Nature: Rethinking the links between genes and disease

_{Denyse O'Leary

October 13, 2016

Genetics, News}

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Because many mutations are benign. From an editorial at Nature:

One of the major findings of the Exome Aggregation Consortium (ExAC), the largest-ever catalogue of genetic variation in the protein-coding regions of the human genome, is that many genetic mutations have been misclassified as harmful (M. Lek et al. Nature 536, 285–291; 2016). Authors of that study estimate that each person has lurking in their genome an average of 54 mutations that are currently considered pathogenic — but that about 41 of these occur so frequently in the human population that they aren’t in fact likely to cause severe disease. That finding is having major consequences for some people with such variants, lifting the equivalent of genetic death sentences. More.

This doesn’t sound like good news for genetic fundamentalism.

See also: Researchers: Early life stress shortens telomeres It’s amazing how genetic fundamentalism is falling by the wayside. The genome has got to be the worst thing that ever happened to the Gene, the Selfish Gene, and all that.

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Besides "Rethinking the links between genes and disease", biologists also need to entirely rethink genetic reductionism, i.e. 'the central dogma', upon which Darwinian evolution is built. DNA, and particularly random mutations to DNA, are simply not the be all-end all explanation for biology that Darwinists envisioned them to be. They are not even close to being the be all-end all explanation.
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 Duality in the human genome - Nov. 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 ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body-plan. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ Stephen Meyer – Functional Proteins and Information for Body Plans – video https://youtu.be/hs4y4XLGQ-Y What Do Organisms Mean? Stephen L. Talbott - Winter 2011 Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: "Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements... take unique meaning from their context.[3]",,, http://www.thenewatlantis.com/publications/what-do-organisms-mean
In other words, reductive materialistic explanations cannot, in principle, account for the single unifying 'context' of a particular organism's form. Genetic Reductionism, and indeed any type of reductive materialism that Atheists would try to postulate, simply cannot account for exactly why the trillions, upon trillions, upon trillions, of molecules in a human body cohere as a single unified whole for 'precisely a lifetime and not a moment longer'.
The Unbearable Wholeness of Beings - Stephen L. Talbott - 2010 Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary. ,,, the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer? Despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity. http://www.thenewatlantis.com/publications/the-unbearable-wholeness-of-beings
In fact, I hold that in order for someone to give an adequate account for exactly why the trillions, upon trillions, upon trillions, of molecules in a human body cohere as a single unified whole for 'precisely a lifetime and not a moment longer', then it is absolutely necessary for that someone to postulate the existence of a single unifying 'soul'.
picture - What power holds off that moment — precisely for a lifetime, and not a moment longer? http://www.crystalinks.com/obe.lady.jpg Scientific evidence that we do indeed have an eternal soul (Elaboration on Talbott's question “What power holds off that moment — precisely for a lifetime, and not a moment longer?”)– video 2016 https://youtu.be/h2P45Obl4lQ
Any other explanation that does not take the concept of a 'single unifying soul' into consideration, in its attempted explanation for why the trillions, upon trillions, upon trillions, of molecules cohere as a whole as a single unified whole for precisely a lifetime and not a moment longer, simply will be on a completely wrong conceptual level to begin with in its attempted explanation of 'form'.bornagain77_{October 14, 2016
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Ian Thompson: That's not at all what irreducible complexity is about. Try again. By the way, both ID theory and IC are perfectly compatible with the idea that most mutations are neutral. It's neo darwinian theory, in its classic form, which requires that a relevant number of mutations are: 1) Positive 2) So positive that they can give some reproductive advantage, and therefore be selected and fixed 3) Miraculously additive towards some new complex function Multiple mutations are neither likely nor unlikely. Multiple mutations simply happen. It's multiple coordinated mutations necessary to give some specific complex function that are exponentially unlikely. IOWs, while starting from any sequence of, say, 50 characters, like: rhoso nfpoena rposlk fdspphurv sbpopet shooqlco ty you can have as many multiple mutations as you like, and get other sequences of characters without any meaning, be sure that you will never get the phrase that starts your post: It may not be good news for genetic fundamentalism which corresponds to a search space of 245 bits. And, as I have shown here: https://uncommondescent.com/intelligent-design/an-attempt-at-computing-dfsci-for-english-language/ with a longer sequence (600 characters, as an extreme example) you can be absolutely certain that you will never get a sequence made of english words even if you use the whole universe for the search (more than 800 bits of functional complexity).gpuccio_{October 14, 2016
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It may not be good news for genetic fundamentalism. But it does chip away (very!) slightly at the foundations of irreducible complexity, which tend to assert that single mutations are harmful and therefore unlikely. And hence that multiple mutations (etc) are even more unlikely.Ian Thompson_{October 13, 2016
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