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Author
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Topic: The process of elimination -> Biosignatures & Designsignatures
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Elend
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Member # 326
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posted 18. October 2002 05:11
quote:
1 chance in 10/150 is the threshold set by Dembski. It is this threshold which must be achieved by Darwinian evolutionists to falsify Dembski.
As far as I understand, that limit was computed for elementary particles, but seems to be freely applied to aminoacids, all kinds of molecules, atoms, etc. In fact I think the method of arriving to this limit is subjective to say at least. Perhaps discussing the method is the subject of another thread...
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Cre8ionist
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Member # 140
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posted 19. October 2002 11:08
Hi,
quote:
Let's first deal with a minor side issue or two. I asked you for evidence of ID and that
science would not ignore it, to which you responded with the non sequitur that there are
scientists who claim that ID is outside of science. What relevance does this have to my
claim? Show evidence of ID and science will deal with it. ID however does NOT deal in
evidence but merely the absence of evidence.
Not exactly, what you said before that was
quote:
As far as your claim that science ignores the possibility of ID, that also is
incorrect.
I was merely disputing that, and particularly in the case of scientific naturalism.
quote:
ID does not propose any mechanisms or pathways which
according to Dembski are irrelevant to ID.
Obviously, I don't speak for Dembski, but I think he's
trying to get people to understand that the two questions ( the if of design & the how of design) are separate. So it would probably be clearer to say that pathways are irrelevant to ID detection (one doesn't have to know how a computer is made by an intelligent designer to know if it was made by one), rather than pathways are irrelevant to ID.
More below on this,
quote:
When I asked you why you considered CSI to be calculated from a chance hypothesis you
responded with a truism, CS has to take into account natural mechanisms but that is not
what your calculation did. You merely proposed a purely chance mechanism.
I'm sure I didn't explain clearly here. What I'm saying is that Dembski's falsifiable claim
is that his upper limit shall not be crossed by any "natural mechanism." It's not that I say CSI is to be calculated from a chance hypothesis, it's that the C in SC is calculated in terms of probability. All you or anyone else needs to do to silence Dembski or me on the issue, is violate the upper limit through a purely natural mechanism.
And this is where pathways are important. It is possible to trace the source or pathway of SC in many cases, but there are cases where the ultimate source is more elusive. Some computer simulations for instance, sneak SC in, making a trace difficult. But, in cases where the pathways are known, Dembski's limit holds.
Now, if Dembski's method is wrong, because of some proposed natural mechanism, please demonstrate this.
BTW, rather than repeat your entire post this dovetails into your next charge, namely, that I said that Darwinism must falsify ID. I did not say must, or intend to lay this task entirely at the feet of Darwinists. IDer's should try to falsify ID as well. You do claim however that it is wrong, I don't think it's too much to ask you show why.
quote:
As far as your question about Mt Improbable, an anthill seems far less of a problem would
you not agree?
I agree totally, which is why I said it, Dembski has made the mountain smaller. Forget about mountains, climb Dembski's anthill, that's all we're asking. Can you do it?
quote:
Now to another one of your claims. I asked about repetition of the protein sequence. Let
me ask you something, if a gene duplicates does the information double or not?
Correct me if I'm wrong, there would be the same qualitative amount, but a different quantitative amount. But let me try to give an example of what I see here with this particular protein, and again, I'm not a bio-chemist or biologist, look at the picture again and imagine it as a full house, in a game of poker, i.e., 3 of a kind + a pair, now you've got 5 specified cards, they must all be there, remove any one of them and the specificity of the hand changes, all are combined to make a different specified object. Therefore, the probability of getting all 5, is smaller than getting 4 or three or 2 etc....But again, even if you disagree here, it won't be very long until we're designing and creating indisputable biological SC all over the place.
In any case, this brings me to something else, why would you even bother discussing the case when you've now admitted that it doesn't matter whether humans create biological specified complexity or not?
Obviously it matters to me, and I'll explain why, but since it doesn't matter to you, why did we even have this conversation?
Anyway, let me recap:
You closed out your section on the scientific veracity of the martian biosignature with
quote:
Not observed naturaly on earth
Yet to be synthesized.
I closed out my section (based on your method), on the scientific veracity of the designsignature with
quote:
Biological specified complexity not observed to originate naturally on earth
Can only be synthesized.
Now, if biological SC could not be synthesized, or, it could be observed to originate naturally, that would be a serious problem for ID, since neither of those things is true though, this gives us the upper hand, in my opinion. We can observe the intelligent creation biological SC, and we cannot observe the natural creation of it.
quote:
When I copy parts of a text that are not CS but together they add up to something that is
CS does this not prove that CS can be generated by such approaches as copying and
pasting and an occasional copying error ? Does that not sound a lot like Darwinism?
That would depend on whether they were random copies or directed copies. Remember, Darwinism, in simulation, is incapable of putting together long pieces of text without going through show stopping transitions.
quote:
And finally you seem to still be claiming that biosignatures and ID are similar but as I have
shown biosignatures propose a theory that is not based on elimination strictly but rather
on the fact that on earth the magnetite signature seems strictly related to biology and
that chance is an unlikely candidate.
What theory does ID propose? I am still waiting....
Seems that ID and biosignatures are inherently different. ID can never be tentative since
that would make it open to false positives and according to Dembski that does not happen
but if it is not open to false positives and if it is never tentative then how can it be
falsified? Dembski hints to the inability to falsify it when discussin Oklo reactor, even if it
could be shown that Oklo is CSI, he would then not allow for elimination of ID as the
explanation despite the absence of any supporting evidence that ID was involved. At most
what can be disproven is a negative claim, xxx can never arise naturally. But that hardly
disproves ID.
Well, I think you're mixing terms here, unintentionally, and we all do it. ID and ID detection, it is Dembski's
detector which can be falsified, whether or not we'll be able to falsify the notion that God created the universe, is another question. Don't think we need to discuss that one here though, I'm just here promoting the similarity aspect of biosignatures and designsignatures. See early on in this thread, where I use your methods to demonstrate that the approach is scientific.
One last thing, whatever the outcome of this overall debate, I recognize that
Behe and Dembski will have contributed no less to it's solution than did Darwin or Paley.....................Cre8
I removed a snippet about cards being replicas (an inadvertent mistake) due to early morning
drowsiness I hope ![[Embarrassed]](redface.gif) , addressed by Frances in the next post. Suits do not matter in a full house.
[ 19. October 2002, 17:40: Message edited by: Cre8ionist ]
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Frances
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Member # 169
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posted 19. October 2002 15:31
Dear C
You still seem to be under the impression that science ignores the possibility of ID. As I have shown that of course is incorrect UNLESS you consider ID to be dealing in supernatural causes. Indeed then science cannot deal with ID but I do not believe that Dembski proposes supernatural 'interventions' through supernatural processes.
To understand that ID is not being ignored, one has but to point to archaeology for instance or forensic sciences or SETI.
When you claim 'scientific naturalism' are you talking about methodological or philosophical naturalism? Science deal merely in methodological naturalism and unless your claims are that ID are ONLY supernatural mechanisms, your claim that science ignores the possibility of ID are erroneous.
Now we get to the 'meat of the discussion' ID pathways. Indeed Dembski suggests that the historical or causal pathway of the suspected designed object is irrelevant but it is trivial to show that one does have to understand this in order to propose probabilistic measures.
When you claim that 'one does not know that a computer was made by ID' you raise a strawman since we do KNOW and OBSERVE such construction, we know the causal pathway. But for the flagellum for instance we do not have any such knowledge. We should thus not let our ignorance conclude ID.
Now about falsifiable claims. Of course CSI cannot be generated by natural processes since then it would not be CSI anymore. Lets step through the Dembski filter once again to realize that the problem is for ID to show that something IS CSI. After all when/if a causal natural pathway can be shown then the object is not CSI anymore since its probability is much larger than the lower bound.
Thus, one may reverse the claim by stating that Dembski has yet to show that CSI systems in biology exist.
But now you reverse your course, pathways are suddenly important again. Of course they are since that's what ID is all about. Now your claim that computer models sneak in CSI. An interesting but somewhat unfounded claim. Could you for instance explain where CSI is smuggled in in the traveling salesman problem? Or what about the CSI as found in simulations by Tom Schneider for instance. And IF it can be shown that algorithms can generate CSI then nature surely can do the same where information is imparted on the genome through the environment?
There are NO known pathways in biology that have been under Dembski's EF scrutiny thus your claim that 'in cases where the pathways are known' Dembski's limit hold seem to be meaningless. Dembski has applied his filter to some trivial examples that are not beyond the usual scientific approach of detecting human design.
The question of course is: Is the 'design' found in nature natural or intelligent?
Can one climb Dembski's mountain? Of course, it's trivially simple. Propose a mechanism for the flagellum and wait to see if Dembski can provide us with the probabilities to disprove it. :-)
You claimed that Darwinism should prove itself but that is not how science works.
Now about gene duplication. I was pointing out the repetition in the protein. So its qualitatively the same but quantitatively different? How do you suggest this to be possible and if it is quantitatively different then information is different?
I do not understand your poker hand example though. The likelihood of any given hand is the same. If you suggest that the cards in 3 of a kind are replicas then you surely are playing with a crooked deck since there is only one of every card in the game (unless there are some spare aces up one's sleeves :-) )
So lets come back to my question: Does gene duplication increase the information?
Now back to the bio signature:
You claim that biological specified complexity not observed to originate naturally on earth. To which I claim that such claim is tautological since there is no such thing as biological CSI since it would not be CSI anymore. There are no competing theories so far for biosynthesis but there are competing theories for biological complexity.
CSI is not a very useful concept anyhow what is more useful is: Are there 'chance' hypotheses that explain XX? And the answer is YES. It's up to ID to eliminate them just like biosignatures. The difference is that biosignatures are tentative while ID cannot be tentative since it has no false positives...
Now about these 'show stopping transitions" that you speak about with Darwinism? Could you provide some evidence of these?
But IF you claim that copying and pasting increases CSI then that's exactly what Darwinism does.
Now about Demsbki's ID detector, the detector cannot even be falsified what can be falsified is a claim that system X cannot arise naturally. As far as the 'claimed similarity' between biosignatures and ID, I believe that I have dealt with them by pointing out that there is NO id hypothesis to be falsified. Merely a claim of ignorance.
Have Dembski and Behe contributed to the debate? Well they may have raised some interest in dealing with issues such as biological complexity but I doubt that a claim of ignorance without any alternative detailed hypotheses are relevant to scientific inquiry.
So let me recap:
Biosignatures and ID are very different, one relies on positive evidence and is falsifiable, the other one relies on absence of evidence and is not really falsifiable.
If copying and pasting increase specified information then why can natural mechanisms such as gene duplication not achieve the same? If 'algorithms can smuggle in SI' what prevents nature from doing this as well? After all an algorithm is just another chance hypothesis?
I hope that my contributions have clarified the many problems with ID. As a Christian I have no problem accepting a Designer but I would not even consider trying to formulate a scientific hypothesis to detect His Design. Who would want to falsify such anyway....
My Designer is evidenced in Faith. As it should be.
Added:
Response to C's statements below:
You still seem to be under the impression that ID should be the default position when in fact the position should be, default 'we don't know'
Now, if science proposes a Darwiniam mechanism for the flagellum, there is no requirement for it to perform probability calculations. Science proposes a hypothesis which is open to falsification. Does ID take on the challenge to falsify such pathways? realize taht there is no need for science to falsify the negative claim of ID since ID does not propose any testable hypothesis. It is enough for science to propose hypotheses to be tested. In fact such hypotheses are quite common place, Dembski calls them 'just so' stories because as is with any natural mechanism, the likelihood that probabilities can be calculated are minimal thus a probability approach seems useless but that does not mean that there are no other ways to falsify these hypotheses but those involve hard scientific work.
Thus as I have shown there is no reason to believe a priori that there is CSI in nature, in fact claims of CSI can only be evaluated when chance hypotheses have been proposed.
Climbing Dembski's ant hill is simple since the hill requires one to only propose mechanisms. If Dembski has better hypotheses or if Dembski can refute the hypotheses then we can discuss what the future is but why one should presume CSI because we may be ignorant of the probabilities involved seems unnecessary.
In fact there have been instances in which people have shown how complexity and information can be added by chance/regularity processes.
Your poker hand was meant to discuss something about the gene duplication and information. Now it is meant to show that if one pre-specifies an outcome (the hand to beat) that probabilities are different but that's the problem with pre-specifying. It already introduces information.
My question is simple: Would gene duplication increase information or not? What about gene duplication and specialization of the duplicated gene while the original gene retains its function? Would that increase the information?
Such events have been documented in literature, I am merely trying to understand what you believe their relevance is to the discussion? I would say that the similarity with your poker example suggests that information did increase.
So when is duplication of information an increase in information and when isn't it?
Let's assume that we start with the original protein with six duplications and then an accidental mutation removes one of the proteins. Would this be an increase in information if now the protein seems to inhibit HIV? What about a single mutation which now inhibits malaria infections?
Without knowing the causal history of the protein, how can we determine if it is CSI? How can we determine if and what caused it to be information? Lets assume that HIV did not exist yet, would such a duplication be increase in information? Or is it merely based on an after the fact specification?
As I have shown it is not trivial to show CSI in nature even when there are ID pathways. Because ID ala Dembski does not really depend on such indirect evidence, after all all it shows is that humans can create certain proteins, what it doesn't show is that such proteins are CSI. That depends on elimination of probable pathways.
In fact when looking at the design of the 5-helix, it is clear that the researchers based it on N36/C34 six helix bundle. Did their changes to this original protein increase or decrease information? After all they deleted one of the helixes? Can information be increased by deletion? Is the 5-helix more specified than the original protein? That surely depends on the specification would you not agree? The specification is arbitrarily set to be binding to HIV. Certainly the original HIV virus from which the protein was obtained seems specified "spreading HIV" and more complex than the 5-helix one. So did the humans create CSI? Or merely moved it around? But that depends on whether or not the original HIV protein was CSI? By adding or deleting some parts the researchers either moved around pre-existing CSI, which does not help one deal with the issue whether or not humans can create CSI, and opens the door for Darwinian pathways which delete and add amino acids appropriately.
Could random mutation and selection lead to such a system and what would that say about mutation and random selection?
Or one argues that the CSI of HIV is specific to 'infection' and that thus its specificity wrt 'binding to the HIV protein' was low and the steps taken by the researchers infused SI into the protein. But then again one has to address if this lead to CSI, which can only be resolved through elimination of competing hypotheses which at this moment may be lacking. But should or ignorance then be used to infer CSI and ID? Certainly the steps taken by the researchers are all natural thus leaving it open to natural pathways.
quote:
The envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) consists of a complex of gp120 and gp41. gp120 determines viral tropism by binding to target-cell receptors, while gp41 mediates fusion between viral and cellular membranes. Previous studies identified an alpha-helical domain within gp41 composed of a trimer of two interacting peptides. The crystal structure of this complex, composed of the peptides N36 and C34, is a six-helical bundle. Three N36 helices form an interior, parallel coiled-coil trimer, while three C34 helices pack in an oblique, antiparallel manner into highly conserved, hydrophobic grooves on the surface of this trimer. This structure shows striking similarity to the low-pH-induced conformation of influenza hemagglutinin and likely represents the core of fusion-active gp41. Avenues for the design/discovery of small-molecule inhibitors of HIV infection are directly suggested by this structure.
Source
and
quote:
The design of 5-Helix was based on the N36/C34 six-helix bundle crystal structure (7).
Source
So how does this help us find CSI in nature? Well, the only way to find, without false positives, CSI in nature is by showing that no chance and/or regularity hypotheses could generate the structure. But such is not a priori logical and thus unless we can show that we have indeed eliminated all such hypotheses we should not jump to an inference of ID since that would make ID fallible (false positives). But the latter one would also make ID scientific. But if ID is open to false positives then it is unreliable and thus we need additional evidence to support our claims of ID. Thus ID becomes tentative. As such it has to show that ID is a better hypothesis than other proposed hypotheses or yet to be proposed hypotheses leading to an interesting contradiction that ID can never be shown to be the better hypotheses since there is not ID hypotheses.
And there are additional problems. If inhibition of HIV infection is evidence of CSI, then what about natural occurrences of such inhibition?
quote:
Population geneticist Stephen O'Brien of the National Cancer Institute, his NCI colleagues Michael Dean and Mary Carrington, and their collaborators provide strong confirmatory evidence that people who have two mutant copies of the gene for CCRS (also known as CKRS), the chemokine receptor that HIV uses when it initially infects infects white cells, are highly resistant to HIV infection. Another, entirely new, finding is that people who get infected with HIV, but have one mutant copy of the CCRS gene, progress to AIDS more slowly than do people without the mutation. (Cohen, 1996, 179
Did the mutation(s) that caused this infuse SI? Did this happen before or after HIV arose?
I do no consider it irrelevant that we can create CSI, I am saying that it has not yet been shown that CSI has been created? Specified? Depends on circumstance, complex? depends on the presence or absence of natural pathways.
Biosignatures have shown that there exists such signatures generated by organisms on earth. ID has yet to show that CSI exists wrt biology. Whether or not something is CS is of great importance to your claim of similarity. And even then this does not prove anything about natural occurrences of structures such as biosignatures.
[ 19. October 2002, 17:38: Message edited by: Frances ]
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Cre8ionist
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Member # 140
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posted 19. October 2002 16:42
Hi Frances,
I'll try again, last time though, I think we've run past each other several times.
You claim it's easy to climb Dembski's mountain, which I called an anthill (compared to what
Dawkins' claimed to climb), please do it with whatever pathway you can so it can be evaluated.
If you can easily do it as you claim, I'll drop my adherence to Dembski's designsignature. If you cannot, please understand that you're overstating your case.
The poker hand is meant to point out that if you need a full house to win, one or two pair won't do. The protein could not be specified without the additional segments, just as the full house cannot be specified without the right cards. 1 of each segment wouldn't do, nor would 1 of each number do.
As to the amount of information, again, 2 copys of Dembski's latest book would seem to be quantitatively more info (a word count is double that of one book), but qualitatively (no new information), the same. But the protein is unlike the book, in that
it's structure depends on the extra information, so it's not superfluous, but necessary to the specificity of the protein. You may see the word "the" many times throughout this post, should we only count it once if we calculate the probability of this post being typed randomly?
Anyway, you consider it irrelevant whether we can create biological SC anyway, remember?
I still maintain that the use of biosignatures is no different than the use of designsignatures and no objection here really changed that, our biggest issues have been over whether or not a given protein is SC according to Dembski's formula.
I'm tempted to engage you on your religious faith, but this isn't the place for that,
however, I will talk to you again, I'm sure............................ Cre8
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Cre8ionist
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posted 19. October 2002 18:00
Hi again, your latest post raises good questions, most of them answered in Spetner's "Not by Chance." I'll pass for now on a detailed response, but let me know if you've read the book. Perhaps someone else would like to carry on, I've got to tend to some other internet related stuff which is getting backlogged.......................Cre8
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Frances
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posted 19. October 2002 18:11
See my addendum to the posting above. One more issue to discuss, does adding multiple copies of a word add information?
Perhaps its important to define the meaning of information here, is it Shannon information? Or is it lexical information. We have to be careful because the term information has a lot of meanings but is quite limited as used by Dembski.
On a lexical level 'the' may or may not add information that we could not obtain from context but on a Shannon information concept information has quite a different meaning.
To give an example, random changes in general will tend to increase the information in a Shannon sense. For instance the string
qmnfsdeqwmfsdjqw
has more information than the string
aaaaaaaaaaaaaaaa
But if one wants to use complexity in the sense of 'meaning' then it depends on circumstances. Which leads to the interesting conclusion that information depends on specification. Before the onset of HIV, the mutations that led to immunity to HIV had limited specification but once HIV arose their specification happened (albeit after the fact).
Information in the sense used by Dembski is nothing more than the negative log of probability however. High information means low probability wrt the relevant hypothesis. Thus gene duplication would have low information since the new structure is highly probable. But information used in this sense makes it hard to judge the information present since it depends on the hypothesis being tested. I would say that the probability of gene duplication as evidenced in the designed protein is quite high as well, thus the information would be arguably quite low with respect to the hypothesis of intelligent design. But to infer Dembski's measure of information one needs to look at other hypothesis than ID. Thus his meaning of CSI is only that which is too improbable under all natural hypotheses. So did humans generate CSI? Certainly the probability of the protein under the hypothesis of human design seems to be quite high and thus the information imparted seems to be quite low. But CSI is defined not under ID hypotheses but under all other hypotheses and as such it is hardly self evident that CSI has been created especially since the steps taken were purely natural. Now one has to eliminate all known and unknown pathways to such structure that involve chance and/or regularity.
Instances of human design may or may not be evidence of CSI but that still does not resolve the issue of whether or not biology complexity contains CSI or not.
Lets assume a biological structure such as the flagellum. What is the probability of such a structure under the hypothesis of design? We really do not know now do we since there is no pathway for us to study unlike in the case of the designed protein. In the case of the designed protein the probability would be high thus the information would be low. But what about the flagellum? How do we determine the probability of design here without knowing the pathways?
Dembski is quite explicit in his latest claims that ID does not deal in pathways so we cannot use the pathway in the case of human design of the protein to show probability but it we would, the information imparted would be quite low by the hypothesis. In fact in case of probability 1, the information would be zero. No specified information would be imparted by the intelligent designer. Does that not seem to conflict with only ID can impart complex specified information? In fact under the inverse approach of using a filter, would one not come to the conclusion that ID cannot generate natural-CSI? Well, that depends on how one defines CSI. In the case of Dembski it is used only wrt natural processes and chance and lets call this ID-CSI as opposed to natural-CSI but then one wonders without knowing the exact pathways how one can determine that CSI content since it depends on the hypotheses involved.
ID-CSI merely means low probability of chance/(law like) regularity
But one could then argue that Intelligent Design cannot add natural-CSI since the probability of the design hypothesis is too high.
So how does one resolve this problem? Simple by generating probabilities for all hypotheses involved. But that's a problem for intelligent design as it is formulated right now since its probability is merely 1-P(E|H) but that requires one to know all relevant H's and we cannot know them all so we cannot really determine the probability of ID. So how can we then determine ID when ID is merely NOT-chance? And if it merely NOT-chance then is it not really an argument from ignorance?
Hmmm time to step back and see where this discussion goes. My head is running over with terms like CSI, probability, information.
I guess my intent was to show that information is a difficult term and that one should not confuse our intuitive understanding of it with how it is being used or we run the risk of equivocation.
Thanks for the reference to Not By Chance which I believe suffers from the same problems. When is a mutation an increase or decrease in information? Spetner iirc argues that mutations merely decrease information but that depends on the hypothesis at hand, and thus the specification. Let's say that we have a protein X with function F_X and a mutation of protein X, name X' with function F_X'.
Wrt to function F_X the information surely decreased when X mutated to X' but it increased with respect to function F_X'. The same applies to the designed protein, which was a variation on the existing proteins in HIV. Certainly the tinkering destroyed the ability of the protein to infect the cells thus information would have decreased but information also increased wrt the function "inhibit HIV infections".
Spetner's concepts seem also self contradictory in that a reverse mutation should also decrease information but then the round trip X -> X' -> X would lead to an X with reduced information. Enough roundtrips and information would be negative... So the concept of information is a tricky one indeed.
So the claims found on for instance here seem to be utterly self contradictory
quote:
He then examines the classic textbook situations that have been used to tell students that, since adaptation by mutation and natural selection is happening in front of our eyes, this process only needs time in order to perform all the miracles credited to evolution. Spetner shows in exquisite (but clear) detail that where these changes are by genuine point mutations (rather than by the 'switching on' of existing genes) they are all, without exception, losses of information.
[ 19. October 2002, 18:23: Message edited by: Frances ]
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