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So creationism works—but only for genes?

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From a bioRxiv preprint:

Abstract: The origin of ‘orphan’ genes, species-specific sequences that lack detectable homologues, has remained mysterious since the dawn of the genomic era. There are two dominant explanations for orphan genes: complete sequence divergence from ancestral genes, such that homologues are not readily detectable; and de novo emergence from ancestral non-genic sequences, such that homologues genuinely do not exist. The relative contribution of the two processes remains unknown. Here, we harness the special circumstance of conserved synteny to estimate the contribution of complete divergence to the pool of orphan genes. We find that complete divergence accounts for at most a third of eukaryotic orphan and taxonomically restricted genes. We observe that complete divergence occurs at a stable rate within a phylum, but different rates between phyla, and is frequently associated with gene shortening akin to pseudogenization. Two cancer-related human genes, DEC1 and DIRC1, have likely originated via this route in a primate ancestor. – Nikolaos Vakirlis, Anne-Ruxandra Carvunis, View ORCID ProfileAoife McLysaght doi: https://doi.org/10.1101/735175 Pdf.More.

So 2/3 of the time, we have “de novo emergence from ancestral non-genic sequences, such that homologues genuinely do not exist?”

Okay. Somebody better go put their arm around the Selfish Gene. It’s tough being the Last Darwinian.

Gene, we did not do this to you. Francis Collins and Craig Venter did this to you. Honest.

Hat tip: Creation-Evolution Headlines

See also: De Novo genes and normal science

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2 Replies to “So creationism works—but only for genes?

  1. 1
    bornagain77 says:

    as to:

    There are two dominant explanations for orphan genes: complete sequence divergence from ancestral genes, such that homologues are not readily detectable; and de novo emergence from ancestral non-genic sequences, such that homologues genuinely do not exist.

    They may be the ‘dominant’ explanations but neither are the correct explanation.

    As to the supposed ‘dominant explanation’ of “de novo emergence from ancestral non-genic sequences”, in the following article Dr Hunter points out that Darwinists believe that “de novo emergence from ancestral non-genic sequences” must be true not because of any substantiating evidence that they may have, but they believe it must be true in spite of the evidence to the contrary, (i.e. they believe it must be true simply because of their apriori belief that Darwinian evolution must be true).

    Is the Origin of New Genes “Basically a Solved Problem”? – September 11, 2014 – Cornelius Hunter
    Excerpt: This evolutionary narrative is certainly not “basically a solved problem.” In fact, what evolutionists have are high claims of the spontaneous evolution of incredibly complex structures, not because of the evidence, but in spite of the evidence.
    So what gives evolutionist’s their confidence? It is not that they understand how such genes could have evolved, but that the genes are observed over and over. And since (in the minds of Darwinists) evolution must be true, then those solo genes must evolved:
    http://darwins-god.blogspot.co.....olved.html

    In the minds of Darwinists, Darwinism is simply never allowed to be falsified by empirical observation. Needless to say, this not science.

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge

    As to their other supposed ‘dominant explanation’ of “complete sequence divergence from ancestral genes”, likewise Darwinists believe “complete sequence divergence from ancestral genes” must be true not because of the substantiating evidence but they believe it must be true in spite of the evidence to the contrary, (i.e. they believe it must be true simply because of their apriori belief that Darwinian evolution must be true).

    Darwinists hold that genes-proteins have, basically, unlimited plasticity in their ability to try new sequences in their search for new functional sequences in sequence space.

    Conservation of Information Made Simple – William A. Dembski – August, 2012
    Excerpt: Biological configuration spaces of possible genes and proteins, for instance, are immense, and finding a functional gene or protein in such spaces via blind search can be vastly more improbable than finding an arbitrary electron in the known physical universe. ,,,
    http://www.evolutionnews.org/2.....63671.html

    Yet directly contrary to their belief that genes-proteins have, basically, unlimited plasticity in their ability to search for new functional sequences in sequence space, genes-proteins are instead found to be highly constrained in their ability to search ‘sequence space’ in order to try to find new functional sequences.

    Stability effects of mutations and protein evolvability. October 2009
    Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,,
    http://www.ncbi.nlm.nih.gov/pubmed/19765975

    Doug Axe and Ann Gauger have done experimental work exploring just how constrained genes-proteins are in their ability to search sequence space. Their work found genes-proteins to be highly, even severely, constrained in their ability to search sequence space.

    “Enzyme Families — Shared Evolutionary History or Shared Design?” – Ann Gauger – December 4, 2014
    Excerpt: If enzymes can’t be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.,,,
    Taken together, since we found no enzyme that was within one mutation of cooption, the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 10^15 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations.
    We have now addressed two objections raised by our critics: that we didn’t test the right mutation(s), and that we didn’t use the right starting point. We tested all possible single base changes in nine different enzymes, Those nine enzymes are the most structurally similar of BioF’s entire family We also tested 70 percent of double mutations in the two closest enzymes of those nine.
    Finally, some have said we should have used the ancestral enzyme as our starting point, because they believe modern enzymes are somehow different from ancient ones. Why do they think that? It’s because modern enzymes can’t be coopted to anything except trivial changes in function. In other words, they don’t evolve!
    That is precisely the point we are making.
    http://www.evolutionnews.org/2.....91701.html

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://www.biologicinstitute.o.....nt-collide

    Thus again, Darwinists believe that “complete sequence divergence from ancestral genes” must be true not because of any substantiating evidence but they believe it must be true in spite of the evidence, (i.e. they believe it must be true simply because of their apriori belief that Darwinian evolution must be true).

    And again, as should be needless to say, this is NOT science:

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge

    Of supplemental note to genes-proteins being highly constrained in their ability to search sequence space:

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
    Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].,,,
    38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142.
    39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432.
    40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654.
    41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997.
    42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.
    43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589.
    http://www.worldscientific.com.....08728_0006

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
    Conclusions: Our analysis confirms mathematically what would seem intuitively obvious – multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations?
    http://www.worldscientific.com.....08728_0006

    Verse:

    1 Thessalonians 5:21
    Test all things; hold fast what is good.

  2. 2
    EDTA says:

    News,
    Unrelated, but new finding:
    Counterintuitive physics property found to be widespread in living organisms
    https://phys.org/news/2019-08-counterintuitive-physics-property-widespread.html
    (Darn those dang counterintuitive findings! 😎

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