Evolution, an irreplicable lightning strike , or an unavoidable lightning bolt in a thunderstorm

Bart V

straw materialist
Member
#21
Douglas Axe has done experiments to try to determine if there are many possible protein sequences that have functions or only a few. If functioning proteins are very common, then evolution by natural selection might seem to be more probable. But if functioning proteins are very rare, then evolution by natural selection might seem to be less probable. The results of these experiments show that functional proteins are very rare and the possibility that many alternate evolutionary paths exist is not a good explanation for the origin of species.

http://www.toriah.org/articles/axe-2000.pdf
How much of protein sequence space has been explored by life on Earth?

3. Discussion
Protein sequence space is often viewed as a limitless desert of maladjusted sequences with only a few oases of working sequences linked by narrow pathways (Axe 2000, 2004). The navigation over this space by natural selection is difficult and could take many different routes thus resulting in organisms with largely different protein compositions. This idea of contingency, if taken at the level of species, led Gould to suggest that if one was to rerun the ‘tape of life’ then evolution would take a totally different path and we, as a species, would only appear as a highly improbable accident (Gould 1991; Luisi 2003; de Duve 2007a,b). However, if there is any merit to our simple calculation then protein sequence analysis provides no support for the idea of contingency at a molecular level and it provides strong support for the ideas of convergence (Conway Morris 2000, 2004; Dawkins 2005; Vermeij 2006; de Duve 2007a,b). If one was to rerun the tape, then the protein composition of organisms would be similar. Our calculation removes the almost impossibly unrealistic pressure on natural selection to navigate through protein sequence space avoiding the vast number of functionless sequences by simply indicating that most sequences have been tried are useful in some way, and that there are many possible routes to obtain proteins with desirable functions (Nagano et al. 2002; Anantharaman et al. 2003; Holliday et al. 2007).

Finally, we conclude that the number 20100 and similar large numbers (e.g. Salisbury 1969;Maynard Smith 1970; Mandecki 1998; Luisi 2003; Carrier 2004; de Duve 2005) are simply ‘straw men’ advanced to initiate discussion in the same spirit as the ‘Levinthal paradox’ of protein folding rates (Levinthal 1969; Zwanzig et al. 1992). 20100 is now no more useful than the approximate 2×101 834 097 books present in Borges' (1999) fantastical ‘Library of Babel’ and has no connection with the real world of amino acids and proteins. Hence, we hope that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention (Bradley 2004; Dembski 2004).

Axe (2004) and the evolution of enzyme function

Summary

To summarize, the claims that have been and will be made by ID proponents regarding protein evolution are not supported by Axe’s work. As I show, it is not appropriate to use the numbers Axe obtains to make inferences about the evolution of proteins and enzymes. Thus, this study does not support the conclusion that functional sequences are extremely isolated in sequence space, or that the evolution of new protein function is an impossibility that is beyond the capacity of random mutation and natural selection.


http://bio-complexity.org/ojs/index.php/main/article/download/BIO-C.2010.1/56
These two are from the "Look mam, we have peer reviewed articles too" magazine of self publishing, so we can safely ignore them.
 

Bart V

straw materialist
Member
#22
Agreed - but it can always be argued that vital intermediate fossils are missing by chance, etc etc. I am happy to give natutaristic explanations a bit of extra rope as compared with explanations that do invoke something beyond materialism, but I am not prepared to offer them an essentially infinite amount of extra rope!
The ID movement has given itself so much rope, it has effectively hung itself on a scientific level. All the arguments are so old and stale, and have been debunked so often, it simply has become ridiculous.
I'm not really disagreeing, all I am really saying is that you can give a great deal away to those who believe in Darwinian evolution, and they will still lose the argument.

I think it is important for people to realise just how seriously Darwinian evolution broke when DNA was discovered. The nature of genes makes it untennable.

David
What the hell are you talking about, David?
A mechanism like DNA was predicted by the theoretic framework of evolution. It is not only evidence for evolution by NS, by it's evidence for common descent, it closes the deal.
 
#23
Now that I see this catch phrase for the 1000th time... I have to ask, why is that?
If we say instead "nobody did it", or "an accident did it", how is that going to change or improve the situation?

We know we're up against a monumental mystery, that doesn't stop us trying to be less wrong (i.e. learn more), but the ultimate answer ... "god did it", "randomness did it", "the grand simulator did it", 42... is out of reach anyway.
Let me put it like this: ID proponents and evolutionary biologists both love a gap... but for entirely different reasons.
 
#24
Let me put it like this: ID proponents and evolutionary biologists both love a gap... but for entirely different reasons.
A serious question for me: Why do evolutionary biologists love such a gap? Is this an allusion to a "job security" joke or something more serious?
 
#25
A serious question for me: Why do evolutionary biologists love such a gap? Is this an allusion to a "job security" joke or something more serious?
Science is, and always has been, about filling gaps.

ID philosophy is to hype and manufacture gaps into which they can squeeze god (or whatever wink, wink).
 
#26
The argument that 'MAL' just decided to 'get extra busy' for the 25 million years of the Cambrian explosion just seems a bit shallow when put up against the multiple strands of evidence supporting common descent.
 
#27
Science is, and always has been, about filling gaps.

ID philosophy is to hype and manufacture gaps into which they can squeeze god (or whatever wink, wink).
I have never read about the "gap filler" theory in many years of reading Philosophy of Science. Causal connectivity in physics and chemistry is driven by empirical measurements and math analysis. Empirical evidence is the backbone of analysis, sorted by logic and reason.

The semantic aspect of science theory for "gap filling" is known as "just so story". I can cite a lot of Phi-o-Sci commentary on the use of narrative by scientists. It is mostly derision and tales of prejudice. In my "book" data rule and b.s. walks.

ID as per Dembski and Behe is one "just so story" promoted to counter-point the "just-so-story" of evolving phenotypes exclusively from RM and NS.

Forget this crap. Look to actual data from Physiology. Look at it objectively - it's a fight of the scientists who model - how biology works from physics/chemistry - vs the ones putting evolutionary "narratives" on top of known phenomena. I simply side with the data-based biologists.

A year ago, Moran posted a piece entitled “Physicists and biologists” on his Sandwalk blog (http://sandwalk.blogspot.com/2011/08/physicists-and-biologists.html). In this post, he ridiculed the enthusiasm I expressed in the book for physicists coming into evolutionary studies and bringing new skills and new ideas.
"Meanwhile, I welcome all those physicists who know nothing about evolution, protein structure, genetics, physiology, metabolism and ecology. That’s just what we need in the biological sciences to go along with all the contributions made by equally ignorant creationists."

What a great way to make new friends for evolution science—equating physicists with creationists and calling them “equally ignorant”!
The scientific community is engaged in an important struggle to convince the public of the reality of evolution and the importance of evolution science. NCSE is the organization entrusted with representing us. The shame in NCSE’s choosing Moran as a reviewer is that he seems to seek to alienate everyone not educated in a certain way; hardly the best choice to convince the public that evolutionists are open-minded and that evolution science is an active, exciting and forward-looking field.

Now that I have seen the review, I have to conclude that my expectations were, sadly, fulfilled. Let me illustrate what I mean by summarizing what I tried to say and giving a few quotations from the review. My argument is that molecular research over the past sixty years on DNA change processes has taught us that virtually all genetic variation results from the action of regulated cell biochemistry, including a wide array of cutting, splicing and polymerizing functions that I summarize under the term “natural genetic engineering”. I assert that this realization represents a fundamental shift from the conventional view that genetic change is a random, accidental process.
http://reports.ncse.com/index.php/rncse/article/view/183/231
 
#28
Science is, and always has been, about filling gaps.
Stephen already covered this, but I've never read nor understand science to be about filling gaps. I actually think most scientists would shirk from such a description. Heck, many scientists have even suggested some gaps (e.g., consciousness) to be beyond their ability to explore.
 
#29
There were suspected gaps in the periodic table. Scientists accurately predicted what would fill them. Other scientists discovered those elements.

This parallels what we have seen on the compilation of the fossil record.
 
#30
There were suspected gaps in the periodic table. Scientists accurately predicted what would fill them. Other scientists discovered those elements.

This parallels what we have seen on the compilation of the fossil record.
Certainly true about atomic weight series in an epistemological sense, which is a subjective view of our knowledge-base from analogy and graphic representation. I was talking about empirical work. Filling-in a chart of trees or bushes with possibilities is not empirical science. At hand is empirical evidence on how regulation (cybernetic control) builds RNA/DNA/Ribosome signalling systems for the communication of information. To understand how it actually works is to lose belief in in "random magic".

Just-So Stories
Loose talk about evolution and storytelling.


The just-so story, as perfected by Rudyard Kipling, is a reverse-engineering narrative. You begin with a phenomenon—an animal with tough scaly skin, or with spots, or with a long prehensile trunk—and you work your way backwards in time until you hit upon a possible explanation for its origin. In the context of stories for children, of course, the explanation is not meant to be likely or even plausible but rather as imaginative and delightful as possible while still qualifying as a kind of "explanation."

In scientific just-so stories, by contrast, it is plausibility that counts—and there have been such accounts as long as there has been inquiry into the curious phenomena of the natural world. - Alan Jacobs
 
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#32
The ID movement has given itself so much rope, it has effectively hung itself on a scientific level. All the arguments are so old and stale, and have been debunked so often, it simply has become ridiculous.

What the hell are you talking about, David?
A mechanism like DNA was predicted by the theoretic framework of evolution. It is not only evidence for evolution by NS, by it's evidence for common descent, it closes the deal.
Bart you are hardly worth discussing this issue with. You outright blindly dismiss all criticism of evolution and consistently assume that everything goes back to the DI or ID, while blatantly ignoring when people challenge you with non-ID sources. David said the most valuable thing in this thread: that just because you don't have a replacement theory, does not make the criticism worthless. I personally believe in common descent (important note, since you seem to think that everyone who disagrees that RM, NS and chance got us here today: lots and lots of people who have huge issues with evolution by that mechanism still buy into common descent), and I believe in evolution. But it seems obvious to me, based on the information available, that evolution by RM and NS is not nearly the whole picture. Does this mean that those mechanisms weren't involved? Of course not. They sure seem to be very involved. But there are plenty, and I mean plenty, of issues with the extended synthesis and gene centric view of evolutionary theory. That criticism is both valuable and significant, even if you don't have a replacement theory. A negative result in science is 100% every bit as valuable as a positive one.
 
#33
Certainly, true about atomic weight series, in an epistemological sense, which is a subjective view of our knowledge-base from analogy. I was talking about empirical work. Filling-in a chart of trees or bushes is not empirical science.
Do you consider the study of the fossil record empirical? The study of the genetic and molecular evidence for common descent? The study of the morphological similarities between species? Because that is what we are talking about.... Is there anything here you consider unempirical?



At hand is empirical evidence on how regulation (cybernetic control) builds RNA/DNA/Ribosome signalling systems for communication of information.
I need to be clear on what you mean here. Have you a link to the empirical evidence? I'm not sure serial chains of chemical reactions are truly transmitting "information" along them, unless of course you consider there is a designed end point 'in mind' from the outset. These propositions seem to be overlaid with vague language and imprecisely defined terms, in order to inject some pseudo-profundity into the argument.
 
#37
Do you consider the study of the fossil record empirical? The study of the genetic and molecular evidence for common descent? The study of the morphological similarities between species? Because that is what we are talking about.... Is there anything here you consider unempirical?
The study of the fossil's materials are empirical. Referring to my primary stand of using the tools of material science and physics is one level of abstraction and the tools of information science are another - your questions tease out my humble worldview. Common descent is a straightforward proposition that biological beings come from a parent. I think is is a certain observation. My take is some believe it means something more magical. Whatever this magical view of bio-evolution is, I think that Lynn Margulis and the merger of bacterial and virus information bearing molecules with other genomes proves it false.

The study of genetics is based on the transfer of information. Here the tools of information science have opened the doors to reality. Open to debate and opinions would be my personal understanding that much of information science and math analysis is quasi-empirical. So therefore; much of the work in genetics is quasi- empirical. The directness of the measurement is in question when mapping function and biochemistry.

Quasi-empirical methods are methods applied in science and mathematics to achieve epistemology similar to that of empiricism (thus quasi- + empirical) when experience cannot falsify the ideas involved. Empirical research relies on empirical evidence, and its empirical methods involve experimentation and disclosure of apparatus for reproducibility, by which scientific findings are validated by other scientists. Empirical methods are studied extensively in the philosophy of science, but they cannot be used directly in fields whose hypotheses cannot be falsified by real experiment (for example, mathematics, philosophy, theology, and ideology). Because of such empirical limits in science, the scientific method must rely not only on empirical methods but sometimes also on quasi-empirical ones. The prefix quasi- came to denote methods that are "almost" or "socially approximate" an ideal of truly empirical methods.

It is unnecessary to find all counterexamples to a theory; all that is required to disprove a theory logically is one counterexample. The converse does not prove a theory; Bayesian inference simply makes a theory more likely, by weight of evidence.
"just-so-stories" are very useful as abduction (considered guessing). They are neither empirical or quasi-empirical.
 

Bart V

straw materialist
Member
#38
Likewise, many dogmatic scientists work backwards from the assumption that their conclusion about blind physical forces and random chance creating life today as we know it. So, that's again complete nonsense. It cuts both ways.
That is simply not true, the theory of evolution is based on observation, and evidence, not on dogma.
In the days of it's inception, there was no dogma to defend, on the contrary it replaced the oldest dogma in the world.

However, it is true that many scientist base their work on the foundations laid by the ones that came before them, that is not dogma, that is how science works.
The field of evolutionary biology is completely open to change through the normal process of research and peer review. This certainly can result in some inertia to accept new ideas, but that can be expected.

Now, do you think the ID crowd is going to change any of their ideas under any circumstance?
Bart you are hardly worth discussing this issue with.
What is this post then, a lecture?
You outright blindly dismiss all criticism of evolution ...
No, i opposed very specific claims made in this thread, i provided links that imo showed these claims wrong.
Please tell me which criticisms of evolution i blindly dismissed?.
... and consistently assume that everything goes back to the DI or ID, while blatantly ignoring when people challenge you with non-ID sources.
Well that is because most of the names mentioned are directly connected to the DI, Berlinski is a senior DI fellow, so is Meyer.
Axe is the director of the Biologic institute, which is funded by the DI.
The Biologic institute publishes the BIO-Complexity Journal, in which Axe and the other discoverites publish most of their 'work.'

Peer review is a lot easier if you keep it in the family, you know.


The third way movement, is interesting, but it is also a very big tent.
if i take a look at the list of authors, and their work, they represent a very wide range of viewpoints.
To me they look a bit to heterogeneous to be one movement.
But, at first sight, most of them seem honestly frustrated scientifically or philosophically.

David said the most valuable thing in this thread: that just because you don't have a replacement theory, does not make the criticism worthless.
David said a lot of things in this thread, without giving any reference, something he threatened to ban people for in other threads.
But this is one i might agree with, although it does not apply to evolution. I do not think evolution is shown to be a "phoney explanation", to use his words.
I personally believe in common descent (important note, since you seem to think that everyone who disagrees that RM, NS and chance got us here today: lots and lots of people who have huge issues with evolution by that mechanism still buy into common descent), and I believe in evolution. But it seems obvious to me, based on the information available, that evolution by RM and NS is not nearly the whole picture.
NS is not the only selection mechanism known, there is genetic drift, sexual selection, migration.
None of these are controversial.
also RM is not the only mechanism, there is epigenetics, horizontal gene transfer, endosymbiosis.
In itself, maybe these are not controversial, but to what degree they (have) play(ed) a part, is certainly ground for healthy scientific debate.


And then there is the question whether DNA maybe has a deeper layer we do not fully understand.

Does this mean that those mechanisms weren't involved? Of course not. They sure seem to be very involved. But there are plenty, and I mean plenty, of issues with the extended synthesis and gene centric view of evolutionary theory. That criticism is both valuable and significant, even if you don't have a replacement theory. A negative result in science is 100% every bit as valuable as a positive one.
I agree, up to some level, but it is not clear to me what has been shown to be a negative result, and by whom.

On the other hand i would be very cautious about anybody who wants to claim a negative result, but already has a faith based replacement in mind.

I think the DI ,and all of it's subsidiaries, definitely fall into that category.
You do not have to take my word for that, research them a bit, their origin, their founding document, etc..

If you really are interested in the legitimate scientific controversies that live at the edge of the research, your viewpoint would probably be further from theirs than from mine, even if we would be at the opposing end of these legitimate controversies.
 
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#39
also RM is not the only mechanism, there is epigenetics, horizontal gene transfer, endosymbiosis.
And then there is the question whether DNA maybe has a deeper layer we do not fully understand.
There is a deep layer in your post. You are fighting the DI (a strawman to me) and in the mean time there is a cadre of elite scientists refuting your rose-colored simplistic view of bio-evolution. DNA and it's genes are not stand-alones - they are part of an elaborate communication system, which has regulation and adaptation as its primary function.
(not evolutionary change)

Yes, RM is not the only "mechanism" it is a minor background factor in terms of proven casual effects. Physiological break-throughs of the last 20 years have found genetic adaptation that encode strategy for future development. Hardly random.

What do you think of the Weismann Barrier?
 
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