Register | Sign In


Understanding through Discussion


EvC Forum active members: 65 (9162 total)
9 online now:
Newest Member: popoi
Post Volume: Total: 915,815 Year: 3,072/9,624 Month: 917/1,588 Week: 100/223 Day: 11/17 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   What I have noticed about these debates...
Tranquility Base
Inactive Member


Message 106 of 238 (26668)
12-15-2002 6:43 PM
Reply to: Message 104 by Mammuthus
12-15-2002 6:25 AM


Mammuthus
Mammuthus writes:
The data from this paper show an extremely well conserved functional domain that is part of a superfamily of proteins indicating that the family evolved from a common ancestor.
This is precisely where you do the jumping to conclusions. You simply have blinkers on. The data is equally conmpatible with God reusing a design.
If you deny identity by descent you cannot believe in the concept of a protein superfamily. To be a "family" means that they have to show similarity by common ancestry.
Correct. If I had my way I would call these protein supergroups or something lke that. Anything that categorizes could be either a 'family' or a 'group'. Semantics cannot help anyone here.
'Superfamily' is an evolutionary misnomer anyway. Members of a superfamily are not necessarily related via divergent evolution even by the evolutionary definiton of superfamily. The term 'family' here simply means 'group'.
Then there should be no reason for KRAB memebers to show ANY sequence similarity. You could get the function multiple ways so why are KRAB proteins in one species more similar to KRAB proteins in the related species than in very distant relatives?
Why do you insist that God could not reuse designs just as a human engineer would?
What a bunch of nonesense TB...so you god follows the rules of chemistry but then ditches the observable rules of transmission genetics? Your independent creation schtick is hardly parsimonious..it requires ignoring a huge amount of data to believe in.
Could you explain what you're getting at here?
TB:
Two proteins with the same fold can have totoally different sequences but the same 'profile' and catalytic residues without being related by evolution. Go look up the definition of a superfamily to prove it to yourself.
M: However, that is not what I posted..and neither are the KRAB family, HOX, HERVs etc.
What's your point precisely? My point is simply that protein superfamilies have certain vauge 'profile' similarities that could be any of:
(i) Convergent evolution
(ii) Divergent evolution
(iii) Creation
I will point out TB, that you almost never post a single reference that supports you claim that I could read. I don't mean creationist literature. I mean, post a section of a genetics, genomics, zoological, or paleontological article or book that you think is a good example of creation and we can discuss it. As to my posting abstracts, I posted references that I felt dealt with the subject at hand. If you don't understand them or some part of them let me know. I thought the KRAB article and the tunicate genome sequencing article are pretty self explanatory.
I haveb't addressed your KRAB stuff. I'm talking it one abstract at a time and your first abstract was compeletley irrelevant. On the surface it kindo f sounds relevant, but in the end it has no relevance as I have explained.
The phophodiesterase article was just to show that evolution works by exon shuffling, duplication, deletion, di-tri-tetra nucleotide expansion etc etc to generate novelty. Horizontal transfer is another mechanism.
Guess what, I agree! If genomes arrived by evoltuion then one mechanism is shuffling, duplication etc. But the evidence that exists only demonstrates allelic examples. No-one has shown where distinct protein families come from. All you guys ever whow is that if evoltuion aoccurred it must have had such and such features. We agree! What we point out is that your mistake is your initial assumption that macroevolution has occurred.
Syncytin was originally an envelope protein for a retrovirus...now it initiates syncytiotrophoblast fusion for Old World Monkey and Great Ape placental development.
But that's simply your assumption. God could have inserted the gene in the genomes of all sorts of organisms of course as he could have for the entire proteomes. EDIT: see below, now that I have read the remainder of your post.
It is all consistent with the fact that in sexually reproducing animals you inherit you genes from your parents who inherited theirs from their parents all the way back to the common ancestor of all living things.
Yes it's consistent. It's also consistent with God creating kinds and then letting them go for it within allelic boundaries as one would expect from an engineering point of view.
[This message has been edited by Tranquility Base, 12-16-2002]

This message is a reply to:
 Message 104 by Mammuthus, posted 12-15-2002 6:25 AM Mammuthus has replied

Replies to this message:
 Message 108 by Mammuthus, posted 12-16-2002 4:24 AM Tranquility Base has replied

  
Tranquility Base
Inactive Member


Message 107 of 238 (26694)
12-16-2002 1:00 AM
Reply to: Message 101 by Mammuthus
12-12-2002 6:55 AM


Mammuthus
Let's now move to your Looman et al ref:
Mol Biol Evol 2002 Dec;19(12):2118-30
KRAB Zinc Finger Proteins: An Analysis of the Molecular Mechanisms Governing Their Increase in Numbers and Complexity During Evolution.
Looman C, Abrink M, Mark C, Hellman L.
Kruppel-related zinc finger proteins, with 564 members in the human genome, probably constitute the largest individual family of transcription factors in mammals. Approximately 30% of these proteins carry a potent repressor domain called the Kruppel associated box (KRAB). Depending on the structure of the KRAB domain, these proteins have been further divided into three subfamilies (A + B, A + b, and A only). In addition, some KRAB zinc finger proteins contain another conserved motif called SCAN. To study their molecular evolution, an extensive comparative analysis of a large panel of KRAB zinc finger genes was performed. The results show that both the KRAB A + b and the KRAB A subfamilies have their origin in a single member or a few closely related members of the KRAB A + B family. The KRAB A + B family is also the most prevalent among the KRAB zinc finger genes. Furthermore, we show that internal duplications of individual zinc finger motifs or blocks of several zinc finger motifs have occurred quite frequently within this gene family. However, zinc finger motifs are also frequently lost from the open reading frame, either by functional inactivation by point mutations or by the introduction of a stop codon. The introduction of a stop codon causes the exclusion of part of the zinc finger region from the coding region and the formation of graveyards of degenerate zinc finger motifs in the 3'-untranslated region of these genes. Earlier reports have shown that duplications of zinc finger genes commonly occur throughout evolution. We show that there is a relatively low degree of sequence conservation of the zinc finger motifs after these duplications. In many cases this may cause altered binding specificities of the transcription factors encoded by these genes. The repetitive nature of the zinc finger region and the structural flexibility within the zinc finger motif make these proteins highly adaptable. These factors may have been of major importance for their massive expansion in both number and complexity during metazoan evolution.
Much of this is again simply assumed. On the other hand I agree that genes can duplicate and mutate. Some of the members of this family probably have their origin in duplicaiton. But they are all still transcription factors and the protein folds are still the same.
You also said:
Sycytin is a HERV-W envelope gene that causes syncitotrophoblast fusion critical in the formation of the placenta. It only does this in Old World Monkeys and the great apes as other primates do not contain this class of HERV. They also require syncitiotrophoblast fusion but it is carried out by an unrelated gene.
I am quite prepared to agree with you that this sort of 'non-homologous replacement' as it is called has occurred in nature. It's clear that this is simply an example of horizontal transfer and that it does not explain how the gene itself arose.
Did it create a novel subsystem? No the system was working nicely. Then the gene hoped into the genome from elswhere and was able to funciton in parallele with the existing gene yielding redundancy. Then one or other gene, in this case the one that had been arond longer, mutated and becomae non-funtional. I agree that that is what may have occurred in this case. But the funciton already pre-existed as did the non-homologous, but similarly functioning, genes.
So that is definitely non-allelic, I'll grant that. But it does not represent the origin of a new gene family or new subsytem. Both were pre-exisiting.
[This message has been edited by Tranquility Base, 12-16-2002]

This message is a reply to:
 Message 101 by Mammuthus, posted 12-12-2002 6:55 AM Mammuthus has replied

Replies to this message:
 Message 109 by Mammuthus, posted 12-16-2002 4:35 AM Tranquility Base has replied

  
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 108 of 238 (26707)
12-16-2002 4:24 AM
Reply to: Message 106 by Tranquility Base
12-15-2002 6:43 PM


Hi TB:
This is precisely where you do the jumping to conclusions. You simply have blinkers on. The data is equally conmpatible with God reusing a design.
Correct. If I had my way I would call these protein supergroups or something lke that. Anything that categorizes could be either a 'family' or a 'group'. Semantics cannot help anyone here.
M: So you do not believe that you pass on any genetic material to your offspring i.e. they are genetically no more related to you than to a housefly? That is what you have to accept in order for you to claim I have blinkers on and that the proteins are similar, can be grouped by related organisms, have conserved functions. You can change it to protein superman groups for all the difference it would make. There is no reason for there to be homology of systematic relevance if the proteins are not similar by descent.
TB:
'Superfamily' is an evolutionary misnomer anyway. Members of a superfamily are not necessarily related via divergent evolution even by the evolutionary definiton of superfamily. The term 'family' here simply means 'group'.
M: Why would you call it a group in any case if you don't believe the proteins are related? You are not being consistent.
Why do you insist that God could not reuse designs just as a human engineer would?
M: Then your god is a pathetically poor engineer? And what human engineer are you claiming built the genome? But you seem to indicate you accept the natural process as it is but then insert god as responsible without evidence. Those are the blinkers you are wearing.
TB:
Could you explain what you're getting at here?
M: You were stating that the rules of chemistry are inviolable and are followed for whatever reason by your god. But then against the rules governing inheritence and population genetics, you claim that there is no identity by descent but rather constant independent creation events that you have no evidence for. How is that a parsimonious or even a testable hypothesis? And why should god obey the rules of physics and chemistry but then ignore the observable rules of inheritence which is ultimately also chemistry?
TB:
What's your point precisely? My point is simply that protein superfamilies have certain vauge 'profile' similarities that could be any of:
(i) Convergent evolution
(ii) Divergent evolution
(iii) Creation
M: Why 3? Convergent evolution (I am not sure what you mean by divergent evolution) but anyway, evolution predicts similarity by because of common ancestry. Why would creation? How would you test it? Created by who? If you answer that how do you know it was not created by something else? What created the creator?...
TB:
I haveb't addressed your KRAB stuff. I'm talking it one abstract at a time and your first abstract was compeletley irrelevant. On the surface it kindo f sounds relevant, but in the end it has no relevance as I have explained.
M: It did have relevance which I explained. However, handwaving away data that you do not like is hardly like you.
TB:
Guess what, I agree! If genomes arrived by evoltuion then one mechanism is shuffling, duplication etc. But the evidence that exists only demonstrates allelic examples. No-one has shown where distinct protein families come from. All you guys ever whow is that if evoltuion aoccurred it must have had such and such features. We agree! What we point out is that your mistake is your initial assumption that macroevolution has occurred.
M: Umm what exactly don't you get TB? If amphioxus has one hox cluster which developmentally restricts it to a very basic body plan and then you see Drosophila with a more complex body plan and more hox clusters and mammals with 4 hox clusters and yet more complicated body plans. The devo's have mapped out the transcription profiles particularly in drosophila for the significance in change in expression upon morphology even among fairly distant related species. How is this not macroevolution? If the duplicates, HERVs, shuffled exons are exclusive to a group and have some impact on the morphology, behavior etc on that group that makes it distinct, that is macroevolution. You are really not clear on what you want in terms of information. When you argued that bacteria have no evidence of hemoglobin I showed that they do and that it has a different function in bacteria. Hemoglobin evolution is macroevolution as well between bacteria and multicellular organisms.
TB:
But that's simply your assumption. God could have inserted the gene in the genomes of all sorts of organisms of course as he could have for the entire proteomes. EDIT: see below, now that I have read the remainder of your post.
M: We know the how and why HERVs transpose just like other proviruses. There have been direct observations as well as experimentall induced cases of retrotransposition. The HERV-W endogenous retroviruses are only known from Old World Monkeys and Great Apes from an infection of the last common ancestor of all. Given that we know how and why retrotranposons work, we know the systematics of primates and can perform tests of the relevant hypothesis involved, what compelling reason should I have for accepting your assertion that none of this occurred by the known natural mechanisms like other HERVs but is a case of "god did it"? I can test retrotranposition mechanisms..I can even find the most closesly related HERV envelope gene to syncytin (well I dont have to, it was alread published)...can you show any positive evidence that all of this entire field of inquiriy (which includes HIV research as it is a retrovirus to) is complete bullshit and that your god did it? Please provide some positive evidence for it.
TB:
Yes it's consistent. It's also consistent with God creating kinds and then letting them go for it within allelic boundaries as one would expect from an engineering point of view.
M: How so? Please detail how it is consisten with god creating kinds and what testable hypothesis there is that would support this view. Also list the kinds of experimental evidence you would gather for god creating kinds and the predictions you would make based on the testable hypothesis.
cheers,
M

This message is a reply to:
 Message 106 by Tranquility Base, posted 12-15-2002 6:43 PM Tranquility Base has replied

Replies to this message:
 Message 115 by Tranquility Base, posted 12-16-2002 5:48 PM Mammuthus has replied

  
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 109 of 238 (26708)
12-16-2002 4:35 AM
Reply to: Message 107 by Tranquility Base
12-16-2002 1:00 AM


TB:
Much of this is again simply assumed.
M: For example? What is assumed?
TB:
On the other hand I agree that genes can duplicate and mutate. Some of the members of this family probably have their origin in duplicaiton. But they are all still transcription factors and the protein folds are still the same.
M: I don't get you point. And didnt you just say in the last point that this was also consistent with your god individually creating each duplicate copy and in the process being so completely incompetent that he littered the genome with pseudogenes, recessive lethal mutations, etc etc.?
TB:
I am quite prepared to agree with you that this sort of 'non-homologous replacement' as it is called has occurred in nature. It's clear that this is simply an example of horizontal transfer and that it does not explain how the gene itself arose.
M: I dealt with that in the last post..HERV's are ancient proviruses..if you want to see a modern one look in the T cells of HIV infected patients and you will find modern versions of HERVs...if any of the HIV proviruses were to infect the germ line they would have a chance at becoming HERVs.
TB:
Did it create a novel subsystem? No the system was working nicely.
M: What are you talking about?
TB:
Then the gene hoped into the genome from elswhere and was able to funciton in parallele with the existing gene yielding redundancy. Then one or other gene, in this case the one that had been arond longer, mutated and becomae non-funtional. I agree that that is what may have occurred in this case. But the funciton already pre-existed as did the non-homologous, but similarly functioning, genes.
M: A completely unrelated gene took over a critical function in a specific group of organisms...and you don't consider this a radical difference? By the way, the envelope gene is not a similarly functioning gene...like hemoglobin in bacteria..it has drastically changed its function.
TB:
So that is definitely non-allelic, I'll grant that. But it does not represent the origin of a new gene family or new subsytem. Both were pre-exisiting.
M: I still get the impression you are looking for the first gene that ever existed i.e. abiogenesis...but in your debates you constantly shift your creation myth in time to it happened in the primate lineage..it happened after bacteria..it happened whenever it is convenient to the arguement. When exactly do YOU think the creation event occurred and what is your evidence for it? Since you on and off accept macroevolution, in some twisted way accept a very odd version of evolution within groups, it is not clear what your position is.
I would like to point out one last thing...we are in amolecular evolution debate and this is the Faith and Belief thread..I have the distinct feeling that we are way off topic for this thread and should perhaps consider moving the entire topic over to the Evolution or Origin of Life thread...what say you Adminaquility ? I would guess we are boring the crap out of the people who are reading this for he "what I have noticed about these debates..."
cheers,
M

This message is a reply to:
 Message 107 by Tranquility Base, posted 12-16-2002 1:00 AM Tranquility Base has replied

Replies to this message:
 Message 119 by Tranquility Base, posted 12-16-2002 8:25 PM Mammuthus has not replied

  
nator
Member (Idle past 2169 days)
Posts: 12961
From: Ann Arbor
Joined: 12-09-2001


Message 110 of 238 (26733)
12-16-2002 9:57 AM
Reply to: Message 97 by Tranquility Base
12-10-2002 5:42 PM


[QUOTE]Originally posted by Tranquility Base:
[B]Schraf
I'll admitt that that evidence is suggestive that Gish ignored facts. I'd like to hear his side of it. Has he commented on this accusation? Have you looked for it?[/QUOTE]
I am glad you do not the ignore the evidence in this case. Considering that one can read the transcripts of his statements and read his books, and SEE that he continued to use misleading or false information years and years after he was corrected, I am not sure why you need "his side" of anything.
Either he is a liar for Jesus or supremely incompetant as a scientist/intellectual.
Gish's side of the stories are linked to at all the talkorigins pages that discuss him. In fact, there are many, many links to Creationist viewpoints and responses on Talkorigins.
I am surprised that you seem to be new to this information, TB. Gish's tactics have been common knowledge for decades.
quote:
Many of your so called 'got yas' turn out to be very hollow. You accuse us of misusing extracts from Riley, Ethridge, Patterson and Gould. I have tracked down the original material in many of these instances in our library and I still agree with the creationist use of this material in almost every case.
Excellent. Post them here and we will discuss if Creationists misrepresented them and also why it is you agree with the use of the material.
BTW, I thought we were discussing if the scientists at the ICR, et. al. were crackpots or not, and their continued acceptance within the Creation 'science' movement is perhaps why mainstream science does not respect creation 'science' very much.
Shall we move on to Henry Morris?
"The entire monstrous complex was revealed to Nimrod at Babel by demonic influences, perhaps by Satan himself . . . Satan himself is the originator of the concept of evolution." (Morris, Troubled Waters of Evolution, 1974, pp 74-75)

This message is a reply to:
 Message 97 by Tranquility Base, posted 12-10-2002 5:42 PM Tranquility Base has not replied

Replies to this message:
 Message 111 by nator, posted 12-16-2002 10:17 AM nator has not replied
 Message 112 by nator, posted 12-16-2002 10:19 AM nator has not replied

  
nator
Member (Idle past 2169 days)
Posts: 12961
From: Ann Arbor
Joined: 12-09-2001


Message 111 of 238 (26739)
12-16-2002 10:17 AM
Reply to: Message 110 by nator
12-16-2002 9:57 AM


deleted to remove double post.
[This message has been edited by schrafinator, 12-16-2002]

This message is a reply to:
 Message 110 by nator, posted 12-16-2002 9:57 AM nator has not replied

Replies to this message:
 Message 113 by funkmasterfreaky, posted 12-16-2002 10:24 AM nator has not replied

  
nator
Member (Idle past 2169 days)
Posts: 12961
From: Ann Arbor
Joined: 12-09-2001


Message 112 of 238 (26740)
12-16-2002 10:19 AM
Reply to: Message 110 by nator
12-16-2002 9:57 AM


Oh, and another thing, TB...
Don't you think that a big reason that Creation 'science' isn't taken seriously by real science might be this statment from AiG that all of their 'scientists' must sign?
Legitimate scientific organizations do not require people to swear to a conclusion about nature before they have even conduced any research, TB. This is uttely anathema to inquiry.
This statement of faith is classic "any evidence which does not fit into the Bible is to be ignored or twisted to fit" dogma.
...and that's why it isn't even close to being real science.
http://www.answersingenesis.org/home/area/about/faith.asp
(I edited to remove items which were not science-related)
Statement of Faith
I. Priorities
1.The scientific aspects of Creation are important, but are secondary in importance to the proclamation of the Gospel of Jesus Christ as Sovereign, Creator, Redeemer, and Judge.
2.The doctrines of the Creator and the Creation cannot ultimately be divorced from the Gospel of Jesus Christ.
II. Basics
1.The Bible is the written Word of God. It is divinely inspired and inerrant throughout. It is the supreme authority in all matters of faith and conduct. Its assertions are factually true in all the original autographs.
2. The final guide to the interpretation of Scripture is Scripture itself.
3. The account of origins presented in Genesis is a simple but factual presentation of actual events and therefore provides a reliable framework for scientific research into the question of the origin and history of life, mankind, the Earth, and the universe.
4. The various original life forms (?kinds?), including mankind, were made by direct creative acts of God. The living descendants of any of the original kinds (apart from man) may represent more than one species today, reflecting the genetic potential within the original kind. Only limited biological changes (including mutational deterioration) have occurred naturally within each kind since Creation.
5. The great flood of Genesis was an actual historic event, worldwide (global) in its extent and effect.
6. The special creation of Adam (as one man) and Eve (as one woman), and their subsequent fall into sin, is the basis for the necessity of salvation for mankind.
7. Death, both physical and spiritual, entered into this world subsequent to?and as a direct consequence of?man?s sin.
Theology
10. Those who do not believe in Christ are subject to everlasting conscious punishment, but believers enjoy eternal life with God.
left this one in just for fun.
IV. General
The following are held by members of the board of Answers in Genesis to be either consistent with Scripture or implied by Scripture.
1. Scripture teaches a recent origin for man and the whole Creation.
2. The days in Genesis do not correspond to geologic ages, but are six (6) consecutive twenty-four (24) hour days of Creation.
3. The Noachian flood was a significant geological event and much (but not all) fossiliferous sediment originated at that time.
4. The Gap Theory has no basis in Scripture.
5. The view, commonly used to evade the implications or the authority of Biblical teaching, that knowledge and/or truth may be divided into ?secular? and ?religious? is rejected.
6. By definition, no apparent, perceived, or claimed evidence in any field, including history and chronology, can be valid if it contradicts the Scriptural record. Of primary importance is the fact that evidence is always subject to interpretation by fallible people who do not possess all information.

This message is a reply to:
 Message 110 by nator, posted 12-16-2002 9:57 AM nator has not replied

Replies to this message:
 Message 116 by Tranquility Base, posted 12-16-2002 6:04 PM nator has replied

  
funkmasterfreaky
Inactive Member


Message 113 of 238 (26741)
12-16-2002 10:24 AM
Reply to: Message 111 by nator
12-16-2002 10:17 AM


quote:
Statement of Faith
I. Priorities
1.The scientific aspects of Creation are important, but are secondary in importance to the proclamation of the Gospel of Jesus Christ as Sovereign, Creator, Redeemer, and Judge.
2.The doctrines of the Creator and the Creation cannot ultimately be divorced from the Gospel of Jesus Christ.
II. Basics
1.The Bible is the written Word of God. It is divinely inspired and inerrant throughout. It is the supreme authority in all matters of faith and conduct. Its assertions are factually true in all the original autographs.
2. The final guide to the interpretation of Scripture is Scripture itself.
3. The account of origins presented in Genesis is a simple but factual presentation of actual events and therefore provides a reliable framework for scientific research into the question of the origin and history of life, mankind, the Earth, and the universe.
4. The various original life forms (?kinds?), including mankind, were made by direct creative acts of God. The living descendants of any of the original kinds (apart from man) may represent more than one species today, reflecting the genetic potential within the original kind. Only limited biological changes (including mutational deterioration) have occurred naturally within each kind since Creation.
5. The great flood of Genesis was an actual historic event, worldwide (global) in its extent and effect.
6. The special creation of Adam (as one man) and Eve (as one woman), and their subsequent fall into sin, is the basis for the necessity of salvation for mankind.
7. Death, both physical and spiritual, entered into this world subsequent to?and as a direct consequence of?man?s sin.
Theology
10. Those who do not believe in Christ are subject to everlasting conscious punishment, but believers enjoy eternal life with God.
Amen to this! I see no problem here. I know you all think I'm nuts, but this is AWESOME!
------------------
Saved by an incredible Grace.

This message is a reply to:
 Message 111 by nator, posted 12-16-2002 10:17 AM nator has not replied

Replies to this message:
 Message 114 by Quetzal, posted 12-16-2002 10:44 AM funkmasterfreaky has not replied

  
Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 114 of 238 (26744)
12-16-2002 10:44 AM
Reply to: Message 113 by funkmasterfreaky
12-16-2002 10:24 AM


Yeah, Funk, it's a pretty succinct statement of faith. The problem is, the entire idea that you start with immutable, untouchable "givens" and then reject anything that might appear to contradict these givens, is diametrically opposite anything that might be construed as science. Hence, if the "creation scientists" are adhering to the above guidelines (and I have no reason to doubt they do just that), then 50% of what they call themselves is an out and out fabrication.

This message is a reply to:
 Message 113 by funkmasterfreaky, posted 12-16-2002 10:24 AM funkmasterfreaky has not replied

  
Tranquility Base
Inactive Member


Message 115 of 238 (26862)
12-16-2002 5:48 PM
Reply to: Message 108 by Mammuthus
12-16-2002 4:24 AM


Mammuthus
Mammuthus writes:
So you do not believe that you pass on any genetic material to your offspring i.e. they are genetically no more related to you than to a housefly? That is what you have to accept in order for you to claim I have blinkers on and that the proteins are similar, can be grouped by related organisms, have conserved functions.
There's nothing wrong with your POV except that it is only one interpretation, hence the blinkers.
There is no reason for there to be homology of systematic relevance if the proteins are not similar by descent.
If God created the genomes the sequence homology could be presnet due to creative reuse. And superfamily simlarity is not necessarily at the sequence level (see next).
TB:
'Superfamily' is an evolutionary misnomer anyway. Members of a superfamily are not necessarily related via divergent evolution even by the evolutionary definiton of superfamily. The term 'family' here simply means 'group'.
M: Why would you call it a group in any case if you don't believe the proteins are related? You are not being consistent.
The proteins are related by 3D structure, that's why they have the same seqweunce profile. A superfmaly is a structural family that does not need to be related deivergenetly. Trust me on this one will you. It's a mainstream definition! I teach it in my lectures.
You were stating that the rules of chemistry are inviolable and are followed for whatever reason by your god. But then against the rules governing inheritence and population genetics, you claim that there is no identity by descent but rather constant independent creation events that you have no evidence for. How is that a parsimonious or even a testable hypothesis? And why should god obey the rules of physics and chemistry but then ignore the observable rules of inheritence which is ultimately also chemistry?
Nature does obey the rules of genetics. But if God created kinds the rules of genetics have been only in action since the gneomes were created. You see tantalizing evidence of common descent in the homologous genes but it never bnothers you that tens of thousands of new unrealted genes have appeared since the simplest bacteria.
All you are doing is putting a slant on reuse. I am putting the other slant on it. Over time one or other of our viewpoints may be ruled out or become hard to justify (as future genomes turn up). Currently both are compatible with the data.
TB:
(i) Convergent evolution
(ii) Divergent evolution
(iii) Creation
M: Why 3? Convergent evolution (I am not sure what you mean by divergent evolution) but anyway, evolution predicts similarity by because of common ancestry. Why would creation? How would you test it? Created by who? If you answer that how do you know it was not created by something else? What created the creator?...
Divergent evoltuion is evolution that leaves undoubted signatures of common descent. For us it is simply reuse of a gene. As you probably know, convergent evolution is a stumbling upon a similar feature without evidence of common descent (for that feature). For us it is resuse of a protein fold without the sme sequence.
M: Umm what exactly don't you get TB? If amphioxus has one hox cluster which developmentally restricts it to a very basic body plan and then you see Drosophila with a more complex body plan and more hox clusters and mammals with 4 hox clusters and yet more complicated body plans. The devo's have mapped out the transcription profiles particularly in drosophila for the significance in change in expression upon morphology even among fairly distant related species. How is this not macroevolution? If the duplicates, HERVs, shuffled exons are exclusive to a group and have some impact on the morphology, behavior etc on that group that makes it distinct, that is macroevolution. You are really not clear on what you want in terms of information. When you argued that bacteria have no evidence of hemoglobin I showed that they do and that it has a different function in bacteria. Hemoglobin evolution is macroevolution as well between bacteria and multicellular organisms.
I get all of that. What you keep forgeting is that in additon to the generation of new paralogs new taxa systematically discover new protein families and systems that did not exist before.
M: We know the how and why HERVs transpose just like other proviruses. There have been direct observations as well as experimentall induced cases of retrotransposition. The HERV-W endogenous retroviruses are only known from Old World Monkeys and Great Apes from an infection of the last common ancestor of all. Given that we know how and why retrotranposons work, we know the systematics of primates and can perform tests of the relevant hypothesis involved, what compelling reason should I have for accepting your assertion that none of this occurred by the known natural mechanisms like other HERVs but is a case of "god did it"? I can test retrotranposition mechanisms..I can even find the most closesly related HERV envelope gene to syncytin (well I dont have to, it was alread published)...can you show any positive evidence that all of this entire field of inquiriy (which includes HIV research as it is a retrovirus to) is complete bullshit and that your god did it? Please provide some positive evidence for it.
I have no problem with horizontal transfer as I have said on many occasions. It does not account fo the origin of any gene family.
TB:
Yes it's consistent. It's also consistent with God creating kinds and then letting them go for it within allelic boundaries as one would expect from an engineering point of view.
M: How so? Please detail how it is consisten with god creating kinds and what testable hypothesis there is that would support this view. Also list the kinds of experimental evidence you would gather for god creating kinds and the predictions you would make based on the testable hypothesis.
The genomes are undoubtedly consistent wiht God creating x thousand gneomes and letting them evolve since then via all the mechanisms of plasticity that you believe in. God created fully working genomes that have evolved allelically and via horizontal transfer and via gene loss. It is perfectly conpatibel with thegenome projects. You just don't like it. You insist on reading the reuse as common descent over time. It could simply be reuse by God.
Experiments? The data comes from the genome projects. If the idea of kinds is true we should be able to catalog life into kinds from genomes. The members of each kind will be distinguished by allelic differences and relative losses. Kinds will be differentiable by relative gene family and paralog gains. Because gene losses vs gains aren't always distinguishable it may not always be possible to identify kinds in this way. Hence it may be difficult to objectively distinguish between the creation and evolution models, as we are finding, becasue the actions of history are not always carefully recoded for us in the genomes.
[This message has been edited by Tranquility Base, 12-16-2002]

This message is a reply to:
 Message 108 by Mammuthus, posted 12-16-2002 4:24 AM Mammuthus has replied

Replies to this message:
 Message 120 by Mammuthus, posted 12-17-2002 3:56 AM Tranquility Base has not replied

  
Tranquility Base
Inactive Member


Message 116 of 238 (26865)
12-16-2002 6:04 PM
Reply to: Message 112 by nator
12-16-2002 10:19 AM


I think AIGs article of faith is a 'necessary evil'. There are so many flavours of OEC and YEC that they want to beable to state how many 'real' YECs they have on the books.
That does not stop a non-member from publishing in the journal however. All it does is stop someone being a member. If I were running the society I would also create an 'observer' membership for the 'unsure', OEC and atheist categories.

This message is a reply to:
 Message 112 by nator, posted 12-16-2002 10:19 AM nator has replied

Replies to this message:
 Message 117 by nator, posted 12-16-2002 7:00 PM Tranquility Base has replied

  
nator
Member (Idle past 2169 days)
Posts: 12961
From: Ann Arbor
Joined: 12-09-2001


Message 117 of 238 (26874)
12-16-2002 7:00 PM
Reply to: Message 116 by Tranquility Base
12-16-2002 6:04 PM


[QUOTE]Originally posted by Tranquility Base:
[B]I think AIGs article of faith is a 'necessary evil'. There are so many flavours of OEC and YEC that they want to beable to state how many 'real' YECs they have on the books.[/QUOTE]
Well, it is completely at odds with the scientific method and is actually akin to the intellectually-stifling atmosphere of several hundred years ago, except that AiG can't throw you in the stockade for publishing non-Biblically consistent work.
My point is that IF AiG requires their members to sign this statement, they are by definition not doing science and therfore should not be surprised that mainstreal scientific entities do not take them at all seriously.
quote:
That does not stop a non-member from publishing in the journal however. All it does is stop someone being a member.
Anyone who is interested in science would not have any respect for a supposed scientific organization which would require such a statment from it's members, and I imagine that they would be very doubtful that they would get a fair evaluation of their work if it contradicted scripture.
quote:
If I were running the society I would also create an 'observer' membership for the 'unsure', OEC and atheist categories.
But don't you get it, TB? There shouldn't be any difference if what you are doing is science!

This message is a reply to:
 Message 116 by Tranquility Base, posted 12-16-2002 6:04 PM Tranquility Base has replied

Replies to this message:
 Message 118 by Tranquility Base, posted 12-16-2002 7:02 PM nator has replied

  
Tranquility Base
Inactive Member


Message 118 of 238 (26875)
12-16-2002 7:02 PM
Reply to: Message 117 by nator
12-16-2002 7:00 PM


They are not just doing science Schraf. I'll agree with that. But an organization that does things other than science can also do science.

This message is a reply to:
 Message 117 by nator, posted 12-16-2002 7:00 PM nator has replied

Replies to this message:
 Message 121 by nator, posted 12-17-2002 9:31 AM Tranquility Base has replied

  
Tranquility Base
Inactive Member


Message 119 of 238 (26899)
12-16-2002 8:25 PM
Reply to: Message 109 by Mammuthus
12-16-2002 4:35 AM


You're right Mammuthus, I'll start a new thread.

This message is a reply to:
 Message 109 by Mammuthus, posted 12-16-2002 4:35 AM Mammuthus has not replied

Replies to this message:
 Message 122 by Adminnemooseus, posted 12-17-2002 11:23 AM Tranquility Base has not replied

  
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 120 of 238 (26943)
12-17-2002 3:56 AM
Reply to: Message 115 by Tranquility Base
12-16-2002 5:48 PM


Mammuthus writes:
So you do not believe that you pass on any genetic material to your offspring i.e. they are genetically no more related to you than to a housefly? That is what you have to accept in order for you to claim I have blinkers on and that the proteins are similar, can be grouped by related organisms, have conserved functions.
TB
"There's nothing wrong with your POV except that it is only one interpretation, hence the blinkers."
Question again, do you or do you not accept the proven facts of transmission genetics? If not, what is you counter evidence to the last 100 years of genetics research.
"If God created the genomes the sequence homology could be presnet due to creative reuse. And superfamily simlarity is not necessarily at the sequence level (see next)."
Why? Why does god have to do anything? I thought this was the supreme being..but here he is limited to "creative reuse". What is the evidence for this?
M: "Why would you call it a group in any case if you don't believe the proteins are related? You are not being consistent.[/qs]
"TB:
The proteins are related by 3D structure, that's why they have the same seqweunce profile. A superfmaly is a structural family that does not need to be related deivergenetly. Trust me on this one will you. It's a mainstream definition! I teach it in my lectures."
M: I don't doubt that you believe and don't doubt you teach it that way but this is not my question. Why if each and every protein is an independent creation of your god, should there be any similartiy between them? Especially like the KRAB family a phylogenetic signal? It only makes sense if they share a common ancestor.
"Nature does obey the rules of genetics. But if God created kinds the rules of genetics have been only in action since the gneomes were created. You see tantalizing evidence of common descent in the homologous genes but it never bnothers you that tens of thousands of new unrealted genes have appeared since the simplest bacteria."
M: Now nature obeys the rules of genetics but a minute ago you basically denied transmission genetics??? Anyway, what are the tens of thousands of unrelated genes between humans and chimps? Or humans and gorillas ? Anyway, as with hemoglobin in bacteria, why should I be troubled by the development of new genes as organisms adapt to new environments or new resources become available? And I have yet to see tens of thousands of new genes that are unrelated to anything. You also make a false assumption about bacteria and that is that you imply they are the same now as they were billions of years ago...that is not true. Bacteria have also evolved and may share very little similarity with their distant ancestors. Look up any bacterial evolution paper and you will see how quickly and dramatically they can change genomically over short periods of time.
"All you are doing is putting a slant on reuse. I am putting the other slant on it. Over time one or other of our viewpoints may be ruled out or become hard to justify (as future genomes turn up). Currently both are compatible with the data."
M: That assumes there are only two possible views on the subject which is not clear. And my slant follows from observations, experiments, and a testable hypothesis and your slant ignores all of these scientific criteria.
"Divergent evoltuion is evolution that leaves undoubted signatures of common descent. For us it is simply reuse of a gene. As you probably know, convergent evolution is a stumbling upon a similar feature without evidence of common descent (for that feature). For us it is resuse of a protein fold without the sme sequence."
M: You might want to use more mainstream terms than divergent evolution. Divergent does not imply "undoubted signatures of common descent". And you are also mis-defining convergent evolution. A birds wing and a bats wing are convergent evolution. Or most of the physical characteristics of the Tasmanian wolf and eutherian canids are convergent evolution..not just protein folds as you state.
Since you are saying all similar sequences are re-use of genes, do you believe you passed on genes to your children? Or were they magically created and have nothing to with you but are genetically more similar to you than to any other male on the planet because of god re-using genes? This is starting to sound like Peter Borger's multipurpose genome ga ga.
"I get all of that. What you keep forgeting is that in additon to the generation of new paralogs new taxa systematically discover new protein families and systems that did not exist before."
M: Except that they exist in all the relatives of the taxa or exceptions such as syncytin where it is known what happened, or inactivation of genes like several differences between humans and chimps etc....this is not a problem for genetics or evolution.
"I have no problem with horizontal transfer as I have said on many occasions. It does not account fo the origin of any gene family."
M: Why not? And actually, HERVs and transposons do account for gene family evolution. They are a great mechanism for causing duplications of chromosomal regions and genes...and in most high copy number regions of the genome..you find retrotransposons i.e. HLA, globin cluster, etc etc.
M: How so? Please detail how it is consisten with god creating kinds and what testable hypothesis there is that would support this view. Also list the kinds of experimental evidence you would gather for god creating kinds and the predictions you would make based on the testable hypothesis.[/qs]
"The genomes are undoubtedly consistent wiht God creating x thousand gneomes and letting them evolve since then via all the mechanisms of plasticity that you believe in. God created fully working genomes that have evolved allelically and via horizontal transfer and via gene loss. It is perfectly conpatibel with thegenome projects. You just don't like it. You insist on reading the reuse as common descent over time. It could simply be reuse by God."
M: If it were undoubtedly consistent then why do most scientists and a large number of non-scientists doubt it? Anyway, what is your evidence for god creating x genomes? If it is undboutebly consistent you should be able to provide the evidence that it was created and not due to natural processes. Your claim that I just don't like it is false. I see no evidence for it. You are claiming in this last paragraph that everything about genetics and evolution I said is correct but then that there is no such thing as common descent (so I guess I can never have kids) and that you have to insert a creator of each genome for which you have no evidence. I could do the same and claim that a big blue monkey with a banana in its nose and a bottle of gin in its hand created the genomes...what is your evidence that your god did it and not my monkey?
"Experiments? The data comes from the genome projects. If the idea of kinds is true we should be able to catalog life into kinds from genomes. The members of each kind will be distinguished by allelic differences and relative losses. Kinds will be differentiable by relative gene family and paralog gains. Because gene losses vs gains aren't always distinguishable it may not always be possible to identify kinds in this way. Hence it may be difficult to objectively distinguish between the creation and evolution models, as we are finding, becasue the actions of history are not always carefully recoded for us in the genomes."
M: Funny, then I see no reason to use a blanket term like "kind" when species, genus, family, order etc. are far more descriptive. How does a gene loss versus gains in any way make it difficult to distinguish evolution and creation? What evidence for creation is there in a HERV deletion or a partial deletion of a HERV in the salivary amylase cluster?

This message is a reply to:
 Message 115 by Tranquility Base, posted 12-16-2002 5:48 PM Tranquility Base has not replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024