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Debate: dandan vs Inferno

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Debate: dandan vs Inferno
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InfernoContributorUser avatarPosts: 2298Joined: Thu Apr 30, 2009 7:36 pmLocation: Vienna, Austria Gender: Cake

Post Re: Debate: dandan vs Inferno

I didn't really want to reply to this post. I really didn't want to reply to this post.
I have posted eight times, this will be my ninth time. Dandan has posted eight times, plus one post right at the beginning and one post explaining an earlier post. In that time, we've talked about platypus venom in Dandan's first post and in his second and in his third and in his fourth and in his... and finally in his eighth. Never during this whole debate have have we really talked about anything that wasn't covered in my second post. I then merely expanded on that, and explained, and explained, and expanded, and explained.

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dandan wrote:No same genes doesn´t mean identical genes, for example humans, chimps and all mammals have the FOXP2 gene, it is said to be the “same gene” but the gene is not identical in all species, if you compare the FOXP2 gene in humans and chimps you will find some differences.

An analogy would be the bible (King James version) and the bible (new international version) it is said to be the same book, but it is not identical.


Entirely different argument.
I specifically quoted portions where you said "exact same mutations" and "same genetic material". You are now trying, in retrospect I might add, to change the intent of what you said.

dandan wrote:Obviously since we are suppose to share a common ancestor with chimps, originally chimps and humans where the same animal and therefore we had the same FOXP2 gene, according to evolution, the differences between the human FOXP2 gene and the Chimp FOXP2 gene evolved after they diverged. ¿Agree?


Not necessarily, but in essence correct. I'll explain that comment shortly.

dandan wrote:Obviously if we compare the human FOXP2 gene with the Cow FOXP2 gene we would expect to find even more differences because we diverged from cows longer ago than we did from chimps ¿Agree?


Again, not with absolute necessity, but in essence correct.
It is possible, though not particularly likely, that a particular gene under a set of similar circumstances can be subject to extreme purifying selection. In that case, it could happen that two gene sequences are almost identical, even though the lineages may have split some time ago. It's not particularly likely, I'm not even sure if an instance of this has been found, but it is theoretically possible. I merely mention this for the sake of accuracy.

dandan wrote:From an evolutionary perspective if humans and cows have a common mutation in the FOXP2 gene, that is absent in other primates, evolutionists would say that cows and humans received the same mutation independently ¿agree?


Given no further information, this would appear to be the most likely explanation. Why, will you claim that FOXP2 shows that they're differently related? Good luck with that...
Image

dandan wrote:This is what happened; scientists study a series of genes that are related to echolocation, these genes are present in all mammals however only a particular variant of these genes allows echolocation.


As far as I'm aware we're talking about "Prestin", not several others?

dandan wrote:The problem is that bats and dolphins being far relatives, have the same variation at least in 200 sites, (closer relatives don´t have these variatons) the implication is that bats and dolphins received the same mutations 200 times independently.


I already told you a few times that this is wrong, but I'll give you the chance to actually prove your point.
The following is the gene Slc26a5, also known as Prestin. In this particular example, it's the variant from Mus musculus or the common house mouse.
A search for orthologues yields 104 results. Sticking with a dolphin/bat comparison, I chose Tursiops truncatus (bottlenosed dolphin) and either Myotis lucifugus (little brown bat), Myotis brandtii (Brandt's bat) or Eptesicus fuscus (big brown bat). By clicking on "FASTA", you can see the whole nucleotide sequence.
Now show me the 200 sites.

dandan wrote:So unless you prove that it is statistically possible and reasonable for 2 independent clades to suffer from the same mutations 200 times independently, I think you are forces to admit that I least this is a valid argument against evolution.


First, I already told you that "suffer" is not the word to be used.
Second, having asked both Rumraket and a biologist from my circle of friends, I still believe I'm correctly interpreting the results and you're dead wrong. Like you were with the platypus-papers, I might add. You made such a fuss for such a long time and you still haven't conceded that you're wrong, you've simply dropped it.
Third, valid argument? It wasn't even a coherent idea most of the time.

dandan wrote:It seems to be a similar case as it is with echolocation, I emailed the author but she told me that she was out of town and that was going to answer until mid-august.


I quoted her E-Mail in the previous post, you simply have to read it. It is now early September, did she answer?

dandan wrote:PF = 0.5 in a hypothetical population of 1 individual, with that clarified, do you agree that both equations are the same one?


No, they're not.
Inferno wrote:As I explained, your original one is: (I erroneously wrote Pt while it should have been Pf in the first post.)
(Mt x Ps x Pf x Nb)/Gs

Your new one is
(Mt x Ps)/Gs x 0.5


As I explained, you didn't correctly substitute your terms. The two are not the same, can you see that?

However, I myself have now made a mistake and I wish to correct that. In the last post, I claimed that Pf = 1/2Ps while it's actually Pf = 1/(2Ps). I then erroneously claimed that the problem is with the 0.5, while it really lay with the number of base pairs, Nb. You suddenly dropped them, which confused the hell out of me. Apologies for the confusion, but to be honest it's quite difficult following posts.

In any case, it doesn't matter because I already presented the correct ones very early on. Do you accept that the ones I provided are correct and accepted by scientists?

That being said, I want you to admit to a very particular point. A post back, I showed that even if I substitute the population of 1 (which you claim helps me) by a population of 1,000,000 (which you claim is detrimental to my position), we find that it actually agrees with what I've been saying all along. I explained that here:
Inferno wrote:You originally claimed
((100)(1)/3,000,0000,000)) x (1/2)
so all we have to do is substitute 1 by 1,000,000 so the new equation looks like this:
((100)(1,000,000)/3,000,0000,000)) x (1/2)
Correct?

Here's an oopsie: When I calculate that, I get 1:60 or one mutation every 60 years. So following your advice, I multiply 1/60 x 1/14 and I get 1/840. Meaning we should hit the 14-amino-acid lottery every 840 years. Strange, didn't you say using a larger population size should give us a lower probability? That's funny, it almost seems like your "equation" doesn't calculate what you think it does.


Do you admit that your equation is simply wrong, that it's never been used in academia?

dandan wrote:However we both agree that it would be impossible for 2 independent clades to suffer from the same 200 mutations, so why are you still making a big deal with the equation?


Not impossible, merely very unlikely.
I am still arguing the point because you're still claiming things that I've shown to be false nearly two months ago.
"Sometimes people don't want to hear the truth because they don't want their illusions destroyed." ― Friedrich Nietzsche

"I shall achieve my objectives through the power... of Science!" --LessWrong
Wed Sep 03, 2014 9:57 pm
dandanPosts: 431Joined: Sat May 10, 2014 2:16 pm Gender: Male

Post Re: Debate: dandan vs Inferno

I didn't really want to reply to this post. I really didn't want to reply to this post.
I have posted eight times, this will be my ninth time. Dandan has posted eight times, plus one post right at the beginning and one post explaining an earlier post. In that time, we've talked about platypus venom in Dandan's first post and in his second and in his third and in his fourth and in his... and finally in his eighth. Never during this whole debate have have we really talked about anything that wasn't covered in my second post. I then merely expanded on that, and explained, and explained, and expanded, and explained.


The reason why this discussion is moving in circles, is because you ae focusing on minor details, and ignoring the important stuff.
Regardless of who is correct in the minor details, it is still a fact that there are examples of distant clades with genetic material in common and it is still a fact that you haven’t presented any testable model that explains this unpredicted similarities.

If you provide a model that explains why how could bats a dolphins share genetic material related to echolocation you would win this debate.
Entirely different argument.
I specifically quoted portions where you said "exact same mutations" and "same genetic material". You are now trying, in retrospect I might add, to change the intent of what you said.


Word Games…this is what I am talking about, you can call it “same mutations” “same genetic material” or whatever, the point is that there are distant clades that have genetic material in common and so far you have failed to provide a model that explains these unexpected similarities


Again, not with absolute necessity, but in essence correct.
It is possible, though not particularly likely, that a particular gene under a set of similar circumstances can be subject to extreme purifying selection. In that case, it could happen that two gene sequences are almost identical, even though the lineages may have split some time ago. It's not particularly likely, I'm not even sure if an instance of this has been found, but it is theoretically possible. I merely mention this for the sake of accuracy.


Ok, so at least we agree on something, it would be very unlikely for 2 distant clades to have genetic material in common, if other closer relative’s don´t have these trades, because these would imply that 2 clades received the same mutations independently.

However the whole point I am trying to make is that you can´t explain echolocation with evolution because dolphins and bats have common genetic material in at least 200 sites. this would imply that dolphins and bats (their ancestors) suffered from the same 200 random mutations independently. This is analogous to you and I rewriting the bible and both of us having the exact same 200 spelling mistakes in the same words and sentences.

So unless you provide your mathematical model that shows that it is reasonably possible for 2 independent clades to suffer from the same 200 mutations I think I can safely claim victory in this debate.

If you don´t think my equations are accurate feel free to provide your own equations with your own assumptions

As far as I'm aware we're talking about "Prestin", not several others?


No I am using presting just as an example of a gene that shows genetic similarities amoug clades that are distantly related, but my point is that there are thousands of similar examples. About echolocation I posted a paper that analyses several genes related to echolocation, where the authors discovered that dolphins and bats have unexpected genetic similarities in 200 sites. So unless you provide a model that explains these 200 homologous sites I will claim victory in this debate.

I already told you a few times that this is wrong, but I'll give you the chance to actually prove your point.
The following is the gene Slc26a5, also known as Prestin. In this particular example, it's the variant from Mus musculus or the common house mouse.
A search for orthologues yields 104 results. Sticking with a dolphin/bat comparison, I chose Tursiops truncatus (bottlenosed dolphin) and either Myotis lucifugus (little brown bat), Myotis brandtii (Brandt's bat) or Eptesicus fuscus (big brown bat). By clicking on "FASTA", you can see the whole nucleotide sequence


However it is still a fact that bats and dolphins have unexpected similarities in these and many othet genes and it is still a fact that you haven´t provide any model that explains this similarities

Now show me the 200 sites.


I already did...

study-sees-convergent-evolution-hundreds-echolocation-loci
http://www.nature.com/nature/journal/v5 ... 12511.html

Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or



So when I say that dolphins and bats have 200 homologous genetic regions I mean exactly what the author of this paper says, so please provide your mathematical model and show that it is possible for 2 distant clades to share 200 genetic variants.
Mon Sep 15, 2014 3:15 pm
InfernoContributorUser avatarPosts: 2298Joined: Thu Apr 30, 2009 7:36 pmLocation: Vienna, Austria Gender: Cake

Post Re: Debate: dandan vs Inferno

dandan wrote:Regardless of who is correct in the minor details, it is still a fact that there are examples of distant clades with genetic material in common and it is still a fact that you haven’t presented any testable model that explains this unpredicted similarities.


No, that's precisely the point. Every time I addressed a point, it again showed that your understanding of what was said in the papers and your understanding of the science behind it was wrong. The only "minor detail" we talked about was that silly equation you brought up to bolster your point, that I showed to be in error and that you still haven't accepted is wrong... after more than two months.

dandan wrote:If you provide a model that explains why how could bats a dolphins share genetic material related to echolocation you would win this debate.


They. Do. NOT. Share. Genetic. Material.

Not in the way you believe, anyway.
I already explained that we would expect to see some level of congruence. I explained that similar living conditions will often require similar genes (convergent evolution anyone?), that similar living conditions might preserve certain genes more strongly but that these genes will not be the exact same.

And what do we find? We find similar genes with very different nucleotide sequences shared by two genera with similar living conditions. It is exactly what we would expect to find.

dandan wrote:Word Games…this is what I am talking about, you can call it “same mutations” “same genetic material” or whatever, the point is that there are distant clades that have genetic material in common and so far you have failed to provide a model that explains these unexpected similarities


First, it's called semantics, if you want to get into it. "Word games" is typically a cop-out move when someone's been shown to be wrong but can't admit it.

Second, this is not a trivial error. I absolutely agree that both genes are "FOXP2" genes. However, they are different in their nucleotide sequence and almost certainly also in their amino acid sequence. I explained this in a PM.

For example, this (alternative) is the FOXP2 gene in humans, this (alternative) is FOXP2 in the common mouse and this shows that there are small, tiny changes. They are the same genes, but they are not identical. That's the crucial point and that's why I've explained it to you so often.

It's not "word games", it's not semantics... it's the crux of the argument. Forget everything else, this is the important bit. What we're trying to establish is: Are the nucleotide sequences (in for example "prestin") in two (more or less) distantly related clades absolutely identical (strong evidence against evolution) or merely remarkably similar (strong evidence for evolution)?

The answer is the latter.

Also, you claim I haven't "provided a model" for this, but I explained this in my second post:

Inferno wrote:Number three already has the answer in the line you quote: "resemble". This means "similar, but not the same". I didn't even have to open the nature article or read the study to know that they were talking about convergent evolution. Turns out I was right: "Poisonous platypuses confirm convergent evolution"

...

I will, however, take the time to link you to the following blog post over at BioLogos. I'm not particularly fond of them, but the post is excellent.
It explains why gene trees are not always exactly the same as the species trees and it's the species trees we're concerned with. (That directly fouls papers 1, 3, 4 and 5) This also explains why the rest of your argument is invalid: You're looking for discordant gene trees, but they're to be expected. That's why you look at multiple loci instead of just one and that's also why you look at multiple lines of evidence.

As Isotelus pointed out, "[d]iscordance would falsify evolution if studies showed both consistent and significant mismatches between gene and species trees". You're showing individual discordant genes, but even they fit into the overall lines established. That's what I showed when I provided the Laurasiatheria paper: Multiple lines of evidence with scientists looking at multiple genes provide the evidence, singular genes might not reflect that due to incomplete lineage sorting.


You're literally asking me for stuff I provided over two months ago!

dandan wrote:However the whole point I am trying to make is that you can´t explain echolocation with evolution because dolphins and bats have common genetic material in at least 200 sites. this would imply that dolphins and bats (their ancestors) suffered from the same 200 random mutations independently. This is analogous to you and I rewriting the bible and both of us having the exact same 200 spelling mistakes in the same words and sentences.


So I went back and read the study... again...

Genome-wide signatures of convergent evolution in echolocating mammals wrote:Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.

...

New evidence supports the former scenario: divergent clades of echolocating bats seem to have undergone convergent amino acid replacements in several genes implicated in hearing

...

Our genome-wide analysis shows that natural selection has acted on three echolocating lineages (cetaceans and two separate bat lineages) to produce a complex pattern of changes in protein sequence, including both divergent and, more surprisingly, extensive convergent changes.


Now as I already explained, we do expect that some genes are more similar to distantly related clades (incomplete lineage sorting et al.), which is why multiple genes are usually used, precisely to avoid errors where a single gene may skew the results:

Molecular Evolution: Gene Convergence in Echolocating Mammals wrote:The incorporation of a wide range of genes in phylogenetic analyses will hopefully reduce problems associated with molecular convergence, as convergence in multiple traits may be unlikely, and as more and more neutral sites are incorporated in datasets. Phylogenomic approaches will go some way to circumventing problems arising from molecular convergence, as will careful selection of genetic data that are probably neutral (intron sequences, for example).


This is also why both Isotelus and I explained that we're looking for multiple and consistent discordance. You've given two examples, one of which the author herself showed to actually agree with what I said and the other where both others and I have repeatedly shown you to be wrong.

dandan wrote:So unless you provide your mathematical model that shows that it is reasonably possible for 2 independent clades to suffer from the same 200 mutations I think I can safely claim victory in this debate.

If you don´t think my equations are accurate feel free to provide your own equations with your own assumptions


Strange, didn't I show your maths to be wrong very early on? Didn't you then berate me for going off topic? And now you're asking me for the exact same thing again? Make up your mind.

As to "assumptions": I quoted the equations from the textbooks they use at University, yours don't even give the results you expect them to:

Inferno wrote:You originally claimed
((100)(1)/3,000,0000,000)) x (1/2)
so all we have to do is substitute 1 by 1,000,000 so the new equation looks like this:
((100)(1,000,000)/3,000,0000,000)) x (1/2)
Correct?

Here's an oopsie: When I calculate that, I get 1:60 or one mutation every 60 years. So following your advice, I multiply 1/60 x 1/14 and I get 1/840. Meaning we should hit the 14-amino-acid lottery every 840 years. Strange, didn't you say using a larger population size should give us a lower probability? That's funny, it almost seems like your "equation" doesn't calculate what you think it does.


I have shown your "mathematical model" to be in error, no contest. I've also explained multiple times that the "200 loci" do not mean what you think they mean. As such, the blog post from BioLogos I've posted about three times now should suffice.

dandan wrote:No I am using presting just as an example of a gene that shows genetic similarities amoug clades that are distantly related, but my point is that there are thousands of similar examples. About echolocation I posted a paper that analyses several genes related to echolocation, where the authors discovered that dolphins and bats have unexpected genetic similarities in 200 sites. So unless you provide a model that explains these 200 homologous sites I will claim victory in this debate.


I understand you think there are thousands of examples, but you've yet to show that even one is correct.
Once again: The SIMILARITIES are to be expected. What would be utterly remarkable is IDENTICAL sequences. How often does this have to be said?

I once again took to BLAST and checked the sequences.

The following is the gene Slc26a5, also known as Prestin. In this particular example, it's the variant from Mus musculus or the common house mouse.
A search for orthologues yields 104 results. Sticking with a dolphin/bat comparison, I chose Tursiops truncatus (bottlenosed dolphin) and either Myotis lucifugus (little brown bat), Myotis brandtii (Brandt's bat) or Eptesicus fuscus (big brown bat). By clicking on "FASTA", you can see the whole nucleotide sequence.
Now show me the 200 sites.


The whole prestin sequence for the bottlenosed dolphin is just over 50.000 letters long. 90-94% (45.000-47.000 letters) are identical with bats, which means we've got 6-10% difference. Now, which of the 3-5.000 letters are we concerned about here? Which of those are the subject of the "200 loci" you're talking about?

I'll repeat myself one more time: You're misunderstanding what the authors have said in the article. They're talking about 200 similar loci due to convergent evolution while you should be searching for 200 identical loci not due to convergent evolution. Do you understand the difference?

You can claim all you want, but here's the great thing: Science works whether you believe it or not. Nature just keeps on doing her thing. You can turn your head all you want, but the fact still remains that you've been arguing a straw-man from the beginning.

dandan wrote:However it is still a fact that bats and dolphins have unexpected similarities in these and many othet genes and it is still a fact that you haven´t provide any model that explains this similarities


Except that they're not that unexpected and that I have provided the models:
Inferno wrote:I will, however, take the time to link you to the following blog post over at BioLogos. I'm not particularly fond of them, but the post is excellent.
It explains why gene trees are not always exactly the same as the species trees and it's the species trees we're concerned with. (That directly fouls papers 1, 3, 4 and 5) This also explains why the rest of your argument is invalid: You're looking for discordant gene trees, but they're to be expected. That's why you look at multiple loci instead of just one and that's also why you look at multiple lines of evidence.


dandan wrote:So when I say that dolphins and bats have 200 homologous genetic regions I mean exactly what the author of this paper says, so please provide your mathematical model and show that it is possible for 2 distant clades to share 200 genetic variants.


Interesting that you'd use that word.

UC Berkley: Homologous structure wrote:Inherited from a common ancestor. Human eyes and mouse eyes are homologous structures because we each inherited them from our common ancestor that also had the same sort of eyes. Contrast this with homoplasious and analogous.


Biology-online: Homologous wrote:Having similar structure and anatomical position (but not necessarily the same function) in different organisms suggesting a common ancestry or evolutionary origin (e.g. wings of bats and arms of humans are homologous).


Well ain't that rad...

Thank you, good night.
"Sometimes people don't want to hear the truth because they don't want their illusions destroyed." ― Friedrich Nietzsche

"I shall achieve my objectives through the power... of Science!" --LessWrong
Tue Sep 16, 2014 5:55 pm
dandanPosts: 431Joined: Sat May 10, 2014 2:16 pm Gender: Male

Post Re: Debate: dandan vs Inferno

We both agree that there are discordances in the alleged family tree, however our point of disagreement in weather if this discordances represent a problem for evolution.

Up to this point you haven’t presented any equations or model that shows that the discordances that we observe are predicted, explainable and/or statistically insignificant. It seems to me that no matter how many discordance we find you will always say “evolution did it” you don´t seem to have any objective metric that allows you to determine if a given scenario would be problematic.

Talking specifically about the 200 discordances described in the paper about echolocation, you haven´t provide any model or equation that shows that these 200 discordances are insignificant. What if instead of 200, scientists would have found 300 or 400, or 1,000 or 1,000,000? At what point would you say that evolution is in trouble? At what point would you consider these discordances valid objections against the evolutionary model?


[No, that's precisely the point. Every time I addressed a point, it again showed that your understanding of what was said in the papers and your understanding of the science behind it was wrong. The only "minor detail" we talked about was that silly equation you brought up to bolster your point, that I showed to be in error and that you still haven't accepted is wrong... after more than two months.
Ok so instead of explaining what you think I understand explain what the papers actually reports, for example explain objectively the 200 discordances found in the echolocation paper. ¿how can darwinain mechanisms account for genetic similarities in echolocation among distant relatives? With genetic similarities I mean what the papers describes as 200 loci.

It's not "word games", it's not semantics... it's the crux of the argument. Forget everything else, this is the important bit. What we're trying to establish is: Are the nucleotide sequences (in for example "prestin") in two (more or less) distantly related clades absolutely identical (strong evidence against evolution) or merely remarkably similar (strong evidence for evolution)?


I never said that dolphins and bats have identical genes, I said that there are portions in the dolphin genome that are more “bat-like” (far relative) than whale-like (close relative) what you have to show is that these discordances are not problematic for evolution, which is why you most provide an OBJECTIVE model.

Form an evolutionary point of view this would imply that bats and dolphins suffered from the same mutation independently, so prove MATHEMATICALLY that it is possible for 2 independent clades to suffer from the mutations.
I apologize for using the term “suffer” but I honestly don´t know what other term to use.

This is also why both Isotelus and I explained that we're looking for multiple and consistent discordance. You've given two examples, one of which the author herself showed to actually agree with what I said and the other where both others and I have repeatedly shown you to be wrong


Ok so what do you mean with “multiple” and consistent? If 200 loci doesn’t count as multiple, then how much is needed in order for you to call it “multiple” and even more important how do you know it?

You originally claimed
((100)(1)/3,000,0000,000)) x (1/2)
so all we have to do is substitute 1 by 1,000,000 so the new equation looks like this:
((100)(1,000,000)/3,000,0000,000)) x (1/2)
Correct?

Here's an oopsie: When I calculate that, I get 1:60 or one mutation every 60 years. So following your advice, I multiply 1/60 x 1/14 and I get 1/840. Meaning we should hit the 14-amino-acid lottery every 840 years. Strange, didn't you say using a larger population size should give us a lower probability? That's funny, it almost seems like your "equation" doesn't calculate what you think it does.


you are wrong ½ stands for 1/2N in an hypothetical population of 1 individual, if you what to use a population of 1,000,000 you have to use 1/2,000,000. Instead of 1/2

I will, however, take the time to link you to the following blog post over at BioLogos. I'm not particularly fond of them, but the post is excellent.
It explains why gene trees are not always exactly the same as the species trees and it's the species trees we're concerned with. (That directly fouls papers 1, 3, 4 and 5) This also explains why the rest of your argument is invalid: You're looking for discordant gene trees, but they're to be expected. That's why you look at multiple loci instead of just one and that's also why you look at multiple lines of evidence.
[/quote]

Your source simply states that discordances are possible and predicted by evolution, it dind´t prove anything

So just a quick summary of the debate so far:
- We both agree that we find some discordances in the family tree of life
*With discordance I mean exacly what your source means (http://biologos.org/blog/evolution-basi ... ge-sorting)

- Our point of disagreement is on weather if the discordances are statistically significant, or problematic for evolution.

- I am arguing that you have provide a mathematical model that demonstrates why aren’t´ the discordances that we observe significant

- For some reason you don´t what to present your model.
Fri Sep 19, 2014 2:59 pm
InfernoContributorUser avatarPosts: 2298Joined: Thu Apr 30, 2009 7:36 pmLocation: Vienna, Austria Gender: Cake

Post Re: Debate: dandan vs Inferno

This will be my last post in this thread, as per the 10 post quota we agreed on in the beginning. Dandan will then have one more post, if he so wishes, even though he already used up his ten posts. I will use this post first to reply to the last batch of points made by Dandan, after which I will finish with some concluding remarks.

Dandan wrote:Up to this point you haven’t presented any equations or model that shows that the discordances that we observe are predicted, explainable and/or statistically insignificant. It seems to me that no matter how many discordance we find you will always say “evolution did it” you don´t seem to have any objective metric that allows you to determine if a given scenario would be problematic.


This is incorrect. In fact, I gave you exactly what you were asking in the second post I made in this thread.

Inferno wrote:As I said, statistics is one of the few areas of science where I have to shamefully hang my head and declare my absolute ignorance. I simply don't know. All I can do is point to the analysis of other scientists and show what they have done:
Ibid. wrote:Two parallel mutations in Pcdh15 (I946M and E1278D) were shared by branches b, d, and g. Parallel evolution was statistically significant (P<0.001) between branches b and g for the following 22 parallel mutations: N218D, Q310E, E393V, T427S, A433V, I438V, T490I, V546F, I643V, N666K, K820R, I853V, K856T, M946I, V952A, R999L, T1139R, F1160L, A1173S, K1275R, D1278E, and I1404V. Parallel evolution was also statistically significant (P<0.001) between branches d and g for three parallel mutations: A726D, M946I, and D1278E. Finally, eight parallel mutations occurred between branches b and d, including L423V, Q468P, H765Y, F876L, M946I, F984S, V1019I, and D1278E (Figure 2C). Parallel evolution between these two branches was statistically significant (P<0.001). The positions of these sites in the domain structure of Pcdh15 were mapped in Figure S4. The BI tree based on amino acids excluding all parallel-evolved sites differed somewhat with the species tree, but it did not group echolocators together (Figure S5).


I have to assume that the authors used a standard p-value test, so a value of p>0.1 would confirm your hypothesis, whatever that might be. That they do share genes for echolocation? I'm not sure I understand your position, but I understand enough to know that it's wrong.


You then went on to calculate the time (likelihood to happen in x number of years) it takes for an event to happen and claimed that this was statistical significance. That was of course very wrong.

I then repeated that point in my third post:
Inferno wrote:So my answer is this: I would use any statistical p-value test (chi-squared or student's t-test, whichever suits the subject studied) and explore whether convergent evolution is statistically significant. (p<0.001) Anything with 0.1<p would confirm your hypothesis. I already explained that, too!


I did so again in my fourth post and even gave you a paper that gives you the very numbers you want, but that I can't give you because I'm not a statistician!
Inferno wrote:Second, I already told you that I know very little about statistics so I'd be hard-pressed to find you a number. I can only repeat what the scientists found. I am taking a course in advanced biological statistics, so feel free to drop me a line in 2-3 months from now if you really want an answer.

Now, as for the scientists answer: They predicted the values using a software (CoalHMM) and then crunched the numbers. The numbers matched up with the prediction. As Isotelus already stated, they predicted 0.9% of orangutan alleles would be more similar to humans and the actual number they found was 0.8%. Now tell me, how can something that's predicted by evolution also falsify evolution? You're making no sense.

Now I wouldn't expect the numbers to deviate too much from the expected value, but I don't know how to calculate it. All I can do is once again refer you to the probability I alluded to above: Anything with a low p-value (p<0.001) would support "my" hypothesis, anything with p>0.1 would confirm your hypothesis. Well no, actually that would just mean that "my" hypothesis isn't correct.

In any case, how can I reasonably calculate what you're asking me for? I'd have to know my way around CoalHMM and know a large deal of statistics. You're in no way being reasonable in your expectations. Know that it's taking trained scientists months to figure this stuff out and you're expecting me to do it in an afternoon?
But I already proved that I don't need to do that because we're already seeing a great deal of concordance between species that, according to you, are supposed to be unrelated. If your pet hypothesis were true, we wouldn't expect to find that ever.


Yet you claim, after all these careful explanations, that I did not furnish you with one? Come now, surely you realize how ridiculous this is.

Talking specifically about the 200 discordances described in the paper about echolocation, you haven´t provide any model or equation that shows that these 200 discordances are insignificant. What if instead of 200, scientists would have found 300 or 400, or 1,000 or 1,000,000? At what point would you say that evolution is in trouble? At what point would you consider these discordances valid objections against the evolutionary model?


If you had applied any of the information in the three quotes above, you might have had an answer to that question. Here, I'll quote the relevant portion of the paper:
By comparing our observed values to null distributions of corresponding values obtained by randomization, we found that hearing genes had significantly more negative average values than expected by chance for bat–dolphin convergence (H2: z = −0.0194, P < 0.05). We repeated this method for 75 genes listed as involved in vision and/or blindness, and found support, although weaker, in both cases of phenotypic convergence (z = −0.0020, P ≤ 0.055 and z = −0.0097, P ≤ 0.09). Loci previously reported to have association with echolocation had strong support by randomization for both hypotheses (P ≤ 0.01 in both cases).


In both cases, the results for convergence are statistically significant. If they weren't, or if discordance were statistically significant, that might be cause for concern.

As for specific numbers: I have no idea. I told you repeatedly that I'm not a statistician, so I can only report what is in the papers. Contact the authors and ask them about the numbers if you're not satisfied with my answer.

I also won't go into your ongoing misunderstanding of the science in the paper.

Dandan wrote:Ok so instead of explaining what you think I understand explain what the papers actually reports, for example explain objectively the 200 discordances found in the echolocation paper. ¿how can darwinain mechanisms account for genetic similarities in echolocation among distant relatives? With genetic similarities I mean what the papers describes as 200 loci.


I did that, too. I explained that you misunderstood the science behind the papers:


Inferno wrote:
Indeed, the same misplacement of dolphin is observed in the Prestin tree reconstructed with only nonsynonymous nucleotide substitutions (Figure S1B); but, when only synonymous substitutions are used, dolphin and cow are correctly grouped with 100% bootstrap support (Figure S1C).


Convergent sequence evolution between echolocating bats and dolphins wrote:The ability of some bats and all toothed whales to produce sonar pulses and process the returning echoes for prey detection and orientation (echolocation) is a spectacular example of phenotypic convergence in mammals.


Trees based on nucleotide alignments from this larger dataset strongly supported the accepted species tree topology, albeit with the clustering of echolocating bats reported earlier [3].


I explained that again:
Inferno wrote:In the exact way Dr. Whittington explained that the amino acids converged in platypus and snakes, meaning the protein sequence, so also do the protein sequences in bats and toothed whales. This is what you get wrong and that's why your example is not valid. Let me make this absolutely clear: When comparing the gene or nucleotide sequence, bats and toothed whales are correctly classified. If the protein sequence is compared, bats are classified with toothed whales. That's the whole deal. The gene sequences are not the same. This is made absolutely clear in a paragraph I quoted earlier:

Convergent sequence evolution between echolocating bats and dolphins (2010) wrote:To test whether convergent changes in bat Prestin genes have also occurred in echolocating whales, we sequenced the entire gene in a range of echolocating toothed whales and non-echolocating baleen whales, as well as additional bats (see Table S1 in the Supplemental Data available on-line with this issue). Trees based on nucleotide alignments from this larger dataset strongly supported the accepted species tree topology, albeit with the clustering of echolocating bats reported earlier [3]. However, in trees based on amino acid sequences, constructed using a range of different phylogenetic methods, we found that the echolocating dolphins now formed a well-supported group with echolocating horseshoe and Old World leaf-nosed bats (node posterior probability = 0.99 or 0.94 depending on the analysis), members of which emit Doppler-sensitive signals dominated by a constant frequency (CF) component [6] ( Figure 1A). Intriguingly, the addition of the sperm whale, which appears to echolocate at much lower frequencies [7], was seen to decrease support for this convergent signal, leading to the cetaceans and bats both forming monophyletic groups. The extent of sequence convergence between bats and whales was thus not sufficient to unite these clades when non-dolphin odontocetes were included in the analysis.


However, in trees based on amino acid sequences, constructed using a range of different phylogenetic methods, we found that the echolocating dolphins now formed a well-supported group with echolocating horseshoe and Old World leaf-nosed bats.


And so on and so forth. I explained how you misunderstand the science three times, yet here you are still asking me the same flawed question. How do you expect me to answer to a question that's based on a number of falsehoods?

dandan wrote:I never said that dolphins and bats have identical genes, I said that there are portions in the dolphin genome that are more “bat-like” (far relative) than whale-like (close relative) what you have to show is that these discordances are not problematic for evolution, which is why you most provide an OBJECTIVE model.

Form an evolutionary point of view this would imply that bats and dolphins suffered from the same mutation independently, so prove MATHEMATICALLY that it is possible for 2 independent clades to suffer from the mutations.
I apologize for using the term “suffer” but I honestly don´t know what other term to use.


I told you here that you can say "have", I guess you could say "be subject to" or some other formulation, but "suffer" has the Mr. Hyde/Hulk connotation.

As for "identical", I already disproved that myth here:
Inferno"[quote="Dandan wrote:Just ot be clear, I never said that snakes and platypus have identical genes, I said that the proteins responsible for the venom have a high degree of homology, which would require homologous and independent mutations in snakes and platypus.


That's simply not true, you specifically stated that they have the same genes, which I have to understand means "identical".
I checked a few dictionaries just to make sure:
Merriam-Webster The same: being one without addition, change, or discontinuance : identical
Oxford Dictionaries (the same): 1 Identical; not different:
...and so on and so forth.

Dandan wrote:That is not true, platypuses and snakes have the same proteins (same genes) for venom, but that is irrelevant you will still invoke convergent evolution as you did with the sonar in whales and bats.

...

I think you are misunderstanding what the authors are saying, when they talk about convergent evolution, they mean that the same genes evolved independently


Will you admit that you definitely said "same genes" meaning "identical genes"? Will you also admit that you claim the same thing (same aka identical genes) for dolphins/bats?

Dandan wrote:The authors explain this by arguing that bats and dolphins received the exact same mutations independently, exactly what you said was impossible.

...

Supposedly the genes evolved twice independently, like in the case of pristine in bats and dolphins the same genetic material evolved independently more than once, exactly what you said was impossible.

...

The whole point I was trying to make is to show that it would be very unlikely for two unrelated clades to suffer from the exact same mutations, since we both agree with that conclusion I see no point in discussing on weather if my equations are correct or not

...

3)I did presented something equivalent, pristine in dolphins is more similar to bats than to whales, which would imply that dolphins suffered from the exact same mutations than bats independently


And so on and so forth. I was only half-way through our conversation at that point, so I assume there are more quotes where these four came from.
[/quote]
The rest was dealt with above, so I won't go into it again.

dandan wrote:Ok so what do you mean with “multiple” and consistent? If 200 loci doesn’t count as multiple, then how much is needed in order for you to call it “multiple” and even more important how do you know it?


I'm not going to deal with a new point in this last post, but suffice it to say Isotelus explained this four months ago. If you didn't understand it in these four months, you won't understand it in this last post.

dandan wrote:you are wrong ½ stands for 1/2N in an hypothetical population of 1 individual, if you what to use a population of 1,000,000 you have to use 1/2,000,000. Instead of 1/2


I'm wrong, am I?

Very well, let's substitute the numbers.

Your original claim with a population size of Ps=1 was
((100)(1)/3,000,0000,000)) x (1/2)
The result is 1.666 x 10^-8 or 1/60.000.000

The new one with a population size of Ps=1.000.000 is
((100)(1,000,000)/3,000,000,000)) x (1/2,000,000)
The result is 1.666 x 10^-8 or 1/60.000.000

Isn't that odd? Well no, any mathematically literate person could have spotted that immediately: The addition of two millions simply cancel each other out, so your result is exactly the same. It does not matter whether you use a population of 1 or 1.000.000, aat least not when using your incorrect mathematics. That's completely contrary to your claim that a larger population size means longer time. (That claim is correct, by the way, you're just using bogus maths to prove it.)

I already gave the correct equations here, but you still refuse to use them. Why is that?

Dandan wrote:Your source simply states that discordances are possible and predicted by evolution, it dind´t prove anything


It wasn't supposed to prove anything, it was supposed to explain why you're wrong.

BioLogos wrote:Now that we have worked this example, hopefully the reason behind the discrepancy is clear – there is no guarantee that alleles will sort in a lineage to match up with the overall species pattern. If a gene has variation in a population undergoing speciation events, it is expected that some of the time it will assort with a pattern that does not match the species pattern – in some cases, it will have a gene tree that is “discordant” with the species tree. For a population with thousands of genes with multiple alleles present, it is a given that some alleles will assort into a discordant pattern. Far from being a problem for evolution, discordant trees are predicted by evolution. It would be a problem if we did not observe them – but in fact we do, and as we shall see next time, we observe them in precisely the pattern that matches what we would expect based on species trees.


I can prove that the post is correct though: Just open either a good university textbook on the subject or read one of the articles either Isotelus or I posted. In one of them, there's even a mathematical model to explain how much is to be expected. (Note: That article was quoted three times in this thread.)

Dandan wrote:So just a quick summary of the debate so far:
- We both agree that we find some discordances in the family tree of life
*With discordance I mean exacly what your source means (http://biologos.org/blog/evolution-basi ... ge-sorting)

- Our point of disagreement is on weather if the discordances are statistically significant, or problematic for evolution.


Agreed. I already showed that they were predicted.

Dandan wrote:- I am arguing that you have provide a mathematical model that demonstrates why aren’t´ the discordances that we observe significant

- For some reason you don´t what to present your model.


Incorrect on both counts, as I showed above.

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Closing remarks...

Since the beginning of this debate, I've read at least ten different papers, read an additional ten or so blog posts and have received an E-Mail from one of the authors in the papers discussed. I believe I have learnt a lot in the course of the debate, even though none of that can be contributed to my opponent. I hope others had the chance to learn something as well. If my opponent learned something, that would really make my day. Dandan, could you comment? Did you learn anything from me at all?

Over the course of this debate, I have had many an opportunity to ridicule my opponents views. I hope that I was able to remain calm and rational, though at times I had insults written out and only deleted them on my final draft. Conducting this debate was not easy, as my opponent frequently repeated points that had been dealt with in previous posts and failed to acknowledge that I had addressed them already.

I also hope that I was able to approach the subject with wit and humour. Debates tend to get stuffy at times, so I wanted to throw in the occasional funny line. I also try to write in an engaging manner, so as not to make you fall asleep. If I've achieved that, that's already a statistically significant win for me.

Finally, I'd like some feedback:
1) Were there any arguments you thought I didn't address well enough? Any that I missed out? Was there any additional information that I could or should have posted? Worse yet, were there grave mistakes I made?
2) Which style of posts did you like best? The one where I quoted Dandan or the one where I made three structured arguments while quoting as little as possible? Or is there an entirely different format I should adopt?
3) Overall, how did I compare? Did I achieve my goals (as set out above) or did I fail miserably? Was I cordial and nice or could I use a refresher there?

I'm looking forward to all of your comments and hope to have another discussion here soon, then with improved l33t skillz.
"Sometimes people don't want to hear the truth because they don't want their illusions destroyed." ― Friedrich Nietzsche

"I shall achieve my objectives through the power... of Science!" --LessWrong
Sun Sep 21, 2014 11:01 pm
dandanPosts: 431Joined: Sat May 10, 2014 2:16 pm Gender: Male

Post Re: Debate: dandan vs Inferno

Ok, I am also ready to make my closing statements.

1 we both agree that we see discordances in the tree of life

2 I say that these discordances are statistically significant relevant and impossible to explain by Darwinian mechanisms
.
3 I tried to prove my point with an equation, and I am happy to report that aside for all the misunderstandings that you finely understood my equation.




Very well, let's substitute the numbers.

Your original claim with a population size of Ps=1 was
((100)(1)/3,000,0000,000)) x (1/2)
The result is 1.666 x 10^-8 or 1/60.000.000

The new one with a population size of Ps=1.000.000 is
((100)(1,000,000)/3,000,000,000)) x (1/2,000,000)
The result is 1.666 x 10^-8 or 1/60.000.000

Isn't that odd? Well no, any mathematically literate person could have spotted that immediately: The addition of two millions simply cancel each other out, so your result is exactly the same. It does not matter whether you use a population of 1 or 1.000.000, aat least not when using your incorrect mathematics. That's completely contrary to your claim that a larger population size means longer time. (That claim is correct, by the way, you're just using bogus maths to prove it.)



So from my equation we can say that the chances of having a single discordance is 1/60,000,000, in the echolocation example I presented a case with 200 discordances, 12,000,000,000 you don´t have enough probabilistic resources to acount for this counsidence.


4 Since the beginning of these debate I´ve been asking you for an equation, mathematical model, or some sort of objective metric that would allow us to determine if a given discordance is statistically relevant, and you failed to do so. You will disagree with this and you will quote from previous post where you supposedly provided such objective metric, I will simply let neutral observers to decide if you provided a satisfactory answer.
5 You keep repeating that my arguments are based on my misunderstanding of the paper, that is wrong and irrelevant, the objective model that you are supposed to presents has to explain what the paper reports concerning the 200 loci, you where expected to provide a model that explains objectively why isn’t this discordance relevant nor problematic for evolution. In other words you are suppose to explain what the author reports, no my understanding of the paper.

In the general sense, obviously this is out of topic, I would say that the main problem with evolutionists is that they typically don´t think quantitatively about their statements.

Evolutionists say thinks like “we share 99% of our genes with chimps” “we shared a common ancestor 5 Million years ago” but they fail to notice that a 1% difference represents around 30,000,000 base pairs, 5 million years is not enough time to evolve 30,000,000 bais pairs, if so we would expect to to see a “speed of evolution” of 6 base pairs per year.

*this means 6 mutations that become selected fixed and dominant in a population per year, (or 120 per generation)
You say things like “convergent evolution” at a genotypic level, but you fail to understand that the idea of 2 clades having the same mutations independently is nearly impossible
.

You say that the eye evolved from a “simple” light sensitive organ, but you fail to notice that it would require thousands of millions of mutations and you have limited time.

At best evolutionists find small cracks in this type of arguments, they say things like “maybe things were different in the past” but they fail to provide any sort of objective model that proves objectively that none of this represents a problem.
Wed Sep 24, 2014 3:20 pm
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