Calling Spade out of phylogenetics

by bohm 16 Replies latest jw friends

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  bohm

  Spade wrote on this thread: http://www.jehovahs-witness.net/watchtower/bible/206699/3/The-Gentile-Times-Reconsidered

  Although phylogenetic trees produced on the basis of sequenced genes or genomic data in different species can provide evolutionary insight, they have important limitations. They do not necessarily accurately represent the species evolutionary history.The data on which they are based is noisy; the analysis can be confounded by horizontal gene transfer, hybridisation between species that were not nearest neighbors on the tree before hybridisation takes place, convergent evolution, and conserved sequences.

  I would characterize myself as someone with more than a working knowledge in this field, given i have developed my own algorithm for doing something similar. In other words, i am happy to meet a person who is apparently willing to question the consencus. In my oppinion your critique miss the point completely, and phylogenetic reconstruction remain one of the most definite evidence in favor of evolution because it is highly quantifiable.

  It is quite true what you highlight; the data is noisy and the posterior will reflect the noise. Said in another way, the model will fit the data rather poorly. In other words, the noise has the effect of discrediting a phylogenetic model compared to other models, eg. a model based on biblical kinds. Thus it become even more remarkable the various phylognetical reconstructions, based on different kind of genetic data, agree to such a high degree, and that they do not favor a biblical kind-like modelling hypothesis.

  Furthermore quantizing the effect of HGT, conserved sequences, etc. is ofcourse a field of study which is being persued agressively, see eg.

  Identification of Horizontal Gene Transfer from Phylogenetic Gene Trees http://www.springerlink.com/content/w22575448864j5mu/

  If you object on the grounds that phylognetic reconstruction has not been tested against a biblical kinds-like hypothesis, i would suggest you look at this nature paper:

  http://xcelab.net/rm/wp-content/uploads/2010/03/common-ancestery-AIC-test-paper.pdf

  (http://www.nature.com/nature/journal/v465/n7295/full/nature09014.html)

  where the assumptions are tested against each other using standard measures of model comparison. i would like you to quantify exactly what effects invalidate their result, specifically which noise effects there is in the data which favor a phylogenetic tree over a (true) biblical kinds-like model (which are the two they test against each other).

  As it is now you seem to explain away an effect by an argument which (if it is true) make the effect even more remarkable. I wonder if you are aware of that.

  I would also briefly note that once again we are in the situation that science has provided a testable, falsifiable hypothesis which it support with an immense statistical material of different kinds, where it does not seem that you even provide a hypothesis. What kind of statistical work on phylogenetics would in your oppinion discredit the biblical kind-model?

  ps.

  Since you mention HGT, are you saying the sequences in the human genomen which look like retroviral insertions or other HGT effects actually are retroviral insertions or other HGT effects? im ofcourse asking because if this is the case, one do have to wonder why they appear in a way which exactly support the evolutionary history; and if it is not the case, I do wonder how you can use eg. retroviral insertions and other HGT effects to discredit evolution when you have not believed these events have occured in the first place; to me it seem a bit like saying the sky is blue because the pixies i dont believe in painted it blue, but i dont want to put words in your mouth...
• 

  bohm

  juuuhuuu spade!

  one may get the idea you just copy-pasted some random crap you didnt really understand :-).
• 

  Mary

  bohm, Spade (who is just Alice.in.wonderland reincarnated) has absolutely no interest in openly debating any subject that requires rational thinking. She's a pathetic moron who has nothing better to do in life than to troll ex-JWs sites with her ridiculous cut-and-pastes that she gets from the Craptower's on-line library.

  On a previous thread done while she was still posting as Alice.in.wonderland, she actually started arguing with one of the lawyers who had worked on the lawsuit against the Organization (for protecting pedophiles) that was eventually settled. When your mental faculties are so screwed up that you pretend to know more about a case than one of the lawyers involved, then that's pretty much a clear sign that you are not capable of rational reasoning.

  So you won't want to hang from the end of a rope waiting for Spade/Alice to reply to your challenge in any sort of normal fashion (other than her possibly doing another useless cut and paste that won't answer any of your questions.)
• 

  Heaven

  Booyah, bohm! Thanks for posting this. While Mary is spot on about Spade (AIW reincarnated), I think it is vitally important for those who are in the know to call these glue sniffers out. So thanks for this bohm because it shows lurkers just how wacked these certain posters are.
• 

  bohm

  Mary, haha, classic spade :-). this troll is such a pathetic case. i have a picture of spade as the kind of person who has no positive interaction with anyone and copy-pasting drivel is the only way to get social interaction.

  at a previous encounter with Spade (in another incarnation, cant remember which one) i asked him/her if a direct quote from the watchtower was true or not. Spade/whatever refused to answer, calling it a loaded question (3 times no less!). Her response to TD on todays thread fall into the same catagory: i wont answer because it will make me look bad.

  so, well, i dont have any illusions of getting a coherent answer :-). Im just having a bit of fun, and i think the nonsense spade spewed should not go unanswered.
• 

  jookbeard

  thanks for your hard work Bohm I've certainly learnt from your articles.
• 

  TheStumbler

  Have any WT publications addressed ERVs and phylogenetic evidence for evolution?
• 

  TheStumbler

  In fact, is there any Creationist rebutal of these lines of evidence?
• 

  bohm

  TheStumpler: Well, its been a while since i read AIG but i believe the typical creationist rebuttal is (first and foremost)

  "Same designer implies similar design"

  Basically whenever something is found which is to suspicious, it is claimed that was the way God made it.

  As for retroviral insertions, another favorite tactic is to find a retroviral insertion where at least part of the insertion does something usefull (which is, ofcourse, entirely compatible with evolution). From this single instance a vague remark is made which sort of implies all retroviral insertions which has not been directly observed to occur could really just be how God made the DNA in the first place.

  The funny part of these objections is that it does not change the fact this is evidence in favor of evolution over creation at all. at most (if the arguments was not so obviously post-hoc) it would change the significance of the evidence somewhat.

  I think Spade actually gave the AiG response to statistical modelling.. she should properly have sprinkled it with implying the scientists who build the models are biased in favor of evolution and somehow cheat. ofcourse the objection only work if one has no clue what is going on, but i would hardly be a first for Ken Ham.

  if there are more sofisticated arguments i dont recall hearing them. its all set to the tune: "it COULD be your wrong and it COULD be i am right, therefore the earth COULD be flat!", while doing nothing to actually study what the majority of the evidence strongly suggest.
• 

  TheStumbler

  The problem with the common designer argument, as I'm sure you are aware, is that any conceivable reality is consistent with design so the idea is not testable.

  I heard the analogy that ERVs are like plagarism. It is possible, although unlikely, that two writers produce remarkably similar pieces of work independant of each other. However, if both pieces of work contain the same typos, formatting errors and spelling mistakes then this strong evidence that both pieces of work share a common origin - plagarism. It is unlikely that a designer would repeat the same mistakes in exactly the same places when creating different kinds. I suppose, you could argue that like how a car manufacter uses common components in diferent models of cars a designer might use common DNA segments and so mistakes are duplicated across different kinds.

  Dont retroviral insertions effectively act as random mutations though, as far as evolutionary selection is concerned, so the fact that some serve a function is really just further evidence for evolution...

  I was just wondering if there were any strong creationists arguments against ERVs.