Whoaaaaa! take a dekko at this

[reen12]

quote: EnterTheBowser

In other words, it seems a little premature to reject a naturalistic explanation of abiogenesis.

I don’t know as it’s a question of out-right “rejecting.”
[And I think you’re correct, in employing the term
“premature.”] I’m willing to…wait.

Still, it was the seeming “premature” treatment of this theory
as fact, that I found troubling.

“abiogenesis” = biological life ‘generated’ through inanimate substances. [correct?]
If that *does *end up to be the case, I will be…stunned.

From what I’ve read - and from presentations I’ve viewed -
[which constitute a small fraction of the type of material I’m
usually occupied with] abiogensis seems…unlikely.
Still, as I said, I’ll continue to follow this theory, with
interest.

Thanks for your thought,

reen12

BTW, I once saw a presentation on how sediment is
laid down…and the effect this has on “dating” objects.
It was a startling reality, I thought. {But then, there
are those who might claim that I “startle” - easy.]

 

[itsjustdave1988]

it seems a little premature to reject a naturalistic explanation of abiogenesis.

I don’t reject it, but understand it for what it is… a postulate. One can certainly reconcile aspects of evolutionary postulates with Catholic teaching. However, must I?

Whether I accept or reject this postulate has little to do with the field of science I work in, which is space operations. In fact, the search for life elsewhere leads me to believe this postulate is at least dubious, as I would think our nearest celestial body, the moon, would be teeming with at least some kind of life. Yet, evidence of life elsewhere is lacking, as of yet, which makes the earth an “extreme outlier” with respect to random distributions of the celestial bodies in our neighborhood. My math brain doesn’t like inferring that extreme outliers are caused by random processes. I look instead for Gaussian distributions when processes are governed by random chance. I look instead for another celestial body similar to earth (either more or less lively, but still close in the distribution).

Granted, space is big (we learned that in Space 101) So perhaps earth is quite similar to many other worlds out there. It’s just that this too is a postulate which all available evidence seems to contradict (thus far). But the search for ET continues.

PS. I worked in NORAD and while the “stargate” makes for good science fiction, we don’t really have one.

 

[reen12]

quote: itsjustdave

I don’t reject it, but understand it for what it is… a postulate.

Preee-cisely.

reen12

 

[hecd2]

itsjustdave1988:

hec2d,

I asked: “is this still a postulate as of yet untested?” I’ll assume your lack subterfual reply to mean that it is still a postulate as of yet unproven by controlled experimentation.

I really don’t know why I bother.

Just for a moment there I thought you were genuinely interested in sharing ideas like real scientists do, but I was disappointed. As it turned out, you weren’t actually interested in exploring how systematists and cladists work out phylogenies, divergence dates, population sizes, population dynamics, and ancestral sequences by using extant molecular sequence data. You weren’t really interested in figuring out how your expertise in designing GAs might be combined with phylogenetic models to determine ancestry and evolutionary trees of your GAs, and to use that as an an illuminating analogue of the biological situation. You just weren’t interested in adding your special expertise to that of the biological scientists to perhaps bring out something new.

No, sadly, you were just out make a point. Basically you are setting your inability to determine which GAs have which ancestors using your naive superficial approach, against a branch of science that has been developed by hundreds of scientists who have dedicated their life studies to it over decades. Don’t you think it would be rather grand to learn something about phylogenetic inference and cladistics rather than just to ridicule them? You are a smart guy; wouldn’t it be so much more fulfilling to contribute to this endeavour, rather than to deny it a priori?

Please surprise me by a unexpected willingness to actually look at the science. For you and for anyone else who reads this who has a genuine desire to learn I’ll post some sources anyway. Hie thee to a library. You know, there is no shame in not knowing about these technical things, but I think there is shame in taking an entrenched poition without really understanding the science.

First of all, here are some reference books and an on-line paper that explain how biologists use genomic data from different species to work out family trees:

Holder, M. T. and P. O. Lewis. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews Genetics 4:275-284, 2003
**tinyurl.com/7vyaq

**
Felsenstein, J,. Inferring Phylogenies Sinauer Associates, Sunderland, Massachusetts, 2004

(Felsenstein is one of the early key figures in this branch of science, along with the great Luigi Luca Cavalli-Sforza)

Graur, D. and W.-H. Li. Fundamentals of Molecular Evolution, second edition. Sinauer Associates, Sunderland, Massachusetts, 2000

Page, R. D. M. and E. C. Holmes. Molecular Evolution: A Phylogenetic Approach. Blackwell Science, Oxford, 1998

Salemi, M. and A.-M.Vandamme The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny. Cambridge University Press, 2003

TO BE CONTINUED

 

[hecd2]

CONTINUATION

Next, specifically to your challenge of whether phylogenetic methods have been verified, all of these papers below contain simulation tests of phylogenetic algorithms against absolute measures and against one another for accuracy (do they recover the actual tree?) and robustness (is the accuracy independent of errors in the assumptions?) (the approaches being neighbour joining, maximum parsimony, minimum evolution, and maximum likelihood techniques with bootstrapping or jack-knife analysis to determine confidence; or Bayesian techniques based on Markov chain Monte Carlo analysis which are becoming more common):

Hillis, D. M. and J. J. Bull. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192, 1993

Hillis, D.M., J. P. Huelsenbeck and C. W. Cunningham. *Application and accuracy of molecular phylogenies. *Science 264:671-677, 1994

Huelsenbeck, J. P. The performance of phylogenetic methods in simulation. Systematic Biology 44:17-48,1995

Takahata N. and Y. Satta, Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences. Proc Natl Acad Sci USA 94:4811-4815, 1997

Huelsenbeck, J. P., F. Ronquist, R. Nielsen and J. P. Bollback Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314, 2001

Kishino, H. J. L. Thorne, and W. J. Bruno Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352-361, 2001

Arbogast, B. S., S. V. Edwards, J. Wakeley, P. Beerli and J. B. Slowinski. Estimating divergence times from molecular data on population genetic and phylogenetic time scales. Annual Review of Ecology and Systematics 33:707-740, 2002

Alfaro M. E., S. Zoller and F. Lutzoni Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20(2):255-266, 2003

Douady C. J., F. Delsuc, Y. Boucher, W. F. Doolittle and E. J. P. Douzery. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20(2):248-254, 2003

Zwickl, D. J. and M. T. Holder, Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst. Biol. 53:877-888, 2004

Sullivan, J., Z. Abdo, P. Joyce and D. L. Swofford, Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Mol. Biol. Evol. 22:1386-1392, 2005

Brookfield, Evolutionary forces generating sequence homogeneity and heterogeneity within retrotransposon families, Cytogen Gen Res 110, 383 - 391, 2005

Now you or anyone else can look these up for yourself, or you can ask me and I’ll do my poor best to explain what any one of these papers say. But, for heavens sake, don’t give us the “I can’t distinguish GA ancestry so all of phylogenomics is phooey and speculation” line. And perhaps there are others on this thread who would like to learn some real science too.

Alec
evolutionpages.com

 

[Anguirus]

“Faith is a disease…just look at Northern Ireland or the Middle East”
Or the sisters at work in Calcutta, or the Missionaries in Africa and Latin America, or Pope John Paul II or…oh.

 

[itsjustdave1988]

No, sadly, you were just out make a point.

Actually, I was hoping for a straight answer about experimental evidence that have tried to test the postulate, and instead I got from you: “The grand experiment of molecular biology.”

Your second attempt is at least more substantial. However, I was interested more in experiements using computer simulations, where offspring analysis is conducted by “experts,” to show that one can reasonably predict common ancestry verses common design in a contolled experiment.

 

[reen12]

hecd2

And perhaps there are others on this thread who would like to learn some real science too.

Perhaps. And perhaps some of the readers of the
thread have other interests - that fill their lives with
satisfaction and meaning, and thus would reluctantly
decline your offer of - instruction.

Additionally, before I accepted such instruction, I would want
the timely (name removed by moderator)ut - of other experts -in terms of any real science
presented - who might also offer a critique of the material
you’ve referrenced:

quote: hecd2

Hillis, D. M. and J. J. Bull. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192, 1993

Hillis, D.M., J. P. Huelsenbeck and C. W. Cunningham. *Application and accuracy of molecular phylogenies. *Science 264:671-677, 1994

Huelsenbeck, J. P. The performance of phylogenetic methods in simulation. Systematic Biology 44:17-48,1995

Takahata N. and Y. Satta, Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences. Proc Natl Acad Sci USA 94:4811-4815, 1997

Huelsenbeck, J. P., F. Ronquist, R. Nielsen and J. P. Bollback Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314, 2001

Kishino, H. J. L. Thorne, and W. J. Bruno Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352-361, 2001

Arbogast, B. S., S. V. Edwards, J. Wakeley, P. Beerli and J. B. Slowinski. Estimating divergence times from molecular data on population genetic and phylogenetic time scales. Annual Review of Ecology and Systematics 33:707-740, 2002

Alfaro M. E., S. Zoller and F. Lutzoni Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20(2):255-266, 2003

Douady C. J., F. Delsuc, Y. Boucher, W. F. Doolittle and E. J. P. Douzery. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20(2):248-254, 2003

Zwickl, D. J. and M. T. Holder, Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst. Biol. 53:877-888, 2004

Sullivan, J., Z. Abdo, P. Joyce and D. L. Swofford, Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Mol. Biol. Evol. 22:1386-1392, 2005

Brookfield, Evolutionary forces generating sequence homogeneity and heterogeneity within retrotransposon families, Cytogen Gen Res 110, 383 - 391, 2005

I will wait to see if your kind offer receives a response.

Best,

reen12