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ORIGINAL: Jhud

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maybe you need to define "novel". Otherwise I am having difficulty seeing how this is an evolutionary relevant difference.

Well, a skeletal system is novel with respect to an organism without one.

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Actually, you have inadvertently stumbled across one of the differences between many regulatory process and what evolutionists ordinarily mean when they talk about mutations; many regulatory processes are responding to specific needs, and do so repeatedly.

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Well, yes again you are starting to answer your own questions. Is one assumes a wing is indeed a “modification of a tetrapod forelimb”, what would a skeletal system be with respect to organisms that have none? What would bilateralism with respect to animals that aren’t bilaterial? What would a nervous system be with respect to an organism that had none?

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But they didn’t ‘speciate’ they simply displayed variations on a common capability.

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Do you think the original organism has the genetic capability to produce every extant structure and system that exists in modern organisms?

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Really? So your argument would be that a skeleton, rather than a specifically engineered structure that support system which allows for the attachment of muscles, the protection of vital nervous tissue, and the production of red blood cells, is simply a a glorified excretion of calcium?

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Okay, so now we are getting somewhere; what evidence is there genetically that small, sequential, incidental changes occurred to allow for the development of a skeleton from a calcium secreting cell; and would changes to this cell alone be sufficient, or would other changes have to occur in the organism to utilize a skeleton?

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I mean "novel" in terms of genetic information.

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I am not sure about this. For example you referred to the development of resistance in a case where stronger resistance was created by increasing the number of pumps that expel toxins from the cell.

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One does not need to assume that a wing is a modification of a tetrapod forelimb. It is a tetrapod forelimb. Whether the forelimb in question is a bird's wing, a dolphin's fin, a horse's foreleg or a baboon's arm, the bones are the same, the bone, blood, muscle and nerve arrangements are basically the same. The source of the tissue comes from the same embryonic cells and the same genes regulate their formation through the same signalling pathways.

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On the others, you are simply moving to items for which we do not have as much information yet. I hope someone is researching it. Obviously for a complete system you have to look at multiple factors. But you don't begin with a complete system. A skeleton is a support system. It may be internal or external as in arthropods. It may also be protective. But even unicellular organisms often produce exquisite "skeletons" like those of diatoms. So even at this level--whether for protection or support or just to get rid of excess calcium or some other mineral--there is a basic capacity to produce what would be needed to build a bony matrix. So we can begin there.

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Are you redefining the term "species"?

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Which original organism?

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You playing with me? Don't be silly. Some cells in bones produce blood cells, for example. But you would hardly have bone without cells which produce a calcium matrix would you? To get to the full system, you would have to look at every type of cell involved. So perhaps what you are really getting to is how multicellular species began to differentiate tissues so that some did one thing and some another. That is something the embryologists are studying too. How do the original stem cells know what sort of cell to become? The answers they come up with may also help us understand better how differentiated tissue developed in the first place.

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Oh, any system is necessarily a matter of various things evolving together. You can't lengthen a bone without also changing nerve pathways and muscle placements for example. I am not sure why you are speaking of changes to a cell. What you need are genetic changes which are carried by the zygote and they will probably be changes that affect embryonic development in one way or another. So in reference to the skeleton itself, you would probably get groups of cells involved from the first. The only single cell involved would be the originating zygote.

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As for evidence, I think you are going to have to go back to the microbiologists who are working on identifying which genes control the development of tissues and organs, and how they work. We have known for a century now that genetic material produces phenotypic effects. But the whole question of which genes on which chromosomes contribute to which phenotypic effects, in what proportion, according to what timetable, under what regulatory conditions, etc. etc is still largely a huge black box.

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One does not need to assume that a wing is a modification of a tetrapod forelimb. It is a tetrapod forelimb. Whether the forelimb in question is a bird's wing, a dolphin's fin, a horse's foreleg or a baboon's arm, the bones are the same, the bone, blood, muscle and nerve arrangements are basically the same. The source of the tissue comes from the same embryonic cells and the same genes regulate their formation through the same signalling pathways.

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ORIGINAL: unclemonkey
Are you saying that because frogs and humans both have five digits on their hands/feet it is evidence of a common ancestor?

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ORIGINAL: Jhud

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I mean "novel" in terms of genetic information.

Well then, the genetic basis for a skeletal system with respect to an organism that doesn’t have one.

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Briefly, prolonged exposure to increasing concentrations of tetracycline cause increased sequential activity of regulatory genes which promote over-expression of genes that code for as many as 9 transporter proteins of distinct efflux pumps which extrude unrelated antibiotics prior to their reaching their intended targets.

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Living organisms have the capacity to adapt to changing environments without the need to rely on mutations, which are infrequent and thereby slow, to be incorporated into a population in a given environment. In the case of the efflux of toxic compounds, physiological adaptation of a cell to a given substance in a given environment begins with an event that takes place at or within the cell envelope and results in a sensor type of stress response. This eventually results in genetic activity that encodes for additional units of that same efflux pump that extrude a broad range of substrates. The addition of more efflux pumps into the cell envelope increases the survival of the organism.

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Actually, whether it is a ‘tetrapod forelimb’ is somewhat irrelevant; the reality is numerous other inherently interrelated and interdependent modifications must occur throughout the genome before a ‘terapod forelimb’ can be any of those other things.

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The ‘skeleton’ of a diatom is vastly different from that of a vertebrate

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Are you redefining the term "species"?

I don’t have to; it has no definitive meaning.

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And more particularly, how does the genetic regulatory networks work together in a system of combinatorial interdependencies if it is as you suggest merely the product of the accumulation of incidental modification?

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You speak of ‘genetic changes’ as if the processes of embryo development and genetic mutation were one and the same.

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The fact that the genome does act systemically, that is that those genes controlling the structure of the skeleton, and the growth of nervous tissue and musculature, are all part of a system of genes. This speaks to the fact that such a system would resist incidental change, as such a change would disrupt entire systems.

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This is perhaps why the genome is designed with self-repair mechanisms that resist incidental modification.

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Yes, and I think increasingly the trend will continue that demonstrates that such complexities are quite ancient, unselected, and highly interdependent, rather than the product of incidental derivation over time.

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ORIGINAL: gluadys

Are you redefining the term "species"?

ORIGINAL: Jhud

I don’t have to; it has no definitive meaning.

For the purposes of clear communication, it would be appropriate to adopt a working definition. I know it is not perfect, but I generally go with the Biological Species Definition, which defines a species as an interbreeding population that does not breed with other populations under natural conditions.

If you wish to use another working definition, please propose it. After all, you cannot argue that they did not speciate without proposing what a species is and showing that none of the finch populations is of a different species than the others in spite of the fact that most of them do not interbreed.

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Do you have a response to this, Jhud?

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ORIGINAL: Jhud

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Do you have a response to this, Jhud?

Well, yes, as I have often responded before I think the term ‘species’ is fairly useless in terms of these broad discussions.

No one definition fits the many cases considered when discussing the mechanisms of evolution, and considering that your proposed definition, an “interbreeding population that does not breed with other populations under natural conditions.” Cannot be applied to any organisms that no longer exists, it really doesn’t help us here. I just don’t speak in terms of it because it isn’t useful except for specific well documented cases.

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But the Galapagos finches do exist. So this is a specific well-documented case.

Are you suggesting that all the biosphere is one species?

Are you suggesting that it is likely that dinosaurs mated with mosasaurs?

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ORIGINAL: Jhud

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But the Galapagos finches do exist. So this is a specific well-documented case.

Are you suggesting that all the biosphere is one species?

Are you suggesting that it is likely that dinosaurs mated with mosasaurs?

What an odd confluence of questions and statements.

I don’t doubt something like a species exists, I simply don’t find it to be a robust demarcation by which one can judge the maxima and minima of biological change.

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In that case you have no basis for the assertion that the finches have not speciated.

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You are simply saying that you cannot or will not define what a species is, therefore you cannot tell whether they have speciated or not.

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I am not sure what you mean by "maxima and minima" of biological change. Do you mean the maximum and minimum in terms of population size and range, in terms of existing and potential variability, or something else?

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Do the cactus finches mate with the ground finches? Do the large ground finches mate with the small ground finches? Do the finches of one island mate with those of another island?

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Does each interbreeding population have distinct morphological characteristics? Does it have correspondingly distinctive genetic characteristics?

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Do the differences each population displays enable it to avoid excessive competition with finches of other populations in terms of food and mate choice?

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ORIGINAL: Jhud

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In that case you have no basis for the assertion that the finches have not speciated.

When did I make that assertion?

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You are simply saying that you cannot or will not define what a species is, therefore you cannot tell whether they have speciated or not.

No, I am saying it's not particularly useful terminology.

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I mean in terms of substantive change in terms of gross morphology, body plans, organs, structures, and systems.

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Do the cactus finches mate with the ground finches? Do the large ground finches mate with the small ground finches? Do the finches of one island mate with those of another island?

What possible difference does it make whether they do?

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Does each interbreeding population have distinct morphological characteristics? Does it have correspondingly distinctive genetic characteristics?

Each individual has distinct physical characteristics, and every population has a range of characterisitics, and occasionally those populations overlap and interbreed; it depends on what year you are looking at them and what the environment happens to be throwing at them that year.

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What doesn't change is the gross morphology, body plans, organ structure, and systems. In terms of genetics, there is very little difference.

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Do the differences each population displays enable it to avoid excessive competition with finches of other populations in terms of food and mate choice?

Again, irrelevant to the larger questions.

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Post 299

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It is not particularly useful to you. But it still speaks of a real natural phenomenon. Mating is not random among individuals. In some cases mating is not possible. Reproductive barriers are real. "Species" is the term used to identify populations separated by reproductive barriers. Since evolution in animals is closely connected to the establishment of reproductive barriers within a framework of common ancestry, it is a very useful terminology for the study of evolution.

I grant that it is by no means perfect. It is useless as a way to verify speciation in a framework of asexual reproduction or in cases (as with fossils) where it cannot be tested. Nevertheless, some analogies can be made because we can see how the distribution of characteristics is connected to the existence of reproductive barriers and we can find analogous distribution patterns in fossil lineages.

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Of course, one has to qualify what is meant by "substantive". What would be a minimum of "substantive change"? One could make a case that the remoulding of a weight-bearing limb to a wing is not a "substantive change" because of the retention of the homologous structure of the appendage. At the other extreme, one could also make the case that the remoulding of the digestive processes of a fruit fly to exclusive nourishment from meat is a substantive change, although "it is still a fruit fly".

One could also make the case that the items in your list never undergo "substantive" change and all one can look for is the initial establishment of the morphology, body plan, organ, structure or system. Historical constraint only allows for subsequent modification, not substantive change to such elements. Note in this respect especially the conservatism of body plans. It would appear that there was a limited historical window in which fundamental body plans could be established and after which , although modified, they have not substantially changed.

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See above. It goes to the framework in which change occurs, and the historical development of evolutionary pathways.

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It also depends on which particular pair of populations you are looking at. That is why I specified cactus finch and ground finch above. The occasional overlap and interbreeding documented by the Grants was among different populations of ground finches. None was observed between ground finches and cactus finches in any year. From an evolutionary viewpoint this is significant.

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Little difference, but still difference. Again, one has to set the parameters of "gross morphology". Are we talking about the gross morphology of finches, the gross morphology of modern birds, the gross morphology of therapod dinosaurs? Some organs and organ systems found in Galapagos finches have been relatively stable since the first appearance of vertebrates. Some since the first appearance of birds (e.g. flow-through lung system), some only since the appearance of modern birds (e.g. lack of teeth, tail). It is easy to discount any intraspecies or intragenus change as not affecting these characteristics, but in fact, we would not really know what present day changes are significant until well into the future. As for features already established, we need to get specific, as different ones go back to different specific changes in the past. What do you consider the past relevant changes in the gross morphology of a finch heart, for example?

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Depends on what you think the larger questions are. This question goes to the heart of why populations diversify in the first place.

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ORIGINAL: Jhud
Well, as I pointed out above, even a ‘model’ case like Darwin’s finches don’t follow the rules very well. So I think it’s unhelpful in a broader context.

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Well, this is where I find that ID definitions are helpful. For a substantive morphological change I like Dembski’s definition of IR:

A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system.

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I think in this respect the bat of a wing differs considerable from the forelimb of a mouse. I suppose the difference really has to do with function;

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what is the function of the structure in question, and how are the changes in the genome related to the required changes in the function of the structure – the degree to which that function depends on multiple specific interdependent changes, the less likely it is that they could be the product of incidental modification.

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Well we know the pathways that led to the differences in Darwin’s finches; they aren’t particularly evolutionary.

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Ground finches and cactus finches have interbred.

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Well, again, it comes done to function; we can define function; so the question becomes, is it a complex and interdependent change that allows for a novel function? Or is it a simple change that enhances a extant function? I would say evolution is great at the latter, but is limited in regards to the former.

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Again, populations can diversify as much as their genetics allow; there seem to be definitive limits to how much they can change, and Darwin’s finches don’t exceed those limits.

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Actually, they do. They are a model of populations that either recently speciated or are on the verge of completing a speciation process. Or, perhaps at the point of reversing a speciation process. Of course, one has to examine the populations by pairs to see what is happening on a case by case basis, as the trend will be different in different cases.

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The function is certainly different. Yet the structure is homologous. Perhaps function follows form instead of being the goal of changes in form.

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Since you are reading Sean Carroll's book, you will be learning about the genetic basis of embryological development. It bears out a speculation I first read in one of Stephen Gould's essays. Given the way embryonic development is regulated in large part by signals which determine when, where and for how long a gene is expressed, a single change, even a fairly minor change in the pattern of development can lead through a cascade of subsequent cueing signals to a significant phenotypic change. This is especially so if the mutation affects development in the crucial early stages. Gould's thesis is that some significant steps in phylogenetic history could be accounted for by such changes affecting embryonic development with subsequent fine tuning taken care of by incidental modification along classic neo-Darwinian lines.

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OK. Either I missed that information or it is a more recent observation. Doesn't change an awful lot though. For the key question is the degree to which the mating is assortative. If the mating is not assortative at all, one definitely has a single species. If it is totally assortative (no mating between groups even when the physical opportunity is available) one definitely has two species. In between these extremes one is somewhere between a single population and a population divided by reproductive barriers. This in-between stage can endure over many generations and even oscillate between a trend toward a permanent establishment of reproductive barriers or the taking down of such partial barriers that have been established.

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So how would you see the change from a three-chamber to a four-chamber heart? Is this novel or merely an enhancement of an extant function?

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ORIGINAL: Jhud
Any hard fast numbers on when they are doing one or the other?

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Well a wheel is homologous to a gear; but the means little interms of their disparate functions.

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Sure; except you still need a specificity that requires the modification of several different aspects of development to work in conjunction. In fact, the specificity is even more critical here because even the smallest changes can have systematic effects.

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This simply confirms to me my suspicion that your opinion on the matter isn’t particularly amenable to the facts, and that my point that a ‘species’ isn’t a particularly robust or clear designation.

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Well, it depends; does the four chamber heart allow the organism to function in a way it couldn’t without it?

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I think the best numbers we have are those of Peter and Rosemary Grant (The Beak of the Finch is a popular summary of their work.) And as far as I know, their numbers were inconclusive. Also they focused on only one island and primarily on the ground finches, so numbers for other islands and other species are spottier.

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Isn't that pretty much what I said? You can get quite different functions from basically similar forms. What is it we are tracing in evolution if not the inheritance of changing forms?

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If the effects are systemic, doesn't that automatically modify several different aspects of development?

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Because of the lack of clarity within the process of speciation? Or are there additional factors involved in your judgment here? I would re-iterate that in most cases the diversification of a single species into two or more species is expected to include a period in which it is difficult to ascertain the precise relationship of the emerging species. So if this is your only reason to consider the 'species' designation unclear, it simply doesn't wash as an objection to evolution, because this is what is expected from a process of speciation.

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In a species which has a history of a four-chambered heart, a three-chambered heart would be problematical. We see a near equivalent in "blue baby syndrome" where the window between the ventricles that exists in the embryo does not fully close at birth. The condition is not necessarily fatal but would certainly be selected against.

But at the time of transition, even partially divided ventricles would likely be advantageous in comparison to a non-divided ventricle. Yet species which have always had three-chambered hearts still thrive.

In all cases the primary function of the heart (to re-oxygenate and circulate the blood) is the same, but that doesn't mean those who have inherited a four-chambered heart could function well, if at all, with a three-chambered heart.

I will leave you to draw the conclusion.

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ORIGINAL: Jhud

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If the effects are systemic, doesn't that automatically modify several different aspects of development?

Sure it changes already extant structures, either through amplification or inhibition; it doesn’t create new structures or functions.

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I am simply pointing out that you threw out your best case and it failed on a number of levels;