Universal Common Descent Dilemma

  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 Replies to “Universal Common Descent Dilemma”

  1. Rumraket Rumraket
    Ignored
    says:

    Mung: They have a reason Rumraket. You may not like their reason, but they do have one.

    Better to try to understand what their reasons are, what your reasons are, and see if any common ground at all can be found, because it not, there are far better ways to spend your time.

    Gee thanks Mung, as if I didn’t know this. I have argued with these people since sometime in 2007 or 2008. I know what their reasons are, and they’re patently irrational. It has nothing to do with evidence or science, they have prior commitments to a particular interpretation of religious scriptures and with that interpretation held aloft as basically unassailable fact, they will arbitrarily decide to delineate organisms into independent, unrelated clades. Like the ludicrous separation of the human species from the rest of life despite our obvious kinship.

    The kinds of arguments that creationists would advance to show that all the different species of rodents (or canines, or felines, etc.) fit together in a unified tree, would show that humans are primates related to all other primates. And one could go on and show that all their independent trees also fit together by the same methodology into bigger more inclusive trees.

  2. Mung Mung
    Ignored
    says:

    Rumraket and I agree!

    It would be quite a trick if you could get them to agree to the common descent of some taxa and then explore how they might going about making a scientific case for the common descent of those taxa.

    Perhaps ask how they would try to convince someone of the shared ancestry of those groups without reference to the Bible.

    If they can’t agree there is any scientific support for the common descent of those taxa, well, what can you do, lol.

  3. John Harshman John Harshman
    Ignored
    says:

    Mung: It would be quite a trick if you could get them to agree to the common descent of some taxa and then explore how they might going about making a scientific case for the common descent of those taxa.

    Yes, that would be quite a trick. I’ve been trying to get Bill, mostly, to agree to any common descent of two or more species of anything for quite some time, and to explore what he would require as evidence for such a thing. No luck so far, and not just with Bill, but thanks for asking.

  4. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Mung has suggested that we could find a creationist who accepts common descent of one group, then ask them to explain their reasoning in accepting it, and whether they aren’t being inconsistent in rejecting common ancestry of apes and humans.

    It would be interesting if one could get them to engage in that exercise. But it’s been tried, with no results. One occasion was my question to Cornelius Hunter at his blog “Darwin’s God” in July, 2010. My initial comment was here. I asked Hunter whether, if there were some group that he accepted had common ancestry, that this would establish that they had evolved. He said here, that sure, that diatoms were an example. I then asked here why, if he accepted this for the 100,000 species of diatoms, he didn’t accept similar evidence for the 59,000 species of chordates.

    He didn’t accept it, claiming that unlike diatoms’ differences which were “modest”, chordates’ differences were much more dramatic “adaptive change” and required detailed explanation.

    This response of Hunter’s is here, a reply by me to that is here. More back-and-forth will be found in a later thread at Hunter’s blog, starting with a comment by me here. But Hunter continues to avoid the issue by claiming that the differences among chordates require detailed explanation — he’s much less impressed with the differences among diatoms. Not being a diatom himself.

    So Mung, it’s been tried and no, it does not lead to the creationist seeing that the logic in the two cases is the same. However logical, your proposed approach doesn’t work in practice.

  5. Nonlin.org
    Ignored
    says:

    Allan Miller: Because the systems are isolated; there is no general homogenising flow between every organism on earth. Much as there exist lakes at various levels, despite the tendency of water to equilibrate. Or, for that matter, separate cups containing black or milky coffee.

    Wrong. Nothing is isolating the cat environment from the human one. And the Darwinist story claims homogeneity transformation into heterogeneity. You’re merely saying that distinct heterogeneous systems remain distinct which is trivial.

    IOW, we’re not talking about “separate cups” but about a cup that separates its ingredients and creates new ones! Based on current knowledge, this is an impossibility without external intervention (aka ID).

    Why do I have to explain the basics all the time?

  6. Allan Miller
    Ignored
    says:

    Nonlin.org: Wrong. Nothing is isolating the cat environment from the human one. And the Darwinist story claims homogeneity transformation into heterogeneity. You’re merely saying that distinct heterogeneous systems remain distinct which is trivial.

    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.

    Why do I have to explain the basics all the time?

    On this showing, your grasp of the basics is atrocious.

  7. Allan Miller
    Ignored
    says:

    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.

  8. Mung Mung
    Ignored
    says:

    Joe Felsenstein: So Mung, it’s been tried and no, it does not lead to the creationist seeing that the logic in the two cases is the same. However logical, your proposed approach doesn’t work in practice.

    Yes, that sort of switching between the evidence that species share a common ancestor to requiring evidence for how it happened, I have seen that, esp from Bill.

    I did not read your interaction with Dr. Hunter, but it seems from your description that he did not agree that the evidence for shared ancestry was based upon phylogenetic methods but rather upon what he could believe was possible given Darwinan mechanisms. So you were probably talking past each other.

    Now I believe that Hunter is bright enough to understand phylogenetic inference. If he is questioning the methods of inference that would be one thing. But it doesn’t appear that he was doing that. It sounds more like he was trying to avoid the question by changing the subject.

    Maybe one day I can have a look at that series.

  9. colewd
    Ignored
    says:

    Joe Felsenstein,

    So Mung, it’s been tried and no, it does not lead to the creationist seeing that the logic in the two cases is the same. However logical, your proposed approach doesn’t work in practice.

    Would you consider it reasonable to say that the greater the differences between species the lower the chance that they share a common ancestor?

  10. John Harshman John Harshman
    Ignored
    says:

    Mung: It sounds more like he was trying to avoid the question by changing the subject.

    But does he know he’s doing it? Bill clearly doesn’t. I don’t think Sal Cordova does either.

  11. John Harshman John Harshman
    Ignored
    says:

    colewd: Would you consider it reasonable to say that the greater the differences between species the lower the chance that they share a common ancestor?

    No. It’s not about difference. It’s about nested hierarchy. Remember the crocodiles?

  12. Allan Miller
    Ignored
    says:

    colewd:

    Would you consider it reasonable to say that the greater the differences between species the lower the chance that they share a common ancestor?

    Surely you would want to make allowance for time? The longer the time till the common ancestor, the greater the difference.

  13. colewd
    Ignored
    says:

    Allan Miller,

    Surely you would want to make allowance for time? The longer the time till the common ancestor, the greater the difference.

    What does this have to do with the probability that two species share a common ancestor?

  14. Rumraket Rumraket
    Ignored
    says:

    colewd:
    Allan Miller,

    What does this have to do with the probability that two species share a common ancestor?

    It shows that you don’t compute the “probability that they share a common ancestor” by how different they are, but by the consilience of independent phylogenies and the nesting hiearchical structure in the data as measured by the consistency index. Predictions 1.2 and 1.3 in Theobald’s 29+ Evidences for macroevolution, read them. For the fiftieth time. At least. Read them and comprehend them.

  15. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    colewd: the chance that they share a common ancestor?

    As far as I know that probability is 100% no matter which two species you are talking about, no matter how great or small are the differences between them.

    Or did you mean to ask some other question?

  16. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Mung: did not read your interaction with Dr. Hunter,

    Maybe one day I can have a look at that series.

    My sympathies with you if you are too busy to find the 15 minutes that this would take.

  17. colewd
    Ignored
    says:

    Joe Felsenstein,

    As far as I know that probability is 100% no matter which two species you are talking about, no matter how great or small are the differences between them.

    The only possibility here is you’re assuming universal common descent is true as there is no other way to claim that the chance a human shares a common ancestor with e coli bacteria is 100%.

  18. Rumraket Rumraket
    Ignored
    says:

    colewd: The only possibility here is you’re assuming universal common descent is true as there is no other way to claim that the chance a human shares a common ancestor with e coli bacteria is 100%.

    No, we either share common descent or we do not. So either the probability is 100%, or 0%. Those are the only two options.

    But there’s a difference between what is the case, and what we know. That depends on what evidence we have. The evidence we have for the common descent of all known life is absolutely incredible. Two types of that evidence is explained quite well here:
    Prediction 1.2: A nested hierarchy of species

    One widely used measure of cladistic hierarchical structure is the consistency index (CI). The statistical properties of the CI measure were investigated in a frequently cited paper by Klassen et al. (Klassen et al. 1991; see Figure 1.2.1). The exact CI value is dependent upon the number of taxa in the phylogenetic tree under consideration. In this paper, the authors calculated what values of CI were statistically significant for various numbers of taxa. Higher values of CI indicate a greater degree of hierarchical structure.

    As an example, a CI of 0.2 is expected from random data for 20 taxa. A value of 0.3 is, however, highly statistically significant. Most interesting for the present point is the fact that a CI of 0.1 for 20 taxa is also highly statistically significant, but it is too low—it is indicative of anti-cladistic structure. Klassen et al. took 75 CI values from published cladograms in 1989 (combined from three papers) and noted how they fared in terms of statistical significance. The cladograms used from 5 to 49 different taxa (i.e. different species). Three of the 75 cladograms fell within the 95% confidence limits for random data, which means that they were indistinguishable from random data. All the rest exhibited highly statistically significant values of CI. None exhibited significant low values; none displayed an anti-correlated, anti-hierarchical pattern.

    Note, this study was performed before there were measures of statistical significance which would allow researchers to “weed out” the bad cladograms. Predictably, the three “bad” data sets considered under ten taxa—it is of course more difficult to determine statistical significance with very little data. Seventy-five independent studies from different researchers, on different organisms and genes, with high values of CI (P ‹ 0.01) is an incredible confirmation with an astronomical degree of combined statistical significance (P ‹‹ 10^-300, Bailey and Gribskov 1998; Fisher 1990).”

    And here:
    Prediction 1.3: Consilience of independent phylogenies

    “In science, independent measurements of theoretical values are never exact. When inferring any value (such as a physical constant like the charge of the electron, the mass of the proton, or the speed of light) some error always exists in the measurement, and all independent measurements are incongruent to some extent. Of course, the true value of something is never known for certain in science—all we have are measurements that we hope approximate the true value. Scientifically, then, the important relevant questions are “When comparing two measurements, how much of a discrepancy does it take to be a problem?” and “How close must the measurements be in order to give a strong confirmation?” Scientists answer these questions quantitatively with probability and statistics (Box 1978; Fisher 1990; Wadsworth 1997). To be scientifically rigorous we require statistical significance. Some measurements of a given value match with statistical significance (good), and some do not (bad), even though no measurements match exactly (reality).

    So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 10^38 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree (see Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies (for consensus phylogenies from pre-molecular studies see Carter 1954, Figure 1, p. 13; Dodson 1960, Figures 43, p. 125, and Figure 50, p. 150; Osborn 1918, Figure 42, p. 161; Haeckel 1898, p. 55; Gregory 1951, Fig. opposite title page; for phylogenies from the early cytochrome c studies see McLaughlin and Dayhoff 1973; Dickerson and Timkovich 1975, pp. 438-439). Speaking quantitatively, independent morphological and molecular measurements such as these have determined the standard phylogenetic tree, as shown in Figure 1, to better than 38 decimal places. This phenomenal corroboration of universal common descent is referred to as the “twin nested hierarchy”. This term is something of a misnomer, however, since there are in reality multiple nested hierarchies, independently determined from many sources of data.”

  19. colewd
    Ignored
    says:

    Rumraket,

    But there’s a difference between what is the case, and what we know. That depends on what evidence we have. The evidence we have for the common descent of all known life is absolutely incredible. Two types of that evidence is explained quite well here:

    You have evidence of similarities. To explain the nested hierarchy you need to explain the differences. I agree we cant quantify the probability only that ancestry is more likely as similarities increase as we have cases where we can establish ancestry. In all these cases genetic similarity is extremely high. This is very different then the case between bacteria and humans.

  20. Rumraket Rumraket
    Ignored
    says:

    colewd: You have evidence of similarities. To explain the nested hierarchy you need to explain the differences.

    What matters is the pattern in the similarities and differences. Why is there so much nested hierarchical structure in the data, and why do independent sets of data corroborate the same hierarchy to such an overwhelming degree? The explanation for those facts is common descent, and there is no sensible alternative. Key word is sensible. God The Designer made it that way isn’t a sensible alternative, because why would the designer make exactly the pattern expected from a branching evolutionary process when there is no functional reason to do so?

    I agree we cant quantify the probability only that ancestry is more likely as similarities increase as we have cases where we can establish ancestry.

    I’m sorry but that sentence does not convey any coherent meaning. What were you trying to say?

    In all these cases genetic similarity is extremely high. This is very different then the case between bacteria and humans.

    No there are still a substantial number of genes shared between humans and bacteria that are very similar. The genes of the translation system for example. Particularly ribosomal RNA and protein. But again, it is not merely about similarity. You keep not fathoming this elementary point. It is not merely about similarity. It is not merely about similarity. Are you equipped to understand those words?

    It is about the nesting hierarchical structure in the data. As in the nesting hierarchical structure in the similarities between different versions of the same genes from different species, is incredibly statistically significant. Why is that the case? That’s exactly what you would expect from a branching evolutionary process.

    Not only that, independent sets of data (different genes for example) corroborate the same hierarchy, as in the same groupings. The same tree. Also to an exceptional degree of statistical significance. Again exactly was one would expect from a branching evolutionary process.

    What, other than prior commitments to some conclusion you desperately want to be true, would explain this fact? You have absolutely no reason to expect a designer to make this the case as there is no functional reason for it. Which means you have to believe the designer is being deliberately deceptive, because it is hyper-astronomically unlikely that a design process just so happens by chance to produce that level of hierarchical structure in different sets of data, and even more unlikely that each independent set of data exhibits so significantly similar topologies.

    Bill, it is not merely about similarity. Okay? It is not merely about similarity.

  21. colewd
    Ignored
    says:

    Rumraket,

    Bill, it is not merely about similarity. Okay? It is not merely about similarity.

    How does the mechanism of reproduction explain the differences?

  22. Rumraket Rumraket
    Ignored
    says:

    colewd:
    Rumraket,

    How does the mechanism of reproduction explain the differences?

    For the inference of common descent, as in our ability to infer that common descent is a fact, it doesn’t even matter. We could be ignorant about that, and the fact that the similarities and differences exhibit nesting hierarchical structure, and that different sets of data corroborate the same nesting hierarchy, is still enough to show that common ancestry is a fact. This has also been explained to you countless times before.

  23. John Harshman John Harshman
    Ignored
    says:

    No matter how many times it’s explained, no matter how it’s explained, no matter who explains it, Bill will never, ever understand how we infer common descent and why we don’t have to know what causes mutations in order to do so. I speak from experience.

  24. colewd
    Ignored
    says:

    John Harshman,

    No matter how many times it’s explained, no matter how it’s explained, no matter who explains it, Bill will never, ever understand how we infer common descent and why we don’t have to know what causes mutations in order to do so. I speak from experience.

    I understand how you infer it. Rumraket calls it fact and Joe calls it 100% true. I respectfully believe these are unsupported claims.

  25. Corneel Corneel
    Ignored
    says:

    colewd: I understand how you infer it.

    Then could you explain, in your own words, how common descent is inferred?

  26. Corneel Corneel
    Ignored
    says:

    colewd: Rum: Bill, it is not merely about similarity. Okay? It is not merely about similarity.

    Bill: How does the mechanism of reproduction explain the differences?

    This made me smile.
    Looking at similarities and looking at differences are two sides of the same coin.

  27. Allan Miller
    Ignored
    says:

    colewd:
    Allan Miller,

    What does this have to do with the probability that two species share a common ancestor?

    Really? Do you think as 2 lineages diverge from a common ancestor the probability they share that common ancestor diminishes?

  28. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:
    Let’s try an HGT case study. Turn to page 294 in your hymn books (Futuyma, Evolutionary Biology 3rd Ed, Fig 10.24. There’ll be an original paper somewhere, but Futuyma points to a book by Li and Graur as his source). Here we see a case where an anomaly has been ascribed to HGT, in order to ‘save the theory’. A virogene is found in all Old World monkeys, and in some, but not all, cats.

    There are several factors to note.

    1) This is only an anomaly because it stands out against the rest of the genome, which largely conforms to simple phylogeny – the same phylogeny already broadly established on morphology alone. This is a point repeatedly stated and repeatedly blanked. Even if the virogene moved by ‘magic’, the rest of the genomes in which it sits appear to have been transmitted by vertical descent, because the data forms the hierarchic relations precisely expected from that mode of tranmission.

    2) Sequence analysis nests the virogene within the viruses. That is, we know it came from a virus because of the assumption of common descent. See, even anomalies aren’t all that anomalous!

    3) Once it transferred, presumably by an ancestor of the small cats catching a bug from a primate, this gene flows into the ‘vertical’ path of descent – it is a heritable change to the genome. And as such, it is a phylogenetic marker for that group. Once again, sequences that are anomalous at one level support common descent at another – because they are just another change, once integrated into the genome.

    Of course, I only think all this because of my metaphysical blinders. So, what should I think instead?

    You have pointed to a particular case where there is good evidence for HGT. But I have never claimed that HGT does not happen. I am saying that because there is evidence of HGT in certain cases of anomalous sequence similarity it should not be inferred in all anomalous cases. IMO to do so in cases where the evidence is lacking would only be done to save one’s preferred theory. That is my point.

    I’m sure you would agree that viruses are fascinating entities. I see life as a whole as being a unity, and that being the case the genetic information contained therein is all part of that unity. Viral transfer is a good way of exchanging information within that unity. Parts within the unity may be adversely affected by viruses but on the whole they have been doing more good than harm. Life is allowed to develop in a way that allows for the evolution of consciousness.

  29. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    colewd: Rumraket calls it fact and Joe calls it 100% true. I respectfully believe these are unsupported claims.

    The evidence for universal common descent being extremely strong, I accept it as true. I have not simply “assumed” that it is true — there actually is very strong evidence to that effect. Strong enough that I regard it as true.

    Given universal common descent, any question about whether, say, king salmon and monarch butterflies have a common ancestor is answered: they do have one, and we don’t have to ask how similar those two different species are. (*)

    The meaningful questions are whether particular sets of species are clades — say metazoans (multicellular animals). Those require more than statements about similarity.

    (*) Philosophy majors who want to quibble about how a true scientist never concludes that anything is absolutely true are invited to do so in a different thread, where I will not appear.

  30. CharlieM CharlieM
    Ignored
    says:

    Entropy:

    CharlieM:
    Here is an article which argues against the proposal that there are “master regulators” controlling development.

    That guy is making the same semantic mistake that you make. Mistaking the complexity of the machinery for what makes the difference between regulating one thing or another. The concept of a master gene is not that it works all by itself, but that it’s product makes the difference between regulating one thing or another. I do understand that in order for, say, the Bicoid protein to exert its regulatory effects, it combines with a bunch of other proteins (TFs), but it is the presence of Bicoid in the complex that provides the specificity for its binding to start a cascade of regulatory events behind cell differentiation

    Yes, the Bicoid is the first link in one specific chain, but the overall regulation is governed by the way the cell uses the materials, mixtures and compounds within it and being exchanged with its environment. The set up as a whole needs to be in organised balance in order for the cell to be viable and productive. There is no master builder among the termite population and likewise there is no master regulator within genes. A vital link is not the same thing as a master regulator. The power source of your TV is a vital link but it is not a master regulator.

  31. CharlieM CharlieM
    Ignored
    says:

    Entropy:

    CharlieM:
    It has been argued that this amount of TF binding events are due to opportunistic binding, but the article demonstrates that certain genes are specific targets for TF binding.

    There’s no contradiction here. The amount of events can be explained by the presence of opportunistic events, while there must be biologically more meaningful events in the mix as well. That’s what TFs are supposed to be about: specific targets. Otherwise there would be no regulation. What I don’t understand, is what you think this demonstrates. If anything, it makes my point: specific interactions are what I’m talking about, and a lot of the “complexity” we might see otherwise is just noise.

    Specific TF binding is achieved by complexes of genes working together. I used to think that transcription and other processes within cells were achieved by the required molecules coming together by chance because they were just floating around in the cell. But because of what I have read about active transport, microtubules, dynein motors, the packaging of DNA and such like, I have realised that this cannot be the case. The closer we look the more coordinated organisation we see.

    In the past we were told that junk DNA was just noise. This is turning out not to be the case.

    Here is just one piece of evidence for the coordination involved:

    These results therefore highlighted the possibility of coordinated binding by c-FOS and/or MITF with a subset of the shared TFs to mast cell-specific regulatory regions…

    One particular puzzling result was the observation that unlike with genes, where genome sequencing showed mammalian genomes to have far fewer genes than had been expected (Lander et al, 2001), TF binding events in many cases far exceeded expectations and commonly outnumber the total number of genes.

    And coordinated activity must have been the norm from the beginning of cellular life.

  32. CharlieM CharlieM
    Ignored
    says:

    Entropy:

    CharlieM:
    Genes don’t regulate themselves. The cell regulates its genes in a controlled way.

    Nothing you cite demonstrates such a thing. How can a cell regulate anything without the tools for such regulation? The tools are proteins, among them TFs. What are these TFs if not the products of genes? What do you think TFs are?

    Sticking with your metaphor I would say that the genes are the tools and the cell uses these tools to produce the materials needed for construction and maintenance. The proteins are the materials.

  33. Mung Mung
    Ignored
    says:

    Joe Felsenstein: My sympathies with you if you are too busy to find the 15 minutes that this would take.

    Well, if you put it like that …

    I really had no idea how long the discussion went on or how much I’d have to wade through. If it’s only 15 mins of my time I might be able to manage that. 🙂

  34. Mung Mung
    Ignored
    says:

    Allan Miller: Do you think as 2 lineages diverge from a common ancestor the probability they share that common ancestor diminishes?

    Only to the extent that they become more dissimilar as they diverge.

  35. Corneel Corneel
    Ignored
    says:

    CharlieM: Sticking with your metaphor I would say that the genes are the tools and the cell uses these tools to produce the materials needed for construction and maintenance. The proteins are the materials.

    I like to think of the genes as a pile of wet autumn leaves, the proteins as a group of Greek sirtaki dancers, and the cell as a smallish ball of pink cotton.

    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.

  36. Rumraket Rumraket
    Ignored
    says:

    CharlieM: Specific TF binding is achieved by complexes of genes working together.

    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.

  37. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:

    CharlieM: Is there a pattern of simple vertical descent in prokaryotes?

    Yes. I would particularly direct your attention to the curious nesting of mitochondria within or near the alpha proteobacteria. Have you encountered this phenomenon … at all … ever … perchance?

    From bacterio.net

    In contrast to eukaryotic nomenclature, there is no such thing as an official classification of prokaryotes because taxonomy remains a matter of scientific judgment and general agreement.

    Your statement above is another reason why the species concept while suitable for eukaryotes should not be applied in a similar fashion to prokaryotes. If what you say is true then eukaryote organisms are really a combination of eukaryote and prokaryotes making up one unified organism. Eukaryotes include prokaryotes and so much more.

  38. John Harshman John Harshman
    Ignored
    says:

    colewd: I understand how you infer it.

    No you don’t. You only imagine you do. I can tell the difference.

  39. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:
    Certainly a funny old world when people stop caring about the evolutionary relationships of multicellular eukaryotes, and instead fall back on “But … but … the prokaryotes”!

    Who are these people? We should put them straight 🙂

  40. CharlieM CharlieM
    Ignored
    says:

    Entropy:
    However, Charlie seems to mistake problems with establishing a phylogenetic vertical history to whether HGT happens. Since Charlie doesn’t think that HGT happens, then why would he quote from an article that talks about how HGT makes it hard to establish vertical histories for prokaryotes?

    The problem with this is that Charlie does think that HGT happens!

  41. CharlieM CharlieM
    Ignored
    says:

    Mung: Especially so because prokaryotes are just devolved eukaryotes.

    Prokaryotes are essential to earthly life in the same way that root systems are essential for the life of plants. They are the foundations that make higher forms of life possible. A vital link in the chain 🙂

  42. colewd
    Ignored
    says:

    Joe Felsenstein,

    The evidence for universal common descent being extremely strong, I accept it as true. I have not simply “assumed” that it is true — there actually is very strong evidence to that effect. Strong enough that I regard it as true.

    I think that some of the evidence is strong and some of the evidence is weak. For universal common descent to be a valid inference all the evidence has to be strong.

    I am much more confident that you and I share a common ancestor then a salmon and a butterfly share a common ancestor. Your position is that they are equally probable and that goes against reasonable intuition in my opinion as there are many more differences to explain.

  43. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:

    CharlieM,

    So what controls the pattern of Sry expression?

    ?

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

    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.

  44. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:
    CharlieM,

    So how come that echolocation’s molecular similarity was not ascribed to HGT?

    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.

  45. CharlieM CharlieM
    Ignored
    says:

    Corneel: What unites the cells in an organism is not, as you previously claimed, the potential to exchange genetic material, but a shared genetic interest; they all are closely related and carry (nearly) the same genome. That close genetic relationship is what makes the division of labour profitable in evolutionary terms

    Profitable for what?

  46. Entropy Entropy
    Ignored
    says:

    CharlieM: The problem with this is that Charlie does think that HGT happens!

    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.

  47. Entropy Entropy
    Ignored
    says:

    CharlieM:
    Sticking with your metaphor I would say that the genes are the tools and the cell uses these tools to produce the materials needed for construction and maintenance. The proteins are the materials.

    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!”

  48. Allan Miller
    Ignored
    says:

    CharlieM: You have pointed to a particular case where there is good evidence for HGT. But I have never claimed that HGT does not happen. I am saying that because there is evidence of HGT in certain cases of anomalous sequence similarity it should not be inferred in all anomalous cases. IMO to do so in cases where the evidence is lacking would only be done to save one’s preferred theory. That is my point.

    It is a strawman of a point. People don’t fall back on HGT where evidence is lacking.

    And don’t forget the nested hierarchy. My choice of the cat/baboon story was to illustrate the point that HGT was inferred from the evidence, and sticks out as an ‘anomaly’ precisely because of its discordance with the predominant signal: that of common descent among the cats and among the primates.

    Can you actually back up your suppositions and think of an unjustified inference of HGT?

  49. Allan Miller
    Ignored
    says:

    Mung: Only to the extent that they become more dissimilar as they diverge.

    So no, then.

  50. Allan Miller
    Ignored
    says:

    CharlieM: Me: Yes. I would particularly direct your attention to the curious nesting of mitochondria within or near the alpha proteobacteria. Have you encountered this phenomenon … at all … ever … perchance?

    Charlie: Your statement above is another reason why the species concept while suitable for eukaryotes should not be applied in a similar fashion to prokaryotes. If what you say is true then eukaryote organisms are really a combination of eukaryote and prokaryotes making up one unified organism. Eukaryotes include prokaryotes and so much more.

    But the mitochondria nest within the alpha proteobacteria. Archaeal relations are a bit less solid, but the bacterial component isn’t. You Google up things you don’t even understand in support of your contention. You are using the tangled roots of the prokaryotes bush/tree to support a contention that NO relationships can be inferred from analysis of prokaryotes. Which would preclude all bacterial taxonomy and, indeed, sequence analysis in epidemiology. That would be plain hogwash. So why do the tangled roots of the entire bacterial clade have any bearing here?

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.