Re: Stereotypes and reputations

Pim:

The fossil data from the Cambrian Explosion shows a morphological explosion. You may appeal to what we may find out someday. That is not falsifiable. But the data that we have in hand right now indicates a morphological explosion which is not consistent with evolution. Nor is it consistent with common descent unless your version of common descent involves pulling rabbits out of hats. A friend of mine took a university biology course. After the "evidences for evolution" lectures he spoke with the professor, asking about all the weaknesses. The professor responded that the evidence would be clarified in the future. You write:

"morphological explosion may fall well within the paradigm of Darwinian/evolutionary theory"

Right. So science is now open to raw speculation about future findings that will fall in our lap favoring our theory. Imagine if a creation researcher said something like this. You write:

"I am not sure why such ignorance should pose a problem to Darwinian theory.

So counter evidences are not problems with the theory but with our understanding. Actually, the state of our knowledge is not quite so mediocre. The problems with evolution and CD are from knowledge, not ignorance. Your argument that better evidence will be forthcoming is an argument from ignorance. You write:

"Woese argues for massive HGT followed by clearly identifiable common descent."

Woese rightly identifies problems throughout the evolutionary tree: "Phylogenetic incongruities can be seen *everywhere* in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves" -- Woese, "The Universal Ancestor," PNAS 95:6854, 1998.

Regarding the Ouzounis paper, they set up an algorithm to model something like Woese's idea and found they needed a special kind of HGT with vines and hubs with rapid transfer abilities. It is true that Woese envisioned massive HGT initially, but then the HGT was to taper off as those early cells rapidly evolved. The Ouzounis group's results may not match closely what Woese envisioned, but that doesn't solve the problem. The Ouzounis group needed to have a non traditional community of cells with vines and hubs conducting a sort of HGT we have never observed. Others have tried equally creative models (Rivera and Lake have used a ring topology). I'm not saying evolutionists cannot dream up solutions to this, given all the powers of their imagination and the freedom to ignore empirical constraint and to overlook the usual group of outliers in their fits. My point is simply that this is what they are forced to do to fit the data.

Regarding phylogenetic mismatches you feel these are minor, often resolved, and outweighed by the matching data. This is simply not true. Mismatches are not typically resolved. If anything they are becoming increasingly apparent. Have you ever looked at any of the problematic sequences? They're not going to be resolved without creative HGT-type stories. And they are by no means minor. The mitochondria mismatches are huge. ORFans constitute something like 10-20% of the genes (and this happens for variants within the same species). The photosynthetic bacteria study used something like 188 genes.

You wondered why non homologous development patterns that make utterly no sense on common descent. Because you wouldn't expect a speciation event to produce two highly similar species, yet their similar designs arise from *different* embryonic development pathways or different genes. Similar designs, in congeneric species, would be expected to arise from the same genes and development pathways. But this prediction is routinely violated.

You also see no problem with detailed designs evolving independently. After all, similar solution can be found by natural selection right? Wrong. Why would we expect natural selection to locate the same design twice, in a huge design space, starting from different initial conditions, and in different environments? This doesn't make sense according to evolution. Remember, play the tape twice and you get different species. It is all about random events and contingencies. Why would the squid and human eyes be so similar, for example, when the conditions are so different? Indeed, one of the major arguments for common descent are the similarities between species. They are supposed to have been inherited from a common ancestor. But why should we believe this if you are now saying that these similar designs arise independently so readily?

Note also the HERVs and UCEs that make no sense on common descent? There is the homologous provirus found in chimps, bonobos and gorillas but not humans; and the homologous provirus mysteriously not found in chimps and gorillas. Common descent needs some clever explanations for how these patterns arose. Likewise for the identical UCEs (ultra conserved sequences) such as between mouse and human. I would have thought Theobald would have found functionally unconstrained yet conserved sequences to falsify common descent. I guess not ...

--Cornelius

  ----- Original Message -----
  From: Pim van Meurs
  To: Cornelius Hunter
  Cc: asa@calvin.edu
  Sent: Saturday, July 30, 2005 8:58 PM
  Subject: Re: Stereotypes and reputations

  Cornelius Hunter wrote:
    Pim:

    The problems with common descent are not minor issues that can be glossed over. I recall speaking with an evolutioniist about abruptness in the fossil record (Cambrian explosion, etc.). She said she did not think that constituted evidence against the theory. So there was no evidence against evolution. Do you see the problem here?

  The Cambrian explosion, while to some, may have appeared problematic to Darwinian theory (Darwin himself acknowledged it), more and more evidence shows that what appears to be a morphological explosion may fall well within the paradigm of Darwinian/evolutionary theory. In fact, the evidence of common descent extends through the Cambrian.

    If one cannot admit to what are clear counter indications, then there is a problem. Woese is not saying that HGT explains early life. He is appealing to a far more aggressive explanation -- HGT on a massive scale -- nothing like it has ever been observed. You also have understated Doolittle, who is one of the early evolutionists to admit to what the data say: the tree model doesn't work very well. You wrote:

  Again this is misleading. There are indications of a problem namely our ignorance of the exact circumstances surrounding the Cambrian explosion. I am not sure why such ignorance should pose a problem to Darwinian theory. Would it not pose a problem to any theory? Woese argues for massive HGT followed by clearly identifiable common descent. Woese's claims hardly seem to be problematic for common descent, although it does pose a problem to extract horizontal versus vertical gene transfer. And yet recent studies have quantified this and found for a set of bacteria that horizontal gene transfer accounts for a relatively small amount of the variation compared to the vertical transfer. The reason why Doolittle states that tree model does not work very well is because of the horizontal transfer, a tree needs to have additional links.
  Once more research becomes available science resolves many of these 'problems' quite easily.

  See
  http://www.pandasthumb.org/archives/2005/07/carl_zimmer_tan.html
  The net of life: Reconstructing the microbial phylogenetic
  network Victor Kunin1, Leon Goldovsky, Nikos Darzentas and Christos A.
  Ouzounis

  [quote]
  Abstract:It has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (HGT) events. Yet, all phylogenetic reconstructions so far have presented microbial trees rather than networks. Here, we present a first attempt to reconstruct
  such an evolutionary network, which we term the "net of life." We use available tree reconstruction methods to infer vertical inheritance, and use an ancestral state inference algorithm to map HGT events on the tree. We also describe a weighting scheme used to estimate the number of genes exchanged between pairs of organisms. We demonstrate that vertical inheritance constitutes the bulk of gene transfer on the tree of life. We term the bulk of horizontal gene flow between tree nodes as "vines," and demonstrate that multiple but mostly tiny vines interconnect the tree. Our results strongly suggest that the HGT network is a scale-free graph, a finding with important implications for genome evolution. We propose that genes might propagate extremely rapidly across microbial species through the HGT network, using
  certain organisms as hubs.
  [/quote]

      That there are problems with morphological and molecular data does not mean that there is no common ancestry. It merely shows that resolving difficulties may be hard. Again, the argument common ancestry is wrong because two methods disagree, is hardly sufficient.

    Unfortunately this is always the explanation, and it makes common descent unfalsifiable.

  Not at all. Common descent would be easily falsifiable. THe problem is that some look at minor/major disagreements about mechanisms and their relative importance as evidence of a larger problem namely that of common descent being wrong

    With every problem, one hears, "well, that doesn't mean the theory is wrong." So here we have all kinds of incongruities -- phylogenetic mismatches abounding.

  Compared to the matching data, the mismatches are in most cases quite minor and often resolve themselves when more accurate data becomes available.

    Non homologous development patterns that make utterly no sense on common descent.

  Why not?

    Detailed designs evolving independently over and over.
  Again no problem for evolutionary theory, once you realize that it is not surprising for similar solutions to be found by natural selection.

    Did I mention fundamental differences at the DNA level where common descent predicts there should be none (proteins involved in DNA replication)?

  Again, you need to be more specific. Where was this prediction made and what evidence was found?

    And of course that little problem that we have no idea how these designs could are arisen. Sure, one can always contrive just-so stories. How many different evidential problems, from how many different angles, do we need before we acknowledge problems? You mentioned, Douglas Theobald's site -- this is yet another problem with talkorigins. That page is problematic. You wrote:

  I agree that the page IS problematic for those arguing against common descent as Douglas has described a wealth of data establishing common descent beyond much reasonable doubt.

      Convergence is also not necessarily a problem for common descent. Nor are ORFans for instance. We should not let our ignorance lead us astray from the solid evidence in favor of common descent.

    I'm sorry but this is not tenable. ORFans and massive convergence not problems? This is a joke right?

  Not at all. Please explain why you believe that these are problems to Darwinian theory or common descent? It may be tempting to reject the vaste amounts of data supporting common descent because of some minor issues, most of them due to our ignorance. Once you realize that evolution is 'constrained' by environment, laws of nature. mechanical constraints etc, finding convergence becomes far less an issue.

  Although convergence may make recovering accurate trees more difficult, it should not be considered a major problem for common descent/.
Received on Sun Jul 31 03:44:36 2005