How paleontology really works

This isn't really a "reply", but more of a way to mention a point that has been overlooked by both sides. Simply put, the idea that the earth of millions of years ago isn't geographically the same as the earth of today. So, you must redefine what you mean by global.

Octipice, most creationists agree with the basic global correlation of the geological epochs and the drift of the continents.

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Originally posted by Tranquility Base:
Mark

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I 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.

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Yup, I think you’ll recognise this. http://palaeo.gly.bris.ac.uk/publs/Benton/2001Treeoflife.pdf

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Benton:

Contrary to these ndings is that a number of studies
have shown congruence between trees and stratigraphy
for a wide range of organisms (Norell & Novacek 1992a,b;
Benton & Storrs 1994; Smith & Littlewood 1994; Benton
& Hitchin 1996; Benton et al. 1999, 2000). Admittedly,
many of the assessed trees cover groups with accepted
`good’ fossil records

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A major criticism of the approach adopted here is that
it can only work when the fossil record is relatively
complete: if there are many gaps, then there is no
evidence that the correct tree will t stratigraphy any
better or worse than any of the numerous incorrect trees
(Fortey & Jeeries 1982; Wagner 2000b).With signicant
missing fossils, the recorded order of origination of groups
could easily be the exact opposite to that implied by the
`correct’ tree. So, hanging over any comparisons between
stratigraphy and phylogeny is the concern that modest
changes in the degree of congruence may say nothing
about improvements in the quality of the cladogram.

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For the LAST time,WHEN THE FOSSIL RECORD IS GOOD, CLADISTISTICS & STRATIGRAPHY MATCH WITH A HIGHER FREQUENCY THAN WHEN THE FOSSIL RECORD IS POOR.Benton cites four studies supporting the correlation between good fossil record & cladistics/stratigraphy, one of his own is among them.It comes to something, TB, when you won’t even accept the words of Benton, your own cite. Why, then, do you believe anything he writes? Could it be because you’ll accept anything that supports your view, & disregard anything that doesn’t, even if it’s presented by the same author?

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Originally posted by Tranquility Base:

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.

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But this is the nature of cladograms, it doesn’t directly show anagenesis, even if it did occur.

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Originally posted by Tranquility Base:

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.

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Hang on a minute! YOU claimed that the fossil record was complete, now you’re asking me for objective determination of good data?Anyhow,

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Benton:

There is growing evidence that the fossil record is well sampled.
For example, in a study of the quality of the
fossil record of tetrapods from 1967 to 1993, there was a
statistically signicant improvement in the quality of t to
a xed set of cladograms (Benton 1994; Benton & Storrs
1994): new discoveries were lling predicted gaps, not
creating new gaps. If, on the other hand, new fossil nds
created gaps more often than they lled them,
palaeontologists would have to retire from the discussion
until they could demonstrate some stability in their
knowledge of the fossil record. Indeed, Weishampel
(1996) found, in comparing the addition of new taxa to
trees of dinosaurs, horses, and hominids through the past
120 years, that many new nds did extend trees, and add
gaps. However, this eect was seen only for dinosaurs and
horses, and the pattern is one of uctuation, with highest
mean ghost range measures in 1900 and 1916, respectively,
and lower values since. For hominids, mean ghost ranges
have declined from1920 onwards.

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The determination of good data, is where a phylogeny/cladogram turns up relatively few unsampled dotted lines. Again, from your own cite.

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Originally posted by Tranquility Base:

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.

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Well, the other half don’t.Then please explain the appearance angiosperms, gymnosperms, lycopsids, & pteropsida.People are killed on coastal mud flats when the tide comes in. Please tell me how mice/gophers etc. are able to outpace an advancing global flood on a flat plain? Or does your model predict convenient mountains every couple hundered yards?

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Originally posted by Tranquility Base:

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'.

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Distinct kinds is not data.The tree of life is evidence of evolution.

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Originally posted by Tranquility Base:

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.

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I'll suspend reality for a moment & assume a global flood happened, what is your positive physical evidence that there was only 1,500 years for organisms to die in pre-flood?

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Originally posted by Tranquility Base:

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.

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Stratigraphy matches phylogeny for horses, YAY, at last. The stratigraphy of horses DOESN’T match hydrodynamic sorting, however.

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Originally posted by Tranquility Base:

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

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(i) the lengthening of a limb
(ii) the gain of genuinely novel genetic and morphological features

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At 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]

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Yeah, thought so. Those balloons & dotted lines on paleontological charts represent created kinds & the gaps are fossil voids, in classifications higher than family. But below family, the balloons & dotted lines represent available fossils, & inferred lineages. This is utterly, utterly hypocritical, you can’t even universally apply the same criteria to the same evidence to support your model.------------------
Occam's razor is not for shaving with.

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[This message has been edited by mark24, 06-24-2002]

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[This message has been edited by mark24, 06-24-2002]

MarkI agree wholeheartedly that there is a correlation with homology and that it will of course only become evident where the data is more complete.But it's still an issue of extents. I still am yet to see an average SCI quoted for 'good' data. The point is you beleive that if the data collection was perfect there would be an infinie SCI. I believe it would level out at some finite value becasue we don't expect a perfect correlation. We can't distinguish between these two possibilities.Whatever the case, you can't go to the fossil record and construct trees from it in most cases.I'm not a zoologists so you'll have to explain the issues about angiosperms, gymnosperms, lycopsids, & pteropsida.You said 'Distinct kinds is not data'. Distinct fossil species are.The 1500 years is obviously a scriptual inference. But we see no evidence of deep non-marine Precambrian beds so I would see that as physical evidence of not much time in between creaiton/flood.We don't put everything down to hydrodynamic sorting - please stop saying that! There is also biogeography and relative mobility.Those balloons are definitely simply collections of family members! You just use the family anme and get a balloon. There are systematically no transition and the SCI values are worse within families than for higher taxa.

OK everyone here's some excerpts from a very nice 1994 paleontolgoy book I'm reading currently (Benton's is also very good but mainly taxonomic):

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p58 "(E)volutionary sequences of anscestor-descendant cannot simply be read from the rocks - fossils first have to be ordered into some form of hierarchy on the basis of their morphology"

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p123 "Recently the correspondence between predicted order derived from phylogenetic analysis and observed order from the fossil record has been tested empirically . . . they obtained very mixed results."

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AB Smith Systematics and the fossil record Blackwell, Oxford (1994)

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I don't deny that the reason may be the incompletness of the fossil eocrd but it is still true that one can't systematically use the fossil record to constuct trees!Eldredge one of the fathers of Punctuated Equilibrium said only seven years ago:

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"No wonder paleontologists shied away from evoltuion for so long. It never seemed to happen. Assiduous collecting up cliff faces yields zigzags, minor oscillations, and the very occasional slight accumulation of change - over millions of years, at a rate too slow to account for all the prodigious change that has occurred in evoltuionary history. When we do see the introduction of evolutionary novelty, it usually shows up with a bang, and often with no firm evidence that the fossls did not evolve somehwere else. Evolution cannot forever be goin on somewhere else. Yet that's how the fossil record has struck many a forlorn paleontologist looking to learn something about evoltuion."

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N. Eldredge (1995) Reinventing Darwin, Wiley, New York p95

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We cannot pretend that the fossil record shows evidence of genuine transforamtions.

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[This message has been edited by Tranquility Base, 06-24-2002]

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Originally posted by Tranquility Base:
Mark

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I agree wholeheartedly that there is a correlation with homology and that it will of course only become evident where the data is more complete.

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But it's still an issue of extents. I still am yet to see an average SCI quoted for 'good' data. The point is you beleive that if the data collection was perfect there would be an infinie SCI. I believe it would level out at some finite value becasue we don't expect a perfect correlation. We can't distinguish between these two possibilities. .

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No, wouldn’t expect it to be infinite (it can only be as high as one, surely), but I would expect it to be relatively high, I accept the real world isn’t perfect. Furthermore, character traits are seen to fluctuate over time, despite showing a general trend, that is, varies around a mean. This has serious repercussions in poorly sampled fossil clades. In studies of stickleback fossils G.doryssus in Miocene strata (Nevada) are found in an unusually complete series of strata spanning 110,000 years. Large numbers of fossil samples were were studied from layers on average 5,000 years apart. When pelvic structure, dorsal spine number, & predorsal pterygiophore number are plotted against time, a general trend is observed. This trend is broken by a wobbling, a zig-zagging around an average increase line, with the prior ancestral character occasionally regaining dominance, before the general trend continues. Meaning morphology doesn’t smoothly transit. (After Bell et. al. 1985). As a result, cladogram nodes based on these characters, vs stratigraphy will rarely correlate into a perfect SCI of 1. In fact, looking at the graphs for dorsal spine number, it shows a general increase in number, but taking each point, there are 12 decreases, & 13 increases. Similarly, the predorsal pterygiophore number shows a general increase, with 11 decreases, & 14 increases. Of course the quantitive value of the increases outweighs the values of the decreases (the increases go up more than the decreases go down, on most occasions).But I wonder what SCI value this would show if some samples were removed? As Benton states, you can potentially get exactly the wrong conclusion if the sampling is poor.Further examples of this non-linear zig-zag across a general trend are abundant. I list only a couple here,Trilobyte rib numbers ; Nileids, Bergamia, Whittardolithus, Ogyginus, Ogygiocaralla, curiously, Noboliosaphus pans out with almost exactly a straight line. (Evolutionary Biology 3rd ed. D Futuyma)Shell shape of Globoritalia (Malmgren 1983)Radiolaran speciation & divergence of Eucyrtidium calvertense, & E.Matuyamai (After Kellog & Hays 1975)My point being, if the above examples were poorly sampled it is possible to get nonsense results from an SCI check. Also, inferring phylogenies from characters that vary about a mean line of progress may trick the SCI into not seeing a nodal correlation because a character has varied too far from the mean for that species/character to be considered on node, particularly if there are potential samples missing, relative to the characters of samples immediately prior & after the sample in question.

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Originally posted by Tranquility Base:

Whatever the case, you can't go to the fossil record and construct trees from it in most cases.

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You can when the data is abundant (see the Horse genera phylogeny in previous posts). You can’t when it isn’t. God of the gaps. You’re just repeating yourself now. You can hang your hat on a 0.5% SCI average if you want, but your shutting your eyes to evidence that points to well sampled fossils deriving cladograms that are highly congruent with fossil stratigraphy. This is the one & only point I wanted to make.In any area of study, no one expects poorly sampled data to give good results, we do expect well sampled data to give good results, however, & that is what we see. From an evolutionary perspective a good result are congruent cladograms/fossil stratigraphy. This is seen, & represents excellent evidence of evolution of higher taxa.I see no point continuing this discussion if you are simply going to deny your own cite, Benton has backed up his conclusion by citing other studies.You seem to be arguing that an SCI average of 0.5 is in some way supportive of the creationist flood model. Please tell me how, supported with positive evidence how this phylogeny of Equidae can be explained with hydrodynamic sorting, biogeography, & relative mobility.

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Originally posted by Tranquility Base:

I'm not a zoologists so you'll have to explain the issues about angiosperms, gymnosperms, lycopsids, & pteropsida.

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Being a botanist would be more help than being a zoologist! Angiosperms are flowering plants, gymnosperms are cone bearing, lycopsids are club mosses, & pteropsida are ferns. I should also include pteridosperms (seed ferns), that have been extinct since the Jurassic.Club mosses, ferns, & seed ferns appear in the devonian/carboniferous.Gymnosperms appear in the triassic.Angiosperms appear in the cretaceous.Why, then do these tree (ferns excepted) to small plant bearing classes of plants appear at different times, & in the case of seed ferns, disappear altogether, under a flood model? I ask you to explain the stratigraphy of these plant taxa, & how it pertains to the flood models hydrodynamic sorting, biogeography, & relative mobility.

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Originally posted by Tranquility Base:

You said 'Distinct kinds is not data'. Distinct fossil species are.

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Distinct fossil species are not distinct biblical kinds. You would obviously argue that the existence of families are evidence of a biblical kind, because the evidence of familial intermediates is poor. But then I could say the same about individual species & genera, but you interpret them to have evolved from a familial ancestor, despite the lack of transitionals.You can’t have it both ways.

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Originally posted by Tranquility Base:

The 1500 years is obviously a scriptual inference. But we see no evidence of deep non-marine Precambrian beds so I would see that as physical evidence of not much time in between creaiton/flood.

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Precambrian non marine sediments cannot have time inferred from them.So, you don’t have any positive evidence with which to infer 1,500 years passed between creation & the flood, then? In which case you cannot infer that the pre-flood period wouldn’t generate many fossils. I think you’ll find that the positive evidence suggests that the pre-cambrian is longer than all of the paleozoic, mesozoic, & cenozoic eras combined, & that they themselves lasted a LOT longer than 1,500/4,500/6000 years.If you are assuming that the Precambrian is pre-flood rock, then you’re in even more trouble.Not a single species of mammal is found in pre Cambrian rock, & not a single species of multicellular life in pre-cambrian rock is found in cenozoic rock. See below. In fact an increasing complexity can be seen over time in pre Cambrian formations, namely, prokaryotes, eukaryotes, & multicellular eukaryotes. How is this explained by hydrodynamic sorting, biogeography, & mobility? Oh, my mistake, it can't! These are precambrian rocks & weren't involved in the flood! Oh, what to do?Explanations based on positive evidence please.

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Originally posted by Tranquility Base:

Not to mention that the flood would have ripped up the local pre-flood shallow deposits.

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So where is the cenozoic Ediacaran fauna?Given soft bodied Ediacaran fauna can manage to fossilise pre-flood, where are the mammals, reptiles, amphibians etc? You reckoned that 1,500 years wouldn’t generate many fossils, yet hard-to-fossilise soft bodied examples can be found. So, where are the easy to fossilise examples, of bone, for example, Which we would reasonably expect to find more of than soft bodies?

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Originally posted by Tranquility Base:

We don't put everything down to hydrodynamic sorting - please stop saying that! There is also biogeography and relative mobility.

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See angiosperms, gymnosperms, lycopsids, & pteropsida, above.Plants of all sizes are immobile, except perhaps Triffida triffida, yet they display exactly the same manner of appearance/disappearance in the fossil record as animals, so the relative mobility dog won’t hunt.

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Originally posted by Tranquility Base:

Those balloons are definitely simply collections of family members! You just use the family anme and get a balloon. There are systematically no transition and the SCI values are worse within families than for higher taxa.

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You miss my point, I’m talking the balloons & lines associated with individual species & genera, within the same family. If you apply your interpretation of these diagrams, as you apply them to family level classifications & above, then each individual species is a separately created kind in its own right. There are NO transitionals, because only a dotted line separates them, & a dotted line to you means a gap where no transitional exists. So, how then do you interpret these charts to mean sub-family classifications are related via common descent, & higher-than-family classifications are specially created, based on EXACTLY the same evidence, without exposing yourself as a colossal hypocrite?I’m on my hols ‘till Tuesday, so won’t be able to reply until at least then. But please, anyone feel free to chip in with your tuppeny worth.Mark------------------
Occam's razor is not for shaving with.

SCI = number of consistent nodes/inconsistent nodes so you do expect an infinite SCI (obviously in practice with N nodes, and one error you expect an SCI of N). It should have been defined as consistent nodes/all nodes and the SCI = 1 would be perfection. I suspect the definer of SCI didn't like the idea of SCI = 0.3. Sounds like a poor correlation doesn't it? Cynical? Yes but with good reason in this case. Every 'order parameter' I have ever used or defined myself is a 0-1.0 parameter.I've already agreed with you that getting improved SCIs with data collecting is what you expect, and I say we partially expect it to.You haven't systematically shown that SCI is good with abundant data? Where is that graph in Benton's papers?I think life sciences needs a term that encompasses zoology and botany. OK - I'm not a systematisist. I agree that creationists must ultimately answer the botanical orderings in the fossil ecord and that we cannot appeal to relative mobility! Biogeography and hydrodynamical sorting is our only possibility.We have it both ways on within/across family evoltuion because there generally appears to be a lack of genuine jumps of novelty within families so why shouldn't they evolve? We're on your side - you should be happy! But beasue of the flood model we don't believe the fossil record is showing us the order of divergence. We distinguish between the origin of genuine biochemical/cellular novelty and morphing of existing elements. No matter how hard you try it's impossible to adaptively morph an immune system from non-immune system genomes without developing completely new protein families that bear no resmeblance to pre-existing ones!I assign the Precambrian rocks to creation day 3 (land appearing out of water) and for theological reasons (2 Pet 3, Ps 90, Heb 4, Rev 20, Gen 1) I suspect the creation days to be 1000 year periods. We expect trivial fosilization during the non-catastrophic pre-flood 1500 years so we expect the entire eidence of pre-flood life to have been washed away early in the flood. Convenient maybe but utterly expected. The Precambrian fossils are marine - why would anyone expect to find amphibians there?

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[This message has been edited by Tranquility Base, 06-25-2002]

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Originally posted by Tranquility Base:
SCI = number of consistent nodes/inconsistent nodes so you do expect an infinite SCI (obviously in practice with N nodes, and one error you expect an SCI of N). It should have been defined as consistent nodes/all nodes and the SCI = 1 would be perfection. I suspect the definer of SCI didn't like the idea of SCI = 0.3. Sounds like a poor correlation doesn't it? Cynical? Yes but with good reason in this case. Every 'order parameter' I have ever used or defined myself is a 0-1.0 parameter.

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It was defined as consistent nodes/all nodes.SCI is the proportion of stratigraphically consistent nodes (those younger than, or equal in age to, the node immediately below) to total nodes in a cladogram (Benton), therefore the highest you can get is a 1. Infinity is impossible.I think the misunderstanding comes from this definition (Benton again). The SCI for a cladogram compares the ratio of the sums of stratigraphically consistent to inconsistent nodes. This isn’t a good definition, since it can mean consistent nodes/total nodes, or total nodes/consistent nodes (it doesn’t tell you what way around they are compared). I must confess, this was the first definition I saw, & the only way I could resolve it was by checking the actual SCI’s from Bentons database. If you check, you will see the SCI can go up to one, but not beyond.Therefore, 0.5 means 50% of nodes correlate.The range is from zero (no correlation), to one (100% correlation).

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Originally posted by Tranquility Base:

I've already agreed with you that getting improved SCIs with data collecting is what you expect, and I say we partially expect it to.

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Then provide a universal model to tell us why homology is expected in a flood scenarios deposition of fossils.

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Originally posted by Tranquility Base:

You haven't systematically shown that SCI is good with abundant data? Where is that graph in Benton's papers?

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What graph? http://palaeo.gly.bris.ac.uk/cladestrat/introduction.htmlI did a little study of my own using Bentons data. I only took SCI readings from samples that showed a 90+ RCI score (100 max). My prediction would be that high RCI (relative completeness index) should show a higher than average SCI score, which you are telling me is 0.5.Out of 75 samples that hit criteria, the average SCI was 0.66. Therefore it is demonstrable that the more complete the sampling from which the cladograms are derived, the better the congruence with stratigraphy. In fact, the only group that fared badly was fishes (0.45 av over 29 samples). If you drop them out of the equation the SCI average jumps to 0.79.For comparison, the same criteria applied to molecular mammalian phylogenies yielded an SCI of 0.78.The prediction has been borne out, the congruence of cladograms & the fossil stratigraphy rises with an increase in RCI.To recap, this means that creationists cannot infer anything negative about the ToE as a whole based on poor sampling. ie. saying we "only" see an average of 0.5 SCI is misleading. The better the sampling, the better the correlation (on average). To do so so would be a god-of-the-gaps argument. Not that I'm saying that the lower RCI phylogenies are worthless, sometimes you have to work with what we have, but that's science.However, I’m not convinced that 0.5 average SCI alone doesn’t adequately demonstrate evolution when taken along with RCI, & SRC metrics, given the potential pitfalls of poor sampling, convergence, homoplasy, non-gradual progression etc. Especially since you have provided nothing to make me believe that homology has anything to do with fossil deposition re. The flood model. The SCI is but one metric used, & quite often a phylogeny that fails one metric (for whatever reason), passes another. http://www.nature.com/nature/debates/fossil/fossil_19.html11 Benton, M. J. & Hitchin, R. Congruence between phylogenetic ands stratigraphic data on the history of life. Proc. R. Soc. Lond. B264, 885-890 (1997).10 Clyde, W. C. & Fisher, D. C. Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis. Paleobiology, 23, 1-19 (1997).12 Benton, M. J. Molecular and morphological phylogenies of mammals: congruence with stratigraphic data. Molecular phylogenetics and evolution, , 398-407 (1998).Putting aside one's personal preferences, what actually happens when cladograms are compared with stratigraphy? Clyde & Fisher10 compared stratigraphic and morphological data with 29 cladograms and concluded "morphologic and stratigraphic information show similarly good fit to these phylogenetic hypotheses. Large, significant increases in stratigraphic fit (49 %) required only small, insignificant decreases in morphologic fit (4 %) when stratigraphic data participated in constraining the structure of the phylogenetic hypotheses."Benton & Hitchin11 applied three metrics (SRC, RCI and Huelsenbeck's stratigraphic consistency index SCI) to 384 published cladograms of echinoderms, fish and tetrapods to test for congruence between stratigraphic and morphological data. The last measures the stratigraphic consistency of each node in a cladogram. Benton & Hitchin found good agreement between phylogenetic and stratigraphic data. They concluded "This congruence of conclusions from two essentially independent sources of data confirms that the majority of cladograms are broadly accurate and that the fossil record, incomplete though it is, gives a reasonably faithful documentation of the sequence of occurrence of organisms. Interestingly, the metric which showed the closest agreement was the SCI.Finally, Benton12 has compared 206 mammal phylogenies based on morphological and molecular data with stratigraphy using the same three metrics. The overall result was broadly the same, although this time it was the RCI which showed closest congruence largely due to significantly better results compared to SRC and SCI for protein-based phylogenies.Taken together these last three papers provide a large enough sample to conclude thatcharacter analysis and stratigraphy are by no means poles apart. Since the data are largely independent, one is forced to conclude that both must be broadly correct. There is independent evidence that the sequence of fossils is reliable: if it were not we wouldn't be able to correlate using fossils. Character analysis is the first step in erecting phylogenetic hypotheses. Where there is a fossil record, it should be used as the first test of these hypotheses.Chris PaulDepartment of Earth Sciences, University of LiverpoolEmphasis mine.See question 5/, below. It seems to me that you need to demonstrate that fossil homology is actually an expectation of the flood model.

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Originally posted by Tranquility Base:

I think life sciences needs a term that encompasses zoology and botany. OK - I'm not a systematisist. I agree that creationists must ultimately answer the botanical orderings in the fossil ecord and that we cannot appeal to relative mobility! Biogeography and hydrodynamical sorting is our only possibility.

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Biology is zoology combined with botany, hence biology. To be fair, it has come to mean much more, particularly with there being more than 2 kingdoms now!You cannot maintain that the flood is the best explanation for the fossil record when you, nor any other creation scientist can explain the record as it stands.

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Originally posted by Tranquility Base:

We have it both ways on within/across family evoltuion because there generally appears to be a lack of genuine jumps of novelty within families so why shouldn't they evolve? We're on your side - you should be happy! But beasue of the flood model we don't believe the fossil record is showing us the order of divergence. We distinguish between the origin of genuine biochemical/cellular novelty and morphing of existing elements. No matter how hard you try it's impossible to adaptively morph an immune system from non-immune system genomes without developing completely new protein families that bear no resmeblance to pre-existing ones!

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1/ Provide scientific references that concludes it is impossible to adaptively morph an immune system from non-immune system genomes without developing completely new protein families that bear no resmeblance to pre-existing ones.2/ You’re evading my argument. You are interpreting the same information on spindle diagrams to mean two different things, when it suits you.The dotted lines are complete gaps because they have no intermediate fossils, or they are NOT.YOU CAN’T HAVE IT BOTH WAYS!!!!!!!I’m assuming, this being the third time I’ve pointed out this inconsistency, that you have no answer that directly addresses my point. We are attempting to do science, & you can’t do this unless you are going to apply universal criteria with which to apply to ALL dotted lines in paleontological diagrams.

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Originally posted by Tranquility Base:

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I assign the Precambrian rocks to creation day 3 (land appearing out of water) and for theological reasons (2 Pet 3, Ps 90, Heb 4, Rev 20, Gen 1) I suspect the creation days to be 1000 year periods. We expect trivial fosilization during the non-catastrophic pre-flood 1500 years so we expect the entire eidence of pre-flood life to have been washed away early in the flood. Convenient maybe but utterly expected. The Precambrian fossils are marine - why would anyone expect to find amphibians there?

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[This message has been edited by Tranquility Base, 06-25-2002]

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But all fossils/evidence of pre-flood life wasn’t washed away, was it? Prokaryotic bacteria are found in the lowest strata, then single celled eukaryotic, then multicellular eukaryotic, found in order of complexity. Saying that all pre-flood life was washed away is not only convenient, it is demonstrably wrong.Amphibians were created pre-flood, were they not? So they walked on the pre-cambrian surface, along with reptiles, mammals. Seed ferns co-existed with angiosperms & gymnosperms, ALL of which fossilise better than the soft bodied organisms that are found in pre-cambrian strata. So, where are they? We would expect to find several orders of magnitude more vertebrates, arthropods, trees, etc. than soft bodied fossils that do exist there. Furthermore, since these pre-cambrian soft bodied organisms (eg Ediacara) managed to fossilise in pre-cambrian rock, why aren’t they found in post-flood strata, like all other taxa?Also, you never answered my questions.1/

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Originally posted by Tranquility Base:

Not to mention that the flood would have ripped up the local pre-flood shallow deposits.

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So where is the cenozoic Ediacaran fauna?2/ Given soft bodied Ediacaran fauna can manage to fossilise pre-flood, where are the mammals, reptiles, amphibians etc? You reckoned that 1,500 years wouldn’t generate many fossils, yet hard-to-fossilise soft bodied examples can be found. So, where are the easy to fossilise examples, of bone, arthropods etc. Which we would reasonably expect to find more of than soft bodies?3/ Why is an increase in complexity seen in pre-flood strata, from older to younger?4/ I’m still waiting for your explanation of the Equidae fossils, with respect to homology, hydrodynamic sorting, biogeography, & relative mobility. I’m particularly interested as to why a phylogeny can be inferred at all, the SCI ranges from 0.67 to 1.0 btw, with over half of Bentons studied samples being in the 0.90 to 1.0 . Or is this something else you can’t explain, after telling me you could, & still maintain that the flood model is the best explanation?5/ (New question) Provide a model (it’s a toughy, I know, but single examples I can always contradict with a counter example. It’s best to cut to the chaste) that universally demonstrates that homology related deposition is expected under the flood model. Otherwise, well, it isn’t, & a 0.5 average SCI is pretty remarkable evidence for evolution, not to mention that when the fossil record is better, so is the SCI, on average.Right, I’m REALLY going on hols this time! Sunny Inverness, scotch, haggis, nessie, men in skirts, bring em’ on! Back tues of next week, so I won’t be able to reply until then.Mark------------------
Occam's razor is not for shaving with.

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[This message has been edited by mark24, 06-26-2002]

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[This message has been edited by mark24, 06-26-2002]

MarkOK, I found a worked example and you're right about the definition of SCI - that was very sloppy writing by my favourite paleontologist!I have seen detailed work on flood ordering but it is clear that mobility, biogeography and hydrological sorting properties are related to homology.That is a good analysis you did using RCI. So what it comes down to is whether we expect homology to order fossils to the extent of about 80%? That is ultimately what we have to show. Your problem is to explain why even when your data is very good 20% of the nodes are incorrectly ordered. You also have to explain why there are many ghost ranges that traverse hundreds of millions of years. Many fossils found (as evidence by thick spindles) but ghost ranges of no appearence for the preceding 100 million years. Go look at Benton's 1994 book to see. For us it's easy - these animals had good flood surivability or where biogeographically separate.If you look here you'll get refs and quotes on the fact that cellular systems are correlated with novel protein families that are unrelated by sequence: http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=5&t=46&m=10#10There is no almost no literature on the origin of protein families. I'm not kidding. It is clear that the veovltuion of distinct protein families is a prohibitive barrier to evolution.Mark, it is quite clear from Bentons book that the family spindles are simply collections of families! Those diagrams put aside within family evoltuion and look at between family evoltuion. There is nothing wrong with doing that but that is what is done. The resolutio of the diagrams is not large enough to show all of the genii (genuses?) sperately. The stratigraphic arrangement of fossils within the families is poorer than the ordering between families - Benton has said that. If you think all those family balloons are proof of hundreds of evolutionary transitions you are completely mistaken.You find it a big surpirise that microscopic creatures found their way into pre-flood cracks? The flood to us is an extinction event with multiple phases. You may need dozens of explanaitons of extinctions but we have one unifying event. The increase in complexity in pre-flood rocks may have to do with something as simple as size.The Equidae ordering is an example where homology correelates very well with stratigraphy. That homology certainly does lead from small horses to large ones and hence differnetial mobility. And I've already given you the qualittive reasons we expect homology to coincide with stratigraphy.

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[This message has been edited by Tranquility Base, 06-26-2002]

quote:

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Originally posted by Tranquility Base:

I have seen detailed work on flood ordering but it is clear that mobility, biogeography and hydrological sorting properties are related to homology.

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Great, then all you have to do is tell me how, if it’s so clear! You have given up on plant fossil stratigraphy, so I’m guessing when push comes to shove, it’s really not that clear, after all!

quote:

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Originally posted by Tranquility Base:

That is a good analysis you did using RCI. So what it comes down to is whether we expect homology to order fossils to the extent of about 80%? That is ultimately what we have to show.

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Yup.

quote:

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Originally posted by Tranquility Base:

Your problem is to explain why even when your data is very good 20% of the nodes are incorrectly ordered.

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Homoplasy. Non linear progression around a mean. Cladogenesis, & varying rates of evolution among traits between sister clades. Reversal of character progression (see Archeohippus & Nannihippus, below).

quote:

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Originally posted by Tranquility Base:

You also have to explain why there are many ghost ranges that traverse hundreds of millions of years. Many fossils found (as evidence by thick spindles) but ghost ranges of no appearence for the preceding 100 million years. Go look at Benton's 1994 book to see. For us it's easy - these animals had good flood surivability or where biogeographically separate.

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Incomplete fossil record. Large radiations from a small population. Examples that fossilise poorly, with occasional good conditions, resulting in snapshots of taxa. Preservation bias of different taxa.Additionally, the overall ghost ranges are becoming fewer as more fossils are found, that is, the net ghost ranges are becoming fewer. This indicates that ghost ranges are correctly inferred as missing lineages, & do indeed contain undiscovered species, this conclusion backed up by molecular evidence. Despite this, you still maintain that the ghost ranges are genuine gaps, when it suits you.

quote:

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Originally posted by Tranquility Base:

If you look here you'll get refs and quotes on the fact that cellular systems are correlated with novel protein families that are unrelated by sequence:

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http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=5&t=46&m=10#10

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There is no almost no literature on the origin of protein families. I'm not kidding. It is clear that the veovltuion of distinct protein families is a prohibitive barrier to evolution.

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I asked,

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Originally posted by Mark:

Provide scientific references that concludes it is impossible to adaptively morph an immune system from non-immune system genomes without developing completely new protein families that bear no resmeblance to pre-existing ones.

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I still can’t see that you’ve done so. Therefore, saying it is clear that the veovltuion of distinct protein families is a prohibitive barrier to evolution is at best premature. If you can’t show this, it’s another God-of-the-gaps argument from incredulity.

quote:

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Originally posted by Tranquility Base:

Mark, it is quite clear from Bentons book that the family spindles are simply collections of families! Those diagrams put aside within family evoltuion and look at between family evoltuion. There is nothing wrong with doing that but that is what is done. The resolutio of the diagrams is not large enough to show all of the genii (genuses?) sperately. The stratigraphic arrangement of fossils within the families is poorer than the ordering between families - Benton has said that. If you think all those family balloons are proof of hundreds of evolutionary transitions you are completely mistaken.

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Very simply, if the stratigraphic arrangement of fossils within the families is poorer than the ordering between families, then this is evidence of special creation of individual species, surely? This is consistent with your interpretation of fossil gaps above family level, I’m merely forcing you to be consistent.How did they all get on the ark?You can’t have it both ways. Gaps in the fossil record are gaps, or they are not. You can’t pick & choose.

quote:

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Originally posted by Tranquility Base:

You find it a big surpirise that microscopic creatures found their way into pre-flood cracks? The flood to us is an extinction event with multiple phases. You may need dozens of explanaitons of extinctions but we have one unifying event. The increase in complexity in pre-flood rocks may have to do with something as simple as size.

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Wrong, bacterial fossils can be found as impressions in sedimentary rock, indicating they were present at the time of lithification, & not added afterwards. Secondly, micro fossils can be found within rock, not just on the surface. Nevertheless, this rather simplistic waving away doesn’t explain,a/ The ordering. Prokaryotes, eukaryotes, & then multicellular eukaryotes.b/ The existence of stromatolites. They found their way into pre flood cracks, & remained in cladistic/stratigraphic order!? If whole colonies of cyanobacteria can be found in 3.0 by old rock, why can’t a SINGLE eukaryotic cell not be found for another 1.0 by?Some "living" stromatolites. Some fossil ones. ( http://cushforams.niu.edu/Stromato.htm )Precambrian conical stromatolite from the McArthur Group, Australia. Field photo showing weathered outcrop of small conical stromatolites (Conophyton) in the Tooganinnie Formation, McArthur Group, near Tanumbirini, 700 km southeast of Darwin, Northern Territory, Australia. 1.6 billion years old. Photo by M. R. Walter, Baas Becking Geobiological Laboratory, Canberra, Australia. Copyright by and used with the permission of the Precambrian Paleobiology Research Group - Proterozoic (UCLA).c/ There are plenty of non-microscopic multicellular forms found in the pre-cambrian.You see your problem, TB? These aren’t things that find their way into cracks, nor do multicellular (eukaryotes).See 3/, below.

quote:

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Originally posted by Tranquility Base:

The Equidae ordering is an example where homology correelates very well with stratigraphy. That homology certainly does lead from small horses to large ones and hence differnetial mobility. And I've already given you the qualittive reasons we expect homology to coincide with stratigraphy.

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[This message has been edited by Tranquility Base, 06-26-2002]

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I’m afraid I missed the qualitative reasons you expect homology to coincide with stratigraphy. See 4/ & 5/, below.Secondly, the fossil record shows that Archeohippus & Nannihippus (among others), became smaller, not larger. Which rather spoils your homology comparison, doesn’t it? Because differential mobility simply can’t be a factor if size isn’t affecting the phylogeny/stratigraphic placement. This is why I’m asking you for a model, because for every example you give me, I can provide a counterexample. If I can do that, then your idea of homology, hydrodynamic sorting, biogeography, & relative mobility being responsible is a poor one, & undemonstrable. Given that size isn’t the sole factor, please then explain how toe number, molar morphology, face length etc. are responsible for stratigraphic position. This will be particularly interesting because after cladogenesis, there are occasions where the ancestral trait was retained by one clade, & changed in another, or even reversed, yet both/all coexisted at the same time! Take the coexisting sizes, for example. Or the preorbital fossa of the Hipparion group, relative to the fossa of Protohippus, Calippus, Astrohippus, Pliohippus, all coexisted. The same is true of toe number, teeth morphology etc.You could potentially argue homology/stratigraphy in a straight line evolutionary pathway, if the traits you are marking as being informational don’t show any reversal. They do (see previous post re. Deviation around a mean), also Equidae growing smaller when others are getting larger.Your position gets absolutely ridiculous when the nature of relationships inferred show a multi-clade tree, with ancestral traits being retained, alongside traits reversing, others progressing, among contemporary species.Please answer these questions in detail.

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Originally posted by Mark:

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1/ "Not to mention that the flood would have ripped up the local pre-flood shallow deposits."

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So where is the cenozoic Ediacaran fauna?

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2/ Given soft bodied Ediacaran fauna can manage to fossilise pre-flood, where are the mammals, reptiles, amphibians etc? You reckoned that 1,500 years wouldn’t generate many fossils, yet hard-to-fossilise soft bodied examples can be found. So, where are the easy to fossilise examples, of bone, arthropods etc. Which we would reasonably expect to find more of than soft bodies?

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3/ Why is an increase in complexity seen in pre-flood strata, from older to younger?

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4/ I’m still waiting for your explanation of the Equidae fossils, with respect to homology, hydrodynamic sorting, biogeography, & relative mobility, taking into account reversing trends. I’m particularly interested as to why a phylogeny can be inferred at all, the SCI ranges from 0.67 to 1.0 btw, with over half of Bentons studied samples being in the 0.90 to 1.0 . Or is this something else you can’t explain, after telling me you could, & still maintain that the flood model is the best explanation?

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5/ Provide a model (it’s a toughy, I know, but single examples I can always contradict with a counter example. It’s best to cut to the chaste) that universally demonstrates that homology related deposition is expected under the flood model. Otherwise, well, it isn’t, & a 0.5 average SCI is pretty remarkable evidence for evolution, not to mention that when the fossil record is better, so is the SCI, on average.

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Mark------------------
Occam's razor is not for shaving with.

Bump......------------------
Occam's razor is not for shaving with.

Bump.....------------------
Occam's razor is not for shaving with.

Your posts make mine look small Mark - I'll get around to it ASAP!

Right! It's been two weeks now, does that mean I can claim victory?Regardless, TB, I will be annoyed if you claim that the fossil record is what would be expected under a flood model. You haven't been able to show how homology, hydrodynamic sorting, biogeography, & relative mobility, are relevant for explaining the fossil record.Mark------------------
Occam's razor is not for shaving with.

MarkThanks for the boot.OK - I was planning to make an informed comment on your stuff. Instead, for now, you'll get my of the cuff comments!I have to disappoint you by saying that(i) I have both faith and scientific intuition of plausibility that our 3-point mechanism could generate the empirical ordering
(ii) I understand some of the very gross patterns (marine/wetland/mobile)
(iii) I really have read some creationist studies which have addressed the issue
(iv) I do trust the mainstream column but nevertheless am convinced that 'out of order fossils' are frequently ignoredYou wont like it and I don't like it bt that's where we are on the issue. I stand by my original statement that the fossil record itself cannot generally generate cladogams. I acknowledge that homology accounts for about 50%-80% of the node orderings correctly on average.It is clear that you put down inconsistencies to homoplasy and incompleteness - fine. vast ghost ranges ar still a major problem.I can't show you refs showing that it is impossible to generate the immune system step by step. But there is a lack of literature doing this. Behe, a mainstream molecular biologists has a book on this that I'm sure you know about.If you want refs on the origin of protein familes see the other threads here.The stratigraphic data argues either for evolution (possible under the guise of progressive creaiton) or else the flood. They are two different scenarios.I'll answer the rest next time.