At Access Research Network: Art Battson on keeping evolution in context

JVL: "You think mutations are not random with respect to fitness? I guess you can believe that if you want to." And yet, "But that assumption is now known to be false."

In the twentieth century, the theory of evolution predicted that mutations are not adaptive or directed. In other words, mutations were believed to be random with respect to the needs of the individual. As Julian Huxley put it, “Mutation merely provides the raw material of evolution; it is a random affair, and takes place in all directions. … in all cases they are random in relation to evolution. Their effects are not related to the needs of the organisms.” (Huxley, 36) Or as Jacques Monod explained: "chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is likely ever to be revised." (Monod, 112) Ronald Fisher wrote that mutations are “random with respect to the organism’s need” (Orr). This fundamental prediction persisted for decades as a recent paper explained: “mutation is assumed to create heritable variation that is random and undirected.” (Chen, Lowenfeld and Cullis) But that assumption is now known to be false. The first problem is that the mutation rate is adaptive. For instance, when a population of bacteria is subjected to harsh conditions it tends to increase its mutation rate. It is as though a signal has been sent saying, “It is time to adapt.” Also, a small fraction of the population increases its mutation rates even higher yet. These hypermutators ensure that an even greater variety of adaptive change is explored. (Foster) Experiments have also discovered that duplicated DNA segments may be subject to higher mutation rates. Since the segment is a duplicate it is less important to preserve and, like a test bed, appears to be used to experiment with new designs. (Wright) The second problem is that organisms use strategies to direct the mutations according to the threat. Adaptive mutations have been extensively studied in bacteria. Experiments typically alter the bacteria food supply or apply some other environmental stress causing mutations that target the specific environmental stress. (Burkala, et. al.; Moxon, et. al; Wright) Adaptive mutations have also been observed in yeast (Fidalgo, et. al.; David, et. al.) and flax plants. (Johnson, Moss and Cullis) One experiment found repeatable mutations in flax in response to fertilizer levels. (Chen, Schneeberger and Cullis) Another exposed the flax to four different growth conditions and found that environmental stress can induce mutations that result in “sizeable, rapid, adaptive evolutionary responses.” (Chen, Lowenfeld and Cullis) In response to this failed prediction some evolutionists now are saying that evolution somehow created the mechanisms that cause mutations to be adaptive. https://sites.google.com/site/darwinspredictions/mutations-are-not-adaptive

JVL goes on to state "I’m trying to explain what a vast majority of working scientists actually believe to be true based on empirical evidence." And yet a 'vast majority of working scientists', according to JVL, and in direct contradiction to empirical evidence, apparently believe 'mutations are random with respect to fitness',,, Go figure!bornagain77

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Seversky, JVL... Darwin's theory of evolution is the biggest fail in the history of science. The only reason why it lasted for so long (150 years), it is because the subject is politically very sensitive. Anyway, it is very disturbing, that so many smart people (after all the discoveries made in 21st century) still support it. The whole theory is absurd to the highest possible degree. Viruses - the MOST ABUNDANT biological entity on Earth, and your theory can't explain where viruses come from :)))) Especially in COVID-19 era. So absurd it is :))))martin_r

January 9, 2021

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Bornagain77: Well JVL,,,, whatever,,, The randomness postulate of Darwinian evolution is what it is, and that postulate has been falsified by empirical observation. PERIOD! You think mutations are not random with respect to fitness? I guess you can believe that if you want to. I am more than satisfied that unbiased readers can see that I have made my case against that primary postulate of Darwinian evolution, and that you are, once again, just trying to blow smoke to CYA, rather than ever honestly admitting the truth. I'm trying to explain what a vast majority of working scientists actually believe to be true based on empirical evidence. You're allowed to disagree of course. You're not a working scientist are you? I'm not being snarky, just asking a question.JVL

January 9, 2021

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Well JVL,,,, whatever,,, The randomness postulate of Darwinian evolution is what it is, and that postulate has been falsified by empirical observation. PERIOD! I am more than satisfied that unbiased readers can see that I have made my case against that primary postulate of Darwinian evolution, and that you are, once again, just trying to blow smoke to CYA, rather than ever honestly admitting the truth.bornagain77

January 9, 2021

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Bornagain77: The fact that we ‘do not observe randomness in all natural things or events or situations’ is a empirical observation that goes directly against the Darwinian presupposition of randomness. It is not an argument that is in favor of the truthfulness of Darwinism. The presupposition of randomness only applies to mutations with respect to health and things like rocks falling, the interactions between individual atoms and molecules and such. But not to classes of objects like molecules in cells. Over the last several decades, Darwinists, because of their reductive materialistic framework, have presupposed there to be far more ‘random thermodynamic jostling’ of atoms and molecules in molecular biology than there is actually turning out to be. That level of randomness is not hypothesised to affect things on a larger scale. For example: even if the position of the electrons in the atoms in your body is undeterminable at some level it doesn't mean your whole body is likely to fly apart at any given moment. Another example: Brownian motion does not apply to multi-cellular organisms; it just doesn't come in the picture. The same can be said for most quantum effects and the weak and strong nuclear force. We don't have to accommodate those things at our level of existence. In the example of the cell . . . the interactions between groups of atoms and molecules is NOT random, there may be some uncertainty exactly when some particular interaction will happen but step back a stage or two and the trends are clear. I think of it like radioactive decay: you can't say when a particular atom will decay but the general flow is predictable and clear. And it's NOT random. And even though Dr. Alberts wrote that article 23 years ago in 1998, Darwinists, because of the ‘randomness’ presupposition held within their reductive materialistic framework, are still very much reluctant to let go of their belief that the cell is “dominated by randomly colliding individual protein molecules”. Again, step back from looking at the individual molecules and look at general trends. That is predictable. This is why drugs work: you can't say when or if a dose of antibiotics will kill a particular bacterium but you know the general trend. And it works.JVL

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Moreover, as if all that was not bad enough for Darwinists, Darwin’s theory holds mutations to the genome to be random. Yet, the vast majority of mutations to the genome are now found to not be random but are instead found to be ‘directed’.

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 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

And yet, in spite of these empirical findings that show randomness to be far less prevalent than Darwinists had presupposed,, Darwinists, because of the 'waiting time problem', have cast natural selection itself under the bus, and Darwinists are now more reliant on chance and/or randomness than they ever were before,, i.e. " It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance."

Austin Hughes and Neutral Theory - Laurence A. Moran - June 19, 2017 Excerpt: Originally proposed by Motoo Kimura, Jack King, and Thomas Jukes, the neutral theory of molecular evolution is inherently non-Darwinian. Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance. http://sandwalk.blogspot.com/2017/06/austin-hughes-and-neutral-theory.html The waiting time problem in a model hominin population – 2015 Sep 17 John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner Excerpt: The program Mendel’s Accountant realistically simulates the mutation/selection process,,, Given optimal settings, what is the longest nucleotide string that can arise within a reasonable waiting time within a hominin population of 10,000? Arguably, the waiting time for the fixation of a “string-of-one” is by itself problematic (Table 2). Waiting a minimum of 1.5 million years (realistically, much longer), for a single point mutation is not timely adaptation in the face of any type of pressing evolutionary challenge. This is especially problematic when we consider that it is estimated that it only took six million years for the chimp and human genomes to diverge by over 5 % [1]. This represents at least 75 million nucleotide changes in the human lineage, many of which must encode new information. While fixing one point mutation is problematic, our simulations show that the fixation of two co-dependent mutations is extremely problematic – requiring at least 84 million years (Table 2). This is ten-fold longer than the estimated time required for ape-to-man evolution. In this light, we suggest that a string of two specific mutations is a reasonable upper limit, in terms of the longest string length that is likely to evolve within a hominin population (at least in a way that is either timely or meaningful). Certainly the creation and fixation of a string of three (requiring at least 380 million years) would be extremely untimely (and trivial in effect), in terms of the evolution of modern man. It is widely thought that a larger population size can eliminate the waiting time problem. If that were true, then the waiting time problem would only be meaningful within small populations. While our simulations show that larger populations do help reduce waiting time, we see that the benefit of larger population size produces rapidly diminishing returns (Table 4 and Fig. 4). When we increase the hominin population from 10,000 to 1 million (our current upper limit for these types of experiments), the waiting time for creating a string of five is only reduced from two billion to 482 million years. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573302/

If Darwinian evolution were a normal science, instead of basically being a religion for atheists, these falsifications of both natural selection and 'randomness' should count as complete falsifications of their theory.,,, and Darwin's theory should be forever relegated to the dustbin of failed scientific theories. But alas, as has been pointed out in the preceding posts, Darwinian evolution is a religion, not a science! Of supplemental note:

Darwinian Materialism vs. Quantum Biology – Part II - video https://www.youtube.com/watch?v=oSig2CsjKbg

bornagain77

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Yet, regardless of their overt bias against anyone daring to see Intelligent Design in the cell, the fact of the matter is that we now have several lines of evidence firmly establishing the fact that the cell is not nearly as random and haphazard in its makeup as Darwinists would prefer people to believe For instance, in the following article from 2014, Dr Jonathan Wells takes direct issue with Carl Zimmer's claim that biological molecules are 'flailing blindly in the crowd' and states,, But that’s not what the biological evidence shows. In fact, kinesin moves quickly, with precise movements, to get from one place to another,,,

Flailing Blindly: The Pseudoscience of Josh Rosenau and Carl Zimmer – Jonathan Wells - April 17, 2014 Excerpt: The new animation (like the old) also includes a kinesin molecule hauling a vesicle, but this time the kinesin’s movements are characterized (in Zimmer’s words) by “barely constrained randomness. Every now and then, a tiny molecule loaded with fuel binds to one of the kinesin “feet.” It delivers a jolt of energy, causing that foot to leap off the molecular cable and flail wildly, pulling hard on the foot that’s still anchored. Eventually, the gyrating foot stumbles into contact again with the cable, locking on once more — and advancing the vesicle a tiny step forward. This updated movie offers a better way to picture our most intricate inner workings…. In the 2006 version, we can’t help seeing intention in the smooth movements of the molecules; it’s as if they’re trying to get from one place to another. In reality, however, the parts of our cells don’t operate with the precise movements of the springs and gears of a clock. They flail blindly in the crowd.” But that’s not what the biological evidence shows. In fact, kinesin moves quickly, with precise movements, to get from one place to another. A kinesin molecule takes one 8-nanometer "step" along a microtubule for every high-energy ATP molecule it uses, and it uses about 80 ATPs per second. On the scale of a living cell, this movement is very fast. To visualize it on a macroscopic scale, imagine a microtubule as a one-lane road and the kinesin molecule as an automobile. The kinesin would be traveling over 200 miles per hour! https://iconsofevolution.com/flailing-blindly/

Moreover, in the following 2016 paper, it was found that “crowding in cells doesn’t hamper protein binding as much as they thought it did.” In fact, finding a lack of ‘collisions’ in the crowded cell was a ‘counterintuitive surprise’ for the researchers: Specifically one of the researchers stated: “This was a surprise,” “It’s counterintuitive, because one would think collisions between a protein and other molecules on DNA would slow it down. But the system is so dynamic, it doesn’t appear to be an issue.”

Proteins put up with the roar of the crowd – June 23, 2016 Excerpt: It gets mighty crowded around your DNA, but don’t worry: According to Rice University researchers, your proteins are nimble enough to find what they need. Rice theoretical scientists studying the mechanisms of protein-DNA interactions in live cells showed that crowding in cells doesn’t hamper protein binding as much as they thought it did.,,, If DNA can be likened to a library, it surely is a busy one. Molecules roam everywhere, floating in the cytoplasm and sticking to the tightly wound double helix. “People know that almost 90 percent of DNA is covered with proteins, such as polymerases, nucleosomes that compact two meters into one micron, and other protein molecules,” Kolomeisky said.,,, That makes it seem that proteins sliding along the strand would have a tough time binding, and it’s possible they sometimes get blocked. But the Rice team’s theory and simulations indicated that crowding agents usually move just as rapidly, sprinting out of the way. “If they move at the same speed, the molecules don’t bother each other,” Kolomeisky said. “Even if they’re covering a region, the blockers move away quickly so your protein can bind.” In previous research, the team determined that stationary obstacles sometimes help quicken a protein’s search for its target by limiting options. This time, the researchers sought to define how crowding both along DNA and in the cytoplasm influenced the process. “We may think everything’s fixed and frozen in cells, but it’s not,” Kolomeisky said. “Everything is moving.”,,, Floating proteins appear to find their targets quickly as well. “This was a surprise,” he said. “It’s counterintuitive, because one would think collisions between a protein and other molecules on DNA would slow it down. But the system is so dynamic, it doesn’t appear to be an issue.” http://phys.org/news/2016-06-proteins-roar-crowd.html

In fact, instead of a biological systems being “dominated by randomly colliding individual protein molecules”, the fact of the matter is that biological systems are now shown to be extremely resistant to random background noise. As the following article on photosynthesis stated, 'These biological systems can direct a quantum process,,, in astoundingly subtle and controlled ways – showing remarkable resistance to the aggressive, random background noise of biology and extreme environments.'

Unlocking nature's quantum engineering for efficient solar energy - January 7, 2013 Excerpt: Certain biological systems living in low light environments have unique protein structures for photosynthesis that use quantum dynamics to convert 100% of absorbed light into electrical charge,,, "Some of the key issues in current solar cell technologies appear to have been elegantly and rigorously solved by the molecular architecture of these PPCs – namely the rapid, lossless transfer of excitons to reaction centres.",,, These biological systems can direct a quantum process, in this case energy transport, in astoundingly subtle and controlled ways – showing remarkable resistance to the aggressive, random background noise of biology and extreme environments. "This new understanding of how to maintain coherence in excitons, and even regenerate it through molecular vibrations, provides a fascinating glimpse into the intricate design solutions – seemingly including quantum engineering – ,,, and which could provide the inspiration for new types of room temperature quantum devices." http://phys.org/news/2013-01-nature-quantum-efficient-solar-energy.html

Likewise the following article on human vision stated that, “Research,, has shown that humans can detect the presence of a single photon, the smallest measurable unit of light”.,,, “it is remarkable: a photon, the smallest physical entity with quantum properties of which light consists, is interacting with a biological system consisting of billions of cells, all in a warm and wet environment,”,, and the researched added, “The response that the photon generates survives all the way to the level of our awareness despite the ubiquitous background noise. Any man-made detector would need to be cooled and isolated from noise to behave the same way.”,,, “What we want to know next is how does a biological system achieve such sensitivity? How does it achieve this in the presence of noise?”

Study suggests humans can detect even the smallest units of light – July 21, 2016 Excerpt: Research,, has shown that humans can detect the presence of a single photon, the smallest measurable unit of light. Previous studies had established that human subjects acclimated to the dark were capable only of reporting flashes of five to seven photons.,,, it is remarkable: a photon, the smallest physical entity with quantum properties of which light consists, is interacting with a biological system consisting of billions of cells, all in a warm and wet environment,” says Vaziri. “The response that the photon generates survives all the way to the level of our awareness despite the ubiquitous background noise. Any man-made detector would need to be cooled and isolated from noise to behave the same way.”,,, The gathered data from more than 30,000 trials demonstrated that humans can indeed detect a single photon incident on their eye with a probability significantly above chance. “What we want to know next is how does a biological system achieve such sensitivity? How does it achieve this in the presence of noise?” http://phys.org/news/2016-07-humans-smallest.html

Moreover, instead of proteins randomly colliding into each other, as the Harvard Biovisions video falsely portrayed them, proteins instead are found to be “analogous to the way wine glasses tremble”,,, "If you tap on a bell, it rings for some time, and with a sound that is specific to the bell. This is how the proteins behave,"

Symphony of Life, Revealed: New Imaging Technique Captures Vibrations of Proteins, Tiny Motions Critical to Human Life - Jan. 16, 2014 Excerpt: To observe the protein vibrations, Markelz' team relied on an interesting characteristic of proteins: The fact that they vibrate at the same frequency as the light they absorb. This is analogous to the way wine glasses tremble and shatter when a singer hits exactly the right note. Markelz explained: Wine glasses vibrate because they are absorbing the energy of sound waves, and the shape of a glass determines what pitches of sound it can absorb. Similarly, proteins with different structures will absorb and vibrate in response to light of different frequencies. So, to study vibrations in lysozyme, Markelz and her colleagues exposed a sample to light of different frequencies and polarizations, and measured the types of light the protein absorbed. This technique, , allowed the team to identify which sections of the protein vibrated under normal biological conditions. The researchers were also able to see that the vibrations endured over time, challenging existing assumptions. "If you tap on a bell, it rings for some time, and with a sound that is specific to the bell. This is how the proteins behave," Markelz said. "Many scientists have previously thought a protein is more like a wet sponge than a bell: If you tap on a wet sponge, you don't get any sustained sound." http://www.sciencedaily.com/releases/2014/01/140116084838.htm

Moreover, in direct contradiction to Carl Zimmer’s claim of molecules flailing blindly in a crowd, in the following article subtitled 'how bio-molecular machines can generate nontrivial quantum states', the authors state that entanglement can be maintained even in the presence of very intense noise,

Persistent dynamic entanglement from classical motion: how bio-molecular machines can generate nontrivial quantum states Gian Giacomo Guerreschi, Jianming Cai1, Sandu Popescu and Hans J Briegel Published 29 May 2012 Excerpt: Very recently (Cai et al 2010 Phys. Rev. E 82 021921), a simple mechanism was presented by which a molecule subjected to forced oscillations, out of thermal equilibrium, can maintain quantum entanglement between two of its quantum degrees of freedom. Crucially, entanglement can be maintained even in the presence of very intense noise, so intense that no entanglement is possible when the forced oscillations cease. This mechanism may allow for the presence of nontrivial quantum entanglement in biological systems. Here we significantly enlarge the study of this model. In particular, we show that the persistent generation of dynamic entanglement is not restricted to the bosonic heat bath model, but can also be observed in other decoherence models, e.g. the spin gas model, and in non-Markovian scenarios. We also show how conformational changes can be used by an elementary machine to generate entanglement even in unfavorable conditions. In biological systems, similar mechanisms could be exploited by more complex molecular machines or motors. http://iopscience.iop.org/article/10.1088/1367-2630/14/5/053043/meta

And in the following article, the authors even go on to state that 'this reverses the previous orthodoxy, which held that quantum effects could not exist in biological systems because of the amount of noise in these systems',,, Environmental noise here drives a persistent and cyclic generation of new entanglement.

Quantum entanglement in hot systems Excerpt: The authors remark that this reverses the previous orthodoxy, which held that quantum effects could not exist in biological systems because of the amount of noise in these systems,,, Environmental noise here drives a persistent and cyclic generation of new entanglement. http://quantum-mind.co.uk/quantum-entanglement-hot-systems/

Thus instead of the molecular machines of the cell being dominated by random noise in the cell, as Carl Zimmer had falsely claimed in his New York Times article, the molecular machines of the cell are instead shown to have ‘remarkable resistance to the aggressive, random background noise of biology and extreme environments.’ Moreover, molecular machines are apparently designed in such an ingenious way so as to feed off the noise in the cell. Quote unquote, “Environmental noise here drives a persistent and cyclic generation of new entanglement.”bornagain77

January 9, 2021

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JVL,

I don’t agree with the argument you posted. We do not observe randomness in all natural things or events or situations.

The fact that we 'do not observe randomness in all natural things or events or situations' is a empirical observation that goes directly against the Darwinian presupposition of randomness. It is not an argument that is in favor of the truthfulness of Darwinism. Over the last several decades, Darwinists, because of their reductive materialistic framework, have presupposed there to be far more ‘random thermodynamic jostling’ of atoms and molecules in molecular biology than there is actually turning out to be. For instance, in the following 1998 article, Bruce Alberts, who was a two time president of the National Academy of Sciences, stated that “We have always underestimated cells.”,,, “But at least we are no longer as naïve as we were when I was a graduate student in the 1960s.”,,, “instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules.”

“We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naïve as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB — and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. Consider an enzyme, for example. If its substrate molecule is present at a concentration of 0.5mM,which is only one substrate molecule for every 105 water molecules, the enzyme’s active site will randomly collide with about 500,000 molecules of substrate per second. And a typical globular protein will be spinning to and fro, turning about various axes at rates corresponding to a million rotations per second. But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.” – Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell, 92 (February 6, 1998): 291-294) https://brucealberts.ucsf.edu/publications/BAPub157.pdf Editor-in-Chief of Science (2009-2013). Dr Alberts served two six-year terms as the president of the National Academy of Sciences

And even though Dr. Alberts wrote that article 23 years ago in 1998, Darwinists, because of the ‘randomness’ presupposition held within their reductive materialistic framework, are still very much reluctant to let go of their belief that the cell is “dominated by randomly colliding individual protein molecules”. For a prime example of this fact, In 2006 Harvard University, via a production company called “BioVisions”, made a video entitled The Inner Life of the Cell

The Inner Life of the Cell http://www.xvivo.net/animation/the-inner-life-of-the-cell/

The video by Harvard BioVisions was one of the first videos on the web that animated some of the amazing molecular machines that are now being found in cells. As you can see, the overwhelming impression of the intelligent design of the cell literally leaps out of the video at you. Since the Intelligent Design of the cell is readily apparent for all to see, Dr. William Dembski, one of the pioneers of the Intelligent Design movement, would, circa 2007, show the video in some of his talks to students on Intelligent Design:

Inner Life of a Cell w William Dembski commentary – video https://www.youtube.com/watch?v=jNs5kBE66Xo

When Harvard BioVisions found out about Dr. Dembski using the video in his lectures to his students they 'warned him’ not to use the video anymore.

William A. Dembski Excerpt: The Inner Life of the Cell copyright controversy,, David Bolinsky, creator of the video, wrote that Dembski was warned about using the video without permission,,, https://en.wikipedia.org/wiki/William_A._Dembski

Their effort to stop Dembski was futile since the video soon went viral on the web and anyone with access to a computer could download the video and watch it whenever they wanted to, and see for themselves the amazing design that is readily apparent in the cell. The Darwinists at Harvard Biovisions who had originally made the video apparently did not like this development one bit. And in 2013, apparently trying to undo the damage that was done to Darwinian thinking by their original video, Harvard BioVisions then made a subsequent video entitled 'Inner Life of the Cell: Protein Packing'.

In 2013, we released The Inner Life of the Cell: Protein Packing, which illustrates the crowded molecular environment present in cells. http://www.xvivo.net/animation/the-inner-life-of-the-cell/

In the 2013 video, as you can see, Harvard Biovisions tried to make the inner workings of the cell look as random, chaotic, and haphazard as possible so as to try to dispel any impression of design in the cell that they had inadvertently created in their first video.

Inner Life of a Cell | Protein Packing https://www.youtube.com/watch?v=uHeTQLNFTgU

In fact, in 2014 New York Times itself ran an article on the 'Protein Packing' video. I’m sure many ID advocates wish they could get such free promotion for their videos on intelligent design in the New York Times. But anyways, in the article Carl Zimmer stated that ' “In the 2006 version, we can’t help seeing intention in the smooth movements of the molecules” but of the 2013 video he said that the molecules of the cell 'flail blindly in the crowd.” And that “Our cells work almost in spite of themselves.'

Watch Proteins Do the Jitterbug - Carl Zimmer - APRIL 10, 2014 Excerpt: In the 2006 version, we can’t help seeing intention in the smooth movements of the molecules; it’s as if they’re trying to get from one place to another. In reality, however, the parts of our cells don’t operate with the precise movements of the springs and gears of a clock. They flail blindly in the crowd. Our cells work almost in spite of themselves. https://www.nytimes.com/2014/04/10/science/watch-proteins-do-the-jitterbug.html

Thus, even though Bruce Alberts himself. all the way back in 1998, had largely dispelled the myth that the cell was “dominated by randomly colliding individual protein molecules”, none-the-less, Darwinists as late as 2014, motivated primarily by their bias against Intelligent Design, were still widely disseminating the false claim that the cell was “dominated by randomly colliding individual protein molecules”.bornagain77

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Bornagain77: Well that is the oft repeated argument, but it is a argument that does not pass the smell test, ,,, as was referenced earlier and you apparently did not bother to read,,, I don't agree with the argument you posted. We do not observe randomness in all natural things or events or situations. In fact, your argument is circular; you assume that the argument is that everything is random including the generation of the universe therefore it's all random. But no one is saying that. The reason that science works at all is because certain situations and material configurations give dependable, predictable results NOT random results. It's NOT random all the way down, no one thinks it is.JVL

January 9, 2021

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JVL, "Natural selection is NOT totally random.",,, Well that is the oft repeated argument, but it is a argument that does not pass the smell test, ,,, as was referenced earlier and you apparently did not bother to read,,,

Assuming Naturalism to be true, Darwin’s god-of-the gaps becomes even less plausible when one realizes that random variations are processed by Naturalism’s randomly generated universe and its randomly generated filter of natural selection making the entire process random all the way down. While there is nothing like a good scientific theory, “everything just happened randomly” is nothing like a good scientific theory. - Art Battson http://www.arn.org/eic/eic/Welcome.html

bornagain77

January 9, 2021

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Bornagain77: rationality can only be grounded within the Theistic worldview and cannot possibly be based on chaos and/or randomness as Darwinists presuppose to be the ultimate source of all things,, (of both physical and mental things). Is that what they really claim though? I don't think so. As far as unguided evolution goes the only part that is claimed to be random is the occurrence of mutations with respect to health. Natural selection is NOT totally random. Certainly some life forms and individuals are snuffed out because of random events like rock falls or some such. But even there, many natural phenomena are not totally random: floods depend on climatic conditions and geography to some extent. Monsoons don't happen everywhere on the planet. You don't find permafrost in Australia. I don't think most physicists think the universe arose out of chaos randomly. It seems to me they are trying to find the most basic building blocks of our universe and the ways those blocks can be put together suggest certain kinds of structures and arrangements; like atoms and molecules. IF there is such a basis to reality (kind of like everything being reduced to a few kinds of Lego bricks) then what happens cannot be completely random as only certain configurations can occur.JVL

January 9, 2021

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Seversky, in order to even argue in a rationally coherent manner in the first place you are forced to adopt a Theological worldview. i.e. If you believe that the universe, and therefore your thoughts, are ultimately the result of chaos and/or randomness, then all rationality is lost. Only in Theism can rationality, and therefore science itself, be coherently grounded:

“It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter.” - J B S Haldane -“When I am dead,” in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209. “Supposing there was no intelligence behind the universe, no creative mind. In that case, nobody designed my brain for the purpose of thinking. It is merely that when the atoms inside my skull happen, for physical or chemical reasons, to arrange themselves in a certain way, this gives me, as a by-product, the sensation I call thought. But, if so, how can I trust my own thinking to be true? It’s like upsetting a milk jug and hoping that the way it splashes itself will give you a map of London. But if I can’t trust my own thinking, of course I can’t trust the arguments leading to Atheism, and therefore have no reason to be an Atheist, or anything else. Unless I believe in God, I cannot believe in thought: so I can never use thought to disbelieve in God.” - C. S. Lewis - The Case for Christianity

Thus Seversky, if you were to truly "strip out all the theological references" that are in 'Origin of Species' then you would necessarily have to strip out rationality itself since rationality can only be grounded within the Theistic worldview and cannot possibly be based upon the chaos and/or randomness that Darwinists presuppose to be the ultimate source of all things,, (of both physical and mental things).bornagain77

January 9, 2021

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Bornagain77/3

And indeed, in Darwin’s book “Origin of Species” you will not find one mathematical equation, nor will you find one laboratory experiment. What you will find in abundance in Darwin’s book is “one long (theological) argument’.

He did, however, compile a great deal of data from observations in the field, which is a perfectly legitimate part of science, as is constructing theories to explain that data. Far more so than relying on holy texts and testaments written long after the events they purport to describe. And, if you wanted, you could do with Origins something like Jefferson did with the Bible, strip out all the theological references and just leave the pure, unadulterated theory behind.

Darwinists, with their vital dependence on faulty theological presuppositions, instead of on any compelling scientific evidence, in order to try to make their case for Darwinian evolution are, as Cornelius Van Til put it, much like the child who must climb up onto his father’s lap into order to slap his face.

The theory of evolution has no need of theological presuppositions, faulty or otherwise. Come to think of it, how do you actually decide if a theological presupposition is faulty or not? As for Van Til's cute little analogy, it's more like the child who gets off Santa's knee at Christmas and walks away shaking his or her head that they were still expected to believe comforting myths about their presents being delivered by a fat old man who comes down the chimney on Christmas Eve. Sooner or later, most people grow out of that sort of belief.Seversky

January 9, 2021

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It is interesting to note that, since all of science is based on presuppositions that can only be grounded within a Theistic worldview,,,

Physics and the Mind of God: The Templeton Prize Address – by Paul Davies – August 1995 Excerpt: “People take it for granted that the physical world is both ordered and intelligible. The underlying order in nature-the laws of physics-are simply accepted as given, as brute facts. Nobody asks where they came from; at least they do not do so in polite company. However, even the most atheistic scientist accepts as an act of faith that the universe is not absurd, that there is a rational basis to physical existence manifested as law-like order in nature that is at least partly comprehensible to us. So science can proceed only if the scientist adopts an essentially theological worldview.” https://www.firstthings.com/article/1995/08/003-physics-and-the-mind-of-god-the-templeton-prize-address-24 Taking Science on Faith – By PAUL DAVIES – NOV. 24, 2007 Excerpt: All science proceeds on the assumption that nature is ordered in a rational and intelligible way. You couldn’t be a scientist if you thought the universe was a meaningless jumble of odds and ends haphazardly juxtaposed. ,,, the very notion of physical law is a theological one in the first place, a fact that makes many scientists squirm. Isaac Newton first got the idea of absolute, universal, perfect, immutable laws from the Christian doctrine that God created the world and ordered it in a rational way. Christians envisage God as upholding the natural order from beyond the universe, while physicists think of their laws as inhabiting an abstract transcendent realm of perfect mathematical relationships. http://www.nytimes.com/2007/11/24/opinion/24davies.html Moreover, contrary to what many people have been falsely led to believe by Darwinian atheists, about Intelligent Design supposedly being a pseudo-science, the fact of the matter is that all of science, every nook and cranny of it, is based on the presupposition of intelligent design and is certainly not based on the presupposition of methodological naturalism. From the essential Christian presuppositions that undergird the founding of modern science itself, (namely that the universe is rational and that the minds of men, being made in the ‘image of God’, can dare understand that rationality), to the intelligent design of the scientific instruments and experiments themselves, to the logical and mathematical analysis of experimental results themselves, from top to bottom, science itself is certainly not to be considered a ‘natural’ endeavor of man. Not one scientific instrument would ever exist if men did not first intelligently design that scientific instrument. Not one test tube, microscope, telescope, spectroscope, or etc.. etc.., was ever found just laying around on a beach somewhere which was ‘naturally’ constructed by nature. Not one experimental result would ever be rationally analyzed since there would be no immaterial minds to rationally analyze the immaterial logic and immaterial mathematics that lay behind the intelligently designed experiments in the first place. Again, all of science, every nook and cranny of it, is based on the presupposition of intelligent design and is certainly not based on the presupposition of methodological naturalism.

,,, since all of science is based on presuppositions that can only be grounded within a Theistic worldview, then it is very interesting to note that Darwinian evolution itself is inextricably wedded to (faulty) Theistic presuppositions, In fact, Darwin's college degree, believe it or not, was in Theology. His degree was not in mathematics, nor was it in any other field that would be conducive to the founding of a new theory in science.

Charles Darwin - Education Charles Darwin entered Shrewsbury School as a boarding student in 1822. He left three years later, at the age of 16, called by his father to study medicine with his elder brother, Erasmus, at Edinburgh University. Repelled by the horror of early 19th century surgery, Darwin dropped out of Edinburgh in 1827 and enrolled in Christ College, Cambridge University, studying to be a clergyman in the Church of England. Charles earned his Bachelor's Degree in Theology in 1831.,,, https://www.allaboutscience.org/charles-darwin.htm

In fact, Darwin himself said that he found mathematics to be quote unquote, 'repugnant',,,

"I attempted mathematics [at Cambridge University ], and even went during the summer of 1828 with a private tutor (a very dull man) to Barmouth, but I got on very slowly. The work was repugnant to me, chiefly from my not being able to see any meaning in the early steps of algebra. This impatience was foolish, and in after years I have deeply regretted that I did not proceed far enough at least to understand something of the great leading principles of mathematics; for men thus endowed seem to have an extra sense. But I do not believe that I should ever have succeeded beyond a very low grade." - Darwin - Autobiography (p. 58 of the 1958 Norton edition)

And indeed, in Darwin's book "Origin of Species" you will not find one mathematical equation, nor will you find one laboratory experiment. What you will find in abundance in Darwin's book is "one long (theological) argument'.

CHARLES DARWIN: VICTORIAN MYTHMAKER By A.N. Wilson (Book Review By Jonathan Wells) - - Wednesday, January 31, 2018 Excerpt: Darwin called “The Origin of Species” “one long argument,” and it was a theology-laden argument against creation by design. Many people have the mistaken impression that Darwin’s theory was accepted because he provided so much scientific evidence for it (he didn’t). Instead, his theory was accepted because it fit the increasingly secular spirit of the times.,,, So Darwinian evolution is not so much a scientific theory as it is a secular creation myth. According to Mr. Wilson, “Darwinism, as is shown by the current state of debate, is resistant to argument because it is resistant to fact. The worship of Darwin as a man, the attribution to him of insights and discoveries which were either part of the common scientific store of knowledge or were the discoveries of others, this is all necessary to bolster the religion of Darwinism.” Mr. Wilson’s book is not flawless, but on this point he’s right. https://www.washingtontimes.com/news/2018/jan/31/book-review-charles-darwin-by-an-wilson/ Charles Darwin, Theologian: Major New Article on Darwin's Use of Theology in the Origin of Species - May 2011 Excerpt: The Origin supplies abundant evidence of theology in action; as Dilley observes: I have argued that, in the first edition of the Origin, Darwin drew upon at least the following positiva theological claims in his case for descent with modification (and against special creation): ?1. Human beings are not justified in believing that God creates in ways analogous to the intellectual powers of the human mind. 2. A God who is free to create as He wishes would create new biological limbs de novo rather than from a common pattern. 3. A respectable deity would create biological structures in accord with a human conception of the 'simplest mode' to accomplish the functions of these structures. 4. God would only create the minimum structure required for a given part's function. 5. God does not provide false empirical information about the origins of organisms. 6. God impressed the laws of nature on matter. 7. God directly created the first 'primordial' life. 8. God did not perform miracles within organic history subsequent to the creation of the first life. 9. A 'distant' God is not morally culpable for natural pain and suffering. 10. The God of special creation, who allegedly performed miracles in organic history, is not plausible given the presence of natural pain and suffering.?http://www.evolutionnews.org/2011/05/charles_darwin_theologian_majo046391.html

To this day Darwinists are still inextricably bound to (faulty) Theological argumentation,

Methodological Naturalism: A Rule That No One Needs or Obeys - Paul Nelson - September 22, 2014 Excerpt: It is a little-remarked but nonetheless deeply significant irony that evolutionary biology is the most theologically entangled science going. Open a book like Jerry Coyne's Why Evolution is True (2009) or John Avise's Inside the Human Genome (2010), and the theology leaps off the page. A wise creator, say Coyne, Avise, and many other evolutionary biologists, would not have made this or that structure; therefore, the structure evolved by undirected processes. Coyne and Avise, like many other evolutionary theorists going back to Darwin himself, make numerous "God-wouldn't-have-done-it-that-way" arguments, thus predicating their arguments for the creative power of natural selection and random mutation on implicit theological assumptions about the character of God and what such an agent (if He existed) would or would not be likely to do.,,, ,,,with respect to one of the most famous texts in 20th-century biology, Theodosius Dobzhansky's essay "Nothing in biology makes sense except in the light of evolution" (1973). Although its title is widely cited as an aphorism, the text of Dobzhansky's essay is rarely read. It is, in fact, a theological treatise. As Dilley (2013, p. 774) observes: "Strikingly, all seven of Dobzhansky's arguments hinge upon claims about God's nature, actions, purposes, or duties. In fact, without God-talk, the geneticist's arguments for evolution are logically invalid. In short, theology is essential to Dobzhansky's arguments.",, http://www.evolutionnews.org/2014/09/methodological_1089971.html Damned if You Do and Damned if You Don't - Steve Dilley- 2019-06-02 The Problem of God-talk in Biology Textbooks Abstract: We argue that a number of biology (and evolution) textbooks face a crippling dilemma. On the one hand, significant difficulties arise if textbooks include theological claims in their case for evolution. (Such claims include, for example, ‘God would never design a suboptimal panda’s thumb, but an imperfect structure is just what we’d expect on natural selection.’) On the other hand, significant difficulties arise if textbooks exclude theological claims in their case for evolution. So, whether textbooks include or exclude theological claims, they face debilitating problems. We attempt to establish this thesis by examining 32 biology (and evolution) textbooks, including the Big 12—that is, the top four in each of the key undergraduate categories (biology majors, non-majors, and evolution courses). In Section 2 of our article, we analyze three specific types of theology these texts use to justify evolutionary theory. We argue that all face significant difficulties. In Section 3, we step back from concrete cases and, instead, explore broader problems created by having theology in general in biology textbooks. We argue that the presence of theology—of whatever kind—comes at a significant cost, one that some textbook authors are likely unwilling to pay. In Section 4, we consider the alternative: Why not simply get rid of theology? Why not just ignore it? In reply, we marshal a range of arguments why avoiding God-talk raises troubles of its own. Finally, in Section 5, we bring together the collective arguments in Sections 2-4 to argue that biology textbooks face an intractable dilemma. We underscore this difficulty by examining a common approach that some textbooks use to solve this predicament. We argue that this approach turns out to be incoherent and self-serving. The poor performance of textbooks on this point highlights just how deep the difficulty is. In the end, the overall dilemma remains. https://journals.blythinstitute.org/ojs/index.php/cbi/article/view/44

Darwinists, with their vital dependence on faulty theological presuppositions, instead of on any compelling scientific evidence, in order to try to make their case for Darwinian evolution are, as Cornelius Van Til put it, much like the child who must climb up onto his father’s lap into order to slap his face.

“The ultimate source of truth in any field rests in him. The world may discover much truth without owning Christ as Truth. Christ upholds even those who ignore, deny, and oppose him. A little child may slap his father in the face, but it can do so only because the father holds it on his knee. So modern science, modern philosophy, and modern theology may discover much truth. Nevertheless, if the universe were not created and redeemed by Christ no man could give himself an intelligible account of anything. It follows that in order to perform their task aright the scientist and the philosopher as well as the theologian need Christ.” – Cornelius Van Til, The Case for Calvinism p.147-148 “In other words, the non-Christian needs the truth of the Christian religion in order to attack it. As a child needs to sit on the lap of its father in order to slap the father’s face, so the unbeliever, as a creature, needs God the Creator and providential controller of the universe in order to oppose this God. Without this God, the place on which he stands does not exist. He cannot stand in a vacuum.” Cornelius Van Til, Essays on Christian Education (The Presbyterian and Reformed Publishing Company: Phillipsburg, NJ, 1979).

In short, Darwinian atheists need God even to be able to have the capacity to argue against Him in the first place. It would be a very comical state of affairs were not the consequences for their own souls, in their rejection of God, not so terrifying.

The Uncomfortable Subject Jesus Addressed More than Anyone Else - MAY 11, 2017 Excerpt: A friend once challenged me to show her where Jesus talks about hell in the Gospels. Even a cursory read-through shows Jesus talked about it plenty. In fact, Jesus talked about hell more than any other person in the Bible. In Luke 16, he describes a great chasm over which “none may cross from there to us.” In Matthew 25, Jesus tells of a time when people will be separated into two groups, one entering into his presence, the other banished to “eternal fire.”,,, "Jesus talks about hell more than he talks about heaven, and describes it more vividly. There’s no denying that Jesus knew, believed, and warned against the absolute reality of hell." https://www.thegospelcoalition.org/article/the-uncomfortable-subject-jesus-addressed-more-than-anyone-else/

bornagain77

January 9, 2021

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Evolution; a 'non-theistic' religion which is "nothing like a good scientific theory'

KEEP EVOLUTION IN CONTEXT Excerpt: He (Pierre-Paul Grasse) goes on to say, "Mutations, in time, occur incoherently. They are not complementary to one another, nor are they cumulative in successive generations toward a given direction. They modify what preexists, but they do so in disorder, no matter how. ... As soon as some disorder, even slight, appears in an organized being, sickness, then death follow. There is no possible compromise between the phenomenon of life and anarchy (pp. 97, 98)." Grasse in several different places in his book provides devastating evidence to show that "chance" cannot account for evolution. He correctly evaluates the attitude of Darwinists toward "chance" when he says: "Directed by all-powerful selection, chance becomes a sort of providence, which, under the cover of atheism, is not named but which is secretly worshipped (p. 107)." Assuming Naturalism to be true, Darwin's god-of-the gaps becomes even less plausible when one realizes that random variations are processed by Naturalism's randomly generated universe and its randomly generated filter of natural selection making the entire process random all the way down. While there is nothing like a good scientific theory, "everything just happened randomly" is nothing like a good scientific theory. Evolution as a secular religion?* Grasse is not alone. Even Michael Ruse recognizes a secular religion when he sees one. "...And certainly, there's no doubt about it, that in the past, and I think also in the present, for many evolutionists, evolution has functioned as something with elements which are, let us say, akin to being a secular religion ... And it seems to me very clear that at some very basic level, evolution as a scientific theory makes a commitment to a kind of naturalism, namely, that at some level one is going to exclude miracles and these sorts of things come what may." - Ruse - "Nonliteralist Antievolution" - AAAS Symposium: "The New Antievolutionism," February 13, 1993, Boston, MA - National Center for Science Education,,,, Bottom line? Always keep "evolution" in context and beware of secular religions. Creation preceded evolution and Mind preceded matter. It matters. * Author's Note: John Calvert has pointed out that "Like Michael Ruse, I refer to materialistic evolution/origins science as a 'secular religion.'" He goes on to state that "I believe that is an oxymoron as 'secular' means 'not religious.' 'Not religious religion' = an oxymoron. So, I would suggest you change 'secular' to 'non-theistic.' ... http://www.arn.org/eic/eic/Welcome.html

bornagain77

January 9, 2021

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the article above quotes Bill Gates... Let me add another, very interesting quote of Bill Gates (all atheists should see this), it is from an interview for RollingStones magazine (from 2014) Bill Gates: "I agree with people like Richard Dawkins that mankind felt the need for creation myths. Before we really began to understand disease and the weather and things like that, we sought false explanations for them. Now science has filled in some of the realm – not all – that religion used to fill. But the mystery and the beauty of the world is overwhelmingly amazing, and there's no scientific explanation of how it came about. To say that it was generated by random numbers, that does seem, you know, sort of an uncharitable view [laughs]. I think it makes sense to believe in God, but exactly what decision in your life you make differently because of it, I don't know." This is another example, where a very smart guy (an engineer) doesn't buy materialistic explanation on how all what we see came to be ...martin_r

January 9, 2021

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