Uncommon Descent Serving The Intelligent Design Community

DLL Hell, Software Interdependencies, and Darwinian Evolution

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In our home we have six computers (distributed among me, my wife, and two daughters): two Macs, two Windows machines, and two Linux (Unix) machines. I’m the IT (Information Technology) or IS (Information Systems) guy in the household — whatever is is.

A chronic problem rears its ugly head on a regular basis when I attempt to update any of our computer systems: Software programs are often interdependent. DLLs are dynamic link libraries of executable code which are accessed by multiple programs, in order to save memory and disk space. But this interdependence can cause big problems. If the DLL is updated but the accessing program is not, all hell will break loose and the program will either severely malfunction or suffer an ignominious, catastrophic, instantaneous death. On the other hand, if the program is updated and the DLL is not, the same thing can happen.

I’m still trying to figure out how the circulatory avian lung evolved in a step-by-tiny-step fashion from the reptilian bellows lung, without encountering DLL hell, and how the hypothesized intermediates did not die of asphyxia at the moment of birth (or hatching), without the chance to reproduce.

Of course, we all know that this kind of challenge — no matter how obvious or compelling — presents no problem for the D-Fundies (Darwinian Fundamentalists), who are true believers in the clearly impossible, based on materialistic assumptions in which design could not possibly have played a role.

Comments
Hi Scott, I don't mean to just jump in here, but I'd like to offer some ideas for consideration. First of all, when we look at extant species, there is an interesting pattern: older lineages tend to have less species diversity than younger, more recent lineages. This is primarily due to extinction-- the older lineages have had more time for competition and natural selection to take their toll. Secondly, consideration must be given to the number of marine niches available. That is because, as a general rule, a niche is occupied by only one species. Two species can do so usually only for a limited time before one either moves away or becomes extinct, or both species 'partition' the niche in some way to avoid directly competing (both species may specialize in non-ovelapping diets, for example). What this means is, without ecological opportunity (i.e, available niches), speciation will not usually occur. So one has to figure out how many actual available niches there are (or were) before expecting how many species of a particular type of organism should have existed. Finally, looking at the fossil record and the conditions required for fossilization, it must always be kept in mind just how few organisms ever get fossilized at all. If we find large numbers of a particular species, that is probably a good indication of just how successful that species was. Less succcessful species (in terms of numbers) may never have been fossilized at all, or are buried in rocks we haven't seen or to which we have no access. to.Dave Wisker
June 20, 2009
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Nakashima @239: Without going into too much about whales, they all have blowholes and blubber. Somewhere a long the way were creatures with no blowholes and no blubber (and perhaps other features common to all whales.) They wouldn't be considered whales. They must have existed for some time. And yet the only descendants appeared to be whales. If dozens of whale species branched off after that point, why are there no living descendants from anything further back in the transition? And why does that pattern seem to appear in so many life forms? Even between amphibians, reptiles, and mammals? I'm not claiming some great knowledge of taxonomy - I might be wrong on every detail. But widespread variations on a relatively smaller number of classifications strikes me as inconsistent with speciation from a number of gradual transitions.ScottAndrews
June 20, 2009
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Mr ScottAndrews, But doesn’t it seem unusual that these ecological niches could be so discriminating that they permit whales but not the descendants of nearby branches, and yet permit so many varieties of whales? I don't understand the distiction you are making between "varieties of whales" and "descendants of nearby branches". All the varieties of whales _are_ the descendants of nearby branches.Nakashima
June 20, 2009
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Hi Paul,
Your translation into flowery evolutionary language is interesting. How many neutral steps and/or how many temporarily deleterious steps can one reasonably allow before a postulated evolutionary pathway becomes unfeasible? In other words, where is the edge of evolution in terms of neutral or deleterious mutations?
The answer to that depends entirely on the genetic and ecological context of the situation. For example, how stable is the environment? If it is changing relatively quickly, then the adaptive problem (which defines the "end' of the sequence of steps) may require more steps to achieve, may render the achievement impossible, or may eliminate the original adaptive problem altogether. So I think the idea of establishing some limit is, in the end, a pointless arbitrary exercise.Dave Wisker
June 20, 2009
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Hi Paul, Actually, when I said 'beginning', I was referring to the beginning of the development of complex order.Dave Wisker
June 20, 2009
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Hi Dave (#229),
I would argue that the beginning of this is the containment of a semi-permeable membrane– a way of creating a more limited internal environment as opposed to be subjected completely to the vagaries of the environment as a whole.
I would almost agree with you. A semi-permeable membrane is a requirement for all known life, for the reason you stated. Whether it is the "beginning" depends on how literally we interpret beginning, and whether life in fact evolved with the first step being a semi-permeable membrane. If you substitute "a presently foundational requirement" for "the beginning of this", I would agree with you.Paul Giem
June 20, 2009
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Nakashima:
They no longer fit the ecological niches that exist today as well as their descendant species.
I considered that. But doesn't it seem unusual that these ecological niches could be so discriminating that they permit whales but not the descendants of nearby branches, and yet permit so many varieties of whales? And the pattern appears to repeat within so many other types of creatures? I don't know that the observation itself means anything, but it seems that speciation should branch at occasional intervals, not just radiate from single points.ScottAndrews
June 20, 2009
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Mr Hunt: Just a reminder: 1] Prigogine et al, 1972:
The point is that in a non-isolated system there exists a possibility for formation of ordered, low-entropy structures at sufficiently low temperatures. This ordering principle is responsible for the appearance of ordered structures such as crystals as well as for the phenomena of phase transitions. Unfortunately this principle cannot explain the formation of biological structures. The probability that at ordinary temperatures a macroscopic number of molecules is assembled to give rise to the highly-ordered structures and to the coordinated functions characterizing living organisms is vanishingly small. The idea of spontaneous genesis of life in its present form is therefore highly improbable, even on the scale of the billions of years during which prebiotic evolution occurred. [Ilya Prigogine, Gregoire Nicolis & Agnes Babloyants, "Thermodynamics of Evolution," Physics Today, (Vol. 25, November 1972) p. 23. (Emphasis added.)]
2] Orgel, 1973:
"[L]iving organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple, well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures which are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity." [[Leslie E. Orgel, The Origins of Life: Molecules and Natural Selection, pg. 189 (Chapman & Hall, 1973). (Emphases added.)]
Onlookers, the above exchange with P Giem simply underscores to me how desperately modern biology needs to listen tot he point being made by design thinkers. GEM of TKIkairosfocus
June 20, 2009
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About my essays:
I looked at his essays. They seem a little short on documented detail.
I'm sorry. This unsupported assertion is just not true. My essays focus on a few interesting aspects of life, and my claims and conclusions are supported by reference to actual experimentation. (I'll admit that one may have to follow a trail through several essays. But laziness is no reason to misrepresent things so.)Arthur Hunt
June 19, 2009
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Art states,
Ask a high school bio student (e.g., perform a sort of “toddler test”) if these characteristics would qualify something as being alive, and the answer very likely would be yes.
But this, rather than supporting his thesis, illustrates the poor quality of biological teaching in the US.
Um, the "toddler test" was something that Mike Gene introduced me to. If you don't like it that this ID tool actually takes one places where one is predetermined never to tread, blame him. Not me, nor our schools.Arthur Hunt
June 19, 2009
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"If computers ever do deserve the epithet “living”, it will be because they have mastered the science of organizing their environment to serve their purposes, including their own preservation, and are able to impose their particular brand of complexity on the relatively simple raw materials they intake, rather than because they can evolve, or fission, or aggregate, or any or all of the other properties Art and you have listed."
Fox's protocells "are able to impose their particular brand of complexity on the relatively simple raw materials they intake". Not that the debate about what is really living is all of what my argument is about. There seems to be a tenuous agreement that the properties I list, that protocells are observed to possess, are also characteristics seen in living cells. What this means is that a DNA code (or whatever "information" the ID proponent wishes to invoke) is quite unnecessary when it comes to the origination and maintenance of these characteristics.
"It is interesting to note that the hypothesis of Yaris et al. required that “highly evolved anabolic pathways” somehow arose without DNA control. It would be reasonable to propose RNA control for these pathways. But it is totally unreasonable to propose that they arose without any control whatsoever. The point is that life requires control. That’s what the membrane is about—control.
Control is an inherent property of chemistry. For example (one quite apart from all that has been discussed in this thread - it's just a simple illustration), consider a 4-step series of irreversible first order chemical reactions that leads from A to B to C to D to E. It turns out that, no matter how you change the rate constants of the second and third reactions, you don't change the overall flux thru the pathway at the steady state. That's quite exquisite control, a simple and strong robustness that we don't see in engineered systems. There's no reason to claim that prebiotic chemistry was without control. We're talking chemistry, not primitive engineering.
And that is why it is difficult, and may be impossible, for RNA to be the control molecule. One needs a way of clearly differentiating the backup from the working copy.
Why? RNA viruses do this just fine. (Remember this conversation next time you come down with a cold.)
If RNA is serving both purposes, it is hard for the cells degradative enzymes to figure out which is which and destroy the working copies when they are no longer needed without destroying the backup copy.
As long as one copy survives, life goes on. Life is about RNA, ribosomal RNA to be specific. This is the central player in the cell - the bulk of the RNA is rRNA, most of the rest "services" rRNA, and the majority of cellular metabolism is geared towards rRNA function. DNA is little more than "the back-up copy" of the rRNA. Any code, control, or other aspect informational aspect that one might see in DNA is actually a reflection of the functioning of rRNA.
DNA solves that problem. I’m still waiting to see evidence that RNA actually does the job in specified circumstances rather than theoretical partial justifications of how it might have happened."
I think I told Paul Nelson this fictional anecdote - if a very advanced alien species did a quick fly-by analysis of life on Earth, their conclusion would run along the lines of "well, rRNA sure has found a lot of interesting ways to propagate itself on this planet". Life is, at its core, all about RNA. Ribosomal RNA. Understand its origins and one understands the OOL. (Heck, if ID proponents weren't so religiously stubborn in their opposition to any and all suggestion that the OOL can actually be studied and understood, I believe they might seize on and study this OBVIOUS candidate for this possible designoid that lies at the core of life as we know it. But that ain't gonna happen. For obvious reasons.)Arthur Hunt
June 19, 2009
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Hi Dave, My original comment and your answer were,
Is it not reasonable to make a fallible tentative conclusion that when the dust is settled, such “highly evolved anabolic pathways” without DNA control will turn out to be not realistically feasible?
I don’t think so, given the state of the research now being done. We haven’t really explored that yet– there is another interesting review by Yarus discussing what he suggests are the precursors to organisms using the genetic code. I was hoping to discuss that in a later comment.
My next comment was,
Whoa. I’ll wait for the discussion. But in the meantime, are you saying that if someone comes up to me and asks whether life arose spontaneously, I am supposed to say, “I have no idea”? I can’t say, “I don’t know for sure, but at present it looks to me like it didn’t”? No conclusions, however tentative and open to revision, are allowed? Does that also apply to the Privileged Planet hypothesis also? If so, have you written to the Iowa State faculty about the gross injustice of closing down the debate prematurely? Or is it only ID adherents who are not allowed to draw any conclusions?
The first part of your reply was,
Of course not. Where did you get the idea I think that? If that is the impression my posts are giving, then maybe I need to polish my communication skills.
That being the case, the questions I asked about the Privileged Planet hypothesis are mostly irrelevant. If tentative conclusions can be drawn, then the faculty at ISU were within their rights to conclude that Gonzalez was wrong on this issue (whether they were correct in fact, or whether their actions were justified if he were wrong, are separate issues). BTW, Gonzalez made one advance from the typical anthropic principles arguments. He introduced the concept that the earth was designed not only for the existence of life but for scientific discovery, which of course has no survival value. This feature, if truly present, is difficult to account for on the basis of either natural selection or an atheistic view of the anthropic principles. It also is positive evidence. Finally, it implies a designer of a particular type; one who is powerful enough and intelligent enough to create a world where scientific discovery is easier than what one would expect from chance, and one who apparently wishes us to engage in scientific discovery. That is, minimalist ID is superseded here. Your translation into flowery evolutionary language is interesting. How many neutral steps and/or how many temporarily deleterious steps can one reasonably allow before a postulated evolutionary pathway becomes unfeasible? In other words, where is the edge of evolution in terms of neutral or deleterious mutations? Are there either calculations or experimental evidence that can help us here? I gather you are not too happy with Behe's answer. Do you have your own, and why?Paul Giem
June 19, 2009
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Hi Paul. However, there is one property that clearly differentiates between life and non-life, and it does not appear in this list. It is organization with the result that the organism imposes a complex order on what it receives from the environment, so that the environment serves the organism rather than vice versa. I would argue that the beginning of this is the containment of a semi-permeable membrane-- a way of creating a more limited internal environment as opposed to be subjected completely to the vagaries of the environment as a whole.Dave Wisker
June 19, 2009
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Hi Dave, Thanks for your note (#184). And thanks for the compliment. On life without DNA, if we are to use Art Hunt's "protocells" we need to define life. I'll discuss that below. On Yarus, I will have to read the entire article before commenting, and do not have immediate access to it. However, in the next few days I should be able to do so, probably Tuesday or Wednesday. Hopefully we can have a good discussion then. In the meantime, if Art Hunt is correct in his claim, protocells are life without DNA. So how does he define life? In #157 he links to an essay of his with very little description. The essay is apparently on 2 mutations changing a plant from a herbaceous annual to a woody perennial. In #160 he links to another essay apparently attempting to refute Behe's The Edge of Evolution. In 162, he links to another essay, and this time lists several properties that it looks like he is suggesting is life (or perhaps protolife): Growth Division Evolution Response to external stimuli Possession of rudimentary metabolism. In #166 he pointed back to his previous post, presumably #160. In #170 he again refers to "my essay" (the one linked in #160, linked 3 times) and to "Fox's critters". I looked at his essays. They seem a little short on documented detail. They are probably reassuring to one who starts out agreeing with him but wavering. But they are less helpful to someone who starts out skeptical and wants evidence rather than assertions. In particular, the claim is made that "the information content of proteins is inherently low." I would appreciate evidence and citations, rather than this assertion that is found halfway through his article. He also posits the frequency of simple nucleotidyltransferases at 10^-14, again without explaining where that figure came from. Hopefully, he has some rationale behind these statements. In the paper he lists several properties of protocells (see #178 for the exact quotes): The ability to sense an electrical field Aggregation Mobility Osmosis The ability to selectively pass materials across a semi-permeable membrane Fission Reproduction Conjugation Communication Excitability This list contains some redundancies. It seems to me that if protocells undergo fission, they have to undergo reproduction. Osmosis is one specific example of the ability to selectively pass materials across a semi-permeable membrane. The list also contains some properties that are not well-defined. It is not clear how we know that the protocells have the ability to sense an electrical field. Does that simply mean that they can be demonstrated to react to an electrical field? I shall assume that this is what he really means, and he can correct me if I am wrong. The same is true for communication, which is defined as the ability to pass information directly to another. Presumably this means another protocell. It is not clear what kind of information is being passed. It seems to be something vague, like passing a molecule with a particular enzymatic activity to another protocell. I am not sure why this would not be considered as an enzyme moving from one protocell to another, rather than a protocell communicating with another. For now, until this property is better explained, I shall ignore it. Finally, excitability is not a clear-cut concept. Capacitors can store and discharge energy. An example of how protocells generate electrical fields is not given, or what form of energy is converted into electrical fields, or for what purpose protocells "utilize" (a word that means put to use and implies purpose) elecrical fields. Again, in the absence of further information, I will consider this to mean that protocells can convert other forms of energy to electrical energy, and then convert electrical energy into other forms of energy. Again, Art can correct me if I misunderstood. Thus our new modified list looks like this: Protocells can react to an electrical field, and transform other forms of energy into electrical energy and electrical energy into other forms of energy, aggregate, move, pass materials across a semi-permeable membrane, split apart, and fuse. Compare this with your list, and we should add grow evolve (change?) Response to external stimuli, and possess a rudimentary metabolism. Art states,
Ask a high school bio student (e.g., perform a sort of “toddler test”) if these characteristics would qualify something as being alive, and the answer very likely would be yes.
But this, rather than supporting his thesis, illustrates the poor quality of biological teaching in the US. Let me explain. The above are properties of most life. But they do not come close to adequately defining life, or getting close to its essence. And they are philosophically unsatisfying. A good definition uses crucial properties, and as few as possible to differentiate the objects included by the definition from those excluded by the definition. Thus the ability to pass materials across a semipermeable membrane is a poor criterion, because non-living membranes have this property, and because although all living things have this property, it does not reach to the core of life. If computers ever become sophisticated enough to be considered alive, they will not have this property, so it is conceivable that life would not have this property. The same goes for fusing. Many living things do not fuse, Soap bubbles fuse. Fusion is not near the core of life. Responding to external stimuli is a poor differentiator, as is movement, aggregation, responding to electrical energy, transforming electrical energy into other forms, and creating electrical energy (thunderstorms, anyone?). Growth is not a criterion, or every adult mammal would be considered dead. Growth is indeed a property of life as we know it, but if we found a living organism that never grew, we could not thereby assert that it was not alive. The same is true for reproduction. Several close relatives of mine can no longer reproduce, and one of them has never reproduced. I would hesitate to call them not alive. Although reproduction is a requirement for living things to continue to exist where death is a reality, philosophically the requirement that the essence of life is reproduction seems misguided. And soap bubbles can fission with the right wind currents; I've seen it happen. Perhaps the most misguided criterion is that life evolves. Change happens to non-living things. The morphology of algae has apparently not changed significantly in 3+ billion years according to standard interpretations. If the genome has also not changed, algae would still be alive. Stasis in the fossil record is not evidence that the organisms are dead. If we somehow developed an organism that had perfect genetic repair, the organism would still be alive. Frankly, I suspect the last one is an attempt to define evolution into life. Perhaps someone was so thrilled with Dobzhansky's statement that he/she tried to define life sot that it would make sense in the light of evolution. Or perhaps someone wanted a definition to knock down those pesky intelligent design creationists. Whatever the reason, it was a lousy definition. It is instructive to note that, other than the membrane properties, none of the above criteria are capable of differentiating life from fire. Fire can react to an electrical field, create and transform electrical energy, aggregate, move, split apart, fuse, grow, evolve, and respond to external stimuli. Fire even possesses a rudimentary metabolism. Chemists familiar with Bunsen burners know that part of the flame is typically oxidizing, and part is typically reducing. There are distinct "metabolic zones." Any definition of life that does not differentiate between fire and life is a failure. However, there is one property that clearly differentiates between life and non-life, and it does not appear in this list. It is organization with the result that the organism imposes a complex order on what it receives from the environment, so that the environment serves the organism rather than vice versa. Food is organized into humans, or pine trees, or bacteria, rather than vice versa That's why we call them organisms. They are organized, and they organize. As kairosfocus (#185) quotes Orgel as saying, "living organisms are distinguished by their specified complexity." He goes on to say,
Crystals are usually taken as the prototypes of simple, well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures which are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity.”
If computers ever do deserve the epithet "living", it will be because they have mastered the science of organizing their environment to serve their purposes, including their own preservation, and are able to impose their particular brand of complexity on the relatively simple raw materials they intake, rather than because they can evolve, or fission, or aggregate, or any or all of the other properties Art and you have listed. It is fascinating to note that neither your list nor that of Art recognizes this aspect of life. Don't feel too bad; the biology textbooks I have read don't either. You may have picked your definition up from them. The high school biology students Art appealed to probably got their definition from the textbook also, and Art's "toddler test" is therefore about as useful as asking an actual toddler. It is interesting to note that the hypothesis of Yaris et al. required that "highly evolved anabolic pathways" somehow arose without DNA control. It would be reasonable to propose RNA control for these pathways. But it is totally unreasonable to propose that they arose without any control whatsoever. The point is that life requires control. That's what the membrane is about—control. That's what the DNA code is about. That's what the anabolic pathways are about—controlling the form of what comes in so that it becomes changed into an integral part of the organism. And that is why it is difficult, and may be impossible, for RNA to be the control molecule. One needs a way of clearly differentiating the backup from the working copy. If RNA is serving both purposes, it is hard for the cells degradative enzymes to figure out which is which and destroy the working copies when they are no longer needed without destroying the backup copy. DNA solves that problem. I'm still waiting to see evidence that RNA actually does the job in specified circumstances rather than theoretical partial justifications of how it might have happened.Paul Giem
June 19, 2009
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Mr ScottAndrews, I neglected to mention the obvious, that the other species descended from intermediates could all be extinct, but why would dozens of species of whale survive and not one pre-whale? They no longer fit the ecological niches that exist today as well as their descendant species.Nakashima
June 19, 2009
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Explanation: I don't think IDers are at all comparable to such deniers. That's just the limit case that Lyotard examines in his book about certain kinds of argumentative impasses.David Kellogg
June 19, 2009
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DW, Yes. Or like the holocaust denier who will only accept accounts from those who actually died in the gas chambers (cf Jean-Francois Lyotard, The Differend).David Kellogg
June 19, 2009
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David Kellogg, Ahh...well, there will always be those who demand every dropped Japanese bomb be accounted for before admitting the Japanese actually attacked Pearl Harbor.Dave Wisker
June 19, 2009
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David Kellogg, I like your humor.Clive Hayden
June 19, 2009
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Dave Wisker, I don't think Clive believes speciation ever happens. That's not, strictly speaking, and ID position, but it's a position of something else from which ID, errr, speciated.David Kellogg
June 19, 2009
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I happened to be reading a book my daughter left on a recent visit, and came across a reference in it to another book entitled The descent of man, and selection in relation to sex. Geoffrey Miller (The Mating Mind) suggests Darwin's discussion of human's descent from ape ancestors was not the main issue of the book, rather it was sexual selection.Alan Fox
June 19, 2009
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Dave Wisker, Of course isolation produces reproductive isolation. The question is whether this produces speciation by virtue of the isolation.Clive Hayden
June 19, 2009
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Clive, theer ius very good evidence for sexual selection maintaining strong reproductive isolation between two otherwise genetically compatible species: Boughman JW (2001). Divergent sexual selection enhances reproductive isolation in sticklebacks. Nature 411: 944-948.Dave Wisker
June 19, 2009
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I neglected to mention the obvious, that the other species descended from intermediates could all be extinct, but why would dozens of species of whale survive and not one pre-whale?ScottAndrews
June 19, 2009
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I think the question makes more sense if I turn it around. If we envision the tree of life as a series of intermediates branched by speciation, why do the majority of living examples of speciation appear to spring from so few points along the tree of life? Why are there dozens of species of whale, and no species of any of the nearest predecessors not recognizable as whales? It suggests that they didn't speciate until they were finished "becoming" whales.ScottAndrews
June 19, 2009
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This also leads me to wonder about the apparent coordination between punctuated evolutionary changes and speciation. As it is, we have many species of related animals in a recognizably similar state of evolution*. That is, we can recognize birds, cats, and dogs all over the world, similar enough that we can tell what they are. But in each case it appears that they speciated after they completed their transitions to being birds, cats and dogs. Given entire populations of animals, all at a sufficient state of fitness to have been selected in their current states, it seems odd that they would wait to speciate until they achieved some significant change in form. Where are the descendants of the species that branched from their intermediates? Shouldn't we see more of them today? *For the sake of discussion.ScottAndrews
June 19, 2009
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Dave, There is no evidence of speciation by virtue of sexual preference or sexual isolation.Clive Hayden
June 19, 2009
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Clive, Dave Wisker, There is no evidence for it, how about that? Are you saying that there is no evidence for population divergence under reproductive isolation? That there is no evidence that this isolation results in enough genetic divergence that interfertility is impaired?Dave Wisker
June 19, 2009
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Dave Wisker, There is no evidence for it, how about that?Clive Hayden
June 19, 2009
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Clive, Ignoring what I wrote supporting it and implying I am just repeating the same sentence undermines the credibility of your point dramatically.Dave Wisker
June 19, 2009
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