How paleontology really works

[/QUOTE][b]Scraf, evolution of new protein folds is a prohibitative barrier to macroevoltuion. Whenever we see the optimization of a trait, even after millions of generations of bacteria, it is invariably due to mutations in pre-existing genes.[/QUOTE][/b]How many traits have been looked at, and have been definatively shown to have not had the alterations due to misfolding? Also, how do you know that folding alterations cannot evolve when protein folding is poorly understood? Also, if the origin of protein folding is somewhere in the genetic code, how can folding be fixed, beyond the range of mutations to alter? Especially since some misfoldings are linked to mutations. Finally, if you are just looking at "optimization" (microevolutionary) adaptations don't you think that a new fold would be a bit drastic?

Thanks for the benefit of the doubt Quetzal. It is certainly true that the flood is absolutely essential to our model. Please do not equate us with the early creationists who claimed that God planted the dinosuars and the strata.How could we decouple the flood from the geological column. Wouldn't you expect a global flood to generate strata?However, I am prepared to discuss the fossil record miuns the flood but just remember that we do not claim to be able to explain the fossil reocrd without it!I have extensively read paleonotology monographs and papers including Benton's papers on the SCI, GER an RCI measures of stratigraphic vs cladistic consistency.My rewrite of 1a has to include the flood I'm afraid:1a. Special Creation and the Genesis Flood predicts the distribution via biogeography, hydrodynamic sorting and differential mobility of taxonomic groups in a 3-part fossil record: pre-flood, flood and post-flood.

MarkI don't deny that consistency could improve with data collection. That is what you expect. Fine.You have to remember that we expect the distributions to partailly match homology as well. Homologous animals have similar traits - so similar biogeogrpahy, similar hydrodynamic sorting properties and similar mobilities.Another point to remember is that consistency doesn't test the relative positions of branches. The positions of plants are not tested realtive to mammals for example becasue this is not predicted by non-molecular cladistics. So it's not as if the tree of life is tested to that extent.I'm not a paleontologist or taxonomist but it seems to me that the gaps between orders and classes are no smaller than those between families. You have to rely on punctuated equilibrium in faith. You can't rely on fossil order becasue the SCI is only about 0.5 on average. If you don't find the systematic lack of gaps a problem, fine, but it was a prediciton made by Darwin and the only 'fix' is PE.The positive evidence to us is distinct kinds. Yes there is a gray line somewhere where we all wonder but for now the data is compatible with this idea. The lack of transitionals is equivalent to stating this so I don't agree on your 'lack' of informaiton not being important. You have to stand in faith that for some reason, whenever novelty arises it comes in jumps. That is your stand of faith.The horses family balloon is simply a set of balloons put together. You can interperet it as evolution but you can't demonstrate gradual evoltuion up the column. Your jumpy evoltuion up the column could just as well be the flood distribution. Interesting how the larger horses tend to be at the top. I am very aware of the trends in bone proportions but this could be due to biogeography and flood escape too. BTW, I'm not necesarily against the idea that horses diverged into multiple forms via primarily genetic mixing, but I don't think that is what is shown in the fossil record. For us it happened pre and post flood.Our two models are very differnet and homology comes into both.Benton's work is excellent, I agree. I've read one of his books and his papers.

Gene90I'm abslutely convinced that misfolding generates traits - I bet half of the sillier dog breds are due to this or some other inactivation of genes.The quesiton is where did the foldable gene come from? If you want to define novelty loosely as new traits then I'll agree that novelty is easy to come by. But genuine biochemical and cellular novelty is systematically associated with novel gene families as evidenced by refs I have posted in the transposon/retroviral thread.Engineered and mutated proteins can misfold into nearby stable folds - I just read a paper on it (a beta-strand became a helix I think). But that fold is easily recognized as evolutionarily related. The SCOP classification (for example) of protein families has not been organized into such a system however.The point is that millions of generations of bacteria have been stressed and whenever the mechanism of adaptation is looked for it turns out to be mutations to an existing gene which maintains it's fold. Who knows what we will find in the future. We'll see, but becasue we know the genomes are constrcutred from hundreds of very differnent protein folds we already know that evoltuion had to fight this problem. So far it is an unsolved problem and there is almost no literature on it. The creationist paper I linked to recently suggests it is a prohibitive barrier.The main point about protein folding is that in going from one fold to another one would generally spend most of the time in non-functional unfolded states. One may as well start a gene from random DNA. There is little or no evidence that the protein fold families evolved from each other.The surprising thing is that life could almost undoubtedly get away with far fewer folds which would be much, much easier for evoltuion. Protein engineering and structure-function work on antibodies shows us how much can be achieved from even a single protein fold (immuoglobulin). It is quite bizaree that evoltuion chose to use differnt protein folds much of the time. Of course for optimal biochemistry more protein folds offers better diversity and hence more specificity etc but life could have easily been quite happy with far fewer folds. Antibodies can bind to just about anything and all have the same fold. Enzymatic activity is harder but preliminary work shows that enzymatic sites can be transplanted from fold to fold.

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[This message has been edited by Tranquility Base, 06-21-2002]

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Originally posted by Tranquility Base:
Mark

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I don't deny that consistency could improve with data collection. That is what you expect. Fine.

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So stratigraphy matches phylogeny when the data is good. This is the point I was trying to make. You would have an argument if stratigraphy didn’t match phylogeny and the data was good. This supports evolution, not special creation or the flood model.

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Originally posted by Tranquility Base:

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You have to remember that we expect the distributions to partailly match homology as well. Homologous animals have similar traits - so similar biogeogrpahy, similar hydrodynamic sorting properties and similar mobilities.

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Right, that’s why the largest mammals are found in the highest strata, right? Contrary to what is expected of hydrodynamic sorting. Mobility is IRRELEVENT, unless all those large mammals are intelligent enough to dig up their dead relatives & carry them to the high ground. Big bones at the bottom, TB, not the top.You have no model that is internally consistent.

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Originally posted by Tranquility Base:

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Another point to remember is that consistency doesn't test the relative positions of branches. The positions of plants are not tested realtive to mammals for example becasue this is not predicted by non-molecular cladistics. So it's not as if the tree of life is tested to that extent.

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Not sure of your point here. If a plant is found in the same strata as a Diplodocus, then it was buried at roughly the same time. It is my understanding that plant phylogenies, below higher taxa, are more difficult to infer because of a paucity of fossils. So it comes back to not having enough data to infer reliable phylogenies, which you manage to interpret as special creation. God-of-the-gaps.Secondly, you’re moving the goalposts slightly, we began discussing the congruence of cladistics & stratigraphy, which Benton agrees occurs when the data is abundant. I’m not trying to show an entire tree of life, nor will I, just that evolution is seen in the fossil record because cladistics & stratigraphy are congruent. Your own cite agrees with me.

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Originally posted by Tranquility Base:

I'm not a paleontologist or taxonomist but it seems to me that the gaps between orders and classes are no smaller than those between families. You have to rely on punctuated equilibrium in faith. You can't rely on fossil order becasue the SCI is only about 0.5 on average. If you don't find the systematic lack of gaps a problem, fine, but it was a prediciton made by Darwin and the only 'fix' is PE.

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In this argument I am not relying on on PE AT ALL. Another fix, is incomplete fossil record.The SCI is 0.5 average. This is based on 1000 phylogenies, regardless of the quality of fossil data. Benton tells us that when the quality that the data is derived is abundant/good, then stratigraphy & cladistics are congruent.Why must I labour this point? WHEN THE FOSSIL RECORD IS ABUNDANT, GIVING GOOD QUALITY DERIVED DATA, STRATIGRAPHY/CLADISTICS/PHYLOGENY ARE CONGRUENT. Finished. Over. Job done.Evolution CAN be seen in the fossil record because traits change progressively over time, that is, morphology changes from older to younger strata. You are attempting to imply that it doesn’t, & in this you are patently, demonstrably wrong. Did you read your own cite?Your argument still relies on gaps & poor data, in spite of the fact that good data shows what you say it does not.I DO NOT CARE HOW MANY GAPS THERE ARE IN THE FOSSIL RECORD, WHEN THE RECORD IS GOOD, STRATIGRAPHY MATCHES PHYLOGENY!!!!! YOU CANNOT INFER ANYTHING FROM WHAT ISN’T THERE!!!!!! GOOD GRIEF!!!!!

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Originally posted by Tranquility Base:

The positive evidence to us is distinct kinds.

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So you think having your conclusion as evidence is scientific?A tree of life is evidence of evolution.

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Originally posted by Tranquility Base:

Yes there is a gray line somewhere where we all wonder but for now the data is compatible with this idea. The lack of transitionals is equivalent to stating this so I don't agree on your 'lack' of informaiton not being important. You have to stand in faith that for some reason, whenever novelty arises it comes in jumps. That is your stand of faith.

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I’m starting to get annoyed, now.The positive evidence points to evolution, stratigraphy & cladistics are congruent when the data is abundant.Gaps & voids are gaps & voids. YOU CANNOT INFER SOMETHING FROM WHAT ISN’T THERE. ESPECIALLY WHEN WHAT IS THERE CONTRADICTS YOU. Get it?The best you can say is that an evolutionary prediction has not been entirely borne out. This is NOT A FALSIFICATION.

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Originally posted by Tranquility Base:

The horses family balloon is simply a set of balloons put together. You can interperet it as evolution but you can't demonstrate gradual evoltuion up the column. Your jumpy evoltuion up the column could just as well be the flood distribution. Interesting how the larger horses tend to be at the top. I am very aware of the trends in bone proportions but this could be due to biogeography and flood escape too. BTW, I'm not necesarily against the idea that horses diverged into multiple forms via primarily genetic mixing, but I don't think that is what is shown in the fossil record. For us it happened pre and post flood.

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It is interesting that the larger Equines are at the top, WHEN THEY SHOULD BE AT THE BOTTOM ACCORDING TO HYDRODYNAMIC SORTING. So the jumpy evolution up the column is actually the reverse of what is expected (small to large).Phylogeny is inferred from characters in existing fossils, no comment is made regarding slow or fast evolution, so saying I can’t demonstrate evolutionary gradualism is a strawman. Nevertheless, the equine fossils DO infer a phylogeny, & OMG! It matches stratigraphy!!!!!! This is consistent with evolution, & on size alone, is the reverse of the expectation of hydrodynamic sorting. One nil to evolution. (Pity England couldn’t have held Brazil to that score! But you can’t have everything )On a side note, do you believe that the members of families are related by common descent, & if so, why?Mark------------------
Occam's razor is not for shaving with.

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[This message has been edited by mark24, 06-21-2002]

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[This message has been edited by mark24, 06-21-2002]

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Originally posted by Tranquility Base:
Thanks for the benefit of the doubt Quetzal. It is certainly true that the flood is absolutely essential to our model. Please do not equate us with the early creationists who claimed that God planted the dinosuars and the strata.

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Sorry to hear this. You may be right, then. It appears impossible to conduct a discussion on a level other than what mark, for instance, is already belaboring.

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How could we decouple the flood from the geological column. Wouldn't you expect a global flood to generate strata?

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The problem is that if you're going to claim a single, massive global flood event, you're going to have to go back and show that there is some consistent global evidence - the exact same sequence all over the world - that shows the specific layer or layers that would be deposited by the flood. And then argue about the distribution of fossils on either side. IOW, your going to have to get REALLY specific on the evidence globally for your event. Sort of like Alverez et al did for the iridium layer they are using as evidence for the asteroid K-T extinction event. Worse still, IMO, you're going to have to show clustering in the record (all animals of a specific body type/size/etc existed on one side of the layer, and didn't exist on the other, for example). IOW, since you're postulating a one-time mass extinction of a huge percentage of all life (except those animals saved on the ark, or that were somehow able to stay alive on floating vegetation, etc), you're going to have to show how the flood could have sorted Eusthenopteran, a lobe-fin fish, below Panderichthys, a bottom dwelling protoamphibian with both lungs and gills, which is sorted below Suaripterus, a bottom dwelling protoamphibian with a tetrapod humerous, and this below Acanthostega a true amphibian with genuine tetrapod limbs, but still water dwelling with an internal gill, but well-defined nasal opening and lungs, and this one below Hynerpeton a true amphibian that could spend time on land, without a gill (but retaining the gill arch).I think you're setting yourself more work than is necessary. However, feel free to try.

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However, I am prepared to discuss the fossil record miuns the flood but just remember that we do not claim to be able to explain the fossil reocrd without it!

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See above - I think you're setting yourself an impossible challenge.

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I have extensively read paleonotology monographs and papers including Benton's papers on the SCI, GER an RCI measures of stratigraphic vs cladistic consistency.

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Mark is already discussing this - and he's got a lot better knowledge base than I do. I just want to talk bones.

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My rewrite of 1a has to include the flood I'm afraid:

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1a. Special Creation and the Genesis Flood predicts the distribution via biogeography, hydrodynamic sorting and differential mobility of taxonomic groups in a 3-part fossil record: pre-flood, flood and post-flood.

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If you insist, but I still think you're actually making life more difficult for yourself. You now have to show: a spontaneous creation event (a globally correlated layer where all taxa appear simultaneously), a one-time extinction event (a layer, globally correlated, where a massive extinction/die-off has occured of all animals with the same size and body plan) and extremely rapid radiation of derived characteristics in the post-flood layers (in order to a) not have too many critters on your ark, and b) account for the 13 million+ species extant today.)I look forward to your discussion.

This is new information to me and I appreciate the post. I will try to keep an eye out in the journals and on the web in the future. Thanks

MarkI didn't agree that stratigrpahy matches phlogeny whenever the data is good. Can you show a reference that states that with supportive statistical data? I don't think Benton has shown this and he's almost the only one doing this stuff systematically. The anecdotal story of the horse is not good enough. We do expect this result to a certain extent becasue we also expect a certain amount of correlation with homology.In our model the order is due to biogeolgoraphy, relative mobility and hydrodynamic sorting properties. This is quite consistent with large mammals at the top. 'Digging up dead relatives' is a red herring - in our model 1500 years of life does not generate substantial fossils. Not to mention that the flood would have ripped up the local pre-flood shallow deposits.My point about the limited testing of the startigrphic/phylogentic ordering is that after branching the order of occurance of species between the new groups is not predicted by non-molecular cladistics.The cladistics & stratigraphy are somewhat congruent. The average SCI is about 0.5. You show me where Bentonhas a separate analysis for objectively determined 'good' data.All we are saying is that the flood is a potential explanation of the fossil ordering and it does predict an approximate ordering with homology. If you want to believe the evolutionary scenario with the rule being sudden appearenace and no transitions with incompleteness being your 'fix' that's your choice. The fact that about half (if not more) of the paleontological community fels that PE is necessary is a telling point.When I said 'The positive evidence to us is distinct kinds' I am talking about the data, not my conculsions. What you see as 'abrupt appearences' we see as the distinctness of fossil fmailies and thus 'kinds'.Stratigraphy matches phylogeny for horses - that's why museums use this example! It's terrible for primates (near zero correlation). See p123 AB Smith Systematics and the fossil record Blackwell, Oxford (1994) for correlation graphs.Our belief that organisms at approximately the family level probably did diverge from common ansestors is primarily due to biochemical, cellular and morphological novelty issues. Unlike some evolutionists we acknowledge a qualitative difference between(i) the lengthening of a limb
(ii) the gain of genuinely novel genetic and morphological featuresAt the genetic level I have posted links demonstrating that novel biochemical and cellular systems are systematically correlated with novel protein families and novel biochemical pathways.

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[This message has been edited by Tranquility Base, 06-23-2002]

QuetzalI agree that to be taken seriously by mainstream science creationists will have to get very detailed. There is more published than you think by these guys in quite good creaitonist journals. I get CEN TJ delivered at home (I don't use my uni address ) and it is a good read. 95% creation/flood science and some Christian apologetics.Are you aware of the extent of global correlation in the geological column determined by mainstream science? The first order sea level curves have global correlation. Most of the large marine beds on the continents (which incidnetally represents most of the geological column) is globally corelated! It really isn't mostly swamps and rivers! That's what I've uncovered from my minastream readings of the last six months.We have coal formation globally in the Carboniferous and Cretaceous. Chalk formation in the Cretateous. Of course there is a lot of localness even in the flood model and the data but it sits on top of an envelope of globality.Some work has been done on accounting for fossil distributions via the flood and it will continue (but not by me). I'll summarize this creationist stuff here some time in the next month but I honestly am mainly reading mainstream geology and paleontology currently.

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[This message has been edited by Tranquility Base, 06-23-2002]

Tranquility Base writes:

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I didn't agree that stratigrpahy matches phlogeny whenever the data is good.

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The evidence for increasing differences from modern forms with increasing depth, and the fact that every fossil is typical in some geologic layers and and never found in others, has been readily apparent since early in the 19th century. It was how they knew evolution had happened before Darwin provided a theory for how it happened.

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Can you show a reference that states that with supportive statistical data? I don't think Benton has shown this and he's almost the only one doing this stuff systematically.

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Benton isn't doing that type of analysis. Probably no one is doing that type of analysis. It would be like doing a statistical study of gravity to see what percentage of objects really fall down.Just to speak generally, below a certain geologic layer there is only unicellular life, and somewhere above those layers back in the late pre-Cambrian the first multi-cellular life appears. The first fish appear in layers above that. The first land animals appear in even higher layers, then the first reptiles, then dinosaurs and mammals. There are no exceptions. No mammals are found in pre-Cambrian rocks. No dinosaurs are found in Devonian layers. And floods don't sort.I hope we spend some time on this because you're ignoring the most extensive and obvious of all evidence for evolution. You can't keep dancing past important evidence to focus on details, because those details can't help but be misinterpreted if you misunderstand the broader context. It's as if you had a painting that you wanted to be of an angel, but it's not, so you've moved in way close so you cannot perceive the picture while you search for angels in the pigments.--Percy

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Originally posted by Tranquility Base:
Are you aware of the extent of global correlation in the geological column determined by mainstream science?

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Actually, I was hoping that no one had noticed.

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The first order sea level curves have global correlation.

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This is a big surprise. You raise the level of one ocean and the rest also rise!

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Most of the large marine beds on the continents (which incidnetally represents most of the geological column) is globally corelated!

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Well, if you are on the continents, yes. And yes, we can correlate units over much of the globe. I'm not sure what this has to do with a flood, however.

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It really isn't mostly swamps and rivers! That's what I've uncovered from my minastream readings of the last six months.

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Nope. But the only person I have heard say this is TB.

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We have coal formation globally in the Carboniferous and Cretaceous.

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Actually, it isn't quite global. There is coal where the environments were/are appropriate.

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Chalk formation in the Cretateous.

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Well, yes, but not everywhere.

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Of course there is a lot of localness even in the flood model and the data but it sits on top of an envelope of globality.

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This is counter to the mainstream interpretation? No, it isn't however, there are other details that your scenario does not account for, such as evaporites, eolian dunes, and dinosaur nests in the middle of your flood. And you never did explain how flowering plants managed to give no evidence of their presence until the Cretaceous. But then, we KNOW that your explanation is better, right?

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Some work has been done on accounting for fossil distributions via the flood and it will continue (but not by me). I'll summarize this creationist stuff here some time in the next month but I honestly am mainly reading mainstream geology and paleontology currently.

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Why wait? We've been trying to get this kind of evidence out of you for months...

PercyBenton has studied the extent to which SCi has changed during the 20th century. It would make a lot of sense to plot SCI vs 'goodness' of data if that could be objectively done. I would expect an increase up to a point becuase we expect homology to be somewhat correlated stratigraphically.You seem to be trying to tie us to hydrodynamics only arguements. Yes, there is an appearance of change in the fossil record but it could be nothing more than biogeographical, hydrological and differnetial escape.

EdgeThe coal (and chalk separately) are non-coincidentally correlated globally. That's how the Carboniferous epoch got it's name.These things are partially counter to mainstream expectation. Why coal formation primarily in two goes? Why correlated chalk deposits? It makes a lot of sense in our scenario but has to be shoehorned into yours.And I've admitted that the flowering plant issue is a major problem for us.

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[This message has been edited by Tranquility Base, 06-23-2002]

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Originally posted by Tranquility Base:
The coal (and chalk separately) are non-coincidentally correlated globally. That's how the Carboniferous epoch got it's name.

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Okay then, tell us where the Carboniferous coals are in Colorado. Your understanding of correlation is pretty sorry.

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These things are partially counter to mainstream expectation. Why coal formation primarily in two goes?

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Because of worldwide transgressions that ameliorated the climate, most likely.

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Why correlated chalk deposits? It makes a lot of sense in our scenario but has to be shoehorned into yours.

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Okay then, tell us where the chalk deposits are in Utah. No, they are not shoehorned anywhere by us, but have been imagined by yourself.

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And I've admitted that the flowering plant issue is a major problem for us.

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But I suppose you you still maintain that your scenario explains it better somehow. Please explain how this can be. Your reasoning defies logic.

EdgeI'm not saying that coal or chalk has to be everywhere. But coal turns up preferentially at certain stages fo the flood via the floating mat model.