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Author Topic:   Definition of created kind!
Zhimbo
Member (Idle past 6012 days)
Posts: 571
From: New Hampshire, USA
Joined: 07-28-2001


Message 32 of 86 (12334)
06-28-2002 9:46 AM
Reply to: Message 25 by Tranquility Base
06-26-2002 10:43 PM


quote:
Originally posted by Tranquility Base:
John
you are quite right that a protein could gradually morph from one fold to another via DNA changes. However in doing so it would spend most of its time unfolded and hence non-funcitonal

Why would a protein *ever* be unfolded?
Proteins fold. Period. Make a protein, it assumes *some* fold. It would never, ever be "unfolded". What would that even mean? That it would be a straight chain of amino acids?
------------------
"Colorless green ideas sleep furiously." - Chomsky

This message is a reply to:
 Message 25 by Tranquility Base, posted 06-26-2002 10:43 PM Tranquility Base has replied

Replies to this message:
 Message 35 by Tranquility Base, posted 06-30-2002 8:37 PM Zhimbo has replied
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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 33 of 86 (12405)
06-30-2002 12:48 PM
Reply to: Message 31 by Tranquility Base
06-27-2002 8:34 PM


quote:
Originally posted by Tranquility Base:
SLPx, you never responded to (at least the second) of the quotes I dug out from the mainstream FEBBs Lett paper later:
quote:
"Using the presence of the protein families as taxonomic traits, and linking them to biochemical pathways . . ."
and
The mere presence or absence of a protein family can be indicative of the existence of an entire cellular process"
[This message has been edited by Tranquility Base, 06-27-2002]

Whats to reply to? I am aware of no criterion that says that all creatures must be in possession of all protein families. I did my graduate work on the molecular systematics of primates using two unlinked loci, one of which was the gamma1 and gamma2 globin genes. Not all mammals have all of the genes in the cluster. Not all Primates have all of the genes (at least not all of the same genes) in the cluster. What IS present, however, is an interesting phylogenetic history laid out by the very presence or absense of the various genes and the changes within them. They match - gasp! - evolutionary hypotheses of descent.
My reply was implicit in my other responses - you are making mountains out of molehills.

This message is a reply to:
 Message 31 by Tranquility Base, posted 06-27-2002 8:34 PM Tranquility Base has replied

Replies to this message:
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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 34 of 86 (12406)
06-30-2002 12:49 PM
Reply to: Message 33 by derwood
06-30-2002 12:48 PM


Oh - and you did not reply to my question re: chimp genomes.

This message is a reply to:
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Replies to this message:
 Message 37 by Tranquility Base, posted 06-30-2002 8:52 PM derwood has replied

  
Tranquility Base
Inactive Member


Message 35 of 86 (12409)
06-30-2002 8:37 PM
Reply to: Message 32 by Zhimbo
06-28-2002 9:46 AM


Zhimbo
99.999% of random protein sequence do not fold! The sequences that fold are either created or selected by evolution. Random protein sequences do not fold except by luck and no-one has ever randomly generated a protein sequence that has folded into a large protein fold. Some small folds have been generated by random means in the cases where all possibilities were exhaustively sampled (ie billions of possibilities).
If you have one protein fold that is 'abbbab' for example (a = alpha helix, b=beta strand). It might fold into a four stranded beta sheet with two alpha helices. It is almost impossible to insert a third alpha helix into the middle of this sequence. If you inserted amino-acids that are likely to form an alpha helix (eg ALVSELVA) betwwen say the 'abb' and 'bab' parts you are almost 100% sure to get an unfolded protein. Proteins fold in a very, very cooperative manner. A single amino acid change can cause it to unravel. This is why one cannot go systematically from one fold to another. One could easily imagine going from a abbbab fold to a abbbaba fold on the other hand but the point is that the known protein folds do not fit a pattern lke this and we know probably 80% to 90% of the water soluble folds.
[This message has been edited by Tranquility Base, 06-30-2002]

This message is a reply to:
 Message 32 by Zhimbo, posted 06-28-2002 9:46 AM Zhimbo has replied

Replies to this message:
 Message 38 by Zhimbo, posted 07-01-2002 11:44 PM Tranquility Base has replied

  
Tranquility Base
Inactive Member


Message 36 of 86 (12410)
06-30-2002 8:44 PM
Reply to: Message 33 by derwood
06-30-2002 12:48 PM


SLPx
My refed quote The mere presence or absence of a protein family can be indicative of the existence of an entire cellular process" shows what I claimed, that protein folds accompany cellular novelty - at least some of the time (if not most of the time). In other words if you pick almost any cellular cystem you will need new protein folds to constrcut them.
Your study of globin genes is a study within a gene family - they are all homologs or orthologs of a single gene. These could have arisen by either creation or evolution.

This message is a reply to:
 Message 33 by derwood, posted 06-30-2002 12:48 PM derwood has replied

Replies to this message:
 Message 45 by derwood, posted 07-04-2002 2:21 PM Tranquility Base has replied

  
Tranquility Base
Inactive Member


Message 37 of 86 (12411)
06-30-2002 8:52 PM
Reply to: Message 34 by derwood
06-30-2002 12:49 PM


SLPx - I said the human/chimp issue will have to await the chimp genome because it is only then that we will find to what extent we (humans) are diferentiated from chimps via
(i) SNPs (single point mutations)
(ii) Regulatory sequences
(iii) Paralogs (extra new funtion copies of genes)
(iv) New gene families (protein folds)
One non-creationist discussion I read recently points out that the 98% similarity experiments (determined by annealing rates) will definitely give an overestimate of similarity (because the non-similar parts wont combine!) and doesn't say much about the presence of new gene families. Human gene families that aren't in pan are known and extrapolation suggests about 30 novel gene families might be present in man. We will just have to see.
[This message has been edited by Tranquility Base, 06-30-2002]

This message is a reply to:
 Message 34 by derwood, posted 06-30-2002 12:49 PM derwood has replied

Replies to this message:
 Message 44 by derwood, posted 07-04-2002 2:14 PM Tranquility Base has replied

  
Zhimbo
Member (Idle past 6012 days)
Posts: 571
From: New Hampshire, USA
Joined: 07-28-2001


Message 38 of 86 (12515)
07-01-2002 11:44 PM
Reply to: Message 35 by Tranquility Base
06-30-2002 8:37 PM


Well, getting rid of a certain fold to me does not mean you have an unfolded protein...
Seriously, what does an "unfolded protein" mean? Unfortunately all my textbooks are currently packed away, and I have yet to find appropriate internet resources that would let me know about "unfolded proteins" in the current context - although the smattering I've looked at have yet to tell me that "most proteins are unfolded". Perhaps this is just a variation of jargon across regions or sub-disciplines.
Anyway, all you've told me is that certain fold patterns are resistant to mutational change (without serious or complete disruption). Where exactly is the absolute barrier to evolutionary change that would make this relevant to "created kinds"?
(Perhaps you've covered this elsewhere, and you could point me there._
------------------
"Colorless green ideas sleep furiously." - Chomsky

This message is a reply to:
 Message 35 by Tranquility Base, posted 06-30-2002 8:37 PM Tranquility Base has replied

Replies to this message:
 Message 39 by Tranquility Base, posted 07-01-2002 11:55 PM Zhimbo has replied

  
Tranquility Base
Inactive Member


Message 39 of 86 (12518)
07-01-2002 11:55 PM
Reply to: Message 38 by Zhimbo
07-01-2002 11:44 PM


Zhimbo
Protein folding is something that happens almost automatically to a protein chain of amino-acids ('chaperones' help but don't change the final structure). Only a very small subset of protein sequences will fold to a compact specific structure with a defined shape and surface that can do a job. It is an optimized process because it has been demonstrated that if the sequence isn't carefully chosen a protein would take millions of years to fold to it's native functional state.
If you constructed a random amino-acid sequence it will probably remain like a semi-extended string flopping around. A folded protein is quite rigid and most of the molecules in a population will have a near identical structure unlike a floppy chain.
The point that your textbooks are yet to make is that the proteins we study most of he time are coded for in genomes and are foldable (ie they automatically find the right shape to do their job). A good textbook will somewhere point out that most random amino-acid chains will not have this property.
And my point is that becasue protein structures are discontinuous in structure from one fold to another, and because protein folding is critically dependent on sequence, a protein typically will be unfolded (and hence non-functional) on the way to morphing into another protein fold via sequence changes. The point is that on the way to the new fold there is nothing good to select for so you are back to random sampling. The other point is that the protein families show no hint of their descendency from each other via their sequences.
[This message has been edited by Tranquility Base, 07-02-2002]

This message is a reply to:
 Message 38 by Zhimbo, posted 07-01-2002 11:44 PM Zhimbo has replied

Replies to this message:
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 Message 41 by Zhimbo, posted 07-03-2002 7:48 PM Tranquility Base has replied

  
SAGREB
Inactive Member


Message 40 of 86 (12573)
07-02-2002 2:40 PM
Reply to: Message 39 by Tranquility Base
07-01-2002 11:55 PM


Invitation
Ive started a msn-group about this subject: Created kinds
Please join!
http://groups.msn.com/Createdkinds
Zauruz

This message is a reply to:
 Message 39 by Tranquility Base, posted 07-01-2002 11:55 PM Tranquility Base has not replied

  
Zhimbo
Member (Idle past 6012 days)
Posts: 571
From: New Hampshire, USA
Joined: 07-28-2001


Message 41 of 86 (12693)
07-03-2002 7:48 PM
Reply to: Message 39 by Tranquility Base
07-01-2002 11:55 PM


OK, I think we're on the same wavelength - by "unfolded", you mean something like "not folded to a single stable conformation"?
I'll have to read up a bit to talk about this intelligently, but some clarification:
Are you saying that protein fold families define, or help define, "originally created kinds"? Or just that this is a problem for current evolutionary theory? (Or both...or something else...).

This message is a reply to:
 Message 39 by Tranquility Base, posted 07-01-2002 11:55 PM Tranquility Base has replied

Replies to this message:
 Message 42 by Tranquility Base, posted 07-03-2002 9:01 PM Zhimbo has replied
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Tranquility Base
Inactive Member


Message 42 of 86 (12698)
07-03-2002 9:01 PM
Reply to: Message 41 by Zhimbo
07-03-2002 7:48 PM


Zhimbo
Not folded = "not folded to a single stable conformation" is a good summary.
Protein fold families, among other things, do help define created kinds IMO, yes, and this is very well supported by studies of the association of fold families with cellular novelties. I also see it as a micro/macro-evolution differentiation which we equate to the kind distinguishment anyway.
It is a difficulty for evolution becasue there doesn't seem to be anywhere near enought time for these families to evolve, let alone organise into pathways, systems and organs. But the only refs on that are creationist so you probably wont buy that. There is a surprising complete silence in the mainstream lit on the issue so I will take that as a sign that the creationists are, at the very least, not stretching the point.

This message is a reply to:
 Message 41 by Zhimbo, posted 07-03-2002 7:48 PM Zhimbo has replied

Replies to this message:
 Message 43 by derwood, posted 07-04-2002 1:51 PM Tranquility Base has replied
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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 43 of 86 (12762)
07-04-2002 1:51 PM
Reply to: Message 42 by Tranquility Base
07-03-2002 9:01 PM


quote:
Originally posted by Tranquility Base:
Protein fold families, among other things, do help define created kinds IMO, yes, and this is very well supported by studies of the association of fold families with cellular novelties. I also see it as a micro/macro-evolution differentiation which we equate to the kind distinguishment anyway.
Then you must be able to easily identify the 'protein fold familiaes' that separate the human-kind from the ape-kind... Or, for that matter, ANY one-kind from another.
quote:
There is a surprising complete silence in the mainstream lit on the issue so I will take that as a sign that the creationists are, at the very least, not stretching the point.
There is an unsurprising lack of coherent positive evidence for any brand of creationism IN the creationist literature. That should be taken as a sign that the creationist position is an undefensible one.

This message is a reply to:
 Message 42 by Tranquility Base, posted 07-03-2002 9:01 PM Tranquility Base has replied

Replies to this message:
 Message 46 by Tranquility Base, posted 07-04-2002 9:24 PM derwood has replied
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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 44 of 86 (12763)
07-04-2002 2:14 PM
Reply to: Message 37 by Tranquility Base
06-30-2002 8:52 PM


quote:
Originally posted by Tranquility Base:
SLPx - I said the human/chimp issue will have to await the chimp genome because it is only then that we will find to what extent we (humans) are diferentiated from chimps via
(i) SNPs (single point mutations)
SNPs are single nucleotide POLYMORPHISMS - that is, point mutations WITHIN a species. This would have no bearing on the human-chimp issue whatsoever.
quote:
(ii) Regulatory sequences
Exactly. Indeed, many evoloutionary biolists think that small changes in regulatory sequence are of great import in macroevolution.
quote:
(iii) Paralogs (extra new funtion copies of genes)
Such as the beta globin cluster.[/quote]
(iv) New gene families (protein folds)[/quote]
If, as you wrote, "99.999% of random proteins" 'do not fold' ( a claim I find fantastic), it stands to reason that selection would weed such sequyences out. Since you admit paralogous duplication, I wonder what the rationale is for the implicit suggestion that such genes could not substantially mutate to produce novel proteins?[/quote]
One non-creationist discussion I read recently points out that the 98% similarity experiments (determined by annealing rates) will definitely give an overestimate of similarity (because the non-similar parts wont combine!) and doesn't say much about the presence of new gene families.[/quote]
You are referring to DNA-DNA hybridization, I assume. Funny thing about those 'overestimates: they have been borne out by direct sequence comparisons.
Chimpanzee Fetal G-gamma and A-gamma Globin Gene Nucleotide Sequences Provide Further Evidence of Gene Conversions in Hominine Evolution
: Slightom et al., 1985
: Mol Biol Evol 2(5):370-389.
: 1.4-2.25% nucleotide difference, depending on which sets of alleles are compared.
Primate Eta-Globin DNA and Man's Place Among the Great Apes.
: Koop et al., 1986.
: Nature 319:234-238.
: 1.7% distance measured by direct comparison of aligned nucleotide sequences (2.2 kilobases)
Mol Phylogenet Evol 2001 Jan;18(1):14-25
Catarrhine phylogeny: noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade.
Page SL, Goodman M.
1.7% difference, 10 kb, serum albumin introns and non-coding globin sequence
I wonder how many creationist 'hypotheses' have actually been borne out by subsequent analyses...
quote:
Human gene families that aren't in pan are known and extrapolation suggests about 30 novel gene families might be present in man. We will just have to see.
What are these 'known' novel gene families? Refs?
[This message has been edited by SLPx, 07-04-2002]

This message is a reply to:
 Message 37 by Tranquility Base, posted 06-30-2002 8:52 PM Tranquility Base has replied

Replies to this message:
 Message 47 by Tranquility Base, posted 07-04-2002 10:47 PM derwood has replied

  
derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 45 of 86 (12764)
07-04-2002 2:21 PM
Reply to: Message 36 by Tranquility Base
06-30-2002 8:44 PM


quote:
Originally posted by Tranquility Base:
My refed quote The mere presence or absence of a protein family can be indicative of the existence of an entire cellular process" shows what I claimed, that protein folds accompany cellular novelty - at least some of the time (if not most of the time). In other words if you pick almost any cellular cystem you will need new protein folds to constrcut them.
I fail to see how that indicates creation. Of course, quite disparate cellular systems utilize quite similar proteins - e.g., type III secretory systems and the flagella of some bacteria.
I think that example alone takes the wind out of your sails.
quote:
Your study of globin genes is a study within a gene family - they are all homologs or orthologs of a single gene. These could have arisen by either creation or evolution.
Yet the products of these genes exhibit distinct characteristics, and not all of the genes in the cluster in humans are found in other creatures. That was my point.

This message is a reply to:
 Message 36 by Tranquility Base, posted 06-30-2002 8:44 PM Tranquility Base has replied

Replies to this message:
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Tranquility Base
Inactive Member


Message 46 of 86 (12792)
07-04-2002 9:24 PM
Reply to: Message 43 by derwood
07-04-2002 1:51 PM


SLPx
I recently read about novel protein fmailies in man vs chimp. The researchers extrapolated to predict about 30 novel families but this could be a lower limit. DNA hybridization experiments that say we are 98% similar almost definetely will generate an underestimate. We'll soon see.

This message is a reply to:
 Message 43 by derwood, posted 07-04-2002 1:51 PM derwood has replied

Replies to this message:
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