Illusions of Phylogeny

lifepsyop said:

Show me where the predictions were made beforehand, and the levels of discordance that were stated on record would falsify Evolution. .

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Protein sequences and the molecular clock

While evolutionary biologists were tentatively branching out into molecular biology, molecular biologists were rapidly turning their attention toward evolution.

After developing the fundamentals of protein sequencing with insulin between 1951 and 1955, Frederick Sanger and his colleagues had published a limited interspecies comparison of the insulin sequence in 1956. Francis Crick, Charles Sibley and others recognized the potential for using biological sequences to construct phylogenies, though few such sequences were yet available. By the early 1960s, techniques for protein sequencing had advanced to the point that direct comparison of homologous amino acid sequences was feasible.[11] In 1961, Emanuel Margoliash and his collaborators completed the sequence for horse cytochrome c (a longer and more widely distributed protein than insulin), followed in short order by a number of other species.

In 1962, Linus Pauling and Emile Zuckerkandl proposed using the number of differences between homologous protein sequences to estimate the time since divergence, an idea Zuckerkandl had conceived around 1960 or 1961. This began with Pauling's long-time research focus, hemoglobin, which was being sequenced by Walter Schroeder; the sequences not only supported the accepted vertebrate phylogeny, but also the hypothesis (first proposed in 1957) that the different globin chains within a single organism could also be traced to a common ancestral protein.[12] Between 1962 and 1965, Pauling and Zuckerkandl refined and elaborated this idea, which they dubbed the molecular clock, and Emil L. Smith and Emanuel Margoliash expanded the analysis to cytochrome c. Early molecular clock calculations agreed fairly well with established divergence times based on paleontological evidence. However, the essential idea of the molecular clock—that individual proteins evolve at a regular rate independent of a species' morphological evolution—was extremely provocative (as Pauling and Zuckerkandl intended it to be).[13]

History of molecular evolution - Wikipedia, the free encyclopedia

"Arguments against macroevolution, based on so-called gaps in the fossil records, are also profoundly weakened by the much more detailed and digital information revealed from the study of genomes. Outside of a time machine, Darwin could hardly have imagined a more powerful data set than comparative genomics to confirm his theory."
--Dr. Francis Collins, "Faith and the Human Genome"
http://www.asa3.org/ASA/PSCF/2003/PSCF9-03Collins.pdf

Loudmouth said:

"Arguments against macroevolution, based on so-called gaps in the fossil records, are also profoundly weakened by the much more detailed and digital information revealed from the study of genomes. Outside of a time machine, Darwin could hardly have imagined a more powerful data set than comparative genomics to confirm his theory."
--Dr. Francis Collins, "Faith and the Human Genome"
http://www.asa3.org/ASA/PSCF/2003/PSCF9-03Collins.pdf

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Ignore Dr. Francis Collins! He's just trying to justify his evil atheist ways!

lifepsyop said:

You do realize the molecular clock has basically been debunked? The current literature is replete with admissions of its failures as any kind of reliable measurement device for determining degrees of evolutionary divergence.

The molecular clock is another failed prediction of the theory.

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The question was on phylogeny, not the molecualr clock, and no it hasn't been "debunked" in any case.

I have one question for you now. How would life on earth look different if common descent were correct?

lifepsyop said:

Another evolutionist apologizing for the fossil record.

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Yea, thats a good one.

lifepsyop said:

You're the one that brought it up.

And yes, the molecular clock has been debunked as any kind of accurate measurement device for which it was first proposed. Biologists don't take it seriously anymore, only evolution salesmen.


This is just one paper of dozens recognizing this fact.

The genetic equidistance result: misreading by the molecular clock and neutral theory and reinterpretation nearly half of a century later
Hu et al. 2013

In 1963, Margoliash discovered the unexpected genetic equidistance result after comparing cytochrome c sequences from different species. This finding, together with the hemoglobin analyses of Zuckerkandl and Pauling in 1962, directly inspired the ad hoc molecular clock hypothesis. Unfortunately, however, many biologists have since mistakenly viewed the molecular clock as a genuine reality, which in turn inspired Kimura, King, and Jukes to propose the neutral theory of molecular evolution. Many years of studies have found numerous contradictions to the theory, and few today believe in a universal constant clock. What is being neglected, however, is that the failure of the molecular clock hypothesis has left the original equidistance result an unsolved mystery. In recent years, we fortuitously rediscovered the equidistance result, which remains unknown to nearly all researchers. Incorporating the proven virtues of existing evolutionary theories and introducing the novel concept of maximum genetic diversity, we proposed a more complete hypothesis of evolutionary genetics and reinterpreted the equidistance result and other major evolutionary phenomena. The hypothesis may rewrite molecular phylogeny and population genetics and solve major biomedical problems that challenge the existing framework of evolutionary biology.

The genetic equidistance result: misreading by the molecular clock and neutral theory and reinterpretation nearly half of a century later - Springer

So the prediction you pointed out has turned out to be a total failure. But since Evolution is a religion and not a science, it doesn't matter how many of its predictions fail.

The funny thing is you can go back a few years and find evolutionist spokespersons (and there are still some today) using the so-called molecular clock as a major evidence for Evolution. But when evolutionist arguments get debunked they are quietly swept under the rug as new replacement stories are packaged for the next round of public consumption.

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That abstract has a very biased undertone in the writing. Doesn't sound like a scientific paper at all. The journal is open access, but claims to be peer reviewed. I doubt they have a particularly good reputation, if this is the level of stuff they are publishing.

lifepsyop said:

Translation: I don't like what this paper says so it must be wrong.

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Actually, I don't care if the paper is right or wrong. I don't care if molecular clocks work or not. It makes no difference to me.

I was merely commenting on the unprofessional sweeping generalizations made in the abstract. For example:

In recent years, we fortuitously rediscovered the equidistance result, which remains unknown to nearly all researchers.

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Plus, the use of the term "ad hoc" when describing a new hypothesis.

Granted, it could be a language barrier thing, since English is probably not the author's first language.

lifepsyop said:

You're the one that brought it up.

And yes, the molecular clock has been debunked as any kind of accurate measurement device for which it was first proposed. Biologists don't take it seriously anymore, only evolution salesmen.


This is just one paper of dozens recognizing this fact.

The genetic equidistance result: misreading by the molecular clock and neutral theory and reinterpretation nearly half of a century later
Hu et al. 2013

In 1963, Margoliash discovered the unexpected genetic equidistance result after comparing cytochrome c sequences from different species. This finding, together with the hemoglobin analyses of Zuckerkandl and Pauling in 1962, directly inspired the ad hoc molecular clock hypothesis. Unfortunately, however, many biologists have since mistakenly viewed the molecular clock as a genuine reality, which in turn inspired Kimura, King, and Jukes to propose the neutral theory of molecular evolution. Many years of studies have found numerous contradictions to the theory, and few today believe in a universal constant clock. What is being neglected, however, is that the failure of the molecular clock hypothesis has left the original equidistance result an unsolved mystery. In recent years, we fortuitously rediscovered the equidistance result, which remains unknown to nearly all researchers. Incorporating the proven virtues of existing evolutionary theories and introducing the novel concept of maximum genetic diversity, we proposed a more complete hypothesis of evolutionary genetics and reinterpreted the equidistance result and other major evolutionary phenomena. The hypothesis may rewrite molecular phylogeny and population genetics and solve major biomedical problems that challenge the existing framework of evolutionary biology.

The genetic equidistance result: misreading by the molecular clock and neutral theory and reinterpretation nearly half of a century later - Springer

So the prediction you pointed out has turned out to be a total failure. But since Evolution is a religion and not a science, it doesn't matter how many of its predictions fail.

The funny thing is you can go back a few years and find evolutionist spokespersons (and there are still some today) using the so-called molecular clock as a major evidence for Evolution. But when evolutionist arguments get debunked they are quietly swept under the rug as new replacement stories are packaged for the next round of public consumption.

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You cited one paper and claimed it represented "dozens." What journal did you pick the paper from? "Science China." Really... is that the best you can do? The writing is awful and a number of incorrect statements are apparent, such as the claim that ENCODE leads to the conclusion that at least 80% of the human genome is functional. This is a gross exaggeration that the ENCODE scientists themselves never made, but one that a non-scientist writer might claim when writing about it on line. Why did you pick that paper? Because you think it supports your position. Did you read it? Can you expalin what the MGD hypothesis they are advocating is? Are they right about the molecular clock, but wrong about common descent (since they clearly accept it)?

I also asked you a question that you ignored. I will ask it again. How would life on earth look different if common descent were correct?

lifepsyop said:

Translation: I don't like what the paper says so it must be wrong.

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Another irony meter just exploded.

You have done nothing but ignore entire swaths of data. Perhaps a little self reflection will help you.

lifepsyop said:

Translation: I don't like what the paper says so it must be wrong.


I could show you more papers but you'll just keep making excuses.

Here's another one (not written by those backwards science-illiterate Chinese.)

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No, I told you exactly why I had issues with the paper in question. And yes, that journal is not well regarded, not even in China. And no, I never claimed Chinese were "backwards" or "science-illiterate." Maybe you are projecting your own short-comings? Freudian??

Since you like to cite papers you don't understand and never read, here are few more for you. Tell me why they are all wrong.

Nature Reviews Genetics 13, 303-314 (May 2012) | doi:10.1038/nrg3186
Molecular phylogenetics: principles and practice
Ziheng Yang & Bruce Rannala
Abstract
Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use
http://www.nature.com/nrg/journal/v13/n5/full/nrg3186.html

The Impact of Molecular Data on Our Understanding of Bee Phylogeny and Evolution
Annual Review of Entomology
Vol. 58: 57-78 (Volume publication date January 2013)
First published online as a Review in Advance on August 28, 2012
DOI: 10.1146/annurev-ento-120811-153633
Bryan N. Danforth,1* Sophie Cardinal,2 Christophe Praz,3 Eduardo A.B. Almeida,4 and Denis Michez5
ABSTRACTOur understanding of bee phylogeny has improved over the past fifteen years as a result of new data, primarily nucleotide sequence data, and new methods, primarily model-based methods of phylogeny reconstruction. Phylogenetic studies based on single or, more commonly, multilocus data sets have helped resolve the placement of bees within the superfamily Apoidea; the relationships among the seven families of bees; and the relationships among bee subfamilies, tribes, genera, and species. In addition, molecular phylogenies have played an important role in inferring evolutionary patterns and processes in bees. Phylogenies have provided the comparative framework for understanding the evolution of host-plant associations and pollen specialization, the evolution of social behavior, and the evolution of parasitism. In this paper, we present an overview of significant discoveries in bee phylogeny based primarily on the application of molecular data. We review the phylogenetic hypotheses family-by-family and then describe how the new phylogenetic insights have altered our understanding of bee biology.
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RECENT ADVANCES IN THE (MOLECULAR) PHYLOGENY OF VERTEBRATES
Annual Review of Ecology, Evolution, and Systematics
Vol. 34: 311-338 (Volume publication date November 2003)
First published online as a Review in Advance on September 2, 2003
DOI: 10.1146/annurev.ecolsys.34.011802.132351
Axel Meyer
Rafael Zardoya
ABSTRACT▪ Abstract  The analysis of molecular phylogenetic data has advanced the knowledge of the relationships among the major groups of living vertebrates. Whereas the molecular hypotheses generally agree with traditional morphology-based systematics, they sometimes contradict them. We review the major controversies in vertebrate phylogenetics and the contribution of molecular phylogenetic data to their resolution: (a) the mono-paraphyly of cyclostomes, (b) the relationships among the major groups of ray-finned fish, (c) the identity of the living sistergroup of tetrapods, (d) the relationships among the living orders of amphibians, (e) the phylogeny of amniotes with particular emphasis on the position of turtles as diapsids, (f) ordinal relationships among birds, and (g) the radiation of mammals with specific attention to the phylogenetic relationships among the monotremes, marsupial, and placental mammals. We present a discussion of limitations of currently used molecular markers and phylogenetic methods as well as make recommendations for future approaches and sets of marker genes
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A Molecular Phylogeny of Phytophthora and Related Oomycetes
D.E.L. Cookea, 1, A. Drenthb, J.M. Duncana, G. Wagelsb, C.M. Brasier
Fungal Genetics and Biology
Volume 30, Issue 1, June 2000, Pages 17–32
Abstract
Phylogenetic relationships among 50 Phytophthora species and between Phytophthora and other oomycetes were examined on the basis of the ITS sequences of genomic rDNA. Phytophthora grouped with Pythium, Peronospora, and Halophytophthora, distant from genera in the Saprolegniales. Albugo was intermediate between these two groups. Unlike Pythium, Phytophthora was essentially monophyletic, all but three species forming a cluster of eight clades. Two clades contained only species with nonpapillate sporangia. The other six clades included either papillate and semipapillate, or semipapillate and nonpapillate types, transcending traditional morphological groupings, which are evidently not natural assemblages. Peronospora was related to P. megakarya and P. palmivora and appears to be derived from a Phytophthora that has both lost the ability to produce zoospores and become an obligate biotroph. Three other Phytophthoras located some distance from the main Phytophthora–Peronospora cluster probably represent one or more additional genera.
A Molecular Phylogeny of Phytophthora and Related Oomycetes

Science 28 January 2005:
Vol. 307 no. 5709 pp. 580-584
DOI: 10.1126/science.1105113
•Report
A Molecular Phylogeny for Bats Illuminates Biogeography and the Fossil Record
Emma C. Teeling1,2,*, Mark S. Springer3,*, Ole Madsen4, Paul Bates5, Stephen J. O'Brien6,*, William J. Murphy
AbstractBats make up more than 20% of extant mammals, yet their evolutionary history is largely unknown because of a limited fossil record and conflicting or incomplete phylogenies. Here, we present a highly resolved molecular phylogeny for all extant bat families. Our results support the hypothesis that megabats are nested among four major microbat lineages, which originated in the early Eocene [52 to 50 million years ago (Mya)], coincident with a significant global rise in temperature, increase in plant diversity and abundance, and the zenith of Tertiary insect diversity. Our data suggest that bats originated in Laurasia, possibly in North America, and that three of the major microbat lineages are Laurasian in origin, whereas the fourth is Gondwanan. Combining principles of ghost lineage analysis with molecular divergence dates, we estimate that the bat fossil record underestimates (unrepresented basal branch length, UBBL) first occurrences by, on average, 73% and that the sum of missing fossil history is 61%.
A Molecular Phylogeny for Bats Illuminates Biogeography and the Fossil Record

Molecular phylogeny and divergence times of drosophilid species.
C A Russo, N Takezaki and M Nei
Mol Biol Evol (1995) 12 (3): 391-404
Abstract
The phylogenetic relationships and divergence times of 39 drosophilid species were studied by using the coding region of the Adh gene. Four genera--Scaptodrosophila, Zaprionus, Drosophila, and Scaptomyza (from Hawaii)--and three Drosophila subgenera--Drosophila, Engiscaptomyza, and Sophophora--were included. After conducting statistical analyses of the nucleotide sequences of the Adh, Adhr (Adh-related gene), and nuclear rRNA genes and a 905-bp segment of mitochondrial DNA, we used Scaptodrosophila as the outgroup. The phylogenetic tree obtained showed that the first major division of drosophilid species occurs between subgenus Sophophora (genus Drosophila) and the group including subgenera Drosophila and Engiscaptomyza plus the genera Zaprionus and Scaptomyza. Subgenus Sophophora is then divided into D. willistoni and the clade of D. obscura and D. melanogaster species groups. In the other major drosophilid group, Zaprionus first separates from the other species, and then D. immigrans leaves the remaining group of species. This remaining group then splits into the D. repleta group and the Hawaiian drosophilid cluster (Hawaiian Drosophila, Engiscaptomyza, and Scaptomyza). Engiscaptomyza and Scaptomyza are tightly clustered. Each of the D. repleta, D. obscura, and D. melanogaster groups is monophyletic. The splitting of subgenera Drosophila and Sophophora apparently occurred about 40 Mya, whereas the D. repleta group and the Hawaiian drosophilid cluster separated about 32 Mya. By contrast, the splitting of Engiscaptomyza and Scaptomyza occurred only about 11 Mya, suggesting that Scaptomyza experienced a rapid morphological evolution. The D. obscura and D. melanogaster groups apparently diverged about 25 Mya. Many of the D. repleta group species studied here have two functional Adh genes (Adh-1 and Adh-2), and these duplicated genes can be explained by two duplication events.
Molecular phylogeny and divergence times of drosophilid species.

lifepsyop said:

Quite the accusation. To be honest, I don't think you understand even half of what you've been posting in this whole thread.

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Psychological projection. I happen to have a Ph.D. in Biology. What is your education in the field?

lifepsyop said:

Most of the conclusions in those papers appear to be based on the assumption that the molecular clock model works in the first place. There exist just as many papers which state the molecular clock data contradicts conventional phylogeny. Dozens of references in the Schwartz paper I linked.

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Did you count them? Sure, there are some known issues with using molecular clock data to determine phylogenetic distance. It doesn't work well for short time frames and very long times frames. Species do not always evolve at equal rates during the same time frames. Nevertheless, what we find is consistant with common descent.

lifepsyop said:

The question is whether or not the molecular clock is actually a reliable model for inferring relatedness between both closely and distantly related taxa, which it clearly isn't.

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Phylogenetic trees do that. You know... the nested hiearchies you alternately say do exist and do not exist... or do not matter even if they do.

lifepsyop said:

What are we left with? Yet another scenario where both the confirmation and contradiction is accommodated into evolution theory. Surprise surprise.

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Once again, you focus on exceptions and ignore the preponderence of the evidence.

Split Rock said:

Psychological projection. I happen to have a Ph.D. in Biology.

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So these would be your peers in this forum? Are we that supportive of your profession? Or do you just like us that much.

lifepsyop said:

This says it all. When the "molecular clock" seems to agree with standard phylogeny, then it "works". When the MC disagrees with standard phylogeny then the "species evolved at unequal rates", or some other kind of irregularity occurred.

More of the same non-falsifiable, ad-hoc, save-the-theory-with-rescue-devices nonsense.

Being a biologist, I would expect you to recognize this type of problem.

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It isn't a problem. Think about the forces that drive evolution. Part of it relies upon frequency of reproduction over time (creatures that reproduce more quickly and arrive at reproductive age more quickly tend to evolve faster, which is why bacteria change so fast). Not only this, but one of the driving forces of evolution is environmental change. If the environment changes drastically in a brief period of time, evolutionary speed tends to skyrocket.