Science and Freethinking

_{Gil Dodgen

September 23, 2011

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

first removing information from a cell, and then either letting the programming of the cell calculate compensatory mutations, and/or introducing some epigenetic information in the form of designed/selected proteins that is then compensated for by the sophisticated programming in the cell.
The question you posed asked for an example of a novel protein originating via Darwinian processes. I cited an example of a novel, functional protein, and asked a simple question: How could it have been designed without using Darwinian selection? How could anyone design a protein coding sequence without using selection? How were the sequence libraries used in the experiment produced? How could they have been designed while not using selection? So far you haven't addressed my question.Petrushka_{September 26, 2011
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ScottAndrews As to:
Only after a set of proteins was selected was any experimentation done on living organisms.
Moreover 4 genes were 'knocked-out' before the designed/selected proteins were even inserted, and when the designed/selected proteins were inserted they merely 'rescued the cells, and did not increase the functional information over and above what was already present before the genes were knocked out! In fact I would hold the position that even after several rounds of 'compensatory mutations', by the highly sophisticated programming that is inside the cell, that the cells still did not return to its original level of 'robustness/fitness' when compared to the parent strains robustness/fitness! It is also interesting to note that in skimming over Behe's 'First Rule' paper,
EXPERIMENTAL EVOLUTION, LOSS-OF-FUNCTION MUTATIONS, AND “THE FIRST RULE OF ADAPTIVE EVOLUTION” http://www.lehigh.edu/~inbios/pdf/Behe/QRB_paper.pdf
,,,that I noticed, in TABLE 4, that both of the supposed 'gain of function' mutations listed by Dr. Behe, that Nick Matzke seems to be so enamored with, are such 'forced' deletions preceding 'compensatory mutations' events,,,
Investigator action- Viruses manipulated to be defective Deletion of 19 intercistronic nucleotides from RNA virus MS2 containing Shine-Dalgarno sequence and two hairpins Underlying mutation - One revertant deleted 6 nucleotides; another duplicated an adjoining 14- nucleotide sequence; missing functional coded elements substantially restored (Compensatory mutations!) Investigator action- 4 nucleotide deletion in lysis gene of MS2 Underlying mutation - Reading frame restored by deletions, insertions (Compensatory mutations!)
Thus as with Petrushka's forced example, it seems that our atheistic neo-Darwinian commentators, have been reduced to beggars of any evidence whatsoever, pathetically searching for proof of neo-Darwinian evolution by first removing information from a cell, and then either letting the programming of the cell calculate compensatory mutations, and/or introducing some epigenetic information in the form of designed/selected proteins that is then compensated for by the sophisticated programming in the cell. note:
Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
bornagain77_{September 26, 2011
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Petrushka, You are right. Selection is possible. No objections. And TOE is possible. No objections. The problem with TOE is that it is highly unlikely in our universe. It is so unlikely that it does not make sense to talk about this as a working scientific theory.Eugene S_{September 26, 2011
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Sorry, the Cyrillics did not work :)Eugene S_{September 26, 2011
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Hi, I think the fallacy of evolutionary thinking is that it puts the cart before the horse. There is no evidence of genuinely complex systems appearing spontaneously. On the other hand, theory of semantic information maintains that for successful transmission of information not only does one have to have an agreement about the language, but also about the alphabet and, most importantly, about information semantics, i.e. what is to be considered "true" or "false". Say, e.g. you have a string "dhfgdhg???????????f", most our colleagues here won't have a clue what it is but to me as a Russian speaker part of it makes sense because the Cyrillic letters in fact read "spanner". However, it is not it. More importantly, the originator of the message must know beforehand that I, as a receiver, have an idea about what a spanner is like. Otherwise, the string no matter how informative it is will remain jibberish for the receiver. So, before information is relayed over a channel successfully, a number of a priori set conditions must be satisfied. To assume that these conditions were being worked out on the way is utterly implausible to me, as we have absolutely no evidence supporting such an assumption.Eugene S_{September 26, 2011
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LOL! How about: "Warning! Materialists are cautioned not to view this material. May cause extreme cognitive dissonance."Eric Anderson_{September 25, 2011
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The selection process used to create the library bears no resemblance to Darwinian selection. It tested individual proteins to see whether they would fold.
LOL. In a living thing that kind of selection would never happen? I'm curious. How is selection not Darwinian? You might think I'm being frivolous, but I'm not. ID proponents are continually using analogies to engineering. Software, airplanes and such. When a human engineer designs a product, he can look up the properties of materials and find their strength, weight, cost and such. There is no such database for protein coding sequences. And ID proponents have gone to great pains to point out that such a database would take more resources than are available in the universe. And Douglas Axe has asserted that there are no shortcuts. No rules of thumb that tell you what the effect will be of modifying a base pair. Sow how does a designer of proteins proceed without using Darwinian selection? How do you build a sequence library that codes for folding, and how do you build a subset that might contain useful folds without selection? Are you really trying to say that that chemistry behaves differently in the lab than it does in the wild? Or are you attacking a fundamental methodology that seeks to isolate the variables being studied?Petrushka_{September 25, 2011
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Nick, I examined the evidence and logic, and determined that you and those of your persuasion are promoting a thesis that cannot be defended on scientific, rational, mathematical or evidential grounds, and have therefore resorted to intimidation and vilification as the only recourse in an attempt to defend an indefensible, dying philosophy, disguised and promoted as "science." The fact that I am a legitimate scientist who followed the evidence where it led, and a former militant, obnoxious atheist like you, is what really pisses you off.GilDodgen_{September 25, 2011
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Now this question is actually interesting, though not for the reason that petrushka would prefer:
Experiments are always designed. Do you think chemistry knows whither it is taking place in a lab or in a living thing?
Personally I don't think atomic particles are aware of anything, and yet:
Genesis, Quantum Physics and Reality Excerpt: Simply put, an experiment on Earth can be made in such a way that it determines if one photon comes along either on the right or the left side or if it comes (as a wave) along both sides of the gravitational lens (of the galaxy) at the same time. However, how could the photons have known billions of years ago that someday there would be an earth with inhabitants on it, making just this experiment? ,,, This is big trouble for the multi-universe theory and for the "hidden-variables" approach. http://www.asa3.org/ASA/PSCF/2000/PSCF3-00Zoeller-Greer.html.ori
Hmmm, and if that wasn't, to use Einstein's word, 'spooky' enough: Here is the key experiment that led Wigner to his Nobel Prize winning work on quantum symmetries:
Eugene Wigner Excerpt: To express this basic experience in a more direct way: the world does not have a privileged center, there is no absolute rest, preferred direction, unique origin of calendar time, even left and right seem to be rather symmetric. The interference of electrons, photons, neutrons has indicated that the state of a particle can be described by a vector possessing a certain number of components. As the observer is replaced by another observer (working elsewhere, looking at a different direction, using another clock, perhaps being left-handed), the state of the very same particle is described by another vector, obtained from the previous vector by multiplying it with a matrix. This matrix transfers from one observer to another. http://www.reak.bme.hu/Wigner_Course/WignerBio/wb1.htm
i.e. In the experiment the 'world' (i.e. the universe) does not have a ‘privileged center’. Yet strangely, the conscious observer does exhibit a 'privileged center'. This is since the 'matrix', which determines which vector will be used to describe the 'symmetry of the atomic particles being 'observed' in the experiment, is 'observer-centric' in its origination! Thus explaining Wigner’s dramatic statement, “It was not possible to formulate the laws (of quantum theory) in a fully consistent way without reference to consciousness.” Now exactly how in blue blazes do photons know billions of years in advance if a experiment will be preformed to see which side of a galaxy they will pass on, and exactly how in blue blazes do atomic particles in a experiment know if a different observer is performing a experiment??? Materialism simply offers no coherent explanation but Theism certainly does!!!,,, As to the chemistry in living systems, there is an interesting anomaly that merits note:
“Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection." Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79 https://uncommondescent.com/evolution/16037/#comment-369806
Spooky huh? Gets spookier to, because that same type of quantum action that caused the photon to 'know' billions of years in advance if a experiment would be preformed on earth to detect the photon,,,
Light and Quantum Entanglement Reflect Some Characteristics Of God - video http://www.metacafe.com/watch/4102182
,,,is the same type of quantum action that has recently been discovered in molecular biology!!!
Quantum Information/Entanglement In DNA & Protein Folding - short video http://www.metacafe.com/watch/5936605/
Now I don't know about atheists, but as for myself, and for several of my close friends, finding something that blatantly defies time and space on a massive scale within our bodies is very comforting to our overall Theistic beliefs!!bornagain77_{September 25, 2011
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Petrushka, The paper specifically refers to the de novo proteins as synthetic and designed. The selection process used to create the library bears no resemblance to Darwinian selection. It tested individual proteins to see whether they would fold. Only after a set of proteins was selected was any experimentation done on living organisms. Thomas Edison tested thousands of filaments for light bulbs and selected what worked best, but we would hardly cite that as evidence that selection trumps design.ScottAndrews_{September 25, 2011
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Petrushka,
Experiments are always designed. Do you think chemistry knows whither it is taking place in a lab or in a living thing?
It doesn't. But a better question is, how can it ever be known whether such chemistry would take place outside of the lab experiment? A designed experiment demonstrates what can happen in a designed experiment but always leaves uncertainty that the same results would occur elsewhere. One illustration (I forget the source) put it this way: Someone can play eighteen holes of golf. Does that demonstrate that the ball can move from the first tee through all eighteen holes without the player?ScottAndrews_{September 25, 2011
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Your failure to answer the question is very obvious to the onlookers.Timbo_{September 25, 2011
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LOL,
Why don’t you just stay on topic and answer my question?
LOL, Petrushka, sorry I thought purely neo-Darwinian evolution was the question. Oh well, since I'm not interested in your 'Design plus Darwinism' question, I guess I will go watch some videos.bornagain77_{September 25, 2011
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Why don't you just stay on topic and answer my question? How do you design protein coding sequences without using selection? Is there some shortcut not known to Douglas Axe?Petrushka_{September 25, 2011
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Petrushka you state:
Experiments are always designed.
OK let's look at experiments 'designed' to detect what ONLY neo-Darwinian processes can do since that is the specific question we want to answer and not at experiments 'designed' to detect what intelligence AND neo-Darwinian processes can do since that is not the question we want to answer. i.e. What can PURELY neo-Darwinian processes do???
Many of these researchers also raise the question (among others), why -- even after inducing literally billions of induced mutations and (further) chromosome rearrangements -- all the important mutation breeding programs have come to an end in the Western World instead of eliciting a revolution in plant breeding, either by successive rounds of selective "micromutations" (cumulative selection in the sense of the modern synthesis), or by "larger mutations" ... and why the law of recurrent variation is endlessly corroborated by the almost infinite repetition of the spectra of mutant phenotypes in each and any new extensive mutagenesis experiment (as predicted) instead of regularly producing a range of new systematic species... (Wolf-Ekkehard Lönnig, "Mutagenesis in Physalis pubescens L. ssp. floridana: Some Further Research on Dollo's Law and the Law of Recurrent Variation," Floriculture and Ornamental Biotechnology Vol. 4 (Special Issue 1): 1-21 (December 2010).) http://www.evolutionnews.org/2010/12/peer-reviewed_research_paper_o042191.html
Four decades worth of lab work is surveyed here:
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/
Michael Behe talks about the preceding paper on this podcast:
Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010 http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00
How about the oft cited example of antibiotic resistance?
List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria: Excerpt: Resistance to antibiotics and other antimicrobials is often claimed to be a clear demonstration of “evolution in a Petri dish.” ,,, all known examples of antibiotic resistance via mutation are inconsistent with the genetic requirements of evolution. These mutations result in the loss of pre-existing cellular systems/activities, such as porins and other transport systems, regulatory systems, enzyme activity, and protein binding. http://www.trueorigin.org/bacteria01.asp
That don't seem to be helping Petrushka! How about we look really, really, close at very sensitive growth rates and see if we can catch almighty evolution in action???
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. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, 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
Shoot that don't seem to be helping Petrushka. Perhaps we just got to give the almighty power of neo-Darwinism 'room to breathe'? How about we 'open the floodgates' to the almighty power of Darwinian Evolution and look at Lenski's Long Term Evolution Experiment and see what we can find after 50,000 generations, which is equivalent to somewhere around 1,000,000 years of human evolution???
Richard Lenski's Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information - September 2011 Excerpt: The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski's research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT. (Michael J. Behe, "Experimental Evolution, Loss-of-Function Mutations and 'The First Rule of Adaptive Evolution'," Quarterly Review of Biology, Vol. 85(4) (December, 2010).) http://www.evolutionnews.org/2011/09/richard_lenskis_long_term_evol051051.html
Now that just can't be right Petrushka!! Man we should really start to be seeing some neo-Darwinian fireworks by 50,000 generations!!! Hey I know what we can do! How about we see what happened when the 'top five' mutations from Lenski's experiment were combined??? Surely now the Darwinian magic will start flowing, baby!!!
Mutations : when benefits level off - June 2011 - (Lenski's e-coli after 50,000 generations) Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually. http://www2.cnrs.fr/en/1867.htm?theme1=7
Now Petrushka, something is going terribly wrong here!!! Tell you what Petrushka, let's just forget trying to observe evolution in the lab, I mean it really is kind of cramp in the lab you know, and now let's REALLY open the floodgates and let's see what the almighty power of neo-Darwinian evolution can do with the ENTIRE WORLD at its disposal??? Surely now almighty neo-Darwinian evolution will flex its awesomely powerful muscles and forever make those IDiots cower in terror!!!
A review of The Edge of Evolution: The Search for the Limits of Darwinism The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have "invented" little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155). http://creation.com/review-michael-behe-edge-of-evolution Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution "Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell--both ones we've discovered so far and ones we haven't--at best extremely limited benefit, since no such process was able to do much of anything. It's critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing--neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered--was of much use." http://www.evolutionnews.org/2009/05/swine_flu_viruses_and_the_edge.html
Now Petrushka, there is something terribly wrong here!!! After looking high and low and everywhere in between, we can't seem to find the almighty power of neo-Darwinism anywhere!! Shoot we can't even find ANY power of neo-Darwinism whatsoever!!! Perhaps you know all this, and this is why you are trying your absolute darnedest to sell the 'Designed' experiment as confirmation of Darwinian evolution??? :)bornagain77_{September 25, 2011
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Chris: "But don’t you think it is sufficient to identify design in nature?" Petrushka: "Absolutely not. As Elizabeth has taken some pains to point out, evolution has a candidate for the designer. ID does not." Sorry, but Elizabeth has missed the boat on this issue. Elizabeth's recent interactions on these threads leave much to be desired from a standpoint of logic and scientific reasoning. There is absolutely no logical reason ID needs to identify the designer, however much you would like, from your own philosophical preferences, for ID to do so. Evolution can't have a candidate for the designer because it claims there isn't one. If you mean that evolution claims things came about through purely mechanistic processes, then sure, evolution has put forth a candidate for its designer substitute: purely mechanistic processes (albeit a wholly vague, highly-disputable, and wildly speculative one). That's what a mechanistic theory needs to show, that a purely mechanistic process did it (or at least is plausible, to be taken seriously in the first place). ID is not a mechanistic theory. ID is not a theory of everything. ID is a very limited ascertainment of certain artifacts of design left behind. It does not pretend to explain the exact mechanistic process *because it is not a mechanistic theory*. You can dislike that all you want. You and Elizabeth can kick and scream and complain and berate design proponents for not going beyond their theory. But that is a problem with your bias, not a problem with ID.Eric Anderson_{September 25, 2011
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Experiments are always designed. Do you think chemistry knows whither it is taking place in a lab or in a living thing? You are avoiding a key question. Is it possible to design proteins without using Darwinian selection? Take a look at how sequence libraries are generated. Find an example where sequences are designed from first principles rather than using selection.Petrushka_{September 25, 2011
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Nick - I am really curious. Have you ever applied actual mathematical/ statistical algorithms to your confidence in the adequacy of darwinism/materialism. All I ever hear from atheist/materialist/physicalist/darwinist types are hand-waving arguments about look at this phenotype similarity ( which does not impress me because it has no bearing on the design/non-design question at all) , or consider how many years and then extend micro arguments to macro... I never see anything which tries to pin down real numbers. The only brave attempts I have seen to actually use real numbers come from design people ( Richard Sternberg, Douglas Axe ) and those who are not for design but publish articles which critique evolution and OOL theories ( Paul Davies, Bob Shapiro ). What I would really like to see from the evolutionary community is an honest statement like "We have no real quantitive arguments - but our gut feeling given this evidence is that it confirms evolution." Without quantitative statistical numbers please get off the high horse of "scientific surety" and admit you are making a choice based on guesswork. Maybe then you will show a little more respect to your ideological opponents.JDH_{September 25, 2011
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Petrushka, with such a 'handicapped' ability to discern what is actually happening in this experiment, and see that intelligence played a foundational role, it is no wonder that you believe in neo-Darwinism no matter what evidence is presented to you!bornagain77_{September 25, 2011
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I butchered my blockquote tag. That's me quoting you, replying, quoting you, and replying again (as I'm sure you guessed.)ScottAndrews_{September 25, 2011
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Petrushka,
I think people understand what the “official” definition is, but I think they get confused by how that translates into typical posts on ID supporting forums. Posts which are frequently religious, and which frequently denounce atheism.
I agree. I think that sends a confusing, mixed signal.
It would seem that ID proponents want to walk mainstream science into a box in which it lacks answers to many questions and in which it is not allowed to seek answers.
ID offers no reason not to consider mechanisms or seek answers. It's just that it, in itself, is not that science. But it might point us in the right direction to find those answers. If we're seeking an undirected explanation for something that was directed, or vice versa, then we're looking in the wrong place. The only case I've seen of not being allowed to seek answers is when investigating the mere possibility of intelligent design is discouraged.
ScottAndrews_{September 25, 2011
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How do you suppose the libraries are “designed”? Check it out. Do you think it is possible to know what an arbitrary coding sequence will produce, or do you suppose sequences are selected? Think about the process, not just the words.Petrushka_{September 25, 2011
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Petrushka, I don't have to think about it,,, Intelligent agents were directly involved!!! The burning question is not whether neo-Darwinian processes, 'aided by a guiding intelligence', can produce functional proteins, the burning question is whether neo-Darwinian processes, and only neo-Darwinian processes, can generate functional genes and/or proteins.bornagain77_{September 25, 2011
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How do you suppose the libraries are "designed"? Check it out. Do you think it is possible to know what an arbitrary coding sequence will produce, or do you suppose sequences are selected? Think about the process, not just the words.Petrushka_{September 25, 2011
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Petrushka, you are simply completely out of touch with reality if you think your cited experiment proves 'purely' neo-Darwinian processes can produce novel functional proteins and or genes. Wishful thinking, denialism, fantasy world, and pseudo-scientific posturing are few other, of the 'nicer', adjectives that come to mind!!!
De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth Excerpt: A central challenge of synthetic biology is to enable the growth of living systems using parts that are not derived from nature, but designed and synthesized in the laboratory. As an initial step toward achieving this goal, we probed the ability of a collection of >10^6 de novo designed proteins to provide biological functions necessary to sustain cell growth. Our collection of proteins was drawn from a combinatorial library of 102-residue sequences, designed by binary patterning of polar and nonpolar residues to fold into stable 4-helix bundles.,,, http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015364
And Petrushka, other than your seemingly pathological need to deny the overwhelmingly obvious evidence for a 'design' in life, why in blue blazes would you be forced to use such a 'Designed' experiment to try to prove purely 'natural' neo-Darwinian processes can generate functional genes/proteins??? Surely it is because you are forced to do so against your will, for if you had any evidence whatsoever, of purely neo-Darwinian processes generating novel functional proteins/genes, then you would do certainly cite that evidence rather than be embarrassed by such a pathetic citation that was supposedly supporting your atheistic neo-Darwinian position!!!bornagain77_{September 25, 2011
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Forgot the link: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015364Petrushka_{September 25, 2011
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Petrushka, perhaps you would care to show the ‘pathetic detail’ of just one novel, functional, protein/gene, that actually does something other than ‘stick’ to ATP every 1 in 10^12 tries, originating by purely neo-Darwinian processes???
Here's some functional proteins derived by selection. You will invoke the buzzword "designed," but be aware that no one can design protein coding sequences. You can only select them. No one knows how to predict how a coding sequence will fold, and Douglas Axe has asserted there are no shortcuts.Petrushka_{September 25, 2011
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as to 'science can only seek regularities'
Meyer and Nelson on a Failed Explanation for the Origin of the Genetic Code - Jonathan M. - August 2011 Excerpt: 'codes and digital information are categories of effects uniformly associated with intelligent causes. Indeed, to the extent that Yarus and others have succeeded in establishing affinities between codons and amino acids, they did so only as a direct consequence of their own intelligent manipulation and intervention.' http://www.evolutionnews.org/2011/08/direct_rna_templating_a_failed050121.html "A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter. Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107." (The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.) The DNA Code - Solid Scientific Proof Of Intelligent Design - Perry Marshall - video http://www.metacafe.com/watch/4060532 The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html The Capabilities of Chaos and Complexity - David L. Abel - 2009 Excerpt: "A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information). http://www.mdpi.com/1422-0067/10/1/247/pdf Stephen C. Meyer - Signature In The Cell: "DNA functions like a software program," "We know from experience that software comes from programmers. Information--whether inscribed in hieroglyphics, written in a book or encoded in a radio signal--always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source." http://www.evolutionnews.org/2009/07/leading_advocate_of_intelligen.html Three subsets of sequence complexity and their relevance to biopolymeric information - David L Abel and Jack T Trevors: Excerpt: Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction...No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization...It is only in researching the pre-RNA world that the problem of single-stranded metabolically functional sequencing of ribonucleotides (or their analogs) becomes acute. http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf Biological Information: The Puzzle of Life that Darwinism Hasn’t Solved - Stephen C. Meyer Thus, as my book Signature in the Cell shows, Joyce’s experiments not only demonstrate that self-replication itself depends upon information-rich molecules, but they also confirm that intelligent design is the only known means by which information arises. http://www.evolutionnews.org//2009/06/biological_information_the_puz.html The Origin of Life: An RNA World? - Jonathan M. - August 22, 2011 (Refutation of Nick Matzke) Excerpt Summary & Conclusion We have explored just a small handful of the confounding difficulties confronting the chemical origin of life. This is not a god-of-the-gaps argument, as Matzke claims, but rather a positive argument, based on our uniform and repeated experience of cause-and-effect. It is not based on what we don't know, but on what we do know: that intelligence is a necessary and sufficient condition for the production of novel complex and functionally specified information. The design inference is based on sound and conventional scientific methodology. It utilizes the historical or abductive method and infers to the best explanation from multiple competing hypotheses. http://www.evolutionnews.org/2011/08/the_rna_world_a_response_to_ni049871.html There remains one and only one type of cause that has shown itself able to create functional information like we find in cells, books and software programs -- intelligent design. We know this from our uniform experience and from the design filter -- a mathematically rigorous method of detecting design. Both yield the same answer. (William Dembski and Jonathan Witt, Intelligent Design Uncensored: An Easy-to-Understand Guide to the Controversy, p. 90 (InterVarsity Press, 2010).)
Stephen Meyer describes the intelligent design argument as follows:
“Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information. “Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information. “Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.” Stephen C. Meyer - The Scientific Basis For the Intelligent Design Inference - video http://www.metacafe.com/watch/4104651
Certainly seems like a solid 'scientific regularity' to me Petrushka!!!bornagain77_{September 25, 2011
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Petrushka, if there was evidence for evolution, I would merely become a theistic evolutionist: my worldview would barely be altered. It would be wrong to say that theistic evolutionists believe that evolution, by itself, designs. No, evolution would just be a mechanism that the Intelligent Designer used. There is no problem for me accepting that possibility if that is where the evidence leads. A number of ID proponents accept common ancestry (I'm not one of them), but, you must agree, there is a crucial and unbridgeable gap between mere evidence for common ancestry and the evidence that you must provide to demonstrate that human beings evolved from a single-celled eukaryote through a process of natural selection acting upon random mutations. This is why I placed the emphasis on atheistic evolutionists: people who believe that the universe and everything in it all made itself, by accident, without purpose or design, people who believe that all life evolved purely naturalistically, from non-living chemicals, and that death brings only oblivion. As all of the greatest scientists who ever lived believed, the regularities that we observe in the universe only make sense in light of the Supreme Being who wrote the Laws of Nature and created an ordered universe for us to dwell in. Or are you saying we can only study things like Stonehenge if we assume it made itself by naturalistic means? Because, you know, design and engineering is ultimately a regular and ordered process: and nature provides us with the highest levels of design and engineering and as such, this can only be explained in terms of Intelligent Design. Truth is not reducible to everything that can be learned from the scientific method. Imposing methodological naturalism on science merely makes it even more difficult for science to determine truth.Chris Doyle_{September 25, 2011
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As Elizabeth and countless others -- including Micheal Denton -- have pointed out, God can use evolution to effect design. One could argue whether the specific current state of life is destiny, or whether evolution is free to explore alternate scenarios, but evolution designs, and it is not automatically atheistic to say so. As others on this site have also pointed out, science seeks to find the background regularities in nature, against which miracles and interventions might be discerned. Even the Catholic church does this when attempting to verify miracles. What other procedure makes sense? If you don't look for regularities, you are blinded by voluntary ignorance. As you point out, science can only seek regularities. that is the point of Lewontin's statement, when you quote the whole statement rather than a snippet.Petrushka_{September 25, 2011
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