Biological Information and Intelligent Design: evolving new protein folds

[Cornelius_Hunter]

@glipsnort

Characters that violate the tree are only falsifying evidence if they occur significantly more often than expected under the model of common ancestry. No one has demonstrated that they do

Actually they have. There are many evidences which surprised evolutionists because they were not expected.

[Cornelius_Hunter]

@sfmatheson

A “broken gene” is only the focus of purifying selection if the loss of function is itself deleterious

Perhaps you didn’t read all of my post, as that is what I said.

[glipsnort (Steve Schaffner)]

@Cornelius_Hunter

Actually they have.

Where has it been demonstrated that violations occur more often than can be expected from known processes?

[Lynn_Munter]

@Cornelius_Hunter

Yes, sure, similarities in species is evidence for evolution, but it is very, very weak evidence.

Just out of curiosity, what is your opinion on the accuracy of paternity testing?

[sfmatheson]

@Cornelius_Hunter

Perhaps you didn’t read all of my post, as that is what I said.[/quote]

I just re-read that very post, and no, it’s not what you said. It’s right here:[quote=“Cornelius_Hunter, post:41, topic:34703”]
Under evolution, broken genes are subject to purefying selection, not positive selection. This is not evidence for evolution, it is evidence against evolution. Of course there are always the just-so stories about how anything can happen. Of course these don’t falsify evolution, if that were so possible. But evidence for evolution, and evolution of the primates of all things?

That paragraph is nonsense.

I’m done here.

[Cornelius_Hunter]

@sfmatheson

I’m done here.

Was it something I said?

[Cornelius_Hunter]

@glipsnort

Where has it been demonstrated that violations occur more often than can be expected from known processes?

You can see them both in the research papers, science magazines, blogs, etc. I’m not talking about creationists saying this, I’m talking about evolutionists expressing surprise that the data made no sense.

[glipsnort (Steve Schaffner)]

@Cornelius_Hunter

You can see them both in the research papers, science magazines, blogs, etc.

I can’t see them until you tell me where they are. Where has it been demonstrated that tree violations occur more often than can be expected from known processes?

[Cornelius_Hunter]

@glipsnort

I can’t see them until you tell me where they are.

OK, did you see Wednesday’s PloS on the finding of internal membrane pores in bacteria, and the “stunning evolutionary convergence” that is implied? They considered the common ancestry hypothesis but found it to be unlikely, and so they are left with a “stunning evolutionary convergence.”

How about Monday’s BMC on the finding of widespread monoamine signaling in bilaterians, implying they and their receptor families were all present in the last common ancestor of protostomes and deuterostomes, and this then must have been followed by a complex history of losses? Complex structures are always getting pushed back to ancient evolutionary history, to be followed by a complicated histories of losses and gains.

How about the week before last article in Nature that the Panda’s thumb must have evolved twice, thus confirming a “growing body of literature that suggests that organisms that face the same challenges often adapt in genetically similar ways,” and that evolution, “is actually much more predictable than anybody predicted.” In other words, it’s not by heritage (common ancestry) but by repeated origin.

Such articles that contradict common descent and make it superfluous, run all through the literature. There are many, many more examples where these came from.

[glipsnort (Steve Schaffner)]

Convergent evolution under selection is a known process – that’s why people look at pseudogenes, you know. So you haven’t answered the question.

[Cornelius_Hunter]

@glipsnort

Convergent evolution under selection is a known process

Divergence is even easier than convergence. Convergence is the independent evolution, at least twice, of the same design. Divergence is the evolution of a design, perhaps only once. And of course divergence is also a “known process.”

So your theory explains, or accommodates, (i) new complex designs arising which evolutionists have failed to explain (as discussed above), (ii) convergence, and (iii) divergence.

Who’s to argue?

It seems like anything goes and there’s not much empirical content left as your theory doesn’t actually say anything of consequence except, of course, that you’re right and that “known processes” can explain everything. You could sit down and arrange m characters in n species pretty much any way you want and explain it on your theory. In spite of the data not falling anywhere close to a “known processes” model, you’ve proven it.

How about the genome of the starlet sea anemone, Nematostella vectensis which turned out to share “a surprising degree” of similarity with the genome of vertebrates, thus “contradicting the widely held belief that organisms become more complex through evolution”!? As one evolutionist admitted:

It is commonly believed that complex organisms arose from simple ones. Yet analyses of genomes and of their transcribed genes in various organisms reveal that, as far as protein-coding genes are concerned, the repertoire of a sea anemone — a rather simple, evolutionarily basal animal — is almost as complex as that of a human.

This makes no sense on the theory.

How about the non homologous development in salamanders, developing their digits (which violate, as well, the pentadactyl pattern by the way) in the wrong order? In fact the salamander character data are full of contradictions:

The evolution and phylogeny of crown group salamanders is plagued by homoplasy. In fact, a large a number of highly derived anatomical characters, including body elongation, tail autonomy, and life history pathways, have been demonstrated or are debated to have evolved multiple times.

You can also add unique genes to that list. These make no sense on common descent.

But alas, none of this matters, for these are but more meaningless examples of convergence, divergence, and new designs arising, and they are not a problem. Lakatos explained this a long time ago: theories are protected. You can’t get at evolution. It is safeguarded from the empirical evidence by a protective belt.

@glipsnort

Convergent evolution under selection is a known process – that’s why people look at pseudogenes

You continue to appeal to this failed argument/evidence that George tried to use. First of all, for pseudogenes falling into the common descent pattern, the (hypothetical) lack of fitness/selection does not help. If it is deleterious, as the loss of vitamin C synthesis likely would be, then it is evidence against the theory, in spite of Steve’s protestations. If it is neutral, or it is positive (which is quite possible), then you have supporting evidence, but not very strong.

All of this is moot, however, since pseudogenes can violate the common descent pattern with no harm to the theory!

And finally, if this wasn’t enough, the whole argument is on the wrong side of centuries of history. Evolutionists have always been claiming disutility, and it just continues to be proven wrong. This applies to pseudogenes just as much as everything else. Now they’re being called “pseudo-pseudogenes,” with the latest study suggesting they may be “a widespread phenomenon.”

[glipsnort (Steve Schaffner)]

@Cornelius_Hunter

It seems like anything goes and there’s not much empirical content left as your theory doesn’t actually say anything of consequence except, of course, that you’re right and that “known processes” can explain everything.

Well, no, not just anything goes. But you’re right: the default approach of scientists is to accommodate anomalies by modifying a successful theory rather than by tossing it out in favor of nothing at all. (And make no mistake: in the eyes of biologists – including myself – common descent is a very successful theory.) There lies your difficulty. You have to demonstrate that some set of findings are actually inconsistent – that is, impossible or so improbable as to be effectively impossible – with common descent, and common descent can produce a wide range of observed data.

The reason you have this problem is that common descent does provide a compelling explanation for the broad patterns we see in living things. For example, in the panda paper you cited, the great majority of the panda genomes suggested a single, consistent phylogeny for them. It was only in a small number of genes that the anomalous pattern was seen. And that’s a problem for you because you don’t have an explanation for the overarching pattern. To replace an existing theory with a new one is easy: just show that the new one explains more data. To exclude an existing theory without an alternative is very hard, as it should be – anything as complex as the history of life is going to produce all kinds of odd phenomena here and there, so the mere existence of anomalies doesn’t count for much.

So unless you have an alternative, testable alternative to common descent, one that explains the large consistent phylogenies, you’re pretty much stuck. Just listing findings that biologists found surprising will get you nowhere.

[Cornelius_Hunter]

@glipsnort

And make no mistake: in the eyes of biologists – including myself – common descent is a very successful theory.

I’m afraid you simply are not familiar with the literature. Failures are ubiquitous and even evolutionists have increasingly acknowledged that the common descent and evolutionary tree model doesn’t work very well. Of course, what scientists think about their theories is of only so much value. Science is not a democracy, and scientists have believed all kinds of things we no longer accept. And, importantly, they were very resistant to changing their minds about their theories, for all kinds of reasons including social, professional, funding, etc. And of course with evolution, the elephant in the room are the metaphysical mandates for naturalism that are so powerful and have motivated the theory for centuries. So when we start talking about what people believe as some sort of justification for our theory, not only is confirmation bias tempting, but the waters get murky very quickly.

@glipsnort

The reason you have this problem is that common descent does provide a compelling explanation for the broad patterns we see in living things.

Again, I think you are simply unfamiliar with the literature. There are many, many more examples of empirical contradictions than those examples from the past few weeks I pasted above. This is why even evolutionists recognize the problem. As for “broad patterns,” this metastudy [Klassen, 1991] showed dozens of data sets which consistently contradicted common descent (especially those data sets with more than about 15 taxa, which were the more significant ones). Most of the sets were actually closer to random than to the common descent model!

@glipsnort

For example, in the panda paper you cited, the great majority of the panda genomes suggested a single, consistent phylogeny for them. It was only in a small number of genes that the anomalous pattern was seen.

I’m not familiar with panda genomes in particular, but if you believe this is true of genomic comparisons, in general, then you are quite mistaken. Genomic comparisons suffer from the same kinds of convergences, divergences, and new structures which have no reasonable explanation on the theory. These are not merely “a small number of genes,” though of course even a small number of contradictions are still contradictions.

@glipsnort

There lies your difficulty. You have to demonstrate that some set of findings are actually inconsistent – that is, impossible or so improbable as to be effectively impossible – with common descent, and common descent can produce a wide range of observed data. … So unless you have an alternative, testable alternative to common descent, one that explains the large consistent phylogenies, you’re pretty much stuck. Just listing findings that biologists found surprising will get you nowhere.

Well your bar for allowing common descent to be questioned seems to be rising. First it was any evidence that common descent could not reasonably explain. Then it became a large amount of such data. Now the data must be impossible or effectively impossible. And also, you need a “testable alternative,” which is self-refuting.

Frankly, these are all age-old, protectionist devices. Your theory is “accepted” and “standard.” What evidence you can find to support it is “normative.” Contradictory evidence is “anomalous” and safely swept under the rug, to the detriment of scientific progress. And philosophical criteria are erected against alternatives.

Your criteria that alternatives must be “testable” is a classic double standard. Even evolutionists admit their theory is not repeatable. And common descent’s incredible flexibility and ability to explain any outcome hardly put its proponents in a position to be demanding testability. As we’ve noted, common descent can basically explain anything. Convergences, divergences, new structures that even evolutionists admit they have no explanation for, are not a problem. So your criteria is self-refuting. Your own science is not testable, but you will use that criterion to reject interpretations of the empirical evidence with which you disagree.

[quote=“glipsnort, post:72, topic:34703”]
And that’s a problem for you because you don’t have an explanation for the overarching pattern. To replace an existing theory with a new one is easy: just show that the new one explains more data. [/quote]

Of course design explains the “overarching pattern.” The existence of complex structures and processes, whose origin is unexplained by natural processes, which appear abruptly in the strata, and their appearance across widely disparate taxa, and differences in neighboring species which also are unexplained by natural processes, all make perfect sense on design. The consistency index is a good way of illustrating this. I’ll be the first to agree that design apparently doesn’t give detailed predictions and can accommodate a range of outcomes. But I trust you won’t complain about that.

[Casper_Hesp]

@Cornelius_Hunter

Of course design explains the “overarching pattern.”

Hi Cornelius, it could be useful for you to check out the thread we had up here a while ago. It was about a comparison of the explanatory power of mere “similarity” with that of “shared history” (i.e., common descent) when analyzing gene sequences. This comparison clearly showed that shared history has more predictive power. Here’s a link to that thread:

Phylogeny vs Similarity and Function

At a genetic level we see a great deal of similarity between organisms. This similarity is a fundamental feature of life, that has to be explained by any theory. Evolution explains that this similarity as largely caused by shared history, by way of common descent. We see function often aligning in sensible ways on phylogenetic trees of sequences and organisms. Of course, this is not perfect, because we also know that life changes over time. As the YEC Walter ReMine accurately points out in The …

As soon as you start elaborating on your alternative to common descent, things become more interesting:

@Cornelius_Hunter

The existence of complex structures and processes, whose origin is unexplained by natural processes, which appear abruptly in the strata, and their appearance across widely disparate taxa, and differences in neighboring species which also are unexplained by natural processes, all make perfect sense on design.

So, according to you, all things that are not easy to make sense of in terms of natural processes are supportive of design? This is an argument from scientific ignorance and God-of-the-Gaps thinking… I can’t see why you would find that kind of approach attractive.

[benkirk (Benjamin Kirk)]

[quote=“Cornelius_Hunter, post:41, topic:34703”]
I am something of an expert at representing views that are not my own.[/quote]
I think we’re asking about your understanding of those views, which is highly inaccurate based on your misrepresentation of them.

[quote]But you are challenging my considerable skills in this area.
[/quote]You forgot to mention your awesome modesty.

[Cornelius_Hunter]

Benjamin:

So what is your opinion of how the salamander evidence bears on evolution or common descent?

@Cornelius_Hunter

How about the non homologous development in salamanders, developing their digits (which violate, as well, the pentadactyl pattern by the way) in the wrong order? In fact the salamander character data are full of contradictions:

“The evolution and phylogeny of crown group salamanders is plagued by homoplasy. In fact, a large a number of highly derived anatomical characters, including body elongation, tail autonomy, and life history pathways, have been demonstrated or are debated to have evolved multiple times.”

You can also add unique genes to that list. These make no sense on common descent.

Secondly, take a look at the consistency index (CI), such as in (Klassen, 1991). It is just what you would expect if you sat down and design a set of things. Consider an architect. The buildings designed by an architect are not going to be completely random. They need to function in similar environments (planet Earth). And you can see his/her style in the buildings. But the various similarities could appear in different ways. A design could be reused in otherwise very different buildings. But there will of course be differences as well. And as with the similarities, the differences could appear in different ways. They could appear in otherwise very similar buildings. And of course there could be completely new and unique designs. This is what we see in biology, and the CI metric is a good demonstration of this. Is this a precise, highly detailed, model? No, it isn’t. But it certainly fits the data.

[Cornelius_Hunter]

@Casper_Hesp

This is an argument from scientific ignorance and God-of-the-Gaps thinking… I can’t see why you would find that kind of approach attractive.

Casper:

Actually it is exactly the opposite. The world “appears” designed. Even evolutionists admit to that. But for centuries evolutionists have been claiming that there is no way that structures could have a function, in spite of the science. Evolutionists just continue to make these claims (about things that are not yet well understood), but the inexorable march of science continues to find function. It is a gap theory, so “I can’t see why you would find that kind of approach attractive.” Now of course I’m not saying every single thing in the world has function. Things do break. But evolution is on the wrong side of history.

[benkirk (Benjamin Kirk)]

@Cornelius_Hunter

So what is your opinion of how the salamander evidence bears on evolution or common descent?

Better to ask what yours is, Cornelius. You’re not citing evidence, just interpretations. Do you not understand the difference?

Secondly, take a look at the consistency index (CI), such as in (Klassen, 1991). It is just what you would expect if you sat down and design a set of things.

Then it should be no problem for you to advance a hypothesis that makes empirical predictions instead of your usual rhetorical bomb-throwing.

But you won’t.

Consider an architect.

No, let’s consider biology. Not what people say about biology, but the evidence itself. You won’t go anywhere near real evidence. That applies in two ways: to evidence produced by others and by your abject failure to produce any new evidence of your own. You can’t even come up with a testable hypothesis, man.

[Cornelius_Hunter]

@benkirk

You’re not citing evidence, just interpretations. Do you not understand the difference?

Wow, I would hope that this simply is a bad joke, but apparently you are serious.

@benkirk

You can’t even come up with a testable hypothesis

That is ironic.

[benkirk (Benjamin Kirk)]

@Cornelius_Hunter

That is ironic.

How so? What is your testable hypothesis?