Unfalsifiable Phylogeny

[lifepsyop]

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.

Hi Engelbert,

Since I've already stated I'm not interested in attempting to advance new scientific models, I'll respond to you on a more personal spiritual level. If I were you, I would honestly consider the possibility that Common Descent is false. I would consider the possibility that different kinds of lifeforms, even in their simplest molecular parts, are far too magnificently and functionally complex to have originated via culled genetic accidents or blind forces of any kind. I would suggest that different kinds of life had a Creator.

The Bible says that God is known by all men through the Creation and Conscience. God is known by the things that are made, and the sense of right and wrong written in our hearts. If I were in your position, questioning how the natural world came to be, I would consider the possibility that you already know the answer to this in your heart, and to humbly ask God yourself for further confirmation.

 

[Darkprophet232]

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

I'm not a scientist, I only have a fundamental-college level understanding of the most basic parts of biology (one intro course in biotechnology). I cannot have a meaningful conversation on most of these topics. As such, could you explain to me how that sentence is any different than saying "Corgi isn't an organism, it's a collection of enzymes that cause height deficiency, and is found in wolves,"?

 

[Inferno]

I'm not a scientist, I only have a fundamental-college level understanding of the most basic parts of biology (one intro course in biotechnology). I cannot have a meaningful conversation on most of these topics. As such, could you explain to me how that sentence is any different than saying "Corgi isn't an organism, it's a collection of enzymes that cause height deficiency, and is found in wolves,"?

Lifepsyop is correct on that one: Nylonase isn't a living organism, it's an enzyme.
Think of it this way: We are humans. We humans can produce haemoglobin. The gene responsible is the HBB-Gene. Would you therefore call humans HBB's? No.

In the same way, the organism you're talking about is called flavobacterium (Strain Sp. K172). It can digest certain by-products of nylon 6 manufacture. The gene responsible is called "nylonase". Would you therefore call this bacterium "nylonase"? No.

That being said, Dustnite's original point still stands, lifepsyop is simply being obnoxious.

By the way, I'll reply in full either tomorrow or on Sunday, RL first and all that jazz.

 

[Darkprophet232]

Thank you kindly, Inferno.

 

[ldmitruk]

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.

Hi Engelbert,

Since I've already stated I'm not interested in attempting to advance new scientific models, I'll respond to you on a more personal spiritual level. If I were you, I would honestly consider the possibility that Common Descent is false. I would consider the possibility that different kinds of lifeforms, even in their simplest molecular parts, are far too magnificently and functionally complex to have originated via culled genetic accidents or blind forces of any kind. I would suggest that different kinds of life had a Creator.

The Bible says that God is known by all men through the Creation and Conscience. God is known by the things that are made, and the sense of right and wrong written in our hearts. If I were in your position, questioning how the natural world came to be, I would consider the possibility that you already know the answer to this in your heart, and to humbly ask God yourself for further confirmation.

So your solution is nothing more than god did it and toss out science in favour of one's feelings?

 

[he_who_is_nobody]

...assumption...

It appears you attended the same university as gilbo12345.

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

This is terrible reasoning.

You are correct; this is terrible reasoning. [sarcasm]I never thought you would use a straw man.[/sarcasm]

However, this does get to the important aspect. It appears you do know the biological definition of evolution. Now, what mechanism stops allele frequency from changing in a population? In order for you to claim that there are different kinds, you would need to point to a mechanism that stops this process so organisms would be unable to change from one kind to another kind.

.

 

[lifepsyop]

...assumption...

It appears you attended the same university as gilbo12345.

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

This is terrible reasoning.

You are correct; this is terrible reasoning. [sarcasm]I never thought you would use a straw man.[/sarcasm]

However, this does get to the important aspect. It appears you do know the biological definition of evolution. Now, what mechanism stops allele frequency from changing in a population? In order for you to claim that there are different kinds, you would need to point to a mechanism that stops this process so organisms would be unable to change from one kind to another kind.

Please quote me where I claimed a mechanism exists that stops allele frequency from changing in a population, because I never said anything of the sort.

I'll explain again for clarity.
Affirming the Consequent is a major fallacy of reasoning. This is because even if the first two statements are true, the conclusion can still be false.

1. If major kinds(families / genera) can evolve into different kinds, than the process occurs via changes in allele frequency.
2. Changes in allele frequency occur.
3. Therefore, kinds of populations can evolve into different kinds.

The first two statements are true. The conclusion is a logical failure. Therefore you have no rational basis with which to shift the burden onto me to show you that changes in allele frequency can not accumulate to produce major new kinds of life.

As a crude analogy, it's like me making the claim:

1. If the complete text from Webster's Dictionary can be naturally written in beach sand, then the process can occur via rearrangement of sand particles due to wind, rain, and waves.
2. Rearrangement of sand particles due to wind, rain, and waves occurs.
3. Therefore, the complete text from Webster's Dictionary can be naturally written in beach sand.

Again, the first two statements are true. The conclusion is absurd. Obviously at this point, any rational person would contend that we must discuss the feasibility of such a large-scale process to occur, regardless of whether or not the most reduced unit of change is observed.

And I'm not comparing beach sand to population genetics, so please don't waste your time telling me I'm not accounting for natural selection. I'm simply giving you an example of the faulty logic you're employing. It might be easier to see with an analogy that isn't protected by your metaphysical belief in Evolution.

 

[lifepsyop]

I'm not a scientist, I only have a fundamental-college level understanding of the most basic parts of biology (one intro course in biotechnology). I cannot have a meaningful conversation on most of these topics. As such, could you explain to me how that sentence is any different than saying "Corgi isn't an organism, it's a collection of enzymes that cause height deficiency, and is found in wolves,"?

Lifepsyop is correct on that one: Nylonase isn't a living organism, it's an enzyme.
Think of it this way: We are humans. We humans can produce haemoglobin. The gene responsible is the HBB-Gene. Would you therefore call humans HBB's? No.

In the same way, the organism you're talking about is called flavobacterium (Strain Sp. K172). It can digest certain by-products of nylon 6 manufacture. The gene responsible is called "nylonase". Would you therefore call this bacterium "nylonase"? No.

That being said, Dustnite's original point still stands, lifepsyop is simply being obnoxious.

You're right, I was being somewhat obnoxious there. I knew what Dusnite was referring to, even though it appears to be a significant error of his in biological classification. But too many times I've watched evolutionists jump all over a creationist for not defining something in quite the correct way, or making other simple errors, and howling with glee at his ignorance. Or otherwise nitpicking at some detail instead of addressing the full thrust of an argument. I consider these dishonest and disingenuous tactics.

I will agree to avoid this type of behavior if the courtesy is returned. It is much better for discussion to deal with each others arguments honestly and charitably.

 

[he_who_is_nobody]

Please quote me where I claimed a mechanism exists that stops allele frequency from changing in a population, because I never said anything of the sort.

I know you have not said that, nor have I claimed you said that. Please work on your reading comprehension. I am asking for it, because without it there is no reason to assume that allelic frequency change stops at some arbitrary point in a population. You would need a mechanism to stop it if your idea were true.

I'll explain again for clarity.
Affirming the Consequent is a major fallacy of reasoning. This is because even if the first two statements are true, the conclusion can still be false.

1. If major kinds(families / genera) can evolve into different kinds, than the process occurs via changes in allele frequency.
2. Changes in allele frequency occur.
3. Therefore, kinds of populations can evolve into different kinds.

The first two statements are true. The conclusion is a logical failure. Therefore you have no rational basis with which to shift the burden onto me to show you that changes in allele frequency can not accumulate to produce major new kinds of life.

I am not affirming the consequence; I am basing a conclusion on the evidence. We have fossil, genetic, and observed laboratory evidence to base these conclusions on. We also know that allelic changes in a population are the only thing that causes these changes. No one is affirming the consequences; there is evidence that points to this as the conclusion.

Furthermore, it appears you are claiming that kind is equal to family/genera, thus all I have to do is show an example of a change above family/genera to show that allelic frequency change can and does lead to population change. Is this a correct statement to make about your position?

As a crude analogy, it's like me making the claim:

1. If the complete text from Webster's Dictionary can be naturally written in beach sand, then the process can occur via rearrangement of sand particles due to wind, rain, and waves.
2. Rearrangement of sand particles due to wind, rain, and waves occurs.
3. Therefore, the complete text from Webster's Dictionary can be naturally written in beach sand.

Again, the first two statements are true. The conclusion is absurd. Obviously at this point, any rational person would contend that we must discuss the feasibility of such a large-scale process to occur, regardless of whether or not the most reduced unit of change is observed.

And I'm not comparing beach sand to population genetics, so please don't waste your time telling me I'm not accounting for natural selection. I'm simply giving you an example of the faulty logic you're employing. It might be easier to see with an analogy that isn't protected by your metaphysical belief in Evolution.

You even point out at the end of this that your analogy is incorrect, so why use it? However, it fails in a larger way in that you are claiming that we are affirming the consequences when we are not, as I have pointed out above. Thus, another straw man.

Furthermore, let us discuss the feasibility of such a large-scale process occurring as rational people without the straw men you created. Please explain the fossil, genetic, and observed laboratory evidence without the theory of evolution and universal common descent.

In addition, it would be nice if you addressed my previous post as well. It covers your claim that evolution is a metaphysical belief.

 

[lifepsyop]

Please quote me where I claimed a mechanism exists that stops allele frequency from changing in a population, because I never said anything of the sort.

I know you have not said that, nor have I claimed you said that. Please work on your reading comprehension. I am asking for it, because without it there is no reason to assume that allelic frequency change stops at some arbitrary point in a population. You would need a mechanism to stop it if your idea were true.

Why are you insisting I defend something I never claimed? I have never implied or assumed any kind of mechanism that stops changes in allele frequency. You have yet to clarify why I need some mysterious mechanism to do this mysterious thing that only you seem to know or care about. Please present a coherent argument if you wish for me to respond.

I'll explain again for clarity.
Affirming the Consequent is a major fallacy of reasoning. This is because even if the first two statements are true, the conclusion can still be false.

1. If major kinds(families / genera) can evolve into different kinds, than the process occurs via changes in allele frequency.
2. Changes in allele frequency occur.
3. Therefore, kinds of populations can evolve into different kinds.

The first two statements are true. The conclusion is a logical failure. Therefore you have no rational basis with which to shift the burden onto me to show you that changes in allele frequency can not accumulate to produce major new kinds of life.

I am not affirming the consequence; I am basing a conclusion on the evidence. We have fossil, genetic, and observed laboratory evidence to base these conclusions on. We also know that allelic changes in a population are the only thing that causes these changes. No one is affirming the consequences; there is evidence that points to this as the conclusion.

You're affirming the consequent when you claim changes in allele frequency demonstrates that accumulated changes can lead to large-scale origins of new kinds of life.

Evolutionists constantly make the absurd argument that if one rejects Evolution, then they reject the observed process of change in allele frequency. This is the logical fallacy I'm addressing. Now that I've exposed it, you are shotgunning wikipedia links at me to attempt to prop up the fallacy that cannot stand on its own weight.

As a crude analogy, it's like me making the claim:

1. If the complete text from Webster's Dictionary can be naturally written in beach sand, then the process can occur via rearrangement of sand particles due to wind, rain, and waves.
2. Rearrangement of sand particles due to wind, rain, and waves occurs.
3. Therefore, the complete text from Webster's Dictionary can be naturally written in beach sand.

Again, the first two statements are true. The conclusion is absurd. Obviously at this point, any rational person would contend that we must discuss the feasibility of such a large-scale process to occur, regardless of whether or not the most reduced unit of change is observed.<i></i>

And I'm not comparing beach sand to population genetics, so please don't waste your time telling me I'm not accounting for natural selection. I'm simply giving you an example of the faulty logic you're employing. It might be easier to see with an analogy that isn't protected by your metaphysical belief in Evolution.

You even point out at the end of this that your analogy is incorrect, so why use it? However, it fails in a larger way in that you are claiming that we are affirming the consequences when we are not, as I have pointed out above. Thus, another straw man.

The analogy was not incorrect, it just went over your head. I'm not making an analogy to population genetics, but an analogy to inferring large-scale accumulated changes from its most reduced unit of change, and the similar logical fallacy of affirming the consequent that results. I highlighted a key statement in red to help you understand why the first two statements in both examples can be true but the conclusion can still be false.

 

[herebedragons]

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.

I don't think you have made a good enough case that the concept of common descent is a metaphysical belief. I understand your contention that common descent is being touted as an undeniable fact lending to the impression that it is protected from falsification. It is easy for people to get carried away and try and lend more credibility to their side than the facts really allow.

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.

No, a replacement model is not needed to identify a broken one. But a model is needed. This is the point I am trying to make. The model can and will not be scratched until a replacement model (one that explains the data better) is proposed. To date, no other suitable model has been offered. So what happens is, we try to fix the problems with the current model. Scientists do acknowledge that there are problems resolving phylogenetic trees and would welcome proposals that would allow 100% resolution. But the current model is what we have to work with at the present time.

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.

If this is your whole point, I personally would concede that the ToE and in particular common descent is not ironclad - pretty darn convincing though, IMO. I think if you asked the question "Could common descent be wrong?" most people would admit, "Yes it could be - but it is highly unlikely that it is." Most honest people leave open the possibility that future evidence could overturn current scientific consensus.

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

This is terrible reasoning.

Yes, terrible reasoning (on your part).

The justification for common descent works this way:

Premise 1. All organisms on earth have descended from organisms that have preceded them. * observed fact

Premise 2. Organisms inherit characteristics from the parent organisms. * observed fact

Premise 3. These characteristics are not inherited perfectly, but are modified so that the offspring are different than the parents. * observed fact

Premise 4. Natural selection acts upon these differences by selection of the most fit phenotypes. * observed fact

Premise 5. If daughter populations are reproductively isolated they can develop significant enough differences so as to be able to identify individuals as members of one population or the other. * observed fact

Now, take any organism, living or dead (fossilized), and ask the question "Is this creature descended from parent organisms that preceded it?" If the answer is "Yes." (which is a logical assumption to make and yes it is an assumption since we were not there to witness its birth - but never-the-less a valid and logical assumption since we know premise #1 to be true) then premise 2, 3, 4 and 5 naturally follow. Now ask this question of every organism known to exist. At what point would you answer "No, this organism did not descend from parent organisms that preceded it?"

This is the contribution Charles Darwin made. Despite the errors he made in the mechanisms involved, he largely worked out this justification for common descent.

Now none of this is proof that common descent is correct, this is the justification for the concept. So there is no assuming the conclusion here, so don't even bring it up . This is the justification for why common descent is a viable model which we can test.

This is where comments such as from HWIN:

you would need to point to a mechanism that stops this process so organisms would be unable to change from one kind to another kind.

What organism could you point to and say "That organism did not descend from a parent organism, with modification." ?

This is why, despite some flaws, a new model would need to be proposed in order for this model to be abandoned. It has very, very strong justification. I think if you took a good, honest look at the evidence for common descent, it would explain > 80% of the data. In other words, more than 80% or the data confirms common descent. (Yes, I puled the 80% out of my hat - it comes from my personal experience and research. I actually think it is higher than that but I chose to be conservative in my estimates) So common descent does a very good job of modeling reality. You are looking at the 20% that doesn't quite fit and suggesting the whole theory be scrapped, which is not really logical is it?

So what do we do with the ~ 20% that doesn't fit? We try to resolve it. We adjust the theory to accommodate the new data. We offer explanations that attempt to resolve the issues. But you call that ad-hoc reasoning. But when there is a model that works for 80% of the data, it won't be discarded until a model is proposed that explains 90% of the data. Until then, we work with what we have.

(though this sounds like the que for a "Evolution is just change over time" equivocation)

That's EFF nonsense, it doesn't fly in the real world.

HBD

 

[he_who_is_nobody]

Why are you insisting I defend something I never claimed? I have never implied or assumed any kind of mechanism that stops changes in allele frequency. You have yet to clarify why I need some mysterious mechanism to do this mysterious thing that only you seem to know or care about. Please present a coherent argument if you wish for me to respond.

Without this mechanism, you have no argument. As I said before, without it there is no reason to assume that allelic frequency change stops at some arbitrary point in a population. In order for there to be a genetic argument for creationism, there needs to be a mechanism that stops evolution from continuing. Do not be angry with me because I know your side of the argument better than you do.

You're affirming the consequent when you claim changes in allele frequency demonstrates that accumulated changes can lead to large-scale origins of new kinds of life.

Again, no. I am not affirming the consequence. I provided evidence that shows large-scale change in organisms. You did not address them, only acted as if they do not exist. Furthermore, I did not argue allelic frequency change demonstrates accumulated change, which is the straw man you created. I argued that we have evidence for large-scale change in organisms and the only thing that we know of that accounts for it is allelic change in populations, tis a difference.

Evolutionists constantly make the absurd argument that if one rejects Evolution, then they reject the observed process of change in allele frequency. This is the logical fallacy I'm addressing. Now that I've exposed it, you are shotgunning wikipedia links at me to attempt to prop up the fallacy that cannot stand on its own weight.

First off, that is not absurd; evolution by definition is change in allelic frequencies in a population over time. Thus, when one says (s)he rejects evolution; that is what (s)he is saying by definition. Second, I did not shotgun wikipedia links (only one of those sites is from wikipedia, so thanks for demonstrating that you did not even look at the other two), I provided evidence for universal common descent, which is what you were arguing against. I am not the straw man you constructed; I know that your argument lies with universal common descent and not evolution. That is why I have provided evidence for universal common descent. You sidestepped that evidence by going back to your straw man argument and claiming that I am shot gunning links. How else do you want me to provide evidence if I cannot use links?

The analogy was not incorrect, it just went over your head. I'm not making an analogy to population genetics, but an analogy to inferring large-scale accumulated changes from its most reduced unit of change, and the similar logical fallacy of affirming the consequent that results. I highlighted a key statement in red to help you understand why the first two statements in both examples can be true but the conclusion can still be false.

Yes the analogy is incorrect. As I pointed out, I am not affirming the consequences, I provided you with evidence that supports universal common descent, and you refused to address it. You keep insisting that I argue for your straw man when I will not. Allelic frequency change is not the evidence we use for universal common descent. This is made the more hilarious when you actually cut out my next paragraph wherein I again point out the evidence, used your own words (the same ones you have just now highlighted), and restate your straw man. Thus, I will just quote what I said back:

he_who_is_nobody[/url]"]Furthermore, let us discuss the feasibility of such a large-scale process occurring as rational people without the straw men you created. Please explain the fossil, genetic, and observed laboratory evidence without the theory of evolution and universal common descent.

In addition, it would be nice if you addressed my previous post as well. It covers your claim that evolution is a metaphysical belief.

 

[Rumraket]

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.

Outright false.

The only thing that is required to falsify common descent is if the number of discordant sites outweigh the number sites congruent with a nested hiearchy to a significant statistical degree. That is all.

Oh by the way, that limitation is actually well defined. You would do well to read up on the mathematics and logic behind the evidence for common descent:
http://www.talkorigins.org/faqs/comdesc/section1.html#independent_convergence

Pay special attention to the references given that define the statistical limitations. This directly contradicts your above claim.

Prediction 1.3: Consilience of independent phylogenies

"It will be determined to what extent the phylogenetic tree, as derived from molecular data in complete independence from the results of organismal biology, coincides with the phylogenetic tree constructed on the basis of organismal biology. If the two phylogenetic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished. Indeed, only the theory of evolution, combined with the realization that events at any supramolecular level are consistent with molecular events, could reasonably account for such a congruence between lines of evidence obtained independently, namely amino acid sequences of homologous polypeptide chains on the one hand, and the finds of organismal taxonomy and paleontology on the other hand. Besides offering an intellectual satisfaction to some, the advertising of such evidence would of course amount to beating a dead horse. Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life."

Emile Zuckerkandl and Linus Pauling, discussing the possibility of the twin nested hierarchy before the first molecular phylogenies had been made.
(1965) "Evolutionary Divergence and Convergence in Proteins." in Evolving Genes and Proteins, p. 101.

Here we commence to beat Pauling's poor 40-year dead horse. If there is one historical phylogenetic tree which unites all species in an objective genealogy, all separate lines of evidence should converge on the same tree (Penny et al. 1982; Penny et al. 1991; Zuckerkandl and Pauling 1965). Independently derived phylogenetic trees of all organisms should match each other with a high degree of statistical significance.

Confirmation:

Well-determined phylogenetic trees inferred from the independent evidence of morphology and molecular sequences match with an extremely high degree of statistical significance. Many genes with very basic cellular functions are ubiquitous—they occur in the genomes of most or all organisms. An oft-cited example is the cytochrome c gene. Since all eukaryotes contain the gene for this essential protein, neither its presence nor its function correlates with organismal morphology. Additionally, because of the fact of DNA coding redundancy, parts of certain DNA sequences have absolutely no correlation with phenotype (e.g. certain introns or the four-fold degenerate third-base position of most DNA codons). Due to these two aspects of certain DNA sequences, ubiquity and redundancy, DNA sequences can be carefully chosen that constitute completely independent data from morphology. (See point 17 and 18 for more background about the molecular sequence evidence and for more detail about how it is independent of morphology.) The degree of phylogenetic congruence between these independent data sets is nothing short of incredible.

In science, independent measurements of theoretical values are never exact. When inferring any value (such as a physical constant like the charge of the electron, the mass of the proton, or the speed of light) some error always exists in the measurement, and all independent measurements are incongruent to some extent. Of course, the true value of something is never known for certain in science—all we have are measurements that we hope approximate the true value. Scientifically, then, the important relevant questions are "When comparing two measurements, how much of a discrepancy does it take to be a problem?" and "How close must the measurements be in order to give a strong confirmation?" Scientists answer these questions quantitatively with probability and statistics (Box 1978; Fisher 1990; Wadsworth 1997). To be scientifically rigorous we require statistical significance. Some measurements of a given value match with statistical significance (good), and some do not (bad), even though no measurements match exactly (reality).

...

Potential Falsification:

When it became possible to sequence biological molecules, the realization of a markedly different tree based on the independent molecular evidence would have been a fatal blow to the theory of evolution, even though that is by far the most likely result. More precisely, the common descent hypothesis would have been falsified if the universal phylogenetic trees determined from the independent molecular and morphological evidence did not match with statistical significance. Furthermore, we are now in a position to begin construction of phylogenetic trees based on other independent lines of data, such as chromosomal organization. In a very general sense, chromosome number and length and the chromosomal position of genes are all causally independent of both morphology and of sequence identity. Phylogenies constructed from these data should recapitulate the standard phylogenetic tree as well (Hillis et al. 1996; Li 1997).

This whole thread is a travesty borne out of your own misunderstanding of the basic facts used in molecular phylogenetics. Oh, and your deliberate leaving out of important details.

If you fundamentalist creationist doctrine was really true, why would you have to lie to support it?

 

[Rumraket]

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.

Hi Engelbert,

Since I've already stated I'm not interested in attempting to advance new scientific models, I'll respond to you on a more personal spiritual level. If I were you, I would honestly consider the possibility that Common Descent is false. I would consider the possibility that different kinds of lifeforms, even in their simplest molecular parts, are far too magnificently and functionally complex to have originated via culled genetic accidents or blind forces of any kind. I would suggest that different kinds of life had a Creator.

The Bible says that God is known by all men through the Creation and Conscience. God is known by the things that are made, and the sense of right and wrong written in our hearts. If I were in your position, questioning how the natural world came to be, I would consider the possibility that you already know the answer to this in your heart, and to humbly ask God yourself for further confirmation.

Well thank you for telling us about how you're here to propagandize for doctrine. Not really needed, we already knew that.

In answer to your last bit, maybe YOU should ask yourself in YOUR heart, why it is that you have to LIE and leave out important details pertaining to molecular phylogenetics, in order to lend support to your creationist doctrine?

Doesn't it strike you as odd that if you're really selling truth, you have to lie about it?

 

[Rumraket]

Anyway, this guy relies on the lack of a deeper understanding of the intricacies of molecular biology among a lay atheist audience to present his arguments.

He's probably the same guy, "Nevertheless" - who got banned from rationalskepticism.org and got relegated to to irrelevancy and jokes over on talkrational.org.

A particular hobbyhorse of his is the subject of computational evolution and molecular phylogenetics. He spends hours scouring pubmed and other sites looking for specific quotemines he can use to present a carefully constructed picture of molecular evolution.

He will frequently cite older studies (but occasionally also newer ones) that show incongruent trees and calls for caution with respect to inferring evolutionary relationships using certain genes or loci otherwise known to be problematic markers. He won't tell you that many of these issues he bring up have already been solved in other works, and as I said he positivel y relies on people's general lack of insight into molecular evolution.

He will neglect to cite key studies resolving earlier difficulties, declare that his carefully handpicked and quotemined studies undermines the whole field and generally insinuate that there is some kind of conspiracy of information going around, perpetrated by evolutionary biologists.

The first ironic thing to note is that, if this supposed conspiracy was real, why is all this information publicly available?

He will insinuate that because different tree-building algorithms sometimes contradict each other, that therefore the trees are statistical artifacts, instead of making any effort to explain what the causes of such incongruencies can be caused by.

He usually won't tell you anything about varying mutation rates between species (or the causes thereof), but if he does, he will spin it to claim that it makes the construction of molecular phylogenies impossible.

He will often cite studies that contradict the commonly established phylogenies for various reasons, which can be anything from lack of data (using single-genes to infer phylogenies, or multiple genes that evolve at different rates and so on and so forth). vHe will cite studies on mitochondrial DNA phylogenies showing problems, neglecting to mention anything about how or why (and who resolved the problem or how).

He will make no effort to shed light on the history of the subject, how or when the problems were first detected and then later resolved both experimentally and theoretically.

He will make conspiratorial claims about the critieria for standard of falsification being moved if contradictions or outliers are found, and declare that resolutions are only applied in an ad-hoc manner to "make it fit".

This is just a fair warning to anyone who wishes to engage with him: He knows some molecular phylogenetics and population genetics, and is deliberately handpicking the papers and quotemining them, neglecting to mention many confounding factors with damning implications for his claims. He will deliberately misrepresent the statistical nature of the evidence for evolution in molecular phylogenetics, including the underlying logic and reasoning that justifies doing the molecula phylogenies.

Basically, he lies a lot. On purpose. And he knows it.

 

[lifepsyop]

The only thing that is required to falsify common descent is if the number of discordant sites outweigh the number sites congruent with a nested hiearchy to a significant statistical degree. That is all.

Can you give an example of common descent being falsified by phylogenetics? And then we can compare it to the data from the OP and see if it can't be rescued.

And you didn't respond to any of the data I presented in the OP. Maybe when you're finished with your lengthy divination of my intentions you could grace me with a substantive response, rather than just telling me I'm wrong and linking to a pro-evolution blog.

 

[lifepsyop]

I am not affirming the consequence.

evolution by definition is change in allelic frequencies in a population over time. Thus, when one says (s)he rejects evolution; that is what (s)he is saying by definition.

You just stated that one can not reject the conclusion without rejecting the second point. This is the same thing as affirming the consequent.

1. If Evolution is true, then it occurs through changes in allele frequency.
2. Changes in allele frequency occur.
3. Therefore Evolution.

Now you will tell me that you didn't just do that, (even though you clearly just did)

I really don't have time to keep playing this game.

 

[he_who_is_nobody]

I am not affirming the consequence.

evolution by definition is change in allelic frequencies in a population over time. Thus, when one says (s)he rejects evolution; that is what (s)he is saying by definition.

You just stated that one can not reject the conclusion without rejecting the second point. This is the same thing as affirming the consequent.

1. If Evolution is true, then it occurs through changes in allele frequency.
2. Changes in allele frequency occur.
3. Therefore Evolution.

Now you will tell me that you didn't just do that, (even though you clearly just did)

Wow, quote mined by a creationist. [sarcasm]Who would have thought that was possible.[/sarcasm]

First, let me put my quotes back into context and see what exactly you left on the cutting room floor.

he_who_is_nobody[/url]"]

You're affirming the consequent when you claim changes in allele frequency demonstrates that accumulated changes can lead to large-scale origins of new kinds of life.

Again, no. I am not affirming the consequence. I provided evidence that shows large-scale change in organisms. You did not address them, only acted as if they do not exist. Furthermore, I did not argue allelic frequency change demonstrates accumulated change, which is the straw man you created. I argued that we have evidence for large-scale change in organisms and the only thing that we know of that accounts for it is allelic change in populations, tis a difference.

he_who_is_nobody[/url]"]

Evolutionists constantly make the absurd argument that if one rejects Evolution, then they reject the observed process of change in allele frequency. This is the logical fallacy I'm addressing. Now that I've exposed it, you are shotgunning wikipedia links at me to attempt to prop up the fallacy that cannot stand on its own weight.

First off, that is not absurd; evolution by definition is change in allelic frequencies in a population over time. Thus, when one says (s)he rejects evolution; that is what (s)he is saying by definition. Second, I did not shotgun wikipedia links (only one of those sites is from wikipedia, so thanks for demonstrating that you did not even look at the other two), I provided evidence for universal common descent, which is what you were arguing against. I am not the straw man you constructed; I know that your argument lies with universal common descent and not evolution. That is why I have provided evidence for universal common descent. You sidestepped that evidence by going back to your straw man argument and claiming that I am shot gunning links. How else do you want me to provide evidence if I cannot use links?

As one can see from my second quote, I am correcting your faulty understanding of the biological definition of evolution. One of my pet peeves is when creationists use the wrong definition of evolution, when their own sources correctly define it.

But wait a minute, it appears, from the bits I underline, that my argument do not make sense compared to the argument you made above. That is probably because I was not arguing against what you stated above, I was arguing against this:

lifepsyop[/url]"]I'll explain again for clarity.
Affirming the Consequent is a major fallacy of reasoning. This is because even if the first two statements are true, the conclusion can still be false.

1. If major kinds(families / genera) can evolve into different kinds, than the process occurs via changes in allele frequency.
2. Changes in allele frequency occur.
3. Therefore, kinds of populations can evolve into different kinds.

The first two statements are true. The conclusion is a logical failure. Therefore you have no rational basis with which to shift the burden onto me to show you that changes in allele frequency can not accumulate to produce major new kinds of life.

Now, when my quotes are read in context with that argument in mind, they make sense. However, if you want me to address your above argument it is easy enough. Your statement of, “f Evolution is true, then it occurs through changes in allele frequency” is false. The phenomenon of allelic change occurs, and we call it evolution, it is as simple as that.

This again, gets back to my pet peeve when it comes to creationists and the biological definition of evolution. Their real arguments are never with evolution, because they actually accept evolution by definition. Their arguments are only with universal common descent and the theory of evolution, However, they are programmed to hate the word evolution, thus they cannot accept that an observed phenomenon is called evolution by definition.

I have to admit that I made the mistake in thinking that you were fine with this definition and moved on to arguing for universal common descent and the theory of evolution. I now see that I was mistaken and you do need a remedial course in biology.

I really don't have time to keep playing this game.

The only one that is playing games is you. We both know why you do not want to move onto the evidence for universal common descent. You would much rather I argue the straw man you keep constructing than deal with the real arguments I have presented. You even went as far as to place two statements I have made, which were unrelated, and claim that I am saying things that I clearly am not. Therefore, whenever you are ready to stop with the games, my actual arguments will be here for you to address:

he_who_is_nobody[/url]"]Furthermore, let us discuss the feasibility of such a large-scale process occurring as rational people without the straw men you created. Please explain the fossil, genetic, and observed laboratory evidence without the theory of evolution and universal common descent.

In addition, it would be nice if you addressed my previous post as well. It covers your claim that evolution is a metaphysical belief.

 

[Rumraket]

The only thing that is required to falsify common descent is if the number of discordant sites outweigh the number sites congruent with a nested hiearchy to a significant statistical degree. That is all.

Can you give an example of common descent being falsified by phylogenetics?

No, because common descent isn't false.

Regardless, I just told you how to do it. If you did a phylogeny with multiple loci you had good reason to think constituted a statistically significant fraction of the genome, that is, "what you would expect to see on average when aligning any shared orthologues loci" - and your finding was that either all the different loci, or a statistically significant majority of them disagreed with each other, such that they did not converge statistically on a single tree.

In other words, instead of seeing this:

We would be seeing this:

In such a case, we would not be justified in inferring common descent.

What is important to remember, and as Douglas Theobald writes on, is that the total number of possible trees you can construct from even a relatively minor dataset is truly staggering. So the odds of finding that all your trees statistically converge on the same general trend is incredibly improbable. The fact that they DO is extremely strong evidence for common descent:

When two independently determined trees mismatch by some branches, they are called "incongruent". In general, phylogenetic trees may be very incongruent and still match with an extremely high degree of statistical significance (Hendy et al. 1984; Penny et al. 1982; Penny and Hendy 1986; Steel and Penny 1993). Even for a phylogeny with a small number of organisms, the total number of possible trees is extremely large. For example, there are about a thousand different possible phylogenies for only six organisms; for nine organisms, there are millions of possible phylogenies; for 12 organisms, there are nearly 14 trillion different possible phylogenies (Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). Thus, the probability of finding two similar trees by chance via two independent methods is extremely small in most cases. In fact, two different trees of 16 organisms that mismatch by as many as 10 branches still match with high statistical significance (Hendy et al. 1984, Table 4; Steel and Penny 1993). For more information on the statistical significance of trees that do not match exactly, see "Statistics of Incongruent Phylogenetic Trees".

The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al. 2002; Penny et al. 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:

"Biologists seem to seek the 'The One Tree' and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al. 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 106." (Penny and Hendy 1986, p. 414)

And then we can compare it to the data from the OP and see if it can't be rescued.

And you didn't respond to any of the data I presented in the OP. Maybe when you're finished with your lengthy divination of my intentions you could grace me with a substantive response, rather than just telling me I'm wrong and linking to a pro-evolution blog.

Maybe you could deal with the facts of the matter instead of propagandizing for doctrine.

 

[Rumraket]

In response to something from your op, you write:

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.

Again it depends on the degree and frequency with which they diverge. Confounding factors exist that make certain relationships difficult to resolve. No, that's not an excuse, it's simply an unavoidable fact.
As the whole genome study goes on to say:

The inconsistency among these results underlines the difficulty in resolving the three-taxon relationship involving rodents, primates, and carnivores. The short branches separating these groups reside deep within the mammalian phylogenetic tree, thereby enhancing the effects of any reconstruction artifacts. These can be related to data quality or any failure to accurately model particular aspects of evolution such as parallel evolution, lineage specific mutation rates, or other changes in the evolutionary process [14].

Long branch attraction (LBA) may occur when an ingroup has a faster rate of evolution, thereby promoting migration of the long branch with accelerated evolution toward the long branch of the outgroup. This phenomenon was first examined by Felsenstein [18], who showed that trees with long branches could be positively misleading when reconstructed under the parsimony criterium. Parsimony, which computes the minimum number of evolutionary steps required to explain the observed sequences, however, does not have the properties of distance and is not additive. Additive means that for a lineage A → B → C, the equation dAB + dBC = dAC is satisfied in the expected value. In case any particular taxon (e.g., mouse [19]) evolves faster than the other two in our three-taxon analysis, LBA could possibly affect the outcome for parsimony or nonadditive distance measures. Additive distance estimates such as those produced by the Markov model of evolution used in this study should not be affected by LBA. However, systematic biases such as those produced by parallel evolution or other deviations from the model can affect any evolutionary distance measure.

Parallel morphological or molecular evolution can occur when two species develop similar characteristics because of adaptation to similar environments or life strategies. A coupling between molecular and morphological evolution among mammals is highly speculative, however. To counter any systematic biases, we have made the precaution of using different phylogenetic methods based on different evolutionary phenomena because it is unlikely that all methods will be affected by systematic biases in the same way.

Taxon sampling may affect the accuracy of phylogenetic reconstruction [20–23]. Some authors argue that increasing the number of characters sampled per taxon improves the accuracy, while others state that accuracy is better improved by subdividing long branches by including more taxa, resulting in fewer characters overall. In any case, the choice of more characters versus more taxa depends on the phylogeny under consideration.

All these different confounding factors aren't erected as excuses for why you potentially get incongruent trees. They're observable facts, we understand how and why this sometimes happens. You could theoretically do phylogenetics on an evolving population of viruses/bacteria/cancer cells in your lab and reproduce the same effect, with multiple close "speciation events" and incomplete lineage sortings making it difficult to resolve the phylogeny of your evolving organisms.

You fail to properly appreciate how the inferences underlying the construction of trees work, and how they support common descent. Evolution is a stochastic process working at a population level, you EXPECT incomplete lineage sorting on speciation events. You EXPECT incongruent trees occasionally. You EXPECT temporally close speciation events on occasion. You must look at the overall pattern instead of ignoring it and focusing on the relatively few and minor incongruencies. Resolving individual closely related species will always be significantly more difficult than resolving relationships at the family or clade level. Regardless of how Primates, Carnivores or Rodents group relatively to each other deep within the mammalian clade, the simple fact is that Primates still group together, Carnivores still group together and Rodents still group together, and that they all still nest within mammals, and that all mammals still nest together within therapsidia, which nests within Animalia etc. etc.

This very same "problem" you see here can be reproduced for many datasets of very closely related species. For example, resolving the internal taxons within snails face the same difficulties. But again, all snails still unambigously nest within Gastropoda, which still unambigously nests within Mollusca and so on and so forth.

You're neglecting the main pattern, focusing on the minor details, thinking that because these difficulties exist we can't be justified in using molecular phylogenies to infer common descent. I'm sorry, but that simply doesn't follow.

Look at my above two pictures again, there are many many more possible ways to construct trees using the same dataset that gives a picture similar to the bottom one, than there are ways to construct trees that statistically converge on the same overall pattern.

Universal common descent for all known species on the planet is still massively statistically supported to an overwhelming degree, even if resolving the within-clade or within-family relationships can be challenging.