intelligence creates intelligence

[Ringer]

Some of that evidence demonstrating the difficulties with mindless natural processes are in that thread I posted earlier. The problem is it's a very long thread and in order to be able to get any further you'd need to have read it and be ready to dispute certain points.

 

However I can't really expect you to plough through all of that by yourself. So perhaps we can use that as a reference and I will sort of talk you through it. Then you can dispute certain points. Unfortunately we do have to do that at some point though, or else you'll be forever waiting for me to "present evidence that mindless natural processes have limitations of relevance to evolution and irreducible complexity", and I'll be forever telling you to "read all of that link".

 

Well if we are talking about not replying to points how about you skipping every link I've sent your way without reading it, I can tell you didn't read them because they address plenty of your 'points', and completely ignoring every single call for evidence. I have personally asked for you to back up your statements with peer-reviewed evidence and you only send me back to the same site over and over again. But thank you for your so generous offer to talk me through the link, but, alas, I have a reason for not reading all of it. You see when someone starts off with a misunderstanding of what they are arguing against I see no reason to continue to waste my time reading a paper written by someone who doesn't understand what they are trying to refute. I see that the author understands the working of proteins and genetic mechanisms, but he misunderstands basic standpoints of evolution. Why would I continue reading a long paper that is introduced with a flawed premise? But, just for your pleasure, if I get extra time this weekend I will go over your link and give you, point by point, what I believe to be wrong with it.

 

We have been waiting for you to produce something real, and I have personally refuted every misunderstanding or anything I don't believe is right. So far you have disputed me by just telling me there's all this evidence you know of that disagrees with what I am saying without ever showing it to me or just plain skipping over that part of my post. I have no idea why you would say it's unfortunate we have to go through your points and discuss them unless it makes you nervous to be shown that you are mistaken.

 

 

 

But before you can say that and have that kind of a statement taken seriously, you'd first have to have gone through the matters in that link on the difficulties of evolving IC machines (like the flagellum). I'm not ahving a go at you, but I note that you are saying repeatedly in this post that I haven't yet offered you any evidence, yet admitting that you haven't read that article in full. Now as I said I didn't really expect you to read all of that, because it is just too long. On the other hand, given that you've admitted that you haven't yet read it, I suggest you back off on the "lack of any evidence" claim for now - at least until we have gone over that article in a bit more depth.

 

I read most of it, and it doesn't give evidence. He had no trials, no data of his own, no supporting research, etc. All he has is pictures of how a flagellum is put together and speculation that it couldn't be that way because he can't think of a way that it could have come about. Supporting a hypothesis is not about speculation, it is about data and evidence. Sure he dresses it pretty fancy but it just still rubbish. We have linked ways in which it could have evolved naturally and your response is just, "Well that's just speculation too." The difference is you have to defend your theory against these types of things for it to hold up. We just defended ours and how it could work out that way and you just say you can't prove it. Well at least we have a feasible mechanism that actually explains something instead of throwing our hands up and exclaiming, "well darn I just can't figure it out, it must be impossible."

 

 

 

It does apply to everything. An eternal mindless universe, and an eternal intelligence. For the same reason that people don't feel the need to explain an eternal universe or eternal energy. If something actually is eternal, it has no origin to be explained. Something after all had to be eternal. We just don't know anything about what exactly that eternal something was. We certainly do not know that whatever the eternal something was had to be simple. That idea is nothing more than a hunch based on being comfortable with the idea of simple going to complex. Something I may add that we never see occurring in mindless nature. But whether simple or complex, something must have been eternal. It is in fact impossible to get something out of nothing. The alternative, that something popped into existence from truly nothing at all (no energy, no laws - nothing) is an impossibility. That is far more illogical a belief, than the idea that something must have always existed.

 

I believe we have an explanation for the universe (that's probably not eternal by the way), but seeing as it is that you have a physics degree I'm sure you knew that. But on the other hand if you meant an explanation for why the universe is here is a pointless question. It is here, we know it's here because we are here. Asking why is philosophical, not scientific. Scientifically we ask if something is here, we know the universe is here so there's your explanation on that. And why do you say that it is more illogical to believe something came from nothing, your belief if you think that god created everything because he had nothing else to work with, than something always existing.

 

Apparently you didn't read, surprise, my link about the yeast forming into proto-multicellularity if you don't think we have ever seen something go from simple to complex. Or maybe you don't believe that our ability to digest lactose into adulthood is a fairly recent incident.

 

 

How is it not the same thing? Explain your objection. A positive SETI inference is the acceptance that it is most likely that an intelligence manipulated laws so that a signal was produced which would most likely have not been able to happen as the result of mindless nature.

 

Sorry I forgot that the signals we produce are supernatural as well. I guess I should call the James Randi Foundation and claim my prize by making him listen to the radio.

 

 

Extra-terrestrial life forms, in all likelihood, will be natural just like us. I'd like to hear your explanation on why they wouldn't be.

 

 

How is intelligence not natural? Because whenever I use the word natural I am referring to mindless natural processes. An intelligence (in a body) is not mindless nature. Mindles nature is natural laws with no intelligence. You claim that intelligence is derived from mindless nature, however that is not known. To assume that to be the case is begging the question that this thread is named after in any case.

 

How about you just use the vocabulary that we all agree on here instead of making your own uses. You have used mindless natural process or MNP when you mean that and that's fine. But when you try to hijack the word nature and use it as such you are creating a gap in our ability to communicate. Intelligence is natural and as such is part of nature.

 

It may not be completely know, but that is what all the evidence points to, except your proof that you are so unwilling to provide.

 

 

I apologize because I don't have the time to respond to the rest of this in detail at the moment as I would like to. So instead of giving you a crappy reply I will respond to it, as well as the link you provided and perhaps others you provided for other people if time allows, in due course.

 

 

[Monsters from the ID]

The idea that evolution is something like wondering through a maze is totally off base, if you must use that analogy then it should be a group of people who explore the maze over many generations and tell each succeeding generation about the false turns so they won't make the same mistakes, reproduction with inherited variation is not like one individual doing anything. I read 800 words a minute give some links to read so I at least know where the stuff you are saying is coming from... right now it seems to be coming from your rectum....

 

 

Also, that model ought to be easily adaptable to populations. You just plop down a whole lot of individuals corresponding to the population onto the plane. Then as they each mutate they go on random walks.

 

Once a population has a set of useful genes (and functinal RNA's), then we could imagine individual organism as having an placeholder existence on each island that corresponds to a functional gene / functional RNA. (A bit weird, but it's hyperdimensions compacted down to 2 dimensions after all). But as far as information about prior false turns? I don't see how that figures in, unless you're just referring to the fact that once an individual is on an island, then it's projeny will tend to stay on the island as well (except that sexual recombination will alter the positions of the progeny according to how their recominations work out. In some rare cases this may push the progeny off some of the islands and into waiting sharks, in the case of some kinds of inheritable lethal diseases.

 

But the central question is - how does a set of initial populated islands, branch out to discover and inhabit the other islands that are waiting out in (potential new useful genes & functional RNA')? The problem is the large distances needing to be covered, and the fact that once in the ocean of nonfunction for some tract of DNA, there is no guidance towards some new island. Only random swims and teleports to random new locations are available. Since the ocean is large and the islands and island clusters are small, then this presents a mechanism problem for the evolution of the protein machinery that now exists in life's repertoire. And not only that, but even evolutionists admit that this must have been pretty much already evolved and in place a billion or two years ago.

 

Here is another site which has been an interesting read: Detecting Design

 

 

 

The following is addressed to Mr. Ringer:

Sorry if you're feeling a little peeved, but you're going to have to evolve some more patience than you're demonstrating at the moment. This discussion is likely to be going on for some months, if we are ever to cover things in any level of detail. I clearly explained that I intend to get to your links in time. I did however cover the video link, but hold my feet to the fire on that if you wish to. Time is what I have plenty of (except I do not intend to spend too many hours of each day glued to this forum).

 

Anyhow, as I said to Moontaman earlier, don't worry, you're not performing for the world here. It's just a forum for science types. It's a pretty good forum, but it's not world class debating. Still, we do need to go through things point for point like I said. You don't get anywhere by making blanket denials. You need to deny first and explain your denial later. And then have an argument about it - over and over and over. You won't get anywhere by trying to rush things along too much. That's not going to happen. Now you claimed that myself and the author of that website have no understanding of how evolution works. If that is really the case, then I will be expecting you to correct me as we go through it, which will take some time, unfortunately. Get used to waiting.

Edited July 2, 2011 by Monsters from the ID

[Moontanman]

Thanks for the link Monster from the ID, lots of misrepresentations, fabrications and out right lies there but that is par for the course from creationist supporter. Now i know who you are and what you are, my conscious will not bother me if i don't get caught up in this debate because like all creationists i doubt you are looking for knowledge, more likely you are looking to ask a question that cannot be answered so I'll give you one, who created God? So far all you have done is obfuscate the issue with straw men and meaningless analogies, your island analogy fails due to the nature of the premise of isolated islands, no organism or chemical in solution is isolated, the very nature of biology is that organisms interact with each other, they mate, pass on genes with inherited variation. For your analogy to work the islands would have to be able to reproduce and come into contact with each, I also thing that virus's have a big role to play in life's very early evolution but that is another line of reasoning. If you continue to obfuscate the discussion by invoking things like ID and using links that suggest not only a total misunderstanding of evolution and spread out right lies I see no reason to take you seriously.

 

From your link:

 

Yet, this disguised religious philosophy has taken the scientific community by storm. The vanguard theory of evolution has taken on an almost sacred status. Who dares question it or openly admit that they do not see the emperor's clothes without putting their reputations and, on occasion, even their careers in jeopardy? I for one have been honestly looking for the emperor's clothes for some time now. But, the more I look the more naked he gets.

Surprisingly, I am not alone in my blindness. A number of very highly educated men and women of science have and are openly questioning the sacred status of the theory of evolution. Of course, we may be too ignorant, stupid, or insane to see the rich clothes that are right there before our very eyes. However, never underestimate the "crazy" or the "blind". History has often shown that those who were crazy and blind in their own day turned out to be right after all.

 

This quote is a classic, a number of scientists are openly questioning the sacred status of evolution, quite the misrepresentation there isn't it? The insinuation that evolution is sacred in some way? Or that scientists are divided in some significant way on the theory of evolution? Are you gonna tell us it's just a theory next? Ahh the smell can't you smell that smell? The link you provided is a creationist link to a guy with a medical degree not a science degree and he is using his MD to try and sell his male bovine excrement (for $12.95) and that is worse than sad, it's wrong, and he is wrong or more accurately lying.

[Monsters from the ID]

Thanks for the link Monster from the ID, lots of misrepresentations, fabrications and out right lies there but that is par for the course from creationist supporter.

 

That's OK. I'm pretty used to it. When discussions get going, sometimes the other side will throw stuff they hope will stick as part of their strategy! As long as you don't hurt yourself doing so, I don't see why that will be much of a problem.

 

Now back to the discussion about protein evolution ...

 

 

, your island analogy fails due to the nature of the premise of isolated islands, no organism or chemical in solution is isolated, the very nature of biology is that organisms interact with each other, they mate, pass on genes with inherited variation. For your analogy to work the islands would have to be able to reproduce and come into contact with each (other).

 

You've mistaken what the analogy is about. Probably because I didn't take the time to specify exactly what it meant. My apologies for that.

 

The 2D plane represents the hyperdimensional coordinates of DNA sequence space as compressed into a 2D surface. For example, a DNA sequence 500 codons long could be thought of as a coordinate system having 500 "dimensions", and each of these 500 dimensions can have 4 possible values: A, C, T or G codons. In such a space there is 4 to the 500th power of possible configurations ~= 1E+301, a large number with 301 zeroes. But to get a visual idea of such a space, we can informally imagine it to be compressed down to 2 dimensions.

 

The islands represent the coordinates of potentially functional proteins (or maybe functional RNA sequences). When you said that no organism or chemical is isolated, well, thats true as a stand-alone statement, but it is irrelevant to this analogy. A bit like you telling me that islands in the ocean consist of isolated populations of humans, and me objecting that "no man is an island!" It's just a category error, but possibly my fault in this case as I may not have explained what they represented thoroughly enough.

 

But you do realize that these Islands certainly do not mate with each other, because the islands are not organisms, they are maps of the outcrops of functionality (and fitness of that function) in protein sequence configuration space (that has been contracted from hundreds of dimensions down to 2 dimensions for the purposes of being able to form a mental image, thus an analogy.

 

If you continue to obfuscate the discussion by invoking things like ID and using links that suggest not only a total misunderstanding of evolution and spread out right lies I see no reason to take you seriously.

 

I don't care if you take me seriously or not. Your schtick is never to take creationists seriously. That's irrelevant to the actual discussion. I just want to see if you can refute my arguments, or not, once they have been thoroughly discussed.

 

 

This quote is a classic, a number of scientists are openly questioning the sacred status of evolution, quite the misrepresentation there isn't it? The insinuation that evolution is sacred in some way? Or that scientists are divided in some significant way on the theory of evolution? Are you gonna tell us it's just a theory next? Ahh the smell can't you smell that smell? The link you provided is a creationist link to a guy with a medical degree not a science degree and he is using his MD to try and sell his male bovine excrement (for $12.95) and that is worse than sad, it's wrong, and he is wrong or more accurately lying.

 

It doesn't matter what you think the creationist medical doctors arguments smell like! What matters is whether you can refute (or ask someone else to refute for you) those smelly arguments he presents demonstrating the infeasibility of the notion that the evolution we observe today, could do anything like having taken us from a common ancestral single celled lifeform(s) to the biology that exists today. I guess it makes sense that any argument that can't be refuted, may indeed smell bad to the poor guy on the other end! Smells like victory.

 

All this talk of creationist odours and lying is funny, entertaining and provides some red meat for your supporters, so I don't mind if you keep it up, as it kind of lightens up the discussion a bit. Some good natured ballyhoo never really hurt anything. Maybe I'll even pretend to be outraged about it once in a while! Why not? Politicians do it all the time. I'll be the straight man, and you can be the funny guy. How about that? But I reserve the right to throw in a few jokes of my own once in a while, OK?

 

By the way, that link was the home page of the website, as you had asked where I was getting some of my material from. But this article in particular contains arguments pertinent to our disussion. We'll be going through them.

 

The evolution of the flagellum (not)

[John Cuthber]

I think it's significant that your reply to my observation

"Any chance of an answer to my point that you seemed to be using the argument from personal incredulity?"

is

 

"Sure. I don't see a problem with that approach."

 

You think that a logical fallacy, duly noted as such, is a reasonable point of view.

[Moontanman]

That's OK. I'm pretty used to it. When discussions get going, sometimes the other side will throw stuff they hope will stick as part of their strategy! As long as you don't hurt yourself doing so, I don't see why that will be much of a problem.

 

Now back to the discussion about protein evolution ...

 

 

 

 

You've mistaken what the analogy is about. Probably because I didn't take the time to specify exactly what it meant. My apologies for that.

 

The 2D plane represents the hyperdimensional coordinates of DNA sequence space as compressed into a 2D surface. For example, a DNA sequence 500 codons long could be thought of as a coordinate system having 500 "dimensions", and each of these 500 dimensions can have 4 possible values: A, C, T or G codons. In such a space there is 4 to the 500th power of possible configurations ~= 1E+301, a large number with 301 zeroes. But to get a visual idea of such a space, we can informally imagine it to be compressed down to 2 dimensions.

 

The islands represent the coordinates of potentially functional proteins (or maybe functional RNA sequences). When you said that no organism or chemical is isolated, well, thats true as a stand-alone statement, but it is irrelevant to this analogy. A bit like you telling me that islands in the ocean consist of isolated populations of humans, and me objecting that "no man is an island!" It's just a category error, but possibly my fault in this case as I may not have explained what they represented thoroughly enough.

 

But you do realize that these Islands certainly do not mate with each other, because the islands are not organisms, they are maps of the outcrops of functionality (and fitness of that function) in protein sequence configuration space (that has been contracted from hundreds of dimensions down to 2 dimensions for the purposes of being able to form a mental image, thus an analogy.

 

 

 

I don't care if you take me seriously or not. Your schtick is never to take creationists seriously. That's irrelevant to the actual discussion. I just want to see if you can refute my arguments, or not, once they have been thoroughly discussed.

 

 

 

 

It doesn't matter what you think the creationist medical doctors arguments smell like! What matters is whether you can refute (or ask someone else to refute for you) those smelly arguments he presents demonstrating the infeasibility of the notion that the evolution we observe today, could do anything like having taken us from a common ancestral single celled lifeform(s) to the biology that exists today. I guess it makes sense that any argument that can't be refuted, may indeed smell bad to the poor guy on the other end! Smells like victory.

 

All this talk of creationist odours and lying is funny, entertaining and provides some red meat for your supporters, so I don't mind if you keep it up, as it kind of lightens up the discussion a bit. Some good natured ballyhoo never really hurt anything. Maybe I'll even pretend to be outraged about it once in a while! Why not? Politicians do it all the time. I'll be the straight man, and you can be the funny guy. How about that? But I reserve the right to throw in a few jokes of my own once in a while, OK?

 

By the way, that link was the home page of the website, as you had asked where I was getting some of my material from. But this article in particular contains arguments pertinent to our disussion. We'll be going through them.

 

The evolution of the flagellum (not)

 

I and many others have answered this creationist bull shit over and over on this site, it gets old to answer those bat shit crazy questions over and over, i see no reason i should break down the site of some dishonest creationist trying to sell a book bit by bit just to satisfy you. the answers you claim to seek are all over this site in many threads about these same dishonest assertions. I suspect no answer I can give will satisfy you, you will just move the goal posts as answers come through as you have already began to demonstrate, it has already been demonstrated how the flagellum could have evolved and still be irreducibly complex as you call it. You cannot go backward and show that something cannot work by removing parts at random because the thing did not evolve at random so why should taking it apart at random have any meaning to how it was produced? The evolution of the flagellum is quite demonstrable as it the eye, the immune system, and your big brain, in fact it can be shown that the human body is IC but that is a false analogy because the human body didn't just pop into existence whole, complex organisms evolved over vast periods of time in small reasonably logical steps. It's all already here go read some of it and if you find a point hard to swallow let me know and I'll do my best to make it easier to understand but this crap of gliding in like you are the first creationist to come here and slowing working your way through all the same crap we have seen dozens if not hundreds of time is a bore. And if you do come up with something that cannot be explained I will applaud you for at least being unique but don't assume I am in awe of your intellect just because you can obfuscate the issue to so well you cause me to loose interest. BTW, the appearance of design does not prove design, there are many crystals that are very complex but do not prove any design or designer. personally i think you should have to prove who the designer is before even suggesting a designer but that is just me and not this site. I always look suspiciously on anyone who is asserting an agenda of denial and selling a book. Does this guy have any peer reviewed papers? No. Does he publish anywhere but his $12.95 book? No. Are you in any way associated with this guy? Can you give examples of any peer reviewed papers that assert a designer? Or IC in the way you are asserting it? I'll ask you directly, are you the one selling this book, are you Dr. Pitman or making money off his book? Have you even read any of the many threads on this subject in this forum? Come on guy give me something i can work with besides a MD pretendign to be a scientist, here is a good one by Dr. Pitman

 

http://dancingfromgenesis.wordpress.com/2007/10/02/detecting-design-by-sean-d-pitman-md-shows-compelling-noahs-flood-evidence-and-reasons-to-doubt-darwins-scheme/

 

 

WOW! What a surprise he is asserting Noah's ark was real and a world wide flood happened, lets see what else Dr. Pitman asserts

 

The author is a young earth creationist, who is commenting on how mainstream scientists and New Agers are missing the boat (willfully in many cases) as they interpret the evidences about our ancient history.

 

He is an Young Earth Creationist, this means by definition he is dishonest because YEC cannot be supported by anything but lies, they are by definition dishonest, you my friend are either deceived and one of the sheep or one of the dishonest shepards. Fell free to mentally masturbate all you want here but I am not into that.

 

BTW, i figured Noah's ark had to be a myth when I was 8 years old, i asked my "public school teacher" yes I said public school teacher where all the water went when the flood dried up and she couldn't answer me with anything other than it dried up, even then i knew that that much water could not hang in the air as vapor, subsequent questions were answered with increasingly less likely answers until i was made to stand in the corner until i admitted the veracity of Noah's flood, I stood in the corner all day and received a spanking that evening, no actually it was a beating, but I never gave in then and I will not give in now, creationism is a lie perpetrated by small minded people who cannot or will not admit that their concept of God cannot be real if they insist the bible equals truth.

 

Another good one by Dr. Pitman,

 

http://naturalselection.0catch.com/Files/humaneye.html

Edited July 3, 2011 by Moontanman

[Ringer]

let's try to at least start this so there's not so much to do at once.

As far as I know such kinds of knockout experiments on the flagellum have been carried out.

 

indeed they have, and your link only talks about how the flagellum doesn't work without them. The problem is that just because the flagella no longer works doesn't mean that it is useless, it doesn't even mean that it's not doing anything. That is what IC argues is that all parts are useless without the whole not that a specific function no longer works without it. If that is it's stance than it misunderstands evolution that I could imagine.

 

One thing Miller says in the youtube video that is weak, is that he claims that irreducible complexity was taken apart at the trial because of the discovery of the strong similarities between the T3SS and the flagellum assembly transportation system. The problem is that the T3SS momologue in the flagellum is all of 10 proteins. The flagellum is 40 to 50 (depending on the version). It's only been suggested that this is an evolutionary waypoint. How does that really defeat irreducible complexity? Miller doesn't say anything about how the T3SS could have formed (it is also very sophisticated in it's own right) nor about what took place from the 10th protein up to the 40th or 50th. Note that he says "that's not evidence, that's an argument". It is a starting point for later investigation perhaps. But such a conjecture which may be the basis for further studies isn't any basis for declaring that IC is a dead in the water concept!

 

Your moving the goalposts, you are doing the same thing as when IDers ask for intermediate species from A to C. You then show them B and ask where the intermediate for that is. It's stupid to ask for ridiculously specific evidence when you provide non of your own.

 

 

IC (don't confuse IC with ID) makes the claim that the evolution of such multi-protein machines is very unlikely based on what we know about proteins and evolution, and the property of irreducible complexity as well. That has never been refuted. All that has happenned is that people like Matzke have proposed hypotheses that may be the basis for future work. But so far that is all there is. We are "incredulous" about such explanations of the possible evolutionary pathways they propose because we know of principles in the laws of nature that would make such evolutionary steps infeasible. You know these princiles too (very likely) but you haven't perhaps imagined they also applied to evolution.

 

What principles do you keep talking about. Name the damned things already, we are not school children that need to be walked through something. If we don't understand it we know how to do research on our own. Just give these principles and evidence you keep talking about.

 

BTW you would be amazed if you just sat down with a scientist and listened to the awe in his/her voice when they talked about there specialty. If you don't think scientists are incredulous about all of these things you are sorely mistaken, they just try to explain these things while being awed. While the IC and ID and creationists, etc. bow down to their incredulity and cry about not being able to understand.

 

 

What do I mean by infeasible? I mean it in this way. If you were in the middle of a very well constructed maze that was say 10km wide, then either you will be going around in circles and walking up blind alleys for a very very long time, or else you could walk out of it in say 12 hours. You really could walk out of it in 12 hours! (That is if the maze actually was built so that you could in fact get out of it). All you'd need to do is to take the correct path out. But is that very likely?

 

IC makes the claim that though you perhaps may be able to walk out of a large maze, in general you will not take the fastest route out. Yet such an argument does fall flat for a tiny maze, because the smaller the maze, the less it matters if you don't take the fastest way out. Right? But as the maze grows larger, the time taken to get out of it grows exponentially. Even though the time taken to walk straight out may only increase linearly.

 

It may be likely enough to happen once in a while for a 10km wide maze that you could find your way out by the fastest path, but most of the time, it will be much much longer before you'd ever get out of it. If such a maze was 1000km wide, is it feasible to think you'd ever manage to get out in 100 days? It would perhaps be possible, but far more unlikely than the likelihood of being able to find the right pathway out of the 10km wide maze.

 

The problem with this comparison, although it could be worked into a very good analogy, is that you assume a starting point without knowledge of the previous generations explorations. I'll try to make it a better example.

 

Say you have multiple G1 families and all of them can only take a single path with one try to get out of the maze. A few get out fast, some get out slow and some don't get out at all. Now those that got out get put back in the same maze except it was extended as you say with their children. Some of the children that had parents that got out fast will get out fast and find the fast way out of the extension, while some will get lost in the extension and get out slowly or not at all. The same goes with the children with slow parents, some may find a different way than their parents and get out fast, some will get out slower, and some will ignore their parents and get out fast. Then the same problem goes with the extension for them. Sooner or later the maze stops extending and the only remaining families will know how to get out of the maze fairly well. If the maze changes again the process will begin again.

 

Now I'll bet that you'll be saying that such examples have nothing to do with the way evolution works. For instance, "evolution isn't trying to get out of a maze". Is the problem completely unlike evolution? Evolution is searching (even though it does not plan or intend to be seraching) for ever more sophisticated function. It must be searching for and finding such functions or else we'd still be just an adapting crude single celled lifeform. One way evolution works is to randomly change DNA codons. It is possible to get from a starting functional protein to a novel functional protein without changing all that many codons for a small protein, perhaps only dozens of them. But say we need to change a certain 40 codons. We could change them in just 40 mutations. But how likely is that to actually happen? The possible number of changes (assuming we picked out all the correct 40 codons to change in the first place) is 4 to the 40th power ~= 1000000000000000000000000 possible codon changes.

 

Apparently you don't realize that changing a single codon, even a single G A T or C, can drastically change the sequence of codons after it. If you change a single start codon, ATG into TTG, that whole sequence will no longer code, the opposite works as well, say GTA gets flipped or gains an AT before the G in crossover you have a new starting sequence and all new codons until it finds a stop codon, TAG TAA or TGA.

 

 

However you might point out that "Evolution isn't aiming for any particulr protein target sequence or solution, so you can't "cheat" in the argument by working backwards."

 

I get your point, but we can show that proteins are in fact so very rare in sequience space that it doesn't matter that no particular target is being aimed at, because there are so few functional protein targets in existence in any case, that evolution is very unlikely to hit any of them. Put it this way, the smaller and simpler the changes needed, the more likely evolution is to succeed, but there comes a point where it gets too slow and never manages to find any "targets" due to the exponential slowing down of the process. Most of that is explained in some detail in the end of that article I referenced earlier.

 

So finding protein function is quite a lot like being in a maze. The outside represents a new higher level (or just new) protein function. The starting point represents the initial function. There are many possible paths. The maze example is a bit forgiving in another way, because we assume there actually is a way from the middle to the outside of the maze. What if there wasn't any such path? Think about it. The walls inside the maze represent the fitness barriers preventing a pathway directly to the higfher function that awaits. Is there a way through? Or not? (There is always a way out of the maze! You can fly out of it.) But evolution has to walk through it gradually and cannot fly out of it. Actually some larger nonpoint mutations could simulate jumping over many walls to a new location, but there is still no guarantee (if the maze wasn't intelligently designed to be solveable) that it is possible to even get out of it.

 

Not only that, but such a maze for evolution is also blind, and has no memories, which makes it harder still.

 

Let's stop you right there. It has no memories huh? What is it with this whole inheritance thing? It must be incredibly unlikely for us to look like our parents without the genetic code having a 'memory' of sorts, right? Also, it is like a maze, just not the one you described.

 

 

See, protein evolution isn't an easy thing to have happen. Proteins are very rare things. Only a small proportion of all possible amino acid sequences are capable of forming functional folds that would be useful in biology. How does evolution find them? Tell me if you know how.

 

It's a little process called natural selection. If something is unhelpful the carrier usually dies or is unable to reproduce. Only the useful proteins are selected for. Let me but it this way, Bovine spongeform encephelopathy (I think that's the right term) or mad cow disease is caused by the secondary form of a folding protein, it's caused by multiple things but that's not the part we are focusing on. Now that unfortunate folding causes all sorts of problems for the cow that would not allow it to find a mate, and even if it did the calf would not be healthy enough to live in the wild. So that fold when mutated in the wild, not fed to other cattle that can absorb and incorporate the protein, it would die without being able to leave a healthy progeny that evolution need for it to succeed.

 

 

I apologize for not getting to the articles yet, I have had much busier weekend than I had planned but will get to it ASAP

[Ringer]

I apologize for the spelling errors and such in my last post, I reread it and my Language Arts teachers would be horrified. For some reason it doesn't have an edit button ATM so the errors shall stay.

 

On to the first link you posted.

http://www.detectingdesign.com/steppingstones.html

Imagine yourself beside a very wide river. As you look out across this river you see various steppingstones. Close to the bank of the river there are lots of these steppingstones such that the average distance between them is rather minimal. However, you notice that the number of steppingstones rapidly decreases as you look out farther and farther from the bank. The average distance between the stones quickly grows, so that a simple jump from one to the next becomes impossible without getting wet. This is the fundamental problem faced by evolutionists. How do the mindless processes of random mutation and natural selection get from one novel steppingstone function to the next without getting wet at higher and higher levels of functional complexity which require greater and greater minimum structural threshold requirements (i.e., more and more specifically arranged amino acid residues)?

 

 

It's odd he doesn't mention what he means by not getting wet. Evolutionary theory, for this analogy, says something more like the stepping stones are far apart and some will have adaptations that survive the swim others will not. That progeny will pass on its 'swimming ability' so they can keep swimming from stone to stone and other adaptations will be produce that make the swim even easier. Getting wet happens all the time, as does drowning, the point is that some of them survive the swim.

 

 

Of course, random mutations (or "letter changes") to the codes of life do occur quite often in every living thing. These letter changes can result in the evolution of a new type or level of function or in no functional change at all. When no functional change is realized, this is called "neutral evolution."¹ For example, a change from the letter sequence grft to agrft via the addition of the letter awould be a neutral change with respect to meaning in the English language system since both letter sequences are equally meaningless.

 

The information systems that code for all the parts of living things often have such functionally neutral mutations. In fact, the large majority of all mutational changes are thought to be functionally neutral. What is especially interesting about these neutral mutations is that nature cannot tell the difference between them, since nature only recognizes differences in function, not "spelling." However, on occasion, a mutation will actually change the meaning or function of a genetic word or phrase.

 

For example, if the spelling of vacation happened to get “mutated†to read vocation or even vucation, there would be a big change in meaning. Of course the word vucation has no meaning in the English language, but a loss of the meaning of the word vacation might be beneficial in certain circumstances, as would the gain of the meaning of the word vocation. Such meaningful changes, when they happen in the genetic codes of living things, can be detected by natural selection as either beneficial or detrimental. If they are deemed to be beneficial, they are kept for the next generation to use, but if detrimental, they are eliminated from the gene pool over the course of time.

 

 

Him talking about how adding a letter does nothing because both are meaningless is a ridiculous analogy. In an intro bio course you find a sentence like 'the sad cat and bat', codons being paired in threes. now you will see that the addition of a single letter will yield 'ath esa dca tan dba t' which is fundamentally useless as a sentence and as a codon because it is no longer in pairs of 3. This is similar to the start/stop codon problem in my last post. Now there are many ways this sentence can change and still be functional, whether it is detrimental or helpful doesn't matter now, such as a codon switching positions 'the cat and sad bat' or 'sad cat and the bat' etc; even whole codons being inserted such as 'now the sad cat and bat'. All of these are still fully functional. You could even look at the sentences that have a somewhat semantically correct structure as helpful functions and semantically wrong mutations as harmful such as a single letter shift, 'tth esa dca tan dba'. Hopefully you get that there are huge amounts of different ways that are functionally sound as well as those that are functionally bunk.

 

 

Another problem he is having is understanding that some evolutionary traits that don't necessarily give benefit now doesn't mean that they will never end up being beneficial. Even some things that are somewhat harmful can still be passed on and end up being beneficial in another sort of environments. Easily done if the animal is migratory.

 

 

In the case of de novo antibiotic resistance, such rapid evolution is made possible because there are so many beneficial "steppingstones" so close together, right beside what the bacterial colony already has. Success is only one or two mutational steps away in many different directions since a multitude of different single mutations will result in a beneficial increase in resistance. How is this possible?

 

In short, this is made possible because of the way in which antibiotics work. All antibiotics attack rather specific target sequences inside certain bacteria. Many times all the colony under attack has to do is alter the target sequence in just one bacterium by one or two genetic "characters" and resistance will be gained since the offspring of this resistant bacterium, being more fit than their peers, will take over the colony in short order. A simple "spelling change" made the target less recognizable to the antibiotic, and so the antibiotic became less effective. In other words, the pre-established antibiotic- target interaction was damaged or destroyed by one or two monkey-wrench mutations. As with Humpty Dumpty and all the king’s men, it is far easier to destroy or interfere with a pre-established function or interaction than it is to create a new one, since there are so many more ways to destroy than there are to create.

 

So, do all functions within living things evolve as easily as the antibiotic resistance function? As it turns out, those independent functions that are not based on the destruction of or interference with other pre-established functions are much more difficult to evolve. For example, single protein enzymes catalyze many biochemical events within living things. They help to build and break down other molecules via their own independent abilities, which are not based on the gain or loss of any other system, function, or interaction.

 

Consider that several forms of antibiotic resistance are based on the production and activity of various enzymes. Perhaps the most famous anti-antibiotic enzyme is the penicillinase enzyme, which is produced by various bacteria having the proper penicillinase code in their DNA. What the penicillinase enzyme does is chop up part of the penicillin antibiotic so that it can no longer attack its target and kill the bacterium. Many people think that bacteria evolve this enzyme just like they can evolve other forms of antibiotic resistance. This is simply untrue.

 

 

Man this one is tricky; not because he's right but because he's so vague as to be useless for any sort of retort. So let's look at some points, he says that there are so many useful stepping stones that can be used. What are these stepping stones, it's kind of useless to make a claim and just say, 'trust me, I know.' Then he talks about how antibiotics target specific areas of the bacteria. He makes points to show how unbelievable improbable that it is to evolve a certain genetic sequence toward a certain specific function, yet says it's perfectly acceptable for bacteria. . . odd. Anyway some fun facts about how else bacteria can do things like this, they have an amazing ability to incorporate genetic sequences into their own code. That's why they are so useful to culture bacteria for gene testing and such. You also have to realize by now that bacteria don't think, 'Oh, look, they're using penicillin. I sure wish I had some penicillinase so it wouldn't hurt me. Oh look, there's some. I think I'll give it to my children.' Some bacteria happen to have a resistance to penicillin, people stop taking it and that bacteria that has a slight resistance survives and infects others. They do the same and the next generation will have an even stronger resistance, ad infinitum.

 

 

 

The information required to produce an enzyme which is specific enough to chop up penicillin is far greater than the information required to block the antibiotic-target interaction, since there are far fewer ways to make such a specific enzymatic function compared to the number of ways to block a specific antibiotic function. Creating a block to a previous function is like breaking Humpty Dumpty, while creating the function of an independent enzyme is like putting Humpty Dumpty back together again.

 

As it turns out, the required code needed for producing the penicillinase enzyme has never been observed to evolve in any bacterial colony de novo. Either a penicillinase-producing colony already had this code before it was exposed to penicillin, or it gained this code by genetic transfer from some other bacterial population that already had the code.² Simply put, the penicillinase enzyme does not evolve, or at least not often enough to have been observed in real time, while other forms of antibiotic resistance that are based on interference with or destruction of pre-established functions or interactions evolve all the time.

 

 

He may be right, if that's how it worked at all. A single bacteria doesn't just come about immune to penicillin, though it may happen by pure chance. The immune strain had parents that were unbelievably immune, which had parents who were extremely immune, which had parents who were ridiculously immune, etc, etc. This is oversimplified but hopefully you get the idea.

 

 

 

But what about other enzymes? Have any novel enzymatic functions ever been shown to evolve in real time? Interestingly enough, several enzymes with entirely new and beneficial functions have been shown to evolve in real time. For example, Kenneth Miller, in his book, Finding Darwin’s God, references a very interesting research study published by Barry Hall, an evolutionary biologist from the University of Rochester.³

 

In this study, Hall deleted the lactase genes in certain E. coli bacteria. These genes produced and regulated the production of a lactase enzyme called b-galactosidase. What this enzyme does is break apart a type of sugar molecule called lactose into two smaller sugar molecules called glucose and galactose — both of which E. coli can use for energy production. Obviously then, without the genes needed to make this lactase enzyme, the mutant E. coli were no longer able to use lactose for energy despite being placed in a lactose enriched environment, unless of course they evolved a new enzyme to replace the one that they lost. And sure enough, they did just that. In just one or two generations these E. coli successfully evolved a brand new gene that produced a new lactase enzyme. Aha! Evolution in action yet again!

 

Although most descriptions of Hall’s experiments stop right here, including the one found in Miller’s book, what Hall did next is most interesting. He deleted the newly evolved gene as well, to see if any other gene would evolve the lactase function . . . and nothing happened! Despite tens of thousands of generations with large population numbers and high mutation rates, no new lactase enzyme evolved. Hall himself noted in his paper that these double mutant bacteria seemed to have "limited evolutionary potential."

 

 

Interesting but not at all as big as he thinks it is. Enzymes are extremely specific because they have been evolving with us for a very long time and have had time to become specialized. I've never heard a biologist say a fully functional specific enzyme just appears out of, although it could. All that matters for evolution is that something give some sort of advantage. Now if a non-specific enzyme that could fit multiple sugars but didn't bread them down as fast as we see now, but still act as a catalyst, there would be an advantage. The problem with saying that this shows evolution stopped is that it measured only the expected reaction rate with the enzyme lactase and not the reaction rate of lactose with bacteria compared to the reaction rate of lactose with no bacteria. If there is a significant measurable difference it could have evolved a novel enzyme that just doesn't work as fast as lactase.

 

 

That's all I can get to today, hopefully I can keep doing this regularly when I have time to sit down

 

 

[Monsters from the ID]

I think it's significant that your reply to my observation

"Any chance of an answer to my point that you seemed to be using the argument from personal incredulity?"

is

 

"Sure. I don't see a problem with that approach."

 

You think that a logical fallacy, duly noted as such, is a reasonable point of view.

 

 

I believe it isn't a logical fallacy to be skeptical about certain claims, if there are accompanying reasons to go along with the skepticism. Because if there are reasons to be skeptical or incredulous, then it isn't personal incredulity in that case, but incredulity (a state of non-belief) based on various avenues of reasoning. I believe the logical fallacy comes in when someone says they don't believe something, and when asked why they say something like; "It just seems ridiculous." And when asked to clarify or give specific reasons why it is ridiculous, they then can't come up with any reasons. They just "feel" that the notion is wrong. That is personal incredulity, and as an argument it is fallacious because no good reasons are given to support the incredulity. In other words, personal incredulity seems to be more of a feeling, than an argument. But incredulity (a state of non-belief) if it has supporting arguments, certainly is not a fallacy. I take it you're not supporting credulousness either, unless it also has some supporting arguments to go along with that state of credulousness.

[Ophiolite]

You have made your point clear, but that clarification was necessary because you had said you saw nothing wrong with the approach of "using the argument from personal incredulity".

 

There is also a difference between well grounded scepticism and knee jerk, dogmatic scepticism. i am not saying you are practicing the latter, but I sense some of your objections come rather close to that position. This devalues such arguments as you may have.

[Monsters from the ID]

... The evolution of the flagellum is quite demonstrable as it the eye, the immune system, and your big brain ...

 

No, these things aren't demonstrable. Perhaps they are in thought experiments, but that doesn't quite count.

 

 

... complex organisms evolved over vast periods of time in small reasonably logical steps.

 

Darwin thought about whether cases could be found that countered the manysmall steps to novelty principle, but couldn't think of any. But now we know more, we have found examples of such cases, one of them being the flagellum.

 

 

... I always look suspiciously on anyone who is asserting an agenda of denial and selling a book.

 

Dr. Dawkins did that though, and probably made millions from the sales. It's OK for him though, right? There's nothing wrong with selling a book! You don't have to buy it, and what's in it is pretty much all on the internet in any case. In fact I'll let you in on my special offer - buy 100 for the price of 1000, and 2% of the proceeds will go directly to a charity of my choice!

 

 

Does this guy have any peer reviewed papers? No. Does he publish anywhere but his $12.95 book? No.

 

According to one site I looked up (which gets you to agree to a confidentiality agreement not to disclose the specific of wht is on the site) he has published 6 papers in various medical journals. I am sure you can find these yourself if you want to. I came across themn after a few minutes of looking. I can tell you he is a hematologist though.

 

Are you in any way associated with this guy? ... I'll ask you directly, are you the one selling this book, are you Dr. Pitman or making money off his book?

 

I wouldn't mind it if I were! Ha! But no, I am not he. But thanks for suspecting I might have been him. You kind of made my day!

 

 

He is an Young Earth Creationist, this means by definition he is dishonest because YEC cannot be supported by anything but lies, they are by definition dishonest ...

 

Then you're using a pretty crap definition of dishonesty aren't you. The two big supporting evidences for a billions of years old earth, are radioactive isotope dating and inferred travel times of starlight in the universe. And I'm not disputing that they are pretty strong evidences. On the other hand, other dating techniques also exist and the majority of them give ages less than billions of years. Interestingly, mica's dated in the millions of years based on their measured decay products, also can be dated to several thousand years via the helium diffusion leak rate. The helium atoms (derived from trapped alpha particles in the mica) are leaking out at a measureable rate, fast enough to bring them to equilibrium with the surroundings very quickly. But nevertheless a high concentration of them remain trapped in the mica. Here we have two radioisotope dating techniques based on the same decay events giving dates that are several orders of magnitude in difference. Such topics are of genuine scientific interest.

 

Have I accused abiogenesis researchers, or even those that believe strongly that abiogenesis took place, of being liars and dishonest? No.

 

Are there people on both sides who do tell actual lies and misrepresent the facts? Of course. But you don't go around generalizing about all the members of a certain group based on a few bad apples. Or do you? If you do, you shouldn't.

 

 

BTW, i figured Noah's ark had to be a myth when I was 8 years old, i asked my "public school teacher" yes I said public school teacher where all the water went when the flood dried up and she couldn't answer me with anything other than it dried up, even then i knew that that much water could not hang in the air as vapor, subsequent questions were answered with increasingly less likely answers until i was made to stand in the corner until i admitted the veracity of Noah's flood, I stood in the corner all day and received a spanking that evening, no actually it was a beating, but I never gave in then and I will not give in now, creationism is a lie perpetrated by small minded people who cannot or will not admit that their concept of God cannot be real if they insist the bible equals truth.

 

Well that was a pretty damn dumb public school teacher! Did she think she'd actually gain your respect that way? Did she really stand you in the corner all day for asking that question though? Or were you being a very naughty boy in other ways? All day in the corner? It's possible of course, but it sounds a little over the top. We'll never know for sure, but how would you like it if I in turn now accused you of being a liar and dishonest? How could you prove me wrong? I could even say that your story (being stood in the corner all day long and receiving a beating afterwards - just for asking where all the water went after Noah's flood - sounds rather like an exaggeration, and many would agree. But I'm not going to, because it's a dumb generalization to make. Neither should you.

 

You have made your point clear, but that clarification was necessary because you had said you saw nothing wrong with the approach of "using the argument from personal incredulity".

 

There is also a difference between well grounded scepticism and knee jerk, dogmatic scepticism. i am not saying you are practicing the latter, but I sense some of your objections come rather close to that position. This devalues such arguments as you may have.

 

 

I should have been a little more careful with my words though I did try to clarify the bit about "personal" versus "reasoned" incredulity. Unless there's a reason (other than a feeling) behind the incredulity, then such incredulity is not worth mentioning in a scientific discussion. Along the same lines, credulousness towards a certain notion based only on the fact that the notion is a consensus viewpoint, ought not to be accepted either, unless the person themselves can reason out why they believe that viewpoint (other than the fact that the notion in question is a consensus notion). Doing THAT, would be the "argument from authority" fallacy.

 

let's try to at least start this so there's not so much to do at once.

 

indeed they have, and your link only talks about how the flagellum doesn't work without them. The problem is that just because the flagella no longer works doesn't mean that it is useless, it doesn't even mean that it's not doing anything. That is what IC argues is that all parts are useless without the whole not that a specific function no longer works without it. If that is it's stance than it misunderstands evolution that I could imagine.

 

I suppose though that you'd need to demonstrate or reason out exactly how the imagined evolution would work in practice. I thnk Matzke did that to a certain extent, though we'd argue that he left out the "how" his proteins would be able to become functional in new ways. We'll come back to that as I think that is one of the major objections. But we need to go over your points in these two most recent posts.

 

Thanks for jumping ahead and doing what I should have started to do. I'm just trying to slow down the pace as lately I have some other things going on, so I haevn't gotten back to it for a few days since last time.

 

 

Your moving the goalposts, you are doing the same thing as when IDers ask for intermediate species from A to C. You then show them B and ask where the intermediate for that is. It's stupid to ask for ridiculously specific evidence when you provide non of your own.

 

I can see your point, biut on the oither hand, if the gaps are wide, then it is justified - justified until the gaps aren't wide that is. When the gaps are small enough to be demonstrably crossed, then you'll have conclusively proved the point - not to our satisfaction, but to yours. As long as the gaps are large and the mechanidms mysterious, there will always be justifiable doubt. But chances are if your side is correct, those gaps will close off in time. If our side is correct, they won't.

 

 

What principles do you keep talking about. Name the damned things already ...

 

You begin to discuss some of them later on yourself - they're in Pitman's article which you begin to go through in these two posts.

 

 

BTW you would be amazed if you just sat down with a scientist and listened to the awe in his/her voice when they talked about there specialty. If you don't think scientists are incredulous about all of these things you are sorely mistaken, they just try to explain these things while being awed. While the IC and ID and creationists, etc. bow down to their incredulity and cry about not being able to understand.

 

I have been near scientists myself (having a BSc.) so I know what you mean.

 

My connection is about to close - will continue tomorrow.

[Moontanman]

No, these things aren't demonstrable. Perhaps they are in thought experiments, but that doesn't quite count.

 

No, the evolution of the eye from a simple light sensitive cell to eyes better than human eyes can be seen in nature, this one at least is not a thought experiment.

 

 

Darwin thought about whether cases could be found that countered the manysmall steps to novelty principle, but couldn't think of any. But now we know more, we have found examples of such cases, one of them being the flagellum.

 

 

The theory of evolution has "evolved" so far past Darwin his name is used only because he first thought up the process of natural selection, it is no longer Darwin's theory and evoking his name to try and refute evolution is silly.

 

 

 

Dr. Dawkins did that though, and probably made millions from the sales. It's OK for him though, right? There's nothing wrong with selling a book! You don't have to buy it, and what's in it is pretty much all on the internet in any case. In fact I'll let you in on my special offer - buy 100 for the price of 1000, and 2% of the proceeds will go directly to a charity of my choice!

 

 

How about you go pound sand...

 

 

 

According to one site I looked up (which gets you to agree to a confidentiality agreement not to disclose the specific of wht is on the site) he has published 6 papers in various medical journals. I am sure you can find these yourself if you want to. I came across themn after a few minutes of looking. I can tell you he is a hematologist though.

 

And this make him an expert on evolution why?

 

 

I wouldn't mind it if I were! Ha! But no, I am not he. But thanks for suspecting I might have been him. You kind of made my day!

 

Of course it did, comparing you to a lying charlatan made your day? Hmm

....

 

Then you're using a pretty crap definition of dishonesty aren't you. The two big supporting evidences for a billions of years old earth, are radioactive isotope dating and inferred travel times of starlight in the universe. And I'm not disputing that they are pretty strong evidences. On the other hand, other dating techniques also exist and the majority of them give ages less than billions of years. Interestingly, mica's dated in the millions of years based on their measured decay products, also can be dated to several thousand years via the helium diffusion leak rate. The helium atoms (derived from trapped alpha particles in the mica) are leaking out at a measureable rate, fast enough to bring them to equilibrium with the surroundings very quickly. But nevertheless a high concentration of them remain trapped in the mica. Here we have two radioisotope dating techniques based on the same decay events giving dates that are several orders of magnitude in difference. Such topics are of genuine scientific interest.

 

So now you are questioning radiometric data? Does it make any sense to you that multiple radiometric methods agree with not only each other but with other methods based on other techniques? No of course not, all you need is one unusual data set and you assume all the rest are incorrect as well but I see nothing to suggest a 6,000 year old earth.

 

Have I accused abiogenesis researchers, or even those that believe strongly that abiogenesis took place, of being liars and dishonest? No.

 

Are there people on both sides who do tell actual lies and misrepresent the facts? Of course. But you don't go around generalizing about all the members of a certain group based on a few bad apples. Or do you? If you do, you shouldn't.

 

 

While everyone lies creationists have to lie to support their assertion of created young earth, not only do they lie your friend does as well, and as I suspect you know he is spouting bullshit so the lie becomes yours. BTW, abiogenesis is not part of evolution, evolution only explains the diversity of life not how life started, get your facts lined up sparky.

 

Well that was a pretty damn dumb public school teacher! Did she think she'd actually gain your respect that way? Did she really stand you in the corner all day for asking that question though? Or were you being a very naughty boy in other ways? All day in the corner? It's possible of course, but it sounds a little over the top. We'll never know for sure, but how would you like it if I in turn now accused you of being a liar and dishonest? How could you prove me wrong? I could even say that your story (being stood in the corner all day long and receiving a beating afterwards - just for asking where all the water went after Noah's flood - sounds rather like an exaggeration, and many would agree. But I'm not going to, because it's a dumb generalization to make. Neither should you.

 

You are correct is wasn't all day, "science" class wasn't till after recess so it was the rest of the day, I apologize. The beating how ever was real, in the early 1960's in WV evolution didn't get much support but genisis was pretty much the absolute truth The flag only had 48 stars too, I guess they didn't believe in Alaska or Hawaii BTW, I was known as an very well behaved child, i just wasn't gullible or stupid enough to believe bible verses as science. .

 

 

I should have been a little more careful with my words though I did try to clarify the bit about "personal" versus "reasoned" incredulity. Unless there's a reason (other than a feeling) behind the incredulity, then such incredulity is not worth mentioning in a scientific discussion. Along the same lines, credulousness towards a certain notion based only on the fact that the notion is a consensus viewpoint, ought not to be accepted either, unless the person themselves can reason out why they believe that viewpoint (other than the fact that the notion in question is a consensus notion). Doing THAT, would be the "argument from authority" fallacy.

 

Now, I gave you neg rep for suggesting I was lying, of course I am sure it is easy to project your faults on me, and again so far your evidence is in sever doubt and easily refuted by simply reading other threads on sfn, until you come up with something new or not easily refuted i am done with this conversation, i see no reason for me to go back and repeat over and over the same stuff just to satisfy you because you are too lazy to read them, if you come up with something new I'll be glad to either applaud you or debate you BTW, are you aware of the Verdict in the trial of ID a few years ago? Yes an actual trial with a Conservative Christian Judge and he struck down ID as nothing but lies being used to support religion. Yes, a Conservative Christian Judge actually agreed after hearing days of testimony that ID was just lies being used to support religion and that ID had no factual support what so ever. And yes the ID people used all the same arguments and examples you are currently using, you have come up with nothing new.

[Ringer]

Just stumbled upon something I thought fit in with this discussion rather well. Behold A scientific look at dinosaur species using creationist hypothesis. Note that this isn't the actual paper just a report of it.

[Monsters from the ID]

The problem with this comparison, although it could be worked into a very good analogy, is that you assume a starting point without knowledge of the previous generations explorations. I'll try to make it a better example.

 

Say you have multiple G1 families and all of them can only take a single path with one try to get out of the maze. A few get out fast, some get out slow and some don't get out at all. Now those that got out get put back in the same maze except it was extended as you say with their children. Some of the children that had parents that got out fast will get out fast and find the fast way out of the extension, while some will get lost in the extension and get out slowly or not at all. The same goes with the children with slow parents, some may find a different way than their parents and get out fast, some will get out slower, and some will ignore their parents and get out fast. Then the same problem goes with the extension for them. Sooner or later the maze stops extending and the only remaining families will know how to get out of the maze fairly well. If the maze changes again the process will begin again.

 

I have a better anaolgy (that of the small islands and large oceans), but as far as the maze analogy goes, it is meant to represent the potential pathways leading (for example) to the evolution of a new functional protein. Now once you are outside the maze, the protein has been evolved. In other words, getting out of the maze means that finally after however long it took to get out of the maze, we hit upon that sequence code that specifies some new function. However, while in the maze, that new function didn't yet exist. If the organism that finally evolves the functional new protein finds that the new function is useful enough, they might have some advantage which can be picked up by evolution and this new protein or protein complex may sart to increase in the population and finally after a much longer time it may even become fixed in the entire population. That's an example of a successfully evolved new protein. But in the case of where nothing has yet emerged from the maze, there isn't a new protein yet. So until the maze is solved, nothing about the route out can be known by the many trials going on inside. While still in the maze, there is no advantageous or disadvantageous mutations with respect to solving the maze. To clarify - there will always be good, bad and neutral mutations as far as the organism is concerned, but whatever happens that is good, bad or indifferent to the organism as a whole, is irrelevant with respect to getting out of the maze. Meaning that the evolution taking place before the evoluton of some new feature appears, then whether a mutation is good bad or neutral to the whole organism, cannot be used as a criteria for guidance by natural selection that has anything to do with the evolution of some new feature before it appears. This means that any evolution that takes place that may be (or may not be) on the way towards some new feature emerging, is unguided (random) with respect to the appearance of a new feature that doesn't yet exist. Only after the new feature has just emerged, can natural selection begin to select for or against it, based on it's fitness contribution to the whole organism. While within the maze, no learning can be undertaken. Evolution has no memories of anything. Evolutions "memories" (so to speak) come only from fixed (or on the way to fixation) already emerged new features that provide an advantage.

 

As an example, if a treasure is at a certain location in a large forest, then though different routes will alternatively provide advantages or problems related to comfort and survival along the way, whether these routes are safe and comfortable, or dangerous and uncomfortable, or dangerous and comfortable, or safe and uncomfortable, all of that guidance is useless as far as finding the treasure is concerned. If I find the treasure, it will be because of luck pure and simple. Nothing about the routes can give me any indication that I am moving towards or away from the treasure.

 

ID believes that we can establish that since the evolutyion of new features that don't yet exist is random evolution (the evolution of these new features that are yet to emerge is not guided towards by natural selection) then if the new features are rare enough entities in coding space, then they will in all likelihoods never be capable of being found by the unguided process of random evolution.

 

It's only after a new feature has emerged that natural selection can begin to provide guidance to the future evolution that can conserve and adapt that feature.

 

 

Apparently you don't realize that changing a single codon, even a single G A T or C, can drastically change the sequence of codons after it. If you change a single start codon, ATG into TTG, that whole sequence will no longer code, the opposite works as well, say GTA gets flipped or gains an AT before the G in crossover you have a new starting sequence and all new codons until it finds a stop codon, TAG TAA or TGA.

 

I did know that. I don't get your particular point with that.

 

 

Let's stop you right there. It has no memories huh? What is it with this whole inheritance thing? It must be incredibly unlikely for us to look like our parents without the genetic code having a 'memory' of sorts, right?

 

As previoulsy pointed out, the inheritance cuts in when we have already emerged already functioning systems in place. But before such systems have managed to emerge, since their functional advantages are as yet non existent, then there can be no "memories" so to speak that can pass along any guidance information. In fact, lethal mutation pathways that got tried once (resulting in the death of the organism that tried them) may be tried yet again - over and over. If a lethal mutation is experienced, then that creature gets deleted, but that same mistake is available for reuse. Nothing is there to prevent such things happening again.

 

 

It's a little process called natural selection. If something is unhelpful the carrier usually dies or is unable to reproduce. Only the useful proteins are selected for.

 

Sure. But first the useful proteins need to have already emerged from nonexistence. Only AFTER they have emerged, can they can be selected for or against. But before a new protein has emerged, natural selection is unable to help it emerge. It must emerge by chance. Once you manage BY CHANCE to find the treasure that was sitting out there somewhere in the forest (or found your way out of the maze), THEN the treasure will give you the advantages that particular treasure provides. And AFTER you benefit from the treasure, then natural selection can favour you over the other poor so and so's who are still wandering around in the forest (or within the maze) not yet having found any treasures. And note that to be a more realistic analogy to evolution, then the people wandering aroud in the forest or inside the maze, cannot have any memories of where they have already been.

 

 

Let me but it this way, Bovine spongeform encephelopathy (I think that's the right term) or mad cow disease is caused by the secondary form of a folding protein, it's caused by multiple things but that's not the part we are focusing on. Now that unfortunate folding causes all sorts of problems for the cow that would not allow it to find a mate, and even if it did the calf would not be healthy enough to live in the wild. So that fold when mutated in the wild, not fed to other cattle that can absorb and incorporate the protein, it would die without being able to leave a healthy progeny that evolution need for it to succeed.

 

That's right. But say the cow was getting by without that protein in the first place (it's a "simpler" cow than our cows) then if a cow happenned to by chance evolve the damaged version of that protein, then it would also be selected against and be more likely to leave less or no) calves as it's descendants. However, despite the fact that natural selection is selecting against that particular mutation whenever it might crop up, the guidance that NS provides against that mutation, cannot assist in evolving that protein (or which the mutation happenned to be a damaged version of). So if our cow is to go from simpler to more complex (by evolving that new useful protein (or protein complex))

then it has luck, not natural selection to thank for it.

 

The question being of course, without natural selection being able to help, and given that we now know that many proteins (all but the very short and simple ones) are so rare as to be infeasible to find via random evolution - then we must ask, is it likely that they can be found at all (in any feasible time period) by such a mindless process as evolution? IDists say that in most cases, the answer is no. Howeve they also admit that in certain limited cases, the answer is yes.

 

Pitman's article establishes that point. So does Doug Axe's paper (in the ID Biocomplexity journal called - "the case against a Darwinian origin of protein folds"). However that ID paper is based on the peer reviewed published work of Axe carried out previousy. Pitman also references other peer reviewed papers from non ID scientists that lead to similar notions, that functional protein folds are such rare entities that the numbers seem to defy the odds. How could nature find them without the help of natural selection? This is known as the "sampling problem". Basically it is a "find the tiny needle in a large haystack in 5 seconds" kind of problem.

 

 

I apologize for not getting to the articles yet, I have had much busier weekend than I had planned but will get to it ASAP

 

Take as long as you need to, and them some. There's no rush. Life is too short to spend it all on the internet, right? I'm starting to realize that more than I used to.

[Monsters from the ID]

http://www.detectingdesign.com/steppingstones.html

 

It's odd he doesn't mention what he means by not getting wet. Evolutionary theory, for this analogy, says something more like the stepping stones are far apart and some will have adaptations that survive the swim others will not. That progeny will pass on its 'swimming ability' so they can keep swimming from stone to stone and other adaptations will be produce that make the swim even easier. Getting wet happens all the time, as does drowning, the point is that some of them survive the swim.

What he meant by steppingstones and the water is this: Each steppingstone is an aquired new beneficial function. If the steppingstones are close together then evolution can quickly find them. Once one is found it may well be able to be preserved by natural selection - thus building up the complexity and sophistication of the organism. Getting wet means basically that in this part of the evolution, the new beneficial function is out there somewhere, but has not yet been found. So being wet means that the part of the DNA that might code (in the future) for some as yet unrealized benefical function (just like the hidden treasure in the forest) is not currently doing so. As a result, natural selection cannot do anything to assist in the finding of the next steppingstone (a beneficial function that may or may not be found).

 

So if the steppingstones are very close together, then evolution can find these new beneficial functions pretty fast. And in some cases this is true, as in examples like the evolution of resistance to antibacterial chemicals. In other cases the new beneficial functions are like distant islands. To get to them you'd have to cross a huge ocean. And that via a random search. There is no guidance to any of these islands or steppingstones. But the closer they are, the faster they will likely be found, and vica versa.

 

Him talking about how adding a letter does nothing because both are meaningless is a ridiculous analogy. In an intro bio course you find a sentence like 'the sad cat and bat', codons being paired in threes. now you will see that the addition of a single letter will yield 'ath esa dca tan dba t' which is fundamentally useless as a sentence and as a codon because it is no longer in pairs of 3. This is similar to the start/stop codon problem in my last post. Now there are many ways this sentence can change and still be functional, whether it is detrimental or helpful doesn't matter now, such as a codon switching positions 'the cat and sad bat' or 'sad cat and the bat' etc; even whole codons being inserted such as 'now the sad cat and bat'. All of these are still fully functional. You could even look at the sentences that have a somewhat semantically correct structure as helpful functions and semantically wrong mutations as harmful such as a single letter shift, 'tth esa dca tan dba'. Hopefully you get that there are huge amounts of different ways that are functionally sound as well as those that are functionally bunk.

I do understand that there are huge numbers of different ways that are functionally sound as well as functionally bunk. However, the longer the sentences get (paragraphs and essays rather than single sentences) and the longer the words get (3 letter words have more functionally dense possibilities than say 7 letter words) then if we are allowing more content such as long essays and long words as well as shorter ones, then even though there are an astronomically large number of ways in which we can express meaningful function, there are a far larger (astronomical to a far greater magnitude) number of ways in which there will be meaningless bunk. So compared to short sentences with short words, multiple long sentences put into paragraphs that can also contain large words as wellas small words, will be far less functionally dense. So the ratio of meaningful arrangements to bunkum arrangements for the longer texts, becomes an exponentially shrinking ratio. This means that mindless process such as evolution will have to search for longer and longer times. And in fact given some calculations you can show that the search time becomes infeasible. This includes having evolution in parallel with huge populations over billions of years. This kind of search for function rapidly becomes an ill conditioned problem.

 

 

Another problem he is having is understanding that some evolutionary traits that don't necessarily give benefit now doesn't mean that they will never end up being beneficial. Even some things that are somewhat harmful can still be passed on and end up being beneficial in another sort of environments. Easily done if the animal is migratory.

That is true, but doesn't really change anything much in the conclusions. I think he well understands all of that, but has realized it makes little difference to his main points.

 

 

What are these stepping stones...?

 

Steppingstones are new useful functions - or even just existing areas of DNA sequence that code for useful function. Whether the function is new or not, is purely dependent on whether the organism has managed to evolve that function already - or not yet.

 

Then he talks about how antibiotics target specific areas of the bacteria. He makes points to show how unbelievable improbable that it is to evolve a certain genetic sequence toward a certain specific function, yet says it's perfectly acceptable for bacteria. . . odd.

 

The reason that evolving resistance to antibacterial agents is easy to do (thus fast in bacteria) is for two reasons. First, there are lots of bacteria evolving in parallel. But more importantly, antibacterial agents are using certain chemicals within the bacteria as attack points. For example, imagine a certain chemical is like a bridge. Then the enemy can use that bridge (the bridge is for the use of the friendlies) to invade the friendly country. Now evolution has two options (among others). It can either evolve a sophisticated mechanism of defense against the antibacterial agent - or else it can simply destry that part of the chemistry that is being used by the antibacterial agent.

 

Thus in the war analogy, is it faster to develop some new weapon to repel the invading forces, oris it faster to just blow up the bridge they are using to cross over on? Option 2 is the fastest and easiset method of evolution. It's always much more probable that some existing feasture will be broken or altered, than it is likely that some new function will be involved.

 

In most cases, altereing or breaking parts of your own chemistry is a bad thing - however if the alternative is to be destroyed, then it is probably better to a certain extent to get crippled and survive, rather than stay healty and get wiped out. This also shows that due to the shortsighted nature of evolution, it usually solves survival problems by breaking, rather than creating existing systems. Thus selection pressures, though enabling survival in some cases (which is better than nonsurvival) , will most of the time lead to a degeneration of functions. Becaue is it much more probable that selection pressure survival problems will be solved "the easy way" via the (beneficial in the short term) breakage and disablement of existing functions.

 

This is what I meant earlier when I mentioned that some examples of apparently poor design may in fact be the damage that evolution has allowed to happen in order to solve selection pressure issues. Evolution almost always chooses the easier way.

 

The harder way to try to win a war - is by conducting an arms race.

 

The easier way to try to win a war - is by conducting a scorched earth policy.

 

 

Anyway some fun facts about how else bacteria can do things like this, they have an amazing ability to incorporate genetic sequences into their own code.

 

Being somewhat simpler than higher organisms are, they are more "modular" so to speak. Such properties are impressive and can in themselves be thought of as supporting evidence that bacteria were designed to be able to take advantage. Being simpler, it is not as big a deal to adapt in such ways as it would be for more sophisticated organisms.

 

 

You also have to realize by now that bacteria don't think, 'Oh, look, they're using penicillin. I sure wish I had some penicillinase so it wouldn't hurt me. Oh look, there's some. I think I'll give it to my children.' Some bacteria happen to have a resistance to penicillin, people stop taking it and that bacteria that has a slight resistance survives and infects others. They do the same and the next generation will have an even stronger resistance, ad infinitum.

 

Yes, but you'll find that newly evolved resistance usually always comes with associated penalties. Why? Because it's likely that the resistance was present because the bacteria that has the resistance had mindlessly evolved in such a way that some function within it became damaged or unregulated. That change is what confered the resistance, but the damage incurred also makes the bacteria less competitive away from the threat.

 

What is happenning is that this kind of "scorched earth policy" evolution is finding the cheap and (non) cheerful solutions to problems that is damaging the organisms that survive. While they do survive (if they even do manage to survive) they are now weaker than they used to be. That's because new machinery isn't being built often enough (if ever) to keep up with the damaged, deregulation and loss of existing machinery via "scorched earth policy" type evolution, wehich is the mos common type of evolution that takes place.

He may be right, if that's how it worked at all. A single bacteria doesn't just come about immune to penicillin, though it may happen by pure chance. The immune strain had parents that were unbelievably immune, which had parents who were extremely immune, which had parents who were ridiculously immune, etc, etc. This is oversimplified but hopefully you get the idea.

Actually, I'm not sure what you mean. I'd be thinking that the immunity developed quickly initially ,and is then carried on down for as long as the threat remains. But if the threat is withdrawn, then that immunity may be perhaps lost agaoin over time, since in most cases the immunity is associated with some damage that took place, so the organisms became less efficient (though that doesn't matter if the damge isn't lethal and allows the organism to overcome the threat). But if the threat ever goes away, then the organism may be at a disadvantage. It has now evolved into a niche that it may find difficult to evolve back out of.

 

Interesting but not at all as big as he thinks it is. Enzymes are extremely specific because they have been evolving with us for a very long time and have had time to become specialized. I've never heard a biologist say a fully functional specific enzyme just appears out of, although it could. All that matters for evolution is that something give some sort of advantage. Now if a non-specific enzyme that could fit multiple sugars but didn't bread them down as fast as we see now, but still act as a catalyst, there would be an advantage. The problem with saying that this shows evolution stopped is that it measured only the expected reaction rate with the enzyme lactase and not the reaction rate of lactose with bacteria compared to the reaction rate of lactose with no bacteria. If there is a significant measurable difference it could have evolved a novel enzyme that just doesn't work as fast as lactase.

 

We don't know this is the case yet, but given the speed with which that initial new enzyme appeared, it seems perhaps there exists a kind of backup system for important enzymes and processes. Building in redundancy would certainly make an organism more robust to the kind of damage I was just talking about. But as Hall did, if you then remove the stand-in as well, well then the organism may be in real trouble as it's "spare tyre" has also been punctured (so to speak).

 

As I said though, that is speculative. But it is an interesting avenue for further research I'd imagine. Are organisms equipped with the capability to backup certain important processes. Perhaps some pseudogenes may be relevant here. On the other hand, some other examples of pseudogenes do in fact appear to be nonfunctional like the human vitamin C case. But other pseudogenes are now being found to have functions of various kinds. It's going to take quite a while to figure out exactly whats going on down there in the DNA, isn't it!

[Ringer]

I have a better anaolgy (that of the small islands and large oceans), but as far as the maze analogy goes, it is meant to represent the potential pathways leading (for example) to the evolution of a new functional protein. Now once you are outside the maze, the protein has been evolved. In other words, getting out of the maze means that finally after however long it took to get out of the maze, we hit upon that sequence code that specifies some new function. However, while in the maze, that new function didn't yet exist. If the organism that finally evolves the functional new protein finds that the new function is useful enough, they might have some advantage which can be picked up by evolution and this new protein or protein complex may sart to increase in the population and finally after a much longer time it may even become fixed in the entire population. That's an example of a successfully evolved new protein. But in the case of where nothing has yet emerged from the maze, there isn't a new protein yet. So until the maze is solved, nothing about the route out can be known by the many trials going on inside. While still in the maze, there is no advantageous or disadvantageous mutations with respect to solving the maze. To clarify - there will always be good, bad and neutral mutations as far as the organism is concerned, but whatever happens that is good, bad or indifferent to the organism as a whole, is irrelevant with respect to getting out of the maze. Meaning that the evolution taking place before the evoluton of some new feature appears, then whether a mutation is good bad or neutral to the whole organism, cannot be used as a criteria for guidance by natural selection that has anything to do with the evolution of some new feature before it appears. This means that any evolution that takes place that may be (or may not be) on the way towards some new feature emerging, is unguided (random) with respect to the appearance of a new feature that doesn't yet exist. Only after the new feature has just emerged, can natural selection begin to select for or against it, based on it's fitness contribution to the whole organism. While within the maze, no learning can be undertaken. Evolution has no memories of anything. Evolutions "memories" (so to speak) come only from fixed (or on the way to fixation) already emerged new features that provide an advantage.

 

As an example, if a treasure is at a certain location in a large forest, then though different routes will alternatively provide advantages or problems related to comfort and survival along the way, whether these routes are safe and comfortable, or dangerous and uncomfortable, or dangerous and comfortable, or safe and uncomfortable, all of that guidance is useless as far as finding the treasure is concerned. If I find the treasure, it will be because of luck pure and simple. Nothing about the routes can give me any indication that I am moving towards or away from the treasure.

 

ID believes that we can establish that since the evolutyion of new features that don't yet exist is random evolution (the evolution of these new features that are yet to emerge is not guided towards by natural selection) then if the new features are rare enough entities in coding space, then they will in all likelihoods never be capable of being found by the unguided process of random evolution.

 

It's only after a new feature has emerged that natural selection can begin to provide guidance to the future evolution that can conserve and adapt that feature.

 

You just turned a decent analogy into a god awful one with lots of word salad and meaninglessness. Inheritance is evolution's memory, it doesn't matter what the traits do all that matters is what was inherited from the parents. Let's say that again, it doesn't matter if the traits are good, bad, ugly, useless, dirty, gross, helpful, or anything they will still be passed on from generation to generation so long as the progeny continues. Since you don't believe new features have evolved does that mean you believe that humans have always had the ability to digest lactose since they have existed? You also need to realize that evolution does not have a direction. That is the flaw in the maze analogy, that's why it's a simplified analogy, evolution doesn't have an end point or a correct solution, just animals that happen to survive and reproduce.

 

 

 

 

I did know that. I don't get your particular point with that.

 

My point was a single inserted letter could make an entirely new amino acid sequence thus making it obvious that a simple mutation could create an entirely novel function. ID's entire premise is that it is impossible to create novel functions through random mutation. So all we have to do to nullify ID is give examples of why it is possible. Every one here has been nice enough to give you evidence, papers, sites, ideas, etc. I believe it's about time you return the favor and start giving your own evidence, not that guys website, to show us why ID is a better alternative to evolution.

 

 

 

As previoulsy pointed out, the inheritance cuts in when we have already emerged already functioning systems in place. But before such systems have managed to emerge, since their functional advantages are as yet non existent, then there can be no "memories" so to speak that can pass along any guidance information. In fact, lethal mutation pathways that got tried once (resulting in the death of the organism that tried them) may be tried yet again - over and over. If a lethal mutation is experienced, then that creature gets deleted, but that same mistake is available for reuse. Nothing is there to prevent such things happening again.

 

As pointed out over and over again, you are wrong. Just because there is nothing to stop a deadly mutation from happening doesn't mean anything whatsoever, there's also nothing to stop beneficial mutations and they will be carried on by the parents children.

 

 

 

Sure. But first the useful proteins need to have already emerged from nonexistence. Only AFTER they have emerged, can they can be selected for or against. But before a new protein has emerged, natural selection is unable to help it emerge. It must emerge by chance. Once you manage BY CHANCE to find the treasure that was sitting out there somewhere in the forest (or found your way out of the maze), THEN the treasure will give you the advantages that particular treasure provides. And AFTER you benefit from the treasure, then natural selection can favour you over the other poor so and so's who are still wandering around in the forest (or within the maze) not yet having found any treasures. And note that to be a more realistic analogy to evolution, then the people wandering aroud in the forest or inside the maze, cannot have any memories of where they have already been.

Get out of abiogensis, if you want to talk about that first read the links I gave then talk to organic chemists.

 

 

That's right. But say the cow was getting by without that protein in the first place (it's a "simpler" cow than our cows) then if a cow happenned to by chance evolve the damaged version of that protein, then it would also be selected against and be more likely to leave less or no) calves as it's descendants. However, despite the fact that natural selection is selecting against that particular mutation whenever it might crop up, the guidance that NS provides against that mutation, cannot assist in evolving that protein (or which the mutation happenned to be a damaged version of). So if our cow is to go from simpler to more complex (by evolving that new useful protein (or protein complex))

then it has luck, not natural selection to thank for it.

 

Really? Do you understand that natural selection isn't an actual entity just an idea? You can call it luck, chance, etc. it's still natural selection.

 

 

The question being of course, without natural selection being able to help, and given that we now know that many proteins (all but the very short and simple ones) are so rare as to be infeasible to find via random evolution - then we must ask, is it likely that they can be found at all (in any feasible time period) by such a mindless process as evolution? IDists say that in most cases, the answer is no. Howeve they also admit that in certain limited cases, the answer is yes.

 

Pitman's article establishes that point. So does Doug Axe's paper (in the ID Biocomplexity journal called - "the case against a Darwinian origin of protein folds"). However that ID paper is based on the peer reviewed published work of Axe carried out previousy. Pitman also references other peer reviewed papers from non ID scientists that lead to similar notions, that functional protein folds are such rare entities that the numbers seem to defy the odds. How could nature find them without the help of natural selection? This is known as the "sampling problem". Basically it is a "find the tiny needle in a large haystack in 5 seconds" kind of problem.

 

I would talk about Axe's paper but I read a reaction to it on Panda's thumb that talked about it much better than I could.

 

 

 

What he meant by steppingstones and the water is this: Each steppingstone is an aquired new beneficial function. If the steppingstones are close together then evolution can quickly find them. Once one is found it may well be able to be preserved by natural selection - thus building up the complexity and sophistication of the organism. Getting wet means basically that in this part of the evolution, the new beneficial function is out there somewhere, but has not yet been found. So being wet means that the part of the DNA that might code (in the future) for some as yet unrealized benefical function (just like the hidden treasure in the forest) is not currently doing so. As a result, natural selection cannot do anything to assist in the finding of the next steppingstone (a beneficial function that may or may not be found).

 

So if the steppingstones are very close together, then evolution can find these new beneficial functions pretty fast. And in some cases this is true, as in examples like the evolution of resistance to antibacterial chemicals. In other cases the new beneficial functions are like distant islands. To get to them you'd have to cross a huge ocean. And that via a random search. There is no guidance to any of these islands or steppingstones. But the closer they are, the faster they will likely be found, and vica versa.

 

Oh, and how exactly do we establish which are further away and which are closer? By thinking, 'damn that must have been pretty difficult.'

 

 

 

 

I do understand that there are huge numbers of different ways that are functionally sound as well as functionally bunk. However, the longer the sentences get (paragraphs and essays rather than single sentences) and the longer the words get (3 letter words have more functionally dense possibilities than say 7 letter words) then if we are allowing more content such as long essays and long words as well as shorter ones, then even though there are an astronomically large number of ways in which we can express meaningful function, there are a far larger (astronomical to a far greater magnitude) number of ways in which there will be meaningless bunk. So compared to short sentences with short words, multiple long sentences put into paragraphs that can also contain large words as wellas small words, will be far less functionally dense. So the ratio of meaningful arrangements to bunkum arrangements for the longer texts, becomes an exponentially shrinking ratio. This means that mindless process such as evolution will have to search for longer and longer times. And in fact given some calculations you can show that the search time becomes infeasible. This includes having evolution in parallel with huge populations over billions of years. This kind of search for function rapidly becomes an ill conditioned problem.

 

Indeed it does take evolution a very long time, if ever, to find an extremely useful trait that seems to be perfect. Luckily it has billions of years to do so and a virtually uncountable number of generations as well.

 

 

That is true, but doesn't really change anything much in the conclusions. I think he well understands all of that, but has realized it makes little difference to his main points.

 

It completely changes his, and your, point that something must be functionally well established to benefit future mechanisms.

 

 

 

Steppingstones are new useful functions - or even just existing areas of DNA sequence that code for useful function. Whether the function is new or not, is purely dependent on whether the organism has managed to evolve that function already - or not yet.

 

Then his analogy is just blatantly wrong and misleading. As I said before, evolution does get wet, it is you that say it can't not us. Prove to us that it can't with data and evidence not opinions.

 

 

 

The reason that evolving resistance to antibacterial agents is easy to do (thus fast in bacteria) is for two reasons. First, there are lots of bacteria evolving in parallel. But more importantly, antibacterial agents are using certain chemicals within the bacteria as attack points. For example, imagine a certain chemical is like a bridge. Then the enemy can use that bridge (the bridge is for the use of the friendlies) to invade the friendly country. Now evolution has two options (among others). It can either evolve a sophisticated mechanism of defense against the antibacterial agent - or else it can simply destry that part of the chemistry that is being used by the antibacterial agent.

 

Thus in the war analogy, is it faster to develop some new weapon to repel the invading forces, oris it faster to just blow up the bridge they are using to cross over on? Option 2 is the fastest and easiset method of evolution. It's always much more probable that some existing feasture will be broken or altered, than it is likely that some new function will be involved.

 

In most cases, altereing or breaking parts of your own chemistry is a bad thing - however if the alternative is to be destroyed, then it is probably better to a certain extent to get crippled and survive, rather than stay healty and get wiped out. This also shows that due to the shortsighted nature of evolution, it usually solves survival problems by breaking, rather than creating existing systems. Thus selection pressures, though enabling survival in some cases (which is better than nonsurvival) , will most of the time lead to a degeneration of functions. Becaue is it much more probable that selection pressure survival problems will be solved "the easy way" via the (beneficial in the short term) breakage and disablement of existing functions.

 

This is what I meant earlier when I mentioned that some examples of apparently poor design may in fact be the damage that evolution has allowed to happen in order to solve selection pressure issues. Evolution almost always chooses the easier way.

 

The harder way to try to win a war - is by conducting an arms race.

 

The easier way to try to win a war - is by conducting a scorched earth policy.

 

I could probably write an entire paper on things that are wrong with this analogy and the misconceptions therein. But to sum it up, it doesn't matter what's easy and organisms don't choose what to evolve. That is your idea, that something chooses how things evolve, not ours. All that matters is something happened to work not whether it was easy or if it was the best option. It worked, that's all that matters.

 

 

 

 

Being somewhat simpler than higher organisms are, they are more "modular" so to speak. Such properties are impressive and can in themselves be thought of as supporting evidence that bacteria were designed to be able to take advantage. Being simpler, it is not as big a deal to adapt in such ways as it would be for more sophisticated organisms.

 

Bolded words are meaningless to living things. There is no hierarchy within the animal kingdom to say we are higher organisms. If anything we are much lower because we are less successful and we would not be able to survive without these 'lower' organisms yet they could easily survive if our entire population were to die.

 

But back to the main point, prove it. That they were designed that way and didn't and couldn't evolve that way.

 

 

 

Yes, but you'll find that newly evolved resistance usually always comes with associated penalties. Why? Because it's likely that the resistance was present because the bacteria that has the resistance had mindlessly evolved in such a way that some function within it became damaged or unregulated. That change is what confered the resistance, but the damage incurred also makes the bacteria less competitive away from the threat.

 

What is happenning is that this kind of "scorched earth policy" evolution is finding the cheap and (non) cheerful solutions to problems that is damaging the organisms that survive. While they do survive (if they even do manage to survive) they are now weaker than they used to be. That's because new machinery isn't being built often enough (if ever) to keep up with the damaged, deregulation and loss of existing machinery via "scorched earth policy" type evolution, wehich is the mos common type of evolution that takes place.

 

What penalties? If you mean that certain adaptations wouldn't work well outside of the niche associated with a certain organism, then I agree. But you know what that sounds like, evolution. Animals evolved certain traits to survive different evolutionary pressures. But how are they weaker? Because they produce an enzyme that breaks downs penicillin before it can kill it.

 

 

Actually, I'm not sure what you mean. I'd be thinking that the immunity developed quickly initially ,and is then carried on down for as long as the threat remains. But if the threat is withdrawn, then that immunity may be perhaps lost agaoin over time, since in most cases the immunity is associated with some damage that took place, so the organisms became less efficient (though that doesn't matter if the damge isn't lethal and allows the organism to overcome the threat). But if the threat ever goes away, then the organism may be at a disadvantage. It has now evolved into a niche that it may find difficult to evolve back out of.

 

Well this is an empirical question not a logical one. Immunity doesn't develop quickly, for the most part. Also even when the threat is gone the trait could remain for quite a long time. How is immunity associated with damage, examples please.

 

 

We don't know this is the case yet, but given the speed with which that initial new enzyme appeared, it seems perhaps there exists a kind of backup system for important enzymes and processes. Building in redundancy would certainly make an organism more robust to the kind of damage I was just talking about. But as Hall did, if you then remove the stand-in as well, well then the organism may be in real trouble as it's "spare tyre" has also been punctured (so to speak).

 

As I said though, that is speculative. But it is an interesting avenue for further research I'd imagine. Are organisms equipped with the capability to backup certain important processes. Perhaps some pseudogenes may be relevant here. On the other hand, some other examples of pseudogenes do in fact appear to be nonfunctional like the human vitamin C case. But other pseudogenes are now being found to have functions of various kinds. It's going to take quite a while to figure out exactly whats going on down there in the DNA, isn't it!

 

Alright I am going to stop responding to you until you actually get to at least some of my earlier posts and links to show you are actually making an effort of seeing both sides of the argument and not just cherry-picking, moving the posts, and all the other things that ID proponents love to do.

 

[edit] I will still go through your links when I have the time if only to show you that the guy you keep going to is full of it[/edit]

Edited July 8, 2011 by Ringer

[Monsters from the ID]

Alright I am going to stop responding to you until you actually get to at least some of my earlier posts and links to show you are actually making an effort of seeing both sides of the argument and not just cherry-picking, moving the posts, and all the other things that ID proponents love to do.

 

 

I've been busier after hours lately than previously. In addition I'm looking at Matzke's paper. It's pretty long, and is taking quite a while to go through. It would be useless to just present a quick "summary" which isn't any summary at all and which ignores most of it's content while also making assertions that fit my viewpoint but ignore his points. This means that our discussion has ground to a halt until I can go through his paper properly. But that would seem to be the proper thing to do.

[Ringer]

All right I can't sleep so back on to the Limited Evolutionary Potential link

Other unfortunate bacteria seem to be just as limited in their evolutionary potential. Even though they would significantly benefit, many types of bacteria, after more than a million generations, have not been observed to evolve a relatively simple lactase enzyme. This is fewer generations than it supposedly took humans to evolve from ape-like creatures. One should also note that these same bacteria, unable to evolve a lactase enzyme, are all able to evolve, in relatively short order, resistance to any antibiotic that comes their way. So what is it, exactly, that "limits" the evolutionary potential of living things, like bacteria, in their ability to evolve some functions but not others?I propose that the answer can be found in the number and density of beneficial “stepping-stones†available (in the form of genetic sequences). For forms of antibiotic resistance that are gained by blocking the antibiotic-target function, there are lots of beneficial steppingstones very close together, but not so for the enzymatic functions of lactase or penicillinase. Relatively speaking, there are very few such enzymes, compared to the total number of possible sequences.

 

For example, there are 676 potential two-letter words in the English language. Of these, 96 are defined as meaningful, creating a ratio of meaningful to meaning- less of 1 in 7. Now, there are 296 more meaningful three-letter words, totaling 972, but the total number of potential words increases 26 fold to 17,576. Since the number of meaningful words only increased by a fraction of this amount, the ratio of meaningful to meaningless dropped to 1 in 18.

 

 

So pretty much what he is arguing is that since the bacteria didn't evolve a very specific enzyme, and because that's the enzyme we want it to evolve, it doesn't evolve. That's like me saying that I can disprove evolution by showing that dolphins could easily survive on land but haven't redeveloped legs. And again we go back to his analogies of language which I have already went over.

 

 

Still, such ratios are relatively high, and random walk can get from any one-, two-, or three-letter words to any other via a path of meaningful words, as in the steppingstone sequence of cat â€" hat â€" bat â€" bad â€" bid â€" did â€" dig â€" dog. "Evolution" (changing meaning or "function") at this level is rather simple because the stepping-stones are so close together. But, with each additional minimum letter requirement, the growth of the meaningless sequences quickly outpaces the growth of the total number of meaningful sequences, and the ratio of meaningful to meaningless gets smaller and smaller at an exponential rate.

 

 

Man I wish I could change the definition of words to suite my argument; I would win every time. Evolution (biological evolution) doesn't mean change in meaning or function, it means change in allele frequency over time. Again he goes back to the letter problem that is more and more meaningless.

 

 

I apologize that I will not, paragraph by paragraph, pick apart every bit of his argument. But to summarize the rest of it he plucks numbers out of the air, he makes more opinions about how natural evolution isn't enough to give us the complexity we have now without anything more than his amazement, then goes back to IC as his main argument.

 

 

Now your links to glial cells means two things. One, that we are learning new things about glial cells all the time. So glial cells work as more support than just structural, which was a theory of only one type of astrocyte, not to mention that only glial cells have the ability to create new cells that can differentiate into neurons (this is ridiculously oversimplified but you get the point). Two, so glial cells do more than we thought, how does that disprove evolution. Or if you were saying this in a big IC argument on the eyes how does this make the eyes more complex than they already were?

 

 

 

[edit] dumb, tired spelling mistakes [/edit]

Edited July 19, 2011 by Ringer

[Monsters from the ID]

I have a problem. In attempting to go over Matzke's paper on the evolution of the flagellum, I find that he makes an assertion and then backs it up with reference to a published paper. Nothing whatsoever wrong with that. The problem for me is that I would need to have access to these papers (or at least a dozen or so) in order to make a meaningful response to what he claims has been demonstrated or is supportable. I am looking into trying to find out what options there are for me to get access. But I can't really afford to spend several hundred dollars purchasing all of these individual papers as I need to. Perhaps I can get by with purchasing just a few. I could ignore all those references of course, but what would be the point of that? I'd then just be giving my opinion, unless I could argue with what Matzke is actually claiming by going to the sources. So I'm working on that.

 

Man I wish I could change the definition of words to suite my argument; I would win every time. Evolution (biological evolution) doesn't mean change in meaning or function, it means change in allele frequency over time. Again he goes back to the letter problem that is more and more meaningless.

 

I don't intend to respond to you until I've solved the literature access problem. It's what you requested and it seems fair. I just want to make this one comment on your statement above. Evolution as it is proposed very definately requires that as well as being defined as the fallback change in allele frequencies over time, is also required to be change in function. That is the major part of Matzke's model of flagellar evolution. It's usually called cooption. The taking of existing proteins being used elsewhere in the cell, and their modification to a form beneficial to our new evolving system. That is absolutely required, and is easily seen in the way that Matzke claims that he has definite protein homologies for many of the proteins involved. We're not just changing definitions to be tricky. This claim (that protein functions must change) is the heart and soul of attempts to explain the evolution of such contrivances.

[Ringer]

I don't intend to respond to you until I've solved the literature access problem. It's what you requested and it seems fair. I just want to make this one comment on your statement above. Evolution as it is proposed very definately requires that as well as being defined as the fallback change in allele frequencies over time, is also required to be change in function. That is the major part of Matzke's model of flagellar evolution. It's usually called cooption. The taking of existing proteins being used elsewhere in the cell, and their modification to a form beneficial to our new evolving system. That is absolutely required, and is easily seen in the way that Matzke claims that he has definite protein homologies for many of the proteins involved. We're not just changing definitions to be tricky. This claim (that protein functions must change) is the heart and soul of attempts to explain the evolution of such contrivances.

 

It is not required, but it does happen. My point was that if someone uses words other than what they actually mean it makes all attempts at discussion useless. When someone uses their own definition instead of the one everyone else is using it causes misunderstanding for everyone. But, the fact that things do change in function, still doesn't do anything for his arguments because he just repeats the exact same thing. He uses the alphabet example over and over and it is as useless this last time as it was the first time.

[Abishai100]

Leviathan: Congruence Cardiology

 

 

This is a really great thread.

 

The backwards method is an interesting way to approach the question posted in this thread.

 

As the thread creator suggested, if we can imagine re-creating intelligent organic life in a petri dish, then surely, we can imagine that an intelligent species implanted certain biochemical algorithmic sequences to set forth in motion the evolution of our intelligent species.

 

Imagine therefore that two human beings, living in close quarters during a time of great climactic turbulence (i.e., Ice Age) start to share all kinds of behaviors and mannerisms and actually start to resemble each other in appearance.

 

This sounds silly, but we've all heard those old lady folk tales and social campfire stories of husbands-and-wives in American small towns who resemble each other or begin to resemble each other after years of marriage. Their values and behaviors are so similar or become similar that they start to look like two 'peas-in-a-pod.'

 

In fact, that "premise" is what the unusual American sci-fi horror film "Leviathan" [1989] is all about --- a group of human undersea miners encounter a terrifying predatory creature that gorges the flesh of its human victims and then absorbs their bodies and brains to grow bigger (into some eerie conglomerate gestating super-being).

 

What can we learn from science studies about morphological adaptations yielding interesting symbiotic structures as extensions of a genetic organic ability to metamorphose during a single lifespan (i.e., caterpillar-to-butterfly)?

 

Certainly, in our modern age of networking wizardry (i.e., Facebook, eTrade, European Union), the ability of a human being to sensitively make profitable (and hence adaptive) networking connections can enhance survivability, which is why Hollywood (USA) makes films such as "The Wolf of Wall Street" [2013].

 

Such a model (albeit generic) could lend credence to the notion that if an intelligent species created us (and then left Earth), then perhaps this ancestral creator actually resembles us in appearance and behaviour.

 

We could arguably use this model to posit the statement that medicines/nutrients/psycho-pharmacologicals that promote circulation enhances a human being's resilience to undesirable changes. After all, doesn't the circulatory system affect the respiratory system and influence our breathing? Easterners argue that yoga, which encourages focused meditative breathing can influence our overall psychological health.

 

Would a hypothetical ancestral super-intelligence alien species resemble us in the circulatory system?

 

 

Edited February 12, 2016 by Abishai100