Nested Biological Hierarchies

It appears to me that a consistent misapplication or a misunderstanding of macroevolution is ever present amongst some dissenters and iconoclasts. On numerous occasions I have requested information that might serve as some actual evidence for any macroevolutionary process. Typically, what I recieve in return is some asinine example or I get the much coveted '29 evidences for macroevolution', hosted by TalkOrigins, thrown at me.29+ Evidences for Macroevolution: The Scientific Case for Common DescentSo, since this site has served so many pro evolutionists as demonstrable evidence, I thought it was time to interject with a contrasting view.I have decided to accomodate Chiroptera's request to go over his favorite example provided by TalkOrigins first, which is, nested hierarchy of species. From there, perhaps we'll go in sequential order down the line. I presume this thread will deteriorate, but perhaps the Mods wil be able to steer it back on course whenever we start to deviate.Read over the information and present your own opnion. We'l pick it up from there.29+ Evidences for Macroevolution: Part 1 Edited by AdminNosy, : To change Thread title and focus on one line of thought.

This is a good start NJ but I think you should focus even more tightly.Change the title to "Nest Hierarchy of Species" to focus on that (other threads can do the other 28). Then in your own words explain what TO is saying and what you agree and disagree with.Then we'll have a good kick off to a focussed topic.

In this topic, I will be going over the alleged instances of macroevolution. As per request, I have accomodated Chiroptera in starting the "29 evidences for macroevolution" hosted by the popular pro-evolution usernet, TalkOrigins, by beginning with Nested Hierarchies.

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"As seen from the phylogeny in Figure 1, the predicted pattern of organisms at any given point in time can be described as "groups within groups", otherwise known as a nested hierarchy. The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes. "

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-Theobald TheobaldHere, the writer describes that the predictable pattern for any organisms that 'groups within groups' will emerge all on their own. I happen to agree with this as it is perfectly compatible with micro-adaptations and we are able to witness these events quite clearly. He also goes on to say that its the known process within the evolutionary model. I happen to agree because the rest is based on interpretation.

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"Mere similarity between organisms is not enough to support macroevolution; the nested classification pattern produced by a branching evolutionary process, such as common descent, is much more specific than simple similarity. Real world examples that cannot be objectively classified in nested hierarchies..."

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I happen to agree with this as well, but most unfortunately, this is an all to common way for many evolutionists to determine lineage."

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Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between "subjective" and "objective" is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically ”perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc."

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Theobald gives a great example on how interpretation can lead some of us to draw unempiricle conclusions that are based more on our predelictions rather than simply making an objective claim.

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"cladistic analysis of cars will not produce a unique, consistent, well-supported tree that displays nested hierarchies. A cladistic analysis of cars (or, alternatively, a cladistic analysis of imaginary organisms with randomly assigned characters) will of course result in a phylogeny, but there will be a very large number of other phylogenies, many of them with very different topologies, that are as well-supported by the same data. In contrast, a cladistic analysis of organisms or languages will generally result in a well-supported nested hierarchy, without arbitrarily weighting certain characters (Ringe 1999). Cladistic analysis of a true genealogical process produces one or relatively few phylogenetic trees that are much more well-supported by the data than the other possible trees."

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Here, I feel that Theobald is being honest, but I get the feeling that he is beginning to lean toward punctuated equilibrium in that if the phylogenic data represented does not show a clear and concise stepwise trend, instead of question whether or not such a broad evolution took place, they make an appeal that we just might not be able to see it as clearly as one would desire."

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There is one caveat to consider with this prediction: if rates of evolution are fast, then cladistic information can be lost over time since it would be essentially randomized. The faster the rate, the less time needed to obliterate information about the historical branching pattern of evolution. Slowly evolving characters let us see farther back into time; faster evolving characters restrict that view to more recent events. If the rate of evolution for a certain character is extremely slow, a nested hierarchy will be observed for that character only for very distantly related taxa. However, "rate of evolution" vs. "time since divergence" is relative; if common descent is true, then in some time frame we will always be able to observe a nested hierarchy for any given character. Furthermore, we know empirically that different characters evolve at different rates (e.g. some genes have higher background mutation rates than others). Thus, if common descent is true, we should observe nested hierarchies over a broad range of time at various biological levels."

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And here, I feel my suspicions are confirmed. While he does not outright mention PE, his description spells it out quite nicely. In other words, he is giving us abstract reasons for why macroevolution should be actual rather than present some actual evidence.Here, AiG gives us a trait matrix as a mock chart that describes how similarities within any given specie can often share similarities that mean very little as far as it would relate in a biological sense. In this chart, the writer uses a simliar diagram that Theobald uses in his description of cars.Heavy truck---Light truck---Automobile---3-wheel motorcycle--- 2-wheel motorcycle---Bicycle---Unicycle
Horn 1 1 1 1 1 1 0
Manual steering 1 1 1 1 1 1 0
Multiple wheels 1 1 1 1 1 1 0
3 ln number wheels 9 7 4 3 2 2 0
Thick tires 1 1 1 1 1 0 0
Motorization 1 1 1 1 1 0 0
Self stability 1 1 1 1 0 0 0
Backrest seating 1 1 1 1 0 0 0
Ln cargo capacity 5 3 1 0 0 0 0
Enclosed cabin 1 1 1 0 0 0 0
Steering wheel 1 1 1 0 0 0 0
Upward exhaust 1 1 0 0 0 0 0
Double wheels 1 1 0 0 0 0 0
Interior partition 1 1 0 0 0 0 0
Detachable units 1 0 0 0 0 0 0
Table 1. Mock character-trait matrix of wheeled vehicles. Most traits are polarized: 0-Absent and 1-Present. The number of wheels is indicated by three times the natural logarithm of the actual number of wheels, rounded off to the nearest whole number. The cargo space is denoted by the ratios of natural logarithms of the cargo volume relative to that of the automobile, based on a guesstimate. Walking Whales, Nested Hierarchies, and Chimeras: Do They Exist? | Answers in Genesis Back to the issue at hand, Theobald goes on to write:"

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If it were impossible, or very problematic, to place species in an objective nested classification scheme (as it is for the car, chair, book, atomic element, and elementary particle examples mentioned above), macroevolution would be effectively disproven. More precisely, if the phylogenetic tree of all life gave statistically significant low values of phylogenetic signal (hierarchical structure), common descent would be resolutely falsified."

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Since we can break things down to its simplest elements, there is always a level of similarity. For instance, all things material, living and non-living are composed of atoms, but to arrive at the conclusion that since we all share similarities on the atomic level, somehow justifies lineage, is suspect."

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Keep in mind that about 1.5 million species are known currently, and that the majority of these species has been discovered since Darwin first stated his hypothesis of common ancestry. Even so, they all have fit the correct hierarchical pattern within the error of our methods. Furthermore, it is estimated that only 1 to 10% of all living species has even been catalogued, let alone studied in detail. New species discoveries pour in daily, and each one is a test of the theory of common descent."

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29+ Evidences for Macroevolution: Part 1Lastly, Theobald provides no actual evidence for anything, about anything, and simply retreates into the hazy cloud that is ToE with its inability to clearly define the theory or even its subtheories and retreats into the plea that moast organisms have yet to be studied thoroughly. This, of course, should make us wonder why he clings to theory so strongly if its basis is on theoretical biology.All in all, the opening segment of '29 evidences' failed to report even one evidence of a macroevolutionary process. Instead, it simply rehashes on certain microadaptations that we already know about and then gives us some abstract reasons for why it theoretically is possible. Edited by nemesis_juggernaut, : Forgot to add sourcesEdited by nemesis_juggernaut, : Trying to reconfigure a chart.... To no avail. Eh, whatever, you get the idea

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“Always be ready to give a defense to
everyone who asks you a reason for the
hope that is in you.” -1st Peter 3:15

So may I change the title of the thread to "Nested Biological Hierarchies"? Then we can promote it.

Yeah, I guess so. The only reason I didn't want to entitle it as such was because I'd be going over all 29 evidences. Nested Hierarchies was just one piece provided.But if you really want to change the title then I guess it isn't critical.Eh, anyway, you're the Mod. Its your site. Do as you please.

Each of them is going to take a lot of posts. They should be organized into individual threads.Thanks.

Thread moved here from the Proposed New Topics forum.

You're really got to bring something better than this, NJ. Surface criticisms that don't even really address Theobald's points are not sufficient.Your criticism that "Theobald implies Punctuated Equilibrium" is meaningless. I get that you don't like PE but that fact is not a refutation of the Theobald's argument.Your criticism that "similiarities don't prove common lineage" is meaningless, because that's not Theobald's argument.Your criticism that he "doesn't present evidence" is outright false. I get that you don't think evolution is true, and therefore that no evidence for it can exist; but the fact that you believe that doesn't make the ample evidence he refers to - even in the sections you've directly quoted - go away. Anybody can read your post and see that, indeed, Theobald has referred to ample and well-known evidence, which you have simply ignored.I would really have thought that, after over 150 posts here, you would have a sense about how an honest debate works. I see from this inital post. however, that that is not the case. Why don't you give it another shot when you're ready to bring your A game?

Hi, nemesis.I apologize, but I can't really figure out what your point is. If you will allow me, I will present a simplified version of Dr. Theobald's case; if you can find criticisms of this simplified version, we can discuss them, otherwise you can add the complications that you find relevant.(1) If the theory of evolution is an accurate description of the history of life, then we should be able to classify the species in a nested, heirarchical scheme.I'm hoping that there is not much dispute over this, but if this isn't accepted, then I suppose we can discuss this point and talk about why common descent must produce a nested heirarchical pattern in the species.(2) The species can be classified in a nested hierarchical scheme.I will point out that this pattern was discovered prior to Darwin's theories, so is not a result of scientists forcing their data to fit a prior held belief in common descent.Now (1) is a prediction of the theory of evolution, and (2) is the confirmation of the prediction. The reason that this is a confirmation is that there is no a priori reason to suspect that the species should be classifiable in a nested hierarchy. Certainly, creationism does not predict what patterns, if any, we should see, and if the creator wanted, the creator certainly could have confounded the future evolutionists by creating each species with a mix-and-match set of characteristics that would have confounded any attempt at finding an objective nested hierarchical pattern.Without the theory of evolution, there is no reason to suspect that this pattern should exist. With the theory of evolution, this pattern must exist. And, lo and behold, we do see this pattern.What are your thoughts?

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"We must respect the other fellow's religion, but only in the same sense and to the extent that we respect his theory that his wife is beautiful and his children smart."
-- H. L. Mencken (quoted on Panda's Thumb)

Surface criticism for a surface paper. Theobald describes nothing that we don't already know, then he goes on to describe theoretical aspects using mathematical analysis. Nowhere does he provide an iota of evidence for macroevolution, which is consequently, the entire premise of the paper. Did you even read the italicized print I provided? Its clear what he was arriving at. He practically spells it out. As far as me not liking PE, no, I don't like it. For one reason only. Providing reasons why we don't find transitional forms is as baseless as you could get. Isn't that the ultimate argument from incredulity? I commended him on not arriving at that conclusion. I was merely mentioning how some of the people on EvC apparently have an inherent agreement on that point. What example does he give us? He simply gave an abstract outline for why we should believe as he does. No, I believe in an evolution of sorts. What I don't believe is the mainstream ToE. I believe that it arrives to some pretty fanciful conclusions holistically. If evolution simply meant, change, I doubt anyone would have a problem with it. Unfortunately, it doesn't stop at a simple genetic change. Instead, it aspires to ask a much broader question that it isn't ready to give. The whole underlying tone within the prevailing theory is highly suspect. Read it again, because he gave no referrences to any studies or conclusive findings. All he says is what you all say, "There is ample evidence of macroevolution." Sorry, but repeating the thing doesn't make it any better or any more true. tThat doesn't cut it. And if any one of you is interested in pragmatism through scientific truisms, then you should al be questioning it. Afterall, the title was '29 evidences for macroevolution.'One down, 28 to go. Mmm, yes, next time I'll bring my A-game dog.

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“Always be ready to give a defense to
everyone who asks you a reason for the
hope that is in you.” -1st Peter 3:15

You didn't address the paper. You've addressed the introduction.Again, to criticize the introduction of a paper for not being the body is pretty ridiculous. So far you're just not producing anything worth taking seriously. Theobald presumes that his reader has at least a passing familiarity with the field of biology. I get that you don't have that familiarity. But if you don't know where to look up examples of papers that arrive at a hierarcheal classification of some group of organisms, isn't the smarter thing to ask? Not simply assume they don't exist at all?Theobald is referring to a well-known phenomenon in biology - when independant sources develop a hieracheral lineage of the same organisms from different data, they arrive at largely the same hierarchy. If you're not even aware that this is true, you don't have the requisite knowledge to address Theobald's arguments.It's like opening a third-year textbook on computer science and openly declaring it invalid because it doesn't tell you how to use a mouse. Sorry, but if you're still back at that level, you're not ready for this class yet. If you don't know about the universal phenomenon of convergence between different means of developing phylogenies in biology, you aren't ready for Theobald's introduction, yet. And you certainly aren't ready to rebut it. Do you have any idea how ridiculous you look?This is what I mean by "bringing your A game." Theobald is presuming that his reader's head is not so crammed full of creationist nonsense that there's no room for knowledge about biology.

Yes, I would agree with that. What I don't understand is how this is supposed to provide us 'evidence' for a macroevolutionary process? Furthermore, he goes on to describe how arriving at any macroevolutionary process is subjective. So, how is that supposed to prove anything? I don't have a problem with the taxonomy chart as far as relates to which animals have more traits that are similar. I mean, is a Dolphin a mammal or a fish? I'm just using this as a referrence. I don't really care if someone said that its a fish because, it has fins, it lives in the water, it has the anatomics of a fish, and so on. On the other hand, its warm-blooded, it recieves its oxygen through the air rather than H2O, etc. On some level, and apparently Theobald agrees, we have the tendency to look at certain characteristics and by human extrapolation, we get to decide what is what and where it belongs in the chain of life. Do you understand what I'm saying? Its completely subject to interpretation based on whatever humans want to call it. This pattern best describes a microadaptive process which is abundantly evident. What it fails to capture is that all living things are ultimately related. We do see some of these mix-match set of characteristics. One such is homo floresiensis, which aparently has the entire paleontological community in disagreement as to what exactly it is. Discovery had a realy good program on it the other night that allowed me to forgive them for airing the program that preceeded it. Again, that's totally subject to a percieved relationship, which Theobald discusses. If you have a group of 100 people in a room, supose that 50 of them are from the same family, and the other half is of another. Just looking at them, could you make the distinction of which ones are actually related? How many of them that weren't related bear a striking resemblance to another?I'm good friends with two brothers. As kids, people often confused me as being the brother of the youngest because we look alike. In fact, the eldest looks nothing like the youngest, and yet, he is by far more closely related to the youngest than I am. I only mention this because its easy for us to make good observations only to arrive at a bad conclusion.

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“Always be ready to give a defense to
everyone who asks you a reason for the
hope that is in you.” -1st Peter 3:15

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So, how is that supposed to prove anything?

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It is evidence, just like the evidence that confirms any scientific theory. Theory A says that we should see phenomenon B. If B is seen, then that counts as confirmation of A, especially if there was no prior reason for suspecting that B would be seen. If an investigator thinks that Amy killed Bob with the chainsaw, what does she do? She makes a prediction: if Amy killed Bob with the chainsaw, then Amy's fingerprints should be on it. If, indeed, Amy's fingerprints are on the chainsaw, that counts as evidence for the suspicion. It is not proof, but it is evidence that will be presented to the jury. Then the investigator says, "If my suspicions are correct, Bob's blood must have splattered all over Amy's clothes." If a search of Amy's house turns up clothes that have Bob's blood on them, then that, too, counts as evidence. Not proof, but that is for the jury to decide how good the evidence is. If either bloody clothes or Amy's fingerprints are not found, then either a good reason must be preented why they have not been found (she wore gloves and burned the clothes), or the theory must be changed or discarded (Amy hired a hitman, or maybe Carla did it!)In the same way, If evolution is true, we should see a nested heirarchical pattern.We look, and, indeed, we see a nested heirarchical pattern.There is no reason why we should see a nested heirarchical pattern, but we do, and evolution has predicted that we should see it. Proof? On its own, no, but good evidence, evidence that we will present to the jury with all the other evidence.-

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I don't really care if someone said that its a fish because, it has fins, it lives in the water, it has the anatomics of a fish, and so on.

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A dolphin does not have the "anatomics" of a fish - the only anatomic traits it shares with fish are the same traits that it shares with all vertebrates. The only traits it shares with crocodiles are the traits it shares with all tetrapods. It is definitely a mammal -- there is no abiguity in this. It has the anatomy of a mammal. It doesn't even have fins -- it has five-digit paws, except that the flesh seperating the digits didn't disapear during development like it does in all other tetrapods.No matter how you look at the dolphin, it's anatomy clearly places it unambiguously in a definite spot in the hierarchical classification, just as the theory of evolution says it should.Now if the dolphin gave birth and nursed its young like a mammal but had eyes like an insect and jointed legs like a lobster -- that would be difficult to classify!-

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What it fails to capture is that all living things are ultimately related.

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What it implies is that all species that can be placed in the same tree are ultimately related. By the 1960s, all metazoan animals (with the possible exception of sponges) could be placed on one definate tree. So the impliation is that all metazoans are related. Now, with the development of molecular biology, all life can be placed on one or another tree, and so far all tested species can be placed on a single tree indicating that all life (so far) is related.-

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One such is homo floresiensis, which aparently has the entire paleontological community in disagreement as to what exactly it is.

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Actually, what is being argued is whether H. floresiensis microevolved from H. erectus or whether it is H. sapiens with some sort of disease. At any rate, these three species are closely related -- I was thinking of mixing and matching characteristics of distant taxa, like otters with bird wings, or sequoias with mammalian circulatory systems, or some such. At any rate, everyone agrees with H. floresiensis' place on the phyletic tree; they just don't know on which very closely spaced branches it belongs to exactly. Now if H. floresiensis teeth like a velocraptor, a turtle shell, and feet starfish tube feet around its mouth, that would be hard to classify!-

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Just looking at them, could you make the distinction of which ones are actually related? How many of them that weren't related bear a striking resemblance to another?

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By examining their anatomy? No, the morphological characteristics that taxonomists use can distinguish species and their relationships, but not the relationships of individuals within a species. Why do you think this failure is relevant to taxonomic classification? It is like saying you don't believe in the existence of space and volume because you cannot measure the space between my teeth with a yardstick. And remember, we are discussing the relationships of species, not individuals. Species evolve, individuals do not.On the other hand, modern molecular biology and genetics can do a very good job of determining the individual relationships between individuals -- the basis of paternity testing, for example. This is now providing an important tool for determining the relationship between taxa for which morphological techniques failed (like bacteria).-At any rate, the heirarchical classification exists. As far as I know, even the creationists accept it -- you may be the first that I know of that is trying to dispute it. At any rate, let's see whether this has cleared anything up.

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"We must respect the other fellow's religion, but only in the same sense and to the extent that we respect his theory that his wife is beautiful and his children smart."
-- H. L. Mencken (quoted on Panda's Thumb)

Maybe he meant aerodynamics, that is the only thing I can think of that makes any sense at all.TTFN,WK

Hi, Wounded King.I figured that nemesis was speaking of the superficial resemblance of dolphins to fish. My point is that this resemblance is only superficial; any detailed examination of dolphins shows without amibiguity that dolphins are mammals.Of course, we expect things like these superficial differences (between the fish-like dolphin shape and the salamander-like shape most other mammals have). After all, if all species were identical, then there would only be a single species, and the whole discussion would be largely moot. But each species is a species precisely because it has differences from the other species. So each species is going to have characteristics that are different from even the most closely related species -- if it didn't, it wouldn't be a different species.That is why it is important to look at many, many different characteristics to determine where in the classification scheme a given species lies. Overall, the gross anatomy indicates the large, general area in which to place the species (dolphins are indisputably chordates), and a not-much-more detailed examination will narrow down the proper category even more (dolphins are clearly mammals, despite superficial appearances). To narrow down the placement further, we start examining the characteristics that differ from the over all, general body plan and compare them to those of other species that share similar differences from the overall body plan.Of course, this is not necessarily easy (I believe that Linnaeus may have classified whales as fish originally), but, then, most of the accepted scientific discoveries and classifications are the result of years and decades of hard, careful work.The interesting thing is as long as you choose a large enough sample of characteristics, it becomes clear which are part of a general plan that characterizes large taxa, and which are the more specific characteristics that determine its proper smaller taxon within the larger one. As long as people choose a large enough number of characteristics, it doesn't matter which ones they choose -- different investigators will produce the same classification.Of course, there will be minor details in how to place individual branches, but two different placements will be very close. (A and B clearly branched off very close to one another, but did A branch off first, or did B? Did C branch off A near its base, or did it branch of the closely related B branch?) Just because one investigator measured the speed of light to be 299,792,458.2 m/s and another measured 299,792,457.9 m/s does not imply that light does not have a speed.(P.S. I am not a taxonomist -- as always, I welcome any corrections from the actual experts.)

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"We must respect the other fellow's religion, but only in the same sense and to the extent that we respect his theory that his wife is beautiful and his children smart."
-- H. L. Mencken (quoted on Panda's Thumb)