Let’s have a serious discussion about phylogenetic systematics.
What are the assumptions, the methods, and the inferences that can be drawn from phylogenetic analysis.
For example, is there anything to the creationist claim that phylogenetic systematics assumes common ancestry and does it even matter?
I’ll be using a number of different references such as Molecular Evolution: A Phylogenetic Approach and Molecular Evolution and Phylogenetics.
This thread will not be password protected, but it will be protected by angels.
Oh Christ, the “it’s inscrutable” bullshit. We’re frogs in a well, but Bill knows all about it because he read about it from other frogs in a well.
See, all you’re doing is sneering without reason or any meaningful argument.
You have nothing, so you just shout louder.
Gee, why don’t you explain it all then?
Well, you certainly won’t.
Well, why don’t birds have to do the same? Oh right, you don’t know, it’s just the nastiness you spew whenever you’ve been given the arguments that persuade people with open minds.
No, again you have nothing, so you attack the messenger. You have no counterargument, no evidence for your claims, nothing but your usual demand that your idiot position be admired because you said it and you have a lot of baseless claims to make against anyone who brings arguments.
As usual, you return to your gullible little “it’s so great it must be designed” with no capacity for dealing with the details. The details undermine your precious little beliefs, and you’re just pissed that they do.
Glen Davidson
GlenDavidson,
You need to think about design tradeoffs and not just point to one weakness without addressing the possible tradeoffs of the design you are critiquing.
You could write that the Mac book pro is too heavy so it was not designed properly. Well, it also has much more memory then the Mac book air at a lower cost so there is a reason for the tradeoff.
You could write that the Mac book air has too little memory. Well, it is lighter and thinner then the Mac book pro. Again, there is a reason for the tradeoff.
Humans can observe the universe. Birds can fly on their own. These are different system designs that require different tradeoffs.
I don’t know, you’re going to have to be more specific about your Theobald quote. Where does Theobald define an “evolutionary process”?
If there has been branching and modification, then yes.
Yes, both manuscript copying and observed instances of multi-generational change and divergence of real organisms.
That’s actually how phylogenetic algorithms are tested: By comparing their results with real observed or experimental phylogenies of branching evolving lineages of organisms. Be they fruit flies, zebra fish, rats and mice, birds, worms, bacteria, fungi, and even phages and viruses.
I consider those to be genealogical processes, yes. But the fact that it was observed is not what makes the resulting nesting hiearchy objective. The data either objectively exhibits hierarchical structure, or it does not. But that fact is not dependent on whether we were there to observe the data form in the first place.
Which is why it is important to test nesting hierarchies inferred from real biological data to see if it exhibits significant hierarchical structure in the same way that nesting hierarchies we did see form, does. And that artificial but subjective hierarchies like a hierarchy of cars, does not exhibit significant hierarchical structure. That was basically the point of my response to fifths, but I think you’ve lost context of what I was responding to and intending to convey.
That’s the message you get from the paper? It contradicts your previous message that the 2003 paper shows common descent within a kind. And “not look like any intentional pattern was created” seems to contradict “one that results from consistent design rules”. I’m not sure you have any sort of coherent opinions.
The message of that paper is that not all data have been correctly understood and that not all hypotheses of homology are correct, and that the coding of some morphological characters was mistaken.
That’s funny.
So consilience of independent phylogenies is not evidence for common descent?
Then what WOULD be evidence for common descent?
Like the process that yields nesting hiearchical structure in the data? The concrete real-world observed empirical fact that consilience of independent phylogenies results from branching genealogical processes?
Except the evidence for common descent.
Aaand we’re back to conspiracy nuttery.
John Harshman,
John. the trees did not match. Stop the bullshit, you are misleading people on your side to support specious arguments.
Okay, I see your point now. But there’s a very significant factor you’re neglecting to consider here: We can potentially (if we are so inclined) go out in the wild and directly observe all living organisms on the planet generate data that exhibits objective hierarchical structure. Basically, that processes we see operate all around us in the present (and for recorded history), predicts the sort of pattern we observe when we analyze the data from all the different species of cellular life on Earth.
On that alone you are erecting a false equivalency. We are not observing the instantaneous magical creation of copies of already existing organisms but with mutations in them, we are observing common descent of organisms take place.
Given that the process empirically determined operating in the present, predicts the sort of pattern we are seeking to explain, why would you ever invoke something unobserved in it’s place?
The level of disagreement between the trees (from John’s paper) is analogus to having two thermometers measure a temperature to be 37.23008 and 37.23007 degrees C, respectively.
Technically those two termometers’ measurements don’t match exactly. They differ by 1 one hundred thousandth of one degrees C.
This when you’d say “John, the thermometers did not match”. That’s basically what you just said.
If you’re going to reject the consilience of independent phylogenies on that miniscule level of disagreement, you’re going to have to reject the consilience of independent thermometers, and rulers, and speedometers in cars, of pocket watches telling time and so on, if they don’t match to an accuracy of 1 in 100.000. Or just be a hypocrite with a double standard.
I believe it’s against the rules to accuse me of lying. The molecular and morphological trees didn’t match. What’s your explanation? You have agreed that crocs are related by common descent, so separate creation can’t be your explanation. Note also that they matched much more than expected by chance, as Theobald explained in his use of the paper as an example. They differ only in the position of a single species. And if you read the paper, I advanced a partial explanation of the difference.
John Harshman,
John, I am not accusing you of lying but you are taking my comment to kieths out of context which will mislead him. The fact that there is probably a common ancestor relationship here but the morphological data does not agree is significant. There is not always correlation between morphological data and phylogenetic data as you pointed out in your paper.
My explanation for mismatch is that morphology match is not just the result of DNA sequence match. Epigenetic factors like gene expression during embryo development are also important.
You don’t seem to understand that gene expression is under genetic control. Gene expression differences between species result from DNA sequence differences. So your “explanation” is nonsense. I don’t think you have any coherent views at all. Incidentally, morphological data are phylogenetic data.
Rumraket,
Your kidding right 🙂
One tree had two crocs sharing a common ancestor and the other had them at the maximum genetic distance among the group.
It was a very simple question. Why can’t you just answer it?
When you say “the objective nested hierarchy” what are you [keiths] referring to? If you don’t know, just say so.
No. As long as the nested hierarchy is “objective” there is no need for consilience. Consilience is superfluous.
Nothing could possibly evidence for common descent in a word where common descent does not exist. Think of it as a world in which God does not exist where there can be no evidence for the existence of God. Call it TSZ.
probably.
John Harshman,
This is not true. Gene expression is not just controlled by DNA sequences. Quantities of small molecules are involved that have nothing to do with DNA. DNA expression can work as a feedback loop so genes are expressed as a result of quantities available of certain molecules.
That’s what I was asking. 🙂
I didn’t see Theobald define it, so I asked keiths, who was going to explain it to me.
That’s a croc! Objectively.
But the small molecules interact with DNA sequences, and differences in expression and response to molecules as well as concentrations of molecules among species depend on differences in DNA sequences. Your idea that species morphology can differ as a result of anything else is contradicted by everything we know.
John Harshman,
Not true. DNA sequences are what code the initial protein but modifications come post transcription splicing and translation. Protein and other molecules that trigger transcription are complex multi molecule structures. Here from wiki:
So activities like phosphorylation happen after protein folding. Ligands can be small molecules that are also mission critical transcription factors. DNA is a critical part of the story but only part of how genes are expressed. Transcription happens when all the proteins and other parts of the transcription complex are together.
That’s the assumption that DNA is the blue print for all the facets of life. That could be an antiquated view based on things like the sugar code and structural inheritance.
But lets just take the coding sequences. For a human that would be about 2%-5% of the 3.3 giga base genome. 5% of the human genome equates to about 40 megabytes of information. You think something as complex as a human is codable by only 40 megabytes of information? I don’t.
3.3 gigabases = 6.6 megabits
6.6 megabits = 6,600,000,000 bits = 6,600,000,000 bits * 1 megabit/ 1,000,000 bits * 1 byte/8 bits = 786 megabytes ~= 800 megabytes
5% * 800 megabytes = 40 megabytes
2% * 800 megabytes = 16 megabytes
Hard to believe something as complex as a human is driven by 16-40 megabytes of information.
Your understanding of mechanisms of development could be going obsolete and colewd is closer to the truth.
Sal,
Except that with your Matryoshka doll, each level of nesting involves just one additional doll. Evolutionary nested hierarchies are not limited that way; think of a Matryoshka doll in which two or more dolls may be nested, at a given level, within the next higher level.
colewd:
You’ve blown it again, Bill.
Read the following once more and see if you can identify which tree I am discussing:
That’s right. I am talking about the tree in Theobald’s Figure 1, not the tree in John’s paper.
You make these dumb mistakes over and over, Bill, and they firmly place you among the worst thinkers at TSZ. It’s time to start taking that into account. When you find yourself disagreeing with folks who are far brighter and better educated — including in this case the entire evolutionary biology community! — your first thought should be “I’m terrible at this, and these guys know what they’re talking about. Where did I screw up?”
Instead you accuse others of “spewing nonsense”, and it makes you look like an idiot.
It’s essentially the same mistake that Sal, fifth, Mung, and Erik are making. Each of you, despite a history of poor thinking and dumb mistakes, takes seriously the thought that you have identified a flaw in evolutionary thinking that has eluded the entire community of evolutionary biologists. It’s a ridiculous notion, and it gets disproven again and again as you make mistake after mistake. Yet somehow it never occurs to you to question yourselves and stop granting yourselves credence, probably because that comes at a steep cost to your egos. But think about it — if someone else screwed up as much as you guys do, would you continue to grant the same weight to their judgments? Not if you had a lick of sense. So why continue to take your opinions seriously, given your demonstrated incompetence?
You guys are here to learn, not to challenge evolutionary biology. The latter is out of your reach. Try to adjust your self-images downward — way downward — so that they match reality, and so that you are properly skeptical of your own poor reasoning abilities.
Rumraket, to colewd:
I predict he’ll choose the latter, as is his tendency.
Mung:
Consilience is what establishes the hierarchy as objective, dipshit.
As I already explained to you:
Mung,
I did, but I made the mistake of urging you to think, when you were expecting me to do your thinking for you.
I wrote:
In that comment, I am obviously telling you that there is more than one ONH, since a given ONH may exclude organisms — like zebras — that could, if we chose, be placed within it.
The ONH without zebras is objective, as is the one with zebras. They are different but compatible.
John explained this to you already. Didn’t you understand what he was saying?
What stuff are you talking about? If manuscript lineages and language families that are used here as analogies to evolutionary descent, then this happens to be the stuff I understand. I understand that the analogies do not show what Darwinians want them to show. The analogies illustrate the pattern, yes, but they say nothing about what causes the pattern. The causes have to be known (not inferred) independently. (Now, Harshman and Felsenstein on the one hand and ID-ists on the other think that the causes can be inferred purely based on a pattern – that’s why they deserve each other.)
The analogies are not mine, by the way. They are by biologists, the analogy with language families is by Darwin himself. In turn, what do you understand?
The data looks like a tree because maybe there are natural reasons why it cannot look like anything else. It’s just a pattern. Is this reaching you? Apparently not. Then you must consider the analogies more fully, until you get it. The analogies should give you the clue that you are looking at effects, not at causes. Sorry, if the analogies are over your head.
I know, which is why you should get this: Darwinian common descent claims are worthless and empty as *explanation of causes of evolution* if, given the same evidence, the causes could be something else. As long as the evidence is just the pattern, then you are actually not touching the causes. We could keep calling it “common descent” and only mean “common descent” in the same sense as in textual studies, without implying that the text self-replicates. Everybody would be fine with “common descent” in that sense and the evidence would work as fine as it does now – except better, because you are not making unwarranted assumptions about the causes. The causes need a whole different category of evidence.
Erik:
Precisely what I said:
Here is the question again. You avoided it last time, falsely claiming that it was a category error. Be brave this time and address it:
Answer, please.
@keiths
I see. Since the answer involved analogies (which are actually used by Darwinian evolutionists to explain their own theory), it went over your head. Since you ignore answers, I’ll ignore you.
Erik:
Yeah, like the fact that it was produced by a process of common descent with gradual changes and primarily vertical inheritance.
That’s our explanation, and it fits the evidence beautifully. What’s yours?
Erik,
To successfully condescend, you need to be in a superior position. You are running away from my question, which means you are not in a superior position, to say the least.
Evolutionists can explain the pattern. What’s your explanation?
Actually, the scribe acts BOTH as a replication process AND as a full-blown efficient cause. Manuscripts themselves do absolutely nothing in this process, they don’t act at all, they just suffer the consequences and embed the effects. The result is in line BOTH with common descent AND with creation plan, but it is not in line with Darwinian (self-running mehanical unguided unaided) common descent.
The conclusion of this discussion is that the analogy is painfully over your head. You consistently fail to connect the most obvious dots.
Yeah, let’s just ignore all this https://en.wikipedia.org/wiki/Living_fossil#References
Erik, to John:
Have you forgotten so soon, Erik? To condescend successfully, you need to be in a superior position, not an inferior one.
Erik,
Are you seriously suggesting that if manuscripts can’t replicate themselves, then neither can organisms? We know that organisms replicate themselves, and we know that the process introduces variation. These are observed phenomena, Erik. Your overreliance on the manuscript analogy is confusing you deeply.
And you still haven’t explained where the objective hierarchical pattern comes from.
Evolutionists can explain it. You can’t.
You see, the analogies are not mine. They are by evolutionists trying to explain their own theory. When they make such analogies, they either know what they are talking about or they don’t. Feel free to guess twice so you definitely get it right at least once.
Yes, tiny variations. Just like in manuscripts: Along a single lineage, the text does not become another story and still be recognized as the same text. For another story, you have another unrelated lineage.
Somebody said something appropriate recently,
Erik,
They do. You don’t.
Analogies are not identities. Savvy people know this and therefore do not assume that everything is analogous in the two phenomena being analogized.
The fact that manuscripts do not self-replicate does not mean that organisms don’t. The analogy does not extend that far.
You are attempting to draw conclusions about biological evolution based on an aspect of manuscript copying that isn.t even analogous.
It’s a dumb mistake, Erik.
Exactly. This is why you have to EXPLICITLY outline the relevance of the analogy, along with the differences, and fill out the differences IN DETAIL.
Not like Harshman, who says without any qualifications, “Manuscripts are a much better analogy to common descent than separate creation, aren’t they?” as if his conclusion were self-evident, without realizing that the opposite conclusion is at least equally valid.
Yes, I agree his mistake is dumb. But it’s also very persistent, probably incorrigible, like your own.
Yes, to you. Ever considered learning a sufficient amount so that analogies are not necessary?
Actually, when Darwin made the analogy, it was to explain his idea of common descent to other biologists. If you are saying that he hadn’t learned enough biology to be able to explain his point without the analogy or didn’t have enough evidence to let the idea stand on its own, then yes, I got the same impression when I read his book.
Now they seem to get it, however. But you still need hand holding. Now is not then. I can see that you don’t understand that concepts may have different levels of understanding over time. Most people could take a stab at what “quantum” means these days, even if they get it wrong in some ways. But that minimal knowledge would have been revolutionary 150 years ago.
But yeah, I get it, you don’t get it.
Understood. And in 1000 years no doubt your name will be remembered over that bloke, D-something, who did not know much biology and who wrote some crappy book.
The book that kickstarted our understanding of biology is underwhelming to Erik, random internet commenter. What a surprise.
In order to begin that process we need to speculate on potential causes. We can then work to design experiments to rule out some of those causes.
Do you have any speculations on what potential causes could form the pattern we observe Erik?
If the analogy applies, then we do not need to speculate on potential causes. If we need to speculate on the causes, then the analogy does not apply. Now please specify – in detail – where, according to you, the analogy ends and the need for speculation begins. And why exactly speculation, not something better such as observation or experiment. Because, given the analogy, the cause is obvious, not subject to speculation: Scribes cause manuscripts.
No. And your reaction just shows you don’t understand what any of this means.
Yeah, there was one mismatching branch. Bill, ALL the branches could be mismatching as there are over 135.000 different ways of representing a tree with 8 species.
The fact that only one branch is mismatching means they are extremely similar. So similar it demands an explanation. And preferably a scientific one (aka it is observationally falsifiable).
Why are the trees so similar when they have over 135.000 ways of failing to corroborate each other?
About here I’d say:
We have a pattern. We have no information on the cause of that pattern. Speculate away.
That doesn’t even make sense. The fact that you can potentially use only a single variable character (such as a single orthologous gene) to construct a nesting hierarchy doesn’t mean that consilience of several independent such nesting hierarchies is not evidence for common descent.
Uhh, yes it can. You don’t seem to understand that there can be evidence for things even if they are wrong.
Imagine a purported crime scene with a dead person A who has been stabbed, and there’s a knife next to the dead person, and the knife has fingerprints on it from person B, and there’s a video camera that has recorded a person B entering the premises around the estimated time of death of the person. And the dead person A was known to have a really bad relationship with the person who’s fingerprints are on the knife, and who has been recorded entering the premises around the time of death.
All those data points are evidence that is consistent with the hypothesis that person B stabbed and killed person A.
But it could simultaneously be true that the evidence has been planted, or doctored in some way. Or they are just unlucky happenstaces that casts a very negative light on person B. It could be the case that person B came to the premises for some other reason entirely, maybe to offer an apology for a fight they had, then discovered that person A had been stabbed, and despite their bad relationship tried to help person A and so on and so forth.
In other words, we could be in a situation where the evidence points to a falsehood. To something that actually didn’t take place. We can only discover that by finding more evidence. Finding more evidence can radically alter where the evidence points.
Yeah I simply don’t agree with that assessment. It is possible for evidence to point in the wrong direction. It is possible for there to be evidence for the existence of God, even if God does not exist, just as it is possible for there to be evidence against the existence of God, even if God really does exist.
That’s why scientific theories are always tentative, and they can change in light of new evidence.
Maybe we don’t have all the evidence. Maybe some of the evidence has been destroyed, leaving what remains pointing in the wrong direction. This is just the nature of the game. You are simply mistaken when you think there can’t be evidence pointing to something false. There can be, which is why we always want more evidence, because the more evidence we find, the less likely it becomes that the evidence just happens to be of the sort that points in a wrong direction.
That’s why consilience of independent phylogenies is important. It is further corroboration of an objective nested hiearchy.
But what causes organisms?
The world may never know.
Glen Davidson
John writes:
colewd disagrees:
Sal pontificates:
Both wrong. The topic of conversation was the differences between extant species with germline-soma distinction; therefore when John wrote “Your idea…is contradicted by everything we know.” he was being 100% correct.
BTW Sal, I am a biochemist, and you have argued with me about biochemistry, so you were wrong when you wrote that 🙂