Unfalsifiable Phylogeny

[lifepsyop]

In my experience, one of the most often used claims for the alleged strength of evolutionary theory is the ability of researchers to construct phylogenetic trees which are said to represent the evolutionary development of major taxonomic groups of life. The main idea conveyed is that such seemingly congruent diagrams would not be possible to construct if Common Descent were false... that is to say, If Common Descent were false, researchers would run into major irreconcilable contradictions while attempting to plot out common ancestry relationships between various major types of life.

My contention here is that the above claim is wrong, and that Phylogeny is, for the most part, unfalsifiable. Instead, what Phylogenetic tree construction appears to be is a Metaphysical statistics program. What I mean is that such systematic constructions proceed only within the prior assumption that Common Descent is true. There are rigorously complex systematic and statistical models for attempting to resolve the 'most-likely' pattern of Common Descent (if it is true), but the model itself lacks any substantial criteria for falsifying the evolutionary assumption it is based on.

The reason I contend this is because of the amount of evolutionary rescue-devices available to reconcile nearly any amount of incongruent or contradictory data.

I will attempt to demonstrate this with the following examples:

Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions
Nishihara et al. 2006

....We propose a superordinal name “Pegasoferae” for this clade of Chiroptera + Perissodactyla + Carnivora + Pholidota. The presence of a single incongruent L1 locus generates a tree in which the group of Carnivora + Perissodactyla associates with Cetartiodactyla but not with Chiroptera. This result suggests that incomplete lineage sorting of an ancestral dimorphism occurred with regard to the presence or absence of retroposon alleles in a common ancestor of Scrotifera (Pegasoferae + Cetartiodactyla), which was followed by rapid divergence into the extant orders over an evolutionarily short period.

http://www.pnas.org/content/103/26/9929.full#B2

First, to show an example of major contradiction in the data... Compare the Human/Mouse/Dog relationship shown above with this study published a year later....

A Phylogenomic Study of Human, Dog, and Mouse
Cannarozzi et al. 2007

In recent years the phylogenetic relationship of mammalian orders has been addressed in a number of molecular studies. These analyses have frequently yielded inconsistent results with respect to some basal ordinal relationships. For example, the relative placement of primates, rodents, and carnivores has differed in various studies. Here, we attempt to resolve this phylogenetic problem by using data from completely sequenced nuclear genomes to base the analyses on the largest possible amount of data. To minimize the risk of reconstruction artifacts, the trees were reconstructed under different criteria—distance, parsimony, and likelihood. For the distance trees, distance metrics that measure independent phenomena (amino acid replacement, synonymous substitution, and gene reordering) were used, as it is highly improbable that all of the trees would be affected the same way by any reconstruction artifact. In contradiction to the currently favored classification, our results based on full-genome analysis of the phylogenetic relationship between human, dog, and mouse yielded overwhelming support for a primate–carnivore clade with the exclusion of rodents.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1761043/

So in a full-genome study we see "overwhelming support" for Primates/Carnivore (Human-Dog) clade, to the exclusion of rodents. But the first study using retroposon insertion sites shows a Primate/Rodent clade with the exclusion of Carnivores(Dogs). This demonstrates that major contradictions are not a problem for phylogeny.

Now, returning to the original Pegasoferae paper, we will highlight a rescue device known as "incomplete lineage sorting" that can potentially be used to explain away large amounts of discordant data.

Here is the explanation for the retroposon presence in the Cetartiodactyla group:

Characterization of an Inconsistent Locus.

In addition to the four loci that support the Pegasoferae clade, we isolated one L1 locus (INT283) that indicates the monophyly of Carnivora, Perissodactyla, and Cetartiodactyla, supporting Fereuungulata. The probability of homoplasy can be considered extremely low for L1 insertions, and the same target-site duplications (that are produced in the process of integration) were clearly observed for both patterns of the insertions (Figs. 3 B and 4F). Thus, this inconsistency cannot be explained by homoplasy, and both of the incongruent trees are convincing gene trees (40). If clear homoplasy-free genetic markers show incongruent trees, it can be interpreted that lineage sorting of polymorphism in a common ancestor of the species was incomplete. Namely, the L1 insertion at locus INT283 occurred in the genome of a common ancestor of Scrotifera, and the ancestral dimorphism of alleles containing or lacking L1 had been retained in the population during the divergence of at least three lineages such as Cetartiodactyla, Chiroptera, and a group of Carnivora + Perissodactyla, followed by random fixation of the alleles. Accordingly, the time period in which the divergences occurred is relatively shorter than the coalescence time of the ancestral population (22, 40). Waddell et al. (8) proposed a likelihood analysis to estimate significance for the lineage supported by retroposon method. According to the estimation, the clade supported by four loci is statistically significant (P = 0.025; ref. 8) despite the existence of one incongruent locus. Therefore, it seems likely that the monophyly of Carnivora, Perissodactyla, and Chiroptera reflect the true species’ relationships, and Fereuungulata (including Carnivora, Perissodactyla and Chiroptera) supported by one locus can no longer be considered a robust clade.

Looking at the tree image again: The researchers found the ERV: INT283 in Perissodactyla, Carnivora, and Certartiodactyla. However Certartiodactyla lacks the four ERVs(165,265,382,391) that unite Pegasoferae. They don't want to propose that INT283 is a homoplasy, (or independently acquired in one group), so the researchers simply conclude that an "incomplete sorting" event took place somewhere between the common ancestor of Pegasoferae and Scrotifera, whereby the lineage representing Certiodactyla avoided gene pools containing the "Pegasoferae" ERV's, but later recombined with gene pools containing the ERV INT283.

Using this methodology, it seems nearly any pattern of retroposon integration could be explained. As a quick experiment, I took the phylogenetic tree from the same study and simulated a new data point that forced me to completely rearrange part of the tree, though I only invoked the same devices as the original paper.

Here's a crude modification of the original diagram with my simulated data point: the presence of a retroposon integration marker: INT138 located in the order Glires (comprised of Rodentia, Lagamoprha). From this I was able to "resolve" a new clade named "Gligasoferae". I included a mock abstract to go with the simulated data.

Following the discovery of the presence of the enigmatic retroposon insertion (INT138), we recover the order Glires (Rodents/Rabbits), as belonging to a clade that is shared with Pegasoferae(Chrioptera, Perissodactyla, Carnivora). We name this newly resolved clade "Gligasoferae".

Since the probability of homoplasy of INT138 is highly unlikely, this clade is resolved by two occurrences of incomplete lineage sorting. (shown in blue labeled ILS1, and ILS2) ILS 1 occurs within common ancestors of the magnorder Boreoeutheria, whereby populations containing insertion sites "A" (labeled in green) were combined with an incompletely sorted polymorphism lacking fixation of insertion sites "B". ILS 2 shows the lineage representing order Glires shared a common ancestor with an incompletely sorted polymoprhism population in the common ancestor of the clade Scrotifera, which had inherited retroposon INT138 (shown in red), but lacked fixation of INT226, INT237.

The point of this was to give a simple example of how easily different data sets can be explained with evolutionary rescue devices such as incomplete lineage sorting.

Evolutionists may counter that "incomplete lineage sorting" is observed in living populations and is an inevitable product of population genetics. But this is not the point. The point is that the evolutionary model is predicting a scenario of unfalsifiability, where discordant data always has an explanation. Regardless of whether or not it is a possible explanation, the model becomes largely removed from falsifiable criteria. The discordant gene trees might be a product of "incomplete lineage sorting", or it might represent true contradictions to phylogeny because Evolution didn't happen.

The latter hypothesis is metaphysically or philosophically unacceptable to evolutionists, so they will simply explain any amount of gene tree discordance as incomplete lineage sorting, or other evolutionary rescue devices.

I believe this is a reoccurring pattern for most of the alleged strengths of the theory of Evolution. Its robustness is an illusion....


For another example: Here's another ERV-based construction attempting to show the phylogeny of the major orders of placental mammals. They found that retroposon integration sites significantly contradicted any single evolutionary tree, which will be more apparent in the images below.

Mosaic retroposon insertion patterns in placental mammals
Churakov 2009

...These findings provide significant support for a “soft” polytomy of the major mammalian clades. Ancestral successive hybridization events and/or incomplete lineage sorting associated with short speciation intervals are viable explanations for the mosaic retroposon insertion patterns of recent placental mammals and for the futile search for a clear root dichotomy.

.....We believe that the most parsimonious interpretation of the current data is that the ancestral placental populations were characterized by severe ancestral subdivisions and rejoinings, leading to a complex mosaic of phylogenetic relationships in recent species (Fig. 4). Effects of alternating divergence, hybridization, introgression, and incomplete lineage sorting might complicate our search for a clear dichotomy at the base of this tree and leave us with an indistinct, effective ‘soft’ polytomy, leading sometimes to one or the other solution depending on the size of the data set and the particular markers examined.

In the first scenario, the Eomaia-like ancestral population probably diverged into three distinct lineages of preAfrotheria, preXenarthra, and preBoreotheria. Limited gene flow and hybridization that occurred among these populations left behind mosaic signs of intermittent relationships that we identify about 125 million years later as a patchwork of Exafroplacentalia (I), Epitheria (II), and Atlantogenata (III) roots (Fig. 4A). This scenario requires temporary overlap of the three lineages or parts of their populations before final speciation occurred (Fig. 4B). A second scenario that could explain the results involves incomplete lineage sorting among the three populations (Fig. 4C). Because retroposon fixation requires possibly millions of years before being consistently represented in a population, alleles with and without certain elements surely coexisted temporarily, and, in the case of rapid speciation, were distributed randomly into different lineages. Such a process could contribute as well to the patchwork presentation of seemingly competing insertion patterns now present in recent species....

....The present example of apparently incongruent markers inherent in the early branching of placentals offers a seminal example of conflicting retroposon presence/absence patterns that, at the same time, shed new light on the decades-old, controversial scenarios of sequence-based phylogenies.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675975/

Isn't it interesting how severely conflicting data just becomes more confirming evidence for Evolution?

This last image (figures A) says it all. Look at the liberty in which the Afrotheria lineage is permitted to skip over the first set of insertions assigned to Boreotheria, but then combines with Boreotheria's second set insertions, finally combining with Xenartha insertions, (Xenartha containing insertions from Boreotheria's first set, but not second)

Here the researchers use the same rescue devices to resolve blatantly contradictory data on a larger scale.

This type of behavior supports my suspicions that Evolutionary Phylogenetics is a metaphysical or philosophical statistics/systematics program, that is largely unfalsifiable. While robust comparative methodology is applied within the model, the model itself does not have a falsifiable scientific basis but a metaphysical one. That is, its practitioners hold a metaphysical, philosophical, or religious conviction that Evolution / Common Descent is true.

I believe this metaphysical conviction to Evolution stems from the root desire to explain existence while denying the obvious: that the Creation had a Creator. But I suppose that is another subject altogether.

 

[he_who_is_nobody]

In my experience, one of the most often used claims for the alleged strength of evolutionary theory is the ability of researchers to construct phylogenetic trees which are said to represent the evolutionary development of major taxonomic groups of life. The main idea conveyed is that such seemingly congruent diagrams would not be possible to construct if Common Descent were false... that is to say, If Common Descent were false, researchers would run into major irreconcilable contradictions while attempting to plot out common ancestry relationships between various major types of life.

This is correct. There would be major contradictions that would make the construction of a phylogenetic tree impossible if it were not for universal common descent.

My contention here is that the above claim is wrong, and that Phylogeny is, for the most part, unfalsifiable. Instead, what Phylogenetic tree construction appears to be is a Metaphysical statistics program. What I mean is that such systematic constructions proceed only within the prior assumption that Common Descent is true. There are rigorously complex systematic and statistical models for attempting to resolve the 'most-likely' pattern of Common Descent (if it is true), but the model itself lacks any substantial criteria for falsifying the evolutionary assumption it is based on.

The reason I contend this is because of the amount of evolutionary rescue-devices available to reconcile nearly any amount of incongruent or contradictory data.

This is incorrect. The model itself would show if universal common descent was incorrect. Again, the reason phylogenetic trees are created at all is because they have similar DNA/ERV/etc… to test. The only way for those to be similar is if they were shared at one point in the past.

You than go on to show data that appears to be contradicting each other and you are correct. In your first example, only one of those could be correct. However, what you are forgetting about is the scientific process, which is what you are seeing. Two different research teams have analyzed the data and come up with different answers. The next step is for both teams to go back into the lab, do more research, and hammer out the details.

There is no rescue device coming to the aid for these ideas. One of those ideas is wrong and will be proven wrong with enough time. Both of the phylogenetic trees presented are hypotheses, and only one of them could be correct. However, another possibility is that they are both wrong and the answer may lie somewhere else. Nevertheless, the main argument still stands, the only way scientists are able to construct phylogenetic trees is because of universal common descent.

I believe this metaphysical conviction to Evolution stems from the root desire to explain existence while denying the obvious: that the Creation had a Creator. But I suppose that is another subject altogether.

Begging the question. Why call it a creation in the first place?

 

[Inferno]

What HWIN said.

Additionally, the most up-to-date research I know of was presented by Isotelus here. Though it applies mainly to Laurasiatheria, it does suggest that humans aren't related as closely to carnivores.

First I'll explain what the PNAS paper said, then I'll explain why keeping up to date with the scientific literature is important. Horses and cows are perhaps not as closely related as you might think; they are, after all, separated into two different orders that split around the early Eocene (perissodactyla and artiodactyla, respectively). That being said, they are grouped in the same superorder, Laurasiatheria, which also includes Ferae (dogs, cats, pangolins), Eulipotyphla (hedgehogs, moles, etc), and most recently, Chiroptera (bats). Sure, that was surprising, but it still didn't harm the "tree of life". Now, when NS reported on the paper in question, they made a mistake by stating that the proposed unranked group within Laurasiatheria that Perissodactyla, Ferae, and Chiroptera were included in, called Pegasoferae, included cows and whales (Cetartiodactyla). This might have given the illusion that the actual PNAS paper showed Cetartiodactyla more closely related to Perissodactyls than they actually are. In fact, Cetartiodactyla was the sister group to Pegasoferae. There is really no excuse for NS to make this mistake, as the members of Pegasoferae are clearly stated within the paper, which is public access. Duh. Furthermore, earlier papers had already suggested that Chiroptera belonged in Laurasiatheria (Liu et al., 2001, as an example). This same paper also found evidence that Chiroptera are most closely related to another basal group within Laurasiatheria, but outside of Pegasoferae: Eulipotyphla. Now I'll highlight the importance of staying up to date with the scientific literature. There have been a number of much more recent papers that have shown Pegasoferae is not actually natural group, i.e., will no longer be used, but nevertheless show Chiroptera as a more basal group within Laurasiatheria; diverging after Eulipotyphla, but prior to Ferae, Perissodactyla, and Cetartiodactyla.
This is what the most current research shows:

Edit 2: Inferno was kind enough (everybody thank him!) to draw up this simplified version of the cladograms provided by the paper linked above. Take note particularly of the positions of Chiroptera, Perissodactyla, and Cetartiodactyla:

 

[he_who_is_nobody]

(everybody thank him!)

Thank you Inferno!

 

[Inferno]

(everybody thank him!)

Thank you Inferno!

:lol:
Thanks, a bit late though!

 

[he_who_is_nobody]

:lol:
Thanks, a bit late though!

Better late then never.

 

[lifepsyop]

What HWIN said.

Additionally, the most up-to-date research I know of was presented by Isotelus here. Though it applies mainly to Laurasiatheria, it does suggest that humans aren't related as closely to carnivores.

First I'll explain what the PNAS paper said, then I'll explain why keeping up to date with the scientific literature is important. Horses and cows are perhaps not as closely related as you might think; they are, after all, separated into two different orders that split around the early Eocene (perissodactyla and artiodactyla, respectively). That being said, they are grouped in the same superorder, Laurasiatheria, which also includes Ferae (dogs, cats, pangolins), Eulipotyphla (hedgehogs, moles, etc), and most recently, Chiroptera (bats). Sure, that was surprising, but it still didn't harm the "tree of life". Now, when NS reported on the paper in question, they made a mistake by stating that the proposed unranked group within Laurasiatheria that Perissodactyla, Ferae, and Chiroptera were included in, called Pegasoferae, included cows and whales (Cetartiodactyla). This might have given the illusion that the actual PNAS paper showed Cetartiodactyla more closely related to Perissodactyls than they actually are. In fact, Cetartiodactyla was the sister group to Pegasoferae. There is really no excuse for NS to make this mistake, as the members of Pegasoferae are clearly stated within the paper, which is public access. Duh. Furthermore, earlier papers had already suggested that Chiroptera belonged in Laurasiatheria (Liu et al., 2001, as an example). This same paper also found evidence that Chiroptera are most closely related to another basal group within Laurasiatheria, but outside of Pegasoferae: Eulipotyphla. Now I'll highlight the importance of staying up to date with the scientific literature. There have been a number of much more recent papers that have shown Pegasoferae is not actually natural group, i.e., will no longer be used, but nevertheless show Chiroptera as a more basal group within Laurasiatheria; diverging after Eulipotyphla, but prior to Ferae, Perissodactyla, and Cetartiodactyla.
This is what the most current research shows:

Edit 2: Inferno was kind enough (everybody thank him!) to draw up this simplified version of the cladograms provided by the paper linked above. Take note particularly of the positions of Chiroptera, Perissodactyla, and Cetartiodactyla:

Thanks for the information, but this really does not address my argument at all. My argument did not hinge in any way on the Pegasoferae phylogeny being correct. Actually my whole point was that it cannot be shown one way or the other if it is correct or incorrect: Unfalsifiability. Evolutionary Phylogenetics is not a scientific pursuit but a metaphysical / philosophical one.

The more recent paper you link to only reinforces this position. It actually reads like one long admission that mammalian phylogeny is a complete mess.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243735/

...The phylogenetic position of Perissodactyla within Laurasiatheria has been another controversial issue. Based on morphological data, Perissodactyla was originally grouped with other hoofed animals in the group Ungulata, which also included Cetartiodactyla, Tubulidentata (aardvarks), Proboscidea (elephants), Sirenia (dugongs and manatees), and Hyracoidea (hyraxes). Subsequently, many molecular studies have placed Perissodactyla and Cetartiodactyla together within Laurasiatheria as members of the clade Fereuungulata....

.... relationships within Fereuungulata are still unclear, and a cascade of studies over the last decade has resulted in many alternative topologies....

....The perceived phylogenetic position of Chiroptera within Laurasiatheria varies depending on the combination of genes selected for analysis. For example, based on mitochondrial genomes, presented strong evidence that Chiroptera is closely related to Fereuungulata. By contrast, several other studies that combined analyses of mitochondrial genomes and functional genes support monophyly of Insectiphillia...

[etc. etc.]

If the hypothesis of Common Descent is false, this is exactly what we would predict: contradiction or lack of concordance in data which would support said hypothesis. But as I mentioned in the OP, that is where evolutionary rescue devices come in.

Here, the 2012 Zhou paper again reinforces my argument, in that the previous 2006 ERV analysis uniting Pegasoferae can easily be discarded by appealing to incomplete lineage sorting... the same way it was resolved. It's a Darwinian grab-bag of unfalsifiable explanations that can be mixed and matched however needed.

Although retroposon analyses (Schwartz et al. 2003, Nishihara et al. 2006) discovered many L1 loci that occur in Carnivora and Perissodactyla but not in Cetartiodactyla (cow or/and pig), we consider it premature to conclude that Zooamata and Pegasoferae are monophyletic because it remains unclear whether the L1 loci are present or absent in the orthologs of Pholidota (pangolins) or other important cetartiodactyl lineages, such as whales and dolphins. It is noteworthy that one locus (INT 283) isolated by Nishihara et al. (2006) supports the monophyly of Carnivora, Perissodactyla, and Cetartiodactyla, which is inconsistent with their preferred hypothesis, which includes monophyly of Pegasoferae. As suggested by Shedlock et al. (2004), such inconsistency can result when species diverged over a short evolutionary time span and there is incomplete lineage sorting of ancestral polymorphisms....

....Many efforts have been made to resolve conflict among retropsoson insertions, presumably as a result of incomplete lineage sorting of polymorphisms.

Also, the 2012 Zhou paper did not even mention the 2007 Cannarozzi paper which reported "overwhelming" full-genome support for Primate/Carnivora clade with the exclusion of Rodentia. Why not?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1761043/

The very notion that any of these researchers are making progress in resolving correct phylogeny is completely reliant on the metaphysical assumption that 'Common Descent is true'. This conclusion clearly does not follow from the data.

 

[lifepsyop]

In my experience, one of the most often used claims for the alleged strength of evolutionary theory is the ability of researchers to construct phylogenetic trees which are said to represent the evolutionary development of major taxonomic groups of life. The main idea conveyed is that such seemingly congruent diagrams would not be possible to construct if Common Descent were false... that is to say, If Common Descent were false, researchers would run into major irreconcilable contradictions while attempting to plot out common ancestry relationships between various major types of life.

This is correct. There would be major contradictions that would make the construction of a phylogenetic tree impossible if it were not for universal common descent.

That's the claim. So what kind of major contradictions should we expect if CD is false? Dogs grouping with termites over other mammals?

My contention here is that the above claim is wrong, and that Phylogeny is, for the most part, unfalsifiable. Instead, what Phylogenetic tree construction appears to be is a Metaphysical statistics program. What I mean is that such systematic constructions proceed only within the prior assumption that Common Descent is true. There are rigorously complex systematic and statistical models for attempting to resolve the 'most-likely' pattern of Common Descent (if it is true), but the model itself lacks any substantial criteria for falsifying the evolutionary assumption it is based on.

The reason I contend this is because of the amount of evolutionary rescue-devices available to reconcile nearly any amount of incongruent or contradictory data.

This is incorrect. The model itself would show if universal common descent was incorrect. Again, the reason phylogenetic trees are created at all is because they have similar DNA/ERV/etc… to test. The only way for those to be similar is if they were shared at one point in the past.

This is a metaphysical claim: "The nature of similarity is inheritance". You're also using the assumption of Common Descent as the evidence for Common Descent.

Furthermore your claim that shared DNA/ERV is a product shared ancestry is contradicted in the literature.

I provide a list of ERV references in this thread where the authors conclude ERV's can be homoplastic and should not be assumed to be inherited: http://www.leagueofreason.org.uk/viewtopic.php?f=8&t=11868

A paper from earlier this year reports widespread "molecular convergence" found in many genes of similar function in distant animal groups. An evolutionary hypothesis is now being advanced that natural selection drives genetic as well as phenotypic convergence.

Genome-wide signatures of convergent evolution in echolocating mammals
Parker et al. 2013
http://www.nature.com/nature/journal/v502/n7470/full/nature12511.html

If Evolution were a falsifiable scientific theory, you would now be considering this data as evidence in contradiction to the theory. However, since Evolution is actually a metaphysical / philosophical / religious ideology, you will automatically absorb this data as just more confirming evidence, and more light shed on how Evolution works.

You than go on to show data that appears to be contradicting each other and you are correct. In your first example, only one of those could be correct. However, what you are forgetting about is the scientific process, which is what you are seeing. Two different research teams have analyzed the data and come up with different answers. The next step is for both teams to go back into the lab, do more research, and hammer out the details.

My argument was not that a contradiction exists, but that the model is unfalsifiable. Those researchers can up-weight or down-weight different data sets, invert structures between homologous and homoplastic, and create imaginary past pathways to have the ancestry of a lineage converge with or diverge with certain data points in order to reconcile a certain relationship.

There is no rescue device coming to the aid for these ideas. One of those ideas is wrong and will be proven wrong with enough time. Both of the phylogenetic trees presented are hypotheses, and only one of them could be correct. However, another possibility is that they are both wrong and the answer may lie somewhere else.

This is an argument to the future. "Someday evidence will show which tree is correct."

And of course, the other possibility is that Common Descent is false. But this is philosophically unacceptable to a committed evolutionist.

Nevertheless, the main argument still stands, the only way scientists are able to construct phylogenetic trees is because of universal common descent.

You've claimed it twice. You have yet to defend it.

 

[Inferno]

Thanks for the information, but this really does not address my argument at all. My argument did not hinge in any way on the Pegasoferae phylogeny being correct. Actually my whole point was that it cannot be shown one way or the other if it is correct or incorrect: Unfalsifiability. Evolutionary Phylogenetics is not a scientific pursuit but a metaphysical / philosophical one.

Actually, you merely focused on the rather less interesting part. The part that does address your argument was this one: "the most up-to-date research"

Stuff I've written way too late at night that might be difficult to understand:

Show More Hide

{TEXT}

Short conclusion:
1) It's no surprise different papers give different answers, that's what we would expect from humans with faults working on complex (scientific) problems.
2) Finding something that's only very slightly out of place isn't much more than a stir. Finding something that's completely out of place (dogs closely related to termites but not to mammals) would be utterly upsetting and would falsify phylogeny. Additionally, you could find a point in the tumbleweed (tree) where taxonomy actually breaks down!

 

[ldmitruk]

I think Aronra might want to have a chat with you regarding the scientific pursuit of Phylogenetics.

Thanks for the information, but this really does not address my argument at all. My argument did not hinge in any way on the Pegasoferae phylogeny being correct. Actually my whole point was that it cannot be shown one way or the other if it is correct or incorrect: Unfalsifiability. Evolutionary Phylogenetics is not a scientific pursuit but a metaphysical / philosophical one.

You might want to check out his video and see if you can meet his challenge.

 

[lifepsyop]

Thanks for the information, but this really does not address my argument at all. My argument did not hinge in any way on the Pegasoferae phylogeny being correct. Actually my whole point was that it cannot be shown one way or the other if it is correct or incorrect: Unfalsifiability. Evolutionary Phylogenetics is not a scientific pursuit but a metaphysical / philosophical one.

Actually, you merely focused on the rather less interesting part. The part that does address your argument was this one: "the most up-to-date research"

Recentness of data does not address the argument.

And each of the preceding studies were "the most up-to-date" when they were generated as well. So you have new data sets with new contradictions to previous data sets. This does not address the underlying argument that the phylogeny is unfalsifiable. And it appears the new paper is only selectively "up-to-date" as it ignores contradictory studies like Cannorozzi 2006 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1761043/

Why is this?

As HWIN said, science constantly updates itself. Jerry Coyne just blogged about two very interesting and very related articles. In these two articles from "The Economist", the authors argue that there are many faults in the scientific enterprise and community.

One particular fact I want to highlight is the following: Many findings are, for a variety of reasons, simply false. Because these findings are rarely replicated, these mistakes tend to crop up in the literature. If they were replicated, they could be redacted.
Now because we know that a lot of research is wrong, we have to do lots and lots of research to be sure that our original research was correct. This was most evident with the Millikan experiment: Research first establishes a value for a phenomenon, in this case electric charge, then future researchers replicate the results and hone in on the correct number in incremental steps.

If you're not willing to honestly deal with the possibility that Common Descent is false, then this may be an extreme understatement.

Now in terms of phylogeny, (we have to assume that a lot of the research is wrong, possibly as much as a third and at least as much as 5%) we have the same problem: At least some of the research is, for whatever reason, simply wrong. Trying to hone in on the correct answer is very difficult indeed.

Indeed, it could be extremely difficult if Common Descent is false and phylogeny represents only a statistical artifact.

I always like to deal in examples people can relate to, so here goes.
Imagine you're trying to construct a (sort of) phylogeny of relatedness between whatever objects, let's say foods. It's pretty obvious that meat and fruit are quite distinct objects, so you'll get that right pretty quick. Upon further sorting, you may notice that fruits and vegetables are slightly more distinct, so you'll separate them. That's more difficult so it'll take you more time.
But even after you've correctly sorted the berry fruits and so on, you might have incorrectly sorted the tomato with the vegetables (it's a fruit!) because of it's taste. Yet when you take into account the classification of fruit, you will notice it belongs in quite a distinct group.

All your research (cutting it, tasting it, mixing it in different salads, etc.) would still have given you an incorrect classification because your methods were flawed.

All that's easy enough to understand and I'm sure you can transfer that to phylogeny.

It's a good demonstration of how similar kinds or types of life can be sorted without the need to assume relatedness. This is where the metaphysics come in and we hear claims like "But only relatedness explains their similarity!" And then we're back on the mystical Darwinian carnival ride.

And I think you're attacking a strawman position here. I have no problem with phylogenetic methodology within the context that it is used. However, it is clear that the context is a metaphysical assumption that is protected from being tested.

Actually, I won't assume that, I'll explain it anyway: Different genes might simultaneously disappear in two distinct branches, so looking at only a few genes might give incorrect answers. Looking at the whole picture or at known pseudogenes will usually give much better answers. That's why one should always be weary of a single gene that "goes against the flow": It might just be a statistical anomaly.

But wait, you say, that still didn't answer my question. Quite right it didn't. I just got through the first part: Why multiple papers might give different results, but also why loads and loads of papers hone in on the right answer.

Now your question was "how could phylogeny be falsified"? This is actually quite simple: Of course we have to assume an evolutionary relationship between organisms to even construct one, but should the results be wildly different from what we've so far constructed... well, then you'd have something.

I'm not talking about minor contradictions. Look again at the Churakov 2009 paper in the OP. The entire tree, down to the root, of placental mammals contradicts each other based on multiple ERV insertions. The invocation of incomplete lineage sorting to rescue the tree is massive. Here is the image again:

Hypothetically speaking, a similar magnitude rescue device could even be used to reconcile ERV's shared only by particular reptile / mammal groups. The evolutionist would simply suggest incompletely sorted polymorphism populations near the "root" of mammalian-reptilian common ancestor, diverging and converging as needed.

If we did indeed find that dogs grouped more closely with termites than with (other) mammals, that would be cause for not only serious concern, but sheer, bloody panic. There is no evolutionary pathway that would link dogs with termites, so the whole picture would crumble. That's what I said earlier about classifying fruit and meat: If it turned out meat was more closely classified with meat than with vegetables, we could chuck everything. But finding that the tomato doesn't belong with veg is an utterly minor change, same with what you mentioned.

I made the dog-termite comment for a reason. The hypothetical data that actually would falsify phylogeny is totally contradictory to basic common sense about nature, completely independent of evolutionary assumptions. It is not rational to expect a dog to be more similar to a termite than another mammal in any capacity.

As a crude example, it's like me saying: "If Biblical Creation is true, then we won't find a cow giving birth to a bird, because animals only follow after their kinds." Can I now present this to you as scientific evidence for Creation because I have laid out a condition of falsifiability? You're presenting a similar scenario by attempting to vindicate Phylogeny by the fact that obviously dissimilar things are dissimilar on a molecular level as well. It is a scientifically bankrupt model if its foundation is this flimsy.

Short conclusion:
1) It's no surprise different papers give different answers, that's what we would expect from humans with faults working on complex (scientific) problems.
2) Finding something that's only very slightly out of place isn't much more than a stir. Finding something that's completely out of place (dogs closely related to termites but not to mammals) would be utterly upsetting and would falsify phylogeny. Additionally, you could find a point in the tumbleweed (tree) where taxonomy actually breaks down!

But evolutionary phylogenetics has rescue devices to reconcile major contradictions. How is the root of all placental mammals a minor "stir" ?

 

[he_who_is_nobody]

That's the claim. So what kind of major contradictions should we expect if CD is false? Dogs grouping with termites over other mammals?

No. dogs not grouping with anything. The fact that groupings are always created is the evidence for universal common descent. In addition, the fact that groupings follow basic patterns that are not based on genetics is another confirmation.

This is incorrect. The model itself would show if universal common descent was incorrect. Again, the reason phylogenetic trees are created at all is because they have similar DNA/ERV/etc… to test. The only way for those to be similar is if they were shared at one point in the past.

This is a metaphysical claim: "The nature of similarity is inheritance". You're also using the assumption of Common Descent as the evidence for Common Descent.

Metaphysical claim? How is that a metaphysical claim, do you not know what DNA is? Have you ever heard of a paternity test? Furthermore, I am not using the assumption of common descent as evidence. If there were not common ancestry between these lineages, they would not create groups in the first place. Do you not know how phylogenetics works?

Furthermore your claim that shared DNA/ERV is a product shared ancestry is contradicted in the literature.

No, it is not. At the most, in your other thread, you have presented outliers in our data. Outliers do not contradict evidence.

If Evolution were a falsifiable scientific theory, you would now be considering this data as evidence in contradiction to the theory. However, since Evolution is actually a metaphysical / philosophical / religious ideology, you will automatically absorb this data as just more confirming evidence, and more light shed on how Evolution works.

First off, these are not contradictions in the way you wish they were. Again, they do contradict each other and only one answer could be correct. The problem here is that you are witnessing the scientific method in action and claiming that there is a problem with it. These scientists are actively researching a subject. The problems they are coming across may be answered in a few years after more data becomes known. It may also never be truly answered based on the nature of what they are studying. Either way, the arguing in active scientific literature does not equal a contradiction of universal common descent.

I could go back and point to several controversies in biology that are now resolved. At the time, you would have been making this same argument against it.

Second, the difference between evolutionary theory (and why it is science) and creationism (and why it is religion) is that evolutionary theory does change with new evidence. You are correct that these new findings can be absorbed into it, which is what science does. If you were correct in claiming that it was a religious ideology, it would be unchanging. Furthermore, any new changes that do happen to religions come under the table years later, new data in science has to be dealt with up front and quickly. Thus, based on your own assumption of what would happen, evolutionary theory is not a religious ideology.

My argument was not that a contradiction exists, but that the model is unfalsifiable. Those researchers can up-weight or down-weight different data sets, invert structures between homologous and homoplastic, and create imaginary past pathways to have the ancestry of a lineage converge with or diverge with certain data points in order to reconcile a certain relationship.

The models are falsifiable. Do you not know that all of these models are only working hypotheses? Any new data can falsify an old hypothesis in this type of study.

This is an argument to the future. "Someday evidence will show which tree is correct."

Argument to the future? Are you saying that new data cannot confirm or disconfirm a scientific hypothesis? I truly do not know what you mean by this.

And of course, the other possibility is that Common Descent is false. But this is philosophically unacceptable to a committed evolutionist.

Again, if common descent were wrong, there would be no way to create phylogenetic trees in the first place. These papers do not throw into question common descent.

You've claimed it twice. You have yet to defend it.

Have a read.

 

[herebedragons]

Hi lifepsyop

First, I want to say that it is refreshing to see a Creationist who works through their own argument and doesn't just regurgitate the same old PRATTs. I can see you have put some work into your argument and that is very commendable.

I just want to throw a couple of things out there for you to consider. The main thing is that science is about developing models that explain how the natural world works. It is not so much about proving any particular concept to be true but that the models we use best explain the data and give us a framework with which to do further research. As an example I was just talking to one of my professors today about a project he has been working on. He had been asked how and why the vapor cloud forms when dry ice is placed in water. In researching it he found that no one had really done any work on this and there was no solid answer. He had a couple of students working on this for their end of the year project and what they found was a direct correlation between surface tension and vapor pressure (both factors of intermolecular forces) and the amount of cloud formation. I told him that what they need to do now is develop a formula (i.e., a mathematical model) that they can plug in the surface tension and vapor pressure of various fluids and predict what the cloud formation will be. This model will strengthen the argument that these forces are responsible for controlling cloud formation.

Would the discovery of contradictions necessarily falsify the model? No, but it may indicate that the model needs to revised to better explain the new data. Let's say they test 30 substances and 29 of them are accurately predicted but one of them is not. Does that mean the whole model is wrong? No, the model is mostly right, but may need to account for some other factor. He already suggested that viscosity (another intermolecular force) may play a part in it as well, so perhaps by including viscosity into the equation, it will be a better model.

Another good example is Newton's law of universal gravitation. In the late 19th century, observations were made that began to contradict the Newtonian model. Did that falsify the model? No not really, it worked for most calculations, but was simply insufficient for some. Einstein proposed general relativity in the early 20th century as a superior model to Newton's and it did a better job of explaining more data. Now general relativity is consider incomplete. Falsified? ... because it doesn't explain all the data perfectly? No, not falsified, incomplete. We may need a better model.

The point is this: evolution is a model (theory of evolution) that attempts to explain the data regarding how living things change through time. Common descent is just a part of that model, it is not the entirety of the model. If it was shown that life originated from 1000 original life forms, the ToE would still be a valid model to explain how life got from then to now - but our understanding of common descent would change.

The problem with your approach is that you think that by pulling out one piece of the model, the whole theory will come crashing down. But that it just not the case. The ToE is built on a tremendous amount of data and facts that have a very solid footing. Showing one piece to be incomplete or even incorrect is not sufficient to bring down the whole model. You may very well be the "Einstein" of common descent and have correctly noted that there are serious problems with the current theory. However, what Einstein did that Creationists are failing to do, is propose a new model that explains more of the data and better fits the data.

The bottom line is that the ToE may very well be completely wrong, but without a sufficient model to replace it, it is unlikely to be abandoned. Don't like it? Understandable, but science needs these kinds of models in order to operate. Without a working model, science just could not function properly. You have probably heard people ask what has the theory of evolution done for science ... it's exactly that; it has given us a model, a framework within which to ask questions, it guides our research (that is it narrows our focus to areas that are most likely to yield results) So, if we tossed out the ToE today, what model should we use? Present a better model.

HBD

 

[lifepsyop]

Hi lifepsyop
First, I want to say that it is refreshing to see a Creationist who works through their own argument and doesn't just regurgitate the same old PRATTs. I can see you have put some work into your argument and that is very commendable.

Hello herebedragons,
Thank you for the compliment. I see evolutionists constantly regurgitating the same PRATTs as well, so I understand the frustration of having to deal with the same arguments over and over again.

I just want to throw a couple of things out there for you to consider. The main thing is that science is about developing models that explain how the natural world works. It is not so much about proving any particular concept to be true but that the models we use best explain the data and give us a framework with which to do further research.

.....Another good example is Newton's law of universal gravitation. In the late 19th century, observations were made that began to contradict the Newtonian model. Did that falsify the model? No not really, it worked for most calculations, but was simply insufficient for some. Einstein proposed general relativity in the early 20th century as a superior model to Newton's and it did a better job of explaining more data. Now general relativity is consider incomplete. Falsified? ... because it doesn't explain all the data perfectly? No, not falsified, incomplete. We may need a better model.

I have no problem with scientific models. As I've already explained, my contention is with metaphysical beliefs that are claimed to be scientific models, but are themselves protected from falsification. (or questioning of any kind really) And then served to the public, dressed up as an undeniable scientific fact, thus bolstering the myth that Common Descent has effectively been proven and only "unreasonable" people doubt it.

The point is this: evolution is a model (theory of evolution) that attempts to explain the data regarding how living things change through time. Common descent is just a part of that model, it is not the entirety of the model. If it was shown that life originated from 1000 original life forms, the ToE would still be a valid model to explain how life got from then to now - but our understanding of common descent would change.

I have no desire to take away Common Descent / Evolution from people who wish to use it as a model. My contention is with individuals and organizations who falsely claim that these models show strong evidence that Common Descent is true, "provisionally" or otherwise, and subsequently encourage campaigns of belittling those who are skeptical or will not conform to that particular model of origins.

The problem with your approach is that you think that by pulling out one piece of the model, the whole theory will come crashing down. But that it just not the case. The ToE is built on a tremendous amount of data and facts that have a very solid footing. Showing one piece to be incomplete or even incorrect is not sufficient to bring down the whole model. You may very well be the "Einstein" of common descent and have correctly noted that there are serious problems with the current theory. However, what Einstein did that Creationists are failing to do, is propose a new model that explains more of the data and better fits the data.

Well, to be more clear, I am not simply picking out conflicting data and waving it around yelling "Look it doesn't fit!".. I am attempting to demonstrate that the Common Descent model has built-in rescue devices to deal with even massively conflicting data.... so it no longer matters what fits and what doesn't fit... I am not so much concerned with the specific data itself, as I am the unfalsifiability of the model. If a model lacks substantial criteria for falsifiability, than the ability to detect data that is for or against, is lost. Therefore it is no longer scientific.

Obviously I disagree with you, and don't believe the ToE is built on a tremendous amount of data or facts. (though this sounds like the que for a "Evolution is just change over time" equivocation) I would say it is one of the most tenuous theories ever conceived, that is, the general belief that culled genetic accidents can turn worms into people given enough time and the right selection pressures. From my observation, the data supporting Evolution is extremely superficial, and requires nearly constant equivocation and obfuscation to support itself as a viable model of origins.

The bottom line is that the ToE may very well be completely wrong, but without a sufficient model to replace it, it is unlikely to be abandoned. Don't like it? Understandable, but science needs these kinds of models in order to operate. Without a working model, science just could not function properly. You have probably heard people ask what has the theory of evolution done for science ... it's exactly that; it has given us a model, a framework within which to ask questions, it guides our research (that is it narrows our focus to areas that are most likely to yield results) So, if we tossed out the ToE today, what model should we use? Present a better model.

If this were really the attitude among evolutionists, we would not see the overarching fear and anxiety of having the model questioned or criticized. There is an entire industry of evolutionists making sure the question you just asked me is *not allowed* to be answered (or even freely discussed) in any open academic forum among scientists. It's really not hard to see that a belief system is being protected underneath all the science claims.

I think the real fear is that when the enforced dogma of Common Descent is finally canned, the life sciences are going to continue unhindered or even improve. Evolutionists seem to enjoy fear-mongering this doomsday scenario that research laboratories around the world will crumble and all science will screech to an immediate halt the moment scientists begin questioning whether or not humans descended from a 400 million year-old population of fish. It's absolutely ludicrous.

 

[he_who_is_nobody]

Obviously I disagree with you, and don't believe the ToE is built on a tremendous amount of data or facts. (though this sounds like the que for a "Evolution is just change over time" equivocation) I would say it is one of the most tenuous theories ever conceived, that is, the general belief that culled genetic accidents can turn worms into people given enough time and the right selection pressures. From my observation, the data supporting Evolution is extremely superficial, and requires nearly constant equivocation and obfuscation to support itself as a viable model of origins.

:facepalm:

Yet another creationist that believes they can question a whole field of science without knowing the first thing about it. The hubris in creationists like this is astonishing.

 

[Engelbert]

The bottom line is that the ToE may very well be completely wrong, but without a sufficient model to replace it, it is unlikely to be abandoned. Don't like it? Understandable, but science needs these kinds of models in order to operate. Without a working model, science just could not function properly. You have probably heard people ask what has the theory of evolution done for science ... it's exactly that; it has given us a model, a framework within which to ask questions, it guides our research (that is it narrows our focus to areas that are most likely to yield results) So, if we tossed out the ToE today, what model should we use? Present a better model.

If this were really the attitude among evolutionists, we would not see the overarching fear and anxiety of having the model questioned or criticized. There is an entire industry of evolutionists making sure the question you just asked me is *not allowed* to be answered (or even freely discussed) in any open academic forum among scientists. It's really not hard to see that a belief system is being protected underneath all the science claims.

I think the real fear is that when the enforced dogma of Common Descent is finally canned, the life sciences are going to continue unhindered or even improve. Evolutionists seem to enjoy fear-mongering this doomsday scenario that research laboratories around the world will crumble and all science will screech to an immediate halt the moment scientists begin questioning whether or not humans descended from a 400 million year-old population of fish. It's absolutely ludicrous.

Hi lifepsyop.
I thought that herebedragons made a pretty good post there. I can't help but feel that you evaded answering and offering thoughts on one of the main questions he asked though. He asked, "if we tossed out the ToE today, what model should we use?"
So, really I was wondering the same thing. If common descent is wrong, then what is right? What is the better explanation that you believe should supercede common descent?
I see common descent as the best explanation for the data and I'm not entirely sure what the alternative that you offer is.
Thanks.

 

[Dustnite]

Obviously I disagree with you, and don't believe the ToE is built on a tremendous amount of data or facts. (though this sounds like the que for a "Evolution is just change over time" equivocation) I would say it is one of the most tenuous theories ever conceived, that is, the general belief that culled genetic accidents can turn worms into people given enough time and the right selection pressures. From my observation, the data supporting Evolution is extremely superficial, and requires nearly constant equivocation and obfuscation to support itself as a viable model of origins.

How exactly is that equivocating? You agree that bacteria can evolve (and I know you can't disagree because organisms like Nylonase exist) and instead of accepting that smaller changes in allele frequency lead to larger ones over time you instead equivocate on what the actual definition of evolution is.

No one can convince you of anything else until you actually take the time to stop arguing from incredulity and look at how the theory of evolution actually works. "Worms into Humans" is not possible and no one ever said it was. Just another standard creotard.

 

[lifepsyop]

Hi lifepsyop.
I thought that herebedragons made a pretty good post there. I can't help but feel that you evaded answering and offering thoughts on one of the main questions he asked though. He asked, "if we tossed out the ToE today, what model should we use?"
So, really I was wondering the same thing. If common descent is wrong, then what is right? What is the better explanation that you believe should supercede common descent?
I see common descent as the best explanation for the data and I'm not entirely sure what the alternative that you offer is.
Thanks.

Discussing replacement models is really not the topic of this thread, nor do I feel a replacement model is necessary to identify a broken one. I think the more scientific attitude would be, when you realize you're using a broken model, you admit so, and encourage discussion (rather than censorship) of seeking alternate models.

I have no problem with scientists who choose to keep using Common Descent models. Just be upfront about your metaphysical dependencies. Stop bluffing about Common Descent being scientifically ironclad.

 

[Engelbert]

Hi lifepsyop.
I thought that herebedragons made a pretty good post there. I can't help but feel that you evaded answering and offering thoughts on one of the main questions he asked though. He asked, "if we tossed out the ToE today, what model should we use?"
So, really I was wondering the same thing. If common descent is wrong, then what is right? What is the better explanation that you believe should supercede common descent?
I see common descent as the best explanation for the data and I'm not entirely sure what the alternative that you offer is.
Thanks.

Discussing replacement models is really not the topic of this thread, nor do I feel a replacement model is necessary to identify a broken one. I think the more scientific attitude would be, when you realize you're using a broken model, you admit so, and encourage discussion (rather than censorship) of seeking alternate models.

I have no problem with scientists who choose to keep using Common Descent models. Just be upfront about your metaphysical dependencies. Stop bluffing about Common Descent being scientifically ironclad.

Hi there Lifepsyop. Thanks very much for your response.

I believe Common Descent to be the most persuasive explanation for the history of biology on Earth. Ironclad - perhaps not philosophically. Extremely persuasive philosophically and scientifically - yes indeed.

It doesn't seem like a broken model to me, but let's assume for the sake of argument that it is false. Let's reject it. As is common in scientific investigation, I would very much like to investigate and explain the lack of understanding (of the natural world) we now have. If you are to be persuasive to me and if we are to do science as you have been advocating, the next logical step is to begin to brainstorm and to create some hypotheses and ideas, so that we may investigate and test. Given this could you please offer some thoughts or even just suggestions of how exactly you believe our current biodiversity came to be, so I can grapple with, investigate and evaluate these new or alternative possibilities. That's what I'd really like to do, if you are to truly persuade me here.

As you say yourself, I would like to "encourage discussion (rather than censorship) of seeking alternate models." So I am encouraging you to offer me something. To make some progress, this is the next step. I'd just like to hear what the alternatives are or at least some suggestions. This is of relevance to this thread, because a cogent alternative argument would increase your chances of finding some agreement here many times over.

(just between the two of us if that helps. I'm not seeking to derail the thread here, so you can answer other posts as required)

Thanks.

 

[lifepsyop]

Obviously I disagree with you, and don't believe the ToE is built on a tremendous amount of data or facts. (though this sounds like the que for a "Evolution is just change over time" equivocation) I would say it is one of the most tenuous theories ever conceived, that is, the general belief that culled genetic accidents can turn worms into people given enough time and the right selection pressures. From my observation, the data supporting Evolution is extremely superficial, and requires nearly constant equivocation and obfuscation to support itself as a viable model of origins.

How exactly is that equivocating? You agree that bacteria can evolve (and I know you can't disagree because organisms like Nylonase exist) and instead of accepting that smaller changes in allele frequency lead to larger ones over time you instead equivocate on what the actual definition of evolution is.

"Nylonase" isn't an organism. Nylonase is a name given to an Esterase enzyme with reduced hydrolytic acitivty, found in flavobacterium.

Small changes in allele frequency are obviously not evidence that such accumulations will eventually lead to the origin of major functional biological structures. Once again, you're using the assumption of Evolution as evidence for it. You're also committing the fallacy of affirming the consequent.

If Evolution is true, then it occurs through changes in allele frequency.
Allele frequency changes.
Therefore Evolution.

This is terrible reasoning.