Science and Freethinking

_{GilDodgen
September 23, 2011

Intelligent Design

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Intelligent Design}

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Everyone has a religion, a raison d’être, and mine was once Dawkins’. I had the same disdain for people of faith that he does, only I could have put him to shame with the power and passion of my argumentation.

But something happened. As a result of my equally passionate love of science, logic, and reason, I realized that I had been conned. The creation story of my atheistic, materialistic religion suddenly made no sense.

This sent a shock wave through both my mind and my soul. Could it be that I’m not just the result of random errors filtered by natural selection? Am I just the product of the mindless, materialistic processes that “only legitimate scientists” all agree produced me? Does my life have any ultimate purpose or meaning? Am I just a meat-machine with no other purpose than to propagate my “selfish genes”?

Ever since I was a child I thought about such things, but I put my blind faith in the “scientists” who taught me that all my concerns were irrelevant, that science had explained, or would eventually explain, everything in purely materialistic terms.

But I’m a freethinker, a legitimate scientist. I follow the evidence wherever it leads. And the evidence suggests that the universe and living systems are the product of an astronomically powerful creative intelligence.

Comments

DrBot, Spontaneous organisation of matter into systems with complex formal relationships between components has not been observed to date. What has been observed is merely self-ordering that has a minimum amount of associated information. This strongly suggests that self-organisation is an impossibility. Common sense suggests that instruction/plan goes before construction of complex systems. At least, the collective experience of humanity teaches us so. Why should biology be an exception? Formally, for information to be transmitted, a number of a priori satisfied conditions must be met, notably as regards the agreement on information semantics between the sender and the receiver. "This is why probability calculations that assumes every bit of functional information has to form all at once is wrong" Is it about climbing Mt Improbable from the back? I think that by the time a trait can be used exaptationally by anything, this anything must already be a very complex system. Exaptation does happen but its capabilities are very limited. The complexity gaps are in fact chasms.Eugene S_{September 27, 2011
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Corrected link: Brooke Fraser – C.S. Lewis Song – Music Video http://www.youtube.com/watch?v=kMRFbc5KVaMbornagain77_{September 27, 2011
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Brooke Fraser - C.S. Lewis Song - Music Video http://www.youtube.com/watch?v=wo-e2BjICCYbornagain77_{September 27, 2011
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The laws of chemistry and physics have absolutely no role in determining the specific sequence of nucleotides in a protein gene that codes for the specific sequence of AAs that gives a functional protein. That sequence is a set of specific configuration of what Abel cals “configurable switches”, that is switches that, in themselves, could take different values according to the laws of chemistry and physics, but take specific functional values because a designer inputs that information. THat has nothing to do with necessity laws. No necessity law of chemistry or physics can make nucleotides assume the sequence in a DNA gene which corresponds, trhough the symbolic key of the genetic code, to the sequence of AAs in myoglobn, just to make an example. That should be very clear to anyone who has a fundamental understanding of biochemistry and biology.
This is a point I've heard before but never so clearly articulated. Kudos to gpuccio.steveO_{September 27, 2011
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Petrushka, you, again with no reference, state:
If things are designed, why are 99 percent of designs extinct?
Yet, contrary to what you may believe, or even 'want' to believe, this is a lie; One persistent misrepresentation, that evolutionists continually portray of the fossil record, is that 99.9%+ of all species that have ever existed on earth are now extinct because of the many 'evolutionary transitions' that must have happened if neo-Darwinism were true. Yet the fact of the matter is that 40 to 80% of all current living species found on the earth are represented fairly deeply in the fossil record.
The Fossil Record - The Myth Of +99.9% Extinct Species - Dr. Arthur Jones - video http://www.metacafe.com/watch/4028115 "Stasis in the Fossil Record: 40-80% of living forms today are represented in the fossil record, despite being told in many text books that only about 0.1% are in this category. The rocks testify that no macro-evolutionary change has ever occurred. With the Cambrian Explosion complex fish, trilobites and other creatures appear suddenly without any precursors. Evidence of any transitional forms in the fossil record is highly contentious." Paul James-Griffiths via Dr. Arthur Jones
In fact, according to this recent census, there are around 230,000 marine species living today,
Marine Species Census - Nov. 2009 Excerpt: The researchers have found about 5,600 new species on top of the 230,000 known. They hope to add several thousand more by October 2010, when the census will be done. http://news.yahoo.com/s/ap/20091122/ap_on_sc/us_marine_census
Whereas, we only have about a quarter of a million different species collected in our museums.
"Now, after over 120 years of the most extensive and painstaking geological exploration of every continent and ocean bottom, the picture is infinitely more vivid and complete than it was in 1859. Formations have been discovered containing hundreds of billions of fossils and our museums now are filled with over 100 million fossils of 250,000 different species. The availability of this profusion of hard scientific data should permit objective investigators to determine if Darwin was on the right track. What is the picture which the fossils have given us? ... The gaps between major groups of organisms have been growing even wider and more undeniable. They can no longer be ignored or rationalized away with appeals to imperfection of the fossil record." Luther D. Sunderland, Darwin's Enigma 1988, Fossils and Other Problems, 4th edition, Master Books, p. 9 "The evidence we find in the geological record is not nearly as compatible with Darwinian natural selection as we would like it to be .... We now have a quarter of a million fossil species but the situation hasn't changed much. The record of evolution is surprisingly jerky and, ironically, we have even fewer examples of evolutionary transition than in Darwin's time ... so Darwin's problem has not been alleviated". David Raup, Curator of Geology at Chicago's Field Museum of Natural History "There is no need to apologize any longer for the poverty of the fossil record. In some ways, it has become almost unmanageably rich and discovery is outpacing integration. The fossil record nevertheless continues to be composed mainly of gaps." Professor of paleontology - Glasgow University, T. Neville George "Evolution requires intermediate forms between species and paleontology does not provide them." David Kitts - Paleontologist "The long-term stasis, following a geologically abrupt origin, of most fossil morphospecies, has always been recognized by professional paleontologists" – Stephen Jay Gould - Harvard "Given the fact of evolution, one would expect the fossils to document a gradual steady change from ancestral forms to the descendants. But this is not what the paleontologist finds. Instead, he or she finds gaps in just about every phyletic series." - Ernst Mayr-Professor Emeritus, Museum of Comparative Zoology at Harvard University "What is missing are the many intermediate forms hypothesized by Darwin, and the continual divergence of major lineages into the morphospace between distinct adaptive types." Robert L Carroll - Paleontologist
,,,Darwinism predicts we should have literally millions and millions of transitional fossil forms yet there are only a few dozen or so highly contested fossils claimed as transitional forms, none of which are uncontested. Moreover, the fossil record is overwhelmingly characterized by sudden appearance and overall stasis of form, with only bounded variation of that form to be found after a species/kind 'sudden' appearance in the fossil record:
Ancient Fossils That Have Not Changed For Millions Of Years - video http://www.metacafe.com/watch/4113820 THE FOSSILS IN THE CREATION MUSEUM - 1000's of pictures of ancient 'living' fossils that have not changed for millions of years: http://www.fossil-museum.com/fossils/?page=0&limit=30 Fossils Without Evolution - June 2010 Excerpt: New fossils continue to turn up around the world. Many of them have an amazing characteristic in common: they look almost exactly like their living counterparts, despite being millions of years old,,, http://www.creationsafaris.com/crev201006.htm#20100618a The Unknown Origin of Pterosaurs - video http://www.youtube.com/watch?v=XP6htc371fM Bat Evolution? - No Transitional Fossils! - video http://www.metacafe.com/watch/6003501/ Australonycteris clarkae is the oldest bat ever found in the fossil record at 54.6 million years old. The ear bones of Australonycteris show that it could navigate using echolocation just like modern bats. https://uncommondescent.com/biology/the-bionic-antinomy-of-darwinism/#comment-340412
============== C. S. Lewis has his own distinctive view on ‘evolution’;
C.S. Lewis - Evolution and The Christian Experience - video http://www.metacafe.com/watch/7060815/
bornagain77_{September 27, 2011
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But my point is very simple: if half of the basic protein domains were designed in the beginning of life, the best expalnation for the remaining half that emerged after is that they were designed too. There is no reason at all to invoke a different mechanism, and especially one that obviously does not work.
Why - given all the evidence for common descent?
Yes, but we are not talking about totally random systems so I think you are missing the point.
You are missing the point. The point is that RV, in the darwinian model, is a totally random system. Do you want to deny that?
Perhaps you didn't read my comment. We were discussing abiogenesis, not evolution. Random variation is random, otherwise it wouldn't be called random variation ;) but we were talking about the ability of the universe to create arrangements of matter that function as a self replicator and I made the perfectly valid point that probability calculations based purely on a random search are not good mo0dels for how the universe works - there are no nested contingencies in a random search, just randomness, but in a complex chemical environment some things naturally follow from others, and consequently lead to more, creating a string of events that are contingent on earlier events - this is what nested contingencies are. The probability of finding matter arranged in orderly layers is different if you are talking about a random search as opposed to a set of physical processes involving tidal forces, liquids and eroding solids.
The laws of chemistry and physics have absolutely no role in determining the specific sequence of nucleotides in a protein gene that codes for the specific sequence of AAs that gives a functional protein. ...
So there is absolutely no physical relationship between the format of a protein gene and the and the protein it produces?
Random systems do not generate regular or complex patterns like crystals or sedimentary layers.
Proteins are not crystals or sedimentary layers.
No. You are not actually addressing the point I am making.
The simplest known biological replicator needs hundreds of complex proteins, and a lot of other information.
Yes, so what is the simplest possible replicator?
Are you saying that proto cell membranes are biologcial replicators?
Nope, I am saying that Lipid bilayers can form naturally.
if you have a minimal replicator of 130 bits and you remove one bit, it stops being a replicator and therefore has zero functional bits – put the bit back and you have 130 functional bits – zero to 130 bits in one move!
This is a common error of thought, too. In your example, the functional information in the 130 bits of the replicator is already there, and working, and you must explain how it was generated. Obviously, you can suppress the function by changing only one bit, at least in some cases. And so? You keep the other 129 functional bits, and so it is perfectly true that one bit mutation (which is in the range of RV) can indeed restore the function. And so? The problem is, still: how did you get the other 129 bits right? By a random search? Can you see the difference?
I think you have misunderstood the concept of functional information. We are talking about a minimal self replicator (one that cannot be any simpler) Function is defined as the ability to self replicate, if it does not self replicate then it does not function. If you remove one bit it will not function (because it cannot be any simpler) so removing one bit leaves you with something that is not a self replicator and by definition has zero functional bits. Here are a couple of examples of cellular components that can form naturally: Lipid bilayers amino acids Now IF these components form part of a functioning replicator then how many bits of functional information does each of these components contribute to the replicator? If these 'building blocks' occur naturally then calculating the probability of the functional bits that they would contribute to a replicator as part of a random search makes no sense - they already exist! - you need to base the probability calculation on the likelihood of these bits coming together, not all being created at once. I'll try the monkey typewriter metaphor - When the monkeys bash away at the keyboard they produce random strings of characters and you can work out some probability of them tying recognisable words, and then phrases. But if the keyboard has keys that produce whole words then the probability of them producing recognisable sentences changes. This is why probability calculations that assumes every bit of functional information has to form all at once is wrong, the calculation should be based on the likelihood of extant building blocks forming the right structure, not on all the building blocks forming all at once in the correct structure at the same time. Do you understand the difference?
It’s in a random walk that you cannot do that. Each single configuration of each bit cannot be implemented or kept, unless it confers a “reproductive advantage”. That’s the hard law of natural selection, the law that makes natural selection as almost useless tool for true evolution.
Again, chemistry is not a random walk. Some 'configuration bits' can be extant, the bits required to describe Lipid bilayers already exist if it has occurred naturally, they do not require selection pressures to exist or to persist, just the right chemical conditions.DrBot_{September 27, 2011
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Your statement which led to this was to the effect that variation in a uniform environment produces little change while variation in a changing environment produces evolution.
If the environment is static then at most you will get neutral drift. What will typically happen is that the population will start to converge at a local maxima. In other words if the population is good enough and there is no pressure to change then there will be little or no change - they will only start to change again of the selection criteria changes.
My response is that variation is just variation, regardless of the environment. You seem to imply that the changing environment raises a challenge, and that life is compelled to rise to it.
No, that is not what I implied.
That a changing environment results in evolution assumes that variation can result in evolution.
The ability to reproduce successfully is determined primarily by two things - the properties of the organism and the environment they exist in. Organisms with certain traits, in a particular environment, will reproduce more than others. If the environment changes then a trait that was beneficial in the old environment may be less beneficial in the new one and a trait that was of no benefit, or even detrimental in the old environment could be an advantage in the new one. And pay attention to my use of the words 'could' and 'may' not 'will'.
There’s a holy grail out there that no one seems to want to bring home and show off. On what do you base the conclusion that any variation, regardless of the environment, results in extensive evolution rather than just small variations?
You can't disregard the environment - It ultimately determines which traits are beneficial. Beneficial traits will tend to dominate a population - this isn't controversial, it is obvious - If a new disease wipes out all but a minority who have some form of resistance then the emerging population will be dominated by organisms with the resistive trait. Can you explain how your domino metaphor relates to the discussion?DrBot_{September 27, 2011
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"If things are designed, why are 99 percent of designs extinct?" I think because we live in an imperfect world. It opens up a vent for philosophical discussions but that the world is imperfect can still be supported scientifically. If you wish to ask further questions such as why is it imperfect, the discourse is bound to be philosophical.Eugene S_{September 27, 2011
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Petrushka: That’s simply untrue. Both in theory and in the data. Most fixed mutations are neutral or nearly neutral. This has been known since before 1950 and has been mainstream for well over 50 years. As it should have been known since the beginning of rational thought that neutral mutations, even if they occasionally and randomly expand, change nothing in the computation of probabilities in a random walk, and therefore are essentially useless and don't explan anything. Occasional random expansion has the same probabilities of hitting a functional target as occasional lucky mutation. That is, practically none. You darwinists shoud make up your minds. If we kindly point out that a random system can generate practically nothing useful, immediately you start adoring the powers of non random natural selection. But if we gently remind you that those powers are minimal, you are ready to seek refuge under the protecting wings of some random component, like genetic drift. Well, I will state it very simply: RV in all its forms, plus natural selection in its only form (expansion of the best replicators) can do practically nothing. Certainly, it cannot generate complex functional information. But don't worry, you can keep your faith and be happy.gpuccio_{September 26, 2011
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Petrushka: For once, I quote myself: But, again, you will pretend not to understand that simple concept. Ditto.gpuccio_{September 26, 2011
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As I have told you many times, intelligent selection is not darwinain selection. It is design.
OK, selection is design regardless of how it happens. "Intelligent" selection monitors on or two dimensions. Natural selection is open to all possible advantages simultaneously, even ones that are invisible to humans. If you want a dog with a longer tail, or a pigeon with some distinctive visual feature, intelligent selection will get you to a goal faster. But natural evolution has no goal. It is simply the result of differential reproduction. It doesn't care which of nearly limitless possibilities confers the advantage. It fixes mutations that confer no advantage, but which occasionally lead to an advantage. It wanders down blind alleys, and most of them lead to extinction. If things are designed, why are 99 percent of designs extinct?Petrushka_{September 26, 2011
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I'm working on it.GilDodgen_{September 26, 2011
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Petrushka, you state (without reference);
It depends on population size. In large populations, favorable mutations tend to get fixed. In small populations, neutral mutations predominate. This fits both observation and simulations of population genetics.
Yet, despite what you believe, most mutations are shown to have a 'unexpectedly' small negative effect;:
Unexpectedly small effects of mutations in bacteria bring new perspectives - November 2010 Excerpt:,,,Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed. http://www.physorg.com/news/2010-11-unexpectedly-small-effects-mutations-bacteria.html
and even granting favorable 'neutral' mutation status to most mutations still does nothing to undermine the CORRECT genetic entropy model of compensating the slightly negative mutations:
Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load: Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space. http://bioinformatics.cau.edu.cn/lecture/chinaproof.pdf MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE http://mendelsaccount.sourceforge.net
As for 'observation' of fixation of mutations
Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies
Moreover, with existing population genetics models, evolution is shown to be impossible:
Whale Evolution Vs. Population Genetics - Richard Sternberg PhD. in Evolutionary Biology - video http://www.metacafe.com/watch/4165203 Waiting Longer for Two Mutations - Michael J. Behe Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that 'for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years' (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless "using their model" gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model. http://www.discovery.org/a/9461 Dr. Sanford calculates it would take 12 million years to “fix” a single base pair mutation into a population. He further calculates that to create a gene with 1000 base pairs, it would take 12 million x 1000 or 12 billion years. This is obviously too slow to support the creation of the human genome containing 3 billion base pairs. http://www.detectingtruth.com/?p=66 Oxford University Admits Darwinism's Shaky Math Foundation - May 2011 Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism within two years. http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html
Perhaps you would like to apply for the job Petrushka since you seem to be so CONNEDvinced that neo-Darwinism is true?!? But I give you a clue Petrushka, population genetics will never, ever, be 'fixed' because neo-Darwinism ain't the way we got here!
All Things Bright And Beautiful - Canon In D - Pachebel http://www.metacafe.com/watch/4082996/
bornagain77_{September 26, 2011
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It’s in a random walk that you cannot do that. Each single configuration of each bit cannot be implemented or kept, unless it confers a “reproductive advantage”.
That's simply untrue. Both in theory and in the data. Most fixed mutations are neutral or nearly neutral. This has been known since before 1950 and has been mainstream for well over 50 years. It depends on population size. In large populations, favorable mutations tend to get fixed. In small populations, neutral mutations predominate. This fits both observation and simulations of population genetics. In living things, selection can monitor unlimited dimensions.Petrushka_{September 26, 2011
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Nice post gpuccio! Petrushka, I'm listing another paper that may help you see just how badly neo-Darwinists have faired in this area of trying to mimic proteins found in nature: Here is a critique of the failed attempt to evolve a 'fit' protein to replace a protein in a virus which had a gene knocked out:
New Genes: Putting the Theory Before the Evidence - January 2011 Excerpt: In this study evolutionists investigated how proteins might have evolved. They attempted to demonstrate the evolution of a virus—a molecular machine consisting of several proteins—in the laboratory. To simplify the problem they started with all but a small part of the virus intact. They randomized the amino acid sequence of one part of one of the viral proteins, and they repeatedly evolved that randomized segment in hopes of reconstructing the entire virus. What they discovered was that the evolutionary process could produce only tiny improvements to the virus’ ability to infect a host. Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved. And the best virus they could produce, even with the vast majority of the virus already intact, was several orders of magnitude weaker than nature’s virus. The reason their evolutionary process failed was that the search for better amino acid sequences, that would improve the virus’ ability to infect the host, became too difficult. A possible evolutionary explanation for these disappointing results is that in such a limited laboratory study, the evolutionists were simply unable to reproduce what the vast resources of nature could produce. Perhaps in the course of time evolution could evolve what the evolutionists could not do in the laboratory. But the results refuted even this fall back explanation. In fact, the evolutionists would not merely need an expanded study with more time in the laboratory, they would need more time than evolution ever had—many times over. The number of experiments they would need to conduct in order to have any hope of evolving a virus that rivals nature’s version is difficult to compute. But it is at least 10^70 (a one followed by 70 zeros). And yet, there it is. This relatively short sequence of amino acids exists as part of of the virus, with its fantastically high infection capabilities. And of course this is not merely a problem for a part of one protein, in one virus. It is a problem for all life, for proteins are crucial molecular machines throughout biology. Did the evolutionists conclude that proteins did not evolve? Did they suggest their findings are a problem for evolution? Did they even do so little as discuss the possibility that this one particular protein they studied may not have evolved? No. There is not even a hint from the evolutionists there is a problem. In fact, the results are, in typical fashion, interpreted according to evolution. As usual, the evolutionists simply explained that evolution must have, somehow, solved the problem: http://darwins-god.blogspot.com/2011/01/new-genes-putting-theory-before.html
Petrushka, I already showed you what this but it bears worth repeating:
Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator - Fazale Rana Excerpt of Review: ‘Another interesting section of Creating Life in the Lab is one on artificial enzymes. Biological enzymes catalyze chemical reactions, often increasing the spontaneous reaction rate by a billion times or more. Scientists have set out to produce artificial enzymes that catalyze chemical reactions not used in biological organisms. Comparing the structure of biological enzymes, scientists used super-computers to calculate the sequences of amino acids in their enzymes that might catalyze the reaction they were interested in. After testing dozens of candidates,, the best ones were chosen and subjected to “in vitro evolution,” which increased the reaction rate up to 200-fold. Despite all this “intelligent design,” the artificial enzymes were 10,000 to 1,000,000,000 times less efficient than their biological counterparts. Dr. Rana asks the question, “is it reasonable to think that undirected evolutionary processes routinely accomplished this task?” http://www.amazon.com/gp/product/0801072093
Petrushka, moreover, the proteins we find in life are found to be optimal which is completely contrary to these results we find, and indeed for what we should expect from some neo-Darwinian process that just so happened to stumble on to appropriate solutions accidentally:
William Bialek - Professor Of Physics - Princeton University: Excerpt: "A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,," http://www.princeton.edu/~wbialek/wbialek.html
bornagain77_{September 26, 2011
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Petrushka: Another point is that while the library used in the experiment is a selected subset of a purely random set, the original set was produces by a stochastic process. I don't think you are right. Here is the procedure followed to build the library: "A general strategy is described for the de novo design of proteins. In this strategy the sequence locations of hydrophobic and hydrophilic residues were specified explicitly, but the precise identities of the side chains were not constrained and varied extensively. This strategy was tested by constructing a large collection of synthetic genes whose protein products were designed to fold into four-helix bundle proteins. Each gene encoded a different amino acid sequence, but all sequences shared the same pattern of polar and nonpolar residues. Characterization of the expressed proteins indicated that most of the designed sequences folded into compact alpha-helical structures. Thus, a simple binary code of polar and nonpolar residues arranged in the appropriate order can drive polypeptide chains to collapse into globular alpha-helical folds." Am I missing something? Protein coding sequences cannot be designed without using the Darwinian process of selection. That is how the “designed” library was produced. The functional set was the result of further selection. Anyone here is free to suggest a method that does not require Darwinian selection. All wrong. First of all, it does not seem that the library was designed using darwinian selection, or any selection at all. It was designed by a specific algorithm. But even if a sequence were designed by coupling RV and selection (which is perfectly possible), still it would be RV + intelligent selection. As I have told you many times, intelligent selection is not darwinain selection. It is design. I hate to remind you, but "darwinan selection" is only, exclusively, "natural selection", that is expansion of the replicators that replicate better. But, again, you will pretend not to understand that simple concept.gpuccio_{September 26, 2011
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DrBot: I see that BA has anticipated me, and quoted the paper by Abel which explains very well a few fundamental concepts: "Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors" The link is: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1208958/pdf/1742-4682-2-29.pdf Another very good paper by Abel is the follwing: "Constraints vs. Controls" http://www.bentham.org/open/tocsj/articles/V004/14TOCSJ.pdf So, I will try to answer briefly your points: If they were intelligently designed with half of the basic protein domains present then that is the point at which evolution starts. But my point is very simple: if half of the basic protein domains were designed in the beginning of life, the best expalnation for the remaining half that emerged after is that they were designed too. There is no reason at all to invoke a different mechanism, and especially one that obviously does not work. That's why the problem of OOL is so strictly connected to the problem of evolution (except in the minds of darwinists): because the same mechanism that generated the tremendous amount of information necessary for the first biological replicators to exist can certainly well explain their successive evolution. Yes, but we are not talking about totally random systems so I think you are missing the point. You are missing the point. The point is that RV, in the darwinian model, is a totally random system. Do you want to deny that? Nested contingencies in this context have nothing directly to do with biology, it is about chemistry and physics. The laws of chemistry and physics have absolutely no role in determining the specific sequence of nucleotides in a protein gene that codes for the specific sequence of AAs that gives a functional protein. That sequence is a set of specific configuration of what Abel cals "configurable switches", that is switches that, in themselves, could take different values according to the laws of chemistry and physics, but take specific functional values because a designer inputs that information. THat has nothing to do with necessity laws. No necessity law of chemistry or physics can make nucleotides assume the sequence in a DNA gene which corresponds, trhough the symbolic key of the genetic code, to the sequence of AAs in myoglobn, just to make an example. That should be very clear to anyone who has a fundamental understanding of biochemistry and biology. Random systems do not generate regular or complex patterns like crystals or sedimentary layers. Proteins are not crystals or sedimentary layers. You are falling here in the common error of conflating what Abel calls "ordered sequences" with what Abel calls "functional sequences" (see the first of the two papers. A crystal is ordered. A protein is not ordered, but is functional. There is a big difference. You cannot apply the concept of self-ordering, a la Prygogine, to proteins or protein coding genes. It does not work. It is simply wrong. The sequence of nucleotides in a protein coding gene does not depend on laws of chenistry, or on self-ordering principles of physics, any more than the sequence of words in Shakespeare's Hamlet depends on the chemistry of ink and paper. Both are examples of functional information obtained by the superimposing of a functional order to configurable switches. Both are the product of conscious design. I keep seeing the ‘randomness cannot generate this’ argument put forth here and I think it is a bad argument because it doesn’t take into account how physics and chemistry work. Again, this is simple nonsense. See before. You don’t need to generate 130 bits in one go, what you have are segmented bit ‘chunks’ which, if put together in the right order, for a replicator. The simplest known biological replicator needs hundreds of complex proteins, and a lot of other information. It is beyonf the dreams of any possible random system. And evolution cannot happen unless you already have a biological replicator. It's as simple as that. Well, indeed evolution, as conceived by darwinists, cannot happen even if you already have biological replicators :) Think about it this way, how many bits are required for a proto cell membrane? If a suitable membrane can result from natural processes (as I think people have already shown) then those bits are already present in the environment, they don’t need to form spontaneously with everything else. Are you saying that proto cell membranes are biologcial replicators? That they can evolve? Where are these strange beings? Where are they gathered in great numbers and concentrations, ready to do their part in the ritual of OOL? Hey, do you really believe these myths? All OOL theories are only that, myths, and bad myths indeed. This reminds me of an issue I have with the whole idea of measuring things in functional bits – if you have a minimal replicator of 130 bits and you remove one bit, it stops being a replicator and therefore has zero functional bits – put the bit back and you have 130 functional bits – zero to 130 bits in one move! Or course I’m not arguing that this happened, I’m trying to make the point that the difference between a replicator with 130 bits of functional information, and a chemical soup with zero functional bits could only be a dozen bits. This is a common error of thought, too. In your example, the functional information in the 130 bits of the replicator is already there, and working, and you must explain how it was generated. Obviously, you can suppress the function by changing only one bit, at least in some cases. And so? You keep the other 129 functional bits, and so it is perfectly true that one bit mutation (which is in the range of RV) can indeed restore the function. And so? The problem is, still: how did you get the other 129 bits right? By a random search? Can you see the difference? In desgin, you can well adjust 130 configurable switches one after another, because you, the designer, know what you want to obtain. And the function can well appear only at the end of the design. What's the problem? It's in a random walk that you cannot do that. Each single configuration of each bit cannot be implemented or kept, unless it confers a "reproductive advantage". That's the hard law of natural selection, the law that makes natural selection as almost useless tool for true evolution. Design can do that. Natural selection can't. It's as simple as that.gpuccio_{September 26, 2011
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DrBot, Understood, that's not what you meant to express. But what did you mean to express? Your statement which led to this was to the effect that variation in a uniform environment produces little change while variation in a changing environment produces evolution. My response is that variation is just variation, regardless of the environment. You seem to imply that the changing environment raises a challenge, and that life is compelled to rise to it. That a changing environment results in evolution assumes that variation can result in evolution. (We're far enough in the discussion that I'll assume we mean the same thing by "evolution.") There's a holy grail out there that no one seems to want to bring home and show off. On what do you base the conclusion that any variation, regardless of the environment, results in extensive evolution rather than just small variations? I can stand one domino on its end and stack ten more on top of it without it falling over. If I told you that by extrapolation I could balance a thousand more on top, would you believe me? Wouldn't you at least question how I came to that conclusion? I've been following this forum for some time and this same question gets raised several times each day. Everyone seems to maintain that is has been answered, but in thousands of posts no one seems to get around to addressing it head on. The one who does will be more famous than Darwin.ScottAndrews_{September 26, 2011
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This statement is fundamentally illogical and highlights the fallacious thinking I’m trying to, well, highlight.
Well I would agree that I expressed it poorly, but as for illogical ...
How is what anything accomplishes ever defined by the criteria for success? What something accomplishes is defined by what it can accomplish and by what it does. If it meets criteria then it does, or else it does not. That statement makes no sense whatsoever.
If the ultimate criteria for success is reproduction then you accomplish nothing if you don't reproduce - How could you accomplish anything if there is no criteria by which you judge accomplishment? Perhaps this is just a muddle over word meanings - when I said "What they accomplish" I was talking about how much a particular trait contributes to reproductive success, not just that organisms with different traits are different.
If some members of a population have a trait …those with the digestive trait will have a greater chance of surviving and reproducing
Do you see why the claim that this happened because it was the criteria for success is not an explanation? What of species that are extinct? Did they have no criteria for success?
No, it isn't an explanation and it is not what I said. I did not claim that the variation happened because of anything, just that variation has consequences in terms of reproductive success. 1-> Organisms are born, each is a little different than others in the population. 2-> Those properties, in the context of the environment, determine reproductive success.
Those are two good reasons why it makes no sense to say that “what they accomplish is actually defined by the criteria for success.”
How do you know if you have actually accomplished anything (as opposed to just doing stuff) if you have no criteria to measure your performance? How could someone claim to have accomplished the task of climbing mount Everest if they do not have 'climbing mount Everest' as the criteria for success?DrBot_{September 26, 2011
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Petrushka, A protein domain of 150 amino acids gives us N=20^150 states max. Proton transfer in hydrogen-bonded water is the fastest chemical reaction known to occur within around femtosecond (10^-15). Let's say we want to check all permutations by blind brute force search at the fastest rate. Simple maths shows it takes much longer than 10^17 seconds, the accepted bound on the age of the universe. That is just for 1 protein domain... Now it depends of course, how many states are meaningful of those N. This varies from protein to protein but overall, meaningful states are known to be very rare AND isolated in the solution spaces. There is simply not enough time to go through all that by blind search. The only other alternative (apart from design) is to say our blind search is lucky to encounter a solution state very early on. But the chance of this happening is ridiculously slim. You may choose to believe in that chance. I don't because it is not physically meaningful. I am not sure if there is any physically meaningful number of that order of magnitude to compare against. Maybe only the number of monkeys...Eugene S_{September 26, 2011
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I agreerhampton7_{September 26, 2011
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The answer to that dilemma is found at Ecclesiastes 9:11.
The race is not to the swift or the battle to the strong, nor does food come to the wise or wealth to the brilliant or favor to the learned; but time and chance happen to them all.
Omnipotence and randomness are not mutually exclusive. Having the ability to foresee the outcome of random events does not necessitate the use of such foresight and does not make those events any less random.ScottAndrews_{September 26, 2011
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Could it be that I’m not just the result of random errors filtered by natural selection? Am I just the product of the mindless, materialistic processes that “only legitimate scientists” all agree produced me?
Since randomness exists as best as we can determine (as defined by mathematics/science) this presents many Christians with the following dilemma: 1) God does not exist, 2) God does exist but is not omnipotent, or 3) God does exist and is omnipotent and so too randomness, for they are not mutually exclusive
Many neo-Darwinian scientists, as well as some of their critics, have concluded that, if evolution is a radically contingent materialistic process driven by natural selection and random genetic variation, then there can be no place in it for divine providential causality. A growing body of scientific critics of neo-Darwinism point to evidence of design (e.g., biological structures that exhibit specified complexity) that, in their view, cannot be explained in terms of a purely contingent process and that neo-Darwinians have ignored or misinterpreted. The nub of this currently lively disagreement involves scientific observation and generalization concerning whether the available data support inferences of design or chance, and cannot be settled by theology. But it is important to note that, according to the Catholic understanding of divine causality, true contingency in the created order is not incompatible with a purposeful divine providence. Divine causality and created causality radically differ in kind and not only in degree. Thus, even the outcome of a truly contingent natural process can nonetheless fall within God’s providential plan for creation.
rhampton7_{September 26, 2011
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You certainly are if you think you're saying anything that will trouble those of us who don't share your blind faith in neo-darwinism. I mean, you're not even giving us pause for thought. Just unsupported claims that are easily refuted. Evolutionists like you, Bot, only seek to reassure ID proponents like me, that the truth is on our side. If you were half as qualified as you think you are this would simply not be the case. You'd present us with debate-ending evidence and cogent arguments, rather than bluffing and blustering your way through. If this is the best that our critics have to offer, then we can be very confident indeed. :-)Chris Doyle_{September 26, 2011
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DrBot, This statement is fundamentally illogical and highlights the fallacious thinking I'm trying to, well, highlight.
Everything but the last bit is correct. Variations are random with respect to fitness. What they accomplish is actually defined by the criteria for success, so the last bit is completely wrong.
How is what anything accomplishes ever defined by the criteria for success? What something accomplishes is defined by what it can accomplish and by what it does. If it meets criteria then it does, or else it does not. That statement makes no sense whatsoever. You say
If some members of a population have a trait ...those with the digestive trait will have a greater chance of surviving and reproducing
Do you see why the claim that this happened because it was the criteria for success is not an explanation? What of species that are extinct? Did they have no criteria for success? Those are two good reasons why it makes no sense to say that "what they accomplish is actually defined by the criteria for success."
But not amongst those who have answered it.
Perhaps you could invite one of them to join the discussion. :)ScottAndrews_{September 26, 2011
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You are a time-waster, sir.
Yes, I often feel like I am wasting my time here ;) I haven't yet been blessed with a knighthood so you need only refer to me as Dr, not Sir.DrBot_{September 26, 2011
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My point is that whether the criteria for success changes or doesn’t has no affect on what type of variations can arise and what they can accomplish.
Everything but the last bit is correct. Variations are random with respect to fitness. What they accomplish is actually defined by the criteria for success, so the last bit is completely wrong. If some members of a population have a trait that makes it easier for them to digest a particular food type, but that food type is rare, then it doesn't give any real advantage. If the environment changes, or the population moves, so that this food source becomes abundant then those with the digestive trait will have a greater chance of surviving and reproducing than those without.
The second question I raised is how changes in the success criteria enable variations to accomplish evolution. That part is very controversial, at least among those who ask the question.
But not amongst those who have answered it.DrBot_{September 26, 2011
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Also, how did you determine that bacteria today are the same as they were 3 billion years ago?
Genomics is allowing us to trace evolution at the gene level, even in microbes. One can find varieties of the same gene, and eventually we will be able to find lineages of individual genes. It's a bit like finding fossils.Petrushka_{September 26, 2011
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DrBot, as to:
I keep seeing the ‘randomness cannot generate this’ argument put forth here and I think it is a bad argument because it doesn’t take into account how physics and chemistry work.
Actually physics and chemistry has been rigidly looked at, and a null hypothesis has been put forth as a result of that thorough examination;
Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,, Testable hypotheses about FSC What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses: Null hypothesis #1 Stochastic ensembles of physical units cannot program algorithmic/cybernetic function. Null hypothesis #2 Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function. Null hypothesis #3 Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function. Null hypothesis #4 Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time. We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified. http://www.tbiomed.com/content/2/1/29 "The Origin-of-Life Prize" ® (hereafter called "the Prize") will be awarded for proposing a highly plausible natural-process mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life. The explanation must be consistent with empirical biochemical, kinetic, and thermodynamic concepts as further delineated herein, and be published in a well-respected, peer-reviewed science journal(s). http://lifeorigin.info/ Of particular interest to you, on the preceding site, is this paper: 'The capabilities of chaos and complexity' Programming of Life - Information - Shannon, Functional & Prescriptive - video http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/1/h3s1BXfZ-3w
bornagain77_{September 26, 2011
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Correction - uniform or ~~static~~ non-uniformScottAndrews_{September 26, 2011
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