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In other words, phylogenetic reconstruction is sheer fantasy …

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Here’s some research done 100 miles down the road from me. Note the sentence highlighted. The actual phylogenies here were experimentally known and yet standard evolutionary theory drew completely wrong conclusions. Oh, but it was a small population, small genomes, and intense selection pressure. Spare me.

“Exceptional Convergent Evolution in a Virus”
Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, Gulati A, Ho C, Molineux IJ.
Department of Zoology, Institute of Cellular and Molecular Biology, University of Texas, Austin 78712, USA. bull@bull.zo.utexas.edu

Replicate lineages of the bacteriophage phiX 174 adapted to growth at high temperature on either of two hosts exhibited high rates of identical, independent substitutions. Typically, a dozen or more substitutions accumulated in the 5.4-kilobase genome during propagation. Across the entire data set of nine lineages, 119 independent substitutions occurred at 68 nucleotide sites. Over half of these substitutions, accounting for one third of the sites, were identical with substitutions in other lineages. Some convergent substitutions were specific to the host used for phage propagation, but others occurred across both hosts. Continued adaptation of an evolved phage at high temperature, but on the other host, led to additional changes that included reversions of previous substitutions. Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data. Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed.

PMID: 9409816 [PubMed – indexed for MEDLINE]

Comments
Jehu:
Phylogenetic trees ultimately fail because the real pattern of life is a mosaic or a web, not a tree.
Were it the case that ALL phylogenetic reconstructions sought ot recontruct the entire history of life, then you might have a point. Let us look at a more manageable scale - look at your family tree going back, say, ten generations. Is it a web, or a tree?
So, the phylogenetic trees always end up containing inconclusive and contradictory data.
Always? Really?
The DNA that leads to one tree could just as easily be used to construct an entirely different tree.
This is true, but very misleading. You can constrain tree reconstruction software to produce arrangements contrary to what the data indicate, and in come software packages you can sort of 'cut and paste' brnaches to rearrange trees. However, in doing so, the reliability scores for the tree drop significantly. I have seen this done in creationist publications, where programs are constrained to prevent humans from grouping with other apes, since the 'researhcers' know that humans and apes are not related. This produces ridiculously low bootstrap values for species that even creationists acknowledge as being related via descent, because it throws the whole tree off, as it were. Simply letting the program produce the tree as indicated by the data will NOT produce any old tree. To claim so is to admit ignorance of the entire field.
Therefore, in order to make the DNA fit the original assumption that a tree even exists in the first place a procrustean bed is fashioned for the data using the twin excuses of horizontal gene transfer and convergent evolution to cover up the contradictions.
The only instances in which this sort of thing needs ot be done is, again, in the case of creationsit baraminological analyses in which outcomes are constrained to reflect Scriptural criteria. Please do not assume that all researchers engage in such manipulation.
A third excuse, mutational hot spots can also be used to defend the tree. However, the mutational hot spot explanation must be handled with care because it is a double edge sword that effectively threatens the very assumptions upon which the tree was built in the first place.
A series of largely unsupportable assertions and a misleading claim. Interesting.derwood
April 26, 2009
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...but scientists try to gloss their dogma in the language of probability
So, apparently, do DI Fellows.derwood
April 26, 2009
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I am wondering why Bill did not bold or comment on this:
Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed.
I also noted the title of the paper: Exceptional Convergent Evolution in a Virus I'm not sure what Dembski =meant when he wrote:
The actual phylogenies here were experimentally known and yet standard evolutionary theory drew completely wrong conclusions. Oh, but it was a small population, small genomes, and intense selection pressure. Spare me.
So, do fasle positives and false negatives in the EF falsify ID? Perhaps if the paper had relied on analogies and bogus probability calculations and unsupported assertions, he would have been more impressed? Heck - maybe we could send a copy to the boys in the ISCID Princeton Office and they could take a look at it...derwood
April 26, 2009
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uoflcard:
If all they have to demonstrate is that it can arise without agency, ID is already defeated.
Why? Such a thing has NOT been acomplished.
It is POSSIBLE, that thousands or millions of genetic mutations occur correctly in a single specimen, creating an entirely new species.
YEC accepts speciation. What's your point?Joseph
April 21, 2009
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uoflcard, whoever that is. Saltation WAS a reality and is believed by this very rational person. There is absolutely no need for any intervention, supernatural or otherwise, in a goal seeking mechanism such as the Prescribed Evolutionary Hypothesis proposes. Where is there intervention in ontogeny? There isn't any. I had planned to abandon this silly "debate" but I cannot abide idiotic statements such as the one that led to this exchange between joseph and yourself. There is no need for any allelic mutations to have a occurred to explain evolution. Allelic mutations never had anything to do with evolution except to ensure extinction. Everything we know pleads for a planned phylogeny now finished. I have presented my case and I might just as well have been talking to the wall. This entire thread has been dominated by a half dozen or so unknowns who would rather "debate" with each other than consider an alternative to Darwinian mysticism presented by a real human being. I hope they know whom they are "debating." I sure don't and don't care to find out. Comments from anonymous sources contribute NOTHING, never have and never will. It is hard to believe isn't it? Not at all. Look around. That is exactly all that you see. "A past evolution is undeniable, a present evolution undemonstrable."JohnADavison
April 20, 2009
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#182 Joseph -
I diodn’t say anything about a possible pathway. They have to demonstrate it can arise without agency involvement. Period.
If all they have to demonstrate is that it can arise without agency, ID is already defeated. Saltation is physically possible. It is POSSIBLE, that thousands or millions of genetic mutations occur correctly in a single specimen, creating an entirely new species. It is astronomically improbable, but still possible. The improbability is why no one believes that actually happened. This is why I say possibility ("can") should be considered along with probability. The example of saltation is an extreme, and not believed by any rational person, but it demonstrates the point.uoflcard
April 20, 2009
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Since Davem woke me up, I might as well show you what scordova did with my last three messages. 379 JohnADavison 04/17/2009 4:39 am e i o. y ai y eae, ooa ai e i oei e o ye. y e ae ei a oe o oi e ae i? I i e you y. ey ae o aei o aiia, a’ y. I i a o eiee i’ i? 380 JohnADavison 04/17/2009 8:28 am a I i you ou aao i ae o e a “i iuee” ui you ae oee you auae uie. oee, I o’ ee o you oiy a ae e ie o i. 381 JohnADavison 04/17/2009 1:07 pm .tfel dna thgir em gniteled erew uoy nehw em ot ti tup uoy sa “flesruoy morf uoy tcetorp ot” gniyrt ylno ma I .laS em natsrednusim t’noD That is the sort of thing one expects at After The Bar Closes. The last one can at least be read, so please do!JohnADavison
April 20, 2009
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I see that "Davem" (#227), whoever that is, waits until I am gone to introduce an incomplete statement in an attempt to denigrate me. That is characteristic of the sort of tactic that typifies internet communication and it invariably comes from some "mighthavebeen" who hasn't the integrity to identify himself. I recommend leaving this sleeping dog alone. If I ever find out who "Davem" is I will expose him to the world as I hope to do with every anonymous blowhard who clutters up internet forums with spiteful, mindless drivel. As David Springer used to say - "Got that? Write that down!" Besides, court cases are not really resolved by debate. If they were there would be no appellate courts, no district courts and no Supreme Court. Even after things finally get "resolved" they are still subject to repeal. The truth has never been subject to repeal. "If you tell the truth, you can be certain, sooner or later, to be found out." Oscar Wilde "Truth is incontrovertible, malice my attack it, ignorance may deride it, but in the end, there it is." Winston Churchill. There is not a word in the entire Darwinian fantasy that ever had anything to do with an ascending, goal directed phylogeny which is no longer in progress - not a single word! "Here I stand. I can do no otherwise." Martin Luther He also said - "When I pass wind in Wittemburg they can smell it in Rome." That is exactly what I have been doing for quite some time. I love it so!JohnADavison
April 20, 2009
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JohnADavison 203 - "I defy anyone, here or elsewhere, to name a single issue, scientific or otherwise that was ever “resolved” through “debate.”" JohnADavison 218 - "Court cases are indeed sometimes resolved by debate..."Davem
April 19, 2009
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Icon, As chameleons go, Icon, you’ve dodged the ball well. All that’s left for you to deny now is that (S)cience disregards agency as a legitimate cause with evidence to support its consideration. Oddly enough this is exactly where you came into this discussion. I had asked another commenter on the thread if he would “be joining materialists everywhere calling for an end to the current default assumption that life began by chance and necessity?" You then took exception to this question by suggesting that ID lacked any real evidence and commented that you “haven’t personally seen any evidence for design in biology” and indeed that you would have “thought that “agency” is readily accepted”. It’s been a shell game of parsed meanings throughout. I’ve repeatedly asked you to be specific and repeatedly you’ve bounced out to “non-natural”, and to “cavemen”, and now to whatever Joseph said. Indeed, you may very well be the perfect example of a materialist ideologue – an enabler of a failed paradigm in the face of overwhelming evidence to the contrary. - - - - - - - - - - Science celebrates positive and parsimonious descriptions of presumed objectivity. But we must never forget that our knowledge is only “best thus far.” Even the most fundamental laws of physics technically must be viewed as “tentative.” We rightly eschew diatribes of metaphysical pontifications. Science proceeds through open-mindedness and the falsification of null hypotheses, not through the rhetorical pronouncement of dogmas. Popper and many since have exposed the problems associated with trying to prove any positive hypothesis [176, 177]. Neither induction nor deduction is foolproof. Theses that cannot be proven ought not to be proclaimed as positive statements of fact. At the same time, we have spent much of the last century arguing to the lay community that we have proved the current biological paradigm. Unfortunately, very few in the scientific community seem critical of this indiscretion. One would think that if all this evidence is so abundant, it would be quick and easy to falsify the null hypothesis put forward above. If, on the other hand, no falsification is forthcoming, a more positive thesis might become rather obvious by default. Any positive pronouncement would only be labeled metaphysical by true-believers in spontaneous self organization. Those same critics would disingenuously fail to acknowledge the purely metaphysical nature of the current Kuhnian paradigm rut [178]. A better tact is to thoroughly review the evidence. Let the reader provide the supposedly easy falsification of the null hypothesis. Inability to do so should cause pangs of conscience in any scientist who equates metaphysical materialism with science. On the other hand, providing the requested falsification of this null hypothesis would once-and-for-all end a lot of unwanted intrusions into science from philosophies competing with metaphysical materialism. While proof may be evasive, science has an obligation to be honest about what the entire body of evidence clearly suggests. We cannot just keep endlessly labeling abundant evidence of formal prescription in nature “apparent.” The fact of purposeful programming at multiple layers gets more “apparent” with each new issue of virtually every molecular biology journal [179-181]. - The Capabilities of Chaos and Complexity (D. Abel) International Journal of Molecular Sciences. 2009, 10, 247-291Upright BiPed
April 19, 2009
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iconofid, Once it is shown that agency involvement is NOT required then ID falls. Period, end of story. Science operates via our existing state of knowledge. Scientific inferences of today cannot and do not wait for what the future may or may not reveal. That said if EVERY time we observe CSI or IC and know the cause it is ALWAYS via agency involvement, then when we observe CSI or IC and don't know the cause, agency involvement is a safe scientific inference. Why does it matter? Experience with reality demonstrates that it matters a great deal to an investigation whether or not that which is being investigated arose via agency involvement or nature, operating freely. So until you have evidence tat nature, operating freely can bring about CSI or IC all you are doing is whining. But somehow I am sure that you don't care.Joseph
April 19, 2009
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Can my six-year old program a computer?
That’s sort of the point. Spiders aren’t taught how to spin webs.-tribune7
And you know that how, exactly?Joseph
April 19, 2009
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I see no point in continuing on this particular thread so I will retire from it now, confident that I have left my convictions behind for others to accpt or reject as they choose. That is all that matters to me anyway. There are matters far more important to me than the mystery of phylogeny. Spring comes to Vermont earlier each year, leaving little doubt in this investigator's mind that we are witnessing what Martin Rees has called "Our Final Century." I hate being right!JohnADavison
April 19, 2009
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It is important to recognize thst it is impossible to reason with ideologues. That does not mean one can't communicate with them. P.Z. Myers has an interesting feature at Pharyngula. While I have been banished from that forum and am now a permanent resident of his "Dungeon," I am still able to reach Myers because I can transmit messages to him. I think anyone can. All you have to do is use your valid email address, compose your message and push the send button. He recognizes your message proving that he received it which is all that matters. 279. John A. Davison - April 18, 2009[Edit] I just sent the following message to P.Z. Myers on Pharyngula. It was accepted but of course will never appear. There are plenty of scientists living and dead who were evolutionists but certainly never Darwinists. Darwinism is dead P.Z. Get used to it as many other evolutionists already have. There is no longer any doubt that evolution WAS a guided process now finished. I love it so! ___________________________________ It is great sport. I recommend it highly.JohnADavison
April 19, 2009
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Icon, If you don’t know the cause, and they don’t know the cause, and no one else knows the cause, then how do we know that agency isn’t the cause? I agree entirely. We don't. Don't mistake Joseph putting words into my mouth further up the thread for anything I've actually said. He said: Joseph: Also it is a bit ironic that icon says that “we don’t know” out of one side of his? mouth but out of the other comes “but we know it wasn’t via a designer”. I doubt if Joseph's fantasies are the origin of your comment, but my position is that we can never know if agency isn't involved in some way in pretty much everything, even if we appear to have very good "non-agency" explanations, let alone in the area we're discussing. I think I said somewhere above that you would be correct in saying that I do "nature of the gaps" in the same way you do "unknown agency" of the gaps. You might want to remember - language, information, and instructions were around and driving life long before there was a caveman to observe it. It is that which must be explained. I don't want to get into semantic arguments, because I'm personally happy with the use of those words in relation to chemical processes, and indeed, I use them. However, the strict traditional use of "language" was only for human languages, although it's recently been extended to other animals and elsewhere. All uses are valid, but I've noticed that some I.D.ers will use the modern sense in which, for example, the chemical messages of ants are language, then associate this with the traditional meaning, and the intelligent design side of our own languages, and start to see sentience in chemical communication and reaction. That point made, I agree with your comment, including the caveman bit. Chemical "codes" appear to be a prerequisite for intelligence, so far as our present empirical observations of the fossil record can tell us, not the other way around. But if we found a large skull of some kind at the ~4 billion year period, I'd consider it direct evidence for I.D. I don't think you should complain that my cavemen are an insult (and they're not intended to be). When someone claims that the only known cause of something is our own volition (and that was the case for the cavemen in relation to fire) then I'm correct to illustrate why that means nothing. If you don't like it, always remember that no-one outside I.D. is forcing I.D.ers to make weak arguments. Because the only time we can be sure of the cause of nuclear fusion is when we do it doesn't mean that the sun was designed. As we already have a reasonable explanation for the formation of stars, few I.D.ers would make that argument, but there are the remains of a natural "power station" where fusion took place in Australia, so, perhaps someone might like to try the I.D. argument there. It won't work.iconofid
April 19, 2009
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...and Icon, I hope you won'tgo back to your cavemen to make your next comment. Its an insult. You might want to remember - language, information, and instructions were around and driving life long before there was a caveman to observe it. It is that which must be explained.Upright BiPed
April 18, 2009
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Icon, If you don’t know the cause, and they don’t know the cause, and no one else knows the cause, then how do we know that agency isn’t the cause?Upright BiPed
April 18, 2009
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Court cases are indeed sometimes resolved by debate and often prove to be in error. Lawyers are not scientists and neither are politicians, or the captains of debating teams. "If you tell the truth, you can be certain, sooner or later, to be found out." Oscar Wilde It is as simple as that.JohnADavison
April 18, 2009
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Upright Biped: And somehow you take from that paragraph the idea that there is no inference to ID being suggested. It is this kind of reasoning that proponents of ID have to contend. It must be difficult. I think I said before that I do not know how "chance and necessity" can account for the systems that they're discussing in that paper, and I certainly can't contradict anything but their final conclusion without searching through hundreds of papers. They, like you, have concluded that every other possibility has been exhausted, and design is required. So, I think I said before that I.D. should definitely claim that intelligent design is required, just as Michael Behe did for the bacterial flagellum. I think it's an ongoing area of research. I think that's what you call "the God of not knowing", but no-one informed me that science would be complete this year. As for the history, the caveman was saying exactly what they're saying in their conclusion in that paper. The same goes for your appeal to consensus power. I think you're referring to my comment that there's no reason why evolutionary processes can't increase complexity and "information". If you disagree, what is that reason?iconofid
April 18, 2009
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Aren't court cases resolved via debate?Davem
April 18, 2009
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Joseph --Can my six-year old program a computer? That's sort of the point. Spiders aren't taught how to spin webs.tribune7
April 18, 2009
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I am no longer allowed to comment on scordova's thread. I have kept a record of all my accepted comments on my "Why Banishent?" thread on jadavison.wordpress.com By comparing that record with the subsequent fate of those comments represents a revealing testimony on the tactics of one "author" here at Uncommon Descent. The most galling aspect of scordova's actions is his insistence that he is "protecting me from myself." I have been quite able to protect myself all by myself all my adult life.JohnADavison
April 18, 2009
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Icon, Well, it seems by your last post that any promise of addressing the actual issues will have to be put on hold. You’ve returned to the safety of fuzzy logic. You start off your post by quoting me when I ask “On what grounds do we justify ignoring agency as a natural force today?” and then you say:
“I understood the point of the paper. As I said, I see no evidence in it for I.D.”
This statement of yours is referring to a peer-reviewed paper in which the authors clearly state: The fundamental contention inherent in our three subsets of sequence complexity proposed in this paper is this: without volitional agency assigning meaning to each configurable-switch-position symbol, algorithmic function and language will not occur. The same would be true in assigning meaning to each combinatorial syntax segment (programming module or word). Source and destination on either end of the channel must agree to these assigned meanings in a shared operational context. Chance and necessity cannot establish such a cybernetic coding/decoding scheme [71]. (emphasis added) In making this statement the authors draw defensible conclusions from an observation-based analysis of the qualitative cause and effect relationship between known causes (chance, necessity, and agency) and their known effects in our natural world. And somehow you take from that paragraph the idea that there is no inference to ID being suggested. It is this kind of reasoning that proponents of ID have to contend. The authors are saying that the pattern in nucleic sequencing is physio-dynamically inert - leading to a conceptual and logical impossibility that physio-dynamics lead to the pattern observed in nucleic sequencing. What part of this do you disagree with? And if you do disagree, then please provide at least some conceptual thoughts as to why the authors are wrong and you are right. The authors are also saying that the algorithmic complexity of the sequencing requires a coordination of disparate systems that is beyond the reach of chance mechanisms given that chance mechanisms operate with equal-probable results at each decision-node along the nucleic chain (the exact opposite of complex coordination). What part of this do you disagree with? And if you do disagree, then please provide at least some conceptual thoughts as to why the authors are wrong and you are right. Further, the authors are saying that the algorithmic instruction in nucleic sequencing are, in fact, imbedded in a conventional code and are therefore subject to a non-physical coordination of symbol meaning between the receiver and the transmitter. What part of this do you disagree with? And if you do disagree, then please provide at least some conceptual thoughts as to why the authors are wrong and you are right. - - - - - - - - - The point you want to return to are the historical mistakes that man has made in the discovery of his world. This is a point that I have already addressed: “…the corrective measure to the historical context you raise is to stop seeing agency where agency is not empirically inferred. It’s been a couple hundred years and several million thinkers since that became clear. Mission accomplished. On the other hand, the irrational corrective measure is to hide our eyes from the evidence and simply say that we must not see agency even under the strongest possible inference to it, and (at the same time) operate with the complete lack of inference to either chance or necessity being able to accomplish what is observed. Now how smart are we?” I still stand by this statement. If you disagree that this is not the appropriate corrective measure, then please be specific in what the corrective measure should be. Also, regarding your cavemen, you have their names wrong. There names are Upright Lemaitre and Icono Hoyle. Now replay your tape and see if it means the same. The same goes for your appeal to consensus power.Upright BiPed
April 18, 2009
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In the meantime I offer some light reading below. http://www.iscid.org/boards/ubb-get_topic-f-6-t-000370-p-108.html April 16, 2009,8:40JohnADavison
April 18, 2009
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uoflcard 169 I'm still trying to figure out why a rodent that had mutated webs between it's digits would have an evolutionary advantage. Furthermore, the webs and digits would have to enlarge through succeeding generations, along with the attendant muscular and vascular changes, until the animal became aerodynamically capable.Davem
April 18, 2009
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I am very much aware of the dual meaning of the word "resolved." I still be back tomorrow morning to see if thare is any answer to my challenge. I am betting there won't be, because there never has been!JohnADavison
April 18, 2009
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77 Pav The change in head morphology is puzzling. I don't see why the lizards with smaller heads would have a tendency to die before reproducing compared to the ones with larger heads, especially if food was abundant.Davem
April 18, 2009
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tribune7:
Joseph, I disagree. I don’t think a spider puts a moment of thought in designing it’s web.
Good luck with your research trying to confirm such a premise.
Can a house spider build an orb web? It’s all in the programming.
Can my six-year old program a computer? I bet if someone could teach the spider how to build something different it could. However one first has to figure out how to communicate with it. Can nature, operating freely create a spider web? If the answer is "No" then it is clear that a spider is an agency and its involvemnet with nature can be detected.Joseph
April 18, 2009
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Any living organism has the ability to be a designer. Joseph, I disagree. I don't think a spider puts a moment of thought in designing it's web. Can a house spider build an orb web? It's all in the programming. “Instinct” is just a word for “we don’t know”. It means in this case 2 a: a largely inheritable and unalterable tendency of an organism to make a complex and specific response to environmental stimuli without involving reason b: behavior that is mediated by reactions below the conscious leveltribune7
April 18, 2009
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OK, JAD. We will make it a "legitimate point of contention"tribune7
April 18, 2009
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