Evolution is well established and accepted by the scientific community, but the door will always remain open to a better explanation. Once upon a time, Newton’s explanation of the universe was also considered immutable.
One facet of science is we never close doors.
I have an irrefutable theory. I can give you the perfect example. My theory is that Sorreentino will not be able to provide you with an all encompassing and irrefutable theory that has become established fact! I would even be willing to put money on it!
You really have no idea do you.
Science does not deal in irrefutable facts.Scientific theories (explantions of observed phenomena] Remain falsifiable. IE they may be proved in error or incomplete as more information is discovered. Simplest explanation I can think of is Newtonian and Einsteinian Physics.; Newton was not disproved by Einstein, only improved upon.
Pretty sure that’s not quite true. Evolution explains the facts of which we are aware, but it is neither perfect nor theoretically irrefutable.
The theory of evolution as posited by Darwin has flaws. I seem to remember reading many years ago that Darwin does not account for the development of flowering plants. That oversight has been rectified.That doesn’t mean that evolution was wrong,only incomplete.
Link below.I think I understand it, but am not sure.I post for more erudite minds to examine if they want.
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2838270/
A skeptic, I’m wary of absolute claims, which is what ‘irrefutable’ means. As I understand it, scientific proofs always have an implicit caveat: Based on available information.
Since you keep repeating this blatant lie, it’s time to break out the ordnance to demolish your bullshit. Given the post count limit enforced here, this will be a multi-part exposition.
However, before moving on to the heavy artillery, I’ll provide a brief exposition of the biological species concept, which is applicable here. The biological species concept is a population concept (as indeed are many other evolutionary concepts), and can be summarised as follows …
A population comprises a species, when:
[1] All members thereof (bar occasional mutants) are reproductively interfertile with other members of the population;
[2] All members thereof (again, bar occasional mutants), when mating, produce offspring that satisfy [1] above.
This provides the foundation for understanding speciation processes. I’ll describe a simple case thereof, while noting that more complex cases, such as ring species, also exist, which properly deserve their own complete post.
The simplest case of speciation occurs when the population undergoes a split for some reason, resulting in two new populations, both sharing the same ancestors, but between which gene flow has ceased. That split can arise as a result of the emergence of a physical barrier, or a behavioural barrier, and instances of both are documented in the relevant literature (more on this later). Once that barrier exists, and gene flow between the two separated populations ceases, the populations start to diverge from each other genetically, and it’s possible for the astute to model this process by spending time writing the relevant code to simulate the process.
Among the genes that exhibit divergence in this respect, are the genes belonging to the Major Histocompatibility Complex family. These genes are responsible for such processes as the immune response, tissue typing, and compatibility of egg and sperm (the fertillin genes governing this last process are part of the MHC family), and these genes have been documented as undergoing mutational change at a rapid rate compared to many other organismal genes.
So, when a population is split into two, for whatever reason, the two populations begin diverging from each other, and that divergence encompasses the MHC gene family, including those all-important fertillin genes. The moment that divergence reaches the point where criterion [1] or [2] above fails to be met, a speciation event has occurred. While the fertillin genes are obvious candidates for this process, there exist other genes that are implicated in the speciation process, and have been documented in the literature as exerting the requisite effect.
Having provided a simple exposition of one operating mechanism (covering some of the others would require me to write a book exceeding 1,000 pages in length), it’s now time to look at the literature, which includes the following papers:
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, [b]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
Reproductive Isolation As A Consequence Of Adaptive Divergence In Drosophila pseudoobscura by Diane M. B. Dodd, Evolution, 43(6): 1308-1311 (September 1989) - DIRECT EXPERIMENTAL TEST OF ALLOPATRIC SPECIATION MECHANISMS, which, if continued for a sufficient period of time, will result in an observable speciation event
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
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
Part 1 ends here. Part 2 follows shortly.
Welcome to Part 2.
Now, it’s important to note that because speciation is a population phenomenon, the phenomenon doesn’t usually appear as a binary “all or nothing” process, but instead, takes place over multiple generations, with increasing instances of interfertility failure between populations over time, until the process becomes complete. Let us hypothesise that we have to hand, a population of organisms, along with the ability to capture complete genetic audits of that population and its descendants. At which point, we introduce a barrier between two subsets of that population, and continue compiling our genetic audits.
When a lineage A diverges into reproductively separated lineages, let’s call these A1 and A2 respectively, then the moment at which A1 and A2 are considered separate species, in accordance with the biological species concept, is the point where all members of lineage A1 become, in some future generation, reproductively incompatible with all members of lineage A2, and vice versa. This arises naturally from the biological species concept, which defines a species as a population within which reproductive compatibility is maintained, but which is reproductively incompatible with other lineages.
Of course, since any population of living organisms is a dynamic entity, as expounded above, this is not an “all or nothing” affair in the space of a single generation. The potentiating mutations driving speciation will appear in one (or possibly more than one) individuals first, and slowly spread through the population, until eventually, all individuals in that population possess those mutations, and reproductive incompatibility with other lineages, including lineages with which the lineage in question shares a common ancestor, will arise.
How long it takes for this to happen, however, is not yet quantitatively predictable. Depending upon many factors, such as the fecundity of the individuals in the population, the generational turnaround, the mutation rates of the genes in question, and how quickly those mutations become fixed in the population, speciation could take place in as little as five years (as happened with Dobzhansky’s laboratory population of Drosophila pseudoobscura, as documented in his 1971 paper), or could take as long as ten million years. Species with fast generational turnarounds and rapid mutation rates in the relevant genes will exhibit speciation events more quickly under relevant circumstances, than species with slow generational turnarounds and slow mutation rates. Unfortunately, we are not yet in a position to use this information in a quantitatively predictive manner, but we can use this in a qualitative manner, to predict that a genetically isolated lineage will eventually exhibit reproductive incompatibility. We will only find out that this has happened, however, when appropriate tests upon the populations in question demonstrate interfertility failure between relevant populations, and of course, with large populations, it will be impractical to test every possible combination of individuals. If you have two populations, each comprising a million individuals, then exhaustive testing would require 1012 trial matings. Sadly, we’re not yet in a position to try this out. In this sense, there is no well-defined point at which speciation occurs, because we lack the ability to perform massive numbers of trial matings to find that point. But that point does exist, as I’ve just explained.
In addition, if there are selective forces at work in the population in question, such as those arising from niche migration and trophic specialisation, or those arising from sexual selection, these forces will act to accelerate the speciation process. See the Lake Victoria Superflock of Cichlid fishes for an example of rapid speciation arising from both mechanisms.
Note however that in some instances thereof, the process is incomplete, as some species in that superflock, despite being defined taxonomically as different species, on the basis of anatomical differences, are still capable of producing fertile hybrids with other members of the same superflock, as Ole Seehausen documented in at least one of his papers, and indeed, as many aquarists have discovered when keeping these fishes in an aquarium. Indeed, the problem of a phenomenon called ‘hyperdominance’, which results in males of extremely aggressive, territorially demanding species, taking over the aquarium and mating with females of other species as well as their own, is a well-known and well-documented problem in the world of Rift Lake Cichlid keeping.
Anyway, let’s move on to what happens to our laboratory population, after the barrier is introduced. We begin taking snapshots of each generation, starting with Snapshot 1 for the first generation after the introduction of the barrier, and continue doing so for however many generations are required to observe the requisite effect. For the first, say, 300 or so generations, no interfertility failure is observed (tested for by appropriate experimental cross matings), while the requisite potentiating mutations are being acquired in each of the two populations. Then, data of the following sort appears in the genetic audit:
Snapshot 751: 1 individual out of 3,726,435 possesses the genes coding for interfertility failure with related populations
Snapshot 752: 3 individuals out of 3,727,201 possess the genes coding for interfertility failure with related populations
Snapshot 753: 9 individuals out of 3,726,974 possess the genes coding for interfertility failure with related populations
Snapshot 754: 17 individuals out of 3,727,032 possess the genes coding for interfertility failure with related populations
Snapshot 755: 30 individuals out of 3,726,883 possess the genes coding for interfertility failure with related populations
Snapshot 756: 47 individuals out of 3,727,265 possess the genes coding for interfertility failure with related populations
…
Snapshot 1,032: 2,788,015 individuals out of 3,727,354 possess the genes coding for interfertility failure with related populations
Snapshot 1,033: 3,113,282 individuals out of 3,726,558 possess the genes coding for interfertility failure with related populations
Snapshot 1,034: 3,305,188 individuals out of 3,727,220 possess the genes coding for interfertility failure with related populations
Snapshot 1,035: 3,497,185 individuals out of 3,726,298 possess the genes coding for interfertility failure with related populations
Snapshot 1,036: 3,592,407 individuals out of 3,726,504 possess the genes coding for interfertility failure with related populations
Snapshot 1,037: 3,664,803 individuals out of 3,726,901 possess the genes coding for interfertility failure with related populations
Snapshot 1,038: 3,709,592 individuals out of 3,726,448 possess the genes coding for interfertility failure with related populations
Snapshot 1,039: 3,747,662 individuals out of 3,727,108 possess the genes coding for interfertility failure with related populations
Snapshot 1,040: 3,726,992 individuals out of 3,727,888 possess the genes coding for interfertility failure with related populations
Snapshot 1,041: 3,727,143 individuals out of 3,727,143 possess the genes coding for interfertility failure with related populations
Snapshot 1,041, if it were possible to take it, would constitute the moment at which the population was genetically separated from surrounding populations of related organisms, to the point of constituting a completely separate species. Of course, we would have, in this hypothetical setup, a series of 10,41 snapshots, constituting perhaps a full genetic audit, beginning from the moment of isolation of the population at Snapshot 1, all the way through to Snapshot 1,041, where the population achieved complete interfertility failure with surrounding populations, including populations that shared a common ancestry.
Of course, the hypothetical data I’ve presented above are highly simplified, and my exposition assumes for simplicity, that the spread of the genes in question would be strictly increasing, whilst of course there is no reason for real world data to conform to this simple model. The actual plot of the numbers could be a curve with both local maxima and local minima (as defined precisely in mathematics), prior to the point at which the entire population possessed the genes in question, and all individuals in that population were no longer able to produce viable offspring with individuals outside the population in question. But of course, those of us who paid attention in class, know that the shape of the curve leading to the end result observed in Snapshot 1,041 above doesn’t in the least change the larger picture.
The issue isn’t that a snapshot such as my hypothetical Snapshot 1,041 could not exist in principle, rather that such a snapshot would be formidably difficult to produce in practice in a real world population. Not that this is regarded as a research obstacle from the standpoint of documenting speciation events. Any snapshot yielding data equivalent to that of the hypothetical Snapshot 1,041 above would be sufficient to document a completed speciation event, even if the actual spread of the genes had taken place some time earlier. We would know, from a rigorous standpoint, that the speciation event ran to completion at some antecedent time to the snapshot being taken in a real world scenario, but we would be unable to know that antecedent time with precision, courtesy of the practical issues I’ve discussed elsewhere.
Indeed, one of my favourite papers documents the first attempt by scientists to produce documentation of a speciation event in the wild, with something akin to the genetic audit trail given above, namely the paper on Cynotilapia afra, and the observed divergence of the two populations at Thumbi Island, those populations having been founded at a known date. Indeed, the Cichlid fish literature alone contains numerous papers, documenting attempts to produce data sets equivalent to the snapshots in my hypothetical example above, some of those papers being:
Adaptive Evolution And Explosive Speciation: The Cichlid Fish Model by Thomas D. Kocher, Nature Reviews: Genetics, 5: 288-298 (April 2004)
African Cichlid Fish: A Model System In Adaptive Radiation Research by Ole Seehausen, Proceedings of the Royal Society of London Part B, 273: 1987-1998 (9th May 2006)
Case Studies And Mathematical Models Of Ecological Speciation. 1. Cichlids In A Crater Lake by Sergey Gavrilets, Aaron Vose, Marta Barluenga, Walter Salzburger and Axel Meyer, Molecular Ecology, 16: 2893-2909 (22nd January 2007)
Cichlid Species Flocks Of The Past And Present by Axel Meyer, Heredity 95: 419-420 (20 July 2005)
Colour Vision And Speciation In Lake Victoria Cichlids Of The Genus Pundamilla by Karen L. Carleton, Juliet W. L. Parry, James K. Bowmaker, David M. Hunt and Ole Seehausen, Molecular Ecology, 14: 4341-4353 (4th August 2005)
Divergent Selection During Speciation Of Lake Malawi Cichlid Fishes Inferred From Parallel Radiations In Nuptial Colouration by Charlotte J. Allender, Ole Seehausen, Mairi E. Knight, George F. Turner and Norman MacLean, Proceedings of the National Academy of Sciences of the USA, [b]100(24): 14704-14079 (25th November 2003)
Divergent Selection On Opsins Drives Incipient Speciation In Lake Victoria Cichlids by Yohey Terai, Ole Seehausen, Takeshi Sasaki, Kazuhiko Takahashi, Shinji Mizoiri, Tohru Sugawara, Tetsu Sato, Masakatsu Watanabe, Nellie Konijnendijk, Hillary D. J. Mrosso, Hidenori Tachida, Hiroo Imai,
Yoshinori Shichida and Norihiro Okada, Public Library of Science Biology, 4(12): e433 (December 2006)
Evolutionary Conservation Of Microsatellite Flanking Regions And Their Use In Resolving The Phylogeny Of Cichlid Fishes (Pisces: Perciformes) by Rafael Zardoya, Dana M. Vollmer, Clark Craddock, Jeffrey T. Streelman, Steve Karl and Axel Meyer, Proceedings of the Royal Society of London Part B, 263: 1589-1598 (1996)
Frequency Dependent Natural Selection In The Handedness Of Scale Eating Cichlid Fish by Michio Hori, Science, 260: 216-219 (9th April 1993)
Genetic And Developmental Basis Of Cichlid Trophic Diversity by R. C. Albertson and T. D. Kocher, Heredity, 97: 211-221 (12th July 2006)
How Many Species Of Cichlid Fishes Are There In African Lakes? by George F. Turner, Ole Seehausen, Mairi E. Knight, Charlotte J. Allender and Rosanna L. Robinson, Molecular Ecology, 10: 793-806 (2001)
Hybridisation And Contemporary Evolution In An Introduced Cichlid Fish From Lake Malawi National Park by J. Todd Streelman, S.L. Gymrek, M.R. Kidd, C. Kidd, R.L. Robinson, E. Hert, A.J. Ambali and T.D. Kocher, Molecular Ecology, 13: 2471-2479 (21 April 2004)
Major Histocompatibility Complex Variation In Two Species Of Cichlid Fishes From Lake Malawi by Hideki Ono, Colm O’hUigin, Herbert Tichy and Jan Klein, Molecular and Evolutionary Biology, 10(5): 1060-1072 (1993)
Male-Male Competition And Nuptial-Colour Displacement As A Diversifying Force In Lake Victoria Cichlid Fishes by Ole Seehausen and Dolph Schluter, Proceedings of the Royal Society of London Part B, 271: 1345-1353 (2004)
Mechanisms Of Rapid Sympatric Speciation By Sex Revesral And Sexual Selection In Cichlid Fishes by Russell Lande, Ole Seehausen and Jacques J. M. van Alphen, Genetica, 112-113: 435-443 (2001)
Mitochondrial Phylogeny Of The Endemic Mouthbrooding Lineages Of Cichlid Fishes From Lake Tanganyika In Eastern Africa by Christian Sturmbauer and Axel Meyer, Journal of Molecular and Biological Evolution, 10(4): 751-768 (1993)
Molecular Phylgeny And Evidence For An Adaptive Radiation Of Geophagine Cichlids From South America (Perciformes: Labroidei) by Hernán López-Fernández, Rodney L. Honeycutt and Kirk O. Winemiller, Molecular Phylogenetics and Evolution, 34: 227-244 (2005)
Multi Agent Simulations Of Evolution And Speciation In Cichlid Fish by Ross Clement, Proceedings of the 15th European Simulation Symposium, 2003
Multilocus Phylogeny Of Cichlid Fishes (Pisces: Perciformes) : Evolutionary Comparison Of Microsatellite And Single-Copy Nuclear Loci by J. Todd Streelman, Rafael Zardoya, Axel Meyer and Stephen A Karl, Journal of Molecular and Biological Evolution, 15(7): 798-808 (1998)
Origin Of The Superflock Of Cichlid Fishes From Lake Victoria, East Africa by Erik Verheyen, Walter Salzburger, Jos Snoeks and Axel Meyer, Science, 300: 325-329 (11 April 2003) #
Phylogeny Of African Cichlid Fishes As Revealed By Molecular Markers by Werner E. Mayer, Herbert Tichy and Jan Klein., Heredity, 80: 702-714 (1998)
Sensory Drive In Cichlid Speciation by Martine E. Maan, Kees D. Hofker, Jacques J. M. van Alphen and Ole Seehausen, The American Naturalist, 167(6): 947-954 (June 2006)
Speciation Through Sensory Drive In Cichlid Fish by Ole Seehausen, Yohey Terai, Isabel S. Magalhaes, Karen L. Carleton, Hillary D. J. Mrosso, Ryutaro Miyagi, Inke van der Sluijs, Maria V. Schneider, Martine E. Maan, Hidenori Tachida, Hiroo Imai & Norihiro Okada, Nature, 455: 620-627 (2nd October 2008)
The Effect Of Male Colouration On Female Mate Choice In Closely Related Lake Victoria Cichlids (Haplochromis nyererei Complex) by Ole Seehausen and Jacques J. M. van Alphen, Behavioural Ecology & Sociobiology, 42: 1-8 (1998) *
The Effect Of Selection Upon A A Long-Wavelength Sensitive (LWS) Opsin Gene Of Lake Victoria Cichlid Fishes by Yohey Terai, Werner E. Mayer, Jan Klein, Herbert Tichy, and Norihiro Okada, Proceedings of the National Academy of Sciences of the USA, 99: 15501-15506 (November 2002)
The Evolution Of The Pro-Domain Of Bone Morphogenetic Protein 4 (Bmp4) In An Explosively Speciated Lineage Of East African Cichlid Fishes by Yohey Terai, Naoko Morikawa and Norihiro Okada, Molecular & Biological Evolution, 19(9): 1628-1632 (2002)
The Species Flocks Of East African Cichlid Fishes: Recent Advances In Molecular Phylogenetics And Population Genetics by Walter Salzburger and Axel Mayer, Naturwissenschaft, 91: 277-290 (20 April 2004)
The Streelman et al paper above on Cynotilapia afra is a particular case in point.
Part 2 ends here. Part 3 follows shortly.
Welcome to Part 3.
But, in order to ram home the fact that speciation has been observed (indeed, there are numerous such documented instances to my incomplete knowledge alone, and almost certainly several thousand in total in the literature), I’ll cover in detail one of the papers above, in which, wait for it, a speciation event was detected as having taken place in the wild, and then REPLICATED IN THE LABORATORY. The paper in question is:
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 here]
The authors continue with:
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.
Moving on …
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?
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 …
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?
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?
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.
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.
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. 
You know that feeling when you get in your driver’s seat, turn on the ignition, and pull out of your driveway - all the while being ignorant of how the transmission, or engine of your car works? Or is it the case for you, that your vehicle won’t operate unless you know where each and every nut and bolt is?
Your assertions are nonsense. If it were placebo effect, it would have stopped working at some point. As far as placebo effect goes, what we know if that mere belief of receiving a treatment is enough to act as a curative source for underlying conditions. As soon as your condition seems to worsen, the placebo effect wears thin (ie. a lack of faith in the treatment is a placebo in reverse).
I have no doubt in my mind that calming my heart down has a positive effect on my lower back inflammation. The fact that I’m not a scientist and can’t conduct a closed study of the phenomenon - nor the fact that other people who may be scientists have never heard of such if phenomenon is irrelevant.
The fact that it is repeated over and over and over again with the same effects is evidence of some mechanism.
So, while you wallow in agony, searching for a peer reviewed method or pill that will numb your pain, I will simply slow down my heart beat; release deep underlying stress patterns in my mind; nullify the inflammation in my lower back; and proceed with the Buddha’s advice - thereby achieving a full body rapture.
You can go suck on a lemon. I’ll induce states of deep well being.
By the way. When you mediate on your breath, do you notice anything of interest in your visual field? Just curious if you’ve discovered the mind-body connection yet …
Thanks Cali.
Butterfly binder 
… Very much appreciated.
No.
My knowledge or lack thereof of them doesn’t affect their efficacy. What has this got to do with you claiming your subjective anecdotal claims mirrored peer review?
Sigh, I never claimed it was a placebo effect, do learn to read. And you will need to demonstrate objective evidence for your claim that a placebo effect has a finite effect. Not that this matters as I was only pointing out your unevidenced assumption involved selection bias.
This in a nutshell is your problem.
On the contrary, it is entirely germane to why your claims are considered subjective woo woo, and not validated objective fact.
Or blind luck, or a placebo effect, or selection bias, or anything at all really since you seem happy to based your conclusion on subjective bias. In fact I’m going to assume meddlesome pixies are doing it for shits and giggles. I mean the fact the result is the same each and everytime, must prove it’s meddlesome pixies according to your rationale.
Or you could ask a witch doctor to lift the curse, all equally valid I believe.
Well I’m happy for you, but this little petulant dismissal of valid objections to your woo woo claims is not a compelling argument.
My eyes are closed.
Pretty sure medical science discovered that quite some time ago.
There you go again. Assumption after assumption. You asked me why I don’t chalk up my experience to placebo - insinuating that it might be - leading to the conclusion that you consider it as possible.
Regardless of how I sift through your underlying assumptions, my answer is sufficient and your reply is utterly beside the point.
If it were placebo it would stop working at some point. Comprehend?
It’s a pattern with a mechanism. And if you’re not suggesting it’s placebo now then what exactly are you doing?
How does my meditative practice differ from yours? Are pixies interceding in your breath meditation? They must be. You’ve made certain claims that it lowers blood pressure and reduces stress, correct?
Yes. And there should be darkness behind your eyelids depending on the lighting. So what do you see in the darkness? Anything?
So you do know? You must have read it somewhere, then?
You dweeb! You just countered your own assertion.
YOU DON’T HAVE A LACK OF FAITH IN THE TREATMENT! THAT IS SIMPLY BECAUSE YOU ARE LIVING IN A DELUSION.
There could be a million reasons why your back pain has left. Simply sitting in a new position has stretched the muscles enabling the tension to be released. You don’t get to rule in woo woo without eliminating all intervening variables. You may have simply had a spontaneous remission in back pain. Correlation is not causation. Please try again after the double blind back pain study.
Uh, you know how often “Christians” are begging 
for us to “let Jesus in” - they all claim the same “effects as evidence of some mechanism” - namely god/Jesus
Changes their lives I tell you!!! Gives them fruits of the spirit and happiness - boy oh boy … gets them “off of” whatever (drugs, alcohol, emotional, mental, physical issues) they needed to be “off of”. OOPS 
should be using the word “saved”. You need to be saved!
No I didn’t, I asked how you ruled out a placebo affect as one example to illustrate your selection bias.
What fucking assumptions? I don’t think you know what it means. I made no assumptions at all.
There was no insinuation at all, I stated plainly and clearly that the existence of a placebo effect can be objectively evidenced, and so we know it is possible, you have since admitted you can’t do that for your conclusion.
Oh fucking stop with this bullshit ffs, your woeful comprehension skills are not my fault, and I make no assumptions.
I never claimed it was a placebo comprehend?
I have asked you to evidence that claim, comprehend?
Asking you to objectively evidence your conclusion with something more robust than your obvious selection bias.
Relaxation techniques that lower heart rate and blood pressure can be objectively tested, as I already said, no assumptions are needed.
Not quite, but the ability to relax has testable benefits, and heart rates blood pressure etc can be easily measured. Your claim went further based solely on subjective assumption.
You’ve lost me sorry, my retinas require light to record images my brain can interpret. Or do you mean am I imagining any images? If so then no, that would be counter productive as focusing solely on the breathing was the entire point.
Know what, that the mind and body are linked, a stroll through a stroke ward would be evidence enough for that.
Same here, Copy and paste to a folder saved to my desktop.
What’s more important? Having the objective evidence or experiencing the benefits for your self through practice?
That’s really all I’m doing with my meditation. I don’t rely on breath. I rely on direct mental control of the apex of the heart. I don’t see why you have to be so contentious.
No. Quite simply, every visual field has a grainy “flickering” quality which is easiest to notice during the night.
Like Night Vision Goggles? That grainy image? Yeah. The same thing exists in our visual field. If you’re not aware of it, then never mind.
That depends.
I’d say certainly the personal experience is more important to ME; EG the benefits of Self hypnosis and the transcendent experience of solving a Zen koan.
BUT there’s a caveat: Only as long as a I don’t want others to accept what I’ve learned. Then the conventions of logic and empiricism become crucial. I can’t prove my experiences. Nor could I care less if others believe me or not. Why should they? Just because I say? Tha’ts blind faith, used by religionists, not me.
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The following just popped into head, I don’t know why 
A bloke is driving along and bam! Blow out.
Pulls over to the kerb, right outside the grounds of the insane asylum (when we had them).
As he gets out of the car, he notices a bloke leaning on the fence on the asylum side. Driver ignores him as he begins to change the tyre. Just as he is about to put the nuts on to the new tire, he drops them and they roll down a storm drain.
“OH Fluck!” He exclaims.
Bloke leaning on the fence says: “Try this: take one nut from each of the remaining three wheels. Put them on this one.They will all be fine long enough for you to get to a repairer”
Driver says: " Well,pickle me grandmother! That’s fantastic!".
Bloke leaning on fence says :" Nah, not really. I’m crazy not stupid"
Goal post shift alert…
Perhaps it’d help you understand if you looked up the meaning of debate, and recognised you have again there made a claim without any objective evidence. How is this control of “the apex of your heart” measured exactly?
If you are getting a transcendent experience from solving a Zen Koan, you don’t fucking understand the Koan. (That’s a Fact)
“Form does not differ from emptiness, emptiness does not differ from form. That which is form is emptiness, that which is emptiness form (…)”
YOU HAVE NOT EVEN GRASPED THE BASICS… “TRANSCENDENTAL” MY ASS!