Science and Freethinking

_{GilDodgen
September 23, 2011

Intelligent Design

2}_{Categories
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

Perhaps the confusion is because no one would suggest that the processes of cell replication are any less natural and mechanical than an IBM reading a punch card and printing an output. That's common ground. So I presumed that we were considering whether natural laws can explain the existence of such a system and the information upon which it operates, not whether that operation follows natural laws. My bad.ScottAndrews_{September 28, 2011
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DrBot: That information you refer to is the physical configuration of the system – nothing more. I asked you to explain how these elements can work together to produce an output, yet have no biochemical relationship. You responded by describing the biochemical relationship. You are really something. So, hamlet is the physical configuration of the ink, and nothing more. And information is a useless concept, certanly! Just to be clear, a functional configuration is not a biochemical relationship, it is an informational relationship realized by imposing a specific form to configurable switches that would never take that form only for spontaneous working of scientific laws. Yes, the functional configuration of a protein is certainly a physical state, but it is not certainly explainable by biochemical laws. To say that biochemical laws explain the sequence of myoglobin means that in some way you can put the necessary aminoacids in some system (where there is no specific information about the myoglobin sequence) and biochemical laws will cause the formation of the myoglobin sequence because of necessity interactions between the molecules. Thagpuccio_{September 28, 2011
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Petrushka,
I do miss the point of asserting that some unspecified thing was done by an unspecified agent having unspecified capabilities at unspecified times and places. That certainly isn’t what archaeologists do. It isn’t what forensic investigators do.
If it were an unspecified thing, what would be even be talking about? Your amplification of "unspecified" is clearly rhetorical. Otherwise that's exactly what forensic investigators do. This person was murdered with a gun. How do you know? From the holes in his chest and back. Who did it? I don't know. Where's the gun? Where's the bullet? I don't know. They draw their conclusions based on historical observations that bullets are the most common cause of such fatal holes, and that they are usually fired by people with guns. They do not draw their conclusions by acquiring every possible piece of information. Rather, their conclusions are the basis for investigating. Knowing the general cause of death tells others where to look for more specific details. That's how it works in real life. We don't prosecute until we know who fired the gun and perhaps prove it by finding the bullet. But imagine if we tied our hands by deciding that the apparent bullet holes were not grounds for an investigation? Imagine telling the guy who found the holes that they weren't even grounds for a murder investigation because he hadn't identified the gun, bullet, or shooter? How absurd. What irks me is that these standards you propose are so selective in their application. In what other context would you discourage the use of limited information to narrow the search for more specific information?ScottAndrews_{September 28, 2011
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If you do not respond to the actual content of my posts because you think I misrepresent you, then there is hardly any reason to continue, is there? I have no desire, nor need, to misrepresent you. So for that I apologize.Upright BiPed_{September 28, 2011
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DrBot, I'm repeating myself and perhaps beating a dead horse because I can't imagine that you are saying what it sounds like you are saying. When an message encoded in abstract symbols is interpreted to follow instructions or produce an object, there is no necessary relationship between either the appearance or the form of the message and the actions or object, even though the process of interpretation follows natural laws. This is evident because a different interpreter can produce different instructions from the same message, just as a word can have two meanings in two languages or number 12 can have multiple meanings within a computer program. I can assign my own meaning to DNA. I can assign various values to different foods and use it to decide what to have for lunch each day. I can have a computer process it for me so that the process is transparently natural. Am I violating laws by associating the code with new outputs? Am I creating new laws? How can there be an intrinsic relationship between a given sequence and chicken noodle soup when there wasn't one yesterday? Some would argue that the existence of any complex functional object requires forward thinking. I'll put that aside. But what about a complex functional object which was produced and assembled from instructions translated from an abstract code expressed in a medium? Seriously, that doesn't require forward thinking?ScottAndrews_{September 28, 2011
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Besides, I consider evolution to be intelligent, at least sufficiently intelligent to do what is attributed to it. Evolution is a learning algorithm. Shapiro, who is supposedly ID friendly, agrees.Petrushka_{September 28, 2011
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And a human being after all is just a composition of 65% of oxigen, carbon 18%, hydrogen 10%, nitrogen 3% Calcium 1.5%, traces of some other elements and enough iron to make one tiny nail.Eugene S_{September 28, 2011
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I agree, and I don't understand what is so controversial. ID theory does not claim that the chemical processes that allow DNA to be copied are not natural and mechanical. If it did, then every instance of cell division would be directly attributed to (an) active intelligent design(ers).rhampton7_{September 28, 2011
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The electromagnetic force (chemical bonding) is what makes "recognition" possible, not any kind of sentience or informational awareness.
Aminoacyl-Transfer RNA Synthetases Read the Genetic Code Each aminoacyl-tRNA synthetase is highly specific for a given amino acid. Indeed, a synthetase will incorporate the incorrect amino acid only once in 10^4 or 10^5 catalytic reactions. How is this level of specificity achieved? Each aminoacyl-tRNA synthetase takes advantage of the properties of its amino acid substrate. Let us consider the challenge faced by threonyl-tRNA synthetase. Threonine is particularly similar to two other amino acids—namely, valine and serine. Valine has almost exactly the same shape as threonine, except that it has a methyl group in place of a hydroxyl group. Like threonine, serine has a hydroxyl group but lacks the methyl group. How can the threonyl-tRNA synthetase avoid coupling these incorrect amino acids to threonyl-tRNA? The structure of the amino acid-binding site of threonyl-tRNA synthetase reveals how valine is avoided. The enzyme contains a zinc ion, bound to the enzyme by two histidine residues and one cysteine residue. Like carbonic anhydrase, the remaining coordination sites are available for substrate binding. Threonine coordinates to the zinc ion through its amino group and its side-chain hydroxyl group. The side-chain hydroxyl group is further recognized by an aspartate residue that hydrogen bonds to it. The methyl group present in valine in place of this hydroxyl group cannot participate in these interactions; it is excluded from this active site and, hence, does not become adenylated and transferred to threonyl-tRNA (abbreviated tRNAThr). Note that the carboxylate group of the amino acid is available to attack the ?-phosphate group of ATP to form the aminoacyl adenylate. Other aminoacyl-tRNA synthetases have different strategies for recognizing their cognate amino acids; the use of a zinc ion appears to be unique to threonyl-tRNA synthetase. The zinc site is less well suited to discrimination against serine because this amino acid does have a hydroxyl group that can bind to the zinc. Indeed, with only this mechanism available, threonyl-tRNA synthetase does mistakenly couple serine to threonyl-tRNA at a rate 10^-2 to 10^-3 times that for threonine. As noted in Section 29.1.1, this error rate is likely to lead to many translation errors. How is a higher level of specificity achieved? Threonyl-tRNA synthetase can be incubated with tRNAThr that has been covalently linked with serine (Ser-tRNAThr); the tRNA has been “mischarged.” The reaction is immediate: a rapid hydrolysis of the aminoacyl-tRNA forms serine and free tRNA. In contrast, incubation with correctly charged Thr-tRNAThr results in no reaction. Thus, threonyl-tRNA synthetase contains an additional functional site that hydrolyzes Ser-tRNAThr but not Thr-tRNAThr. This editing site provides an opportunity for the synthetase to correct its mistakes and improve its fidelity to less than one mistake in 10^4...
rhampton7_{September 28, 2011
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You conspicuously excuse any non-intelligent explanation from this strict requirement. And, apparently without hope, you miss the point of Intelligent Design, which is demonstrated billions of times per day. I don’t think you want to understand it.
I haven't excused evolution from this requirement. Thousands of biologist labor every day to demonstrate that evolution has the physical capability of doing what is necessary to explain common descent. Read the Koonin or Shapiro books and tell me what physical capability is lacking in order for the evolutionary explanation to be valid. I do miss the point of asserting that some unspecified thing was done by an unspecified agent having unspecified capabilities at unspecified times and places. That certainly isn't what archaeologists do. It isn't what forensic investigators do.Petrushka_{September 28, 2011
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All this is possible not because any chemical law connects CGU to Argninine, but because the 20 enzimes that read the genetic code have in their sequence the correct information to associate the correct aminoacid with the correct tRNA, bearing the correct anticodon. That’s how the information in the DNA, and then in the mRNA, is translated into its purposeful output, the protein.
Yes - it is a physical mechanism. The information you refer to is a property of the arrangement of matter and the rules that govern their interactions. This is what you just described. Change the configuration of the chemicals involved and you change the behavior of the system.
it is only the information ib the DNA and in the enzymes that ensures the correct decoding of the symbolic information in the gene.
That information you refer to is the physical configuration of the system - nothing more. I asked you to explain how these elements can work together to produce an output, yet have no biochemical relationship. You responded by describing the biochemical relationship.DrBot_{September 28, 2011
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Not until it makes some point other than what I just said, and is corrected to remove things I didn't. I've been arguing the process is physical. Everyone should be able to agree with that. I haven't said the "association is caused by the physical properties" or "acquired because of those physical properties." I would say it is a physical system that functions with certain physical properties. These functions were acquired.DrREC_{September 28, 2011
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Do you plan to address the actual content of my post?Upright BiPed_{September 28, 2011
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"acquired or given to it because of those physical properties." "Or it is an acquired property directly related to its physical make-up." Distinction?DrREC_{September 28, 2011
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"I agree that all the process is physical" Excellent start. "The relationship is created by the information in the synthetase." The the relationship is mediated by the physical properties of the synthetase, which physically matches the anticodon with the cognate amino acid. A number of biologists have suggested proto-tRNAs were self-charging, and I think some have been created by directed evolution, but I'd have to check for references. At any rate, these are acquired properties directly related to its physical make up of the system. "You confound the laws of necessity that govern chemistry and physoics with the laws of information that govern machines, including biological machines." 1) The laws of necessity? Please list them? 2) Why would you predict something like translation must be governed by a law (I'll define it Law universal and invariable)? Translation is governed by physical properties. It is also plastic, with different systems using different codons and amino acids. You seem puzzled that by this, and seem to equate it with unnatural, or designed. Why would such conformity, such that the 'law of translation' could be writ be an evolutionary prediction? 3) "laws of information that govern machines, including biological machines" And what do you propose those are?DrREC_{September 28, 2011
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This is plainly an equivocation. Either the association is caused by the chemical properties, or it is not. a) If it is caused by the physical properties, then it is not informational. b) If it it not caused by the physical properties, yet an association is nonetheless observed, then its inclusion within the system comes by some other means. In instance (b), the observed association would not have been caused by the physical properties of the component, but acquired or given to it because of those physical properties. It is a distinction you need to keep in mind. Now, you may wish to argue (and make your case) that the other means mentioned above is a completely unguided natural process. But what you cannot do is first claim the association is caused by the physical properties of the component, then failing any demonstration of that, come back to claim that its acquired because of those physical properties, and yet still fail at any demonstration.Upright BiPed_{September 28, 2011
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DrBot, Of course we are describing a system made of physical components. But how do you explain the presence of a mediator that produces a functionally useful output rather than a useless one? How do you explain the presence of a code with the potential to be translated into a functional output? I can scribble letters and numbers all day long, and nothing is going to convert them into a functional anything. The process functions by natural laws, but what laws put it in place?ScottAndrews_{September 28, 2011
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DrRec: They have no biochemical relationship. The relationship is created by the information in the synthetase. To have a biochemical relationship means that the codon has some biochemical reason to react with Arginine, or to make it mounted in the protein. That is not true. The codon never interacts with Arginine. I agree that all the process is physical, exactly as the working of a software is physical. But that does not mean that the sequence of bits in a password has some specific electromagnetic connection with the output that the password commands in the software. The connection is created by the information by which the software works, not by the laws of physics, athough obviously the laws of physics are used by the designer to structure that information in a machine. I will not enter into the debate physyiocal not physical about information. I am not intersted in that. The simple point is that, without the information in the software, not physical laws would make the sequence of bits in a password have any power. or give any output. You confound the laws of necessity that govern chemistry and physoics with the laws of information that govern machines, including biological machines. Or maybe you just want to confound them, for your own purposes.gpuccio_{September 28, 2011
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DrBot: There is a specific enzyme, that is called Arginyl-tRNA synthetase. It is one of the 20 fundamental enzymes that decipher the genetic code. In E coli, it is made of 577 AAs, just to give an idea of its complexity. It recognizes the correct tRNA, with the anticodon corresponding to Arginine. It then binds Arginine to that tRNA, in a position that is completely separated from the anticodon. So, the tRNA with the anticodon for Arginin is charged with Arginin, and will mount Arginine at the correct site on the ribosome, guided by ots anticodon which interacts with the mRNA. All this is possible not because any chemical law connects CGU to Argninine, but because the 20 enzimes that read the genetic code have in their sequence the correct information to associate the correct aminoacid with the correct tRNA, bearing the correct anticodon. That's how the information in the DNA, and then in the mRNA, is translated into its purposeful output, the protein. Chemical laws are obviously respected in all these chemical interactions, but it is only the information ib the DNA and in the enzymes that ensures the correct decoding of the symbolic information in the gene. And, as I have already pointed out, the information in the enzymes is derived, too, form information in other DNA genes (the genes that code for those 20 enzymes). I hope I don't have to repeat all that again.gpuccio_{September 28, 2011
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Petrushka, You say this,
He describes evolution as possibly conscious, and asserts that cells have trigger mechanisms that spur the creation of variation.
and this
But the simple fact is he asserts that purely physical processes are capable of driving evolution.
but then mysteriously with regard to ID you say this:
If you want to counter it you must demonstrate that it can be done. You must reinvent methods that could have been available, and you must show that they work.
You conspicuously excuse any non-intelligent explanation from this strict requirement. And, apparently without hope, you miss the point of Intelligent Design, which is demonstrated billions of times per day. I don't think you want to understand it.
That is what a search for a designer would look like. A description of the design process and a process by which it can be verified.
I'm not aware of anyone scientifically searching for such a designer. Are you? If I heard of anyone I would pass your suggestion along, except that it's wrong. Reverse engineering does not necessarily identify the engineers.ScottAndrews_{September 28, 2011
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That the meaning of the codons is determined by the mediator, not by their own physical properties, indicates that with a different mediator they could have different meanings.
For a given mediator and codon the output will change when you change the codon, if you change the mediator you can also change the output - both are physical components of the system so their output is always determined by their physical properties.DrBot_{September 28, 2011
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DrREC,
Their biochemical relationship is mediated by the aminoacyl tRNA synthetase, which recognizes the anti-codon, and loads the tRNA with the appropriate amino acid.
The ASCII code 65 is mediated by software in my computer, both of which are physical entities, and interpreted as the letter "A." Does that indicate a necessary physical relationship between the stored bits and the number 65, or between the number 65 and the letter "A?" That the meaning of the codons is determined by the mediator, not by their own physical properties, indicates that with a different mediator they could have different meanings. I could assign values to combinations of them and use them to write sentences in English. The functions of coded information and interpreters may themselves depend on physical laws, but cannot be explained by them. There is a difference.ScottAndrews_{September 28, 2011
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For instance, the following codons: CGU, CGC, CGA, CGG correspond symbolically to Arginine in the code. They are recognized by the translation system as a command to mount Arginine. But they have no special biochemical relationship with Arginine.
If there is no physical correspondence then explain how I can make CGU, CGC, CGA, CGG mount Tyrosine?DrBot_{September 28, 2011
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OK, let me rephrase. In the latest Shapiro book he describes evolution as a design process. He describes evolution as possibly conscious, and asserts that cells have trigger mechanisms that spur the creation of variation. He says cells obtain information from the environment and incorporate it into the genome. He likens biological evolution to the process by which the immune system generates antibodies. He invokes no miracles, no intervention, nothing but known physical processes. Now if you think he supports ID -- as many people do -- you can read between the lines and conclude he thinks this system is designed (possibly incorporated at creation?). But the simple fact is he asserts that purely physical processes are capable of driving evolution. Just as computers can process information by purely physical processes. Whatever his mainstream colleagues think of his book (apparently not much), he is well within the mainstream because he does not call upon unnamed entities, and he presents suggestions for research to validate his conjectures. That is what a search for a designer would look like. A description of the design process and a process by which it can be verified. All investigations of design begin with hypotheses about the nature of the designer, whether it be birds and nests, bees and hives, or humans and stone tools. You mention Stonehenge. You might mention the pyramids. There have been many books written asserting that humans are not capable of creating such large scale works without modern technology. Now one could approach this claim by calculating how much a human can lift without modern machinery, or one could go a bit farther and investigate how cathedrals were build and project these techniques backwards. If you did so you might come to the conclusion that the pyramids could not be built by humans unaided by some sort of alien technology. There in no logical or mathematical way to counter this. If you want to counter it you must demonstrate that it can be done. You must reinvent methods that could have been available, and you must show that they work. Of course this has been done in the case of Stonehenge. The interesting thing is that even if you do this you don't really know how it was done. You only know it was physically possible. In the same way, we do not know that stone tools and ancient pottery were made by humans. We only know that it is highly plausible. Plausibility and consistency with all known facts are the criterion for detecting and validating design inferences.Petrushka_{September 28, 2011
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DrRec, One should distinguish self-ordering (e.g. crystallisation) from genuine spontaneous self-organisation. There is a huge difference between the two. The latter has never been observed. Self-organisation involves formal relationships between components of a complex system. Crystallisation is far from this. More details on this, see David Abel on Capabilities of Chaos. Complex systems are routinely organised by intelligent agents.Eugene S_{September 28, 2011
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Petrushka,
ID supported have no agreement on whether intervention is continuous, sporadic, or just once time at creation. And more importantly, no interest in reaching agreement.
BTW, I wasn't aware that the abiogenesis or darwinist camps (pretending they are separate) had come to any consensus on anything except that life formed and then something called "evolution" occurred, and that no intelligence was involved. When you claim to explain everything at least a little more consensus is reasonable to expect. You're still stuck on your strawman concept of ID as an alternative explanation to all of biology, and that's why you're puzzled by the lack of consensus on matters ID does not address. Let me connect the dots from ID to specific explanations for what we observe in biology, as they are not the same thing: The first step in reverse-engineering is to determine that something was engineered. You cannot or will not even begin to reverse-engineer something if you do not know whether it was engineered or incorrectly assume that it was not. Actually it's only one dot.ScottAndrews_{September 28, 2011
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Petsrushka,
I’m merely pointing out the obvious, that if you don’t look for regularities you don’t find them.
I'll point out the equally obvious, that if you don't look for design you don't find it. What does either have to do with anything? And what is this "fruitful" thing you keep mentioning, and how is it relevant? What is true of one thing may not be true of another. If I see a thing and wish to determine whether it was designed, should I examine, analyze, and reason, or should I just decide which conclusion is more fruitful? What is the "fruit" in "fruitful?" A correct conclusion, or just any conclusion at all? Please help me to understand.ScottAndrews_{September 28, 2011
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"Either it is an inherent physical property, or it is a given/acquired property unrelated to its physical make-up." Or it is an acquired property directly related to its physical make-up.DrREC_{September 28, 2011
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I'm glad we agree on that. "But they have no special biochemical relationship with Arginine." Is false. Their biochemical relationship is mediated by the aminoacyl tRNA synthetase, which recognizes the anti-codon, and loads the tRNA with the appropriate amino acid. Physical recognition. Physical process. That you can imagine alternatives (and indeed, humans have expanded the genetic code--mostly by directed evolution) doesn't make it a non-physical process.DrREC_{September 28, 2011
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I apologize for mis-posting. Post 32.2.1.1.i was in response to 32.2.1.2.1Upright BiPed_{September 28, 2011
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