Uncommon Descent Serving The Intelligent Design Community

Does an Element of Subjective Judgment Exclude a Research Program from the Realm of “Science”?

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Congratulations to all of those Darwinists who seek to exclude ID from science whenever the CSI in a structure or DNA sequence is difficult to quantify exactly.  You’ve just excluded a highly influential form of evolutionary analysis (cladistics) from science as well.  The following lengthy quote is from Adrain, Jonathan M.; Edgecombe, Gregory D. & Lieberman, Bruce S., Fossils, Phylogeny, and Form: An Analytical Approach, New York: Kluwer Academic (2002), pp 56-57:

Phylogenetic inference is pivotal to an understanding of the systematics of any group.  Cladistics offers an objective framework for the analysis of data that inevitably incorporates elements of subjectivity (Hennig 1966, Swofford 1993).  A cladogram is a hypothesis of relationships derived from a set of putatively homologous morphological and/or molecular characters (Forey 1992), to which is added information on character polarity or the nature of an outgroup.  If homologous organs or characters are defined as those jointly inherited from a common ancestor (Simpson 1961, Hennig 1966), it becomes impossible to identify homologies without access to the true phylogeny (a problem of circularity:  Jardine and Sibson 1971).  Hence, criteria of compositional and structural similarity are used in practice.  Compositional similarity refers to resemblance in terms of biological or chemical constituents (the composition of the organs).  Structural correspondence refers to the spatial or temporal arrangement of parts, structure of biochemical pathways, or the sequential arrangement of organized structures (Sneath and Sokal 1973).  The number of potential characters is limited only by our ability to recognize putative homologies at increasingly fine scales.

Inevitably, even the most rigorous tests of homology can fail to identify character states that are similar because of convergence or ‘reversal’ (‘homoplasy’, rather than direct, common descent).  Most real data sets therefore contain character conflict (Strauch 1984, Deleporte 1993).  This is usually resolved using some optimality criterion (e.g., parsimony) to derive one or more cladistics hypotheses (which will reject some fraction of the supposed homologies).

Various types of data and analytical techniques are employed in cladistics, sometimes yielding widely differing results (Wiley 1981).  Nonetheless, there is consensus on the nature of the pattern being sought, and the objective reality of the process that produced it (cladogenesis).  There is only one true evolutionary tree, and the diversity of approaches therefore all have the same ultimate goal (Wilkinson 1992).  Inevitably, the process of selecting characters for analysis is subjective, and amounts to a radical form of character weighting (Meacham 1994, Wilkinson 1994a).  The sample is also likely to be biased towards more obvious features, and frequently towards those with some form of historical precedence (Pearson 1999).

The absence of complete objectivity at all stages in a cladistics analysis in no sense detracts from its value in producing hypotheses of relationships.  Other (non-cladistic) approaches in systematics also operate on finite data sets and incorporate similar assumptions.  Often, these do not produce hypotheses directly, but serve to describe aspects of the data, frequently offering additional insights into evolutionary processes (Foote 1996).  All results (phylogenetic and otherwise) should therefore be presented along with the original data and sufficient information to all the analysis to be repeated.

(emphasis mine)

Let’s count up the subjective judgments that go into constructing a cladogram.  I see at least the following (there are almost certainly more).

  1. Which characters am I going to select for analysis?
  2. Are these structures homologous?
  3. Is there “resemblance” of biological or chemical constituents?
  4. Are the spatial and temporal arrangement of parts similar?
  5. Are the character differences upstream or downstream?
  6. Homology or Homoplasy?
  7. Is there “structural correspondence”?

No wonder different scientists’ analyses yield “wildly differing results.”

Consider the following sentence extracted from the quotation above:

The absence of complete objectivity at all stages in a cladistics analysis in no sense detracts from its value in producing hypotheses of relationships.

Is the following a fair extrapolation of the authors’ logic:

The absence of complete objectivity at all stages in a ID analysis in no sense detracts from its value in producing hypotheses of design.

Comments
wd400?Mung
November 10, 2014
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wd400, does that answer your question, and if not, why not?Mung
November 8, 2014
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wd400:
What’s the point of calculating CSI and these other information measures?
Did you calculate the probability of "METHINKS IT IS LIKE A WEASEL" and compare it with Dembski's UPB? Let me guess. It was produced by an algorithm, so the probability cannot be simply calculated by assuming a probability distribution in which all outcomes are equally likely. Does that answer your question, and if not, why not?Mung
November 6, 2014
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wd400:
What’s the point of calculating CSI and these other information measures?
Well gee, you got me there! Did you ask Elizabeth Liddle when she set off to demonstrate that "unguided evolution" could generate CSI? How did Dawkins decide? I don't know. That's why I was asking. What's the point of claiming that random mutations and natural selection can produce the appearance of design if the claim that random mutations and natural selection can produce the appearance of design is untestable?Mung
November 6, 2014
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R0bb:
In other words, if we can apply Durston’s method to entities that we agree were produced naturally, and the result is a high number of fits, will you “abandon ID, shut down this site, and become a dyed-in-the-wool Darwinist”?
The methodology pertains to proteins. Good luck demonstrating proteins arising via blind and undirected processes, but have at it.Joe
November 5, 2014
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wd400- There isn't any evidence that blind and undirected processes can produce proteins, let alone proteins that have over 500 Fits.Joe
November 5, 2014
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Mung, What's the point of calculating CSI and these other information measures?wd400
November 4, 2014
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wd400:
Anyway, I don’t think the problem most people have with CSI is that is requires some sort of subjectivity. What a IDist would need to do is define CSI is a way that it can at least be estimated for a sequence, show that biology has it and then show that natural selection and other mechanisms can’t achieve it. I’ve not seen anyone get close to that.
ah yes.
If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.
Natural selection and other mechanisms must be able to achieve CSI because it hasn't been shown that they cannot. Let's return to reality for just a moment. It is the evolutionists who claim that design is an illusion and that teleology is useless. How have they shown this to in fact be the case? The "Blind Watchmaker" can produce the appearance of design without the designer. Of course, there's no objective definition of design offered that anyone can use to test the claim. Dawkins at least offers a subjective one. "METHINKS IT IS LIKE A WEASEL" is designed. If evolution can do this, then evolution can produce the appearance of design. That's 29 characters. That's got to be WAY over Dembski's UPB, right?Mung
November 4, 2014
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"I believe the true strength of evolutionary theory can be best shown using the evo-imaginogram. It’s like a just-so story, but with pictures!" Just like Sunday school.william spearshake
November 4, 2014
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I believe the true strength of evolutionary theory can be best shown using the evo-imaginogram. It's like a just-so story, but with pictures!Mung
November 4, 2014
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Ppolish: "ID is at the deep end of the pool." Without weights tied on its ankles and no floatation device. But it is in the shallow end of the gene pool.william spearshake
November 4, 2014
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There are deep questions in Theoretical Physics and deep questions in Theoretical Biology. ID is at the deep end of the pool. Deep questions and deep mysteries. Darwinists stay in the shallow end. From where I sit watching, Darwinists are waist deep in water flailing their water wings:)ppolish
November 4, 2014
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Barry: "The absence of complete objectivity at all stages in a ID analysis in no sense detracts from its value in producing hypotheses of design." We agree. Remind me again what hypotheses of design have been produced? Mechanism? Nature of the designer? Is the designer constrained by physical laws? Does the designer affect non-living or just living? And explain how these hypotheses, whatever they are, have been tested. What predictions do they make? Even if evolution as we know it is proven to be wrong, what makes you think that this is evidence for creationism?william spearshake
November 4, 2014
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Joe: "Well MT, until you address my arguments I don’t have anything else to say." If only that were true.william spearshake
November 4, 2014
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But, Joe, earlier you told me that Durston's paper didn't establish wether "chance" (by which I guess you mean evolutionary processes?) could do it. You'll confuse me for being a little confused by your comments? How does Durston's paper help us know if a protein arose via standard evolutionary processes?wd400
November 4, 2014
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Barry:
It is made incessantly on these pages. It is implicit every time an anti-ID poster insists that ID has nothing to say unless the CSI in a particular feature can be calculated with precision.
I agree that this is a lame criticism of ID, but I don't believe that you can support your claim that it's made incessantly on these pages.
Have you asked a cladistics scientist to give you any kind of quantitative result, be it a rough estimate, a range, a lower limit, or whatever” of the degree of “similarity” of two putatively homologous character traits?
Of course I haven't. Do cladistics scientists claim that the similarity is quantifiable, provide a formula to calculate it, encourage us to do the calculation and take the numbers seriously, and declare a numerical limit on how much similarity nature can produce, as Dembski does with CSI?
I am not saying that CSI is never objectively measurable. It is. See Joe’s comment at 7.
Now we're getting somewhere. Are you claiming that the method used by Durston in the paper referenced by Joe objectively calculates CSI? If so, are you willing to plant the goalpost there with regards to your challenge? In other words, if we can apply Durston's method to entities that we agree were produced naturally, and the result is a high number of fits, will you "abandon ID, shut down this site, and become a dyed-in-the-wool Darwinist"?R0bb
November 4, 2014
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MT- The paper talks about FSC as if it was Dembski or Meyer discussing CSI with respect to biology. If you read "No Free Lunch" by Dembski, "Signature in the Cell" by Meyer and the Durston paper (include the Abel & Trevor paper too), the conclusion is FSC and CSI wrt biology, are one in the same. They are just two different ways to discuss the same thing.Joe
November 4, 2014
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wd400:
OK, so if CSI/ FSC just quantifies the observation that proteins takes up a limited part of the space of all sequences then why is it an important thing to calculate?
The calculation reveals if chance had a chance or notJoe
November 4, 2014
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LH:
IDists claim their work can overthrow all of modern biology,...
Umm, no. It supersedes blind watchmaker evolution, which is useless to modern biology. If CSI doesn't work in the real world then neither does Crick's biological information. Heck the real world doesn't exist if CSI doesn't exist in the real world...Joe
November 4, 2014
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I have criticized CSI for being subjective, although not because I believe that science precludes subjective judgements. I was under the impression that IDists claimed CSI objectively demonstrated the existence of design. If that's not correct, then my criticisms weren't either. This post seems to miss the underlying point, though. The claim is that CSI can distinguish between designed and undesigned subjects; it doesn't matter whether it has a subjective element if the tool works. What we've seen recently, and historically, at Uncommon Descent is the tacit admission that CSI is useless. When the subject of actually using CSI, or any other design-detection tool, in the real world comes up, IDists vacillate between indignant outrage at the suggestion and politely ignoring the challenge. See the infamous Mathgrrrl thread, or KF's recent (if probably inadvertent) reminders that CSI remains obstinately theoretical rather than something used in the real world. IDists claim their work can overthrow all of modern biology, but the tool only seems to work on that one very specific subject: life. Not coincidentally, it's the same subject that IDists already believed was designed, on the basis of religious precommitments. CSI doesn't seem to be applicable to any subject where there isn't already a design commitment, rather than an inference (much less proof). What's most interesting to me is that the refusal of IDists to contemplate serious testing seems to suggest that we're all more or less on the same page. I doubt that anyone reading, or writing, these posts thinks that CSI works in the real world. I don't doubt that their belief in ID is sincere, but they are fully aware that the tools have no applicability outside ID blogs. It's why ID proceeds through angry rhetoric, complaints about "Darwinian Debating Devices," KF's "FTR" posts, and other pieces of rhetoric that have nothing to do with actually detecting design. Even Dembski doesn't bother to pretend that his tools work in the real world. When I asked him whether such a thing was possible, he was taken aback. And why not? ID isn't about determining whether things were designed. It's about using rhetoric to persuade people that life was designed. Testing the tools to see if they work is irrelevant to the goal, since the conclusion is assumed. I think there's an interesting comparison between the ID approach and, for example, the research someone linked to a little while ago testing to see whether phylogenetic analyses were accurate. The scientists wanted to see whether their tools worked, so they tested them. IDists know their tools don't work, and they know it doesn't matter. Their program doesn't depend on being able to actually detect design, only on persuading people that it has been detected. You can't lose a bet you don't make, and your beliefs are never threatened if they're never tested. There is a reason that Dembksi wrote Being as Communion and not The Empirical Success of Design Detection: In Multiple Studies, Zero False Positives and 80% Accuracy. As long as he never tests the ideas, he can try to persuade people on the promise of success without running the terrible risk of failure. He sacrifices the tremendous persuasive power that successful tests would have, though, which rather suggests he doesn't believe they would. ID reader, you and I and Dembski agree: CSI doesn't work in the real world, subjective or not.Learned Hand
November 4, 2014
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OK, so if CSI/ FSC just quantifies the observation that proteins takes up a limited part of the space of all sequences then why is it an important thing to calculate?wd400
November 4, 2014
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Joe @ 45 You can see in the paper and in the python code given in the supplementary material that FSC is different from CSI. Also ID proponents have equated Fit to Bit !Me_Think
November 4, 2014
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Just a quick reminder: ?= –log2[10^120 · ?S(T)·P(T|H)] ;)Rich
November 4, 2014
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wd400- It shows us how to measure CSI/ FSC wrt proteins.Joe
November 4, 2014
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Abel and Trevors have delineated three qualitative aspects of linear digital sequence complexity [2,3], Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC) and Functional Sequence Complexity (FSC). RSC corresponds to stochastic ensembles with minimal physicochemical bias and little or no tendency toward functional free-energy binding. OSC is usually patterned either by the natural regularities described by physical laws or by statistically weighted means. For example, a physico-chemical self-ordering tendency creates redundant patterns such as highly-patterned polysaccharides and the polyadenosines adsorbed onto montmorillonite [4]. Repeating motifs, with or without biofunction, result in observed OSC in nucleic acid sequences. The redundancy in OSC can, in principle, be compressed by an algorithm shorter than the sequence itself. As Abel and Trevors have pointed out, neither RSC nor OSC, or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life [5]. FSC includes the dimension of functionality [2,3]. Szostak [6] argued that neither Shannon's original measure of uncertainty [7] nor the measure of algorithmic complexity [8] are sufficient. Shannon's classical information theory does not consider the meaning, or function, of a message. Algorithmic complexity fails to account for the observation that 'different molecular structures may be functionally equivalent'. For this reason, Szostak suggested that a new measure of information–functional information–is required [6]. Chiu, Wong, and Cheung also discussed the insufficiency of Shannon uncertainty [9,10] when applied to measuring outcomes of variables. The differences between RSC, OSC and FSC in living organisms are necessary and useful in describing biosequences of living organisms.
Wow, that describes CSI- as in you can easily replace FSC with CSI and nothing changes.Joe
November 4, 2014
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Joe @ 41 " I don’t have anything else to say" Joe @ 42 " Be a man, Rich. Take on my arguments" Oh Gallien, thou art the font of comedy! Now be patient, my little cupcake.Rich
November 4, 2014
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Joe -- can you answer my question in 28? What is important about the Durston paper?wd400
November 4, 2014
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Be a man, Rich. Take on my arguments as opposed to acting like the child that you areJoe
November 4, 2014
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Well MT, until you address my arguments I don't have anything else to say.Joe
November 4, 2014
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Be patient, Joe. I know you can read many articles on something you've never heard of before in 4 minutes to the point at which you're an expert, but this isn't your dance. Talk with Me_Think. He/She can expedite your butthurt.Rich
November 4, 2014
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