Darwinism Epigenetics Intelligent Design

Epigenetics may explain how Darwin’s finches respond to environment

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From ScienceDaily:

Epigenetics may explain how Darwin’s finches respond to rapid environmental changes, according to new research published in the open access journal BMC Evolutionary Biology.

By studying rural and urban populations of two species of Darwin’s finches on the Galapagos Islands, researchers were able to show that while there was very little genetic variation, there were substantial epigenetic differences that could be related to environmental differences resulting from urbanization.

Sabrina McNew, PhD student at the University of Utah and lead author of the study said: “Urbanization of the Galapagos has happened relatively recently, so this is a good opportunity to study how animals respond to rapid environmental change.”

Genetic analysis of the birds revealed very little differences in genetic make-up between the rural and urban populations of both species. Analysis of DNA methylation patterns revealed significant differences between urban and rural populations for both species.

This study compared just two populations of finches so it cannot be said with certainty that urbanization is the key influencer of epigenetics or morphology. However the results are consistent with a potential role of epigenetic variation in rapid adaptation to changing environments. Future studies are needed to determine what direct effects DNA methylation has on physical traits, and to what extent these methylation patterns may play a role in evolution. Paper. (public access) – Sabrina M. McNew, Daniel Beck, Ingrid Sadler-Riggleman, Sarah A. Knutie, Jennifer A. H. Koop, Dale H. Clayton, Michael K. Skinner. Epigenetic variation between urban and rural populations of Darwin’s finches. BMC Evolutionary Biology, 2017; 17 (1) DOI: 10.1186/s12862-017-1025-9 More.

Between epigenetics and hybridization among closely related species, it is beginning to look as though Darwin’s finches, like Hollywood jeanswear, are marketed to the public mainly on branding.

Note: Darwinians will sometimes claim that Darwin’s finches demonstrate natural selection hard at work. But they are relying on public confusion. Natural selection can mean two different things. It can mean merely what Lynn Margulis said in an interview with Suzan Mazur, that not all life forms that come into existence can live. Only the traits of survivors can be passed on in some form. No one doubts that.

The second meaning is the Darwinian claim that the process of natural selection as above, acting on random mutations, creates large amounts of complex specified information by itself, turning cows into whales, etc. There is little evidence that big changes happen so simply.

And if the famed Darwin’s finches turn out to reflect the ceaseless back and forth flow of genetic information via epigenetics, hybridization, etc.—which results in an ongoing finch population of some type in the Galapagos—the finches are just another branded Darwin canard marketed to the public. They deserve better.

See also: New book: Evolution happens more quickly than we think

Darwin’s finches not a good example of Darwinian evolution

and

Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

The classic tale retold:

26 Replies to “Epigenetics may explain how Darwin’s finches respond to environment

  1. 1
    Dionisio says:

    Exuberantly obscene extrapolation from the embedded variability framework (EVF) operating within the biological systems? At the end of the day birds remain birds, antibiotic resistant bacteria remain bacteria, amphibians remain amphibians, apes remain apes, humans remain humans,
    Where’s the beef?
    They have to present real cases that satisfy the fundamental evo-devo formulation:
    Dev(d) = Dev(a) + Delta(a,d)

  2. 2
    PaV says:

    wd400:

    Are you paying attention? Remember some of my remarks?

  3. 3
    Mung says:

    Obviously evolution can happen far quicker than Darwin, and biologists for 100 years after Darwin, ever thought possible.

    And natural selection must be responsible.

  4. 4
    Anaxagoras says:

    Random mutation is something that the organism experiments or suffers.

    An adaptive variation driven by epigenetic marks on the genome, in response to changes in the environment, is something that the organism “does”. The organism is the agent, not the victim of the variation. The cause is not pure chance, the cause of the variation is the inherent teleology of the living being.Nothing to do with standard darwinian evolutionary theory.Just the opposite.

  5. 5
    aarceng says:

    Evolution depends on changes in the genomes. Since epigenetic changes allow adaptation without change of the genome they will work to prevent evolution.

  6. 6

    Darwinian evolution is indistinguishable from magic. It’s a magical “just so” origins story for a/mats.

  7. 7
  8. 8
    Dionisio says:

    Eukaryotic cells condense their genetic material in the nucleus in the form of chromatin, a macromolecular complex made of DNA and multiple proteins. The structure of chromatin is intimately connected to the regulation of all eukaryotic organisms, from amoebas to humans, but its organization remains largely unknown.

    https://www.researchgate.net/profile/Antoni_Luque/publication/303846274_Correlation_among_DNA_Linker_Length_Linker_Histone_Concentration_and_Histone_Tails_in_Chromatin/links/5760828208aeeada5bc3061c/Correlation-among-DNA-Linker-Length-Linker-Histone-Concentration-and-Histone-Tails-in-Chromatin.pdf

  9. 9
    Dionisio says:

    While much is known about DNA structure on the basepair level, this scale represents only a fraction of the structural levels involved in folding the genomic material.

    http://www.cell.com/biophysj/p.....0034-6.pdf

  10. 10
    Dionisio says:

    Cells sense physical and chemical signals from their local microenvironment and transduce them to the nucleus to regulate genomic programs.

    http://www.cell.com/trends/cel.....17)30104-6

  11. 11
    Dionisio says:

    Cell geometry is tightly coupled to gene expression patterns within the tissue microenvironment. This perspective synthesizes evidence that the 3d organization of chromosomes is a critical intermediate for geometric control of genomic programs.

    Cells seamlessly transition through the epigenetic landscape during differentiation and trans-differentiation programs in our body.

    http://www.tandfonline.com/doi.....ccess=true

  12. 12
    Dionisio says:

    Note that the comment @1 refers to the macroevolutionary fairytale that was mistakenly associated with the Galapagos finch variations.

    If one carefully analyzes the discoveries reported in the latest biology research papers, this obvious conclusion comes to mind:

    They ain’t seen nothin’ yet

    🙂

  13. 13
    Dionisio says:

    We must encourage the young generations to be sharp discerners, always testing everything and holding only what is good.
    But first they’ll have to know what’s good.
    There’s only one true source of wisdom required to be a sharp discerner.
    Run to it!

  14. 14

    Dionisio @ 7-13: Amazing comments. Thank you.

  15. 15
    Dionisio says:

    A history of hybrids? Genomic patterns of introgression in the True Geese

    Jente Ottenburghs,
    Hendrik-Jan Megens,
    Robert H. S. Kraus,
    Pim van Hooft,
    Sipke E. van Wieren,
    Richard P. M. A. Crooijmans,
    Ronald C. Ydenberg,
    Martien A. M. Groenen and
    Herbert H. T. Prins

    BMC Evolutionary Biology
    2017 17:201
    https://doi.org/10.1186/s12862-017-1048-2

    https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-017-1048-2

    https://rd.springer.com/content/pdf/10.1186%2Fs12862-017-1048-2.pdf

  16. 16
    Dionisio says:

    Researchers: Darwin’s finches not typical example of evolution at all

    https://uncommondescent.com/evolution/researchers-darwins-finches-not-typical-example-of-evolution-at-all/

  17. 17
    Dionisio says:

    Epigenetic variation between urban and rural populations of Darwin’s finches

    Sabrina M. McNew,
    Daniel Beck,
    Ingrid Sadler-Riggleman,
    Sarah A. Knutie,
    Jennifer A. H. Koop,
    Dale H. Clayton and
    Michael K. Skinners

    BMC Evolutionary Biology
    https://doi.org/10.1186/s12862-017-1025-9
    https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-017-1025-9

  18. 18
    Dionisio says:

    Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

    M. Ravinet, R. Faria, R. K. Butlin, J. Galindo, N. Bierne, M. Rafajlovi?, M. A. F. Noor, B. Mehlig, A. M. Westram

    Journal of Evolutionary Biology
    DOI: 10.1111/jeb.13047

    http://onlinelibrary.wiley.com.....13047/full

  19. 19
    Dionisio says:

    […] the heterochromatin core in the A. azarae rod nucleus was newly formed in A. azarae or its recent ancestor, and supports the hypothesis that A. azarae, and with all probability other Aotus species, secondarily acquired night vision.

    Co-Opted Megasatellite DNA Drives Evolution of Secondary Night Vision in Azara’s Owl Monkey.
    Koga A1, Tanabe H2, Hirai Y1, Imai H1, Imamura M1, Oishi T1, Stanyon R3, Hirai H1
    Genome Biol Evol. ;9(7):1963-1970.
    doi: 10.1093/gbe/evx142.

    “was newly formed”?
    “secondarily acquired”?

    Huh?

    Where’s the beef?

  20. 20
    Dionisio says:

    Rods and cones are photoreceptor cells in the eyes of vertebrates.

    These cells have an elongated shape, and light passes through the cell nucleus on its way to the outer segments of photoreceptors.

    Rods are more sensitive to weak light than cones.

    It was recently found that rod cells of many nocturnal mammals, including mice, rats, deer, cats, ferrets, and lemurs, possess a unique “inverted nuclear architecture”, in which heterochromatin localizes to the central portion of the nucleus […]

    Co-Opted Megasatellite DNA Drives Evolution of Secondary Night Vision in Azara’s Owl Monkey.
    Koga A1, Tanabe H2, Hirai Y1, Imai H1, Imamura M1, Oishi T1, Stanyon R3, Hirai H1
    Genome Biol Evol. ;9(7):1963-1970.
    doi: 10.1093/gbe/evx142.

    Complex functionally specified informational complexity.

  21. 21
    Dionisio says:

    The inverted nuclear architecture clearly represents an exquisite adaptation to nocturnal life.

    Co-Opted Megasatellite DNA Drives Evolution of Secondary Night Vision in Azara’s Owl Monkey.
    Koga A1, Tanabe H2, Hirai Y1, Imai H1, Imamura M1, Oishi T1, Stanyon R3, Hirai H1
    Genome Biol Evol. ;9(7):1963-1970.
    doi: 10.1093/gbe/evx142.

    Where’s the beef?

    Complex functionally specified informational complexity.

  22. 22
    Dionisio says:

    Our future goal is to test the two hypotheses concerning the origin of owl monkey night vision: Long-time maintenance or reacquisition.

    Co-Opted Megasatellite DNA Drives Evolution of Secondary Night Vision in Azara’s Owl Monkey.
    Koga A1, Tanabe H2, Hirai Y1, Imai H1, Imamura M1, Oishi T1, Stanyon R3, Hirai H1
    Genome Biol Evol. ;9(7):1963-1970.
    doi: 10.1093/gbe/evx142.

    Work in progress… stay tuned.

    Complex functionally specified informational complexity.

  23. 23
    Dionisio says:

    We propose that during karyotype evolution, arvicolines underwent a significant number of complex intrachromosomal rearrangements that were not previously detected.

    It is clear that inversions and centromere repositioning in mammalian species still remains poorly documented.

    A reliable evaluation of the importance of these types of rearrangements for karyotype evolution and their utility for phylogenomics will require further investigations involving a broader array of species, and wider application of region-specific probes.

    Intrachromosomal Rearrangements in Rodents from the Perspective of Comparative Region-Specific Painting.
    Romanenko SA1,2, Serdyukova NA3, Perelman PL4,5, Pavlova SV6, Bulatova NS7, Golenishchev FN8, Stanyon R9, Graphodatsky AS10,11.
    Genes (Basel). 8(9). pii: E215.
    doi: 10.3390/genes8090215.

    Does this have to do with microevolution?

    Complex functionally specified informational complexity.

  24. 24
    Dionisio says:

    […] detection and investigation of intrachromosomal rearrangements in Arvicolinae with microdissection-derived or other region-specific probes will be useful not only for resolving complex phylogenetic relationships, but also for uncovering the mechanisms of chromosome evolution, and for the clarification of the role of chromosome rearrangements in the speciation of this spectacularly diverse taxon.

    Intrachromosomal Rearrangements in Rodents from the Perspective of Comparative Region-Specific Painting.
    Romanenko SA1,2, Serdyukova NA3, Perelman PL4,5, Pavlova SV6, Bulatova NS7, Golenishchev FN8, Stanyon R9, Graphodatsky AS10,11.
    Genes (Basel). 8(9). pii: E215.
    doi: 10.3390/genes8090215.

    Complex functionally specified informational complexity.

  25. 25
    Dionisio says:

    Although the genomes of some songbird species were sequenced recently, the chromosomal organization of these species is mostly unknown.

    […] a complete karyotypical characterization–including the distribution of heterochromatic blocks and rDNA blocks–may be important to complete the interpretation of data obtained by sequencing.

    A clear example of this is the fact that, because of the peculiar nature of the avian karyotype, the number of syntenic groups generated by bioinformatic approaches are not accurate, and usually do not match with the actual diploid number [11].

    Comparative Cytogenetics between Two Important Songbird, Models: The Zebra Finch and the Canary.
    Dos Santos MD1, Kretschmer R2, Frankl-Vilches C3, Bakker A3, Gahr M3, O Brien PC4, Ferguson-Smith MA4, de Oliveira EH5,6.
    PLoS One. 12(1):e0170997.
    doi: 10.1371/journal.pone.0170997.

    Complex functionally specified informational complexity.

  26. 26
    Dionisio says:

    If there is one certainty about speciation, it is that those who research the process are able to disagree about almost anything.

    […] there is clearly still room for discussion and deeper understanding […]

    Understanding the evolution of reproductive isolation will not always be plain sailing.

    We may need information from diverse, sometimes challenging approaches including theory, modelling, experiments, field surveys and new sequencing technologies.

    Land ahoy? Navigating the genomic landscape of speciation while avoiding shipwreck
    A. M. Westram, M. Ravinet
    DOI: 10.1111/jeb.13129
    Journal of evolutionary biology.

    Complex functionally specified informational complexity.

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