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Switch to Forum Live View Phylogenetic analysis -- no separate "kinds"
2 years ago  ::  Apr 27, 2012 - 1:10PM #1
lucaspa
Posts: 557

DM Hillis, Biology recapitulates phylogeny, Science (11 April) 276: 276-277, 1997.  Primary articles are JX Becerra, Insects on plants:  macroevolutionary chemical trends in host use.  Science 276: 253-256, 1997; VA Pierce and DL Crawford, Phylogenetic analysis of glycolitic enzyme expression, Science 276: 256-259; and JP Huelsenbeck and B Rannala, Phylogenetic methods come of age:  testing hypotheses in an evolutionary context. Science 276: 227-233, 1997.


Phylogenetic analysis is based on the analysis of DNA sequences, and thanks to new technology of automated DNA sequencers and supercomputers, now large data sets of of hundreds or thousands of DNA sequences, each of which has thousands of nucleotides, are now routinely being analyzed.


"As phylogenetic analyses became commonplace in the 1980s, several groups emphasized what should have been obvious all along:  Units of study in biology (from genes through organisms to higher taxa) do not represent statistically independent observations, but rather are interrelated through their historical connections."

Everyone look at that quote carefully.  A deduction of creationism is that at least some groups (kinds) must be "statistically independent observations".  That is the "barrier" between kinds.  A barrier that prevents one kind from becoming another kind thru "descent with modification" is going to give you a "statistically independent observation" from every other DNA sequence of that gene or sets of genes. 

OTOH, if evolution happened (the "goo to you"), then all taxas will be "interrelated through their historical connections". 

The results from analyzing large sets of DNA sequences (and not just between polar and brown bears, but between humans, corn, rats, salamanders, alfalfa, E. coli, etc) show that ALL taxa are "interrelated by historical connections".  Creationism falsified, evolution supported.

"If sound science appears to contradict the Bible, we may be sure that it is our interpretation of the Bible that is at fault."  Christian Observer, 1832, pg. 437

"Christians should look on evolution simply as the method by which God works."  James McCosh, theologian and President of Princeton, The Religious Aspects of Evolution, 2d ed. 1890, pg 68.
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2 years ago  ::  Apr 27, 2012 - 3:27PM #2
MMarcoe
Posts: 14,684

Creationists will go through hell and high water to put a spin on all this so that their kinds can stay fixed. We can show them all we want how interrelated everything is, but they'll come up with some spin.


Their spins are growing increasingly thin and pathetic. It's just a matter of time before they have no choice but to give up and accept the truth.


 

There are three sides to every story: your side, my side, and the truth.

God is just a personification of reality, of pure objectivity.
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2 years ago  ::  Apr 28, 2012 - 8:32AM #3
rsielin
Posts: 3,933

Apr 27, 2012 -- 1:10PM, lucaspa wrote:


DM Hillis, Biology recapitulates phylogeny, Science (11 April) 276: 276-277, 1997.  Primary articles are JX Becerra, Insects on plants:  macroevolutionary chemical trends in host use.  Science 276: 253-256, 1997; VA Pierce and DL Crawford, Phylogenetic analysis of glycolitic enzyme expression, Science 276: 256-259; and JP Huelsenbeck and B Rannala, Phylogenetic methods come of age:  testing hypotheses in an evolutionary context. Science 276: 227-233, 1997.


I would be interested if you could provide any links outside the subscription wall on these. I appreciate the real science you have been expressing on this forum. 


Phylogenetic analysis is based on the analysis of DNA sequences, and thanks to new technology of automated DNA sequencers and supercomputers, now large data sets of of hundreds or thousands of DNA sequences, each of which has thousands of nucleotides, are now routinely being analyzed.


Just as Galileo's new telescope technology created an explosion of knowledge about our place in the universe, so will the new technology of genome sequencing create an explosion of new knowledge in evolutionary biology. Though you have correctly stated that creationism has been falsified (by Christians, no doubt) since 1831, this new technology will be the stake in the heart of our vampire creationist of today.  


... if evolution happened (the "goo to you"), then all taxas will be "interrelated through their historical connections".  


The results from analyzing large sets of DNA sequences (and not just between polar and brown bears, but between humans, corn, rats, salamanders, alfalfa, E. coli, etc) show that ALL taxa are "interrelated by historical connections".  Creationism falsified, evolution supported.


Our creationists here cannot understand the implications of the empirical evidence you have highlighted here. The science is way over their heads to grasp. If any respond at all there will be no academic discourse, expect taunts and insults, then a hissy fit or two, then a personal threat and promise of eternal damnation. That's been the pattern for the years I've been involved here.


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2 years ago  ::  Apr 28, 2012 - 1:20PM #4
iamachildofhis
Posts: 10,000

Apr 28, 2012 -- 8:32AM, rsielin wrote:



lucaspa: DM Hillis, Biology recapitulates phylogeny, Science (11 April) 276: 276-277, 1997.  Primary articles are JX Becerra, Insects on plants:  macroevolutionary chemical trends in host use.  Science 276: 253-256, 1997; VA Pierce and DL Crawford, Phylogenetic analysis of glycolitic enzyme expression, Science 276: 256-259; and JP Huelsenbeck and B Rannala, Phylogenetic methods come of age:  testing hypotheses in an evolutionary context. Science 276: 227-233, 1997.


rseilin: I would be interested if you could provide any links outside the subscription wall on these. I appreciate the real science you have been expressing on this forum.



iama: Here is an abstract for one of the above articles:


Science
Vol. 276 no. 5310 pp. 256-259
DOI: 10.1126/science.276.5310.256

  • Report

Phylogenetic Analysis of Glycolytic Enzyme Expression


  1. D. L. Crawford


+ Author Affiliations


  1. Department of Organismal Biology and Anatomy, University of Chicago, 1027 East 57 Street, Chicago, IL 60637, USA.



Abstract


"Although differences among species in enzyme maximal activity or concentration are often interpreted as adaptive and important for regulating metabolism, these differences may simply reflect phylogenetic divergence. Phylogenetic analysis of the expression of the glycolytic enzymes among 15 taxa of a North American fish genus (Fundulus) indicated that most variation in enzyme concentration is due to evolutionary distance and may be nonadaptive. However, three enzymes’ maximal activities covary with environmental temperature and have adaptive value. Additionally, two pairs of enzymes covary, indicating coevolution. Thus, metabolic flux may be modulated by many different enzymes rather than by a single rate-limiting enzyme."



iama:  Obviously, there is ongoing research, and, currently, speculations... indicating new hypothesis-testing is required to validate the evolutionary speculations.


The use of the term "may" indicates the, currently, speculation aspect of this Abstract.



"Phylogenetic" is an evolution-based-speculation-arena, where the evolution-presuppositioned-scientists are researching in hopes of finding evidence for their paradigm.  Again, note the use of the speculation-terms, for example, "may," "regarded as," "represents a hypothesis," "are assumed to have occurred," etc.:


Construction of a phylogenetic tree


Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, hybridize together, or terminate by extinction. This may be visualized in a phylogenetic tree.


The problem posed by phylogenetics is that genetic data are only available for living taxa, and the fossil records (osteometric data) contains less data and more-ambiguous morphological characters.[6] A phylogenetic tree represents a hypothesis of the order in which evolutionary events are assumed to have occurred.


Cladistics is the current method of choice to infer phylogenetic trees. The most commonly-used methods to infer phylogenies include parsimony, maximum likelihood, and MCMC-based Bayesian inference. Phenetics, popular in the mid-20th century but now largely obsolete, uses distance matrix-based methods to construct trees based on overall similarity, which is often assumed to approximate phylogenetic relationships. All methods depend upon an implicit or explicit mathematical model describing the evolution of


characters observed in the species included,


and are usually used for molecular phylogeny, wherein the characters are aligned nucleotide or amino acid sequences." - wiki


iama: NOTE that the "characters observed in the species included" is where the actual science-observations are taking place.  From the observed "characters" the grand "leap of faith" takes place and the "tree of life" is speculated / built as a diagram to convince the world's gullible.


.


The wonder of Christmas is that the God Who dwelt among us, now, can dwell within us. - Roy Lessin
.
"Father, forgive them for they know not what they do."
.
Justice is receiving what you deserve.
Mercy is NOT receiving what you deserve.
Grace is receiving what you DO NOT deserve.
.
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2 years ago  ::  Apr 28, 2012 - 1:31PM #5
amcolph
Posts: 16,280

Apr 28, 2012 -- 1:20PM, iamachildofhis wrote:


 



iama: NOTE that the "characters observed in the species included" is where the actual science-observations are taking place.  From the observed "characters" the grand "leap of faith" takes place and the "tree of life" is speculated / built as a diagram to convince the world's gullible.


.





It is what it is, Iama, incomplete and partially speculative.


But you don't have a better explanation which deals with all the data.


All you have is a shallow and ignorant interpretation of a Bronze-age "how-so" story even more incomplete and speculative than what science has to tell us.


That's why we'll stick with the science.




 

This post contains no advertisements or solicitations.
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2 years ago  ::  Apr 28, 2012 - 1:37PM #6
rsielin
Posts: 3,933

Iama, this post and what you have highlighted with your assumption it exposes some weakness in this science research is a primary example that you are totally clueless about how real science works.  I'm embarassed for you. Everyone sees through your science ignorance. 


Apr 28, 2012 -- 1:20PM, iamachildofhis wrote:

iama: Here is an abstract for one of the above articles:


Science
Vol. 276 no. 5310 pp. 256-259
DOI: 10.1126/science.276.5310.256

  • Report

Phylogenetic Analysis of Glycolytic Enzyme Expression


  1. D. L. Crawford


+ Author Affiliations


  1. Department of Organismal Biology and Anatomy, University of Chicago, 1027 East 57 Street, Chicago, IL 60637, USA.



Abstract


"Although differences among species in enzyme maximal activity or concentration are often interpreted as adaptive and important for regulating metabolism, these differences may simply reflect phylogenetic divergence. Phylogenetic analysis of the expression of the glycolytic enzymes among 15 taxa of a North American fish genus (Fundulus) indicated that most variation in enzyme concentration is due to evolutionary distance and may be nonadaptive. However, three enzymes’ maximal activities covary with environmental temperature and have adaptive value. Additionally, two pairs of enzymes covary, indicating coevolution. Thus, metabolic flux may be modulated by many different enzymes rather than by a single rate-limiting enzyme."



iama:  Obviously, there is ongoing research, and, currently, speculations... indicating new hypothesis-testing is required to validate the evolutionary speculations.


The use of the term "may" indicates the, currently, speculation aspect of this Abstract.



"Phylogenetic" is an evolution-based-speculation-arena, where the evolution-presuppositioned-scientists are researching in hopes of finding evidence for their paradigm.  Again, note the use of the speculation-terms, for example, "may," "regarded as," "represents a hypothesis," "are assumed to have occurred," etc.:


Construction of a phylogenetic tree


Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, hybridize together, or terminate by extinction. This may be visualized in a phylogenetic tree.


The problem posed by phylogenetics is that genetic data are only available for living taxa, and the fossil records (osteometric data) contains less data and more-ambiguous morphological characters.[6] A phylogenetic tree represents a hypothesis of the order in which evolutionary events are assumed to have occurred.


Cladistics is the current method of choice to infer phylogenetic trees. The most commonly-used methods to infer phylogenies include parsimony, maximum likelihood, and MCMC-based Bayesian inference. Phenetics, popular in the mid-20th century but now largely obsolete, uses distance matrix-based methods to construct trees based on overall similarity, which is often assumed to approximate phylogenetic relationships. All methods depend upon an implicit or explicit mathematical model describing the evolution of


characters observed in the species included,


and are usually used for molecular phylogeny, wherein the characters are aligned nucleotide or amino acid sequences." - wiki


iama: NOTE that the "characters observed in the species included" is where the actual science-observations are taking place.  From the observed "characters" the grand "leap of faith" takes place and the "tree of life" is speculated / built as a diagram to convince the world's gullible.


.






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2 years ago  ::  Apr 28, 2012 - 3:08PM #7
57
Posts: 20,547

Apr 27, 2012 -- 1:10PM, lucaspa wrote:


DM Hillis, Biology recapitulates phylogeny, Science (11 April) 276: 276-277, 1997.  Primary articles are JX Becerra, Insects on plants:  macroevolutionary chemical trends in host use.  Science 276: 253-256, 1997; VA Pierce and DL Crawford, Phylogenetic analysis of glycolitic enzyme expression, Science 276: 256-259; and JP Huelsenbeck and B Rannala, Phylogenetic methods come of age:  testing hypotheses in an evolutionary context. Science 276: 227-233, 1997.


Phylogenetic analysis is based on the analysis of DNA sequences, and thanks to new technology of automated DNA sequencers and supercomputers, now large data sets of of hundreds or thousands of DNA sequences, each of which has thousands of nucleotides, are now routinely being analyzed.


"As phylogenetic analyses became commonplace in the 1980s, several groups emphasized what should have been obvious all along:  Units of study in biology (from genes through organisms to higher taxa) do not represent statistically independent observations, but rather are interrelated through their historical connections."

Everyone look at that quote carefully.  A deduction of creationism is that at least some groups (kinds) must be "statistically independent observations".  That is the "barrier" between kinds.  A barrier that prevents one kind from becoming another kind thru "descent with modification" is going to give you a "statistically independent observation" from every other DNA sequence of that gene or sets of genes. 

OTOH, if evolution happened (the "goo to you"), then all taxas will be "interrelated through their historical connections". 

The results from analyzing large sets of DNA sequences (and not just between polar and brown bears, but between humans, corn, rats, salamanders, alfalfa, E. coli, etc) show that ALL taxa are "interrelated by historical connections".  Creationism falsified, evolution supported.




Do you have an actual example of descent with modification?


Backed up by science?  You know, testable? repeatable? predictable?

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2 years ago  ::  Apr 28, 2012 - 5:38PM #8
MMarcoe
Posts: 14,684

Apr 28, 2012 -- 3:08PM, 57 wrote:


Do you have an actual example of descent with modification?


Backed up by science?  You know, testable? repeatable? predictable?





Look in the mirror. You and everyone else are actual examples of descent with modification.


That's how God made it.

There are three sides to every story: your side, my side, and the truth.

God is just a personification of reality, of pure objectivity.
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2 years ago  ::  Apr 28, 2012 - 6:59PM #9
Midutch
Posts: 3,525

Apr 28, 2012 -- 3:08PM, 57 wrote:


Apr 27, 2012 -- 1:10PM, lucaspa wrote:


DM Hillis, Biology recapitulates phylogeny, Science (11 April) 276: 276-277, 1997.  Primary articles are JX Becerra, Insects on plants:  macroevolutionary chemical trends in host use.  Science 276: 253-256, 1997; VA Pierce and DL Crawford, Phylogenetic analysis of glycolitic enzyme expression, Science 276: 256-259; and JP Huelsenbeck and B Rannala, Phylogenetic methods come of age:  testing hypotheses in an evolutionary context. Science 276: 227-233, 1997.


Phylogenetic analysis is based on the analysis of DNA sequences, and thanks to new technology of automated DNA sequencers and supercomputers, now large data sets of of hundreds or thousands of DNA sequences, each of which has thousands of nucleotides, are now routinely being analyzed.


"As phylogenetic analyses became commonplace in the 1980s, several groups emphasized what should have been obvious all along:  Units of study in biology (from genes through organisms to higher taxa) do not represent statistically independent observations, but rather are interrelated through their historical connections."

Everyone look at that quote carefully.  A deduction of creationism is that at least some groups (kinds) must be "statistically independent observations".  That is the "barrier" between kinds.  A barrier that prevents one kind from becoming another kind thru "descent with modification" is going to give you a "statistically independent observation" from every other DNA sequence of that gene or sets of genes. 

OTOH, if evolution happened (the "goo to you"), then all taxas will be "interrelated through their historical connections". 

The results from analyzing large sets of DNA sequences (and not just between polar and brown bears, but between humans, corn, rats, salamanders, alfalfa, E. coli, etc) show that ALL taxa are "interrelated by historical connections".  Creationism falsified, evolution supported.


Do you have an actual example of descent with modification?


Backed up by science?  You know, testable? repeatable? predictable?


As if "creationists" could even recognize real science.


2000+ years worth of ABYSMAL FAILURE is a hard habit to break.


BTW, descent merely means offspring. Modification merely means that the offspring are different from the parents. How, in heavens name, could you NOT see descent with modification.

"creationism" ... 2000+ years worth of ABYSMAL FAILURE ... and proud of it.
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2 years ago  ::  Apr 29, 2012 - 7:15AM #10
57
Posts: 20,547

Apr 28, 2012 -- 5:38PM, MMarcoe wrote:


Apr 28, 2012 -- 3:08PM, 57 wrote:


Do you have an actual example of descent with modification?


Backed up by science?  You know, testable? repeatable? predictable?





Look in the mirror. You and everyone else are actual examples of descent with modification.


That's how God made it.




Do you really think that's what I'm talking about?  Seriously? 


Come on my evo friend. Molecules to man...testable, repeatable and predictable.

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