Universal Common Descent Dilemma

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  1. Despite lack of observational basis, Darwin proposed Universal Common Descent (UCD) saying: “Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed“. He also said elsewhere (referring to UCD): “…the littlest creature (or four or five of them)…” With his remarks, Darwin left the door open to creation (“life was first breathed”), but since then, Neo-Darwinists have rejected creation and replaced it with belief in undirected abiogenesis while maintaining belief in UCD.

  2. UCD is incompatible with the current view of Earth as just an ordinary planet circling an ordinary star located nowhere special inside an ordinary galaxy. If Earth is “nothing special” and abiogenesis is an ordinary “arising” of life from non-living matter, spontaneous abiogenesis would be a trivial common occurrence here on Earth as well as throughout the Universe, and we would have many “trees of life” instead of one. However, until now, all abiogenesis experiments have failed to produce life, spontaneous generation has been rejected, and the Fermi paradox stands, all these keeping the single “tree of life” and UCD hypothesis still alive and still inexplicable.
  3. Conditions for starting life should be similar to those required for sustaining it. The Big Bang model mandates a beginning of life. Furthermore, once started life must be sustained by the same or very similar environment. And since life is being sustained now on Earth, abiogenesis should be ongoing contrary to all observations to date. Tidal pools, deep sea hydrothermal vents, and the undersurface of ice caps have been hypothesized to originate abiogenesis due to their persistent energy gradients, but no abiogenesis or its intermediate phases have been observed around these sites. Given these, the only methodological naturalistic alternative is ‘limited window of opportunity for abiogenesis which suggests primordial life substantially different than all known forms of life, and perhaps originating on another planet followed by panspermia. However, this alternative defies Occam’s razor and the absence of supporting evidence including the earliest ever known fossils (stromatolites) that are of commonly occurring cyanobacteria rather than of alien origin.
  4. Universal Common Descent requires an inexplicable biologic singularity. All known forms of life are based on the same fundamental biochemical organization, so either abiogenesis happened only once or it happened freely for a while but then it stopped when the ‘window of opportunity’ closed and only one organism survived to become the Last Universal Common Ancestor (LUCA) of all existing life on Earth. However, these two biologic singularities should be unacceptable given the lack of evidence and the assumption of continuity in nature. Furthermore, the second scenario requires two discontinuities: one for the cessation of abiogenesis and the second one for the bottleneck leading to LUCA.
  5. In conclusion, UCD hypothesis leads to a number of bad and very bad scenarios: a) Earth is “nothing special” should lead to a “forest of life” rather than a single “tree of life” and to ubiquitous abiogenesis (unobserved); b) Alien life plus panspermia is refuted by the Fermi paradox and oldest known stromatolites fossils; c) Single event abiogenesis is an unsupported and therefore unacceptable singularity; d) ‘Window of opportunity’ abiogenesis followed by LUCA bottleneck is even less acceptable double-singularity. And this brings us back to Darwin’s “open door” to creation, perhaps the most rational alternative that fits all biologic observations.

Pro-Con Notes

Con: Maybe abiogenesis is happening a lot. I think the already existing life would dispose of it quickly though.

Pro:  if so, 1. We should be able to duplicate abiogenesis in the lab; 2. We should see at least some of the intermediate abiogenesis steps in nature; 3. Existing life can only process what looks like food. Cellulose is a well known organic material that cannot be broken down by a lot of organisms and is known to last as very long time in dry conditions.

1,101 thoughts on “Universal Common Descent Dilemma”

  1. CharlieM: ?

    Me: Whether or not it is present in the genome, of course. Did Professor Google not tell you this?

    Charlie: So in that case why are not all proteins expressed in every cell that contains the genome? The genes that code for them are contained in every genome.

    People have already explained gene regulation. The fundamental trigger is Sry. It’s a transcription factor which binds to other genes, turning them on or off, which in turn causes expression of other TFs. There is no master control, but a cascade of downstream effects.

  2. CharlieM: Who are these people? We should put them straight

    You. You keep insisting whatever might be clear cut in eukaryotes falls to pieces when looking at prokaryotes. So by implication we can be happy about the relations of humans and chimps, but not about alpha proteobacteria. Or are prokaryotes just a Wedge?

  3. CharlieM: Because it had already been put down to a case of convergent evolution before the genetic evidence came to light. The genetic similarity came as a surprise.

    What prevented them from changing their minds? And do you know how much molecular similarity there actually is, percentage wise?

  4. Joe Felsenstein:

    ChalieM: And drift allows for a certain plasticity of the population to cater for fluctuations in the local environment.

    Let me see whether I can follow the part about genetic drift. Genetic drift allows plasticity (by “coping with fluctuations in the local environment”). Pandas are in trouble because they have too little plasticity. That must mean that they have too little genetic drift, which implies that they have too large a population size.

    Now actually, pandas have too small a population size, hence by that argument they must have too much genetic drift, and must be too plastic.

    I suppose that explains the problems of pandas. One way or the other.

    You have quite rightly highlighted my confused statement about genetic drift here. I was wrong in saying that genetic drift allows plasticity. As far as I can see genetic drift is just an indication of the dynamic fluctuations of living populations. And any population will experience genetic drift. What effect drift has on panda populations I don’t know. Maybe if there is an answer and someone knows that answer then they will tell me what the effect is.

  5. Corneel: That’s exactly the wrong way around: their limited numbers increases the impact of genetic drift which poses a major concern for conservation, as drift depletes genetic variation and increases the rate of fixation of deleterious mutants.

    I should have read on. You have basically answered my question above. Thanks to you and Joe for the correction.

  7. CharlieM: I should have read on. You have basically answered my question above. Thanks to you and Joe for the correction.

    My pleasure,

  8. Corneel:

    CharlieM: Growth and decay are not some vague forces, they are a fundamental feature of life. Binary fission, cell death, apoptosis, photosynthesis, need I go on.

    Yes, please.

    Binary fission, cell death, and apoptosis somewhat work as proxies for growth and decay in development (I am giving you a lot of leeway here: apoptosis is programmed, so not really decay). In phylogenesis, not so much, and I am at a loss to name the analogous processes. Spelling those out would help filling in some details.

    I certainly don’t know what photosynthesis is doing in your list.

    I think your confusion lies in the way I am using the word, “decay”. What I mean by “growth and decay”, could also be termed anabolism and catabolism, or building up and tearing down.

    Growth:
    Binary fission – The liver is an organ which can regrow if part of it is removed. Human red blood cells are produced at a rate of at least 2.5 million per second.

    Photosynthesis – Plants take enegy from the sun, H2O and CO2 and build up carbohydrates.

    Decay:
    Cell death – We lose hundreds of skin cells every second. They are then broken apart by microbial action.

    Apoptosis – Cells are broken down in a controlled manner. Not decay as you envision it, but it is still decomposition.

    Death of organisms – Life begins with growth and ends in death, decay.

  9. CharlieM: I think your confusion lies in the way I am using the word, “decay”. What I mean by “growth and decay”, could also be termed anabolism and catabolism, or building up and tearing down.

    Yes, that is where the confusion lies, and not just on my end.

    When you make associations between loosely connected terms like you do here, that counts as “vague” in my book. All of these terms need to function in a specific context (e.g. anabolism and catabolism belong to biochemistry). You divorce those specific terms from their context and subsume all under the umbrella of “growth and decay”. That is all nice and dandy, but I would be very surprised if anybody else but you accepts that e.g. anabolism and population growth are similar in any meaningful sense.

    So pointing out superficial resemblances like “the forces of growth and decay” won’t cut it: You need to make explicit that the specific features that ensure a predetermined outcome in development are also present in phylogenesis. I don’t think you can.

  10. Corneel: I like to think of the genes as a pile of wet autumn leaves,

    I can see that. Dead and inactive in themselves, but very valuable to the living creatures that use them. 😉

    the proteins as a group of Greek sirtaki dancers,

    Yes, a dynamic, living chain, moving beautifully. I can see the connection, nice image 🙂

    and the cell as a smallish ball of pink cotton.

    Add a host of tiny organisms, scuttling about, living and breeding within, moving in and out of it. That would make it a better model of the cell. 🙂

    I am not really sure how that fits into the metaphor, but I don’t see why you would get to have all the fun.

    I knew you could do it! 😉 🙂

  11. Rumraket: It has to start somewhere. Initiation of transcription can take place because a particular molecule (the transcription factor) binds to a promoter region of some sort. The efficacy of binding is dependent on the mutual affinity between the DNA and the TF. The TF is usually a protein, and the protein’s shape of course depends on it’s sequence, and it’s affinity to the DNA depends on it’s own shape and the DNA sequence (different DNA sequences have slightly different surface topologies).

    Transcription factors have been tested on random DNA and found to reproducibly yield similar patterns of transcription initiation as found in the genomes of living organisms. Basically the TFs bind all over the place, but most of it weakly, and will only occasionally manage to recruit the transcriptional machinery successfully and result in transcription in places where binding is weak. Particular sequences of DNA that are more similar to the canonical promoter region will exhibit better binding affinity between DNA and the TF, so successful transcription is more likely to take place when the TFs binds to those regions.

    This indicates the process is fundamentally stochastic, that there is no overarching coordination required to get varying levels of specific binding, and that in the end it all depends on the mutual affinities of molecules coming into close proximity to each other under the conditions of brownian motion.

    For anyone who thinks that translation begins with a simple binding of a transcription factor, I would strongly advise that they follow this video carefully. I hope that they will then get an idea of the complexity of the preparation involved. But I’m sure most of the posters here are aware of this complexity.

    From the complexity of RNA polymerase II to the rest of the complex molecules with which it needs to interact before transcription can even begin. In the video it is stated that “RNA Pol II requires a group of >85 associated factors and regulatory proteins to control transcription.”

    He goes on to say:

    Well, I think I gave you a little taste of the level of complexity that’s probably going to be needed to be able to build the machine that’s ultimately going to be able to allow you to transcribe every gene in every cell of the human body. So that turns out to be a much more elaborated machine than what I just showed you. So I want to show you now what is sort of our state-of-the-art thinking about what is actually needed to build the machinery at a gene to allow it to be expressed and transcribed. And the term I want to introduce you to is the “pre-initiation complex,” and its pretty much what it says, It’s the complex of multiple sub-units that has to essentially land on the promoter of a gene, which will be designated for later expression. And this is a process that is probably quite orderly,; that is, there is an order of events that happens, which we, by the way, are not entirely sure exactly what the order is or even if the order is the same from one gene to the next, and the pathway in between, I would say, is still a little bit murky. And the story here again starts with a little snippet of DNA called the TATA box, which I already introduced to you briefly. It’s an AT-rich sequence which sits at the 5′ end, or the beginning of many genes, but not all genes…maybe 20% of the genes might contain this AT-rich region. And that AT sequence is the signal or landmark, if you like, for a particular protein to bind to it. and that protein is called, not surprisingly, the “TATA-binding protein,” because it’s the TATA sequence. And so this represents a second class of transcription factors,. These are not the type that I introduced you to, which are going to be different for every gene. The TATA sequence is present in a very large number of genes, so it can’t be gene-specific. But it turns out to be very crucial for our understanding of how gene regulation works. So you start with a TATA-binding protein finding a TATA box. We later found out that the TATA-binding protein rarely functions on its own and has a bunch of friends that we call “TAFs,” for “TBP-associated factors.” And now your talking about an assembly, a multi-sub-unit complex of almost a million daltons. There are somewhere between 12 to 15 sub-units in addition to the TATA-binding protein that make up this little complex of proteins that kind of travels around together, and this is found in most cell types. And later on I’ll show you in a subsequent lecture that not every cell type might have exactly the same complement of these sub-units, but many of them have this prototypic complex. Is this enough for building the pre-initiation complex? Unfortunatley not. It turns out there are a host of other, I’ll call them “ancillary factors” in addition to the multi-sub-unit tRNA polymerase itself, that are necessary for you to build up an ensemble that is necessary to form an active, ready-to-activate transcriptional pre-initiation complex or the, PIC. And this is kind of the picture we are getting to and even this picture, with many, many colours and many, many different polypeptides, that adds up to probably greater than 85 individual proteins that all have to kind of fit together like a jigsaw puzzle. Its probably not even the whole story. You’ll have noticed I still have one big red question mark there because I think as we begin to study specific cell types and specific processes like embryonic development or germ layer formation, additional components that are not present here in this prototypic pre-initiation complex will come into play. And that’s a subject of a subsequent lecture. But already you can tell that the transcription machinery is anything but simple

    And don’t forget that this initiation process will have been activated by a specific need to produce proteins for use wherever they are needed within the organism, it could be intra-cellular or extra-cellular. For instance if I cut a finger this will stimulate a vast amount of transcription, translation and protein transportation. The instigator of all this activity will be my careless action.

  12. Entropy: Then why did you quote a note about how HGT makes it difficult to establish the phylogenetic histories of prokaryotes? If you think it doesn’t happen, then quoting that note was a contradiction of terms.

    ??

  13. Entropy: But how Charlie? How does the cell accomplish such a thing? You said they’re not conscious. So then how? Everything i have studied shows chemicals being chemicals. Whether the cell wants them to be or not is impossible to tell, so why jump there when the explanations work without such extra, and useless, claim as “the cell controls it all!”

    You have probably typed the paragraph you have written above. Now you can describe it in chemical and physical terms. The processes within nerve and muscle cells, the electrical signals responsible for the patterns of pixels on the screen as you typed. That will give us the finer details of the mechanics involved but it tells us nothing about the actual causes behind this multitude of activities. Focusing on the pixels tells us very little about the letters on the screen, focusing on the individual letters tells us very little about the words, focusing on the words tells us very little about the sentences. It is only when we understand the sentences in their context as a whole do we begin to understand the real cause of all this activity.

    Focusing in on the chemical processes going on in the nucleus of a cell from start to finish will never tell us the the way a leopard uses its senses and mobility to hunt its prey and it won’t tell us how a monoocyte uses its senses and mobility to hunt its prey. The chemical processes are just the means by which these creatures achieve their aims. The leopard may have a higher conscious awareness than a monoocyte but the principle is basically the same.

  14. Charlie, it is true that one can study something at the wrong level of abstraction. Given your constant appeal to some vague unspecified vitalism, you might want to ponder on that point.

    CharlieM: Focusing in on the chemical processes going on in the nucleus of a cell from start to finish will never tell us the the way a leopard uses its senses and mobility to hunt its prey and it won’t tell us how a monoocyte uses its senses and mobility to hunt its prey. The chemical processes are just the means by which these creatures achieve their aims. The leopard may have a higher conscious awareness than a monoocyte but the principle is basically the same.

    Similarly, focusing in on the chemical processes going on will never tell us the way a lambda lysogen uses its senses to decide to induce. The chemical processes are just the means by which lambda excises itself. The leopard may have a higher conscious awareness than lambda but the principle is basically the same.
    Woo-hoo!
    And whether to lyse or lysogenize is an even more complicated decision, not amenable to biochemical analysis.

  16. Allan Miller: Nothing? The fact they can’t interbreed is hardly nothing. Are you saying that such genetic isolation cannot occur through evolution? That’s quite the claim.

    Yes, I am saying “evolution” cannot occur through genetic isolation (and your story is backwards).

    Why should “genetic isolation” lead to anything new in spite of the second law of thermodynamics? Homogeneity just doesn’t “evolve” into heterogeneity in nature. Not when there are no barriers between populations. Take man and ape still living in Africa and elsewhere in the same environment – there was never any barrier. Now take chimps and bonobos – you can hardly tell the difference after 3 mil years of complete separation by the Congo river! And they still gladly mate with each other.

  17. Allan Miller: Nonlin’s thesis appears to be that evolution can’t be true because everything is not the same, and there is only one way to get everything not the same, and that is to will it. This is what we are up against.

    You understand nothing. Evolution fails because it’s logically impossible as demonstrated repeatedly. The fact that it fails second law of thermodynamics is just another nail in its coffin… one of many.

  18. Nonlin.org: You understand nothing. Evolution fails because it’s logically impossible as demonstrated repeatedly. The fact that it fails second law of thermodynamics is just another nail in its coffin… one of many.

    It’s impossible for complexity to spontaneously emerge in a closed system. If only there were some staggeringly vast source of energy that was constantly bombarding the planet with all the power necessary to drive complexity.

  19. Kantian Naturalist: It’s impossible for complexity to spontaneously emerge in a closed system. If only there were some staggeringly vast source of energy that was constantly bombarding the planet with all the power necessary to drive complexity.

    I know what you mean, and you’re wrong. There is absolutely no basis for “energy creates complexity”, let alone life in a closed or open system. Feel free to reply with counterexamples if any.

  20. Nonlin.org: I know what you mean, and you’re wrong. There is absolutely no basis for “energy creates complexity”, let alone life in a closed or open system. Feel free to reply with counterexamples if any.

    Good to see you’ve come to a reasoned conclusion from your years of close study of far-from-equilibrium thermodynamics in open systems and molecular biology.

  21. Nonlin.org: Why should “genetic isolation” lead to anything new in spite of the second law of thermodynamics? Homogeneity just doesn’t “evolve” into heterogeneity in nature. Not when there are no barriers between populations.

    Wow. I think this is saying that “genetic isolation” cannot lead to anything because there are no barriers — no “genetic isolation”.

    Somebody tell nonlin.org about allopatry.

  22. Also the proof that evolution cannot happen because of the Second Law of Thermodynamics is (a) totally wrong, and (b) has failed so badly that Answers in Genesis outrightly recommends that creationists not use that argument. If nonlin.org thinks that the SLOT argument is valid, nonlin.org should start by reading the posts here refuting that. They’re easy to find. And any arguing about that should be a separate thread.

  23. Nonlin.org: I know what you mean, and you’re wrong. There is absolutely no basis for “energy creates complexity”

    Burning your toast is a direct refutation of that claim. The atomic structure of the charred material is incredibly more complex than what was there before. Better yet, put table sugar on a hot frying pan for too long and you basically get asphaltenes from sucrose.

  24. CharlieM,

    You didn’t read what I wrote carefully enough Charlie. Read it again. You’ll notice that your answer didn’t help at all.

    Here for your convenience:

    Entropy:
    But how Charlie? How does the cell accomplish such a thing? You said they’re not conscious. So then how? Everything i have studied shows chemicals being chemicals. Whether the cell wants them to be or not is impossible to tell, so why jump there when the explanations work without such extra, and useless, claim as “the cell controls it all!”

  25. Joe Felsenstein: Somebody tell nonlin.org about allopatry.

    Someone tell Joe about grizzly-polar hybrid bears. They are fertile.

    You have been taught lies.

    Bears are bears, dogs are dogs.

  26. Nonlin.org: Yes, I am saying “evolution” cannot occur through genetic isolation (and your story is backwards).

    Why should “genetic isolation” lead to anything new in spite of the second law of thermodynamics?

    The second law of thermodynamics really has very little to do with it. Because you can think of a miscible fluid with low viscosity, everything must be treated as a miscible fluid with low viscosity? Including diverging gene pools. And because you can think of an example where separation has not led to complete genetic isolation, it is impossible that there be any cases where it has!

    One suspects that, if presented with an example, you would say it’s not an example because it wasn’t shown to evolve. Any putative cases on the way to isolation are not examples because they can still interbreed! The old Creationist one-two.

    What do you think of this, Mung? Nonlin thinks genetic relationship is impossible at ANY level, if interbreeding cannot presently take place. Even the ‘orchard’ would be rejected.

  27. phoodoo: Someone tell Joe about grizzly-polar hybrid bears.They are fertile.

    And here’s another one. He can think of an example of interbreeding after separation, and so this must be a universal principle. No amount of divergence can lead to a biological barrier to introgression. Another Orchard Model skeptic.

  28. Nonlin.org: You understand nothing. Evolution fails because it’s logically impossible as demonstrated repeatedly. The fact that it fails second law of thermodynamics is just another nail in its coffin… one of many.

    Logically impossible, huh?

  29. Allan Miller: What do you think of this, Mung? Nonlin thinks genetic relationship is impossible at ANY level, if interbreeding cannot presently take place. Even the ‘orchard’ would be rejected.

    Probably not, since Nonlin is rarely consistent in his/her reasoning. My impression is that Nonlin is fine with any type of relationship, as long as the differences are the handiwork of the Designer, not any impersonal “random” evolutionary process (human relationships remain a touchy subject of course).

    I suspect Mung can relate to that, but has taken the somewhat more mature position of not being grossed out by distant simian cousins. 😉

  30. phoodoo: Someone tell Joe about grizzly-polar hybrid bears.They are fertile.

    Their ranges also overlap in the polar region, so they’re not really geographically isolated.

    You have been taught lies.

    By whom and what did they lie about?

    Bears are bears, dogs are dogs.

    Ahh the good old one therefore all-fallacy. Are cats all cats? Can all cats interbreed? Can all bears? Can you extract a general principle from one example?

  31. Corneel:
    I suspect Mung can relate to that, but has taken the somewhat more mature position of not being grossed out by distant simian cousins.

    Yes, though my reason for elbowing Mung on this occasion relates to his proposition upthread that other Creationists are cool with a bit of twig-tip speciation. I rarely encounter them: pushed, they all seem to deny speciation in toto, even while, apparently, accepting divergence as a thing (a “logically impossible” thing, chortle!)

  32. Rumraket: Their ranges also overlap in the polar region, so they’re not really geographically isolated.

    Then why do we call them species, skeptic?

  33. Corneel: I suspect Mung can relate to that, but has taken the somewhat more mature position of not being grossed out by distant simian cousins.

    That certainly does pale next to actually being able to agree on something with atheists on the internet!

    Allan Miller:
    Yes, though my reason for elbowing Mung …

    Ouch!

    Allan Miller: … on this occasion relates to his proposition upthread that other Creationists are cool with a bit of twig-tip speciation.

    I seriously doubt that Nonlin.org believes that all modern species were created in their present forms. I prefer to think that he just hasn’t ever taken time to seriously think about his position. As far as me actually engaging with Nonlin.org to try to find out what he really thinks, how’s that working out for you guys?

    phoodoo: Then why do we call them species, skeptic?

    To give the second law of thermodynamics something to do.

  35. I see that you ignored the rest of my post.

    phoodoo: Then why do we call them species, skeptic?

    Well first of all there are different species concepts, you knew this right? Let’s try to read something: Species Concepts and Species Delimitation

    The reason for these incompatibilities has to do with the different biological properties upon which several of the alternative concepts are based; for example, intrinsic reproductive isolation in the case of the isolation version of the biological species concept, occupation of a distinct niche or adaptive zone in the case of the ecological species concept, and fixed character state differences in the case of the diagnosable version of the phylogenetic species concept (Table 1). Moreover, these differences in emphasis are to be expected, because the various properties are of greatest interest to different subgroups of biologists. For example, reproductive incompatibilities are of central importance to biologists who study hybrid zones, niche differences are paramount for ecologists, and diagnosability and monophyly are fundamental for systematists. Similarly, morphological differences are central for paleontologists and museum taxonomists, whereas genetic ones are key for population geneticists and molecular systematists. On the other hand, for biologists who adopt a multidisciplinary approach, or those who can step back from their own personal investments and research interests, all of the concepts seem to have some merits. They are all based on important biological properties.

    More specific on the Ecological species concept: http://www.blackwellpublishing.com/ridley/a-z/Ecological_species_concept.asp

    The ecological species concept is a concept of species in which a species is a set of organisms adapted to a particular set of resources, called a niche, in the environment. According to this concept, populations form the discrete phenetic clusters that we recognize as species because the ecological and evolutionary processes controlling how resources are divided up tend to produce those clusters.

    Ecological research, particularly with closely related species living in the same area, has abundantly demonstrated that the differences between species in form and behavior are often related to differences in the ecological resources the species exploit.

    The ecological species concept should be contrasted with the biological, recognition and cladistic species concepts.

    On polar bears as species: https://en.wikipedia.org/wiki/Polar_bear#Taxonomy_and_evolution

    “Polar bears can breed with brown bears to produce fertile grizzly–polar bear hybrids,[4][31] rather than indicating that they have only recently diverged, the new evidence suggests more frequent mating has continued over a longer period of time, and thus the two bears remain genetically similar.[30] However, because neither species can survive long in the other’s ecological niche, and because they have different morphology, metabolism, social and feeding behaviours, and other phenotypic characteristics, the two bears are generally classified as separate species.[32]”

    So Polar bears and Grizzly bears are ecological and phylogenetic species, but have not biologically speciated. Man it’s like when you want to learn something and you go on the internet, in less than 10 minutes you can come to know a lot you didn’t know before if you just think a little about what to search for.

  36. Mung: As far as me actually engaging with Nonlin.org to try to find out what he really thinks, how’s that working out for you guys?

    It’s a waste of time trying. The gal/guy cannot engage with explanations or reasoning. (S)he asked me once for examples of testing assumptions in the hard sciences, I provided plenty, and her/his answer was to call a main journal in physics a cargo-cult site.

  37. Rumraket: Ahh the good old one therefore all-fallacy. Are cats all cats? Can all cats interbreed? Can all bears? Can you extract a general principle from one example?

    Isn’t evolution a general principle exactly like this? Something like: Such-and-such finches have common descent, therefore all species have common descent.

    ?

  38. Mung:
    To give the second law of thermodynamics something to do.

    I love this one.

    It’s true, the second law is precisely the reason why species diverge and why they are so damn hard to delimit in precise terms. IOW the second law is the reason why there’s evolution in the first place.

  39. Erik:
    Isn’t evolution a general principle exactly like this? Something like: Such-and-such finches have common descent, therefore all species have common descent.

    ?

    Do you actually believe it’s just about finches?

  40. Erik: Isn’t evolution a general principle exactly like this? Something like: Such-and-such finches have common descent, therefore all species have common descent.

    No. How did you ever get to have that impression?

  41. Erik: Isn’t evolution a general principle exactly like this? Something like: Such-and-such finches have common descent, therefore all species have common descent.

    ?

    Absolutely not, no.

  42. Mung:
    I seriously doubt that Nonlin.org believes that all modern species were created in their present forms. I prefer to think that he just hasn’t ever taken time to seriously think about his position.

    That much is clear, but it’s a lark to point out the inconsistencies.

    As far as me actually engaging with Nonlin.org to try to find out what he really thinks, how’s that working out for you guys?

    You could ask that about pretty much any interaction with Creationists. It’s a hobby, is all.

    The problem that can’t be underestimated is that there is belief in eternal reward/damnation on the one side, without even a bag of sweeties to offer on the other. No contest.

  43. Rumraket: No. How did you ever get to have that impression?

    By what reasoning is the principle of evolution (of species by common descent) established then?

    My prediction: No explanation forthcoming.

  44. Erik: By what reasoning is the principle of evolution (of species by common descent) established then?

    I think we have been over this, but here you go:
    http://www.talkorigins.org/faqs/comdesc/section1.html

    In particular, by the overall shared characteristics of all known life.
    By the nesting hierarchical structure in the data.
    By the consilience of independent phylogenies on a common topology.
    By the existence of transitional species in the fossil record.
    By the chronology of common ancestors in the fossil record.

    And last and perhaps most importantly, the mutual corroboration of all these independent lines of evidence on a particular common history of life.

  45. Erik:
    By what reasoning is the principle of evolution (of species by common descent) established then?

    Well, let’s start by explaining that the book on the origin of species doesn’t have anything about finches. Is tis clear so far?

    If clear, let’s follow by explaining that it’s not just reasoning in the air, but about putting together several lines of evidence. By way of example I’ll list a few of the things Darwin put together (but much more has been done in the following years after that):

    1. Lots of quite divergent forms can be “shaped” by breeders by selecting generation-after-generation for features of interest. Darwin used to breed pigeons, if I remember correctly. So pigeons were exemplified, with shapes I had never seen myself before reading the book. (This is why Darwin named the process he proposed “natural selection” as a simile to breeder’s selection.)

    2. It’s obvious that not every offspring lives to reproduction, since if they did, populations would grow beyond the resources of the planet very quickly. It’s therefore possible that there’s at least some competition for survival.

    3. Variation exists between individuals in a population of any species. Since the offspring tends to look like their parents (even if not perfectly), it makes sense that if some hereditary characteristics are behind survival to reproduction, then such characteristics will be passed on to the offspring. As the process goes on and on, the populations should consists of better adapted individuals.

    4. Is this so? Any evidence of diverging populations? Well, Darwin found that fossils that looked similar to current species in some geographical location were located within such geographic location. For example, giant sloth fossils in places where today’s sloths live.

    5. Is this so? Any evidence of diverging populations? Darwin noticed that the more similar two species, the closer they lived. Distance seemed to correspond with divergence in the looks of species in the same families. I don’t remember which examples he used.

    6. How far does this go? Any evidence that, say, something like eyes could evolve? Darwin showed that today’s life forms showed examples of eyes, from very simple to the complex eyes we’re used to think about exist, which show that eyes could evolve in “stages” “each useful to its bearer.”

    7. Etc.

    So, as this small list, obviously not possibly making too much justice to that 600 pages book, shows that the 600 pages didn’t just say “finches! look at finches! therefore evolution!” I’d advice reading it, even if enormous amounts of evidence have accumulated ever since, and even though Darwin didn’t know much about how heredity works, and even though there’s more to evolution besides natural selection.

    For much more than that you can use google scholar to find the latest research about evolution in scientific journals, and, as Rum showed, there’s also online explanations that try and make it accessible to the more general public.

    Erik:
    My prediction: No explanation forthcoming.

    Why would you say this? There’s lots of explanations all over the place, many of them more comprehensive and better written than mine above. It’s all a matter of actually caring to read and understand, rather than looking at creationist bullshit that misinforms and pretends that the evidence doesn’t exist, that Darwin is all there is, and that Darwin wrote the word “finches” time and again all through 600 pages.

    My prediction, you really don’t care because you already made your mind that only what creationist charlatans say about evolution counts.

  47. phoodoo: Yea…that’s what I hear. Lots of them.

    The irony here is that it’s precisely because of evolution that species are so damn hard to delimit, thus the many attempts at defining the term both conceptually and in practice.

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