The threats to the DNA in our cells are incredible. Radiation, carcinogens and even chemicals produced within the cell attack the DNA thousands of time every day. What is more incredible though is the cell’s DNA repair system, which you can read more about here and here. The worst kind of DNA damage is the so-called double-strand break where both strands of the double helix break. In response the cell mounts a swift and sophisticated response which new research is helping to elucidate.One of the key proteins involved in this DNA repair, known as CtIP, has a 49 amino acid DNA-binding segment that has an important role in the repair job. Interestingly, this segment appears to be normally buried within the interior of CtIP. It is exposed when chemical signals indicating DNA damage modify the CtIP structure. The tool is now flipped open and ready to do its job.
Obviously this repair kit wouldn’t work without the CtIP protein. But it also wouldn’t work without the chemical signal that opens it up. Remove either one and the repair kit doesn’t work very well. Of course CtIP needs to have a binding site for the chemical signal, and CtIP needs to undergo just the right conformational change under the influence of the binding.
This is only the beginning of the repair kit’s complexity. There are several more important players in the choreography, without which the repair job would suffer. Nothing in biology makes sense in the light of evolution.
Without molecular biology evolution would be reasonable. When you take molecular biology in account, the light of evolution fades away quickly
ReplyDeleteSpeaking of "the light of evolution".
ReplyDeleteThere never was much light, if any, in evolution.
Darwinism has "screwed up" the world in a major way.
Ideas have consequences and "Darwin's simple idea" has devastating consequences on any society that tries to put it in practice. Understanding the moral and philosophical implications involved is vital.
Even when his evil idea is finally undone and removed from both science and social applications the consequences involved will take many decades if not centuries to assuage.
But, by then some other selfish materialist bastard(s) like Darwin, Marx, Machiavelli, Hitler, Nietzsche, Dawkins, Mao, ... (there is no lack of such) will have come along promoting some other inane but sophistic doctrine to ensure the world remains screwed.
In spite of the immeasurable damage done to the world through ideas, promoted by idiots like them, thankfully truth always prevails in the end because truth cannot be undone.
No doubt the future society will look on this generation and be thankful for all those, like Dr. Hunter, Stephen Meyer, Behe, Berlinski, Abel, Dembski, Wiker, Sanford et al., who did their best to rid the world of seductive lies like Darwin's asinine idea.
Great paper!
ReplyDeleteThought it is curious the authors decided to study this process in Xenopus (an African frog). Who cares? Why would they be confident the process they are studying impacts human health?
In the light of evolution and genomics, they can know the proteins in this process are found from Xenopus to humans. Moreover, they can know the exact percentage similarity, and infer the evolutionary history of the proteins. Conservation of function makes these studies useful.
Try it yourself:
Here is the amino acid sequence of CtIP:
http://www.ncbi.nlm.nih.gov/protein/Q99708.2
Cut.
Here is BLAST (pick protein blast):
http://blast.ncbi.nlm.nih.gov/
Paste.
And you have a sequence alignment:
In similarity to human, the order produced is chimp, other apes and monkeys, rabbit, horse, dog, mouse, rat, chicken, finch, frog, zebrafish. (With some paralogues interspersed).
No presuppositions, no bias in interpretation-just molecular phylogeny from sequence alignments.
What is the alternative to common descent that produces such alignments? What is the design explanation for the use of model organisms? How do you know (without studying all processes in all organisms) that the designer chose to keep the processes the same?
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ReplyDeleteRobert said: "What is the alternative to common descent that produces such alignments? What is the design explanation for the use of model organisms? How do you know (without studying all processes in all organisms) that the designer chose to keep the processes the same?"
ReplyDeleteThese are all excellent questions. I suspect though that Cornelius is not likely to offer any answers, even speculative ones (hypothesis-making is not his thing). But no doubt we'll see lots more posts like this one, splattered with words like "incredible" and "amazing". Unfortuntely until Cornelius (or somebody else) is prepared to offer a better explanatory alternate framework, a hypothesis, or even some postivie evidence for design (other than arcane mathematical musings), this gets precisely nowhere.
Robert said: "What is the alternative to common descent that produces such alignments?"
ReplyDeleteIf you have ever done any software development you would know that this is exactly the kind of thing you want to do. It covers just about every aspect of software development from the big things to the small things. Google "DRY" (Don't repeat yourself). It seems to me that such base functionality i.e. DNA repair mechanisms being shared across organisms is very good engineering.
Andrew-
ReplyDeleteAnd I'm the one accused of metaphysics!!! So it is all about the software designer in the sky?
There is a fundamental difference between conservation of design and the little 'code' changes in evolution that often have no apparent change in function. The DNA repair complexes largely do the same thing-and can be swapped between organisms-but have accumulated changes in their nucleotide 'code' during evolution.
I know I'll be admonished for inferring the will of the designer, but why change the code, but keep the function the same? Why aren't the proteins identical across species? Why make the illusion of common descent and a tree of evolution?
Robert:
ReplyDelete"And I'm the one accused of metaphysics!!! So it is all about the software designer in the sky?"
This is classic evolutionary thought in action. The evolutionist, motivated by metaphsical interpretations of the evidence, concludes that evolution is a fact. When challenged by normal people, who look at the evidence without using such metaphysical premises, the evolutionist retorts: "well what's your explanation?" As if that somehow justified his metaphysics.
When the normal person suggests what is painfully obvious, namely design or creation explanations, the evolutionist exclaims "ah haa!!, you're science is metaphysical!" The evolutionist conveniently is unable to distinguish between metaphysics as a rationalistic starting point versus metaphysics as an empirically-based conclusion.
I think, Cornelius, if you read the rest of Robert's post that you quote, that you will find there is a much more important point at hand. Perhaps you care to respond to that instead?
ReplyDeleteWhy indeed should functionally identical homologous genes differ systematically in a pattern that indicates common descent?
Andrew proposes the software development principle "DRY" as a design-based answer - yet this is not a sufficient solution. The reason is that while DRY potentially explains the similarities between sequences it says nothing of the differences.
Specifically, the proportion of nucleotides that vary between species increases with other measures of distance under common descent - even when those sequences code for the same gene that performs the same function. Why should this be? And, critically, why should the sites that are most likely to vary be those that do not affect the resulting amino acid sequence at all?
The most parsimonious answer is that the sequences have descended from a common ancestor, and that level of sequence divergence indicates approximately the degree or time since separation from that common ancestor. Change occurs in a stochastic fashion, and at a population level the retained changes are those that do no harm. This explains both the similarities and the differences.
Does anyone has a design-based explanation for this pattern that does not invoke common descent?
Thanks Abner-I'm used to the partial rebuttal against the least consequential part of my post. I doubt our questions will be answerer.
ReplyDeleteRecapping the rest:
Robert: Evidence. Naturalistic reasoning. Goodness, I can't believe I'm the one accuse of injecting religion (in response to interjection of a supernatural software engineer as response to nested hierarchies).
Cornelius: AHA! Metaphysics!!! Damn evolutionists and their poor logic. I present NO alternative explanation for the data, therefore avoiding making a metaphysical claim. I win.
"normal person suggests what is painfully obvious, namely design or creation explanations, the evolutionist"
So now its normal people vs. evolutionists. A bit insulting no? We're abnormal? Don't worry, I've been called worse here, but I'm sure you've had evolutionist colleagues in the past. Were they so bad?
Robert said: "Cornelius: AHA! Metaphysics!!! Damn evolutionists and their poor logic. I present NO alternative explanation for the data, therefore avoiding making a metaphysical claim. I win."
ReplyDeleteTo be clear then, when Cornelius said as he did on 3/30
1) Of course I think supernatural causation played a role, because of the science.
2) Timcol: "I think it's also clear you think that this supernatural entity is the Christian God. Cornelius: "Of course"
...he is not doing "metaphysics", no siree! He be doin' science!
Cornelius has still yet to explain the "because of the science" part and why exactly this points to a supernatural cause (and no, it is only painfully obvious if you are already a born-again evangelical as is Cornelius and most of the people on this forum).
Robert: In similarity to human, the order produced is chimp, other apes and monkeys, rabbit, horse, dog, mouse, rat, chicken, finch, frog, zebrafish. (With some paralogues interspersed).
ReplyDeleteNo presuppositions, no bias in interpretation-just molecular phylogeny from sequence alignments.
Jeff: No presuppositions? Are you kidding? You're ASSUMING you're modeling a genealogical tree in the first place. That claim is not demonstrated BY the analysis. The analysis also ASSUMES that degree of similarity indicates degree of genealogical relatedness even for degrees of phenotypical differences we've never seen produced by reproductive variation. And then, on top of those, you assume that there are DNA sequences that will produce all the hypothetical intermdiates posited for the whole genealogical lineage AND that the blind mutational to those functional, HYPOTHETICAL intermediates will occur with a realistic probability in the posited time-frame. In short, you're assuming EVERYTHING that you need to DEMONSTRATE. Amazing!
Robert: Cornelius has still yet to explain the "because of the science" part and why exactly this points to a supernatural cause (and no, it is only painfully obvious if you are already a born-again evangelical as is Cornelius and most of the people on this forum).
ReplyDeleteJeff: What universe are you living in? Virtually all people are teleologists. Teleology involves final causes. Final causes are not natural causes. Yet they are subject to analogical inferences as is done in courts of law all the time. Thus, making analogical inferences about final causes is inductive just like making analogical inferences about efficient causes.
Libertarian free-will is just another name for final causality. In that sense, libertarian free-will, itself, is supernatural. To say that only Christians believe in free-will is absurd beyond belief.
In short, the inference to design is an analogical inference just as is an inferences to a natural cause. But there is no way to test ID inferences or the inference to macroevolution. They are MERELY analogical inferences that can not be tested.
"No presuppositions? Are you kidding? You're ASSUMING you're modeling a genealogical tree in the first place. That claim is not demonstrated BY the analysis."
ReplyDeleteWrong. Sadly for you, the opposite is true. The alignment algorithm works by sequence comparison only. No phylogeny is fed in at the beginning. The result, when results are clustered by relatedness, is a tree, the simplest interpretation for which is that organisms share common descent. Empirical sequence data yields phylogeny.
Read here:
http://en.wikipedia.org/wiki/BLAST
Try here:
http://blast.ncbi.nlm.nih.gov/
In your second post, you are quoting TimCol, not me. Words keep getting put in my mouth here!
Nevertheless, in the same breath where I'm accused of jumping to conclusions, you proceed to defend metaphysical/teleology. Interesting, but not a rebuttal to anything I've said. In this thread, I am merely defending common descent as a explanation for observed data. No origins, etc.
Theistic evolution would be a teleological explanation consistent with the empirical data*. I've also argued above that ID seems a poorly competitive hypothesis based on design principles (see Abner's post above), which no one has answered.
*(And for all you know, I believe in it. Or I don't. Who knows, as we don't really need to discuss teleology to discuss data. As I've mentioned before, we could teach meteorology, discuss and predict the weather without discussing natural evil and the will of God. Same here, no?)
Jeff states: You're ASSUMING you're modeling a genealogical tree in the first place.
ReplyDeleteThis is in fact an inference that stems from the observation of phylogenies, not an assumption of them. The inference is made as a parsimonious explanation for the observed patterns of varied interrelatedness, which produces clustering patterns.
The inference of common descent from phylogeny is supported by independent molecular data from other genes/chomosomes and genomes (e.g. chloroplast or mitochondrial vs nuclear). It is supported by patterns in the fossil record as well as the systematics of extant species. It is supported by embryology. As such, we are not simply talking about a series of baseless assumptions here.
If you can provide a better explanation for the observed patterns please do so. For example, if you have an alternative explanation for why patterns in synonymous sequence divergence match patterns in systematics that does not invoke common descent, then please discuss it.
abimer:
ReplyDelete===
Why indeed should functionally identical homologous genes differ systematically in a pattern that indicates common descent?
===
I don't know why. There certainly are such cases if one narrows one's view. Stepping back and widening the view, we might next ask: "Why indeed should functionally identical homologous genes (and DNA sequences in general) differ systematically in a pattern that does not indicate common descent?"
===
Andrew proposes the software development principle "DRY" as a design-based answer - yet this is not a sufficient solution. The reason is that while DRY potentially explains the similarities between sequences it says nothing of the differences.
===
I don't know enough about that to add anything. You may well be right about that.
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Specifically, the proportion of nucleotides that vary between species increases with other measures of distance under common descent -
===
That is false. You are filtering the data according the theory. Remember, I don't agree that evolution must be true to begin with. I need theory-neutral empirical evidence in order to believe it is true or a good theory. From a theory-neutral perspective, phylogenies based on specific characters are not congruent, they conflict in important ways.
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even when those sequences code for the same gene that performs the same function. Why should this be? And, critically, why should the sites that are most likely to vary be those that do not affect the resulting amino acid sequence at all?
===
Yes, another surprise for evolution which expected the non synonymous changes to predominate. Good questions. Ultimately, the answer right now has to be "we don't know." Clearly it would be unwise, following this false prediction and in addition to the many other false predictions, to hastily conclude that the answer is "because they evolved." That would be penny-wise and pound-foolish, in the sense of resolving an interesting, probably important, question which we don't yet understand at the cost of swallowing evolution's myriad problems.
Now we could try to imagine some possible explanations. It is always interesting how evolutionists, masters of imagining things, suddenly come up short when it comes to thinking about how a design might actually make sense rather than being a fluke. How about the possibility that the coding instructions are more constrained as they must produce a functioning protein, but synonymous changes fulfill other purposes which vary more between species? Funny thing is, when such functional reasons are later discovered, evolutionists never think twice.
===
The most parsimonious answer is that the sequences have descended from a common ancestor, and that level of sequence divergence indicates approximately the degree or time since separation from that common ancestor.
===
Ah, there you go.
===
Change occurs in a stochastic fashion, and at a population level the retained changes are those that do no harm. This explains both the similarities and the differences.
===
Except when it doesn't. Which happens all the time.
Robert:
ReplyDelete"So now its normal people vs. evolutionists. A bit insulting no? We're abnormal? Don't worry, I've been called worse here, but I'm sure you've had evolutionist colleagues in the past. Were they so bad?"
Maybe I'm wrong about that. Maybe I'll have to retract that. I always thought it was odd for folks to make religious claims and mandate absurd theories, distribute blacklists of those who don't agree, deny everything from grades to grants and generally ruin people's careers. But maybe that is normal.
Timcol62:
ReplyDelete===
To be clear then, when Cornelius said as he did on 3/30
1) Of course I think supernatural causation played a role, because of the science.
2) Timcol: "I think it's also clear you think that this supernatural entity is the Christian God. Cornelius: "Of course"
...he is not doing "metaphysics", no siree! He be doin' science!
===
Hmmm, just when I finished explaining this classic evolutionary canard. The evolutionist, motivated by metaphsical interpretations of the evidence, concludes that evolution is a fact. When challenged by people who look at the evidence without using such metaphysical premises, the evolutionist retorts: "well what's your explanation?" As if that somehow justified his metaphysics.
When the person suggests what is painfully obvious, namely design or creation explanations, the evolutionist exclaims "ah haa!!, you're science is metaphysical!" The evolutionist conveniently is unable to distinguish between metaphysics as a rationalistic starting point versus metaphysics as an empirically-based conclusion.
===
Cornelius has still yet to explain the "because of the science" part and why exactly this points to a supernatural cause (and no, it is only painfully obvious if you are already a born-again evangelical as is Cornelius and most of the people on this forum).
===
You keep forgetting that the reason it is painfully obvious to me is that I don't have a religious ax to grind. My God can use evolution as a creation tool, can create miraculously, or anything in between. You are the one who rejects what is painfully obvious because it cannot be true for you. Now I'm not saying you don't have your reasons, and for you they are powerful reasons. But from an empirical science perspective (which I favor), there is no doubt what the score it.
Robert:
ReplyDelete===
Cornelius: AHA! Metaphysics!!! Damn evolutionists and their poor logic. I present NO alternative explanation for the data, therefore avoiding making a metaphysical claim. I win.
===
Again, let's keep the metaphysics straight. There are metaphysical premises and there are metaphysical conclusions. You do the former, I do the latter.
I'm happy to speculate about possible explanations from an empirical perspective. That is, after minimizing the premises and cleansing them of religous beliefs, I'm happy to consider everything from naturalistic explanations to full blown miracles. I have no problem with metaphysical conclusions, but I prefer to keep the metaphysics out of the premises. I'm not saying what you are doing is necessarily out of bounds, but it isn't empirical science.
Robert:
ReplyDelete===
In similarity to human, the order produced is chimp, other apes and monkeys, rabbit, horse, dog, mouse, rat, chicken, finch, frog, zebrafish. (With some paralogues interspersed).
No presuppositions, no bias in interpretation-just molecular phylogeny from sequence alignments.
===
Are there presuppositions in BLASTing sequences? Of course not. Are there presuppositions in claiming, as evolutionists do, that aligned sequences are powerful evidence for evolution? Of course.
Abimer says: Andrew proposes the software development principle "DRY" as a design-based answer - yet this is not a sufficient solution. The reason is that while DRY potentially explains the similarities between sequences it says nothing of the differences.
ReplyDeleteAgain if you had developed software you would know that for example in object orientated programming you can define a base class(object definition) say that has the common functionality, attributes and properties contained within it. You can then define other classes which inherit the functionality, attributes and properties and then you can add or override this functionality. In some languages you can even inherit from multiple classes. You can of course use these new classes as a base for another class. So again its just good engineering to share whats common.
Abimer: If you can provide a better explanation for the observed patterns please do so. For example, if you have an alternative explanation for why patterns in synonymous sequence divergence match patterns in systematics that does not invoke common descent, then please discuss it.
ReplyDeleteJeff: First of all, all "explanations" of hypothetical events and causal capacities are mere HYPOTHETICAL explanations. ID hypothetical explanations are merely analogical inferences just like yours is. There are no tests to confirm either. Only metaphysics can determine which analogical inference seems the least speculative to us. As mere analogies, they all work as hypothetical explanations. But metaphysics can render one analogical inference more speculative than another. And that's what's going on.
So now its normal people vs. evolutionists. A bit insulting no? We're abnormal? Don't worry, I've been called worse here, but I'm sure you've had evolutionist colleagues in the past. Were they so bad?
ReplyDeleteIt looks like Hunter meant normal in both a descriptive and normative sense so I'll let him define his own meaning.
But I would note that you can't have things both ways in the sense of being normal/average because arguments based on professional status combined with consensus are common and arguments of this sort assume that the average person who has not been trained in evolutionary "theory" (such as it is) generally cannot or does understand it. Evolutionists often argue that ignorance and misunderstanding of this sort is why the normal/average person tends to reject evolutionary creation myths. I would actually argue the opposite because it is not as if the "theory" is generally the equivalent of Einstein's theories or Newton's calculus. The problem is probably not that normal people do not understand it, as any ignorant schoolboy can understand most of its core tenets in a matter of weeks. Instead it's more likely that many people recognize that it conflicts with their metaphysics because it begins with and is based on naturalism and atheism. This is probably why the story of a provincial rube finding answers to their former metaphysics and religion in a metaphysical "theory" of evolution are common.
At any rate, proponents can't have things both ways with evolutionists being the Real Scientists© who can cite their own consensus against what the average person thinks due to their expertise and training while also claiming to be just another normal, average person. Any training which caused people to begin to cite their own imaginations as the equivalent of empirical or historical evidence would cause them to be abnormal in a normative sense as well.
Jeff: First of all, all "explanations" of hypothetical events and causal capacities are mere HYPOTHETICAL explanations.
ReplyDeleteThe hypothesis is the primary tool of the scientific method. We propose a hypothesis, then test for its entailed empirical implications. Common Descent across many taxa is supported based on morphology, genetics and embryology. It makes specific and distinguishing empirical predictions. ID does not provide a scientific explanation of any sort.
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ReplyDeleteCOrnelius still hasn't explained the "because of the science". The best he can say is that is "painfully obvious". I do get that everybody brings their own presuppositions to the table in any kind of epistemological endeavor such as this.
ReplyDeleteHowever, we are to believe that in Cornelius's case he is somehow pure and uncontaminated and that he does not bring "metaphysics" into his science (whatever that is - hopefully it is more than just writing this blog). The evidence for this? Simply his own self-referential assertions and nothing else. If Cornelius says he is not doing metaphysics then it is so! Despite the fact that he teaches at a fundamentalist Bible college, freely discusses his faith, we are supposed to believe that he is doing something "empirical". Frankly, whatever.
In the end it comes down to a simple act of whether we want to believe him or not. Until he is prepared to offer the beginnings of a alternative hypothesis, I will remain skeptical.
We propose a hypothesis, then test for its entailed empirical implications.
ReplyDeleteThe notion of common descent does not entail or specify much of anything, a few predictions can be derived from it but it generally remains hypothetical goo.
Common Descent across many taxa...
It's not clear what that hypothesis entails because it's generally not specified. It's supported across "many taxa" yet there could be a "few" unknown and unspecified common ancestors for all taxa? This isn't exactly a rigorously specified scientific theory. And that would be fine if so many didn't try to play pretend as if it is the epistemic equivalent of all "science." (Enter the theory of gravity, the earth revolving around the sun, assorted mythologies of "purely" scientific Progress, etc.)
It makes specific and distinguishing empirical predictions.
It's actually fairly vague, to the point that there is often little distinction between observed patterns and imagining things about ancestry. In the minds of some the data seems to seamlessly merge with their way imagining things about the past to the point that they begin treating imaginary events in the past as the epistemic equivalent of empirical evidence. It seems that every single organism observed can be "predicted" based on "a few" imaginary events in the past.
Despite comparisons to the theory of gravity it's not as if trajectories of adaptation and divergence have been generally predicted and then verified in groups of organisms. Instead it seems that the "theory" of evolution is generally based on observing patterns of similarity and imagining (for one reason or another, usually something about God) that the only explanation for such patterns is that everything has a common ancestor. Or a "few" ancestors... note the specificity of what the hypothesis entails.
Apparently we can have a knowledge of the ancestry of every living thing that exists even if no actual line of ancestry can be identified in the past or predicted in the future. It would be one thing if you had a specified theory that predicted trajectories of adaptation and lines of divergence which had been generally verified. Then all one would need to do was to imagine that the same sort of thing applied in the past, a reasonable assumption. But instead it seems that we're being asked to imagine that patterns of similarity are evidence of constructive and progressive forms of descent with no known cause. Ironically that type of descent may violate known processes like natural selection. One has to imagine causes and processes not known to exist while also imagining that patterns of similarity should be treated as evidence of ancestry (God wouldn't do it that way. Etc.). It's generally a lot to imagine.
mynym-
ReplyDeleteWhere in this thread have I made an argument from authority? I'm arguing my point from the data-and actually arguing quite the the opposite-that anyone can search the public data and test their own hypotheses. Don't believe me--be your own scientist--but present some plausible explanation for the results.
Jeff-
"ID hypothetical explanations are merely analogical inferences just like yours is. There are no tests to confirm either"
Maybe instead of whose metaphysics is 'better,' we should use scientific standards like parsimony and falsifiability? I understand the point of the blog is to argue science isn't scientific, and therefore on equal footing with creationism, but come on. I'd even settle for plausibility as a rubric, but no one here can even argue why "indeed should functionally identical homologous genes differ systematically in a pattern that indicates common descent?......Does anyone has a design-based explanation for this pattern that does not invoke common descent?"
Other than standing back and marveling at the data, what do you propose we do?
I'll even present a falsifiable, scientific? design hypotheses to explain the data:
ALL OBSERVED DIFFERENCES RELATE TO THE FUNCTION OF THE PROTEIN. Different animals, different phenotypes, different design requirements.
Of course, this hypothesis is:
1) Less parsimonious than common descent (though we'll let that slide)
2) More importantly, already falsified. Non-coding changes in DNA (e.g. wobble positions) and many amino acid changes have no impact, and proteins can be functionally swapped between organisms.
Cornelius-
The data isn't filtered. It is true that phylogenetic trees can be confused by horizontal gene transfer, insufficient numbers of sequence, or paralogues. However, the vast majority of the time (and virtually 100% of the time in vertebrates) it works. This presents an inconvenience that I really don't see an alternative explanation for.
Note also that I've only said common descent. Not atheistic evolution, theistic evolution, Zoroastrianism, creationism, abiogenesis, etc. Just an explanation for the data. I again find it funny to be accused of metaphysical premises and conclusions, when in the next post up, you describe creationism as a competitive hypothesis.
I suppose it is, but it seems a double standard when I go from data, to result using an unbiased algorithm (nested hierarchies that I argue conflicts with design criteria), to a parsimonious conclusion (common descent) without reference to theology; that you can introduce creationism as a competitive hypothesis, and still accuse me of inserting religion into science.
And I suppose if I ask why this competing hypothesis explains the data (why would the creator make it look that way) I'll be accused of making a metaphysical argument?
Robert:
ReplyDelete===
The data isn't filtered. It is true that phylogenetic trees can be confused by horizontal gene transfer, insufficient numbers of sequence, or paralogues. However, the vast majority of the time (and virtually 100% of the time in vertebrates) it works. This presents an inconvenience that I really don't see an alternative explanation for.
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Which is an excellent example of evolutionary thinking. You have a theory that consistently produces false predictions yet it must be true because we "don't see an alternative explanation." The metaphysics is subtle and people think their doing science.
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Note also that I've only said common descent. Not atheistic evolution, theistic evolution, Zoroastrianism, creationism, abiogenesis, etc. Just an explanation for the data. I again find it funny to be accused of metaphysical premises and conclusions, when in the next post up, you describe creationism as a competitive hypothesis.
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No, I was reporting on the article which explained the usual evolutionary metaphsyics of rejecting creation.
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I suppose it is, but it seems a double standard when I go from data, to result using an unbiased algorithm (nested hierarchies that I argue conflicts with design criteria), to a parsimonious conclusion (common descent) without reference to theology;
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What you have are confirmed predictions (on circumstantial evidence) amidst false predictions. This DNA repair mechanism is just one of myriad examples that make evolution unlikely, to say the least. But evolutionists focus on the circumstantial evidence. They don't understand the reasons for it, it doesn't appear designed or created to them, and so they jump to the "evolution created all life" conclusion. There are several problems here, not the least of which are the metaphysics and then denial thereof. The reason why you are persuaded is you think the likelihood of the alternatives is tiny or zero given the evidence.
Robert this *is* evolutionary thinking. There's nothing necessarily wrong with your logic, and it has been driving evolutionary thought for centuries. But you end up with a silly theory based on religion. Not where I want to be.
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And I suppose if I ask why this competing hypothesis explains the data (why would the creator make it look that way) I'll be accused of making a metaphysical argument?
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You and evolution have already made the metaphysical argument, by saying that creation or design is disproved by the evidence. Evolution is based on contrastive thinking. It is the very essence of evolutionary thought, going back long before Darwin. You've probably not read many of the early thinkers, but you're making precisely the same arguments. New data, old arguments.
Timcol62:
ReplyDelete===
However, we are to believe that in Cornelius's case he is somehow pure and uncontaminated and that he does not bring "metaphysics" into his science
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I know this is hard for rationalists to believe, but there is a whole lot of folks out there who are not like you. We don't all decide what the answer is based on our religious sentiment.
And so the rationalist is left imagining and imputing motives. Evolutionists and creationists repeatedly state the religious premises, but those who are looking at the evidence, they must have ulterior motives. For rationalists, its all about imputed motives. Don't look at the evidence, look at the person.
Timcol62:
ReplyDelete"(other than arcane mathematical musings), this gets precisely nowhere."
Wow. I'll bet you're so impressed... with yourself.
Denial of the math involved?
The typical Darwinist "I don't know what I'm talking about so I'll just deny the existence and importance of 'arcane' probabilities", response.
It is so obvious how you Darwinists assume evolution then make conclusions by reading your presumptions into the data.
This whole thread could have avoided a ton of unnecessary discussion if Rob had not started his usual "assume common descent then read and stuff the data into it" barrage of ill premised reasonings.
Rob:
ReplyDelete"And I'm the one accused of metaphysics!!! So it is all about the software designer in the sky?"
Pretty amazing response but not surprising Rob.
Why are foolish atheists so obsessed with the 'fill in blank' "in the sky" phrase?
I see this stupid little phrase everywhere and its almost always given by teenagers (or those with 13 year-old angst) who think atheism is smart or cool or ...
"There is a fundamental difference between conservation of design and the little 'code' changes in evolution that often have no apparent change in function."
Really? Prove it.
I can point out literally hundreds of software designs wherein basic functions, like sorting, creating objects, parsing etc. have near identical code yet differ in subtle ways that changes the exact sequence of commands or the variable init values yet without adding or subtracting any vital function.
You ought to study up on what we software engineerings call "Design Patterns" - Google it.
"The DNA repair complexes largely do the same thing-and can be swapped between organisms-but have accumulated changes in their nucleotide 'code' during evolution."
Well as CH pointed out you've already once again, ad nauseum, assumed evolution, read it into the data and then concluded it.
I can also guarantee that about half the software being designed on the planet today uses design patterns loaded from purchased or public domain software builders. They take what they need, "paste" it into their own code and it works.
ANY intelligent designer will seek the same type of building system - reuse, polymorphism, etc.. Which is what we see in biological systems.
Big surprise huh.
I conclude design because I already know that prescribed information, meta information etc., cannot arise by any random process.
Code cannot exist without a mind having founded its symboology -syntax and semantics - get over it for petes sake!
You conclude evolution because you deny this fact and have already assumed it in your premises!
A clear logical fallacy evolutionists are always guilty of but never admit.
Now, what's your point again?
Hutch-could you present a nested hierarchy, based on the alignment of the letters/symbols of designed computer code alone? Simple reuse, cut and paste will not form a nested hierarchy that is best explained by common descent.
ReplyDeleteIn no instance of human design will you end up with a nested hierarchy. Never. What you invariably end up with is a complex network of interrelationships-with starts, stops, complete redesign, etc. A nested hierarchy is only formed when a current design is constrained to its ancestral history and is independent of designs outside its 'lineage'. Only common descent explains the pattern. (Again, why design in non-functional changes that give the appearance of evolution?)
"ANY intelligent designer will seek the same type of building system - reuse, polymorphism, etc.."
Really? So the OS on my computer is built up from SHARE or GECOS? Or did engineers at some point make independent lineages of operating systems, with totally novel features and distinct codes?
You act like there are universal, defining features of design, but our experience as designers tell us there are few. There are inventors and refiners. Is the light-bulb a refinement of a flaming torch? Why nothing novel in the designer's special creation? Why nothing that would stick out as a smoking gun, with no precursors, therefore refuting evolution?
"I already know that prescribed information, meta information etc., cannot arise by any random process. "
You know this? Is selection acting on genetic diversity truly random, or does it act as a filter to select for certain information? What happens when we observe novel traits in the lab, field, or nature? Do you believe each time we observe an information increase or novel functional protein formed, it is the direct influence of the designer?
Andrew says "Again if you had developed software you would know that for example in object orientated programming you can define a base class(object definition) say that has the common functionality, attributes and properties contained within it. You can then define other classes which inherit the functionality, attributes and properties and then you can add or override this functionality. In some languages you can even inherit from multiple classes. You can of course use these new classes as a base for another class. So again its just good engineering to share whats common.
ReplyDeleteYour answer has exactly no explanatory power for what I have discussed above. I have said that DRY could potentially explain commonalities - but what about the differences? Again, the majority of nucleotide substitutions in almost all coding sequences are synonymous, with little or no effect on fitness as the resultant proteins are unchanged. In what sense is that "good engineeering"?
abimer: Again, the majority of nucleotide substitutions in almost all coding sequences are synonymous, with little or no effect on fitness as the resultant proteins are unchanged. In what sense is that "good engineeering"?
ReplyDeleteJeff: Is it "little" or "no?" Because if it's "little," then why wouldn't "good engineering" be a possible cause? A little fitness cost is worse than no fitness cost.
Robert: The alignment algorithm works by sequence comparison only. No phylogeny is fed in at the beginning. The result, when results are clustered by relatedness, is a tree, the simplest interpretation for which is that organisms share common descent.
ReplyDeleteJeff: No. Rather, IF all the hypothetical genotypes and phenotypes you posit are possible and probabilistically derivable in the posited time-frame, THEN common descent would be a simpler explanation. For now, there are only mutually exclusive HYPOTHETICAL analogical explanations. And they aren't testable or falsifiable.
IOW, until you show empirically or by modeling from an empirically-derived causal theory that such hypothetical genotypes produce the hypothetical phenotypes and can be attained blindly with realistic probability in the posited time-frame, all you have is a huge set of such hypotheses that can not yet be tested. "Trees" don't tell us thing about the truth or possibility of those hypotheses.
IOW, macroevolution is more parsimonious IF true. We don't even know it's possible yet, much less true. Nothing but metaphysics can get you to belief that those hypothetical genotypes existed and produced hypothetical phenotypes.
IOW, the most parsimonious explanation of observable, repeatable events (or modeled events modeled after a causal theory tested against observations) is one thing. The most parsimonious HYPOTHETICAL explanation of HYPOTHETICAL events, is not an explanation of known events. It's a HYPOTHETICAL explanation in the sense that the events posited are not even empirically known to have occurred or even to have been possible.
All we know is that there are analogical grounds for both kinds of inference. When the very events that are being "explained" are, themselves, hypothetical (in the sense that they aren't and never have been observable or modelable), you're in purely hypothetical land only. And in that case, you are using "explanation" in a completely different sense than how we mean it with respect to OBSERVABLE or MODELABLE events.
Jeff,
ReplyDeleteZachriel has answered this line of reasoning above:
http://darwins-god.blogspot.com/2010/04/dna-repair-with-molecular-tool.html?showComment=1271339364709#c5023305485236025355
Again, you're putting the cart before the horse. Hypotheses are formed to explain the data. Hypotheses stand until falsified, and evolution has the backing of multiple independent lines of evidence. I have presented nested hierarchies here, and as yet, no one has presented a reasonable alternative (except design, which is being soundly refuted as a having explanatory power) to me.
So, common descent is a falsifiable hypothesis that best explains nested hierarchies. The nested hierarchies are observable, and fit what is known about mutation rates and molecular evolution. In the many posts above, we explain why design does not. Your argument amounts to a "shut up, you don't know everything, so I forbid you from talking about anything. P.S. designer did it." No?
Jeff: Is it "little" or "no?" Because if it's "little," then why wouldn't "good engineering" be a possible cause? A little fitness cost is worse than no fitness cost.
ReplyDeleteJeff, it's "little or no" because there may be small fitness differences between synonymous codons in terms of factors such as translational efficiency.
In the context of this discussion, it is important to note that those differences occur between species and within populations. So, if we were to look for good engineering, we would expect that either a single codon would be used, or there is no important fitness effects from different codons.
So, in order to not outrightly reject the "good engineering" argument, we must accept that the changes have no effect on fitness, such that all homologues are approximately equivalent.
This leaves us with a mass of variation that fits the evolutionary interpretation of a nested hierarchy resulting from common descent. The amount of sequence variation increases with other measures of relatedness such as morphology and body plan.
Further, we know a fair bit about the mutational pressures that drive 4-fold degenerate site evolution in vertebrate mitochondrial DNA. These mutational pressures affect all sites but the changes that are most commonly retained in populations are those in the third (commonly synonymous) position. This is the signature of mutation and drift. Look at third position nucleotide composition in mtDNA. The extraordinarily low proportion of guanine is the result of this mutational pressure.
I said:"Specifically, the proportion of nucleotides that vary between species increases with other measures of distance under common descent -
ReplyDeleteAnd Cornelius replied:That is false. You are filtering the data according the theory. Remember, I don't agree that evolution must be true to begin with. I need theory-neutral empirical evidence in order to believe it is true or a good theory. From a theory-neutral perspective, phylogenies based on specific characters are not congruent, they conflict in important ways.
Agreed. Phylogenies do sometimes conflict in important ways. However, it is a gross overstatement to state that what I have said is simply 'false'. I know of no theory in ecology (and population genetics is heavily ecological in an empirical context) that does not have conflicts and contradictions.
It is the work of scientists to determine whether those conflicts falsify the theory or whether there are ways to refine the theory. We want the simplest explanation that fits the data.
A large part of resolving such phylogenetic disparities has simply been to increase the amount of data. Mutation is a stochastic process, so this makes sense. Phylogenetic models must estimate parameters from models (or have them input externally) - these sorts of things are prone to error as the parameters are never completely knowable and never likely to be stable. Further, weighting character states in other systematics analyses is prone to similar error.
Does the balance of the data in light of such variation truly warrant rejecting phylogenetics as supporting common descent? Further does anything in the evidence suggest another interpretation?
Cornelius also said: Yes, another surprise for evolution which expected the non synonymous changes to predominate. Good questions. Ultimately, the answer right now has to be "we don't know."
No, the right answer is to be found in the last 40 years of population genetics, and is well understood. The idea that non-synonymous change should predominate was indeed a fallacy in the modern synthesis - but we must at least note that it is one that ultimately dates to at least Fisher in 1930, decades before the structure of DNA was determined and as such was highly speculative. In no small part, this is also due to another fallacy in the MS, that mutation is a uniformly weak force in evolution. You are right about the early modern synthesis, and some people probably hold onto some of those fallacies now, but the story hardly stops there. In contemporary terms, the debate at the molecular genetics level is over the extent to which genetic drift and genetic draft control stochastic fixations when we don't hold such ill-founded ideas about mutation. As drift and draft are likely to vary with other population demographic factors such as population size and density, there is likely no singular answer here, but clearly models that can explain much of the pattern.
And regardless of whether or not you wholly accept this answer yourself, the evidence indicates a stochastic process rather than a finely guided one. This is not to reject all models of theistic creation/evolution, rather to address the claim of 'good engineering' as an alternative to common descent.
Finally, I said: Change occurs in a stochastic fashion, and at a population level the retained changes are those that do no harm. This explains both the similarities and the differences.
To this, Cornelius responds: Except when it doesn't. Which happens all the time.
Except when what doesn't? When change is not stochastic or when deleterious mutants are fixed? I think it is clear I am talking about the bulk of fixed mutations - and the bulk of fixed mutations do no harm. You seem to be vaguely implying that this is not the case. Perhaps you could clarify your position.
abimer:
ReplyDelete===
Agreed. Phylogenies do sometimes conflict in important ways. However, it is a gross overstatement to state that what I have said is simply 'false'. I know of no theory in ecology (and population genetics is heavily ecological in an empirical context) that does not have conflicts and contradictions.
===
Well, at issue here are the high claims. Evolution comes with a "Truth inside" tag unlike those other theories. When you make categorical statements, in support of evolution, which are false, it isn't OK just because those other theories have problems as well. Those other theories are not making truth claims with empirically unlikely explanations.
===
It is the work of scientists to determine whether those conflicts falsify the theory or whether there are ways to refine the theory. We want the simplest explanation that fits the data.
===
Evolution does not merely claim to be the simplest explanation. It claims to be a scientific fact.
===
A large part of resolving such phylogenetic disparities has simply been to increase the amount of data. Mutation is a stochastic process, so this makes sense. Phylogenetic models must estimate parameters from models (or have them input externally) - these sorts of things are prone to error as the parameters are never completely knowable and never likely to be stable. Further, weighting character states in other systematics analyses is prone to similar error.
===
Phylogenetic incongrueties are way beyond the noise level. Even evolutionists admit to this (when talking to each other).
===
Does the balance of the data in light of such variation truly warrant rejecting phylogenetics as supporting common descent?
===
It is not controversial that phylogenetics contradicts common descent. Yes there are plenty of data that conform to common descent, but there are important contradictions. So to answer your question, it is not even debatable that from an empirical science perspective, phylogenetics is a problem for common descent. It is not a question of whether or not it supports CD, it is a *problem* for CD. Now of course we can always add patches to the theory if we are sufficiently committed to the theory. So we can create a Rube Goldberg CD theory to absorb the data. In that case, you then have a theory that *is* supported by the evidence, and there is no warrant for rejecting phylogenetics as supporting common descent. But now you have a complicated, not a simple, theory. That is where we are today.
===
Further does anything in the evidence suggest another interpretation?
===
There you go. We don't know of another interpretation, so evolution is the answer, no matter that it has empirical problems. That is deeply metaphysical.
===
Finally, I said: Change occurs in a stochastic fashion, and at a population level the retained changes are those that do no harm. This explains both the similarities and the differences.
To this, Cornelius responds: Except when it doesn't. Which happens all the time.
Except when what doesn't? When change is not stochastic or when deleterious mutants are fixed? I think it is clear I am talking about the bulk of fixed mutations - and the bulk of fixed mutations do no harm. You seem to be vaguely implying that this is not the case. Perhaps you could clarify your position.
===
No, I simply meant that with evolution we must believe in more than the conventional story. For instance:
http://darwins-god.blogspot.com/2010/02/hopeful-monsters-endless-list-of.html
http://darwins-god.blogspot.com/2010/02/persistence-of-saltationism.html
Robert: So, common descent is a falsifiable hypothesis that best explains nested hierarchies. The nested hierarchies are observable, and fit what is known about mutation rates and molecular evolution.
ReplyDeleteJeff: No, what we know about mutation rates and molecular evolution doesn't imply a thing about whether there are DNA sequences that would produce the myriads of hypothetical phenotypes you posit. Nor does it imply a thing about whether the blind mutational search through DNA space to "find" those hypothetical phenotypes could occur with realistic probability in the posited time frame. Nor does tree generation tell us a thing about these. And yet THESE are the very hypotheses you are saying you KNOW to be true.
Robert: In the many posts above, we explain why design does not. Your argument amounts to a "shut up, you don't know everything, so I forbid you from talking about anything. P.S. designer did it." No?
Jeff: By definition, a hypothesis is not knowable until other analogical, hypothetical explanations of the same data is falsified. No one has done that. How do you falsify the inference that eyes can only arise, as seems to be the case with cars, via final causes? You have not remotely demonstrated you've done that.
So ID'ists are saying that certain configurations of matter SEEM to require final causality for their origin. It's an analogical inference. It's not testable. It's only falsifiable if and when a naturalistic alternative is tested SUCCESSFULLY. We're nowhere near that. Macroevolution can't even be tested at all, much less successfully.
abimer: Further, we know a fair bit about the mutational pressures that drive 4-fold degenerate site evolution in vertebrate mitochondrial DNA. These mutational pressures affect all sites but the changes that are most commonly retained in populations are those in the third (commonly synonymous) position. This is the signature of mutation and drift. Look at third position nucleotide composition in mtDNA. The extraordinarily low proportion of guanine is the result of this mutational pressure.
ReplyDeleteJeff: This kind of info doesn't hurt or help either side. It is consistent with both kinds of hyptheses. No ID'ist is arguing against the idea that tons of natural causes are involved in biological variation. Tons of natural causes are involved in the writing and executing of programs as well. That doesn't mean that NO final causes were involved. You're conceiving of ID inferences in a way that we don't. So your comparison isn't addressing the point of contention.
You say that matter will naturally arrange into configurations that we observe today but have never observed configure that way naturally. Like a program, it may do impressive things once it's configured. It's the getting configured that we think might require final causes, not all that happens thereafter.
Rob:
ReplyDelete"Hutch-could you present a nested hierarchy, based on the alignment of the letters/symbols of designed computer code alone? ...."
First, your nested hierarchy is yet another Darwinian myth -for the most part- since life is not neatly arranged in the infamous nested hierarchy at all.
The so-called "evolutionary tree of life" is bogus and out of date. The data reveal not a tree but a forest.
Next, indeed one could form a kind of nested hierarchy out of much of modern computer code.
You didn't look up Design Patterns did you?!
There are pieces of code that I could easily copy and paste from one OS to another without breaking anything at all.
Indeed, a huge part of all modern software is built upon existing libraries which were coded using "Object Oriented" design.
These are nested hierarchies by definition!
You have a series of global root objects or classes giving generalized functions and properties in a system. From these roots are inherited objects that specialize, add to or slightly modify the behavior of the root object. Any derived class "recognizes" the methods and properties used by the root.
Ex. a Square is a Polygon is a Shape.
Square and Rectangle are objects both derived from Shape.
Ex. Sapiens is a Homo is a Primate is a Mammalia is a Animalia
See?
These structures are also polymorphic, can be overridden and overloaded -just like in nature.
http://en.wikipedia.org/wiki/Polymorphism_in_object-oriented_programming
This kind of internal structuring is ubiquitous in software development!
If you fail to see the similarities between this and evols nested hier. then you need to study Object Oriented theory and languages (like C++, C#, Java, etc.) -among the most common programming languages on the planet.
How in the world do you think "evolutionary algorithms" or "genetic algorithms" are coded!?!
Thus, you're way off on this Rob on 2 distinct levels!!
Me - "intelligent designer will seek the same type of building system - reuse, polymorphism.."
Rob: "Really? So the OS on my computer is built up from SHARE or GECOS? Or did engineers at some point make independent lineages of operating systems, with totally novel features and distinct codes?"
Irrelevant. You're merely avoiding the truth of my statement.
The concepts and algorithms used in the original GECOS OS are still being used today in many other systems built under different languages.
continued...
continued...
ReplyDeleteRob: "act like there are universal, defining features of design, but our experience ...tell us there are few."
Wrong. Indeed, there ARE universal design principles.
One of them is that of economy -re-use, polymorphism etc.
A major force against everything you state here is the FACT that the ONLY empirical evidence we have of formal informational structures with function is where intelligences are involved.
There are no other sources of structured functional information.
Indeed, as I continue to point out to you -CODE intrinsically implies intelligence! There is no other possible source!
Rob, you're avoiding the obvious because you don't WANT to see what's wrong with Darwinism -it would upset your current comfort in your whole world view and you would be intellectually forced to consider the alternative.
Rob: "Is the light-bulb a refinement of a flaming torch?"
Well, in a sense yes.
The word torch is still used in Britain for our word "flashlight"! We took the original idea but found a better way to make the fire -smaller and brighter.
"Why nothing novel in the designer's special creation?"
Now you're smoking something nasty.
Nothing novel?!?! Look around you man are you blind?
"Why nothing that would stick out as a smoking gun, with no precursors, therefore refuting evolution?"
How's DNA sound?
Me : "I already know that prescribed information, ...cannot arise by any random process. "
Rob: "You know this?"
Yes, everyone should and apparently only Darwinists don't.
If you can prove otherwise I'd be happy to see your proof.
So go ahead -show the world how an algorithm can be encoded without first inventing a coding convention. Nobel if you do!
Indeed, information has strict laws, some of which are:
*"It is impossible to set up, store, or transmit information without using a code."
*"It is impossible to have a code apart from a free and deliberate convention."
*"It is impossible for information to exist without all five hierarchical levels: statistics, syntax, semantics, pragmatics, and apobetics..."
"It is impossible that information can originate in statistical processes."
Douglas Hofstader wrote, "A natural and fundamental question to ask on learning of these incredibly, intricately interlocking pieces of software and hardware is : 'How did they ever get started in the first place?" Werner Loewenstein, world renown for his work on cell communication and bio-information transfer says, "This genetic lexicon goes back a long long way. Not an iota seems to have changed over 2 billion years; all living beings on earth from bacteria to humans use the same 64 word code"
DNA is genetic software.
The 2 base pair molecules forming the ends of any given rung in the DNA ladder are held together by weak chemical bonds. But the rungs themselves, whose sequence codes the information, have no chemical bonds between them.
Polanyi explains the implications of this, "Suppose the actual structure of the DNA molecule were due to to the fact that the bindings of it's bases were much stronger than the bindings would be be for any other distribution of bases, then such a DNA molecule would have no information content. It's code-like character would be effaced by an overwhelming redundancy... Whatever may be the origin of a DNA configuration, it can function as a code only if it's order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words on a printed page."
In other words, contrary to what all Darwinists are trying to insist here, the message is not derivable from the physics and chemistry itself! The genetic text is not generated by the chemistry of the bonding between molecules.
Cool stuff! Can I share something interesting with you? The “Manga Guide to Molecular Biology” is a comic book that teaches students the basics of molecular biology. It is an entertaining way for students to be educated and entertained simultaneously. Might be helpful. http://cbt20.wordpress.com/2010/04/15/molecular-biology-comic-book-style/
ReplyDeleteThis comment has been removed by the author.
ReplyDelete"Next, indeed one could form a kind of nested hierarchy out of much of modern computer code."
ReplyDeleteI guess that is the difference between you and I. I presented my data that forms a nested hierarchy earlier. You merely invoke it. Designs will form a web over time, not a nested hierarchy. They are NOT a feature of design, and a black eye for ID.
And again, presenting data otherwise would really hurt our cause. Yet NO ID advocate has ever made a nested hierarchy of a succession of designs, which mimics an evolutionary tree of life, with proper branch distances reflecting time, etc...
Your examples of hierarchies in computer software are examples of single designs used in code. They are not nested hierarchies describing the ORIGINS of that software-that is, its development over time. The succession of designs over time will form a web, not a nested hierarchy.
Me: Why nothing that would stick out as a smoking gun, with no precursors, therefore refuting evolution?"
You:How's DNA sound?"
RNA world, reverse transcription.... Try again
"You: "I already know that prescribed information, ...cannot arise by any random process. "
Me: "You know this?"
You: Yes, everyone should and apparently only Darwinists don't. If you can prove otherwise I'd be happy to see your proof."
My argument has already been made. Selection can generate information. Roll dice. Random numbers. Now add selection for 6s. Non-random output via a simple selector. Line up non-random outputs, and what's that, information!!! And what is the theory of evolution based on? Natural selection. Funny how the SELECTION always gets left out. Because it does things you'd rather ignore!
""This genetic lexicon goes back a long long way. Not an iota seems to have changed over 2 billion years; all living beings on earth from bacteria to humans use the same 64 word code"
DNA is genetic software."
He's using an analogy. The genetic 'code' comes from the complexity of our understanding or 'decoding' it. Post-WWII engima days, 'crack the code' etc. This does not mean it is not physio-chemical. I like the quote too-great evidence for evolution.
"The 2 base pair molecules forming the ends of any given rung in the DNA ladder are held together by weak chemical bonds. But the rungs themselves, whose sequence codes the information, have no chemical bonds between them."
You might want to review your biochemistry. All the bases on one side or the other of the 'ladder' are connected by phosphodiester bonds. Across the ladder, there are hydrogen bonds, and shape complementarity that govern A:T G:C pairs. These bonds and shapes are exploited in the physical processes of replication, transcription and translation, where incoming based or amino acid loaded tRNAs come in and pair with the bases (physiochemical). Where's the algorithm?
The last quote you present just states that to carry genes, dsDNA structure must not depend on the base content. That is what makes it useful as the genome.
No scientist would argue transcription and translation are metaphysical and not dependent on physics and chemistry. Their function is thoroughly understood, and related to structure by techniques such as X-ray crystallography. Nice try though.
Rob said...
ReplyDelete"I guess that is the difference between you and I. I presented my data that forms a nested hierarchy earlier."
Your data? Rob you're dreaming. There is no universal Darwinian "tree of life".
rob- "Designs will form a web over time, not a nested hierarchy. They are NOT a feature of design, and a black eye for ID."
I see denial is your main defense.
Rob- "And again, ...which mimics an evolutionary tree of life, with proper branch distances reflecting time, etc..."
There is NO overall Darwinian tree of life
Dr. Hunter et al. (including some more honest Darwinists) have already discussed the evidence for this on this site.
Also:
http://www.sciencemag.org/cgi/content/summary/280/5364/672
Your persistence at skewering data in favor of an inane theory is one of the most striking aspects of all your arguments here.
My OO programming analogy is just that -an analogy.
Software in computers is not alive and does not mutate over time. If it did it would cease to function -completely.
Just as with genetic entropy, which leads to mutational meltdown.
Like I said its a FOREST or NETWORK not a tree.
http://www.ncbi.nlm.nih.gov/pubmed/19594957
http://www.biology-direct.com/content/4/1/34
rob- "RNA world, reverse transcription.... Try again"
RNA world?
Another Darwinian dead duck as you would know if you understood what all the research into that really shows - i.e. intelligent designers can get some interesting results -in a lab with strict controls and purified resources and by controlling the whole intelligently.
Rob- "My argument has already been made."
What argument? You don't even have an argument on this!
Rob-"Selection can generate information."
Totally wrong. I strongly suggest you learn something about what prescribed information is and algorithmic information theory.
Rob- "Roll dice. Random numbers. Now add selection for 6s."
You can't be serious.
Selection for 6's??!!! Robert said...
"I guess that is the difference between you and I. I presented my data that forms a nested hierarchy earlier."
Your data?
Rob you're dreaming. We already know there is no universal Darwinian "tree of life".
rob- "Designs will form a web over time, not a nested hierarchy. They are NOT a feature of design, and a black eye for ID."
I see denial is your main defense.
Rob-"And again, ...which mimics an evolutionary tree of life, with proper branch distances reflecting time, etc..."
There is NO overall Darwinian tree of life
Dr. Hunter and many others (including some more honest Darwinists) have already discussed the evidence for this on this site. Look it up.
http://www.sciencemag.org/cgi/content/summary/280/5364/672
Rob-"...hierarchies in computer software are examples of single designs used in code. They are not nested hierarchies describing the ORIGINS of that software-that is, ..."
You didn't get the point. And nor does any bio hierarchy describe its ultimate origins unless you force it fit NDE theory.
Your persistence at skewering the data in favor of an inane theory is one of the most striking aspects of all your arguments here.
You refuse any other possible explanation in this topic except Darwinian ones. Indeed you can't even see them!
My OO programming analogy is just that -an analogy.
Software in computers is not alive and does not mutate over time. If it did it would cease to function -completely.
Just as in genetic entropy which leads to mutational meltdown.
You should apply your web analogy to evolutionary data - it fits far better than your hierarchy. Like I said its a FOREST or NETWORK not a tree.
http://www.ncbi.nlm.nih.gov/pubmed/19594957
http://www.biology-direct.com/content/4/1/34
rob- "RNA world, reverse transcription.... Try again"
continued...
"RNA world"?
ReplyDeleteAnother Darwinian dead duck as you would know if you understood the research really shows
-i.e. intelligent designers can get some pretty interesting results -in a lab with strict controls and purified resources and by controlling the whole intelligently.
Rob- "My argument has already been made."
What argument? You don't even have an argument!
Rob-"Selection can generate information."
Totally wrong. Learn something about prescribed information and algorithmic information theory.
Rob- "Roll dice. Random numbers. Now add selection for 6s."
Seriously?! Since when does nature deliberately select for anything at all!? You've skewered the whole process in your own desired direction.
You'll need to read the rest before answering.
Rob- "Non-random output via a simple selector. Line up non-random outputs, and what's that, information!!!"
Rob, get out and learn something about information processing.
Your "selected" outputs are NEVER prescribed information, never will be. Indeed, they constitute mere Shannon info.
You have a serious lack of understanding of what kind of information is involved here!
Lined up 6's (which is the only thing you'll get with your filter) have no meaning or function! That is so far from genetic information its ridiculous.
rob- "..Natural selection. Funny how the SELECTION always gets left out..."
No one ever denies selection.
Obviously you don't understand selection yourself.
"natural selection" is a creationist concept - E. Blyth etc. -before Darwin- and many other naturalists - most of which were creationists knew of selection long before Darwin
What is selection? Its just a filter. It never creates anything -certainly not functional information. Selection only operates on information already present! Selection eliminates things - it does not and cannot create anything.
Rob- "He's using an analogy."
How much more wrong can you be!! keep reading ...
Rob: "The genetic 'code' comes from the complexity of our understanding or 'decoding' it. ..."
Where do you get this trash!?
Hubert Yockey is the foremost living specialist in bioinformatics.
He demonstrated that the coding process in DNA is identical to the coding process and mathematical definitions used in Electrical Engineering.
This isn't subjective or debatable or even controversial. It is a brute fact: "Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies." (Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)
"The information content of amino acid sequences cannot increase until a genetic code with an adapter function has appeared. Nothing which even vaguely resembles a code exists in the physio-chemical world. One must conclude that no valid scientific explanation of the origin of life exists at present." -H Yockey, "Self Organization Origin of Life Scenarios and Information Theory,"
Indeed, bioinformatics - which along with biosemiotics is something you're completely ignorant of and yet still trying to disprove to someone who is not ignorant of! Amazing.
" You might want to review your biochemistry."
Duh, that was a quote from Douglas Hofstader, You might it up
Rob:"Where's the algorithm?"
Obviously you don't even understand what we're talking about here.
Rob: "No scientist would argue ...are metaphysical and not dependent on physics and chemistry. ...Nice try though."
Indeed, not even the staunches of creationists scientists would argue such.
... continued
...
ReplyDeleteYou don't know what you're talking about Rob -that's what is devastatingly clear here.
Your basic problem? You understand so little of information processing and theory.
You conflate and mix very different aspects here just like someone who neither sees nor understands those differences.
I'm certainly not going to attempt to educate you in this limited space.
Very poor try Rob
Hitch:
ReplyDeleteProof is not in 1 line insults....
Please present:
1) A nested hierarchy describing the development of a designed product over time.
-Designs will not form nested hierarchies.
-Your reference critiquing nested heirarchies describes examples where nested hierarchies break down-in prokaryotes, and the deep roots of evolution. In higher organisms, they are very obvious, and trivial to generate. I have done so in this thread and others.
And DO YOU EVEN READ THE ABSTRACTS? Goodness. Your choice of reference REFUTES your points. Event eh most complex prokaryotic trees they looked at were discernible, and supported evolutionary models:
RESULTS: A comprehensive comparative analysis of a 'forest' of 6,901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal, particularly among 102 nearly universal trees.....Horizontal gene transfer is pervasive among prokaryotes...making the original tree of life concept obsolete. A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria
2) A disproof of why selection cannot generate novel functions. I argue selection is your intelligent designer. Random+Selection->Not Random
Since we're on the subject, lets bring up an old question of mine:
Every time a protein with novel function (increased information?) is formed, is the designer involved? Why/why not?
3) Why we should ever treat DNA->RNA->Protein as a code, an algorithmic process, that must be designed? (By the way, the whole argument is weak: all known codes/information have a human designer, here is a naturally existing code by analogy, therefore designer). What if DNA is the exception to the rule, as a naturally occurring, evolving physiochemical process?
Back to the arguement:
"Rob: "No scientist would argue ...are metaphysical and not dependent on physics and chemistry. ...Nice try though."
Hitch Indeed, not even the staunches of creationists scientists would argue such.
Ouch Hitch. Foot, gun shoot. You do understand if DNA transcription, and translation are merely physical, and not code, it kinda kills the whole 'information theory' business? And life processes are merely chemical, not algorithmic. Where is the genetic algorithm in the cell? "Code" is an analogy you software engineers have gone too far with. ID has to argue there is more than physiochemistry going on.
You seem to further support this here:
"My OO programming analogy is just that -an analogy. Software in computers is not alive and does not mutate over time. If it did it would cease to function -completely. "
And if software was alive, and did mutate over time, with selection, you know what we might have? Novel algorithms and information. Evolution.
By the way, your expert Yockey, the "foremost living specialist in bioinformatics" soundly refutes ID. Even granting his point that DNA is 'code' he does not find it irreducibly complex, or in need of a designer!!! Pick a better ally to misappropriate quotes from next time!
www.idnet.com.au/files/pdf/Doubting%20Yockey.pdf