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Other bad news from the genome for neo-Darwinism


File:DNA simple.svg Philip Cunningham hat tipped us earlier on the article at Quartz that raised the possibility that all genes affect every complex trait. He also writes to say, “The paper makes the genotype-phenotype mapping problem that much worse for neo-Darwinists. Here are few notes to that throw a little light on how bad the problem is:”

These news items from recent years give some sense of the issues, he says:

The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology (Bard, 2011) Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation. (BioSignaling)

Not Junk After All—Conclusion (August 29, 2013) Excerpt: Many scientists have pointed out that the relationship between the genome and the organism — the genotype-phenotype mapping — cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]

Gene previously linked to obesity is unrelated (June 29, 2015)
Excerpt: … in the real world of careful analysis, scientists are just not finding the “genes” that the headline writers need. British geneticist Steve Jones points out that most human traits are influenced by so many genes that there is no likely systematic cause and effect:
“We know of more than 50 different genes associated with height … That has not percolated into the public mind, as the Google search for “scientists find the gene for” shows. The three letter word for — the gene FOR something — is the most dangerous word in gen etics.”And the craze is not harmless, he warns. …

What If (Almost) Every Gene Affects (Almost) Everything? (Atlantic, 2017)
Excerpt: If you told a modern geneticist that a complex trait—whether a physical characteristic like height or weight, or the risk of a disease like cancer or schizophrenia—was the work of just 15 genes, they’d probably laugh. It’s now thought that such traits are the work of thousands of genetic variants, working in concert. The vast majority of them have only tiny effects, but together, they can dramatically shape our bodies and our health. They’re weak individually, but powerful en masse.

Genetic fundamentalism is probably not due for a revival any time soon.

The Fairyland of Evolutionary Modeling (ENST, May 7, 2013)
Excerpt: Salazar-Ciudad and Marín-Riera have shown that not only are suboptimal dead ends an evolutionary possibility, but they are also exceedingly likely to occur in real, developmentally complex structures when fitness is determined by the exact form of the phenotype.

See also: Do all genes affect every complex trait? Veronique Greenwood: The roots of many traits, from how tall you are to your susceptibility to schizophrenia, are far more tangled. In fact, they may be so complex that almost the entire genome may be involved in some way


New book from Michael Behe on how today’s DNA findings “devolve” Darwin. Devolution… at last, something Darwinism really explains!

If the starting point of evolution is a 'simple single cell', and they can't demonstrate that starting point, they're cheating. They have brought a store bought cake to a bake-off. The creationist
To put the insurmountable genotype-phenotype mapping problem for Darwinian explanations even more clearly, in the following article Dr. Wells states, "I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism."
Ask an Embryologist: Genomic Mosaicism - Jonathan Wells - February 23, 2015 Excerpt: humans have a "few thousand" different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,, The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It's called genomic mosaicism. In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,, ,,,(then) "genomic equivalence" -- the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA -- became the accepted view. I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common. I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism. http://www.evolutionnews.org/2015/02/ask_an_embryolo093851.html
Simply put, and directly contrary to Darwinian presuppositions, mutations are now, empirically, shown to NOT be random mutations but to be directed mutations:
How life changes itself: the Read-Write (RW) genome. – 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. http://www.ncbi.nlm.nih.gov/pubmed/23876611 WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Fully Random Mutations – Kevin Kelly – 2014 Excerpt: What is commonly called “random mutation” does not in fact occur in a mathematically random pattern. The process of genetic mutation is extremely complex, with multiple pathways, involving more than one system. Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur. Rather, the idea that mutations are random is simply a widely held assumption by non-specialists and even many teachers of biology. There is no direct evidence for it. On the contrary, there’s much evidence that genetic mutation vary in patterns. For instance it is pretty much accepted that mutation rates increase or decrease as stress on the cells increases or decreases. These variable rates of mutation include mutations induced by stress from an organism’s predators and competition, and as well as increased mutations brought on by environmental and epigenetic factors. Mutations have also been shown to have a higher chance of occurring near a place in DNA where mutations have already occurred, creating mutation hotspot clusters—a non-random pattern. http://edge.org/response-detail/25264 Duality in the human genome – November 28, 2014 Excerpt: The results show that most genes can occur in many different forms within a population: On average, about 250 different forms of each gene exist. The researchers found around four million different gene forms just in the 400 or so genomes they analysed. This figure is certain to increase as more human genomes are examined. More than 85 percent of all genes have no predominant form which occurs in more than half of all individuals. This enormous diversity means that over half of all genes in an individual, around 9,000 of 17,500, occur uniquely in that one person – and are therefore individual in the truest sense of the word. The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time.,,, According to the researchers, mutations of genes are not randomly distributed between the parental chromosomes. They found that 60 percent of mutations affect the same chromosome set and 40 percent both sets. Scientists refer to these as cis and trans mutations, respectively. Evidently, an organism must have more cis mutations, where the second gene form remains intact. “It’s amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula,” says Hoehe. http://medicalxpress.com/news/2014-11-duality-human-genome.html
The following video goes over many more lines of evidence that have falsified the Darwinian presupposition of ‘random thermodynamic jostling’ within molecular biology.
Darwinian Materialism vs. Quantum Biology – video https://youtu.be/LHdD2Am1g5Y
In fact, due to quantum non-locality, and the necessity to postulate a ‘beyond space and time’ cause in order to explain quantum entanglement within molecular biology, advances in quantum biology have now falsified the entire reductive materialistic foundation that lays beneath Darwinian thought. Verse:
Psalm 139:13 For it was You who formed my inmost being; You knit me together in my mother’s womb.
Recipe metaphor? But people think up and create recipes that are delicious whereas randomly throwing stuff, and steps, together results in disaster and/or food that tastes horrible. Moreover, the recipe metaphor as applied to Darwinian mechanisms, is just plain nonsense, as Stuart A. Newman noted, "Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent."
The Gene Myth, Part II - August 2010 Excerpt: “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, (intrinsically disordered proteins), taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions. ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent. Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy http://darwins-god.blogspot.com/2010/08/gene-myth-part-ii.html
Once again, you, the atheistic Darwinist, simply have no evidence for your claims. and/or for your 'just so stories' (which is what all Darwinian claims ultimately turn out to be.)
Intelligent Design and the Advancement of Science - Brian Miller December 11, 2017 Excerpt: DNA was expected to be the primary source of causality behind the operation and development of life. Such beliefs have previously raised concerns from leading scientists and mathematicians. For instance, physicist Walter Elsasser argued that the unfathomable complexity of the chemical and physically processes in life was “transcomputational” — beyond the realm of any theoretical means of computation. Moreover, the development of the embryo is not solely directed by DNA. Instead, it requires new “biotonic” principles. As a result, life cannot be reduced to chemistry and physics. An unbridgeable gap separates life from non-life. Similarly, mathematician René Thom argued that the 3D patterns of tissues in an organism’s development from egg to birth and their continuous transformation cannot be understood in terms of isolating the individual proteins generated by DNA and other molecules produced in cells. The problem is that the individual “parts” composing tissues and organs only take on the right form and function in the environment of those tissues and organs. More recent work by Denis Noble further has elucidated how every level of the biological hierarchy affects every other level, from DNA to tissues to the entire organism. Based partly on these insights, Thom concluded in his book Structural Stability and Morphogenesis that the process of development should be thought of as being controlled by an “algebraic structure outside space-time itself” (p. 119). Likewise, Robert Rosen argued that life can only be understood as a mathematical abstraction consisting of functional relationships, irreducible to mechanistic processes. He observed that life is fundamentally different from simple physics and chemistry. It embodies the Aristotelian category of final causation, which is closely related to the idea of purpose. The conclusions of these scholars challenge materialistic philosophy at its core. https://evolutionnews.org/2017/12/intelligent-design-and-the-advancement-of-science/ Darwinism vs Biological Form – video (2017) https://www.youtube.com/watch?v=JyNzNPgjM4w "Since the 1980s, developmental and cell biologists such as Brian Goodwin, Wallace Arthur, Stuart Newman, Fred Nijhout, and Harold Franklin have discovered or analyzed many sources of epigenetic information. Even molecular biologists such as Sidney Brenner, who pioneered the idea that genetic programs direct animal development, now insist that the information needed to code for complex biological systems vastly outstrips the information in DNA. DNA helps direct protein synthesis. Parts of the DNA molecule also help to regulate the timing and expression of genetic information and the synthesis of various proteins within cells. Yet once proteins are synthesized, they must be arranged into higher-level systems of proteins and structures. Genes and proteins are made from simple building blocks—nucleotide bases and amino acids, respectively—arranged in specific ways. Similarly, distinctive cell types are made of, among other things, systems of specialized proteins. Organs are made of specialized arrangements of cell types and tissues. And body plans comprise specific arrangements of specialized organs. Yet the properties of individual proteins do not fully determine the organization of these higher-level structures and patterns. Other sources of information must help arrange individual proteins into systems of proteins, systems of proteins into distinctive cell types, cell types into tissues, and different tissues into organs. And different organs and tissues must be arranged to form body plans." [S.Meyer, ‘Darwin’s Doubt’, Ch.14]
Moreover, this failure of the reductive materialistic explanations of Darwinian evolution occurs at a much lower level than DNA itself:
Quantum physics problem proved unsolvable: Godel and Turing enter quantum physics - December 9, 2015 Excerpt: A mathematical problem underlying fundamental questions in particle and quantum physics is provably unsolvable,,, It is the first major problem in physics for which such a fundamental limitation could be proven. The findings are important because they show that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,, A small spectral gap - the energy needed to transfer an electron from a low-energy state to an excited state - is the central property of semiconductors. In a similar way, the spectral gap plays an important role for many other materials.,,, Using sophisticated mathematics, the authors proved that, even with a complete microscopic description of a quantum material, determining whether it has a spectral gap is, in fact, an undecidable question.,,, "We knew about the possibility of problems that are undecidable in principle since the works of Turing and Gödel in the 1930s," added Co-author Professor Michael Wolf from Technical University of Munich. "So far, however, this only concerned the very abstract corners of theoretical computer science and mathematical logic. No one had seriously contemplated this as a possibility right in the heart of theoretical physics before. But our results change this picture. From a more philosophical perspective, they also challenge the reductionists' point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description." http://phys.org/news/2015-12-quantum-physics-problem-unsolvable-godel.html
If Darwinism were a real science instead of a unfalsifiable pseudoscience, this finding, by itself, should be fatal for Darwinian explanations, bur alas, Darwinian evolution is not a science but is instead, in reality, a religion for atheists who are afraid of the Light.
Darwin’s Theory vs Falsification – video https://www.youtube.com/watch?v=8rzw0JkuKuQ "Atheism is a fairy story for people afraid of the light" - John Lennox
Philip Cunningham hat tipped us earlier on the article at Quartz that raised the possibility that all genes affect every complex trait. He also writes to say, “The paper makes the genotype-phenotype mapping problem that much worse for neo-Darwinists. Here are few notes to that throw a little light on how bad the problem is:”
This is why Dawkins wrote in The Blind Watchmaker (32 years ago! And it was old news then) that "blueprints" is a bad analogy for genes, and that a better one is a "recipe". If you change part of a blueprint, you're likely to only change that part of the building, but if you make a change to a recipe (an ingredient, cooking time, etc), you're likely to change the whole cake. He talks about this throughout the book, so it's hard to find a single part to quote, but here's a try:
Cakes baked according to the 'mutated', higher-temperature version of the recipe will come out different, not just in one part but throughout their substance, from cakes baked according to the original lower-temperature version. But the analogy is still too simple. To simulate the 'baking' of a baby, we should imagine not a single process in a single oven, but a tangle of conveyor belts, passing different parts of the dish through 10 million different miniaturized ovens, in series and in parallel, each oven bringing out a different combination of flavours from 10,000 basic ingredients. The point of the cooking analogy, that the genes are not a blueprint but a recipe for a process, comes over from the complex version of the analogy even more strongly than from the simple one.

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