Creationist argument about DNA and information

Daniel: A lie about FSC which is Functional Sequence Complexity (not ID)

FSC = Intelligent Design Construct.
18 March 2016 Daniel: A lie about FSC which is Functional Sequence Complexity in biology (nothing to do with intelligent design).
This is Shannon uncertainty with the addition of a functionality variable as in sources that Daniel has cited before :jaw-dropp!
Measuring the functional sequence complexity of proteins
Background
Abel and Trevors have delineated three aspects of sequence complexity, Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC) and Functional Sequence Complexity (FSC) observed in biosequences such as proteins. In this paper, we provide a method to measure functional sequence complexity.

Methods and Results
We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families. Considerations were made in determining how the measure can be used to correlate functionality when relating to the whole molecule and sub-molecule. In the experiment, we show that when the proposed measure is applied to the aligned protein sequences of ubiquitin, 6 of the 7 highest value sites correlate with the binding domain.
 
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Oh Enoch, you know damn well Abel's theory for FSC doesn't reconcile these issues and Dembski's hijacking of Orgel's metaphor (should read the entire thing you know...pg 196 would do you some good) of specified complexity are pseudoscience.

So here we stand, you have the words of Abel, Trevors, and I assume Dembski at just a copypaste away, and actually demonstrate my previous point elegantly that the use and misuse of Information Theory (Shannon) and Kolmogorov Complexity are just a new coat of paint for the Watchmaker Analogy.

The idea of irreducible complexity and your argument about the bike are a nonstarter and are rejected as they cannot adequately compare to the biochemistry. ID (and IrrCom) present an irrelevant problem meant to lead to an irrelevant conclusion and you repeatedly using your space shuttle plant belies your commitment to said irrelevance.
 
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Daniel: An implied lie by highlighting the "specified complexity" phrase in a source

"In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity"
Leslie E. Orgel, The Origins of Life: Molecules and Natural Selection, pg. 189 (Chapman & Hall: London, 1973
8 March 2016 Daniel: An implied lie by highlighting the "specified complexity" phrase in a 1973 source as if it were IDs later and discredited "specified complexity".
The date is when I first pointed this lie out in another thread:
Your "FSC" is not part of the pseudoscience of Intelligent Design or science
Functional sequence complexity is a concept in science, e.g. Functional Sequence Complexity in Biopolymers
 
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"The attempts to relate the idea of order...with biological organization or specificity must be regarded as a play on words that cannot stand careful scrutiny. Informational macromolecules can code genetic messages and therefore can carry information because the sequence of bases or residues is affected very little, if at all, by [self-organizing] physicochemical factors".
H.P. Yockey; "A Calculation of Probability of Spontaneous Biogenesis by Information Theory"; Journal of Theoretical Biology 67, 1977; p. 390.
A track record of parroting or writing lies by quote mining and you expect us to believe any quote with ellipsis from you, Daniel :eye-poppi!
What is obviously dubious about this citation is the usual Daniel stuff: the age, author and maybe contents of the paper!
This is from 1977 - papers get invalidated by later papers.
Hubert Yockey is not a biologist.
The abstract of A Calculation of Probability of Spontaneous Biogenesis by Information Theory suggests a "747 from a junkyard argument" with the use of "simple combinatorial analysis".
 
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Oh Enoch, you know damn well Abel's theory for FSC doesn't reconcile these issues


Ohhh Lowpro: How so....?

Do you understand the concept of SUPPORTING what you say? Or do you think floating Ipse Dixit Baseless 'bald' Assertions Fallacies in lieu of anything of SUBSTANCE will save the day??


...and Dembski's hijacking of Orgel's metaphor (should read the entire thing you know...) of specified complexity are pseudoscience.


Sure. Do you know Dembski's favorite color? How about his position on Integrity in State Government?? Did he hold that up @ gun point too?

"Orgel's Metaphor :confused: What on Earth LOL.


The idea of irreducible complexity and your argument about the bike are a nonstarter


So you're rebuttal is "Na'ahhh"?? Riveting. You wouldn't happen to be Pre-Law by chance?

regards
 
There are 3 Types of Complexity 1) random sequence complexity (RSC), 2) ordered sequence complexity (OSC), or 3) Functional Sequence Complexity (FSC)."
These are all arbitrary divisions that humans use to make it easier to analyze systems, but there is no fundamental difference between them.

If we had big enough brains or powerful enough computers we could derive it all from the behavior of subatomic particles. Since we can't do that for more than a few molecules we must simply the problem by looking for patterns and differences at the macro scale. But the underlying structure that they 'emerge' from is still unintelligent interactions that are described by quantum physics and mathematics.

"In brief, living organisms are distinguished by their specified complexity.
This is an arbitrary distinction, and 'Specified Complexity' is pseudoscience - but you already knew that. :(

"The attempts to relate... specificity must be regarded as a play on words that cannot stand careful scrutiny.
So why do you keep doing it? :(

Please Reconcile this Irreducibly Complex System.
'Irreducibly Complexity' is pseudoscience.

how are you getting the first "Functional Proteins" when you need "Functional Proteins" (CODED Specifically for on DNA), to make "Functional Proteins"?
We are working on it. Eventually we will work out how DNA emerged, and be able to reproduce the process using unintelligent non-living chemicals in the same environment - then your argument will be shot full of holes.

And as those gaps get smaller, your 'God' will shrink until He completely disappears in a puff of logic!
 
Ohhh Lowpro: How so....?

Do you understand the concept of SUPPORTING what you say? Or do you think floating Ipse Dixit Baseless 'bald' Assertions Fallacies in lieu of anything of SUBSTANCE will save the day??

Pfft if I tried I'd just be scooped by Reality Check. He has your bs on lockdown.


Sure. Do you know Dembski's favorite color? How about his position on Integrity in State Government?? Did he hold that up @ gun point too?

"Orgel's Metaphor :confused: What on Earth LOL.

Looks like someone's got some required reading to do (of their own posted source no less!)

Can we avoid frivolous absurdities as retort? It's bad enough you use them for assertion, but doubling down on them? That dog won't hunt sir!

So you're rebuttal is "Na'ahhh"?? Riveting. You wouldn't happen to be Pre-Law by chance?

regards

Actually if I were Pre-Law I would ask for summary judgment as you did not provide merit to your case.
 
It’s got nothing to do with what we can or cannot do. We simply do not know what information is…any more than it is known what you or I actually are (it’s hardly a stretch to notice the obvious connection). There are patterns, and there is the ability to adjudicate the patterns. Patterns are information. The ability to adjudicate the patterns is intelligence. The ability to intentionally create patterns is also intelligence.




Look in the mirror. Otherwise…see below.




Anything from which meaning can be extracted by an intelligent agent possesses information. Which would mean that everything is information.




…of course there are no intelligent agents. Waves, sand, wind…they’re all a result of the laws of physics.

Ooops, forgot…they’re not actually the result of the laws of physics…the laws of physics just describe what happens. Nobody has ever discovered any ‘laws of physics’ causing anything to happen.

So…the waves, sand, wind…they’re the result of the interaction of matter and energy.

…ooops, forgot again. There is no such thing as matter and energy. Those are, once again, merely phenomena described by our models. Physics quite effectively demonstrates that neither matter nor energy occur as anything but…something else.

Questions for smart people:

What actually is ‘reality’?
What makes it occur / function / happen the way it does?
If we ‘discover’ the laws of physics, does that mean they actually exist (…that’s a slightly incoherent question…we obviously couldn’t discover them if they didn’t exist)?
Since ‘intelligence’ is the only thing we know of with the capacity to create / discover / comprehend a ‘law of physics’…how is it not reasonable to conclude that …since the laws of physics exist (since we discover rather than create them)…some manner of superior intelligence is somehow behind them?
Am I the only one here who finds this sort of undergraduate, 3am, pot-fuelled solipsistic, shadows-on-the-walls-of-the-cave intellectual meandering both boring and pointless?
 
"The attempts to relate the idea of order...with biological organization or specificity must be regarded as a play on words that cannot stand careful scrutiny. Informational macromolecules can code genetic messages and therefore can carry information because the sequence of bases or residues is affected very little, if at all, by [self-organizing] physicochemical factors".
H.P. Yockey; "A Calculation of Probability of Spontaneous Biogenesis by Information Theory"; Journal of Theoretical Biology 67, 1977; p. 390.

If people are wondering, this is one of the cases where quote mining was done by someone else, and Daniel happened upon it.

Let's follow the trail! The original paper is actually titled "A calculation of the probability of spontaneous biogenesis by information theory", note the missing 'the' in his citation. This helps trace the history. The paper was published in 1977 in the Journal of Theoretical Biology. Abstract:

The Darwin-Oparin-Haldane “warm little pond” scenario for biogenesis is examined by using information theory to calculate the probability that an informational biomolecule of reasonable biochemical specificity, long enough to provide a genome for the “protobiont”, could have appeared in 109 years in the primitive soup. Certain old untenable ideas have served only to confuse the solution of the problem. Negentropy is not a concept because entropy cannot be negative. The role that negentropy has played in previous discussions is replaced by “complexity” as defined in information theory. A satisfactory scenario for spontaneous biogenesis requires the generation of “complexity” not “order”. Previous calculations based on simple combinatorial analysis over estimate the number of sequences by a factor of 105. The number of cytochrome c sequences is about 3·8 × 1061. The probability of selecting one such sequence at random is about 2·1 ×10−65. The primitive milieu will contain a racemic mixture of the biological amino acids and also many analogues and non-biological amino acids. Taking into account only the effect of the racemic mixture the longest genome which could be expected with 95 % confidence in 109 years corresponds to only 49 amino acid residues. This is much too short to code a living system so evolution to higher forms could not get started. Geological evidence for the “warm little pond” is missing. It is concluded that belief in currently accepted scenarios of spontaneous biogenesis is based on faith, contrary to conventional wisdom.

If anyone wants the full PDF and don't have access, as is the tradition with academic papers, you know what to do. The quote does not appear in the paper. Here's the full paragraph:

Order, as so conceived, may be very useful in crystallography and in other fields but it will not lead to specificity in molecular biology. Polanyi (1968) has pointed out that the orderliness of the crystal precludes the capacity to function as a code. As we discussed previously (Yockey, 1974) the crystal carries very little information. Attempts to relate the idea of “order” in a crystal with biological organization or specificity must be regarded as a play on words which cannot stand careful scrutiny. Informational macromolecules can code genetic messages and therefore can carry information because the sequence of bases or residues is affected very little if at all by physicochemical factors.

So he's making a statement here about entropy and information. The lower the entropy of something, like a crystal, the lower the potential information content. The paper is of course a paper about abiogenesis and not about evolution. If you want to talk about abiogenesis, a paper that is nearly 40 years old is not a good place to start anyway, many of the ideas discussed have been discarded. And of course, he manages to disagree with Daniel's central premise about thermodynamics "As far as the origin of life is concerned thermodynamics and “heat death” of the universe are irrelevant." You'll also of course note this on a his webpage:

This post is written by Cynthia Yockey. The first thing I want noted about my father is that he is not in any way, shape or form a Creationist. He does not support Intelligent Design. He supports Darwin’s theory of evolution and points out that it is one of the best-supported theories in science.

So on to the next user of this quote, you'll note that the bit about crystal was removed and the [self-organizing] bit was added. This comes from a 1998 book, 'Mere Creation: Science, Faith & Intelligent Design" from the Discovery Institute. The citation is "Yockey, H. P. 1977. A calculation of the probability of spontaneous biogenesis by information theory. Journal of Theoretical Biology 67:377-98"

You can imagine that this being a Discovery Institute text that's been around for 18 years or so, it's got quite a bit of mileage with creationists. The citation with the 'the' removed has quite a bit of traction with creationists, appearing all over the internet. It looks like it came from a pamphlet entitled, "The Evolution Cruncher" from Evolution Facts, Inc. It was written in 2001, but still manages to blame the communists. However, the citation look like this:

"Hubert P. Yockey, “A Calculation of Probability of Spontaneous Biogenesis by Information Theory,” Journal of Theoretical Biology, Vol. 67, 1977, p. 398)."

Daniel's citation for reference:

H.P. Yockey; "A Calculation of Probability of Spontaneous Biogenesis by Information Theory"; Journal of Theoretical Biology 67, 1977; p. 390.[/quote]

The citation actually contains an error (both actually, page 398 is pretty much a blank page). The page is 380, which should help track down the place Daniel is pulling the quote from, but I think the transcription error may be his as many citations include "esp 380", but oddly, many of those citations include the 'the' in the paper title missing in his citation.

Care to enlighten us Daniel?
 
If people are wondering, this is one of the cases where quote mining was done by someone else, and Daniel happened upon it.
Great research, RussDill. The quote was mangled by the Discovery Institute:
  • took away the context of a discussion of order (the quote mine),
  • added a "The", removed quotes? and replaced "in a crystal" with ellipsis to conceal the quote mine and
  • inserted a word to change the meaning of the quote.
Order, as so conceived, may be very useful in crystallography and in other fields but it will not lead to specificity in molecular biology. Polanyi (1968) has pointed out that the orderliness of the crystal precludes the capacity to function as a code. As we discussed previously (Yockey, 1974) the crystal carries very little information. The aAttempts to relate the idea of order in a crystal with biological organization or specificity must be regarded as a play on words which cannot stand careful scrutiny. Informational macromolecules can code genetic messages and therefore can carry information because the sequence of bases or residues is affected very little if at all by [self-organizing] physicochemical factors.

One wonders if Daniel will be honest enough to acknowledge that the Discovery Institute lied about Yockey's paper?
 
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Am I the only one here who finds this sort of undergraduate, 3am, pot-fuelled solipsistic, shadows-on-the-walls-of-the-cave intellectual meandering both boring and pointless?

I don't find it boring or pointless, just tangential to the discussion. By waving away the essential premises, there's not much left to talk about. It's like informing me, in a conversation about racially motivated violence, that there is no biological basis for race. Um, OK, so? There goes the bathwater, and there goes the baby too.
 
Ohhh Lowpro: How so....?

Do you understand the concept of SUPPORTING what you say? Or do you think floating Ipse Dixit Baseless 'bald' Assertions Fallacies in lieu of anything of SUBSTANCE will save the day??
Odd coming from someone who cannot provide same.

Especially given the demonstrated quote-mining and alteration that has been pointed out.


Sure. Do you know Dembski's favorite color? How about his position on Integrity in State Government?? Did he hold that up @ gun point too?
Yes.

Dembski's favourite colour is LIE.
Dembski's position on Integrity in State Government is LIE.
"Did he hold that up @ gun point too?" Courts decide such matters.

"Orgel's Metaphor :confused: What on Earth LOL.
I agree. You are confused.

So you're rebuttal is "Na'ahhh"?? Riveting. You wouldn't happen to be Pre-Law by chance?
What difference would that even make?

You still have no regard for anything but your own superstitious nonsense ideas.
 
@annoid.

Since single nucleotides contain the information to make every possible known (and currently unknown) ribozyme, how then is that information accessed to decide what ribozyme to create when you string them together randomly?

Because right now all experiments seem to suggest there IS no pattern, and therefore they do NOT contain actual information. You claim otherwise. What experimental evidence do you have?
 
Care to enlighten us Daniel?
He won't. At best we will get a comment about Pol Pot, then he will ignore it all, and in a few pages, he will bring the entire quote again, hoping that people will have forgotten.

Thanks, RussDill for checking this.

In the future I shall avoid reading any quotes that he brings, unless he claims that he has checked the quote himself, and that it conveys the intention of the author. At least, then I know that any misrepresentation is intended, and not just the result of sloppy work.
 
Am I the only one here who finds this sort of undergraduate, 3am, pot-fuelled solipsistic, shadows-on-the-walls-of-the-cave intellectual meandering both boring and pointless?


How impressively condescending of you!

…is it worth pointing out that it is you folks who never stop equivocating between “the laws of physics exist” ("we discover them"..."everything follows them")...and “…nope, they don’t”.

Do they…or do they not…exist?

For those who are silly enough to attempt an answer…the correct response is: We do not know…but it sure freakin looks like they do! The INDISPUTABLE facts that A)…we can create these laws and B)…it very very very convincingly looks like everything follows them…

…are, in themselves, evidence in support of some kind of conclusion (why do they constitute such evidence…and how substantive is the argument?). So far, we do not (empirically) know what that conclusion may actually be. If it can be empirically established that something equivalent to the ‘laws of physics’ are actually the cause of everything that is…how would that discovery rate in the history of science?

…would (just for example) the individual who made the discovery be eligible for a Nobel prize? If you were to place a bet...what do you think the odds would be of this discovery actually winning a Nobel prize (personally...I'd wager my entire past, present, future, and my collection of jelly beans)?



...this is hilarious… coming, as it does, from someone who emphatically insists that mathematics / logic are manifest in the fundamental nature of the universe. That there IS some variety of 'thing' that you call 'number' that actually does exist in nature (this despite the indisputable fact that no one anywhere anyhow [including you] has ever explicitly adjudicated such a thing).

The fact that I happen to agree with this variety of conclusion does not mitigate the indisputable fact that it neither has nor can be empirically confirmed in any way shape or form what-so-ever. Thus it is categorically impossible to unconditionally assert it as you do.

I don't find it boring or pointless, just tangential to the discussion. By waving away the essential premises, there's not much left to talk about. It's like informing me, in a conversation about racially motivated violence, that there is no biological basis for race. Um, OK, so? There goes the bathwater, and there goes the baby too.


Except that I’m not waving away the essential premise, I’m asking what it is. The (unanswerable) questions merely illustrate the dimensions of our ignorance. What we have…is reasonably convincing circumstantial evidence that A)…the ‘stuff’ of everything is information and B)…this ‘information’ proceeds according to ‘the laws of physics’ that C)…are somehow discovered [NOT created] by something we call intelligence that is manifest through something we call consciousness. It is therefore reasonable to conclude that there is some kind of explicit and fundamental relationship between these phenomena (information, laws of physics, intelligence, consciousness).

…as Wittgenstein said…”there is that which we must pass over in silence.” Perhaps the ‘truth’ of information is actually such a thing.

…and while I’ve got Wittgenstein in my corner…this one is always good for a laugh:

“Man has to awaken to wonder - and so perhaps do peoples. Science is a way of sending him to sleep again.”

...blasphemer!

@annoid.

Since single nucleotides contain the information to make every possible known (and currently unknown) ribozyme, how then is that information accessed to decide what ribozyme to create when you string them together randomly?

Because right now all experiments seem to suggest there IS no pattern, and therefore they do NOT contain actual information. You claim otherwise. What experimental evidence do you have?


…oooh, a trick question. Perhaps you should review what you write before you post it. You asked if nucleotides contain information.

I replied yes.

Sorry…claiming that a nucleotide has no information is not even stupid. I could explain why this is blindingly obvious but it would only make you look rather foolish. Just take a quick glance at how that (or any molecule) is described / represented…and tell me again how there is no information there.

Here’s a hint: If there is no information…then it could not be described.

You’re making what I call the Massimo-mistake. IOW…your ideological zeal is getting the better of you.
 
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annnnoid,

As I see it, what is being objected to in your arguments is it seems you are saying because we don't know, we can't know.

We don't need to understand all the laws of nature, to use those parts that we do understand. We don't need to completely understand matter, to use matter. We don't have to completely understand energy in order to produce and harness energy. We don't really understand gravity, but we can understand how to use it.

Your arguments just make me want to say, "So?".

It is because we don't know that we seek the answers. If we waited until we knew all the answers, how would we get any answers. We don't know all the properties of gravity, so we shouldn't use gravity, or even inquire about gravity, because how do we know what we know about gravity?

And no, I do not think we create the laws of nature. That is tantamount to saying Columbus created the New World. It was always there, he just found it.* We discover them. I will admit that what we think are the fundamental laws of nature might not be fundamental, there might be something else a layer below them, but how do we know if we don't look. And why can't we explore and use the laws that we have now, and refine them as new information arises? Why do we have to accept some intelligence, when there is no evidence for intelligence.

Science is about facts. Testable and verifiable facts. Theories are built and tested using observation and experiment. If observation does not match the theory, then the theory gets modified. This happens again and again until a completer picture of our universe and how it works is formed. Will the next accepted theory answer every question. Nope, but it answers more than the one that came before. And we can, no I say must, use the knowledge we have now. To do other wise is idiocy.

Bottom line is that Creation science isn't science. Throwing up our hands and declaring there must be a god an intelligence just because there are gaps in our understanding is anti-science, and ignorance of the most basic kind. Creation science has never produced any new breakthroughs. It never will, as all it can do is tear down the real scientists doing real science that will ultimately benefit all human kind. Creationist are actively trying to hinder that progress. Shame on them.
 
…is it worth pointing out that it is you folks who never stop equivocating between “the laws of physics exist” ("we discover them"..."everything follows them")...and “…nope, they don’t”.

Do they…or do they not…exist?

For those who are silly enough to attempt an answer…the correct response is: We do not know…but it sure freakin looks like they do! The INDISPUTABLE facts that A)…we can create these laws and B)…it very very very convincingly looks like everything follows them…
[My bolding]
You can see this is why I find this sort of superficial philosophising pointless. You really think that it is an indisputable fact that we create the laws of physics and then it looks like everything follows them. The obvious and trivial response is to ask what does everything do until we create the laws. But I'm not going to be that cheap because I know that's not what you really meant (in spite of the fact that you shouted INDISPUTABLE). Especially when you wrote further down the post:

Except that I’m not waving away the essential premise, I’m asking what it is. The (unanswerable) questions merely illustrate the dimensions of our ignorance. What we have…is reasonably convincing circumstantial evidence that A)…the ‘stuff’ of everything is information and B)…this ‘information’ proceeds according to ‘the laws of physics’ that C)…are somehow discovered [NOT created] by something we call intelligence that is manifest through something we call consciousness.
{My bolding]

That this species of philosophising is at all useful or illuminating is an open question, but what is clear is that engaging in this discussion without defining and sticking to the agreed definitions of critical terms (eg, information, laws of physics, creation, intelligence, consciousness) is not useful in the slightest, and leads to the sort of internal inconsistencies that are so starkly on display here, not just across different pronouncements based on your thesis, but even within this single post.

You then follow on directly from the post above with this:
It is therefore reasonable to conclude that there is some kind of explicit and fundamental relationship between these phenomena (information, laws of physics, intelligence, consciousness).

It is not reasonable to conclude any such thing - you have not demonstrated that the premises are true, and even if you had done so, the conclusion doesn't follow. None of these terms are defined in an unambiguous way - all I see is a lot of impressive words, arranged in some sort of sensible syntax, bearing very little clear and unambiguous meaning.
 
Annnnoid:


...this is hilarious… coming, as it does, from someone who emphatically insists that mathematics / logic are manifest in the fundamental nature of the universe. That there IS some variety of 'thing' that you call 'number' that actually does exist in nature (this despite the indisputable fact that no one anywhere anyhow [including you] has ever explicitly adjudicated such a thing).

The universe demonstrates its mathematical nature to the same degree as it demonstrates the existence of e.g.: protons. Protons exist -- all our observational and experimental evidence confirms it. The universe is mathematical -- all our observational and experimental evidence confirms it.
Unless contrary evidence is discovered, that is the way it is.
 

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