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Author Topic:   Where is the evidence for evolution?
Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 251 of 367 (33696)
03-05-2003 9:43 AM
Reply to: Message 245 by DanskerMan
03-05-2003 12:33 AM


Re: Some comments
Hi Sonnikke, I have been gone for a while, had to switch jobs when my old BioTech turned turtle, although hopefully it will transmute into a Phoenix. You asked for more info concerning pathways for gene control and duplication of genes for evolution. One major family of pathways involved in gene control which crosses species lines are the MAP Kinase proteins and their related protein families. Here is one very good reference providing informatio concerning the relationships
http://link.springer-ny.com/...als/00239/papers/49n5p567.pdf
(Sorry that I am not putting it in HTML format but I am short on time this morning). PLease note the clustering of the related p38 and JNK families with the related Yeast gene family for osmotic shock. These genes and their associated proteins play a different role than the mitogen activated proteins. Control generally occurs via a feedback style loop of the transcription factor substrates and the initiated gene product. Some of the apparently unrelated or difficult to trace families may be the result of looking at the active site rather than the docking site, of course the docking site data was not available at the time of publication of the paper. Here is a short reference for that as well.
http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=...
This type of duplication of a gene and use of the protein for a different function is rather common.
Another pathway, although not dealing with translational control of genes, is the clotting activity of horseshoe crabs. This is important as, based on current understanding, the Horseshoe crab is a very old and succesfull species. The reason that I like this pathway is that it trashes one of Dr. Behe's examples of Irreducible Complexity, namely blood clotting. Here is a little info on the crab and the clotting system.
Page Not Found | Marine Biological Laboratory
Please note the occurance of one the signs of an "Unsuccessful" pathway acording to Behe, namely the clotting of the entire organism due to an unusually severe infection. However, in the open circulatory pathway of the crab this generally is not a problem. Subsequent modifications to a similar pathway is a likely pathway for the evolution of clotting in animals with closed circulatory systems, here is a decent paper on this.
Page not found – Department of Biochemistry and Molecular Biophysics
So you see, duplication of genes for both individual proteins and portions of pathways really can account for complex, even "Irreducibly complex", pathways and systems.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz
[This message has been edited by Dr_Tazimus_maximus, 03-06-2003]

This message is a reply to:
 Message 245 by DanskerMan, posted 03-05-2003 12:33 AM DanskerMan has replied

Replies to this message:
 Message 306 by DanskerMan, posted 03-13-2003 5:58 PM Dr_Tazimus_maximus has replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 266 of 367 (33832)
03-07-2003 8:34 AM
Reply to: Message 263 by DanskerMan
03-06-2003 10:13 PM


Re: !!
"I'm glad you added the edited part, but I find this infuriating.
For instance, Dr. Page and many others basically dismiss *any* reference to any "creationist" literature, and essentially call it crap, yet I'm supposed to bow at your feet and soak up the information from the evo's *without* questioning or insinuating that it might be wrong. Talk about a biased view."
Sonnikke, please take a look at post 251, it gives intial answers to a part of your question in an earlier post concerning control of genetic pathways by gene duplication. I said initial because you can not put the entire answer into one paper. Hell, you can not even put the entire answer into a series of very large books. The reason for this is that there is no "one" mechanistic answer but rather a wide range or variety of mechanism that all essentially revolve around a theme, that theme being genetic alteration and its phenotypic effects.
As to the creationist cites and sites (sorry for the pun) that you are placing on these boards, part of the problem is that many of them have already been refuted. I do not trash all of them but I DO trash anything from the ICR as I have repeatedly exposed two of the principles (Gish and Morris) for their dishonesty and blatent lies. The same holds true from people such as Hovind and his group, anyone who has to lie about their academic credentials deserves only scorn. Their constant willful misquotes of reputable scientists completely disgusts me. I actually do not mind Dr. Behe so much, although I do disagree with him (as I pointed out in my earlier post) and do feel that his view on evolution is seriously flawed. These flaws have been repeatedly demonstrated in the ID section of this board.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz

This message is a reply to:
 Message 263 by DanskerMan, posted 03-06-2003 10:13 PM DanskerMan has replied

Replies to this message:
 Message 269 by DanskerMan, posted 03-07-2003 9:50 AM Dr_Tazimus_maximus has replied
 Message 270 by nator, posted 03-07-2003 9:52 AM Dr_Tazimus_maximus has not replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 276 of 367 (33860)
03-07-2003 12:09 PM
Reply to: Message 269 by DanskerMan
03-07-2003 9:50 AM


Re: lies
quote:
Most creationist are bible believing christians, as such they hold to a higher calling, upholding truth at all cost. Evolutionists on the other hand are not accountable to a Higher Being, and thus whether lies or truths come out of their mouths, is irrelevant to them because there is no specified benchmark. Also, morals are a product of mindless evolution according to them. Now how is it that I'm supposed to believe an evolved microbe, over a designed human who serves his God?
First, I have seen far too many bible believing Christians bend and distort the truth to agree with your statement. Also, many people who understand that evolution has occurred, and likely through one of the forms of natural selection, are also Christians (or Jews or Moslems) and hold in a higher being. I am married to one. Finally, if you had been paying attention to some of the earlier threads you would have seen proven examples of where people such as Gish have been caught misrepresenting others statements or work. A while ago someone posted a link to an expose of Hovinds doctorate. A degree purchased from a diploma mill. Some of the tracks at Paluxy were staged by your truthful, god-fearing Christians. So please do not tell me about their higher morals.
Now, as I was pleasant and polite in my earlier post to you I intend to take a little bit of a personal affront to te obvious implications in your post. You are correct in stating that I do not think that I am accountable to a higher being. However you could not be more mistaken in your statement whether lies or truths come out of their mouths, is irrelevant to them because there is no specified benchmark. My benchmark is my personal honor and frankly I have found that I stick to that far, far better than most Christians stick to their book. And there is no comparison to the state of my honor and the lack thereof with many of the lying miscreants at ICR. Musashi wrote in the Book of Five Rings that small deviations from the path become large deviations. Well the deviants at the ICR are so far off the path of personal honor and truthfulness that they are going in circles.
As to the other parts of my post, do you have any comments on the evolutionary question at hand or is SLPx correct in that all you want to do is hand wave. The ball is very much in your court on this one.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz
[This message has been edited by Dr_Tazimus_maximus, 03-07-2003]
[This message has been edited by Dr_Tazimus_maximus, 03-07-2003]

This message is a reply to:
 Message 269 by DanskerMan, posted 03-07-2003 9:50 AM DanskerMan has replied

Replies to this message:
 Message 278 by DanskerMan, posted 03-07-2003 12:46 PM Dr_Tazimus_maximus has replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 279 of 367 (33863)
03-07-2003 1:06 PM
Reply to: Message 278 by DanskerMan
03-07-2003 12:46 PM


OK, my statements concerning the ICR is not propaganda. Rather they are drawn from personal experience where I have hunted down original quotes and proven that the ICR representative was lying concerning those quotes. You can believe that or not but I have done it repeatedly on this and other boards.
As to the paper(s), they simply put, follow a line of genetic sequence comparison, coupled with comparison of the pathways which turn on the genes, and by this I mean both which genes are turned on due to different environmental conditions and how they are turned on. A very clear line of descent for duplication and modification of PATHWAYS is demonstrated for those pathways most functionally similar while those less functionally similar are not clear cut, and in fact have a far lower degree of relationship. The paper also references papers which describe genetic mechanisms for the dunplication of either whole or sections of pathways. Simply put they papers and those they reference describe how chuncks of DNA are copied and duplicated and then how the genes contained in the chunks of DNA may have been modified (ie mutated) w.r.t. new functions and environmental responses. There is a lot more but it acts as a start and actually refutes a umber of the points made in your citation in the earlier post w.r.t. control of genes and gene products w.r.t. evolution of pathways.
As to the Horseshoe Crab, the first site was a laymans site so you may find it interesting. Essentially it shows that the very proto style blood clotting system that Dr. Behe of LeHigh University said could not exist, DOES exist. And works quite well. The second paper is a desription of up and down stream (before and after reactions for certian biochemical events) mutations could, and likely did, result in an efficient clotting mechansim for a close circulation animal vs insects (and Horseshoe crabs, which are really more closely related to spiders than crabs).
Hope that helps.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz
PS The way your earlier post read indicated that, not believing in a diety, that supporters of evolution (and by extension me) lie to support our nefarious purposes. That was the reason for the backlash. We have supported our assertions concerning the ICR and people such as Hovind with a great deal of facts and examples, if you think that WE lie please try to provide support for that statement. For the record, I don't.
PPS.
I generally go by Taz.
[This message has been edited by Dr_Tazimus_maximus, 03-07-2003]
[This message has been edited by Dr_Tazimus_maximus, 03-07-2003]

This message is a reply to:
 Message 278 by DanskerMan, posted 03-07-2003 12:46 PM DanskerMan has not replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 281 of 367 (33889)
03-07-2003 6:19 PM
Reply to: Message 280 by wj
03-07-2003 5:41 PM


WJ
WJ, I think that his comments re: a lack of understanding were in reference to my request that he look at the references provided rather than to my comments on honesty and honor. Although I disagree with him and think that his faith in the integrity of the people at ICR is sorely misplaced, I would be dishonest if I didn't point out what I think is a misunderstanding.
Once again I come to Musashi, the way of the sword, narrow paths and attempting not to stray. Just wish I could get time from my new job to stray into the school and practice at least twice a week .
------------------
"Chance favors the prepared mind." L. Pasteur
Taz

This message is a reply to:
 Message 280 by wj, posted 03-07-2003 5:41 PM wj has replied

Replies to this message:
 Message 282 by wj, posted 03-07-2003 10:09 PM Dr_Tazimus_maximus has not replied
 Message 283 by DanskerMan, posted 03-07-2003 10:54 PM Dr_Tazimus_maximus has not replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 291 of 367 (34132)
03-11-2003 3:29 PM
Reply to: Message 286 by DanskerMan
03-10-2003 11:42 PM


Flaws
Sonnikke,
First, none of the articles were ad hominum attacks but were from documented cases of falsehoods largely told by Duane Gish. The same is true of the lies concerning credentials by people like Baugh and Hovind.
Second, many of the so called flaws that you and people at the ICR have discussed been pointed out (and again largely documented) as not being flaws at all. For instance, you asked about evolution of genetic control mechanisms, I answered. You asked for clarification and explaination which I provided. Now, please point out the flaws in their support for the basic Neo-Darwinian/Natural Selection mechanism for evolution, assuming that you can find any.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz

This message is a reply to:
 Message 286 by DanskerMan, posted 03-10-2003 11:42 PM DanskerMan has not replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 311 of 367 (34349)
03-14-2003 8:45 AM
Reply to: Message 306 by DanskerMan
03-13-2003 5:58 PM


Re: Crab
Good Morning Sonnikke,
I have actually read that piece by Dr. Behe. I actually thought that he was the one who skirted the issue. I do not have time for a full criticism now but I hope to have more time tonight. To put it simply, IC relies on the theoretical inability for systems to be cobbled together from existing system or pieces. First off there is a paper in the Journal of Theoretical Biology (By D. Ussery,, if I remember correctly) that destroys this arguement from a theoretical standpoint. Here is the link
http://www.cbs.dtu.dk/staff/dave/JTB.html
Second, he (Behe) totally ignored the point re: crustacians. Namely that they have an OPEN circulatory system (hence my point w.r.t. the Horseshoe crab), allowing for the simpler form of the clotting cascade for a different purpose, namely bacterial defense. The modified reuse of systems is a central point in evolutionary biology, as M. Behe should well know. As to the "problem" with the existence of the horseshoe crab, it is no such thing. The three remaining species are a small remenant of a once much larger family (read "Creation in a Crucible") and have done quite well in a rather small ecological niche, as would be expected under evolutionary theory whether you go with pure neodarwinian or PE based theory.
Actually neither Behe nor Miller use the Horseshoe crab much becuase they are both academics. ANyone in Biotech knows about the LAL assay, it is a key component in the testing of recombinant proteins derived from gram negative bacteria. It (the system) EVOLVED as a defense against bacteria, it was not created for our use, we have co-opted it. Biotech used to use rabbits and look for temperature spikes to determine the level of pyrogens, but that assay stunk.
As for the Pasteur quote, it has to do with keeping your mind primed for alternative explainiation or for the unexpected when reviewing data and events. It has served me well in the lab many times.
Got to get back to the lab now, I will try to go into the flaws of Behe's arguements in more detail later.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz
[This message has been edited by Dr_Tazimus_maximus, 03-14-2003]

This message is a reply to:
 Message 306 by DanskerMan, posted 03-13-2003 5:58 PM DanskerMan has not replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 341 of 367 (34669)
03-19-2003 8:12 AM
Reply to: Message 339 by Mammuthus
03-19-2003 7:35 AM


Re: Crab
Mammuthus, I am not sure that a translation would make much difference anyway. While Sonnikke did reply to the minor part of my earlier post, re: the Horseshoe crab, he completely ignored the major part where I translated data concerning the gene duplication of the MAP Kinase translational control pathways from simpler organisms. And that was the part which was a direct answer to one of his earlier questions concerning gene control and evolution. I intend to go ahead and answer his crab one concerning Dr. Behe when I can get the spare time as I like trashing this particular writting of Dr. Behe's. It is the one which I believe, I am sorry to say, is either the most duplicious or the one which highlights his lack of understanding of the basic tenats of the general theories of evolution.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz

This message is a reply to:
 Message 339 by Mammuthus, posted 03-19-2003 7:35 AM Mammuthus has replied

Replies to this message:
 Message 344 by Mammuthus, posted 03-19-2003 9:53 AM Dr_Tazimus_maximus has replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 342 of 367 (34673)
03-19-2003 8:24 AM
Reply to: Message 339 by Mammuthus
03-19-2003 7:35 AM


Re: Crab
ARRGGHHHHHH
Delete Duplicate post
[This message has been edited by Dr_Tazimus_maximus, 03-19-2003]

This message is a reply to:
 Message 339 by Mammuthus, posted 03-19-2003 7:35 AM Mammuthus has not replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 346 of 367 (34686)
03-19-2003 10:36 AM
Reply to: Message 306 by DanskerMan
03-13-2003 5:58 PM


Re: Crab
OK, Sonnike, here is a short list a just a few of the problems with M. Behe's concepts concerning blood clotting, evolution via natural selection and IC/ID. I will start with Dr. Behe's own words.
quote:
Since my book came out, as far as I am aware there have been no paprs published by the scientific literature giving a detailed scenario or experiments to show how natural selection could have built the system
Sonnikke, the second paper which I cited to you earlier began to do just this. Now, I am aware that Dr. Behe could not have known this as it post-dates this article, however as I sent you the URL you have no such excuse.
The biggest problem with this publication is that it make numerous gross error w.r.t. what Darwin, and subsequent evolutionary biologists have been saying. For example, in Behes paper he writes
quote:
EVIDENCE OF COMMON DESCENT IS NOT EVIDENCE OF NATURAL SELECTION. Homologies among proteins (or organisms) are the evidence for descent with modificationthat is, evolution. Natural selection, however, is a proposed explanation for how evolution took place--
I hate to be the one to tell you this but Darwin called his mechanism Descent with Modification, precisely what Dr. Behe admits is being proven by the demonstrated homologies among proteins. Now, the THEORY for a portion of the driving force/filtering mechanism of evolution is Descent With Modification, AKA Natural Selection. Now while I will agree that a single pathway or a single organ or a single aspect of an organism is capable of providing it with a competitive edge, nowhere in the theory does it state that every single aspect of an organism must be competitively superior for the organism to leave progeny. This is actually a very key point and a major flaw in some of Behe reasoning (also a flaw in certain Ultra-NeoDarwinian camps as well IMO). It is the overall organism which leaves modified descendents, not a specific system within that organism. This error creeps up again and again in Dr. Behe’s discussion, in fact it is one of the chief flaws in his discussion of Keith Robison’s ideas. A specific mutation, duplication, system does not have to be specifically advantageous to be carried along with an organism which, as a whole, is superior enough to leave a greater number of descendents. As has been demonstrated by neutral or semi-neutral theory. One side comment on the section concerning K. Robisons ideas was the oft repeated statistical error (it was actually found in Dr. Behe’s book) of pre-supposing an individual, single outcome and then calculating a probability from it. This has often been called the Fallacy of Large Numbers and has been explained ad nausium on this and other boards.
Dr. Behe’s comments on the statements by Kenneth Miller contain a number similar flaws, and one new one. The statements concerning the irrelevancy of the Lobster clotting system which in a number of ways is very similar to the system which I posted from the Horseshoe Crab. The key point which Behe either misses or ignores is that, under Evolution by Natural Selection systems used by one organism can be used in modified forms by other descendent organisms. The reason to being up the Crab cascade is that a simpler form of clotting would be expected from an organism (from an evolutionary older lineage) with a simpler circulatory system. Please look at the map contained in the site below
Xiphosura
The point here is that the genetic maps and the fossil maps MATCH UP, which is what would be expected if these organisms were linked through evolution. Here is a little more info on the same subject,
http://www.peripatus.gen.nz/Taxa/Arthropoda/Index.html
Essentially it demonstrates that the fossil data and the molecular phylogeny data on the evolution of the clotting systems match up w.r.t. the evolution of open vs closed circulatory systems. Expected in Evolution, but not in creation or even necessarily in design.
This is just a brief set of problems with this "paper". I did not even address the theoretical problems which I pointed too earlier.
Ball is back in your court.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz

This message is a reply to:
 Message 306 by DanskerMan, posted 03-13-2003 5:58 PM DanskerMan has replied

Replies to this message:
 Message 364 by DanskerMan, posted 03-23-2003 8:38 PM Dr_Tazimus_maximus has not replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 347 of 367 (34696)
03-19-2003 12:35 PM
Reply to: Message 344 by Mammuthus
03-19-2003 9:53 AM


Re: Crab
Do you know the sad thing for my current feelings about Dr, Behe's work is that I went into his book with a totally open mind. Not sad because of the open mind but sad because of the final result. Behe actually admitted that ID was non-falsifiable in the creationist book "Mere Creation", and therefore admitted that their scientific enterprise was non-scientific. While I do not agree wth the more drastic aspects of the Popperian concept of science his base concept of falsifiable is, IMO, sound.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz
[This message has been edited by Dr_Tazimus_maximus, 03-19-2003]

This message is a reply to:
 Message 344 by Mammuthus, posted 03-19-2003 9:53 AM Mammuthus has replied

Replies to this message:
 Message 349 by Mammuthus, posted 03-20-2003 3:40 AM Dr_Tazimus_maximus has not replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 354 of 367 (34823)
03-20-2003 9:42 PM
Reply to: Message 353 by peter borger
03-20-2003 9:12 PM


Trouble!!!
Peter, you mean your theory is in trouble, fancy that .
Sorry I just could not resist .
------------------
"Chance favors the prepared mind." L. Pasteur
Taz

This message is a reply to:
 Message 353 by peter borger, posted 03-20-2003 9:12 PM peter borger has replied

Replies to this message:
 Message 355 by peter borger, posted 03-20-2003 10:01 PM Dr_Tazimus_maximus has replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 359 of 367 (34885)
03-21-2003 8:26 AM
Reply to: Message 355 by peter borger
03-20-2003 10:01 PM


Re: Trouble!!!
Hi Peter, I do not have much time this morning but my biggest problems with your stated theory are:
1)that it mis-uses randomness/probability in that you appear to be mixing pre-determined with increased probability and they are not the same, and
2)that you provide no evidence for either the existence or mode of action of your "creatons" or your "morphogenic fields", as well as little in explaination for what they are.
For example, I am just satrting Dr. Caporale's book but I am getting the general gist of it already (actually I also got it form literature for the last couple of years). When she discusses random vs non-random mutations she is in actuallity discussing varying degrees of probability over time at specific sites, she also provides data and mechanisms for the means of action. This is largely what you appear to lack. Not to mention that some of your early examples did not appear to back up your assertions, namely the biosynthetic pathway for ascorbic acid which you later abandoned, and the studies on australian mDNA which appeared to go against your stated theory.
Got to go, running lots of (as in far to damn many) gels and westerns today
------------------
"Chance favors the prepared mind." L. Pasteur
Taz

This message is a reply to:
 Message 355 by peter borger, posted 03-20-2003 10:01 PM peter borger has not replied

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