Comparing human and chimp DNA, using a software analogy

If we treat the protein coding sections as a "dispatch"; basically a token resolution function, usually based on a switch statement, calculated goto, or array of function pointers; these are natural functional bottlenecks in a codebase, which will naturally reduce to the same general shape as other codebases with even just vaguely similar functionality operating in the same environment. Most of the functional complexity will be resting on either side of these dispatches; behind, in the token sequence generation (in terms of biology, what's probably largely hiding in what has been foolishly referred to as "junk DNA"); and in front, in the emergent results of the token resolution (the resultant organism). You don't even need a different dispatch for practically infinite differences in the emergent result in general software terms; it can all lie within the sequence generation; as programming language compilers can be boiled down to dispatches, and we should all know how different the emergent functionalities of the products of such can be.LocalMinimum

March 25, 2018

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Although the purported evidence for human evolution is far weaker and illusory than most people realize, it is interesting to note that leading Darwinists themselves admit that they have no clue how evolution could have produced the particular trait of language in humans.

Leading Evolutionary Scientists Admit We Have No Evolutionary Explanation of Human Language – December 19, 2014 Excerpt: Understanding the evolution of language requires evidence regarding origins and processes that led to change. In the last 40 years, there has been an explosion of research on this problem as well as a sense that considerable progress has been made. We argue instead that the richness of ideas is accompanied by a poverty of evidence, with essentially no explanation of how and why our linguistic computations and representations evolved.,,, (Marc Hauser, Charles Yang, Robert Berwick, Ian Tattersall, Michael J. Ryan, Jeffrey Watumull, Noam Chomsky and Richard C. Lewontin, “The mystery of language evolution,” Frontiers in Psychology, Vol 5:401 (May 7, 2014).) Casey Luskin added: “It’s difficult to imagine much stronger words from a more prestigious collection of experts.” http://www.evolutionnews.org/2014/12/leading_evoluti092141.html

Tom Wolfe was so taken aback by this confession by leading Darwinists that he wrote a book entitled 'Kingdom of Speech' on the subject. The following quote provides an overview of Tom Wolfe's main argument in his book:

“Speech is not one of man’s several unique attributes—speech is the attribute of all attributes! Speech is 95 percent plus of what lifts man above animal! Physically, man is a sad case. His teeth, including his incisors, which he calls eyeteeth, are baby-size and can barely penetrate the skin of a too-green apple. His claws can’t do anything but scratch him where he itches. His stringy-ligament body makes him a weakling compared to all the animals his size. Animals his size? In hand-to-paw, hand-to-claw, or hand-to-incisor combat, any animal his size would have him for lunch. Yet man owns or controls them all, every animal that exists, thanks to his superpower: speech.” —Tom Wolfe, in the introduction to his book, The Kingdom of Speech http://www.nationalreview.com/corner/439553/tom-wolfe-human-exceptionalist

In other words, although humans are fairly defenseless creatures in the wild compared to other creatures, such as lions, bears, and sharks, etc.., nonetheless, humans have, completely contrary to Darwinian ‘survival of the fittest’ thinking, managed to become masters of the planet, not by brute force, but simply by our unique ability to communicate information and, more specifically, infuse information into material substrates,, What is more interesting still, besides the fact that humans have a unique ability to understand and create information and have become 'masters of the planet' through the ‘top-down’ infusion of information into material substrates, is the fact that, due to advances in science, both the universe and life itself are now found to be ‘information theoretic’ in their foundational basis. Renowned physicist John Wheeler stated “in short all matter and all things physical are information-theoretic in origin and this is a participatory universe”.

“it from bit” Every “it”— every particle, every field of force, even the space-time continuum itself derives its function, its meaning, its very existence entirely—even if in some contexts indirectly—from the apparatus-elicited answers to yes-or-no questions, binary choices, bits. “It from bit” symbolizes the idea that every item of the physical world has a bottom—a very deep bottom, in most instances, an immaterial source and explanation, that which we call reality arises in the last analysis from the posing of yes-no questions and the registering of equipment—evoked responses, in short all matter and all things physical are information-theoretic in origin and this is a participatory universe.” – Princeton University physicist John Wheeler (1911–2008) (Wheeler, John A. (1990), “Information, physics, quantum: The search for links”, in W. Zurek, Complexity, Entropy, and the Physics of Information (Redwood City, California: Addison-Wesley))

In the following article, Anton Zeilinger, a leading expert in quantum mechanics, stated that ‘it may very well be said that information is the irreducible kernel from which everything else flows.’

Why the Quantum? It from Bit? A Participatory Universe? Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: “In the beginning was the Word.” Anton Zeilinger – a leading expert in quantum mechanics: http://www.metanexus.net/archive/ultimate_reality/zeilinger.pdf

In the following video at the 48:24 mark, Anton Zeilinger states that “It is operationally impossible to separate Reality and Information” and he goes on to note, at the 49:45 mark, the Theological significance of “In the Beginning was the Word” John 1:1

48:24 mark: “It is operationally impossible to separate Reality and Information” 49:45 mark: “In the Beginning was the Word” John 1:1 Prof Anton Zeilinger speaks on quantum physics. at UCT – video http://www.youtube.com/watch?v=s3ZPWW5NOrw

Vlatko Vedral, who is a Professor of Physics at the University of Oxford, and who is also a recognized leader in the field of quantum mechanics, states, The most fundamental definition of reality is not matter or energy, but information–

“The most fundamental definition of reality is not matter or energy, but information–and it is the processing of information that lies at the root of all physical, biological, economic, and social phenomena.” Vlatko Vedral – Professor of Physics at the University of Oxford, and CQT (Centre for Quantum Technologies) at the National University of Singapore, and a Fellow of Wolfson College – a recognized leader in the field of quantum mechanics.

Moreover, besides being foundational to physical reality, information, as Intelligent Design advocates have been pointing out to Darwinists for years, is also foundational to biological life. Here are a few references to get that point across:

Information Enigma (Where did the information in life come from?) – – Stephen Meyer – Doug Axe – video https://www.youtube.com/watch?v=aA-FcnLsF1g Complex grammar of the genomic language – November 9, 2015 Excerpt: The ‘grammar’ of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world. The findings explain why the human genome is so difficult to decipher –,,, ,,, in their recent study in Nature, the Taipale team examines the binding preferences of pairs of transcription factors, and systematically maps the compound DNA words they bind to. Their analysis reveals that the grammar of the genetic code is much more complex than that of even the most complex human languages. Instead of simply joining two words together by deleting a space, the individual words that are joined together in compound DNA words are altered, leading to a large number of completely new words. http://www.sciencedaily.com/releases/2015/11/151109140252.htm Information is Physical (but not how Rolf Landauer meant) - video https://www.youtube.com/watch?v=H35I83y5Uro

It is hard to imagine a more convincing scientific proof that we are made ‘in the image of God’ ,,, than finding both the universe, and life itself, are both ‘information theoretic’ in their foundational basis, and that we, of all the creatures on earth, uniquely possess an ability to understand and create information, and, moreover, have come to ‘master the planet’ precisely because of our unique ability infuse information into material substrates. Verses:

Genesis 1:26 And God said, Let us make man in our image, after our likeness: and let them have dominion over the fish of the sea, and over the fowl of the air, and over the cattle, and over all the earth, and over every creeping thing that creepeth upon the earth. John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. The same was in the beginning with God. All things were made by Him, and without Him was not anything made that was made. In Him was life, and that life was the Light of men.

Perhaps a more convincing evidence that we are made in the image of God and that our lives have meaning and purpose could be if God Himself became a man, defeated death on a cross, and then rose from the dead to prove that He was indeed God. But who has ever heard of such a thing as that?

“Christianity is not merely religious truth, it is total truth — truth about the whole of reality.” - Francis Schaeffer - Gödel, Infinity, and Jesus Christ as the Theory of Everything https://www.youtube.com/watch?v=x1Jw5Y686jY Copernican Principle, Agent Causality, and Jesus Christ as the “Theory of Everything” https://www.youtube.com/watch?v=NziDraiPiOw Colossians 1:15-20 The Son is the image of the invisible God, the firstborn over all creation. For in him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things have been created through him and for him. He is before all things, and in him all things hold together. And he is the head of the body, the church; he is the beginning and the firstborn from among the dead, so that in everything he might have the supremacy. For God was pleased to have all his fullness dwell in him, and through him to reconcile to himself all things, whether things on earth or things in heaven, by making peace through his blood, shed on the cross.

bornagain77

March 25, 2018

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3. To further drive this point home, Dolphins and Kangaroos, although being very different morphologically from humans, are found to have very similar DNA sequences.

Dolphin DNA very close to human, - 2010 Excerpt: They’re closer to us than cows, horses, or pigs, despite the fact that they live in the water.,,, “The extent of the genetic similarity came as a real surprise to us,” ,,, “Dolphins are marine mammals that swim in the ocean and it was astonishing to learn that we had more in common with the dolphin than with land mammals,” says geneticist Horst Hameister.,,, “We started looking at these and it became very obvious to us that every human chromosome had a corollary chromosome in the dolphin,” Busbee said. “We’ve found that the dolphin genome and the human genome basically are the same. It’s just that there’s a few chromosomal rearrangements that have changed the way the genetic material is put together.” http://www.reefrelieffounders.com/science/2010/10/21/articlesafari-dolphin-dna-very-close-to-human/ Kangaroo genes close to humans - 2008 Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome," http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118 First Decoded Marsupial Genome Reveals "Junk DNA" Surprise - 2007 Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,, The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off. http://news.nationalgeographic.com/news/2007/05/070510-opossum-dna.html Frogs were also found to be unexpectedly similar: Frogs and humans are kissing cousins - 2010 Excerpt: What's the difference between a frog, a chicken, a mouse and a human? Not as much as you'd think, according to an analysis of the first sequenced amphibian genome. The genome of the western clawed frog, Xenopus tropicalis, has now been analysed by an international consortium of scientists from 24 institutions, and joins a list of sequenced model organisms including the mouse, zebrafish, nematode and fruit fly. What's most surprising, researchers say, is how closely the amphibian's genome resembles that of the mouse and the human, with large swathes of frog DNA on several chromosomes having genes arranged in the same order as in these mammals. The results of the analysis are published in Science this week1. "There are megabases of sequence where gene order has changed very little,,,” http://www.nature.com/news/2010/100429/full/news.2010.211.html

4. Where differences are greatest between chimps and humans are in alternative splicing patterns. In fact ., due to alternative slicing, “Alternatively spliced isoforms,,, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,,” and “As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms,,”

Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F Frequent Alternative Splicing of Human Genes – 1999 Excerpt: Alternative splicing can produce variant proteins and expression patterns as different as the products of different genes. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC310997/ Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing - 2016 In Brief Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,, Page 806 excerpt: As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms (Smith and Kelleher, 2013). http://iakouchevalab.ucsd.edu/publications/Yang_Cell_OMIM_2016.pdf

5. Although the behavioral differences between man and apes are far greater than many Darwinists are willing to concede, the one difference that most dramatically separates man from apes, i.e. our ability to speak, is the one unique attribute that leading Darwinists themselves admit that they have no clue how it could have possibly evolved, and is also the one attribute that most distinctly indicates that we are indeed 'made in the image of God'.

Comparing the human and chimpanzee genomes: Searching for needles in a haystack – Ajit Varki1 and Tasha K. Altheide – 2005 Excerpt: we have many characteristics that are uniquely human. Table 1 lists some of the definite and possible phenotypic traits that appear to differentiate us from chimpanzees and other “great apes”2. For the most part, we do not know which genetic features interact with the environment to generate these differences between the “phenomes”3 of our two species. The chimpanzee has also long been seen as a model for human diseases because of its close evolutionary relationship. This is indeed the case for a few disorders. Nevertheless, it is a striking paradox that chimpanzees are in fact not good models for many major human diseases/conditions (see Table 2) (Varki 2000; Olson and Varki 2003). http://genome.cshlp.org/content/15/12/1746.full.pdf+html Table 1. Unique phenotypic traits of humans compared to those of great apes http://genome.cshlp.org/content/15/12/1746/T1.expansion.html In “Science,” 1975, M-C King and A.C. Wilson were the first to publish a paper estimating the degree of similarity between the human and the chimpanzee genome. This documented the degree of genetic similarity between the two (approx. 99% amino acid similarity) ! The study, using a limited data set, found that we were far more similar than was thought possible at the time. Hence, we must be one with apes mustn't we? But…in the second section of their paper King and Wilson honestly describe the deficiencies of such reasoning: “The molecular similarity between chimpanzees and humans is extraordinary because they differ far more than sibling species in anatomy and way of life. Although humans and chimpanzees are rather similar in the structure of the thorax and arms, they differ substantially not only in brain size but also in the anatomy of the pelvis, foot, and jaws, as well as in relative lengths of limbs and digits (38). Humans and chimpanzees also differ significantly in many other anatomical respects, to the extent that nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart (38). Associated with these anatomical differences there are, of course, major differences in posture (see cover picture), mode of locomotion, methods of procuring food, and means of communication. Because of these major differences in anatomy and way of life, biologists place the two species not just in separate genera but in separate families (39). So it appears that molecular and organismal methods of evaluating the chimpanzee human difference yield quite different conclusions (40).” King and Wilson went on to suggest that the morphological and behavioral differences between humans and apes,, must be due to variations in their genomic regulatory systems. David Berlinski - The Devil's Delusion - Page 162&163 Evolution at Two Levels in Humans and Chimpanzees Mary-Claire King; A. C. Wilson – 1975

bornagain77

March 25, 2018

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A few notes: Dr. Paul Giem is up to part 8 in his series reviewing John Sanford's new book "Contested Bones":

Review of "Contested Bones" (Part 8 - Chapter 8 "Homo habilis") 3-24-2018 by Paul Giem - video playlist https://www.youtube.com/watch?v=C68QYWePB64&index=8&list=PLHDSWJBW3DNU_twNBjopIqyFOwo_bTkXm Chapter 8 (Homo habilis - Crucial "Missing Link" or Invented Species?) - Contested Bones (by Christopher Rupe and John Sanford) is the result of four years of intense research into the primary scientific literature concerning those bones that are thought to represent transitional forms between ape and man. This book's title reflects the surprising reality that all the famous "hominin" bones continue to be fiercely contested today - even within the field of paleoanthropology.

Besides the fossils themselves failing to support the supposed gradual evolution of man from some apelike creature, the genetic evidence itself, although often touted by Darwinists as undeniable proof that man evolved from some apelike creature, fails to support the claim that man evolved from some apelike creature. In establishing this fact there are a few points that need to be made. 1. The DNA similarity is not nearly as close to 99% as Darwinists have falsely portrayed it to be.

Monkey Business in the Chimp Genome - Jeffrey P. Tomkins, Ph.D - Jan 31, 2017 Excerpt: An analysis of the seemingly less-contaminated data sets indicate that the chimpanzee DNA sequences are no more than 85% identical overall to human. When the chimpanzee DNA sequences that did not have matches with the human genome were compared to the chimpanzee genome, the matched regions were very short and full of unexplainable gaps. For the chimp DNA sequences that matched onto the chimp genome assembly, they were only 85% identical on average. If the current chimpanzee genome were an accurate representation, these chimp DNA sequences should have been matching up on the chimp genome at a level of 99.9% similarity. These results clearly show that many regions of the chimp genome are mis-assembled and therefore can’t be used to support human evolution. http://www.icr.org/article/monkey-business-chimp-genome DNA Science Disproves Human Evolution by Jeffrey P. Tomkins, Ph.D. - 2017 Excerpt: 1970s, very crude and indirect techniques were utilized to unzip mixtures of human and chimpanzee DNA, which were then monitored to see how fast they would zip back up compared to unmixed samples.5 Based on these studies, it was declared that human and chimpanzee DNA was 98.5% similar. But only the most similar protein-coding regions of the genome (called single-copy DNA) were compared, which is an extremely small portion—less than 3%—of the total genome. Also, it was later discovered by an evolutionary colleague that the authors of these studies had manipulated the data to make the chimpanzee DNA appear more similar to human than it really was.6,,, So, how similar is chimpanzee DNA to human? My research indicates that raw chimpanzee DNA sequences from data sets with significantly lower levels of human DNA contamination are on average about 85% identical in their DNA sequence when aligned onto the human genome. Therefore, based on the most recent, unbiased, and comprehensive research, chimpanzee DNA is no more than 85% similar to human. 6. Marks, J. 2011. The Rise and Fall of DNA Hybridization, ca. 1980-1995, or How I Got Interested in Science Studies. In Workshop on “Mechanisms of Fraud in Biomedical Research,” organized by Christine Hauskeller and Helga Satzinger. The Wellcome Trust, London, October 17-18, 2008. 7. Tomkins, J. P. 2011. How Genomes are Sequenced and Why it Matters: Implications for Studies in Comparative Genomics of Humans and Chimpanzees. Answers Research Journal. 4: 81-88. 8. Tomkins, J. 2016. Analysis of 101 Chimpanzee Trace Read Data Sets: Assessment of Their Overall Similarity to Human and Possible Contamination with Human DNA. Answers Research Journal. 9: 294-298. http://www.icr.org/article/10016 The 98.5% Chimp Human DNA similarity comparisons, according to a Darwinist, “needs to be treated like nuclear waste: bury it safely and forget about it for a million years”,,, The Rise and Fall of DNA Hybridization – Jonathan Marks - 2011 Excerpt: the technique of DNA hybridization had devolved into being doubly “tricky” – but more significantly, the outstanding charge of data falsification was there in black-and-white in the leading science journal in America. It seemed as though nothing more needed to be said for the “wheels of justice” to begin turning. Yet they didn’t. In 1993, I was asked by The Journal of Human Evolution to review Jared Diamond’s book, The Third Chimpanzee. Noting that the book’s “hook” was based on the Sibley-Ahlquist work, which Diamond was still touting uncritically, I said: Perhaps you recall Sibley and Ahlquist. In a nutshell, their results were: (1) chimp-gorilla DNA hybrids were more thermally stable than chimp-human hybrids; (2) the differences were insignificant; and (3) reciprocity was very poor when human DNA was used as a tracer. Unfortunately, the conclusions they reported were: (1) chimp-human was more thermally stable than chimp-gorilla; (2) differences were significant; and (3) reciprocity was near-perfect. And they got from point A to point B by (1) switching experimental controls; (2) making inconsistent adjustments for variation in DNA length, which was apparently not even measured; (3) moving correlated points into a regression line; and (4) not letting anyone know. The rationale for (4) should be obvious; and if (1), (2) and (3) are science, I'm the Princess of Wales. This work needs to be treated like nuclear waste: bury it safely and forget about it for a million years.31 31Marks, J. (1993) Review of The Third Chimpanzee by Jared Diamond. Journal of Human Evolution, 24:69-73. http://webpages.uncc.edu/~jmarks/dnahyb/Sibley%20revisited.pdf

2. Even if DNA were as similar as Darwinists have falsely portrayed it to be, the basic 'form' that any organism may take is not reducible to DNA, (nor is the basic 'form' reducible to any other material particulars in molecular biology, (proteins, RNAs, etc.. etc.. ,,), that Darwinists may wish to invoke. That is to say, 'you can mutate DNA til the cows come home' and you will still not achieve a fundamental change in the basic form of an organism. And since the basic 'form' of an organism is forever beyond the explanatory power of Darwinian mechanisms, then any belief that Darwinism explains the 'transformation of forms' for all of life is purely a pipe dream that has no experimental basis in reality.

"you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form." - Stephen Meyer - Functional Proteins and Information for Body Plans – video – 5:55 minute mark https://youtu.be/hs4y4XLGQ-Y?t=354 Quantum physics problem proved unsolvable: Godel and Turing enter quantum physics - December 9, 2015 Excerpt: A mathematical problem underlying fundamental questions in particle and quantum physics is provably unsolvable,,, It is the first major problem in physics for which such a fundamental limitation could be proven. The findings are important because they show that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,, "We knew about the possibility of problems that are undecidable in principle since the works of Turing and Gödel in the 1930s," added Co-author Professor Michael Wolf from Technical University of Munich. "So far, however, this only concerned the very abstract corners of theoretical computer science and mathematical logic. No one had seriously contemplated this as a possibility right in the heart of theoretical physics before. But our results change this picture. From a more philosophical perspective, they also challenge the reductionists' point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description." http://phys.org/news/2015-12-quantum-physics-problem-unsolvable-godel.html Darwinism vs Biological Form - video https://www.youtube.com/watch?v=JyNzNPgjM4w

bornagain77

March 25, 2018

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I think you would find that even excluding the operating system that Facebook, Instagram, and Snapchat have substantial amounts of similar or identical code.aarceng

March 24, 2018

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An excellent article. I was a software developer/systems engineer for close to 40 years and expended much sweat, blood and tears over those decades working to chase down those many bugs that "killed" the prospects of a robust and fully functional system. I started chasing bugs in 1970, and had I been a whole lot smarter, or had instead majored in Evolutionary Biology, I could have just quite trying and let "deep time" solve these many problems. Of course a new and different bug (problem) would have surfaced -- having been fired for the cause of non-production, how was I to feed myself and my family? How was I to pay the rent? Seriously, how many of us have, throughout life, witnessed so many of the things around us, and within us, decay and disintegrate over time? Old cars, houses, sidewalks, muscles, lungs, mountains, trees ... Can someone please point out to me something, either man made or natural, that when left alone to the constantly changing world around us, has improved over time. Time -- even "deep time" is a measure of destructiveness, and not an agent of creation.ayearningforpublius

March 23, 2018

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