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Author Topic:   Teaching evolution in the context of science
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 31 of 76 (12797)
07-04-2002 10:55 PM
Reply to: Message 29 by Tranquility Base
07-04-2002 9:07 PM


Tranquility Base writes:

The gist of the abstract itself is that there is a discontinuity.
Just as Doug Erwin points out in the three separate quotes, Creationists are misusing the information in his papers. I believe his words were, "deliberate and pernicious misreading of the papers." And in your case you're not even referencing a paper but only an abstract.

Allelic variation in every known case in the moelcualr medicine literature would be due to SNPs or a gross chromosomal rearrangement resulting in a missing or misfolded gene.
I won't comment on the accuracy of this statement, but the abstract you're referencing to support it doesn't even use the words "allelic", "variation", "SNP" or "fold".

But I look at the genomic data and see distinct creation.
Right, and you look at the geologic data and see a global flood. You look at any data and see evidence for your own particular interpretation of the Bible.
The problem for you is that not only do specialists in these fields not agree with you, even your fellow Creationists don't agree with you. The inductive reasoning that is so much a part of the scientific interpretation of data is in your case seriously distorted by your religious beliefs. I know you sincerely believe your conclusions *do* follow from the evidence, but if Creationists were truly listening to the evidence with their minds rather than their hearts then there wouldn't be so wide a range of Creationist belief.

Your attmepts to a priori pronounce everything we say as silly, naive, pseudo-science or misleading is doomed to utter failure. The devil is in the details but what we have to say is, at least a priori, very sensible.
As others have already pointed at many times, you love to dance past the first-order issues and bury them in a mass of second-order detail that makes no sense since you've got the first-order issues wrong. And you've already yourself conceded that what you're doing is not yet science (see your Message 88 in the Non-Marine Sediments thread), but that you hope to one day find sufficient support for your ideas that it may one day qualify as science. So if you're not yet doing science then you're either doing pseudo-science or religion, take your pick.
--Percy
[This message has been edited by Percipient, 07-04-2002]

This message is a reply to:
 Message 29 by Tranquility Base, posted 07-04-2002 9:07 PM Tranquility Base has replied

Replies to this message:
 Message 32 by Tranquility Base, posted 07-04-2002 11:22 PM Percy has replied

  
Tranquility Base
Inactive Member


Message 32 of 76 (12799)
07-04-2002 11:22 PM
Reply to: Message 31 by Percy
07-04-2002 10:55 PM


Percy
I have ordered the Erwin paper and will carefully read it but you tell me exactly how I've misused it? I simply want to point out the distinctness of micro/macro and that's what both the abstract and it's title says.
Erwin does use the term allele. Non-homologous genes have completely unique folds about 10% of the time, ie, thousands of genes have their own corresponding fold family. Whether Erwin knows it or not, what he is saying is essentially about protein fold families! We'll see when I get the paper.
I stand by what I said in that post you cited - most of what we do is indistinguishable from what you would call science.

This message is a reply to:
 Message 31 by Percy, posted 07-04-2002 10:55 PM Percy has replied

Replies to this message:
 Message 35 by Percy, posted 07-05-2002 1:03 AM Tranquility Base has replied
 Message 39 by nator, posted 07-06-2002 11:35 PM Tranquility Base has replied

  
John
Inactive Member


Message 33 of 76 (12802)
07-05-2002 12:26 AM
Reply to: Message 30 by Tranquility Base
07-04-2002 9:19 PM


quote:
Originally posted by Tranquility Base:
My statement about speciaiton is what I meant to say. We beleive in speciation! I don't believe God created hundreds of species of finch! But I do beleive he created horses and giraffes seperately. Very, very different.
Didn't this start out with a discussion of the difference between micro and macro-evolution? And didn't you point me to mainstream literature to prove that the difference is recognized in mainstream biology? I looked it up and stand corrected on the terminology, though you've still not shown a hard-line of demarcation between the two.
Mainstream > macro > speciation
Now you've redefined macro to not be speciation per se.
quote:
I don't link micro/macro to speciation per se
------------------
www.hells-handmaiden.com

This message is a reply to:
 Message 30 by Tranquility Base, posted 07-04-2002 9:19 PM Tranquility Base has replied

Replies to this message:
 Message 34 by Tranquility Base, posted 07-05-2002 12:44 AM John has replied

  
Tranquility Base
Inactive Member


Message 34 of 76 (12803)
07-05-2002 12:44 AM
Reply to: Message 33 by John
07-05-2002 12:26 AM


John
I don't think mainstream evolution researchers would say that speciation had to be macroevoltuion. I think the Erwin ref supports my statement. Allelic variation can no doubt lead to speciation but Erwin wouldn't call that macroevoltuion.

This message is a reply to:
 Message 33 by John, posted 07-05-2002 12:26 AM John has replied

Replies to this message:
 Message 37 by John, posted 07-05-2002 11:08 AM Tranquility Base has replied

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 35 of 76 (12805)
07-05-2002 1:03 AM
Reply to: Message 32 by Tranquility Base
07-04-2002 11:22 PM


Tranquility Base writes:

Erwin does use the term allele. Non-homologous genes have completely unique folds about 10% of the time, ie, thousands of genes have their own corresponding fold family. Whether Erwin knows it or not, what he is saying is essentially about protein fold families!
Only on the Internet can one get arguments about simple matters of fact. Erwin not only doesn't use the word "allele", he doesn't use any of the other terms you've mentioned either, like "genes", "non-homologous", "folds" and "protein". Or "allelic", "variation" and "SNP" from your previous message. How you see any correspondence between Erwin's abstract and your ideas is beyond me. It would make as much sense to cite the sports page.
Why don't you take a step back and ask yourself why you keep seeing correspondences where it appears to everyone else that none exist? Either you're wrong, or you're just capable of making huge leaps of induction that no one else can see, in which case could you please fill in all the missing steps for the rest of us?
--Percy

This message is a reply to:
 Message 32 by Tranquility Base, posted 07-04-2002 11:22 PM Tranquility Base has replied

Replies to this message:
 Message 36 by Tranquility Base, posted 07-05-2002 1:23 AM Percy has replied

  
Tranquility Base
Inactive Member


Message 36 of 76 (12808)
07-05-2002 1:23 AM
Reply to: Message 35 by Percy
07-05-2002 1:03 AM


Percy
I quote Erwin from the abstract:
quote:
"These discontinuities impose a hierarchical structure to evolution and discredit any smooth extrapolation from allelic substitution to large-scale evolutionary patterns."
He says exactly the point I wanted to make. Allelic subsitution is microevolution. He is ultimately talking about the orign of new folds which are non-allelically derived.
If you think an abstract entitled
"Macroevolution is more than repeated rounds of microevoution"
is irrelvant to our POV you are utterly deluded.
PS - and an SNP is an allelic variation which is an allelic substitution. My use of these terms with reference to this abstract was entirely correct and it seems you are simply using a 'find' button. If you don't believe me about folds being non-allelically related then you go find another mainstream structural biologist and he/she will confirm it. I'm simply putting this abstract in the language of structural biology.
[This message has been edited by Tranquility Base, 07-05-2002]

This message is a reply to:
 Message 35 by Percy, posted 07-05-2002 1:03 AM Percy has replied

Replies to this message:
 Message 38 by Percy, posted 07-05-2002 12:27 PM Tranquility Base has replied

  
John
Inactive Member


Message 37 of 76 (12828)
07-05-2002 11:08 AM
Reply to: Message 34 by Tranquility Base
07-05-2002 12:44 AM


quote:
Originally posted by Tranquility Base:
John
I don't think mainstream evolution researchers would say that speciation had to be macroevoltuion. I think the Erwin ref supports my statement. Allelic variation can no doubt lead to speciation but Erwin wouldn't call that macroevoltuion.

Do you depend upon the nebulous nature of your ideas?
If not, please post a detailed rundown of your theory tying this all together-- macro/micro, novelty, protein folding, etc.
------------------
www.hells-handmaiden.com

This message is a reply to:
 Message 34 by Tranquility Base, posted 07-05-2002 12:44 AM Tranquility Base has replied

Replies to this message:
 Message 40 by Tranquility Base, posted 07-07-2002 8:56 PM John has replied

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 38 of 76 (12836)
07-05-2002 12:27 PM
Reply to: Message 36 by Tranquility Base
07-05-2002 1:23 AM


Tranquility Base writes:

He says exactly the point I wanted to make. Allelic subsitution is microevolution.
Execpt that in Message 24 that I originally replied to you were making a different point, saying, "Microevolution is identified with allelic variation = same fold but with SNP(s)."
And I replied that the abstract does not equate allelic variation with "same fold but with SNP(s)." Erwin's abstract is silent in this regard, yet you cite it in support anyway.
The more fundamental issue is why you keep seeing supporting evidence in data irrelevant to your point. Either you're seeing correlations not apparent to everyone else, in which case could you please fill in the missing pieces for the rest of us, or you're way out in left field.
--Percy

This message is a reply to:
 Message 36 by Tranquility Base, posted 07-05-2002 1:23 AM Tranquility Base has replied

Replies to this message:
 Message 41 by Tranquility Base, posted 07-07-2002 9:11 PM Percy has replied

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


Message 39 of 76 (12933)
07-06-2002 11:35 PM
Reply to: Message 32 by Tranquility Base
07-04-2002 11:22 PM


[QUOTE] I stand by what I said in that post you cited - most of what we do is indistinguishable from what you would call science.[/B][/QUOTE]
It's very distinguishable, actually.
Creation "science" isn't falsifiable, because, as it is based upon a certain interpretation of the Bible being infallibly true, nothing can falsify it. Falsifiability is a required component of all science, and Creation "science" thoroughly violates this tenet.
Science is evidence-driven, not pre-held conclusion-driven. Science looks to see what the evidence in nature suggests is the case, while Creation "science" has jumped far ahead to the conclusion about what is supposed to be found. Real science does not ignore evidence, while Creation "science" must ignore evidence to shoehorn it into what they have already decided the "truth" must be.
------------------
"We will still have perfect freedom to hold contrary views of our own, but to simply
close our minds to the knowledge painstakingly accumulated by hundreds of thousands
of scientists over long centuries is to deliberately decide to be ignorant and narrow-
minded."
-Steve Allen, from "Dumbth"

This message is a reply to:
 Message 32 by Tranquility Base, posted 07-04-2002 11:22 PM Tranquility Base has replied

Replies to this message:
 Message 42 by Tranquility Base, posted 07-07-2002 9:13 PM nator has not replied

  
Tranquility Base
Inactive Member


Message 40 of 76 (12980)
07-07-2002 8:56 PM
Reply to: Message 37 by John
07-05-2002 11:08 AM


John, I would have hoped that the extensive posts I have made in this BBS on geology, paleontology, systematics, molecular biology and genome sciences were beginning to be seen as a rather systematic view of creation/flood with, yes, (i) gaps in my personal understandings in some areas and (ii) some gaps in answers by creationists, but otherwise rather neatly consistent.
On this particular issue I see it as follows:
Micro/macro evolution although used by both evolutionists and creationists are not a perfectly defined set of terms. However, a definition that might pass mainstream muster in various fields from paleotology to genome sciences might be one that is also compatible with creationism and the kind concept. It didn't have to turn out that way, but boy, it comes pretty close without working hard at all.
So we simply see the created kinds as genomic stock, distinguishable primarily by ultimately cellular novelties that are nevertheless frequently evident anatomically. This discontinuity is manifest as novel gene families that bear no resemblance to other famiiles in the genome. Many of these gene families turn out to have new protein folds. Regardless of philosophical bias, it is harder to imagine between fold molecular evolution than within fold evolution. Within fold optimization is continuous at every point - exsiting function optimized by evoltuion. This is the evoltuion of an allele coding for a selectable trait. A new protein function on an existing fold requires a chance event to generate some novel, selectable funciton. Once this occurs there can be optimization up to a point dictated by the potential of that fold to allow that eg enzymatic activity. Even harder to imagine is going from one fold to another. It requires a chance event to generate something very different that is immediately useful. If it is not immediately useful then one may as well start from random DNA. Once the function is useble then optimization via natural selection can do its job. This is utterly standard of course but I have put it into the words of structural biology whihc is where the action actually occurs. The point is that in either getting a new funcition or a new fold you are not simply doing optimization. That is the discontinuity that differentiates micro/macro or existing gene/novel fold. In your scenario it could be the reason behind punctauted equilibriu although, for you, that probably requires even a bigger step - the tying together of multiple new pathways to get a new cellular/anatomical feature.
Whatever the case the optimization of a gene (for disease resitance for example) is very different to generating a gene with a new funciton/fold. At the very least one is something we see real examples of in viruses and bacteria - the other has never yet been seen. So regardless of creation/evoltuion there is a discontinuity in expectations and reality. In our scheme it is simply becasue God created distinct genomes abut allowed them to optimze.
[This message has been edited by Tranquility Base, 07-07-2002]

This message is a reply to:
 Message 37 by John, posted 07-05-2002 11:08 AM John has replied

Replies to this message:
 Message 43 by John, posted 07-07-2002 9:41 PM Tranquility Base has replied

  
Tranquility Base
Inactive Member


Message 41 of 76 (12982)
07-07-2002 9:11 PM
Reply to: Message 38 by Percy
07-05-2002 12:27 PM


Percy
I stand by "Microevolution is identified with allelic variation = same fold but with SNP(s)." How have I contradicted this elsewhere?
Erwin does equate microevoltuion with allelic subsitution as stated by yourself but the key point is that moelcular biologists know that allelic subsituion will either be same fold or unfolded! It is irrelvant whether Erwin himself knows this or not. Alleles are either same fold or misfolded. Brown/blue eyes. Long/short nose. Sickle cell/healthy. I have made a statement that covers every allele ever studied by molecular methods. It is the bread and btter of structural biology. One might be able to demonstrate special artificial cases (such as the Nat Struc Biol paper recently) but that is not what generally distinguishes a allele.
You just think Erwin is irrelevant becasue you don't know enough about the structural biology of proteins Percy. Alleles are fixed folds or unfolded faults!

This message is a reply to:
 Message 38 by Percy, posted 07-05-2002 12:27 PM Percy has replied

Replies to this message:
 Message 45 by Percy, posted 07-07-2002 10:51 PM Tranquility Base has replied

  
Tranquility Base
Inactive Member


Message 42 of 76 (12983)
07-07-2002 9:13 PM
Reply to: Message 39 by nator
07-06-2002 11:35 PM


Schraf
Every complex theory is difficult to falsify. It has been said about evolution itself. There are mainstream quotes that state that evolution could be compatible with anything!

This message is a reply to:
 Message 39 by nator, posted 07-06-2002 11:35 PM nator has not replied

  
John
Inactive Member


Message 43 of 76 (12988)
07-07-2002 9:41 PM
Reply to: Message 40 by Tranquility Base
07-07-2002 8:56 PM


quote:
Originally posted by Tranquility Base:
John, I would have hoped that the extensive posts I have made in this BBS on geology, paleontology, systematics, molecular biology and genome sciences were beginning to be seen as a rather systematic view of creation/flood with, yes, (i) gaps in my personal understandings in some areas and (ii) some gaps in answers by creationists, but otherwise rather neatly consistent.
Well, yes, I was getting an idea of what you proposed; but this is much more clear.
[QUOTE][b]So we simply see the created kinds as genomic stock, distinguishable primarily by ultimately cellular novelties that are nevertheless frequently evident anatomically.[/QUOTE]
[/b]
For example....? One genomic stock whould be ________, another would be _______; and the cellular novelties would be _______?
quote:
This discontinuity is manifest as novel gene families that bear no resemblance to other famiiles in the genome.
How does one determine resemblance? How does one determine a gene family within this scenario?
quote:
Many of these gene families turn out to have new protein folds.
But not all? So folding isn't the primary determinant?
quote:
Within fold optimization is continuous at every point - exsiting function optimized by evoltuion. This is the evoltuion of an allele coding for a selectable trait. A new protein function on an existing fold requires a chance event to generate some novel, selectable funciton. Once this occurs there can be optimization up to a point dictated by the potential of that fold to allow that eg enzymatic activity.
What determines the potential of a fold?
quote:
That is the discontinuity that differentiates micro/macro or existing gene/novel fold.
Sorry, still foggy about exactly where this line falls as far as real world critters. New folding/function marks the edge of a family (although you seem a bit hedgie about that-- new folding would be an undebatable hard line but new function is much more subjective), but how does this apply to animals. Your theory should be easily testable. Has it been? Do these criteria line up with genus/species lines or family/genus or order/family?
Take care.
------------------
www.hells-handmaiden.com

This message is a reply to:
 Message 40 by Tranquility Base, posted 07-07-2002 8:56 PM Tranquility Base has replied

Replies to this message:
 Message 44 by Tranquility Base, posted 07-07-2002 10:31 PM John has replied

  
Tranquility Base
Inactive Member


Message 44 of 76 (12992)
07-07-2002 10:31 PM
Reply to: Message 43 by John
07-07-2002 9:41 PM


John
Are you aware that European artificial selection over about 200 years on the wild mustard led to cabbage, brocolli and cauliflower? That is the power/allelic variation within existing genes in the genomes.
OK, our genomic stock could have been the horse family inlcuding donkeys, perhaps including the zebra. 2 or 3, maybe 1 big/small cat families etc.
Cellular novelties? Origin of life issue of course invovles all systems. After that: Multicellularity. Respiratory proteins. Immune system proteins. Plant unique metabolic. Animal unique metabolic. Etc.
The genomes document non-stop cellular nmovelty. A mammalian cell is very different to a prokaryotic cell.
Gene families can be identified by sequence similarity. After 3D protein structure deterimnation, or fiunctional identification, many genes can go into existing fold families. Regardless there are tens of thousands of gene families and probably between 3,000 and 10,000 fold families.
members of a gene family will always have the same fold. But some gene famiiles may share a fold with another gene family. Someteims considered divergent someteims convergetn by evolutionists.
The potential of a fold is ultimately determined by it's ability to display sidechains (amino-acid (AA) chemical groups that vary from one AA type to antoher) in 3D. Each fold will hav a differnet repotoir of possibilities. It is not well understood by any means. But we all (TB puts his mainstream hat on) suspect that certain folds are better for some tasks than others but we also know that the same fodl can do multiple jobs. Evoltuionists predicted far, far more reuse of folds within bochemical enzymatic pathwyas tha nis observed in genomes.
The discontinuity occurs as to whether it is an optimization issue (exisitng functional gene) or a discovey issue (new function needed). Regardless of bias these isseus differ in difficulty markedly and in time expected.
Most (all?) studies deomnstrate that genuses, if not families, contain the same gene families. Obviously there are genes that are lost along the way which makes this issue not as easy as one would like. Mouse and man are only seperated by 300 gene families. Nevertheless it is a discontinuity.

This message is a reply to:
 Message 43 by John, posted 07-07-2002 9:41 PM John has replied

Replies to this message:
 Message 47 by John, posted 07-07-2002 11:41 PM Tranquility Base has replied

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 45 of 76 (12994)
07-07-2002 10:51 PM
Reply to: Message 41 by Tranquility Base
07-07-2002 9:11 PM


Tranquility Base writes:

You just think Erwin is irrelevant because you don't know enough about the structural biology of proteins, Percy. Alleles are fixed folds or unfolded faults!
Erwin's abstract is irrelevant because he's completely silent on the matter. I wasn't addressing whether your claims were right or wrong, but simply noting that you find support for your views in places where no one else sees any connection.
I haven't yet commented about whether you're right or wrong, but since you keep pressing me as if I had I'll address the issue. I'm pretty sure you're wrong to equate allelic variation with only SNPs, regardless of folding. Take this allelic example from The Science of Genetics, Atherly, Girton, McDonald, 1999, p86:
...more than 350 alleles of the human cystic fibrosis gene have been discovered in the last few years.
I very much doubt that every single one of the 350 alleles is a polymorphism of only a single nucleotide, and whether they are or not for this particular case, there is no requirement or reason that an allele be an SNP (beyond that increasing differences make allelic substitution less likely). They could also be double nucleotide polymorphisms, or triple, or quadruple.
The reason SNPs have received so much attention recently is because they are so easy to find, and because they are the most common type of allele, making them the most significant.
This is sort of a side point, but I'll address it anyway:

Erwin does equate microevoltuion with allelic subsitution as stated by yourself...
Since I never questioned or even addressed the point about microevolution being equated with allelic substitution, I obviously never said this, and Erwin's abstract doesn't say this, either. But if you can make as big an error as thinking I said this, then I can certainly understand you thinking that Erwin said this, too.
What Erwin does mention in the abstract is a range of evolution "from allelic substitution to large-scale evolutionary patterns." He is silent concerning where in this range he considers the transition from microevolution to higher levels to take place. He might consider allelic substitution to be the only form of microevolution, he might not, he doesn't say either way. He also says nothing about SNPs, protein folds or allelic variation. Since Erwin's abstract doesn't say, you can't cite it as if it had. I can't believe this has to be explained.
--Percy

This message is a reply to:
 Message 41 by Tranquility Base, posted 07-07-2002 9:11 PM Tranquility Base has replied

Replies to this message:
 Message 46 by Tranquility Base, posted 07-07-2002 11:06 PM Percy has replied

  
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