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DLL Hell, Software Interdependencies, and Darwinian Evolution

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In our home we have six computers (distributed among me, my wife, and two daughters): two Macs, two Windows machines, and two Linux (Unix) machines. I’m the IT (Information Technology) or IS (Information Systems) guy in the household — whatever is is.

A chronic problem rears its ugly head on a regular basis when I attempt to update any of our computer systems: Software programs are often interdependent. DLLs are dynamic link libraries of executable code which are accessed by multiple programs, in order to save memory and disk space. But this interdependence can cause big problems. If the DLL is updated but the accessing program is not, all hell will break loose and the program will either severely malfunction or suffer an ignominious, catastrophic, instantaneous death. On the other hand, if the program is updated and the DLL is not, the same thing can happen.

I’m still trying to figure out how the circulatory avian lung evolved in a step-by-tiny-step fashion from the reptilian bellows lung, without encountering DLL hell, and how the hypothesized intermediates did not die of asphyxia at the moment of birth (or hatching), without the chance to reproduce.

Of course, we all know that this kind of challenge — no matter how obvious or compelling — presents no problem for the D-Fundies (Darwinian Fundamentalists), who are true believers in the clearly impossible, based on materialistic assumptions in which design could not possibly have played a role.

Comments
pubdef-- OK, so let me get this straight: The “programming of life” is way beyond the capabilities of any intelligence we know about or can even conceive of. Therefore, life must have been designed by some intelligence. Um no. It's that the programming of life is way beyond the capabilities of any intelligence we know about so we can be confident that it didn't come about by accident. Now, you really didn't mean to imply that since the programming of life is way beyond the capabilities of any intelligence we know about it means it came about by accident, did you?tribune7
June 7, 2009
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#7:
A great analogy. And then consider that the programming of life is far more sophisticated than even the most advanced OS.
#15:
Nakashima-san, I think the point to consider isn’t that an undirected avian lung evolution is a logical impossibility, but rather an unreasonable assumption considering the issues involved with making changes to already highly related programming work together by those consciencely trying hard to do so per Gil’s example.
OK, so let me get this straight: The "programming of life" is way beyond the capabilities of any intelligence we know about or can even conceive of. Therefore, life must have been designed by some intelligence.pubdef
June 7, 2009
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I’ll let you figure out what that means.
Interesting that you won't come right out and claim that the people involved in information theory, computer programming, engineering, mathematics, and other rigorous scientific disciplines don't support the Darwinian theory. Why is that, Gil?Freelurker_
June 7, 2009
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Hey Gil, I remember a post you did one time a few years back about intelligent design found throughout the universe from the big bang to life... Here is a article I am still working on that covers most of the high points of that fact,,There may be a few gems in it you can use, especially towards the end. Intelligent Design - The Anthropic Hypothesis http://docs.google.com/View?id=dc8z67wz_0hm7ftjfn You might like this two: Turin Shroud Hologram Reveals The Words "The Lamb" - short video http://www.youtube.com/watch?v=7XLcdaFKzYg Shroud Of Turin Carbon Dating Overturned By Scientific Peer Review - Robert Villarreal - Concluding statement of Press Release video http://www.youtube.com/watch?v=UEJPrMGksUgbornagain77
June 7, 2009
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Hmmm… on one side we have scientists of all political persuasions and all religions, all of whom come to the conclusion that evolution is true. Dear Mr. Legend, Where on earth did you get the idea that I don't believe evolution is true? Of course I believe evolution is true. Living things are not now as they once were, so by definition life has evolved. The question is whether or not random changes can accumulate to produce highly complex, functionally integrated, interdependent, information-processing machinery and the information such systems process, given the available probabilistic resources, and even given unrealistically optimistic assumptions. These are the kinds of questions engineers, mathematicians, and computer scientists tend to ask. These questions are never asked by pseudo-scientists like Darwinian evolutionists -- they just make up stories with no rigorous analysis, and declare the problem solved. Those of us who are involved in information theory, computer programming, engineering, mathematics, and other rigorous scientific disciplines tend not to be convinced by hand-waving declarations of consensus. In our engineering department we have a saying: "Does it pass the beverage-out-the-nose test?" I'll let you figure out what that means. The Darwinian mechanism does not pass the test.GilDodgen
June 7, 2009
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"An earlier study published in 1999 estimated the minimal gene set to fall between 265 and 350. A recent study making use of a more rigorous methodology estimated the essential number of genes at 382." John I. Glass et al., "Essential Genes of a Minimal Bacterium," Proceedings of the National Academy of Sciences, USA103 (2006): 425-30. "No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" - David L. Abel and Jack T. Trevors, “Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information,” Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 On top of the fact that we now know the genetic code of the simplest organism ever found on Earth has a highly advanced algorithmic code that surpasses man's ability to devise as such, we also know for a fact that no operation of logic ever performed by a computer will ever increase the algorithmic code inherent in a computer's program, i.e. Bill Gates will never use random number generators and selection software to write highly advanced computer codes: "... no operation performed by a computer can create new information." Douglas G. Robertson, "Algorithmic Information Theory, Free Will and the Turing Test," Complexity, Vol.3, #3 Jan/Feb 1999, pp. 25-34. The Evolutionary Informatics Lab: http://www.evoinfo.org/index.html Thus evolution is soundly defeated at even the most basic level of what we now know for Functional Information generation, namely it is shown that no sequence of events, in the foundational logic of computer language, can ever produce complex functional information. Defeating Evolution With The "Simple Cell" - video http://www.youtube.com/watch?v=giO7UmH7Zw4 Global Organization of Metabolic Fluxes in the Bacterium, Escherichia coli Excerpt: Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological organization of individual reactions into metabolic networks is increasingly well understood, the principles governing their global functional utilization under different growth conditions pose many open questions.bornagain77
June 7, 2009
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Mr Dodgen, Man, that Darwinian stuff sure is amazing. No planning, understanding, or intelligence required. Just add water, random chance, lots of time, and poof: the human mind emerges in 10^17 seconds. And beetles! Remember, the main product of evolution is bacteria.Nakashima
June 7, 2009
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Mr Bornagain77, You've quoted this section of the book before. It is a laundry list of different possibilities, not a desription of how every possibility applies to the whole genome. Is there support for the number 382? I don't see it. As I've said before, every time the same protein is produced by multiple genes/loci, there is less poly-constraint on that protein.Nakashima
June 7, 2009
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Hmmm... on one side we have scientists of all political persuasions and all religions, all of whom come to the conclusion that evolution is true. Also on that side we have reams of carefully produced and peer-reviewed evidence. On the other side we have a group of conservative fundamentalist Christians, some of whom are lawyers, some engineers, and some lay-people who cite "common sense" as the reason they doubt evolution. I need to weigh this carefully to determine which side is more likely to be right.Legendary1
June 7, 2009
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vpr: Gil you can overcome dependency hell, but it takes a lot of planning and compensation. apt-get upgrade Yeah, I know. I upgraded one of my Linux boxes from an old Xandros distro to the latest Ubuntu. I spent the entire day working through the problems. One of my favorite apps, the GMP big-number math library, didn't work after I downloaded GCC and attempted to compile the GMP source with it. The GMP ./configure script gave me error messages, so I went online and found that I had to do a sudo apt-get to fix the problem. All is well now. Man, that Darwinian stuff sure is amazing. No planning, understanding, or intelligence required. Just add water, random chance, lots of time, and poof: the human mind emerges in 10^17 seconds.GilDodgen
June 7, 2009
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"There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns - which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture - which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes). (Dr. John Sanford; Genetic Entropy 2005) Moreover, single genes are shown to code for multiple protein products: Human genes are multitaskers: abstract: Genome-wide surveys of gene expression in 15 different tissues and cell lines have revealed that up to 94% of human genes generate more than one (protein) product. http://www.nature.com/news/2008/081102/full/news.2008.1199.html And multiple genes are shown to code for single protein products Multiple genes code for high-molecular-mass rhoptry proteins of Plasmodium yoelii excerpt: The genes in the family were distributed on 6 chromosomes probably at 9 or more loci. http://www.sciencedirect.com/science?_ob=ArticleURL&bornagain77
June 7, 2009
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Joseph, I don't know. some extant reptiles have air sacs in the tail, so doing some comparative genetics/development between them and reptiles without air sacs and birds might be a good place to start. but the fossil evidence is certainly compelling, and the pathway they propose is plausible and is a good starting point for investigation. or do you disagree? if so, what specifically about the pathway do you think is implausible?Khan
June 7, 2009
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Mr Joseph, There is a new book, How To Build A Dinosaur. Some of it is amusing, but it is a start on answering your request for an objective test. Hopefully it took less than two specified mutations or your position is in a lot of trouble. Luckily, it took more than two, but they were unspecified! :)Nakashima
June 7, 2009
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Mr Bornagain77, Where does the number 382 come from? There are 12 ways to read a DNA strand, 2 directions X 2 strands X 3 reading frames. While each of these is possible, it does not happen in practice that overlapping readings are used. If it were common, then frameshifts due to indel mutations would not be so harmful. We have already discussed this.Nakashima
June 7, 2009
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Khan, What genes/ DNA sequences are involved? IOW how can one objectively test the premise that an accumulation of genetic accidents led to the evolution of the avian respiratory system. Hopefully it took less than two specified mutations or your position is in a lot of trouble.Joseph
June 7, 2009
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Gil, I pointed jerry to this open access paper a little while ago.. they again show air sacs present in theropod dinosaurs and present a hypothetical pathway for the evolution of the avian respiratory system using fossil evidence. what part of this proposed pathway do you find unreasonable? http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003303Khan
June 7, 2009
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However, bi-directional air flow could work in structures that allow uni-directional flow, just less efficiently. Nakashima-san, I think the point to consider isn't that an undirected avian lung evolution is a logical impossibility, but rather an unreasonable assumption considering the issues involved with making changes to already highly related programming work together by those consciencely trying hard to do so per Gil's example.tribune7
June 7, 2009
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Your in good company Gil, Michael Denton wonders about the avian lung in this video: No Beneficial Mutations - Not By Chance - Evolution: Theory In Crisis http://www.youtube.com/watch?v=OdZYguRuzn0 if we were to get a proper “beneficial mutation’ in a polyfunctional genome of interdependent genes then instead of the infamous “Methinks it is like a weasel” single function information problem for Darwinists, we would actually be encountering something more akin to this illustration found on page 141 of Genetic Entropy by Dr. Sanford. S A T O R A R E P O T E N E T O P E R A R O T A S Which is translated ; THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS. This ancient puzzle, which dates back to 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation. This is what is meant when it is said a poly-functional genome is poly-constrained to any random mutations. The puzzle I listed is only poly-fuctional to 4 elements, as stated earlier the minimum genome is poly-constrained to approximately 382 elements (genes). For Darwinist to continue to believe in random mutations to generate the staggering level of complexity we find in life is absurd in the highest order! And in reflection to your computer crashing Gil, Should you not just start randomly changing code until the problem is fixed and you have evolved a OS that is far superior?bornagain77
June 7, 2009
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Hi jerry, I am sure we will be treated to all the underwhelming evidence for avian lung development in the near future and the one or two steps necessary for a gene duplication event with an appropriate deletion and reversal to accomplish it all in just one set of gametes. Nah. Just evidence that the pulmonary system was probably present in the theropod dinosaurs long before birds: O’Connor PM & LPAM Claessens (2005). Basic avian pulmonary design and flow-through ventilation in non-avian theropod dinosaurs. Nature 436:253-256 http://oak.cats.ohiou.edu/~ridgely/OconnorClaessensairsacs.pdf I hope the link worksDave Wisker
June 7, 2009
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Mr Sewell, Very nice article! I was struck by this quote:
When Dr. Behe was at the University of Texas El Paso in May of 1997 to give an invited talk, I told him that I thought he would find more support for his ideas in mathematics, physics and computer science departments than in his own field.
Given the way his own department treats him, I also think it would be wise for him to appeal to a non-biological audience, especially the math, computer science, and engineering crowd. These are the folks who have a chance to understand the information-theoretical basis for modern ID anyways.herb
June 7, 2009
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Mr Jerry, We should alert all readers that we do not pay Nakashima to make his comments here. What?! I was wondering why the check was slow in arriving. :) But seriously, the ad hominem is a poor comeback. PM Erasmus immediately!Nakashima
June 7, 2009
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We should alert all readers that we do not pay Nakashima to make his comments here. The master of the unnderwhelm and the just so story does it all on his own. The denier of all things reasonable makes his claims out of ether. The magic of Darwinism. I am sure we will be treated to all the underwhelming evidence for avian lung development in the near future and the one or two steps necessary for a gene duplication event with an appropriate deletion and reversal to accomplish it all in just one set of gametes. It will be fun to watch this simple process unfold before our very eyes just as the slicer and dicer on the boardwalk with his handy dandy gadget make great epicurean delights. I passed one last night but I do not think it was Nakashima.jerry
June 7, 2009
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Flow-through respiration is hypothesized to have appeared in theropod dinosaurs long before there were birds. See, for instance, http://oak.cats.ohiou.edu/~ridgely/OconnorClaessensairsacs.pdf. Does intelligent design offer an alternative hypothesis?PaulBurnett
June 7, 2009
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Mr Dodgen, First, welcome back to UD! Where exactly is your problem with avian lung evolution? With the evolution of the structures or the evolution of the process? It seems from your comment about asphixiation that you are concerned about process. However, bi-directional air flow could work in structures that allow uni-directional flow, just less efficiently. BTW, you don't have to figure this out yourself. If you Google "evolution avian lung" you can find plenty of resources to help! Again, welcome back!Nakashima
June 7, 2009
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I’m still trying to figure out how the circulatory avian lung evolved in a step-by-tiny-step fashion from the reptilian bellows lung, without encountering DLL hell, A great analogy. And then consider that the programming of life is far more sophisticated than even the most advanced OS. And then close your eyes, put your hand over your ears and repeat "It all happened by chance. It all happened by chance.tribune7
June 7, 2009
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Gil, Yes, welcome back. This is one of the main points I made in my Mathematical Intelligencer article. Granville Sewell
June 7, 2009
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Take your holistic reasoning back to the Dark Ages Gil. We have advanced beyond common sense. Scientists can draw imaginary lines to make a closed system in nature wherever and whenever it is convenient. No need for this "big picture" stuff.tragic mishap
June 7, 2009
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vpr, for even better overcoming dependency hell I think "aptitude upgrade" will do the job!sxussd13
June 7, 2009
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Gil you can overcome dependency hell, but it takes a lot of planning and compensation. apt-get upgrade :)vpr
June 7, 2009
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Welcome back Gil!kairosfocus
June 7, 2009
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