise, Cys and Trp are siblings of the Ser family, and Ile and Met are siblings of the Thr family. Of the seven pairs of amino acids in Table 1 that share the first two bases, Ile-Miet, Asn-Lys, and Cys-Trp are siblings. His-Gln are precursor-product, and Asp-Glu are either siblings or precursor-product. Only Phe-Leu and Ser-Arg are unrelated pairs. There are 190 possible amino-acid pairs amongst the 20 amino acids, and the four families of siblings generate a total of eight sibling pairs. Accordingly the probability of randomly finding as many as three out of any seven amino-acid pairs to be sibling pairs is only 0.00161 on the basis of Eq. 1 (a = 8, b = 182, n = 7, x = 3). If Ile-Met are not regarded as siblings, this probability would be raised to 0.0224, but then there are also grounds to consider Asp-Glu as siblings of the tricarboxylate cycle, whereupon it would be reverted to 0.00161. In any case the enrichment of siblings amongst amino-acid pairs sharing the same first two bases appears strongly nonrandom, and provides further evidence against a chance origin of the correlation between amino-acid biosynthesis and codon distribution.

The rest of the paper can be read in full by downloading the PDF from here.

Moving on, let's look at the Copley et al paper, which can be downloaded from here. This opens as follows:

The genetic code has certain regularities that have resisted mechanistic interpretation. These include strong correlations between the first base of codons and the precursor from which the encoded amino acid is synthesized and between the second base of codons and the hydrophobicity of the encoded amino acid. These regularities are even more striking in a projection of the modern code onto a simpler code consisting of doublet codons encoding a set of simple amino acids. These regularities can be explained if, before the emergence of macromolecules, simple amino acids were synthesized in covalent complexes of dinucleotides with α-keto acids originating from the reductive tricarboxylic acid cycle or reductive acetate pathway. The bases and phosphates of the dinucleotide are proposed to have enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution.

The authors continue thus:

The genetic code has many regularities (1), of which only a subset have explanations in terms of tRNA function (2) or robustness against deleterious effects of mutation (3, 4) or errors in translation (3, 5). There is a strong correlation between the first bases of codons and the biosynthetic pathways of the amino acids they encode (1, 6). Codons beginning with C, A, and U encode amino acids synthesized from α-ketoglutarate (α-KG), oxaloacetate (OAA), and pyruvate, respectively. These correlations are especially striking in light of the structural diversity of amino acids whose codons share a first base. For example, codons for Glu and Pro both begin with C, and those for Cys and Leu begin with U. Codons beginning with G encode amino acids that can be formed by direct reductive amination of a simple α-keto acid. These include glycine, alanine, aspartate, and glutamate, which can be formed by reductive amination of glyoxalate, pyruvate, OAA, and α-KG, respectively. There is also a long-recognized relationship between the hydrophobicity of the amino acid and the second base of its codon (1). Codons having U as the second base are associated with the most hydrophobic amino acids, and those having A as the second base are associated with the most hydrophilic amino acids.

We suggest that both correlations can be explained if, before the emergence of macromolecules, simple amino acids were synthesized from α-keto acid precursors covalently attached to dinucleotides that catalyzed the reactions required to synthesize specific amino acids (see Fig. 1). This is a significant departure from previous theories attempting to explain the regularities in the genetic code (3). The ‘‘stereochemical’’ hypothesis suggests that binding interactions between amino acids and their codons or anticodons dictated the structure of the genetic code (7–10). The ‘‘coevolution’’ hypothesis (6) suggests that the original genetic code specified a small number of simple amino acids, and that, as more complex amino acids were synthesized from these precursors, some codons that initially encoded a precursor were ceded to its more complex products. Finally, the genetic code has been proposed to be simply a ‘‘frozen accident’’ (11).

Recent analysis suggests that the reductive tricarboxylic acid cycle could serve as a network-autocatalytic self-sufficient source for simple α-keto acids, including glyoxalate, pyruvate, OAA, and α-KG, as well as the carbon backbones of sugars and nucleobases (12). α-Keto acids can also be generated from the reductive acetyl CoA pathway (13). Most simple amino acids can be reached from an α-keto acid precursor by a small number of relatively simple chemical transformations, and the synthetic pathway that will be followed is determined within the first three steps. We propose that the positions of functional groups in a dinucleotide–[chr]945[/chr]-keto acid complex determine what reactions can be effectively catalyzed for a given α-keto acid. An example of a series of reactions leading from α-KG to five amino acids, each attached to the first two bases of its codon, is shown in Fig. 2, which can be regarded as a ‘‘decision tree’’ in which the nature of the bases in the dinucleotide determines which types of reactions occur. The pathways proposed follow closely those in extant organisms (14), differing primarily in the timing of the reductive amination leading to the final amino acid. The motivation for this approach is that modern biosynthetic pathways likely emerged by gradual acquisition of enzymes capable of catalyzing reactions that had previously occurred in the absence of macromolecular catalysts. Thus, modern pathways are ‘‘metabolic fossils’’ that provide insight into prebiotic synthetic pathways, although some refinements and permutations are expected to have occurred.

Once again, I'll let everyone read the full paper at leisure, as it's a fairly large and complex one. :)

Moving on, we have the Vetsigian et al paper, which is downloadable from here. This paper opens as follows:

A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early communal life generically lead to refinement and selection of innovation-sharing protocols, such as the genetic code. Our proposal is illustrated by using a simplified computer model and placed within the context of a sequence of transitions that early life may have made, before the
emergence of vertical descent.

The authors continue with:

The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving.

There would seem to be four reasons for this paradoxical situation, all of which reflect the reductionist molecular perspective that so shaped biological thought throughout the 20th century. First, the basic explanation of gene expression appears to lie in its evolution, and not primarily in the specific structural or stereochemical considerations that are sufficient to account for gene replication. Second, the problem’s motto, ‘‘genetic code,’’ is a misnomer that makes the codon table the defining issue of gene expression. A satisfactory level of understanding of the gene should provide a unifying account of replication and expression as two sides of the same coin. The genetic code is merely the linkage between these two facets. Thus, and thirdly, the assumption that the code and the decoding mechanism are separate problems, individually solvable, is a reductionist fallacy that serves to deny the fundamental biological nature of the problem. Finally, the evolutionary dynamic that gave rise to translation is undoubtedly non-Darwinian, to most an unthinkable notion that we now need to entertain seriously. These four considerations structure the approach we take in this article.

To this point in time, biologists have seen the universality of the code as either a manifestation of the Doctrine of Common Descent or simply as a ‘‘frozen accident.’’ Viewing universality as following from common descent renders unthinkable the notion explored here that a universal code may be a necessary precondition for common ancestry, indeed even for life as we know it.We will argue in this article [a maturation of the earlier concept of the progenote (1)] that the very fact of the code’s evolvability, together with the details of its internal structure, provides strong clues to the nature of early life, and in particular its essential communal character (2).

Beyond the code’s universality we have very few clues to guide us in trying to understand its evolution and that of the underlying decoding mechanism. The principal ones again are properties of the code itself; specifically, the obvious structure of the codon table. The table possesses (at least) two types of order: synonymorder and relatedness order. The first is the relatedness of codons assigned to the same amino acid; the second is the relatedness of codons assigned to related amino acids. Relatedness among the amino acids is context-dependent and in the context of the codon table could a priori reflect almost anything about the amino acids: their various properties, either individually or in combination; the several macromolecular contexts in which they are found, such as protein structure, the translation mechanism, and the evolution of translation; or the pretranslational context of the so-called RNA world. Although we do not know what defines amino acid ‘‘similarity’’ in the case of the code, we do know one particular amino acid measure that seems to express it quite remarkably in the coding context. That measure is amino acid polar requirement (3–5). Although the relatedness order of the code is marginally evident from simple inspection of the codon table (3, 4, 6–8), it is pronounced when the amino acids are represented by their respective polar requirements (4).

A major advance was provided by computer simulation studies (9–14) of the relatedness ordering of the amino acids over the codon table, which showed that the code is indeed relationally ordered and moreover is optimized to near the maximum extent possible. Compared with randomly generated codes, the canonical code is ‘‘one in amillion’’ when the relatedness measure is the polar requirement. No other amino acid measure is known to possess this characteristic (14) (in our opinion, the significance of this observation has not been adequately recognized or pursued). These precisely defined relatedness constraints in the codon table were unexpected and still cry out for explanation.

As far as interpretation goes, the optimal aspect of the genetic code is surely a reflection of the last aspect of the coding problem that needs to be brought into consideration: namely, the precision or biological specificity with which translation functions. Precision, along with every aspect of the genetic code, needs to be understood as part of an evolutionary process. We would contend that at early stages in cellular evolution, ambiguous translation was tolerated (there being no alternative) and was an important and essential part of the evolutionary dynamic (see below). What we imply by ambiguity here is inherent in the concept of group codon assignments, where a group of related codons is assigned as a whole to a corresponding group of related amino acids (3). From this flows the concept of a ‘‘statistical protein,’’ wherein a given gene can be translated not into a unique protein but instead into a family of related protein sequences. Note that we do not say that these are an approximation to a perfect translation of the gene, thereby implying that these sequences are in some sense erroneous. Early life did not require a refined level of tolerance, and so there was no need for a perfect translation. Ambiguity is therefore not the same thing as ‘‘error.’’

I'll break off from here, because this paper is very heavy with respect to mathematical content, and some of the relevant expressions are extremely difficult to render in board tags. However, this paper should prove interesting to read.

Next, we have the Lehmann et al paper, which can be downloaded from here. This opens as follows:

AbstractThe origin of the genetic code in the context of an RNA world is a major problem in the field of biophysical chemistry. In this paper, we describe how the polymerization of amino acids along RNA templates can be affected by the properties of both molecules. Considering a system without enzymes, in which the tRNAs (the translation adaptors) are not loaded selectively with amino acids, we show that an elementary translation governed by a Michaelis-Menten type of kinetics can follow different polymerization regimes: random polymerization, homopolymerization and coded polymerization. The regime under which the system is running is set by the relative concentrations of the amino acids and the kinetic constants involved. We point out that the coding regime can naturally occur under prebiotic conditions. It generates partially coded proteins through a mechanism which is remarkably robust against non-specific interactions (mismatches) between the adaptors and the RNA template. Features of the genetic code support the existence of this early translation system.

The authors continue with:

Introduction

A major issue about the origin of the genetic system is to understand how coding rules were generated before the appearance of a family of coded enzymes, the aminoacyl-tRNA synthetases. Each of these ~20 different enzymes has a binding pocket specific for one of the 20 encoded amino acids, and also displays an affinity for a particular tRNA, the adaptor for translation [Fig. 1(a)]. These adaptors are characterized by their anticodons, a triplet of base located on a loop. The synthetases establish the code by attaching specific amino acids onto the 39 ends of their corresponding tRNAs, a two-step process called aminoacylation [1]. The first step (activation) involves an ATP, and leads to the formation of a highly reactive intermediate, aa–AMP (aa= amino acid). The second step consists of the transfer of the amino acid from AMP onto the 39 end of the tRNA. Those tRNAs can subsequently participate in the translation of RNA templates, during which codons about to be translated are tested by the anticodons of incoming tRNAs. When anticodon-codon complementarity occurs, an amino acid is added onto the nascent protein through the formation of a new peptide bond [2].

How could a translation system operate in the absence of the synthetases? Recent works have shown that particular RNA stemloops of ~25 bases can self-catalyze the covalent binding of amino acids onto their own 39 ends [3,4]. These RNAs however require aa–AMP as a substrate because they cannot manage the activation step in their present form. In addition, they show little specificity for the amino acids, raising the question of how a code could be generated by them. Some answers will likely be provided by the activation step if possible to implement on these small RNAs. This issue is not examined in the present paper.

Based on an earlier investigation [5], the present analysis shows that the translation process itself can contribute to the establishment of coding rules. Consider an elementary translation system constituted by RNA templates made up of two types of codons {I, II}, tRNAs with anticodons complementary to these codons, and two types of amino acids {1, 2}. Suppose that the tRNAs are not selectively loaded with amino acids (i.e. the rates of loading only depend on the relative concentrations of the amino acids). Our analysis shows that it is possible to observe a coded polymerization. We calculate the probability of codon I being translated by amino acid 1 and the probability of codon II being translated by amino acid 2, the coding regime occurring when both probabilities are simultaneously higher than 0.5. These probabilities are functions of the anticodon-codon association and dissociation rate constants, the amino acids concentrations and their respective kinetic constants of peptide bond formation. One general configuration allows a coding regime to occur: the amino acid with the slow kinetics (i.e. the ‘‘slow’’ amino acid) is more concentrated in solution than the ‘‘fast’’ amino acid. Given two appropriate codons, the competition for the translation of the codon dissociating quickly from its cognate tRNA (i.e. the ‘‘weak’’ codon) is won by the fast amino acid. As for the ‘‘strong’’ codon, for which the amino acid kinetics are equal or higher than the anticodon-codon dissociation rate constant, the higher concentration of the slow amino acid makes it a better competitor in that case. Although other types of polymerization are possible, we show that this coding regime is favored under prebiotic conditions. It is furthermore remarkably robust against anticodon-codon mismatches. We conclude our analysis by showing that this model can naturally be implemented by a system of four codons and four amino acids thought to be a plausible original genetic code.

Next, we have the Brooks et al paper, which can be downloaded in full from here. The authors begin with:

To understand more fully how amino acid composition of proteins has changed over the course of evolution, a method has been developed for estimating the composition of proteins in an ancestral genome. Estimates are based upon the composition of conserved residues in descendant sequences and empirical knowledge of the relative probability of conservation of various amino acids. Simulations are used to model and correct for errors in the estimates. The method was used to infer the amino acid composition of a large protein set in the Last Universal Ancestor (LUA) of all extant species. Relative to the modern protein set, LUA proteins were found to be generally richer in those amino acids that are believed to have been most abundant in the prebiotic environment and poorer in those amino acids that are believed to have been unavailable or scarce. It is proposed that the inferred amino acid composition of proteins in the LUA probably reflects historical events in the establishment of the genetic code.

I'll move quickly on, and cover in slightly more detail the Novozhilov et al (2007) paper, which opens as follows:

Abstract

Background: The standard genetic code table has a distinctly non-random structure, with similar amino acids often encoded by codons series that differ by a single nucleotide substitution, typically, in the third or the first position of the codon. It has been repeatedly argued that this structure of the code results from selective optimization for robustness to translation errors such that translational misreading has the minimal adverse effect. Indeed, it has been shown in several studies that the standard code is more robust than a substantial majority of random codes. However, it remains unclear how much evolution the standard code underwent, what is the level of optimization, and what is the likely starting point.

Results: We explored possible evolutionary trajectories of the genetic code within a limited domain of the vast space of possible codes. Only those codes were analyzed for robustness to translation error that possess the same block structure and the same degree of degeneracy as the standard code. This choice of a small part of the vast space of possible codes is based on the notion that the block structure of the standard code is a consequence of the structure of the complex between the cognate tRNA and the codon in mRNA where the third base of the codon plays a minimum role as a specificity determinant. Within this part of the fitness landscape, a simple evolutionary algorithm, with elementary evolutionary steps comprising swaps of four-codon or two-codon series, was employed to investigate the optimization of codes for the maximum attainable robustness. The properties of the standard code were compared to the properties of four sets of codes, namely, purely random codes, random codes that are more robust than the standard code, and two sets of codes that resulted from optimization of the first two sets. The comparison of these sets of codes with the standard code and its locally optimized version showed that, on average, optimization of random codes yielded evolutionary trajectories that converged at the same level of robustness to translation errors as the optimization path of the standard code; however, the standard code required considerably fewer steps to reach that level than an average random code. When evolution starts from random codes whose fitness is comparable to that of the standard code, they typically reach much higher level of optimization than the standard code, i.e., the standard code is much closer to its local minimum (fitness peak) than most of the random codes with similar levels of robustness. Thus, the standard genetic code appears to be a point on an evolutionary trajectory from a random point (code) about half the way to the summit of the local peak. The fitness landscape of code evolution appears to be extremely rugged, containing numerous peaks with a broad distribution of heights, and the standard code is relatively unremarkable, being located on the slope of a moderate-height peak.

Conclusion: The standard code appears to be the result of partial optimization of a random code for robustness to errors of translation. The reason the code is not fully optimized could be the trade-off between the beneficial effect of increasing robustness to translation errors and the deleterious effect of codon series reassignment that becomes increasingly severe with growing complexity of the evolving system. Thus, evolution of the code can be represented as a combination of adaptation and frozen accident.

Again, this paper involves some heavy mathematics, and a rather involved computer simulation, so I'll jump straight to the discussion and conclusion:

Discussion and Conclusion

In this work, we examined possible evolutionary paths of the genetic code within a restricted domain of the vast parameter space that is, in principle, available for a mapping of 20 amino acids over 64 nucleotide triplets. Specifically, we examined only those codes that possess the same block structure and the same degree of degeneracy as the standard code. It should be noticed, however, that this choice of a small part of the overall, vast code space for further analysis is far from being arbitrary. Indeed, the block structure of the standard code appears to be a direct consequence of the structure of the complex between the cognate tRNA and the codon in mRNA where the third base of the codon plays a minimum role as a specificity determinant. Within this limited – and, presumably, elevated – part of the fitness landscape, we implemented a very simple evolutionary algorithm by taking as an elementary evolutionary step a swap of four-codon or two-codon series. Of course, one has to realize that the model of code's evolution considered here is not necessarily realistic and, technically, should be viewed as a "toy" model. It is conceivable that codon series swaps were not permissible at the stage in the code's evolution when all 20 amino acids have been already recruited. Nevertheless, we believe that the idealized scheme examined here allows for meaningful comparison between the standard code and various classes of random codes.

The evolution of the standard code was compared to the evolution of four sets of codes, namely, purely random codes (r), random codes with robustness greater than that of the standard code (R), and two sets of codes that resulted from optimization of the first two sets (o and O, respectively). With the above caveats, the comparison of these sets of codes with the standard code and its locally optimized version yielded several salient observations that held for both measures of amino acid replacements (the PRS and the Gilis matrix) that we employed.

1. The code fitness landscape is extremely rugged such that almost any random initial point (code) tends to its own local optimum (fitness peak).

2. The standard genetic code shows a level of optimization for robustness to errors of translation that can be achieved easily and exceeded by minimization procedure starting from almost any random code.

3. On average, optimization of random codes yielded evolutionary trajectories that converged at the same level of robustness as the optimization path of the standard code; however, the standard code required considerably fewer steps to reach that level than an average random code.

4. When evolutionary trajectories start from random codes whose fitness is comparable to the fitness of the standard code, they typically reach much higher level of optimization than that achieved by optimization of the standard code as an initial condition, and the same holds true for the minimization percentage. Thus, the standard code is much closer to its local minimum (fitness peak) than most of the random codes with similar levels of robustness (Fig. 9).

5. Principal component analysis of the between amino acids distance vectors indicates that the standard code is very different from the sets r (all random codes) and O (highly optimized codes produced by error cost minimization for random codes that are better than the standard code), and more similar to the codes from o (optimized random codes) and R (the robust subset of random codes). More importantly, the optimized code produced by minimization of the standard code is much closer to the set of optimized random codes (o) than to any other of the analyzed sets of codes.

6. In this fitness landscape, it takes only 15–30 evolutionary steps (codon series swaps) for a typical code to reach the nearest local peak. Notably, the average number of steps that are required for a random code to reach the peak minus the number of steps necessary for the standard code to reach its own peak takes a random code to the same level of robustness as that of the standard code.

Putting all these observations together, we conclude that, in the fitness landscape explored here, the standard genetic code appears to be a point on an evolutionary trajectory from a random point (code) about half the way to the summit of the local peak. Moreover, this peak appears to be rather mediocre, with a huge number of taller peaks existing in the landscape. Of course, it is not known how the code actually evolved but it does seem likely that swapping of codon series was one of the processes involved, at least, at a relatively late stage of code's evolution, when all 20 amino acids have already been recruited. If so, perhaps, the most remarkable thing that we learned, from these modeling exercises, about the standard genetic code is that the null hypothesis on code evolution, namely, that it is a partially optimized random code, could not be rejected. Why did the code's evolution stop where is stopped, i.e., in the middle of the slope of a local fitness peak (Fig. 9), rather than taking it all the way to the summit, especially, as the number of steps required to get there is relatively small? It appears reasonable to view the evolution of the code as a balance of two forces, the positive selection for increasing robustness to errors of translation and the negative selection against any change, i.e., the drive to "freeze an accident". Indeed, codon series swapping is, obviously, a "macromutation" that simultaneously affects all proteins in an organism and would have a deleterious effect that would become increasingly more severe as the complexity of the evolving system increases. This is why, in all likelihood, no such events occurred during advanced stages of life's evolution, i.e., after the cellular organization was established. Conceivably, such an advanced stage in the evolution of life forms was reached before the code reached its local fitness peak, in support of a scenario of code evolution that combines selection for translational robustness with Crick's frozen accident.

Needless to say, the rest of the papers in my above list are freely downloadable via Google Scholar, and also contain much of interest to the serious student of this topic.

Moving on ...

It would be like tossing up all the scrabble prieces in the air and in the fallen mess there reads some distinct and meaningful message. These are not interpretations from theists but by the science community as a whole.

See the above peer reviewed papers and weep.

Nowhere in the natural world do we see information!

Poppycock. See my above dissertation on the subject.

The ONLY time information exists is because there is a mind behind it.

Poppycock. See my exposition above.

DNA alone by default should clue us in to the fact that there is very good probable cause for a creator.

Poppycock. See the above.

2. Nature is made up entirely of mathematical properties and the universe is extremely FinED tuned.

Poppycock. Fine tuning is a myth. We are here because the laws of physics permitted our emergence, and the relevant physically permitted interactions took place. All you're doing here is regurgitating the fallacy known as Douglas Adams' Puddle.

Even the famous cosmologist and atheist Lawrence Krause compared the Fine tuning of the universe to that of a pencil balancing on its tip... for billions of years.

Why do I smell a quote mine at this point?

He went on to explain that our universe is constantly on the brink of collapse because of the extreme precision of all its properties. Almost as though some entity or property is balancing it?

Again, citation?

3. Quantum physics shows us that reality is made up of tiny pixels. At our most sub atomic level we are made up of pixels and empty space similar to *cough computer simulation cough* quantum physics also reveals that our reality is in a constant state of possible realities (double split experiment) and that only through observation do our realities manifest. In other words, if no one is in a room, the room exists in a state of potentials. similarly in video games When your character is not on a certain part of the game, that part of the map is currently in a state of non existence.

Drivel. You obviously haven't the faintest idea what quantum physics actually states on this matter. Namely, that a wavefunction is in a superposition of states until it interacts with another wavefunction. That other wavefunction can be associated with something as simple as a photon.

4. Irreducibly complex cells.

Oh, you're not going to peddle Michael Behe's garbage, are you?

If you haven’t, please research this.

I have, and I'm about to tell you why it's garbage. That's because "irreducible complexity" was actually first described way back in 1918, by an evolutionary biologist, namely Hermann Joseph Müller. Müller alighted upon the concept sixty years before Behe was born, and his deliberations on this phenomenon were published in a scientific paper in 1918. I've cited this paper repeatedly in past posts whenever this topic as arisen, but, for your benefit, I'll provide not only the citation, but the relevant quote. The paper in question is:

Genetic Variability, Twin Hybrids and Constant hybrids in a Case of Balanced Lethal Factors by Hermann Joseph Müller, Genetics, 3(5): 422-499 (1918) [Original paper downloadable in full from here]

I shall quote directly from that paper for your convenience, highlighting the relevant parts in blue (bottom of page 464 to top of page 465 in original paper):

Most present-day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect upon which it produced upon the 'reaction system' that had been brought into being by the many previously formed factors in cooperation; thus, a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent upon the former. It must result, in consequence, that a dropping out of, or even a slight change in any one of these parts is very likely to disturb fatally the whole machinery.

In other words, "irreducible complexity" was arrived at by Müller before Behe was born and was posited by Müller not as a problem for evolution, but as a natural outcome of evolutionary processes. The so-called "Müllerian Two Step" is summarised succinctly as follows:

[1] Add a component;

[2] Make it necessary.

This was placed upon a rigorous footing by Müller himself, along with others such as Fisher, by the 1930s, and so Behe didn't even find a gap for his purported god to fit into. Biologists have known that Behe's "irreducible complexity" nonsense has been precisely that - nonsense - for a minimum of six decades. Indeed, the community of evolutionary biologists have a term to describe the Müllerian Two Step in more formal language, namely 'bricolage'.

If you are thinking that this has already been debunked, it has not.

Wrong. See above.

Sure biologists have found the components of the flagellum elsewhere in the cell but they have not in no way addressed the real issue here.

Yes they have. Müller solved the problem sixty years before Behe was born.

I can explain this further upon request. I do believe irreducibly complex cells evolved, but not without intention.

Poppycock. See above. Oh, and I have a wealth of other scientific papers destroying Behe's canards that I can bring to the table here.

5.Nobel prize winner Barbara McClintock conducted an experiment which showed cells actively taking initiative to heal themselves. After damaging only a part of a cell she was able to see the cell “make decisions” and “figure out” how to fix the damage area. Additionally there are many examples of cells interacting and behaving in such a way that suggests autonomy, As if they have a mind of their own. Cells often communicate, exchNge information, solve problems and innovate solutions. These behaviors indicate more than simple reactions but are examples of cells taking free willed action.

Cock. You do realise there's a voluminous literature on cell signalling, and the evolution of the requisite signalling molecules? I'm aware of papers in the literature covering the bmp proteins, the wnt proteins, the fgf family, dlx2, and numerous others. None of which are sentient.

Oh, by the way, you are aware that none other than Alan Turing devised a mechanism for tissue morphogenesis that didn't need a magic man, way back in 1952? Which has since been found to be in operation in a wide range of systems, including butterfly wings? I have at least two dozen papers covering the application of Turing morphogenesis to butterfly wings alone.

Your ignorance and incredulity doesn't validate an imaginary magic man. Go and learn some fucking science.

Old man shouts at clouds's picture
@ Calli

@ Calli

Please let me marry your mind...stole all this post. I fucking love your brain.

Jordan's picture
@old man shouts

@old man shouts

She copied and pasted other people’s work which now you are going to do,nice job

Old man shouts at clouds's picture
@ Jordan

@ Jordan

Are you accusing Calli of plagiarism?

Calilasseia's picture
Bit difficult to substantiate

Bit difficult to substantiate that charge when I explicitly state citations for the work in question, and litter my posts with phrases such as "The authors then state the following" ... :D

I'm going to enjoy seeing that accusation crash and burn the same way his canards have done ...

Old man shouts at clouds's picture
@ Cali

@ Cali

Yeh I was soo hoping he would commit to that....but apparently he has enough brain cells left over after breathing that he can spot a trap...

Sheldon's picture
Jordan"She copied and pasted

Jordan"She copied and pasted other people’s work which now you are going to do,nice job"

He, not she, and he posted proper citations, but like all creatards you want to ignore objective evidence when it is demonstrated with hand waving, whilst ignoring all request you demonstrate objective evidence for your creation myths and religious superstition. try addressing the content of his post.

There is no objective evidence for any design or creation in nature.

Cognostic's picture
@Jordan:

@Jordan:
RE: Calilasseia.... OMG! Calilasseia is a plagiarizing bastard? Who would have thought? Not only that!!! Holy hell "HE" has had a sex change operation unbeknownst to all of us. OMG - my bubble has burst and I will never trust anyone again no matter how articulate or educated they appear to be. I can't type any more, I have to go find the tissue box......

Cognostic's picture
@Calilasseia: "You couldn

@Calilasseia: "You couldn't find a cartoon?" I am fairly certain you lost Jordan after the first sentence.

Jordan's picture
@calilasseia

@calilasseia

Thank you for the information I will definitely read up on this. I will say however, of coarse we can look at any given language and dissect it, it does not take away from the fact that it is a system of intelligent information. And to clarify I do belive in evolution I just have a suspicion that it is not all do to natural processes and random chance rather conditions were pre concieved for such life forms to unfold. I think it is counter intuitive for order to arise out of disorder and I don’t profess to believe in God no matter what and with all my night, I just wanted to open up discussion.

Talyyn's picture
@Jordan Of course...

@Jordan

Of course...

Nyarlathotep's picture
Jordan - Quantum physics

Jordan - Quantum physics shows us that reality is made up of tiny pixels.

Nyarlathotep - I guess I missed that day of class. Can you tell us if magnetic moment of an electron is normal to the plane of the pixel, and if so is it with a right or left handed rule? I won't hold my breath.

I'm serious. How do you generate the magnetic moment (3 dimensional vector) of a "pixel" (2 dimensional) electron?

Talyyn's picture
@Nyarlathotep

@Nyarlathotep

Maybe he think about quantization of space-time like in quantum-loop theory? Not that it helps...

Nyarlathotep's picture
I guess she isn't going to

I guess she isn't going to tell us.

rat spit's picture
I like how a generation of

I like how a generation of children who grew up knowing nothing about a world prior to computers and “The Matrix” trilogy always seem to think that existence is a computer program.

A little bit like how the ancients (Moses, maybe?) concluded that man must have been made out of mud (and women from one of his ribs).

Jordon; I think you’re kind of a jack of all trades, you know? Master of none? You know?

Pick a trade; pick a science; and learn it. It’s like spreading things to thin. Would you rather have a piece of bread with A LOT of jam on it; or just a thin layer? So thin, all you can taste is the bread?

By the way - I’m a believer. My advice. Do more drugs. Hallucinogens. Do A LOT of hallucinogens and smoke A LOT of crack. Steal from old ladies to support your habit. AND THEN God will literally pop His mighty head out of the wood work - and you will hear His voice.

If you’ve got anything less than a personal relationship with God, you’re basically just speculating.

As I said; SMOKE CRACK AND STEAL FROM SENIOR CITIZENS TO SUPPORT YOUR CRACK HABIT!!!

Then you will know the truth and the truth will set you apart from the majority of other people.

rat spit's picture
But seriously - you’re

But seriously - you’re getting ripped apart by people here who are experts in their fields. Physicists, Historians, Biologists - they’re all hanging out here ready to tear your pithy speculations to pieces. And then you have Sheldon. Now Sheldon just has a really (I mean seriously) LARGE PENIS. And that obviously makes him intimidating. So watch out for him. He’ll steal your girl if you’re not careful.

But a guy like you - if you’re going to devote time and money into anything, study Buddhism. It’s kind of a religion that’s says “Okay. So maybe there is a God. So what? What about happiness? What about freedom from mental and physical pain and suffering?”

There’s a shit tonne of knowledge in the Buddhist scriptures.

https://www.accesstoinsight.org/

https://suttacentral.net/

Start with the Majjhima nikayas.

What am I an expert at? I’m a nut case. I talk to the OverLord (who is kinda kinda not like “God). And I talk to the Evil One - who is the OverLord’s mouth piece to the human species.

A word to the wise. As you age questions about God’s existence become replaced with “why am I so depressed?” “Why can’t I find the will to get up in the morning and go to work?” “Fuck this shit, I’m checking out!” - ya know?

If you let shitty thoughts overwhelm you, you might just get depressed, give up, or (worst case scenario) check your self out at the door.

We all have to develop coping devices. I’ve derived a lot of faith and inspiration in and from Buddhism. And I have to cope with directly knowing the highest, most Supreme Being in the Universe.

Do you think that’s easy. I’m like a cock roach to him. Like a pesky rat. He’s constantly pissed off that His omniscience includes the sound of my thoughts. But what am I going to do? Check out? Fuck that.

So I develop meditation and I enter states of calm and happiness. And then I go about living my life.

Another word to the wise. Figure out how you want to make a living in life BEFORE you go ahead and get a degree in RELIGIOUS FUCKING STUDIES. You know? That shit don’t pay.

What does pay? Law Enforcement. Truck driving. Manual labour.

What else doesn’t? A degree in math. A degree in philosophy.

Of course if you’re already hooked up with cash and connections because your parents are wealthy - well; that’s not who I’m referring to.

Anyway. Take away message. If you’re going to study something in your spare time, study Buddhism.

- rat spit

Cognostic's picture
Rat Spit: Before you get

@Rat Spit: Before you get into Buddhism - Take a look a J. Krishnamurti's interactions with Buddhists.
(This is a fantastic little clip if you can apply it to buddhist teaching.)

Paraphrased:
JK: "Buddhists cripple themselves with knowledge. Can a mind perceive what is truth? Or must it be free from knowledge? "
Buddist: To perceive truth the mind must be free from all knowledge. (Presuppositions influence the perception of knowledge)
JK: "So... why should one accumulate knowledge (Buddhist Teachings - 8 fold path - Three universal truths -etc...) and then abandon it, and then seek truth?

An old Buddhist saying, I do not recall by whom. "If you meet the Buddha on the road, kill him." Everything you need to know about Buddhism is contained in this expression.

NOTICE THIS INTERPRETATION AND COMPARE IT TO THE MESSAGE OF JK above.
"Once you stand nose to nose with the Buddha (YOU BECOME A BUDDHA YOURSELF) (you "meet him on the road") then you have no more to learn from the Buddha. ****At that point, holding on to those teachings becomes a crutch.****** an identity. *****No teaching is meant to be held onto.****** (IF YOU CAN SAY "I AM A BUDDHIST" YOU KNOW NOT WHAT IS BEING TAUGHT.) They are meant to provide an experience for where you are at in the moment. Hear the same thing later, and it will provide a new meaning, and a new experience." (YOU CAN NOT PUT THE SAME FINGER IN THE SAME RIVER TWICE.)

All mystics are con-men. There is no reason to "LEARN" Buddhism. There is just being here and now. (PD Ouspenski, The Fourth Way.)

rat spit's picture
I’m not a Buddhist. In order

I’m not a Buddhist. In order to “be” a Buddhist you must ordain as a monk or take the 5 precepts as a layman. Even if I took the five precepts in a private manner, I would still not be a Buddhist.

Above all I admire the life of the Buddha and find the amount of scripture attributed to him amazing in both quantity and quality (especially where contradictions are concerned - ie. there are few contradictions in the Tripitaka).

You can evaluate all the historical figures throughout time - Socrates, Aristotle, Andre the Giant; IMO no one sacrificed as much as did Gautama; nor did anyone attain as much.

Jesus’ ministry lasted, what? Two years?

I’ve conversed with a lot of historical figures. None were as compassionate and as enigmatic as Gautama. And funny as Hell. Almost as funny as the Evil One.

Even if his doctrine is antiquated from a practical point of view, it is still interesting from a historical point of view.

And there’s a lot more there to gain than any treatment of Western Philosophy.

Cognostic's picture
@RatSpit: The Life of the

@RatSpit: The Life of the Buddha? Might you possibly mean the "Myth of the Buddha." What do you imagine is actually known about the Buddha? The Buddha himself wrote nothing. Buddhism was a pre-oral tradition and anything attributed to him was written by followers centuries after the fact, just as with Muhammad and his Quaran or Jesus and the New Testament.

Like Jesus there are several amazing magical birth stories for the Buddha, which place him clearly in the realm of fantasy. Yes, there might have been a revered teacher at one point in history, but he was no more the Buddha than Jesus is Jesus or Muhammad is Muhammad. It is all made up BS.

*I find many useful things in some Buddhist thought. Like Christianity or Islam, Buddhism comes in many flavors. Zen has been my choice though I am currently surrounded by the Korean mythology. Japanese have different names for the same monks that Koreans ascribe stories to and of course the Japanese enlightened monks are all Japanese while the Korean enlightened monks are all Korean - "Lucky for us, some of the basic stories remain the same."

Zen stories or Buddhist stories, like Aesop's fables are designed to point to the very nature of the human mind and get us to look at ourselves here and now. This is the one good thing Buddhist thought (Not The Buddha) has going for it.

RE: "to “be” a Buddhist you must ordain as a monk or take the 5 precepts as a layman."
If anyone has told you this, that person is a liar and a con man. If an organization has told you this, they are seeking recruits. If you call yourself a Buddhist, you are not a Buddhist. You do not understand the meaning of the word.

There is a story about a young man who was listening to a Buddhist monk talk in the town square. When the monk had finished his talk, the young man went to him and asked if he could become a Buddhist. The monk looked at him with delight in his eyes. "Yes" said the monk. "Meet me here in the morning at sunup and I will gather the other monks and you can recite the 5 precepts. We will have a conversion ceremony." The young man ran away happy because he was going to be a Buddhist.

The next morning he woke early and raced to the town square where the Buddhist had been. He waited and waited and waited. He waited until the sun was high in the sky. And then he became a Buddhist.

There are schools of thought that have ceremonies rituals and all the trappings of any religion. Avoid them.

Terraphon's picture
This whole thing is just one

This whole thing is just one big, long, boring, poorly constructed teleological argument.

PROTIP - Teleological arguments have been debunked over...and over...and over...and over...and over. I'd venture to say the various teleological arguments have been debunked more times than there are words in this whole, long, boring, poorly constructed teleological argument.

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