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Comment of the week: Physics so uncertain, biology so certain?

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From bFast, appended to Baffling but undead physics results:

Physicists always seem to end up with puzzles: what is dark energy, what is dark matter, what caused the big bang, how big is a proton. I love the honest puzzles that physicists bring to the table.

Evolutionary biologists, however, never seem to be puzzled about nuthin’. First life? Don’t know how yet, but its not a problem. Cambrian explosion, wasn’t mutch,a and it had millions of years. Irreducible complexity? No deal, we did this experiment that produced two mutations to produce a single function — after 1/2 million years worth of evolving. HAR1F pulls off 18 mutations, no problem, millions of years. No issues, not problems, no puzzles. Its as settled as the earth goes around the sun.

In a nutshell, that is the difference between science, like the physics of the Large Hadron Collider, and ideology, like the defense of Darwinism (the only known theory that is in principle capable of explaining certain aspects of life. (p. 287, Blind Watchmaker, 1986)), as the creation story of naturalism.

Physics can shake off its problems mainly by chucking non-evidence-based nonsense. It’s done that before.

The problem in biology is, once we start chucking, half the foundations will be in the dumpsters.

Sure, we can fix things up, but we need a new building. Too much sanctified rot has been left for too long.

See, for example, What the fossils told us in their own words.


In search of a road to reality

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Phinehas: Most well-designed fitness functions are nonrandom, in favorable ways. The universe has many sources of order, if that is what you are asking. Grow upward, young tracheophyte, grow upward! Zachriel
Phinehas: Where did the relationship of the genotype or phenotype to the environment come from? Was its origin nonrandom? It may have started with a simple molecular replicator. No one knows for sure. Zachriel
Z: Where did the relationship of the genotype or phenotype to the environment come from? Was its origin nonrandom? Most well-designed fitness functions are nonrandom, in favorable ways. This doesn't necessarily mean that all fitness functions that are nonrandom in favorable ways are well-designed, but neither should the correlation be ignored. Phinehas
Phinehas: I wonder what fitness function chose the fitness function. The fitness function is an abstraction that represents the relationship of the genotype or phenotype to the environment. Zachriel
...but the actual fitness function biological organisms are subject to is very strongly nonrandom, and in favorable ways.
How very fortunate for us. I wonder what fitness function chose the fitness function. Phinehas
Um, 'twas not I that wrote "we need a new building", it was news. bFast
@bfast wrote: "we need a new building" Choosing is the mechanism of creation. I have seen science about it, mathematics / physics, but nothing on uncommon descent. How can you have a creationist or intelligent design website, without any science whatsoever on how things are chosen in the universe? mohammadnursyamsu
Gordon, who argued gravity implied "intelligent falling". That would be a dumb argument. Gravity's fine tuning does imply design though. That's the physicists conundrum. Not chance. Gravity could not arise by chance. How will biology accept not unguided? Won't be pretty. Lots of kicking, lots of screaming. ppolish
Yes and models of directed evolution are useful for showing the power and creativity of the mechanism. Virgil Cain
asauber: I consider Science to be a limited tool utilized by flawed human beings. Sure. asauber: It doesn’t and can’t explain everything. Right again. asauber: In others, it becomes an enabler of error. Of course. Sometimes, though, science leads to valuable understandings of the natural world. Meanwhile, you might want to read the Asimov essay in light of this statement: "All models are wrong, but some are useful." — George E. P. Box Zachriel
Gordon Davisson,
Did you read the Asimov essay? He answers basically this objection, except about physics. Do you dismiss physics as “wrong”? Chemistry? Astronomy? All of science?"
No. I did not ready the essay. I consider Science to be a limited tool utilized by flawed human beings. It doesn't and can't explain everything. In some instances it works very well. In others, it becomes an enabler of error. So If I were you, I would ditch the assumption that Science is god. It actually makes for better science. Andrew asauber
as to:
Do you dismiss physics as “wrong”? Chemistry? Astronomy? All of science? If not, why single out evolutionary biology?
Actually all of science is based on Theistic presuppositions about the intelligibility of the world and man's ability to understand that intelligibility. In so far as a 'science' tries to deny those Theistic presuppositions, it winds up in epistemological failure. (Boltzmann's Brains, Plantinga's Evolutionary Argument Against Naturalism, Nancy Pearcey's loss of free will and personhood.) In fact, 'modern science' was born out of Christian presuppositions, and was certainly not born out of atheistic/naturalistic and/or materialistic presuppositions which hold that there is no true rhyme or reason for why the universe or anything in it exists. (i.e. the 'chaos' postulate of naturalism)
Science and Theism: Concord, not Conflict* – Robert C. Koons IV. The Dependency of Science Upon Theism (Page 21) Excerpt: Far from undermining the credibility of theism, the remarkable success of science in modern times is a remarkable confirmation of the truth of theism. It was from the perspective of Judeo-Christian theism—and from the perspective alone—that it was predictable that science would have succeeded as it has. Without the faith in the rational intelligibility of the world and the divine vocation of human beings to master it, modern science would never have been possible, and, even today, the continued rationality of the enterprise of science depends on convictions that can be reasonably grounded only in theistic metaphysics. http://www.robkoons.net/media/69b0dd04a9d2fc6dffff80b3ffffd524.pdf
as to:
"We don’t know why e.g. the constants of physics have the particular values they have, but to claim that they must have been intelligently chosen is a pure ID-of-the-gaps argument."
"God is not a “God of the gaps”, he is God of the whole show." John Lennox - video https://www.youtube.com/watch?v=BaXO_wkwtCI Lecture by John Lennox. Are all arguments for the existence of God nothing more than God-of-the-gap arguments? Are Christians just saying God-did-it? Lennox explains why arguments for the existence of God are not arbitrary.
And indeed, contrary to what Gordon and other atheists imagine to the contrary, all of modern science, save for the intellectually bankrupt pseudo-science of Darwinism, points to God as being "God of the whole show":
1. Naturalism/Materialism predicted time-space energy-matter always existed. Theism predicted time-space energy-matter were created. Big Bang cosmology now strongly indicates that time-space energy-matter had a sudden creation event approximately 14 billion years ago. 2. Naturalism/Materialism predicted that the universe is a self sustaining system that is not dependent on anything else for its continued existence. Theism predicted that God upholds this universe in its continued existence. Breakthroughs in quantum mechanics reveal that this universe is dependent on a ‘non-local’, beyond space and time, cause for its continued existence. 3. Naturalism/Materialism predicted that consciousness is an ‘emergent property’ of material reality and thus should have no particularly special position within material reality. Theism predicts consciousness precedes material reality and therefore, on that presupposition, consciousness should have a ‘special’ position within material reality. Quantum Mechanics reveals that consciousness has a special, even a central, position within material reality. - 4. Naturalism/Materialism predicted the rate at which time passed was constant everywhere in the universe. Theism predicted God is eternal and is outside of time. – Special Relativity has shown that time, as we understand it, is relative and comes to a complete stop at the speed of light. (Psalm 90:4 – 2 Timothy 1:9) - 5. Naturalism/Materialism predicted the universe did not have life in mind and that life was ultimately an accident of time and chance. Theism predicted this universe was purposely created by God with man in mind. Scientists find the universe is exquisitely fine-tuned for carbon-based life to exist in this universe. Moreover it is found, when scrutinizing the details of physics and chemistry, that not only is the universe fine-tuned for carbon based life, but is specifically fine-tuned for life like human life (R. Collins, M. Denton).- 6. Naturalism/Materialism predicted complex life in this universe should be fairly common. Theism predicted the earth is extremely unique in this universe. Statistical analysis of the hundreds of required parameters which enable complex organic life to be possible on earth gives strong indication the earth is extremely unique in this universe (G. Gonzalez; Hugh Ross). - 7. Naturalism/Materialism predicted it took a very long time for life to develop on earth. Theism predicted life to appear abruptly on earth after water appeared on earth (Genesis 1:10-11). Geochemical evidence from the oldest sedimentary rocks ever found on earth indicates that complex photosynthetic life has existed on earth as long as water has been on the face of earth. - 8. Naturalism/Materialism predicted the first life to be relatively simple. Theism predicted that God is the source for all life on earth. The simplest life ever found on Earth is far more complex than any machine man has made through concerted effort. (Michael Denton PhD) - 9. Naturalism/Materialism predicted the gradual unfolding of life would (someday) be self-evident in the fossil record. Theism predicted complex and diverse animal life to appear abruptly in the seas in God’s fifth day of creation. The Cambrian Explosion shows a sudden appearance of many different and completely unique fossils within a very short “geologic resolution time” in the Cambrian seas. - 10. Naturalism/Materialism predicted there should be numerous transitional fossils found in the fossil record, Theism predicted sudden appearance and rapid diversity within different kinds found in the fossil record. Fossils are consistently characterized by sudden appearance of a group/kind in the fossil record(disparity), then rapid diversity within that group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. - 11. Naturalism/Materialism predicted animal speciation should happen on a somewhat constant basis on earth. Theism predicted man was the last species created on earth – Man (our genus ‘modern homo’ as distinct from the highly controversial ‘early homo’) is the last generally accepted major fossil form to have suddenly appeared in the fossil record. (Tattersall; Luskin)– 12. Naturalism/Materialism predicted that the separation of human intelligence from animal intelligence ‘is one of degree and not of kind’(C. Darwin). Theism predicted that we are made in the ‘image of God’- Despite an ‘explosion of research’ in this area over the last four decades, human beings alone are found to ‘mentally dissect the world into a multitude of discrete symbols, and combine and recombine those symbols in their minds to produce hypotheses of alternative possibilities.’ (Tattersall; Schwartz). Moreover, both biological life and the universe itself are found to be ‘information theoretic’ in their foundational basis. 13. Naturalism/Materialism predicted much of the DNA code was junk. Theism predicted we are fearfully and wonderfully made – ENCODE research into the DNA has revealed a “biological jungle deeper, denser, and more difficult to penetrate than anyone imagined.”. - 14. Naturalism/Materialism predicted a extremely beneficial and flexible mutation rate for DNA which was ultimately responsible for all the diversity and complexity of life we see on earth. Theism predicted only God created life on earth – The mutation rate to DNA is overwhelmingly detrimental. Detrimental to such a point that it is seriously questioned whether there are any truly beneficial, information building, mutations whatsoever. (M. Behe; JC Sanford) - 15. Naturalism/Materialism predicted morality is subjective and illusory. Theism predicted morality is objective and real. Morality is found to be deeply embedded in the genetic responses of humans. As well, morality is found to be deeply embedded in the structure of the universe. Embedded to the point of eliciting physiological responses in humans before humans become aware of the morally troubling situation and even prior to the event even happening. 16. Naturalism/Materialism predicted that we are merely our material bodies with no transcendent component to our being, and that we die when our material bodies die. Theism predicted that we have minds/souls that are transcendent of our bodies that live past the death of our material bodies. Transcendent, and ‘conserved’, (cannot be created or destroyed), ‘non-local’, (beyond space-time matter-energy), quantum entanglement/information, which is not reducible to matter-energy space-time, is now found in our material bodies on a massive scale (in every DNA and protein molecule).
As you can see when we remove the artificial imposition of the materialistic philosophy (methodological naturalism), from the scientific method, and look carefully at the predictions of both the materialistic philosophy and the Theistic philosophy, side by side, we find the scientific method is very good at pointing us in the direction of Theism as the true explanation. - In fact science is even very good at pointing us to Christianity as the solution for the much sought after 'theory of everything'
General Relativity, Quantum Mechanics, Entropy & The Shroud Of Turin - (video) http://www.godtube.com/watch/?v=9FCEMJNU
Verses and Music:
Psalm 139:7-16 Where can I go from your Spirit? Where can I flee from your presence? If I go up to the heavens, you are there; if I make my bed in the depths, you are there. If I rise on the wings of the dawn, if I settle on the far side of the sea, even there your hand will guide me, your right hand will hold me fast. If I say, “Surely the darkness will hide me and the light become night around me,” even the darkness will not be dark to you; the night will shine like the day, for darkness is as light to you. For you created my inmost being; you knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well. My frame was not hidden from you when I was made in the secret place, when I was woven together in the depths of the earth. Your eyes saw my unformed body; all the days ordained for me were written in your book before one of them came to be. You Are God Alone-Phillips, Craig, & Dean - video https://www.youtube.com/watch?v=9xPzTSpbYmk&list=PLECF3BAB277F09F2C&index=1
asauber @10:
“last year’s understanding of evolution was incomplete and only approximately correct” In other words, “wrong”.
Did you read the Asimov essay? He answers basically this objection, except about physics. Do you dismiss physics as "wrong"? Chemistry? Astronomy? All of science? If not, why single out evolutionary biology? bFast @11: I don't see any good reason why not. Genetic algorithms work, as long as the fitness function is favorable (selectable intermediates are critical). The "No Free Lunch" theorem shows that random fitness functions are not favorable, but the actual fitness function biological organisms are subject to is very strongly nonrandom, and in favorable ways. Whether it's favorable enough to explain all the functional complexity we see is IMO an open question, but it seems to be at least close. (And it's been claimed this deviation from randomness -- "active information" and its relatives -- must derive from an intelligent source. I don't see any good basis for this claim.) ppolish @12: I assume you're referring to fine tuning? If so, be aware that "not chance" does not equal "intelligence". Gravity is (as far as we can tell) completely nonrandom, but that doesn't support the theory of intelligent falling. We don't know why e.g. the constants of physics have the particular values they have, but to claim that they must have been intelligently chosen is a pure ID-of-the-gaps argument. Gordon Davisson
Physics is coming to grips with the evidence/maths that show Nature could not emerge from chance. Won't be a pretty picture when biology reaches the same conclusion. ppolish
Gordon Davisson, "Most of my actual background is in computer science ... " Hmmm, My background is in computer science as well. It is my skill as a software developer that has me baffled that anyone could envision the intricacy of a human being coded via chance, one working mutational event at a time. Everything I see in DNA is coding at a level far above my pay grade. bFast
"last year’s understanding of evolution was incomplete and only approximately correct" In other words, "wrong". And the future looks just as bright! Andrew asauber
Gordon, "tis but a scratch to neo-Darwinism I tell ya!" Black Knight Scene - Monty Python and the Holy Grail https://www.youtube.com/watch?v=RG1P8MQS1cU :) bornagain
News, I'm not anything like an expert on the subject of evolution, but I'd consider myself a well-educated layman. (Most of my actual background is in computer science and physics.) I've also been following UD for quite a long time (since William Dembski ran it), and I'm reasonably familiar with the arguments for ID. I just find them seriously unconvincing. Some are just plain wrong (see Vincent Torley's recent debunking of a couple of points -- unfortunately, that seems to be just the tip of the iceberg). These are going to be rightly ignored by real scientists (much as physicists will generally ignore people who think, for example, that the twin paradox represents an actual problem for relativity). A lot of the other arguments I see against evolution (such as bornagain's points at #7) really only indicate that last year's understanding of evolution was incomplete and only approximately correct. Just like our current understanding of evolution. Just like our current understanding of physics, chemistry, geology, astronomy, and any other (active) field of science you care to name. You seem to think these indicate terrible problems with evolutionary theory, but they look just like normal, incremental, progress in any other field. Again, go read the Asimov piece I linked. Do it now. And get some experience with what the messy process of normal science actually looks like, so you'll have a better idea how to recognize it. Gordon Davisson
as to:
"Probably the biggest single change was in the early 20th century, when Darwin’s theory of natural selection got put together with Mendelian genetics and a population-level statistical approach to genetics (known as population genetics), forming what became known as the new synthetic theory of evolution, or neo-Darwinism." - Gordon Davisson
And neo-Darwinism is now known to be false:
Modern Synthesis Of Neo-Darwinism Is False – Denis Noble – video http://www.metacafe.com/w/10395212 ,, In the preceding video, Dr Nobel states that around 1900 there was the integration of Mendelian (discrete) inheritance with evolutionary theory, and about the same time Weismann established what was called the Weismann barrier, which is the idea that germ cells and their genetic materials are not in anyway influenced by the organism itself or by the environment. And then about 40 years later, circa 1940, a variety of people, Julian Huxley, R.A. Fisher, J.B.S. Haldane, and Sewell Wright, put things together to call it ‘The Modern Synthesis’. So what exactly is the ‘The Modern Synthesis’? It is sometimes called neo-Darwinism, and it was popularized in the book by Richard Dawkins, ‘The Selfish Gene’ in 1976. It’s main assumptions are, first of all, is that it is a gene centered view of natural selection. The process of evolution can therefore be characterized entirely by what is happening to the genome. It would be a process in which there would be accumulation of random mutations, followed by selection. (Now an important point to make here is that if that process is genuinely random, then there is nothing that physiology, or physiologists, can say about that process. That is a very important point.) The second aspect of neo-Darwinism was the impossibility of acquired characteristics (mis-called “Larmarckism”). And there is a very important distinction in Dawkins’ book ‘The Selfish Gene’ between the replicator, that is the genes, and the vehicle that carries the replicator, that is the organism or phenotype. And of course that idea was not only buttressed and supported by the Weissman barrier idea, but later on by the ‘Central Dogma’ of molecular biology. Then Dr. Nobel pauses to emphasize his point and states “All these rules have been broken!”. Professor Denis Noble is President of the International Union of Physiological Sciences. "Physiology Is Rocking the Foundations of Evolutionary Biology": Another Peer-Reviewed Paper Takes Aim at Neo-Darwinism - Casey Luskin March 31, 2015 Excerpt: Noble doesn't mince words: "It is not only the standard 20th century views of molecular genetics that are in question. Evolutionary theory itself is already in a state of flux (Jablonka & Lamb, 2005; Noble, 2006, 2011; Beurton et al. 2008; Pigliucci & Muller, 2010; Gissis & Jablonka, 2011; Shapiro, 2011). In this article, I will show that all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproved." Noble then recounts those assumptions: (1) that "genetic change is random," (2) that "genetic change is gradual," (3) that "following genetic change, natural selection leads to particular gene variants (alleles) increasing in frequency within the population," and (4) that "inheritance of acquired characteristics is impossible." He then cites examples that refute each of those assumptions,,, He then proposes a new and radical model of biology called the "Integrative Synthesis," where genes don't run the show and all parts of an organism -- the genome, the cell, the body plan, everything -- is integrated. http://www.evolutionnews.org/2015/03/physiology_is_r094821.html Die, selfish gene, die - The selfish gene is one of the most successful science metaphors ever invented. Unfortunately, it’s wrong - Dec. 2013 Excerpt: But 15 years after Hamilton and Williams kited [introduced] this idea, it was embraced and polished into gleaming form by one of the best communicators science has ever produced: the biologist Richard Dawkins. In his magnificent book The Selfish Gene (1976), Dawkins gathered all the threads of the modern synthesis — Mendel, Fisher, Haldane, Wright, Watson, Crick, Hamilton, and Williams — into a single shimmering magic carpet (called the selfish gene). Unfortunately, say Wray, West-Eberhard and others, it’s wrong. https://uncommondesc.wpengine.com/darwinism/epigenetics-dawkins-selfish-gene-discredited-by-still-more-scientists-you-should-have-heard-of/ Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble 07/09/2014 Excerpt: Suzan Mazur: In recent years the modern synthesis has been declared extended by major evolutionary thinkers (e.g., "the Altenberg 16" and others), as well as dead by major evolutionary thinkers, the late Lynn Margulis and Francisco Ayala among them. Ditto for the public discourse on the Internet. My understanding is that you are now calling for the modern synthesis to be replaced. Denis Noble: I would say that it needs replacing. Yes. http://www.huffingtonpost.com/suzan-mazur/replace-the-modern-sythes_b_5284211.html Exposing the impotence of the Neo-Darwinian theory - By Dick Peterson - Jan. 2, 2015 Excerpt: Scientists who reject the Neo-Darwinian theory of evolution are getting bolder about publicly proclaiming their skepticism of the explanation for the origins of life once universally accepted in the scientific community. During a mid-November conference in Sao Paolo, Brazil, 350 mostly young research scientists and scholars from Brazil, the United States, Canada, Egypt, Uruguay, Argentina, and Peru gathered to discuss intelligent design (ID). The conference dealt “directly with ID evidence and proof, and how the present scientific paradigms fail to explain the origin and evolution of the universe and life on Earth,” ,,, Neo-Darwinian evolution, or what evolutionary biologists refer to as the Modern Evolutionary Synthesis (MES), is fraught with fundamental problems,,, “As a matter of fact, Modern Evolutionary Synthesis is a dead scientific theory since 1980,” Filho said. Several cell structures discovered since then cast doubt on the previously held notion that the DNA-to-RNA-to-protein process alone determines the basic features of living cells. Such doubt led to what has become known as the Altenberg 16 conference in 2008, when 16 evolutionary biologists and science philosophers met in Altenberg, Austria, and called for an Extended Evolutionary Synthesis (EES) to modify and eventually replace MES. The Altenbeg 16 meeting gave voice to the growing realization of the inadequacy of MES to explain evolution. Proponents of creation theory and ID theory point to conclusions from the meeting as evidence that MES, still taught in classrooms and accepted by most practicing biologists, is a framework beginning to topple. EES will be announced as a new general theory of evolution in 2020, but if the scientific literature on the subject is any indication, it won’t include the origin of genetic information. Filho predicts that without complex specified information, EES will be stillborn as a scientific theory. In the past year, an expanding group of researchers and authors seeking a forum to voice their beliefs that other mechanisms would better explain evolutionary processes are joining a website called The Third Way. http://www.worldmag.com/2015/01/exposing_the_impotence_of_the_neo_darwinian_theory Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf 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 - 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
Gordon Davisson, did you drop in from the 1980s? Hey great, welcome to 2015, where basic physics theories are still pretty sound, but Darwinian biology has morphed so much that it is impossible to say what it is any more. Keep checking the site here for updates. News
I don't see any actual difference between physicists and evolutionary biologists here. In both cases, the basic attitude is "we don't understand X, Y, or Z, but we can use our understanding of A, B, and C to try to figure them out." Neither group is going to say "we don't understand X, Y, or Z, so I guess we should throw out our understanding of A, B, and C." There are indeed plenty of unknowns in both physics and evolutionary biology; in both areas scientists treat them as targets for research, not as reasons to throw up their hands and abandon all current theory. Ask a physicist about dark matter, and you're likely to get an answer along the lines of "we don't know what it is yet, and there's relatively little direct evidence about it, but we're squeezing as much information as we can out of the evidence we do have." Ask an evolutionary biologist about the origin of life, and you're likely to get an answer along the lines of "we don't know how it happened yet, and there's relatively little direct evidence about it, but we're squeezing as much information as we can out of the evidence we do have." Neither one is going to deny that there are unknowns, and that our current understanding is significantly incomplete. But both will treat this as part of the normal process of science: you find answers to some questions, but they raise more more questions; you find answers to those, but they raise more questions; you find the answers to those... etc etc etc. Science is a progressive process of understanding. At any given point our knowledge will be incomplete and only approximately correct. But new theories build on past theories to push our knowledge further and further out, and also better and better approximations to reality. (Go read Isaac Asimov's "The Relativity of Wrong for a quick intro to science as a way of making closer and closer approximations to reality.) I have a feeling someone's going to ask why Darwinism hasn't been overthrown and replaced by something better; the answer is that it has, but the change has been evolutionary rather than revolutionary -- there's been lots of change in the theory, but most has been in the form of a huge number of small changes rather than one big change. Probably the biggest single change was in the early 20th century, when Darwin's theory of natural selection got put together with Mendelian genetics and a population-level statistical approach to genetics (known as population genetics), forming what became known as the new synthetic theory of evolution, or neo-Darwinism. Since then there've been many other advances, including better understandings of the underlying genetics (DNA, the genetic code, etc) and finding more and more processes that contribute to evolution (neutral evolution, jumping genes, ERVs, polyploidy, meiotic drive, hypermutation, hitchhiking, etc etc etc). We've also extended & improved (and complicated) Darwin's theory of common ancestry, adding endosymbiosis, horizontal transfer, etc. And there's no reason whatsoever to think we'll stop learning new things about evolution; scientists are certainly trying their best to improve and extend our understanding. What they're not going to do is throw everything out and start over, any more than physicists are going to throw out their current understanding of gravity just because of dark matter. In a mature field (which, like it or not, evolutionary biology is), progress comes by building on past theory, not by throwing it out and starting over. Even in massive revolutions, like general relativity and quantum mechanics, the new theory derives significantly from the old theory. Gordon Davisson
Defining and Utilizing Intelligent Design in Science - Kirk Durston - Nov. 4, 2015 Excerpt: The first project was to develop a method to measure the minimum level of functional information required to code for a protein family. The results were published, Measuring the functional sequence complexity of proteins- 2007 http://www.tbiomed.com/content/4/1/47 and I then moved on to my first major ID-inspired project. As a result of my experience in testing experimental aircraft engines I observed that an intelligent designer usually specifies a higher degree of information for interdependent components. What if I applied this ID observation to the functional information encoding the 3D structure of globular proteins? My prediction was that it should reveal interdependencies within the primary structure. This, in turn, would reveal key sub-molecular structural components within the larger 3D structure. To test this hypothesis and prediction, I ran a large multiple sequence alignment for ubiquitin through a pattern discovery program that searched for patterns of high information content between sites in the sequence, and clustered the sites accordingly in a nested hierarchy. I was thrilled when the results revealed a cluster tree that predicted important structural interdependencies as well as key binding areas and possible stages of the folding sequence. Comparison with the known 3D structure for ubiquitin, together with published research on binding areas and unfolding experiments, confirmed that the results were meaningful. These were published in a subsequent paper. Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring - 2012 http://www.bsb.eurasipjournals.com/content/2012/1/8 This approach could give rise to an enormous ID-inspired research program that would give further understanding into protein structure and folding, should someone decide to pursue it. http://p2c.com/students/defining-and-utilizing-intelligent-design-in-science-2/
Actually, this whole line of reasoning (the humility of physics) was brought into much clearer a few years ago when I had opportunity to put up a theoretical physicist for a few days. He discussed with me how a few decades back physicists thought they had it in the bag too, then Einstein came along and ruined everything. It got even worse when quantum physics poked its nose into the pristine Newtonian world. I have been waiting for biology to have their Einstein moment ever since. Maybe it'll come with de-novo genes. No, probably not. bFast
Here's a better link to the same phenomenon: https://youtu.be/CEYcGPF00l0 bFast
News, sometimes you just got to use the unsolved mysteries of science to your advantage even before you fully understand them: Case in point: https://assets.rbl.ms/1511120/980x.jpg :) bornagain

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