Here, at Sandwalk: “A twofer” Here’s Jonathan M’s post: “Thoughts on the ‘C-Value Enigma’, the ‘Onion Test’ and ‘Junk DNA.’”
Comments
Larry,
Natural selection is an integral part of evolutionary theory, unless someone decides tomorrow that it isn't.
I ask you to provide an evolutionary explanation of something, just pick something, that demonstrates the explanatory power of evolutionary theory.
You respond with trees, which indicates that you are unable to integrate natural selection with your explanation, or that you view it tautologically.
Natural selection is an integral part of evolutionary theory but you cannot incorporate it in an evolutionary explanation.
Apparently those are the only parts of my post that you didn't read.
So I'm wrong. You didn't run away from the tough question. You just dance in circles around it, waving your spear and chanting your holy incantations to make it disappear.
Am I really asking you a difficult question? Would you like to refer me to an expert in the field?ScottAndrews
October 16, 2011
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ScottAndrews says,
BTW, this is my big chance? Wow, you really are full of yourself.
Translation: "Intelligent Design Creationism can't explain the fossil record or phylogenetic trees. I prefer to concentrate on attacking evolution."
When that doesn't work you can always fall back on ...
Only the most feeble-minded fool would be distracted from such details by name-calling and attempts to intimidate. I can’t tell whether I’m taking to a professor or a child. It is disgraceful. I wouldn’t let you teach my child arithmetic.
Larry Moran
October 16, 2011
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Larry,
Are you saying that they have never constructed phylogenetic trees of chordate proteins, noted that they are basically congruent with the morphological trees and the fossil record, but never offered an explanation based on evolutionary mechanisms?
No, Larry, what I am saying it what I said, and what I cited.
Evolutionary theory posits (today or last week at least) that unintentional variations and environmental pressures result in differential selection. Then it happens again. And again. Throw in drift, HGT, and whatever is popular that week.
Now let me repeat my exact words: The thousands of them together with thousands of years of combined research have yet to use any evolutionary mechanisms to explain any evolutionary change greater than bird beaks, lizard heads, and bacteria that eat nylon.
Then
What changes have you explained in those terms - specific mutations, specific selective pressures, drift, HGT?
You mention construction and comparison of trees as if that were the same thing. They are not, and that is what I am pointing out. How does a tree indicate the something was or was not selected, except tautologically?
Only the most feeble-minded fool would be distracted from such details by name-calling and attempts to intimidate. I can't tell whether I'm taking to a professor or a child. It is disgraceful. I wouldn't let you teach my child arithmetic.
That being said, my original statement stands. Let's see if you avoid the tough questions.
BTW, this is my big chance? Wow, you really are full of yourself.ScottAndrews
October 16, 2011
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ForJah, look at my comment #11.1 where I said,
Hardly anyone thought that all non-coding DNA was junk. That’s a “myth” made up by Jonathan Wells and his supporters. He should know better because he studied molecular biology.
Later on I explained why I said "hardly anyone." It's because there are some examples in the scientific literature of scientists who said that all non-coding DNA is junk. (They probably just misspoke but that's not relevant.)
Then I said (#12.2) ...
The quotes do not reflect the huge majority of scientists who were/are well aware of functional non-coding DNA. It’s just another example of how IDiots distort scientific consensus by selective quote-mining.
You immediately followed up with what you must have thought was a very important question ...
So does that mean there were/are scientists who claim all non-coding DNA was or still is junk?
What kind of reply did you expect? When I said "huge majority" did you think I meant "every single scientist, without exception"?
It was a stupid question.
IDiot.Larry Moran
October 16, 2011
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Joseph says,
ID is not anti-evolution ...
You are correct. If one scours the Intelligent Design Creationist literature one will occasionally stumble upon some article or book that tries to offer some positive evidence for the existence of intelligent design in nature.
On the other hand, 99.9% of that literature is anti-evolution.
Here's a challenge for you, Joseph. Look at all the postings on Uncommon Descent over the past few months. Tote up the number that are anti-evolution and those that offer a positive case for Intelligent Design Creationism.
Post your results here and then we can decided whether, to a first approximation, Intelligent Design Creationism is anti-evolution.
Larry Moran
October 16, 2011
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ScottAndrews said,
... I like to keep in mind that guys like him talk about how evolution works like they’re describing yesterday’s football game, that the thousands of them together with thousands of years of combined research have yet to use any evolutionary mechanisms to explain any evolutionary change greater than bird beaks, lizard heads, and bacteria that eat nylon.
Are you saying that evolutionary biologists have never used evolutionary mechanisms to explain the fossil record of, say, chordates?
Are you saying that they have never constructed phylogenetic trees of chordate proteins, noted that they are basically congruent with the morphological trees and the fossil record, but never offered an explanation based on evolutionary mechanisms?
Do you actually think about what you're writing before you click on "Post Comment"?
Over on my blog I made note of the fact that Intelligent Design Creationists are notoriously deficient in the "explaining" game. They spend most of their time attacking evolution and hardly ever offer their own explanations.
Here's your big chance, ScottAndrews, how do you explain the fossil record and molecular phylogeny using Intelligent Design Creationism? You could start by telling me whether you accept the scientific evidence for the age of the Earth and the age of fossils and whether Intelligent Design Creationists have to accept the scientific evidence for common descent.
I'm betting that you avoid the question. You and your fellow IDiots will probably launch into an attack on interpretations of the fossil record and the failings of molecular evolution.
That's why we call you IDiots. You always avoid the tough questions.Larry Moran
October 16, 2011
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Dear Jammer,
Yes, in a sense I am "afraid" to debate the issue raised by Upright BiPed. When he/she/it said ...
These observations establish that the entailed objects (and dynamic relationships) exist the same in the translation of genetic information as they do in any other type of recorded information (in every example from human language, to computer and machine code, to a bee’s dance).
... that goes well outside of my area of expertise. I don't know anything about how the word "information" is used in human language and in computer code.
I know that most IDiots are expects in almost everything so they are completely fearless about plunging into debates on all kinds of topics.
Scientists like me, however, are much less intelligent. We tend to be experts on only a few things and we try to avoid pretending otherwise.
I guess that means I'm a coward.Larry Moran
October 16, 2011
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Perhaps I wasn't being very clear when I said ...
In common parlance we refer to these sites as containing “information” in the form of specific nucleotide sequence. It’s a very useful analogy and I think everyone knows what we mean when we use it. Nobody expects it to conform to the meanings of “information” in other disciplines.
Nobody, that is, except some IDiots who like to play semantic word games instead of addressing real science.
I hope you’re not one of those people.
What I should have said was "I'm not going to debate the meaning of information in computer science or any other discipline and whether it applies to the 'information' contained in a sequence of nucleotides."
There are two reasons for my lack of interest in such a debate.
1. I don't think there's any connection between the colloguial use of the word "information" in genetics and molecular biology and its use in other disciplines.
2. I don't know anything about the other disciplines and how they use the word "information."Larry Moran
October 16, 2011
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Att UD rebel forces:
I think upright bipeds post should be moved to the reference area (or a version of it). this is a fundamental issue that rarely gets explained/understood in the manner posted @:
Upright Biped 8.1.2.1.4junkdnaforlife
October 15, 2011
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Larry Moron: Sorry, I’m not interested in that kind of “debate.”
Dr. Moron, are you afraid to debate Upright Biped? You seemed so confident at first, yet after UB posted his opening entry, you seem to have gotten cold feet. Are you a coward, as I suspect?
Also, am I correct in concluding that you are a bio-information denialist, i.e., one who denies that actual information exists in biology? That seems to be par-for-the-course with designophobes. It's really quite telling.Jammer
October 15, 2011
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ForJah,
When someone such as Larry attempts to insult and intimidate me, I like to keep in mind that guys like him talk about how evolution works like they're describing yesterday's football game, that the thousands of them together with thousands of years of combined research have yet to use any evolutionary mechanisms to explain any evolutionary change greater than bird beaks, lizard heads, and bacteria that eat nylon.
You can understand it or not, but it's about as relevant the inner mythology of Harry Potter. Despite being hailed as the cornerstone of biology, it has yet to provide an explanation of anything that isn't one third imagination and one third
'somehow/something/evidently.' It is the emperor's new clothes. Only fools like you can I can't see them.
I remind myself of that and it's like that old public speaking trick - imagining them naked.ScottAndrews
October 15, 2011
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Geez Kelly, even Richard Dawkins said it would make a difference- he said it would be a totally different type of biology- I would say something similar to the difference between geologists and archaeologists.Joseph
October 15, 2011
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Larry,
ID is not anti-evolution and I would say that any and all regulatory sequences refute the claim that evolution occurs via blind, undirected chemical processes.
ID claims that evolution occurs (mostly) via directed processes such as those found in targeted searches.
But then again evotards like you don't seem to understand anything about Intelligent design.Joseph
October 15, 2011
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Dr Liddle, what is it about the following exchange that causes you to describe it with the word "surprise" and indicates to you in some way that the exchange is illegitimate in some sense. What I am asking - is why do you think Dr Moran needs your assistance in interpreting his exchange?
BIPED: It is the information in DNA that I am concerned with, its physical existence within the medium...So firstly, I would like to ask if you agree that there is information in DNA, or not?
MORAN: The specific order of nucleotides in DNA determines whether certain biochemical activities will occur at that site...In common parlance we refer to these sites as containing “information” in the form of specific nucleotide sequence. It’s a very useful analogy and I think everyone knows what we mean when we use it.
I told Dr Moran upfront that I had a specific interest, he responded to that, and after describing my interest, he commented that he was not interested in the same thing. It seems pointless for you to be going on about it.Upright BiPed
October 15, 2011
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Elizabeth, in response to you complaint on the other thread, (paraphrase), 'If God can do such powerful miracles why does he allow little children to die':
Natalie Grant - Held - music
http://www.youtube.com/watch?v=8GDUBd2eWFw
bornagain77
October 15, 2011
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No, I'm suggesting that Larry offered to debate a specific topic and you seemed surprised when he declined to debate a different one.
But I might come back to your post myself tomorrow. You seem to have laid out your thoughts in a nice essay format.
Cheers
LizzieElizabeth Liddle
October 15, 2011
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Lol, as someone who is just getting used to the name calling tactic of evolutionists...I LOVE IT! haha...it's like talking with a child. Thank you for finally answering my question and proving my point. I think I'm satisfied with stopping here.ForJah
October 15, 2011
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Dr Liddle ,
You might have noticed in my post where I stated:
I am concerned with, its physical existence within the medium.
To which Dr Moran responded with his comments on that subject.
Are you suggesting that I should be limited in my comments and interests, or are you suggesting that I should be subjected to a test of bona fides on all subject matter in order to comment at all?Upright BiPed
October 15, 2011
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Larry:
Are we debating whether your understanding of the Onion Test is correct?
Go for it
UBP:
[long post that has nothing to do with UBPs understanding of the Onion Test]
Larry:
@Upright BiPed,
Sorry, I’m not interested in that kind of “debate.”
UBP:
ahem...
;)
UBP, why don't you want to debate your understanding of the Onion Test with Larry?Elizabeth Liddle
October 15, 2011
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ahem...
;)Upright BiPed
October 15, 2011
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Yes, of course, that's exactly what I meant.
IDiot.Larry Moran
October 15, 2011
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So does that mean there were/are scientists who claim all non-coding DNA was or still is junk?ForJah
October 15, 2011
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This isn't an answer to my question.ForJah
October 15, 2011
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ForJah says,
First, I don’t believe Wells thinks that all non-coding DNA was considered junk.
That's not the impression he conveys in his book. He never gives a proper scientific definition of "junk DNA." He constantly uses "non-coding" DNA as a synonym for "junk." And he "forgets" to mention that we were aware of many functions for non-coding DNA before the discovery of junk.
He tells his readers about those functions (regulatory sequences, genes for RNA, centromeres) as though they were discoveries that came after the discovery of junk DNA and helped destroy the myth.
Second, I find it interesting that you said “hardly anyone”…So does that mean there were/are scientists who claim all non-coding DNA was or still is junk?
I said "hardly anyone" because I'm well aware of the quote-mining powers of the IDiots. They can comb through the scientific literature and find the odd example of a scientist who implied that all non-coding DNA was junk. If I had said "nobody" those quotes would have popped up immediately in the comments.
The quotes do not reflect the huge majority of scientists who were/are well aware of functional non-coding DNA. It's just another example of how IDiots distort scientific consensus by selective quote-mining.Larry Moran
October 15, 2011
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ForJah says,
Do I have this backwords or something for, although it does seem to prove your point, what I conclude is that molecular biolgists say there is “little junk DNA” but in fact they are wrong and we would expect “a lot of junk DNA”.
Junk DNA is like the Spanish Inquisition, nobody "expected" it.
The presence of large amounts of junk DNA is incompatible with Darwinism but compatible with modern evolutionary theory. Note that I said "compatible." Large amounts of junk DNA were not predicted and were not anticipated.
The presence of large amounts of junk DNA is not proof of evolution and if it turns out that most of the putative junk DNA is functional it will not refute evolution.
Why do IDiots have such a hard time understanding basic evolution?
I suppose I shouldn't be surprised. If you were capable of understanding science you probably wouldn't be IDiots in the first place.Larry Moran
October 15, 2011
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@Upright BiPed,
Sorry, I'm not interested in that kind of "debate."Larry Moran
October 15, 2011
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Dr Moran, sorry for the delay. Other responsibilities intervened for a bit.
Certainly the sequence in DNA is driving reactions. (And there are many varieties)
In your comments you refer to the use of the term “information” within nucleic sequences as a useful analogy, and you say that there is no expectations that it should “conform to the meanings of “information” in other disciplines.” I certainly agree with you that it conforming to other meanings would be a telling turn of events. And I assume your comment suggests that the nucleotide sequence isn't expected to share any of the same physical characteristics as other forms of information - given that we live in a physical universe where information has physical effects. Ones which we can observe.
I think it makes an interesting comparison; the comparison between the physical characteristics of information transfer in the genome, versus information transfer in other forms. Just recently on this forum we were having a conversation about recorded information, and a question arose if a music box cylinder 'contained information'. Speaking to its physical characteristics, the answer I gave was “yes”. Just like any other form of recorded information, the pins on a music box are an arrangement of matter to act as a representation within a system. No differently than ink on paper, or the state of a microprocessor, or the lines left on a recording tape, or an ant's pheromones, or the tone of vibrations we make when we speak; they are all matter/energy arranged in order to represent an effect within a system.
It was also pointed out that a physical arrangement of matter (like the pins on a music box cylinder) cannot by themselves convey information - they require a second coordinated physical object. This second object is easily referred to as a protocol, but physically its is a rule (a protocol) established in a material object. The necessity of this physical protocol is something easily understood; for one thing to represent another thing within a system, it must be separate from it, and if it is truly a separate thing, then there must be something to establish the relationship that exist between the representation and the effect it is to represent (within that system). That is what the second physical object accomplishes, it establishes the relationship between a representation and the effect it represents, which is a relationship that otherwise wouldn't exist.
There have been examples of this dynamic given in previous conversations. For instance, an apple is an apple, but the word “apple” is a separate thing altogether. Being a separate thing from the apple, there must be something that establishes the relationship between the two. In the case of the word “apple” we as humans have learned the protocols of our individual languages, and they physically exist as neural patterns within our brains. These neural patterns are material things, and they establish the immaterial relationship between a physical representation and its physical effect. This same dynamic is found in all other cases of recorded information. I have previously used the example of a bee's dance; a bee dancing in a particular way during flight is a separate thing than having the other bees fly off in a particular direction, and the relationship between the two is brought about by a protocol which physically exist in the sensory system of the bee.
In the dynamics of information transfer, the operative observation is that each of these physical things (the representations, the protocols, and their resulting effects) always remains discrete. This is one of the key observations that allows information to exist at all. The input of information is always discrete from the output effect, and the protocol that establishes the relationship between the two, remains discrete as well. They are three completely independent physical realities which share a relationship, with the protocol establishing the relationship between the representation and its effect within the system. In no case does the representation (or the protocol) ever become the effect.
This same dynamic is found in all forms of recorded information; including those used in the information processing systems created by intelligence. As an example, the first automated fabric looms used an arrangement of holes punched into paper cards (which acted as physical representations of the resulting effects within the fabric). Sensors and pins within the machine would sense where the holes were punched, and it would use that information to change and control the colors of threads being woven. In this instance, the configuration of holes served as the representation, and the configuration of sensors served as the protocol, leading to the specified effects. Each of these is physically discrete, while sharing the immaterial relationship established by the protocol.
So here we have a series of observations regarding the physicality of recorded information which repeat themselves throughout every form – no matter whether that information is bound to humans, or human intelligence, or other living things, or non-living machines. There is a list of physical entailments of recorded information that can therefore be generalized and compiled without regard to the source of the information. In other words, the list is only about the physical entailments of the information, not its source. I am using the word “entailment” in the standard sense – to impose as a necessary result (Merriam-Webster). These physical entailments are a necessary result of the existence of recorded information transfer. And they are observable.
That list includes the four material observations as discussed in the previous paragraphs: a) the existence of an arrangement of matter acting as a physical representation, b) the existence of an arrangement of matter to establish the relationship between a representation and the effect it represents within a system (the protocol), c) the existence of physical effects being driven by the input of the representations, and d) the dynamic property that they each remain discrete. Observations of systems that satisfy these four requirements confirms the existence of actual (not analogous) information transfer.
These same entailments are is found in the transfer of information from a nucleic sequence. During protein synthesis a selected sequence of nucleotides are copied, and the representations contained within that copy are fed into a ribosome. The output of that ribosome is a chain of amino acids which will then become the protein being prescribed by the input sequence. The input of information is therefore driving the output production. But the input and the output are physically discrete, as evidenced by the fact that the don't directly interact, and that the material output is not assembled from the material input.
The exchange of information (from input to output) is facilitated by a set of special physical objects – the protocols – tRNA and its entourage of aminoacyl synthetase. Acting together they make it possible for the input to alter the output, and they do so by allowing them to remain separate. The tRNA physically bridges the gap between the input and the output, acting as a passive carrier of the physical protocol. It accomplishes this by being charged with the correct amino acid by the synthetases (the only molecules in biology which actually hold the rules to the genetic code). The synthetases accomplish their tasks by being able to physically recognize both the tRNAs and the amino acids. They charge the tRNAs with their correct amino acids before they ever enter the ribosome. The actions of the synthetases are therefore completely isolated from both the input and output. In other words, the only molecules in biology that can set the rule that "this maps to that" are physically isolated from both the input and output, while the input and output remain isolated themselves.
These observations establish that the entailed objects (and dynamic relationships) exist the same in the translation of genetic information as they do in any other type of recorded information (in every example from human language, to computer and machine code, to a bee's dance). These observations have been attacked as being as a misuse of the definition of words (a semantic word game, as you call it). But I have already produced the definitions of the words from a standard dictionary; I've restated the observations using those definitions in place of the words themselves; and I have asked the question: “If in one instance we have a thing that actually is a symbolic representation, and in another we have something that just acts like a symbolic representation – then someone can surely look at the physical evidence and point to the distinction between the two. There is also the simple fact that there is nothing about the attachment of cytosine to thymine to adenine that intrinsically means “bind leucine to a nearby polypeptide” as an inherent property of its matter. That is a quality beyond its mere materiality, one it takes on by being in a system with the correct protocol to cause that effect from that arrangement of matter.
There has also been the profoundly illogical objection that because these things follow physical law (and can be understood), they cannot be considered symbols or symbolic representations. Not only does this deny the existence of any symbol in the extreme, it fails for the obvious reason that everything follows physical law. If something can't be true because it follows the same laws as everything else, then we have entered the Twilight Zone.
So going back to your comment, a fair reading suggests that the information transfer in the genome shouldn't be expected to adhere to the qualities of other forms of information transfer. But as it turns out, it faithfully follows the same physical dynamics as any other form of recorded information. As for “disciplines”, you will notice that these observations are very much in the domain of semiotics. Demonstrating a system that satisfies the entailments (physical consequences) of recorded information, also confirms the existence of a semiotic state. It does so observationally. Yet, the descriptions of these entailments makes no reference to a mind. Certainly a living being with a mind can be tied to the observations of information transfer, but so can other living things and non-living machinery. It must be acknowledged, human beings did not invent iterative representative systems, or recorded information. We came along later and discovered they already existed.
Therefore, the search for an answer to the rise of the recorded information in the genome needs to focus on mechanisms that can give rise to a semiotic state, since that is the way we find it. We need a mechanism that can cause an arrangement of matter to serve as a physical representation. We need a mechanism that can establish within a physical object a relationship between two discrete things. To explain the existence of recorded information, we need a mechanism to satisfy the observed physical consequences of recorded information
Do you agree, or do you have evidence that attaching adenine to thymine to guanine is mapped to “start a new protein” in any physical context?Upright BiPed
October 15, 2011
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So I'm a little confused by your response Nick. Now I just want to make sure I undersand what you are saying...
1: there were evolutionists who once rejected the idea of "Junk DNA"(just like Wells does)
2: now its hard to find a "serious" evolutionist that does reject the idea of "junk DNA"
3: Being that Molecular biologists don't have proper training in evolution now-a-days, they are more likely to reject the idea of "junk dna".
Do I have this backwords or something for, although it does seem to prove your point, what I conclude is that molecular biolgists say there is "little junk DNA" but in fact they are wrong and we would expect "a lot of junk DNA".
I can't be correct in my analysis here...could you help me please?ForJah
October 15, 2011
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Kelly, your comparison to physics is deliciously appropriate: the standard model is in a flux. It's an exciting time. Right now you could have a discussion with your physics professor about results that contradict "fundamental understandings" and unless he was an ideological tyrant he would be overjoyed to debate the possibilities. Oh and Guillermo Gonzales did question certain "fundamental understandings" of astrophysics. . .see his bio to find out the results.MedsRex
October 15, 2011
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Kellyhomes, While I believe you make a good point, I just don't agree. I am somewhat ashamed of myself for allowing this conversation to diverge into something irrelevant to the topic. SOo while I would love to address your points, even though you put an extreme amount of words in my mouth, I don't feel this is the proper place to do so.
Getting back on topic though, can someone please address my points and not the education I have.ForJah