I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.
Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.
If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.
One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.
Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.
That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).
Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.
The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”
So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.
So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.
As many people have tried to point out to you, it is not a stupid hypothesis. You even admit that it’s logically possible and could happen given certain conditions.
You need to evolve
Both can be subject to concerted evolution, as far as I am aware.
Could you please explain what you think the “Sternberg-Collins pattern” is, what it has to do with the number of SINEs inserted, and what Collins actually said (with a real citation)?
No he isn’t. In fact he has specifically denied, at various times, any interest in evolution. He’s a self-described structural biologist. I, on the other hand, am an evoutionary biologist. I have a PhD in evolutionary biology from the prestigious University of Chicago, and have published on evolutionary biology in the prestigious journal Science. Prestigious!
If there were indeed 300,000 convergent insertion points, you would have something there. But if you’re just amazed that there were approximately equal numbers of SINE insertions in two species, that doesn’t seem like so much. Could you perhaps clarify what you’re talking about, if you in fact know?
Sternberg has a PhD in Evolutionary Biology and a PhD in another biological field. He is a Process Structuralist which is NOT the same thing as a structural biologist.
As a complete aside, and you don’t have to answer, but really I was just curious given that you said Jerry Coyne banned you from his website. Since Coyne is at University of Chcago, did you ever meet him there? Just a curious question, nothing to do with the OP.
That makes too much sense.
But it also helps explain why some people here are so averse to showing their work in constructing a GA. It would expose them to “well, why did you choose that” questions.
Ah, I see his degree is in molecular evolution, which I suppose counts. But is that degree from a Prestigious University?
UCD? You mean UC? Yes, I met him quite frequently. I had a seminar with him, in fact. He’s prestigious.
By the way, why do you consistently ignore my main points and respond to trivial points?
Because when I get annoyed with what I consider trivial complaints, I put you on ignore. But since you responded to my question, in reciprocity, I should respond to you main points.
If you can, and I apologieze for having to do this to you, can you state the main points you think I haven’t addressed. I felt I gave you direct answers like, “NOI” when you asked if I can identify the Baramin. Or “NO” I can’t explain or predict why the designer would created a nested hierarchy any more than I can explain why or predict why Rachmaninoff chose the notes to his melodies. I personally thought I addressed your main points with direct answers, and when you kept saying I didn’t, I put you on ignore.
So, we can try again to set the record straight. I appreciate you answering my question about Coyne. It really had nothing to do about anything, but personally, I felt bad for you and I thought that was rather rude treatment on Coyne’s part toward you. FWIW, it actually bothered me that he treated you that way, especially given your credentials.
Sorry I must ask you to restate what you really want me to address. I want to set the record straight once and for all.
No, I have no interest in restating my points. Look at my recent posts in this very thread, most of which you have ignored in their entirety. And look at the very post to which you responded, the one with the claim about Sternberg as evolutionary biologist.
So you can’t identify any baramins. Why should that be so? Shouldn’t they be obvious if in fact they were separately created?
So you can’t explain the nested hierarchy of life, and you can’t explain why we see a pattern that would have been generated unavoidably by common descent. Why then don’t you accept common descent of life as a feature of god’s means of creation? Why do you reject evidence pointing to common descent in favor of a process, separate creation of baramins that you can’t even define, that would not be expected to produce such a pattern of evidence?
I was asking for your main points regarding the OP, not your trivial ones, since I’m trying to set the record straight once and for all.
Here is an example. You’re contesting despite that fact that he’s an evolutionary biologist. That’s a trivial mincing of words and ideas. He has more education in evolutionary biology than Charles Darwin had.
From his website:
http://www.richardsternberg.com/biography.php
So you’re straining at trivialities at least in relation to the OP. But there he said he’s an evolutionary biologist, he worked at the NIH NCBI as a staff scientist. You’re saying he’s not an evolutionary biologist, he’s saying he is. In my view you’re just mincing over definitions and words.
So, if not for my sake, how about the readers. What are your top 5 main points you felt needed to be addressed regarding the OP.
stcordova,
What’s it doing in this thread then?
Many things are nonrandom in the genome without even a whiff of [common?] design.
One is still left with the case where a clade possesses flank-SINE-flank when all outgroups do not. I realise my repetition of this point is getting tiresome, but you simply aren’t addressing it with a piece of coarse genome-wide comparison which has nothing to do with it.
flank-SINE1-flank in one species and flank-SINE2-flank in another, aren’t, taking the sequences as a whole, evidence for common descent of those species. Nonetheless, if we ignore the insertion, we have flank-[]-flank in both species, which is evidence for common descent.
But in any case, the SINE sequences used in phylogeny are those in which all sequences are flank-[SINE1]-flank or flank-flank. SINE2, as a hypothetical convergent insert, is a red herring. How do we even come to declare it inconsistent? Could it be its very incongruity with phylogenetic expectation given by everything else in the genome? Once again, as I have noted throughout this thread, you are relying on phylogenetics to destroy phylogenetics.
This appears to go right past your filter as if it weren’t there. It needs explanation. How come so many clades share a particular SINE within the same flanking sequence? Different SINEs probe different taxonomic levels, up to and including close familial relations. How can this be valid at one level but not at another? At what level does the discontinuity arise?
stcordova,
Again you ignore the points I made in the very comment you are replying to in order to concentrate on the trivial bit about whether Sternberg should be called an evolutionary biologist. I have already agreed that there is some argument to be made that he is. Forget that and answer the rest of what I say. That’s where the important points are.
Here’s a suggestion. Stop making trivial points if you don’t want him to respond to them.
ETA: Or label your points as either “main” or “trivial” so that we can see whether Salvador consistently ignores your main points and responds to trivial points.
But things are all better now.
No, that isn’t what it does at all. Either your teacher is very bad or you’re a very bad student. What maximum likelihood does is determine the conditional probability of observing the data given the model. In phylogenetic analysis, the model includes relative rate parameters for different sorts of transitions and sites, as well as a tree. Many trees are examined and the one that maximizes the conditional probability of the data is accepted as the best tree. While most programs consider only connected trees (as opposed to separate trees), it’s possible to evaluate disjoint trees, as Theobald did. And one can also test whether one tree is significantly better supported than another; it if is, that’s evidence of common descent.
I’d like to see you try. And why, if there is no common descent, would we expect those nested hierarchies to exist? Why would we even look for them?
DNA_Jock,
You’re just digging the hole deeper. Not a smart move.
You’re trying to pretend that the three comments merely provided “supporting data” for your counterargument, which is why you linked to them:
Unfortunately, your earlier words betray you:
You went from saying “everyone’s been trying to explain this to you; look at all these linked examples”, to saying “Um, well, three of them are just ‘supporting data’ and the real argument is in the fourth.” Yet even that isn’t true, because the three of them that supposedly supply ‘supporting data’ are in perfect agreement with my own argument.
You were confused and made a mistake. I pointed it out, and instead of acknowledging it, you tried to rewrite history in a decidedly Alan-like way in order to avoid admitting your mistake. Not a very admirable perfomance.
Now that you’ve been caught, will you finally own up to your mistake so that we can move on and discuss the fourth linked comment?
I said:
in pretended contrast:
Mincing words again John. If you really wanted to say the opposite of what I said, you would say, “Maximum Likelihood picks the tree with the least likelihood of being true”. If you believe ML doesn’t pick the best tree, then why use it?
Well, yeah, formally you don’t get the best tree given with 20 taxa you won’t be able to exhaustively explore all possible trees. So you apply heuristics to get you at tree that lies in the right ball park.
So you complain about me not identifying Baramin, You can’t identify the exact right tree anyway, you can only pick one that is approximately close to the correct one. Given the number of trees is astronomical, the chances of you describing the correct tree are astronomically remote, you can only get less astronomically remote to the actual tree. Pot calling the kettle black eh.
That’s possible. So why don’t you tell the readers then what the probability is you got the exact tree out of the buzzillion trees possible?
I actually don’t work with confidence intervals. But say the tree you’ve picked is in the 95% confidence interval after you’ve done all the bootstrapping and whatever else you could do. That means you’re in the 5% region where the right answer lies. So….
5 % of 1 out of a buzullion = 1 out of (.05 buzillion) which is still astronmomically unlikely of being correct. And yet you complain I can’t absolutely identify baramin, when you can’t absolutely identify the correct evolutionary tree. If you suggest my views are worthless because they are inexact, the same criticism could be leveled at your views.
Regarding the possible number of trees, our very own Joe Felsenstein wrote this:
http://www.nematodes.org/phylogenetics/Bayesian_Workshop/PDFs/Felsenstein.pdf
How about the number of bifurcating trees with a mere 19 species?
The forumula is
13,113,070,457,687,988,603,440,625 for only a mere 19 species. Given there are a milliions of species out there, the actual number of possible trees is like a buzzillion. What are the chances any evolutionary biologist will get the tree right even with the heuristics being applied like bootstrapping? And John Harshman complains about my methods being inexact? That is straining at gnats and let camels through.
If universal common descent is false and special creation is true, then distanced based/orphan based methods of taxonomic classification are the best way to do taxonomy, and phylogenetic trees are only beautiful fictions.
Hey, I have no problem with evolutionary fictions as fictions. They are quite entertaining and can be quite beautiful. This is such a beautiful evolutionary fiction, it would almost make a Darwinist out of me:
https://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/protein-classification/what-are-protein-families
No need to define the protein taxonomy based on some mythical (likely wrong) phylogenetic relationship. The Taxnomies are definable by structure and function and sequence.
Here is an example of protein taxonomy. Do we need any phylogenetic methods to build this? Doubtful.
Here is one problem for common descent, the supposed phylogenetic trees of protein domains. Especially when the domains appear in different protein families.
https://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/protein-classification/family-and-domain-based-protei
Note how the red-colored domain appeared in proteins of different families. How did that evolve? Not my problem, because God created it via a miracle.
How do you decide what can be explained without miracles and what can?
More to the point, what’s the actual point of any of this work you are doing? Why not just write “God created it via a miracle” and take your applause from the church basement audience?
Nobody is stopping you doing that are they? And yet you don’t seem to be doing it…
It’s no wonder you are afraid you publish your work in a reputable venue.
And here we see Mung’s confusion, and usual modus operandi, on display again. Mung primarily argues by word-seaching in the literature for little quotes that he thinks he can pick out and throw doubt on some field of study. As is in the nature of any science, there is debate about methods, results and interpretations, so there isn’t any field of science where you can’t cherrypick some quotes to make it appear as if nobody knows anything.
In this particular case, Mung is confusing several things. First of all, he’s confusing being able to infer that species share common descent with inferring the true branching relationship of all species with a great level of certainty. He’s also trying to cast doubt on the validity of phylogenetic inferences by pointing out that using different phylogenetic methods on the same data sets, give different phylogenies. Which really shouldn’t be a surprise to anyone.
In other words, if you do a maximum parsimony phylogeny on a set of DNA sequences, you will get a particular tree. Then, using the same set of DNA sequences, you can try another method, like maximum likelihood, and this will give a tree that isn’t exactly like the maximum parsimony tree. They will have some incongruent branches. And of course it is debated which method to use, when to use it, and so on.
So what Mung is trying to achieve by that Elliot Sober quote, taken completely out of any clarifying context, is to make it appear as if the whole subject of phylogenetic inference is up for grabs and nobody can say anything with any appreciable level of certainty regarding interspecies relationships. Which is of course complete fucking horseshit if you think about it for even less than twenty seconds.
To make a few points in that regard, there is no phylogenetic conflicts that put… whales with squid, for example. Or birds with insects. Or primates with jellyfish. Those are not the natures of the disagreements between methods. Yet if you knew nothing of phylogenetics and read Mung’s quote, that might be the kind of impression you’d be left with. Probably what Mung intended.
Another point to consider is that if you use the same method on independent data sets from the same collection of species, the trees you get still match with an extremely high level of statistical significance. This is often times even the case if you use different algorithms.
The trees, despite having several incongruent branches, are still significantly similar in the way I alluded to above. The trees still correctly groups all mammals together, all birds together, and so on. Where you will see disagreement is in the branching order of very closely related species (like, which one of these mice is more closely related to this particlar rat?), or in general when branching events have been close together in time (exactly where is the root of the jellyfish clade?), which means there has not been enough time for differences in character states to unambigously resolve “which bifurcation came first?”.
There’s something very dishonest and rather perverse about the way Mung argues.
And here we have the double standard of creationism highlighted for all to see.
Sal is fine with an ulfalsifiable conjecture that never explains what we see, as long as it comes in the form of “God did it”. But if the explanation doesn’t involve God, then Sal wants an atom-by-atom world-history of the pattern from the beginning of time.
And just to emphasize the point about unfalsifiable conjecture here. Try to imagine for a second how the distribution of protein domains in Sal’s copied graphic could ever conflict with the claim “God made it like that!”. What you will see is that there is no such pattern even in principle. No matter how those protein domains are arranged, it could never ever conflict with the claim “my unlimited God wanted to make it exactly like we see”.
Thus is relevealed the astonishing hypocricy of creationists.
stcordova,
Can I recommend SINE data as a useful way out of this thicket? 🙂
Given the nature of transposition, and its expected lack of homoplasy (and the possibility of adding multiple ‘cross-ref’ inserts to eliminate even that source of exponential increase in search space) one does not have to sift through anything like this number of trees. In fact, one can do the whole exercise with a pencil and a sheet of paper, no fancy computation required.
stcordova,
OK, place your marker: where does phylogenetic analysis break down? Are there no clades that can be resolved by it, at any taxonomic level? Are you, in fact, a ‘species-immutablist’? Or is it just cladogenesis you disbelieve?
The cuteness continues. I never claimed that the four links were an exhaustive list of the counter-arguments that you had ignored. Sadly, your only mode of engagement seems to be to accuse others of “mistakes” that are, by and large, entirely figments of your own poor comprehension skills (e.g. ‘DNA_Jock’s bizarre “You think we’re closet IDers!” claim.’ — I mean, WTF? )
And I stand by my statement that “This has been explained to you multiple times by multiple posters, yet you fail to address their points, merely rabbiting what you said previously.”
I find it strange that you would insist on my admitting to some mythical error before condescending to discuss my counter-argument. Particularly when the mythical error involves my claim that you have failed to address said counter-argument.
Not really covering yourself in glory there, are you?
But hey, I’m a generous guy, so I won’t put any pre-conditions on actually discussing how guided evolution might produce an ONH. I don’t expect you to own up to your mistakes. 😉
Here’s the fourth linked comment.
Note the emphasis.
keiths:
No, actually, I am not.
Oh, I’m not supporting guided evolution – I am not aware of any evidence to support that concept. I am merely trying to explain to you how (partially) guided evolution could lead to the ONH that we observe.
Well then, that makes three of us, doesn’t it?
^This^ is where your dichotomous thinking has gotten you confused. The best explanation that I can arrive at is that you are considering the hierarchy of changes introduced by the guider in isolation. That’s wrong. We agree that we have descent with modification, which produces a mind-blowingly powerful phylogenetic signal. Buried inside this, we have some aberrations, which we ascribe to convergent evolution (or HGT across taxons…). The sum total of all of these anomalies does not lead sane people to doubt the fact of common descent, because the signal is still there, loud and clear. Because there’s a lot of signal, the analysis can tolerate a pretty large number of anomalies…
Now, the guider’s tinkering, in and of itself, may or may not produce an ONH, depending on his (unknown) preferred mode of operation. Doesn’t really matter, since even a goodly dose of non-hierarchical tinkering would not stop the John Harshman’s of this world from revealing an ONH, albeit one with some anomalies.
If, and only if, the guider was motivated to deliberately obscure the phylogenetic signal would we NOT expect to see such a signal. It isn’t me that’s making assumptions about the goals and abilities of the guider.
It seems that only you fail to understand this. Well, maybe you and phoodoo. That ought to give you pause.
Just to labour the point on SINEs some more: when you don’t have an annotated genome to search, you need some biological material and a couple of designed RNA primers. You look for a SINE sequence of interest, find where it starts and ends, and design a primer for each end. Each primer is complementary to one strand of the flanking sequence, sense one way, antisense the other. Then, you set your primers loose in a PCR. RNA has great specificity, so it can bind to the flanking sequence precisely. DNA polymerase grips this handle and amplifies that which lies between – either it has the SINE, or it doesn’t. This creates molecules of different sizes. Plate them out on a gel, the larger travels at a different speed.
Now of course one could have stumbled upon a homoplasious site – eg one where a different SINE has independently inserted in exactly the same place in the genome. This would be rather unlikely to happen commonly – it is hard to see where this information would be encoded in the transposons. Especially since the same transposon is often found all over the genome. Perhaps there is a site-specific ‘attractor’ for transposons? Again unlikely, since the flanking sequence differs for every insert copy. So maybe someone stuck them there? Yeah, maybe.
The so-called Sternberg-Collins paradox appears to be an attempt to dismiss the use of SINEs due to extensive homoplasy (in two particular species at least). But are we powerless in the face of this? Is there no way we can characterise the SINE that sits between the primers to determine if it’s the one we are interested in or not? If we just look at a band on a gel plate, we don’t know what we are looking at. But we can design an RNA probe for our SINE sequence, make it fluoresce if it’s the right one. If we have an annotated genome sequence, we can just check sequence identity of the insert (commonly descended with other instances of the insert!). And of course we can just pick a few more SINEs to look at, enriching our dataset and allowing any anomalies to stick out.
So … back to why. Why do two unrelated genomes have the same flanking sequences? Why do some genomes with those flanking sequences also have the same SINE in them? If one is looking for functional reasons, one may need to account for the functional absence, as well as functional presence. And one might ask what locus-specific function is served that must be achieved by a transposon, most of whose bits are occupied with the stuff of transposition?
Well, first of all, in the chapter on bootstrapping in my 2004 book, there is a section discussing an argument by John. He’s published on that. And correctly, too.
The whole point of bootstrapping is to assess which branches of the tree are most likely accurate. Not to somehow make them totally accurate. Short branches, reflecting events long ago, are less likely to be accurate. And different methods of inferring phylogenies do find a lot of common signal, just not exactly identical trees.
In addition to which, the formulas and numbers given happen to be inaccurate. For rooted bifurcating trees, the number of possible trees is
which is also the product of the odd integers up to
. and which for 19 species is 221,643,095,476,699,771,875. Still a big number but about 65,000 times smaller.
DNA_Jock:
Exhaustiveness is not the issue, as you know perfectly well.
The issue is your rewrite of history.
You went from “look at these people making the same counterargument I am” to “Oh, those three comments are just ‘supporting data’ for my counterargument, which is in the fourth comment.” (And even that isn’t true, as I’ve already explained.)
Why the rewrite? To cover up your mistake. You were confused, and you thought that what Zachriel and Rumraket wrote was a successful counterargument against mine. You only realized your mistake after I pointed it out. Then your personal spin machine whirred into action, and those comments were magically transformed into mere ‘supporting data’ for the actual counterargument in the fourth comment.
You got caught, Jock. Deal with it.
Jock,
Speaking of your personal spin machine, here is another doozy:
Not only is that false, but in the case of Rumraket I even addressed his point in the very next comment after he made it:
Rumraket:
keiths:
So much for my supposed “complete and utter failure to address the counterpoints”.
You got caught — again. You’re just making shit up and hoping people will believe it. Definitely not your finest hour, Jock.
Since you are in a state of Alanesque denial, I’m not expecting an acknowledgement of your mistakes. I’ll address the fourth comment later today.
LoL.
Here we are, 30 years after Sober wrote those words. So going on 50 years now without an answer to the methodological question. Or are you saying that’s all been resolved now.
Why not face up to the facts?
Questions of method are often raised in science, and often they are routinely dispatched. But this has not happened in the present case. For some fifty years the debate has continued, with no resulting consensus.
We don’t know which one is best, and we don’t know why it’s best, but that doesn’t matter, because common descent is true. Evolutionism rots your brain.
It’s a kind of glory peculiar to one particular poster.
Oh keiths,
I know you think you have addressed the counter-arguments from the Four Horsemen. It’s just that you failed, that’s all.
It’s okay.
I recommend that you try the Active Listening trick: honestly, accurately, and without emotion, try to describe the counter-argument in your own words, as I have done with your argument.
Or have a cookie, your choice.
Jock,
So now you’re back to claiming that Rumraket’s comment was a counterargument, and not merely ‘supporting data’ for your counterargument?
When you find yourself contradicting yourself again and again, that’s a good time to pause and reconsider your approach.
I recommend that you try the “Being Honest” approach.
See this relevant comment in Noyau.
No. Use them all you want to argue for common descent. I already said, in that case we assume for the sake of argument, like evolutionary biologist Richard Sternberg did, that there was common descent. The problem is why the insertion sites are so correlated and not just that, that the epidemic insertion of SINES happened about the same time. That is not consistent with random mutation.
So you have a case of possible common design along with common descent. That demonstrates then that common design can TRANSCEND common descent.
Stop embarrassing yourself. What I said isn’t the opposite of what you said, just different. You may consider the difference to be quibbling, but you really should understand what a method does rather than a garbled form of that. Now of course ML doesn’t pick a tree at all; it just assigns a likelihood to each tree examined. You pick the tree with the highest likelihood, which is “best” by that criterion.
If you do the search right, you are pretty much guaranteed to get the best tree with 20 taxa.
No, you misunderstand. I complain that you don’t realize that your inability to identify baramins is data. If there were baramins, they ought to be obvious. Therefore there aren’t: common descent.
And the number of trees is not at all an obstacle to choosing the correct one, heuristics being quite good. The obstacle is that the data are sometimes indecisive, don’t fit the model, or track a tree other than the species tree. Fortunately, these problems can be dealt with. You are in fact repeating the common creationist claim that if we don’t know everything, therefore we know nothing.
That’s possible. So why don’t you tell the readers then what the probability is you got the exact tree out of the buzzillion trees possible?
I’m sorry, but all that does is show that you don’t understand confidence intervals or bootstrapping. You might want to read Joe’s book. Your attempt to equate your inability to identify a single baramin with the provisional nature of all science is just plain silly.
So now try answering the question: Why, if there are separate kinds, aren’t they obvious?
Yeah, yeah. You really shouldn’t quote-mine a person who actually reads this forum. Marshall McLuhan could show up at any moment.
Bootstrapping isn’t a heuristic. The number of possible trees is not a serious impediment to phylogenetic analysis. And I don’t complain about your methods being inexact; I complain that you don’t address the obvious point that you inability to recognize a single baramin suggests that there are no such things, since if they existed they should be easy to detect.
…how can we possibly explain all the data we have that shows a nested hierarchy of life? That’s what you really need to address, and yet you never have.
relative lack of homoplasy; there are a few examples of identical retroelement insertions in distantly related taxa.
The phylogenetic relationship for Protein trees breaks down when the host organisms in play have substantial amounts of Taxonomically Restricted Features demarcating a group. I avoid the term Orphan Gene as orphan genes are usually short peptides.
Some morphological gaps are brutally obvious, but in doubtful cases hybridization or ring species evidence might help identify an applicable domain of phylogeny as there is indeed good direct evidence of common descent from a created kind. My point about not being exact in the identification of Baramins is that phylogenetic methods aren’t exact either!
Sure there are clades, we may identify them by alleles, and the alleles may or may not be created.
Look at the demosntrable clades within these baramin:
https://en.wikipedia.org/wiki/Brassica_oleracea
But in that case we don’t need phylogenetic methods since we have agricultural records that help us reconstruct the REAL phylogeny.
But one thing I’m noticing in my cloning of plants in my amateur garden, there are rather severe differences in the plants that are cloned. There are lots of “epigenetic” factors that change along the new cloned lineages and these factors are pretty hard to track down relative to genetic characteristics.
As far as I can tell, there is no homoplasy in the SINE insertions he mentions. There is only a) a similar number of insertions between species and b) a similar pattern in the frequency of insertions over gross (megabase scale) regions of the genome. I’m not sure Sal understands this, and I’m not sure Sal understands the figure he keeps posting. I’m pretty sure he has never looked for an explanation of that pattern.
What do you mean “these baramin”? Are you suggesting that Brassica oleracea consists of multiple created kinds?
God did it by miracles because the real TAXONOMIC hierarchy is defined by the miracles of Taxonomically Restricted Complex Features. One does not need phylogenetic methods to see these definable gaps.
What counts as an adequate explanation for me does not count as an adequate explanation for you.
The problem is that you insist that an explanation is adequate if it follows a mechanistic predictable path that goes something like:
State 0:
State 1 result of Set of Events 1
….
State N result of Set of Events N
But miracles don’t follow that. I’m satisfied the gaps for Complex Taxnomically Restricted Features are big enough to argue for miracles. You aren’t. In fact, the sentiment of your side is there will be no gap big enough that you’d believe an orphan system defining a group emerged via a miracle. Given that sort of epistemology, even if a miracle was the cause, you’d never ever be able to see the truth. That’s fine, I’m not here to persuade people who are unwilling to consider the possibility of miracles.
I addressed it in a way satisfying my criteria, not yours, but let’s not pretend I didn’t discuss it.
Random point mutations and indels may create a new peptide, it doesn’t create coordinated protein systems like an insulin regulated metabolism.
As far as taxnomic classification of proteins, this is done mostly on structural and functional grounds, NOT phylogenetic grounds. The reason? Understanding the operation of biological organisms in the present day is dependent on structure and function, not phylogeny. One can do comparative anatomy with the assumption of common design just as well as the assumption of common descent, and I actually suspect even better. Example: there are protein functions that share convergence (common design) that even evolutionists admit have no common descent. From a functional perspective, the present-day design is what is important, not the supposed ancestry.
I’m relatively confident, protein classifications will always be along structural and functional lines and phylogenetic classifications will just be a passing amusement because that’s the way they are already being classified. This begins from the very basics like Quauntum Mechanics generating the periodic table. Just as we wouldn’t classify atoms and molecules by “phylogeny” in the field of chemistry, there is no need to classify proteins (which are also chemicals) based on phylogeny. We classify them on chemical and structural properties. If this is how we do taxnomy at the molecular level.
At the morphological level it may be another story. As Lewontin noted, it bothered him that there are no birds that eat leaves, even though from a nutrition standpoint, it would make some level of sense that they should evolve such a capability. But if we are talking molecular phylogenies, I don’t see much need for them except maybe trying to reconstruct the genealogies towards the creatures on Noah’s ark — but even then, a lot of creationists like me could almost care less exactly what creatures were on the ark. Biochemistry seems to me more interesting than such questions, personally speaking anyway.
No the exact opposite. Recall I said ring species, that is extensible to situations where we actually have agricultural records demonstrating common ancestry.
Then why did you say “these baramin” when referring to the species? Could I ask you to be more careful in your language? You say little enough about “kinds” that confused language when you do say something is especially problematic. What do you think the baramin is here? The species? The genus? Something else? And why?
You say that hybridization is a reason to believe that two species are in the same baramin. Why? Is lack of hybridization a reason to believe that they aren’t? Why can’t we easily identify baramins?
John:
Sal:
Then why did you write “these baramin”?
ETA: Ninja’d by John.
Yes. My apologies. I will try. That is a fair and accurate criticism.
But those definable gaps have two problems for you: 1) they don’t contradict common descent, which you have in fact occasionally admitted, and 2) they aren’t apparently gaps between baramins but mostly between larger groups, and are in fact nested groups.
That much is clear. “Goddidit” is not an explanation that any rational person would accept. It’s a substitute for an explanation. And it prevents further inquiry, the antithesis of science.
In fact you didn’t. You discussed the origin of features, not their arrangement in a nested hierarchy.
I’m surprised that Lewontin had never heard of hoatzins. And many birds eat leaves if you count grass blades as leaves. What relevance does this have?
So to you, biology is boring. Odd. So why is there a nested hierarchy of life? Is your answer “I don’t care” or “Goddidit” or both? Neither of these is an explanation.