Uncommon Descent Serving The Intelligent Design Community

Do we imagine we see patterns in nature where there are none?

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That is called cherrypicking patterns. A common argument against design in nature is that humans randomly evolved to see patterns where there are none. Many a Darwinian airhead advances such received wisdom at the usual bongfests.

He can be fairly sure that few bong-ees are going to point out the obvious: We evolved to see patterns that are there, for our own best interests. We are sometimes mistaken, but disparaging the seeking of patterns supported by evidence is hardly a solution.

Most often the patterns we see are there. Indeed, more people come to grief by not noticing than by noticing them. (“But I thought this would be an exception, you see…” or “But I never thought it would happen to me… ”)

Darwin’s followers themselves are constantly attempting to impose patterns in the fossil record, and watching them disintegrate in the light of evidence.

Casey Luskin notes that:

cladistics and other phylogenetics methods do not demonstrate common ancestry; they assume it. In other words, these methods don’t test whether all organisms fit into a nested hierarchy (i.e., phylogenetic tree). Rather, evolutionary systematics assumes that common ancestry is true and therefore all organisms belong within a nested hierarchy, and then it uses methods to force-fit any organism into the tree, even if that organisms has traits that don’t fit neatly within the tree.

Common ancestry, therefore, is a starting assumption about the data — not a conclusion from it. Another key lesson is this: just because you see evolutionary biologists creating an impressive-looking phylogenetic tree doesn’t mean that all of the organisms or their traits shown within that tree fit neatly into a nested hierarchy (i.e., a tree structure). One could cite many examples of organisms that don’t fit cleanly into a tree. Here are a few:

Sahelanthropus tchadensis is widely touted as a human ancestor that lived about 6-7 million years ago, sometime very soon after the supposed split between the human line and the chimp line. But it’s rarely mentioned that this specimen doesn’t fit into the standard hominin tree at all.

In any case, an evolutionary biologist could decide to group phyla according to early developmental processes, or according to symmetry, and that’s fine. If you weight one trait heavily, you’ll get one tree. But switch that weight to another trait and you’ll get another, conflicting tree. Either way, when you use one character set to create your tree, then the other character set is no longer distributed in a treelike fashion, and vice versa. That’s a major problem. More.

But they can get away with scuffing out serious discussion of genuine problems, questions, and puzzles to the extent that everyone “knows” that Darwinism is true. (“The debate is OVER, etc.”)

One of the serious harms done by court and other judgments demanding the teaching of “evolution” (that is, Darwinism) in the schools is that it helps raise generations not accustomed to asking intelligent questions when the data don’t fit. From Head Teacher Troll:

When the pattern doesn’t work, there is no pattern anyway, you see. Only ID people look for patterns… But now, if we can just tweak this, and then that, we could get our pattern to fit… You! You there! I can tell that you are thinking Wrong Thoughts! Stop thinking now!

Don’t believe me? See the Darwin in the schools lobby hard at work.

Rob Sheldon writes to say, re the claim about detecting patterns that aren’t there:

If all that is meant by this statement, is that people have an unusual gift to see teleology when mathematical algorithms cannot, then this is a truism that a man can be proud of.

But if this is a statement that only mathematical algorithms are justified in finding patterns, then I would have disagree, and ask if a computer made that judgment as well?

Or if this is a statement that you can fool people by claiming to find patterns that aren’t there, then I would say you are a naive Wall Street investor who has learned his first lesson.

The apparent pattern in the clouds may not be there; the apparent pattern in biotechnology stocks may be there after all.

ID is concerned not with finding patterns, which obviously exist in the mathematics of nature, (consider fractals or the golden ratio). Rather, ID studies patterns that look like they were generated by intelligence. A mere pattern endlessly repeats. A thought-out pattern stops at a point where purpose is detectible.  See the CSI
formulation of ID
.

This may be as good a place as any to note that I (O’Leary for News) will shortly be starting a series, “Talk to the Fossils,” at Evolution News & Views that talks about what we really know about situations where evolution does occur. What patterns do we really see?

Follow UD News at Twitter!

Comments
wd400: Why does the tree estimated from synonymous mutations match the standard phylogeny? Because they both use the same assumptions and the same techniques?Mung
June 24, 2015
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wd400 @ 61
Back on an envelope, say changing a Proline to a Histidine would be favoured in an echolocating lineage.
Any evidence that this is the case? And what, precisely are the required changes in the gene to move from non-echolocating to the echolocation function?
Half of the second position mutations in a Pro codon will lead to His.
Could you reference this please?
Precise calculations would require us to know about the way mutations interact with each other to create the phenotype and their respective selective advantages.
Did you include random environmental factors in your calculations?
Calculating the probability that each lineage would find the same substitutions would require us to know about what other mutations might have the same effects (or to turn it around,, this finding is evidence that only a few mutations are able to generate better high-frequency hearing).
I don't think that evidence showing that the same substitutions may appear in different lineages does much to explain the origin of similar complex features arising independently.Silver Asiatic
June 24, 2015
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Virgil Cain (we know who you are) single handedly kicked every Darwinist's arse in this thread. Oh, the shame. Oh, the humiliation. Oh, the humanity.Mapou
June 23, 2015
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As I have said before I am perfectly happy with much of the genetic code being far more similar in the past in the gene coding regions. Micro evolution is one explanation for nested hierarchy. Genomic instability contributes. Multiple functions of DNA contributes.
What? How?
You downplay the exceptions that violate this massively and the improbability of convergence being so common. Rapid diversification following special creation of kinds with common blueprint use can explain nested hierarchies. Anyone who is honest with themselves must come to question the molecular probabilities of convergence of distant species at the molecular level yet you accept the magic by stating Darwin predicted convergence so it’s fine. Even though Darwin knew nothing of molecular sequence and convergence at that level.
You really do love a rant. When you've climbed down, I made a back of the envelope calculating for how surprised we should be about molecular convergences here.wd400
June 23, 2015
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Wd400: No actually I am not saying everything has an altORFor mounting a high horse overvthstb (despite the fact you seem to downplay their exexistence more than it deserves) I am suggesting there are multiple complexities to the genetic code and highlighting the way in which a materalist cannot really think outside their limitations of their favoured theory. As I have said before I am perfectly happy with much of the genetic code being far more similar in the past in the gene coding regions. Micro evolution is one explanation for nested hierarchy. Genomic instability contributes. Multiple functions of DNA contributes. You downplay the exceptions that violate this massively and the improbability of convergence being so common. Rapid diversification following special creation of kinds with common blueprint use can explain nested hierarchies. Anyone who is honest with themselves must come to question the molecular probabilities of convergence of distant species at the molecular level yet you accept the magic by stating Darwin predicted convergence so it's fine. Even though Darwin knew nothing of molecular sequence and convergence at that level....... (And they say theists are crazy for believing in miracles)Dr JDD
June 23, 2015
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It's a loaded question.
Why does the tree estimated from synonymous mutations match the standard phylogeny?
It should as "the standard phylogeny" is actually "the standard deviations from a common design".Virgil Cain
June 23, 2015
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So you aren't going to answer the question?wd400
June 23, 2015
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wd400- We don't have any peculiar ideas about nested hierarchies. You are just ignorant of the concept. Don't blame us for your ignorance. Everything we have ever said about nested hierarchies we have supported.
Why does the tree estimated from synonymous mutations match the standard phylogeny?
Why does standard phylogeny match variations from a common design?Virgil Cain
June 23, 2015
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Joe -- forget you peculiar ideas about nested hierarchies and answer the question. Why does the tree estimated from synonymous mutations match the standard phylogeny?wd400
June 23, 2015
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Zachriel:
Can you explain why the synonymous substitutions form a nested hierarchy consistent with the standard phylogeny?
Umm, phylogeny and nested hierarchy are two different concepts.Virgil Cain
June 23, 2015
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Yes it is the same question as I was giving you a chance to.not look foolish by thinking in.such a blinkered manner. By definition, if some mutation alters a protein sequence or rate of turnover – now listen carefully ...
Oh really JDD... It's prefectly obvious from Zach's first comment that this is irrelevant ot the point he was making. That even in the very rare cases that molecular convergences mean a gene tree doesn't match the species it's common for the synonymous mutations to follow the expected pattern. For some reason you see it as a chance to mount some high horse about alternative ORFs, without mentioning most such ORFs are small, in UTRs and relatively poorly conserved at the a/a level. Meaning (in addition to the fact you point doesn't have much to do with Zach's comment) most synonymous mutations in one ORF are just synonymous.wd400
June 23, 2015
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Zach,
Dr JDD: By definition, if some mutation alters a protein sequence or rate of turnover – now listen carefully – by definition, that is NOT redundant.
Zach: Redundancy refers to the fact that more than one codon may encode a particular amino acid.
And non-redundancy refers to the fact that there is something more going on (see Dr JDD comment).Box
June 23, 2015
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That's Darwin, not the theory of evolution. We asked specifically for the theory of evolution. And your quote seems to say that Darwin was against convergence but that was on the grand scale- ie, whole organismVirgil Cain
June 23, 2015
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Virgil Cain: Can you please link to this alleged theory of evolution so we can all see what it really says?
Darwin, Origin of Species fifth edition 1869, Convergence of Character: "It is incredible that the descendants of two organisms, which had originally differed in a marked manner, should ever afterwards converge so closely as to lead to a near approach to identity throughout their whole organisation."
Zachriel
June 23, 2015
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Zachriel:
Convergence has been part of the theory of evolution since Darwin.
How would you know? Can you please link to this alleged theory of evolution so we can all see what it really says?Virgil Cain
June 23, 2015
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Dr JDD: By definition, if some mutation alters a protein sequence or rate of turnover – now listen carefully – by definition, that is NOT redundant. Redundancy refers to the fact that more than one codon may encode a particular amino acid. Dr JDD: On one layer of code it may be redundant in that context alone, but it cannot be referred to in the general sense as “redundant” or the synonym “synonymous”. Which is why we suggested talking about silent mutations instead. Dr JDD: we can just explain those violations as “convergence”. Convergence has been part of the theory of evolution since Darwin. You ignored the example. Can you explain why the synonymous substitutions form a nested hierarchy consistent with the standard phylogeny?Zachriel
June 23, 2015
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Yes it is the same question as I was giving you a chance to.not look foolish by thinking in.such a blinkered manner. By definition, if some mutation alters a protein sequence or rate of turnover - now listen carefully - by definition, that is NOT redundant. On one layer of code it may be redundant in that context alone, but it cannot be referred to in the general sense as "redundant" or the synonym "synonymous". Which is why given our slow moving towards a deeper understanding of the genetic code, it's complexity and layers of code contained within, how can we assume something is synonymous just because in the traditional ORF and 1-dimensional understanding of genetic code it appears so. But you hold on to that 1-dimensional thinking because you need it to be true for evolution and UCD to be true. As for the other aspect of your comments, I'm not sure it matters how many times you say to yourself "nested hierarchies prove UCD" it still doesn't make it true. Specifically it doesn't make sense when so many violations occur. But I forgot - we can just explain those violations as "convergence". Funny that exceptions usually prove the rule yet convergence is no longer an exception; it is the rule as it is so commonplace. This making nested hierarchies a bit if a joke in the context of UCD.Dr JDD
June 23, 2015
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How are you defining "nested hierarchy"? You seem to be unclear on what it entails.Virgil Cain
June 23, 2015
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Dr JDD: Okay, let me rephrase: it’s a redundant mutation/substitution? Isn't that the same question? It's redundant because of the nature of the genetic code. There are various reasons why a particular synonymous mutation may not be silent, such as an alternate reading frame, or biasing due to how proteins are produced. However, that doesn't change the fact that most synonymous sites form a nested hierarchy consistent with common descent. Consider prestin in mammals, a protein which is important to the sensitivity of hearing. When we sequence the gene, we can see that, while strongly conserved, it forms a nested hierarchy consistent with mammalian phylogeny, except in the case of whales and bats, both of which evolved high frequency hearing for echolocation. However, when we look only at synonymous substitutions, whales and bats are no longer exceptional, but fit the mammalian phylogeny.Zachriel
June 23, 2015
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Okay, let me rephrase: How do you know it's a redundant mutation/substitution?Dr JDD
June 23, 2015
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Dr JDD: yes I understand redundancy but again I ask how do you know it’s synonymous? Synonymous refers to the redundancy by definition. Perhaps you mean how do we know it is silent. One way we can crosscheck is to determine whether the pattern matches what would be expected of genetic drift. We can also look for biasing in the frequency of synonymous substitutions. In any case, most synonymous sites form a nested hierarchy across taxa largely consistent with the fossil pattern. Selection is observed as contrary to this overarching background pattern.Zachriel
June 23, 2015
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Zachriel: yes I understand redundancy but again I ask how do you know it's synonymous? In other words, it may well be synonymous for the traditionally understood and accepted "primary" layer of code but what about other layers of codes and reading frames? A synonymous mutation in the +1 ORF will have a very different impact than in the +3 ORF. So again, I ask, how do you know it's synonymous?Dr JDD
June 22, 2015
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Synonymous substitutions should not be confused with not altering the protein. We know of synonymous substitutions that cause problems because the protein didn't fold properly, most likely due to timing from lack of certain tRNAs. And tryptophan has only one codon that represents it. It doesn't have any redundancy.Virgil Cain
June 22, 2015
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Dr JDD: How do you know the substitutions are synonymous? Redundancy is part of the genetic code. More than one codon may encode a given amino acid. http://www.zachriel.com/blog/GeneticCode.jpgZachriel
June 22, 2015
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Zachriel @8: How do you know the substitutions are synonymous?Dr JDD
June 22, 2015
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Nothing's perfect and this is our scheme so exceptions would be expected. Under unguided evolution exceptions would be the rule, so much so that it may be impossible to objectively group organisms.Virgil Cain
June 21, 2015
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"pristine in the most part". Lol.wd400
June 21, 2015
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Animalia, the most part, with few exceptions, yes.Virgil Cain
June 21, 2015
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wd400:
Why does Linnaues’ biological classification worked so well, when his attempts to apply the same system to rocks and minerals failed so badly?
Good question. Maybe life isn't like other matter. Perhaps life is not just chemistry after all.Mung
June 21, 2015
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And does life have "distinct and pristine groups"? Snakes, moa , archaeopteryx....wd400
June 21, 2015
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