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.
Well fuck me, Mung makes a genuine contribution that is in the realm of reason.
I think it’s wrong, but at least you’re not saying stuff just to be a contrarian.
I think it’s wrong because theories can both explain and predict what they explain. To gave an example, Newton’s theory of gravity would explain the shape of the orbit of some planet around the Sun, given their masses and orbital velocity. But it would also predict it far into the future. Recording the orbit of the planet far into the future and finding that it agrees with the prediction, then also means the predicted and explained orbit is evidence for Newton’s theory.
It is like this with the nested hiearchy. It is both predicted, and explained, by the theory of common descent.
But Newton’s theory of gravity in and of itself, does not explain why there are stars and planets in the first place. Where they come from. It can explain that, once you combine it with theories of nuclear physics and some initial conditions about large gaseous clouds in interstellar space.
Again, it is like that with common descent. It does not explain why there comes to be new features of organisms, it just explains why they are distributed in groups within groups (Why is there are group of organisms with mammary glands and a group of organisms without mammary glands, inside a group of animals with spines? Why is there a group of organisms with spines and a group of organisms without spines, in a larger group of multicelluar eukaryotes?).
Common descent is the theory that explains such a distribution. It implicitly assumes new features arises, but doesn’t say how or why. Just that they do and are then passed on.
To explain the origin of new features, you need another additional theory. Theories of molecular evolution, which means copying of DNA, mutation, natural selection, and so on.
I never said they did! I pointed out they couldn’t evolve by point mutation, you took that to mean I advocated they did. That was a mischaracterization on your part, not a mistake on mine.
You apparently didn’t recognize the form of the argument which was a reduction ad absurbdum refuation. For the reader’s benefit:
https://en.wikipedia.org/wiki/Proof_by_contradiction
That’s all a lot of the way goes around here at TSZ. You guys don’t actually engage the points, you engage arguments I didn’t make. I put data on the table to back up my argument you complain of Gish Gallops. I don’t put data on the table because it floats over John Harshman’s head, you say I didn’t justify my point.
TO THE READERS:
But, first, if I may criticize rather sharply a disagreement I have with something my long-time friend and ID advocate Casey Luskin said. It is unfortunately something that is circulated in the ID community and it has been a credo for some strange reason. It actually conflicts with what a revered (albeit unwitting) founder of ID Michael Denton said.
Here is Casey Luskin:
NO. NO. NO. NO. NO!
The phylogenetic tree is not the only nested hierarchy! Taxonomic nested hierarchies also exist — it is the old school Linnaen hierarchy approach to classification. Denton pointed this out.
Taxonomic nested hierarchies are easily demonstrable, one merely needs to look at groups that are clusterable by structure. It’s not that hard. One doesn’t need all the uncertain cherry-picked phylogenetic methods to see it.
A parrot is a member of the bird (aves) group…etc.
An elephant is a member of the placental mammals, placental mammals are member of mammals, mammals a members of vertetbrates, vertebrates are members of animals, etc.
A magnoilia is an angiosperm, an angiosperm is a plant
One doesn’t need phylogenetic methods to arrange things according to structural similarity. Can only one nested hierarchy be made with structural techniques? Most likely not, but neither can phylogenetic trees! So what if people have different structural classification than someone else. A rose is another rose, in contrast phylogeticists keep aiming to find the right tree which even they admit they’ll never find.
Sheesh with a mere 20 species you get a buzzilion possible phylogenetic nested-hierarchical trees. I think it’s rather absurd to have exponentially more possible nested hierarchies to choose from using phylogeny than the number of species under examination! At worst with structural methods, if you’re dealing with 20 species, you get at worst 20 structural categories if the data are amenable to structural aggregation, not a buzillion of them!
http://www.nematodes.org/teaching/tutorials/phylogenetics/Bayesian_Workshop/PDFs/Felsenstein%20Syst%20Zool%201978a.pdf
I mean, seriously, with those numbers of possible nested hierarchies to choose from, what the heck more can one accomplish compared to simply building classifications based on structure. With those astronomical numbers of possible nested hierarchies to choose from, the odds of getting “the right” phylogeny are pretty remote anyway. Phylogeny is no better than arranging things in terms of structural similarity, probably worse because then you start calling birds “Sarcopterygiian fish”.
Structural biology is far more compelling, imho. How do they go about their business? With chemistry and physics and high-tech machines, not with phylogenetic methods. One would think with all the print invested in phylogenetic methods it would return some fruit in understanding how systems are structured and actually work. Instead, professional phylogenists have been among the most to resist the onslaught of “-omes” as symbolized by ENCODE and several other “-ome” project. Of these, John Harshman said:
ENCODE has pioneered a lot of work on the epigenome, and consequently added knowledge to the methylome (of DNA), the methyl proteome, acetyl proteome, the phosphoproteome. Serveral follow-on projects have resulted including the 4D nucleome. Instead of celebrating the advent of these immensely interesting explorations of biology, we have guys like Dan Graur going ballistic and calling these researchers ignoramuses and crooks. John Harshman has echoed Graru’s disdain for these datapoints many times in this discussion.
Seems to me, John Harshman and Dan Graur find the structural complexity of biology quite unsettling rather than something to wonder at. Why is that?
Sal,
What’s your view of duons; overlapping genes etc?
One man’s contrarian is another man’s skeptic. 🙂
There seems to be a consensus that common descent does not explain the differences.
Given that common descent does not explain the differences among taxa, the nested hierarchy cannot be evidence for common descent, because the nested hierarchy is based on the presence of differences between taxa. Without those differences there would be no nested hierarchy.
You can’t have evidence for a theory that does not explain the evidence.
The orbits can be evidence for the gravitational theory because the gravitational theory explains the orbits. You’re comparing apples and oranges.
There’s a difference between explaining why they exist(they evolve by mutation, natural selection etc. etc.) and why they are distributed the way they are(can be objectively sorted into nesting hiearchies of groups within groups because they go through a branching genealogical process).
Without common descent there would be no good reason to expect a nested hiearchy. So it’s simply not correct what you say.
You are confusing what is to be explained. The existence of differences among groups, with the fact that they can be objectively sorted into nesting hiearchies.
This is like confusing the fact that a planet with some trajectory exists, with it having an elliptical orbit around some mutual center of mass.
Yes. But it doesn’t explain why stars and planets exist in the first place, you need to combine it with something more to get a full description of a solar system. Why is there that planet in the first place? Or why is there three of them, where did they come from? Merely explaining why they conform to some trajectory is on thing. Accounting for their existence is another.
Perhaps another analogy could be explaining why some rocks are sorted differently in some pattern on the beach (as the water ebbs and flows, they are affected differently by it and settles in that pattern), and explaining why the rocks are different from each other in size and composition, in the first place. Well you see different rocks are made by different processes in the Earth’s crust and mantle, and they have existed longer than others and been worn down more bla bla bla.
Or an even more direct analogy. Common descent does not explain why mutations happen, so common descent just explains why we can objectively sort different DNA sequences into branching tree-like pattern if mutation happens.
Why do mutations happen? The explanation for that isn’t common descent, it’s the physics and chemistry of DNA and the proteins that replicate it. Strand-slippage, tautomeric shifts, unequal crossing over and so on and so forth.
But another cause could hypothetically speaking, be making mutations happen, as long as those mutations are passed on to new copies and there is splitting of lineages, we will be able to sort DNA sequences with those mutations, objectively into branching tree-like patterns.
Common descen’t doesn’t explain why the DNA sequences differ from each other in the first place. That takes a theory of causes of mutations.
I’m sorry but no, the analogy here is fine. But if you don’t like it, the rocks on the beach analogy seems even better to me. And the direct analogy to DNA, it’s replication, and the causes of mutation is, well because it is an instance of the very subject, actually perfect.
Phylogeneticists treat unconserved regions in proteins like they are meaningless filler, and thus the patterns of differences in the same gene between species is merely the product of a random walk in such variable/unconserved regions. Far be it for them to even suspect unconserved/ variable regions may have functional significance on a species-specific basis. If the diversity is species-specific and functional, then the differences look more designed than just a random set of mutations because random mutations are not expected to make designs. One such design is a “reader” of histone memory devices in chromatin, known as the bromo domain.
We’re finding some of the differences in the same protein between species has functional significance because each species may implement the protein with a different set of domains — remember that Zinc Finger (hehe).
https://www.ncbi.nlm.nih.gov/pubmed/10892642
Koonin and Kondrashov note:
Below is a diagram of the same protein in different species with different domains inside of them. This shows species-specific function of the same homologous protein by different species.
Just because part of a gene is NOT conserved in a species does not mean it is non-functional. Larry Moran seems to swear by the notion that “conserved means functional” with the insinuation that unconserved regions are just non-functional padding. Well, unconserved species-specific differences in a gene could be functional too!
This is illustrated in Koonin’s paper by this diagram (below):
Now I should point out something that I took issue with John Harshman about, namely the Histone “readers”, “writers”, and “erasers”. One such chromatin/histone “reader” on lysines is the bromo domain (pictured below, marked “Br”.)
TAF145p in yeast does not have this bromo domain “reader” but TAFii250 in A. Thaliana (a plant) TAFii250 does. C. elegans and D. melanogaster have dual memory reader side by side.
These readers are acetylation readers. Recall I mentioned the Acetyl proteome. This bromo domain memory “reader” is one of the molecular machines that implement the acetyl proteome.
The pattern of diversity between species then looks DESIGNED, because it suggests species-specific function, not some mindless mutational random variation in a protein between species. Hence, common design is a better explanation for the pattern of diversity than common descent when the differences are functionally important.
Click to enlarge:
http://theskepticalzone.com/wp/wp-content/uploads/2017/12/domain_accretion.jpg
The Bromo domain from Wiki:
https://en.wikipedia.org/wiki/Bromodomain
Relevance, Dr. Gish?
Hey! Happy Thankgiving and Merry Christmas.
I’m not very familiar with duons. Overlapping genes exists even in humans, but I’ve found only a few papers. But “etc.”? Bwahaha!
A good fraction of my comments in this thread have been on the Polyfunctional features of DNA and the sequences it transcribes to (RNA) and translates to (Proteins). I think you’re the one that found the paper on Polycontraints by Montanyez, Fernandez, Robert Marks, and John Sanford.
Polyconstraints/multi-functional aspects of DNA sequences can account for the patterns of differences in genes, thus the patterns of differences, to the extent they have functional significance support the viewpoint of Common Design toward functional complexity vs random mutation during Common Descent with no functional significance.
The DNA sequence is meaningful in generally 3-6 levels:
Genome and Epigenome
Transcriptome and Epitranscriptome
Proteome and Epiproteome (epiproteome isn’t a standard word, but I mean by that post-translational modification).
John Sanford uses the word “polyconstrained”, but the idea is really multi-functional. One example that I showed John last April that really made him smile was the example of the FIRRE lincRNA which connects to locations on DNA to bring DNA from different chromosomes to create a molecular factory.
DNA doesn’t just provide coding and blueprints, it also provides locations for molecular machines to park. These concentrations of molecular machines creates amazing little molecular factories for the machines to work.
For example:
https://en.wikipedia.org/wiki/Transcription_factories
How FIRRE lncRNA is involved to create these amazing molecular factories is described here:
http://www.lncrnablog.com/tag/firre/
It shows DNA isn’t just about blue prints, it’s about parking lots and factories of molecular machines that use DNA as a parking lot.
Here is a conceptual diagram of a transcription factory.
Rumraket,
Is a “branching genealogical process” the same as reproduction and genetic variation?
The following was the exchange that gave me an extremely low opinion of John Harshman’s knowledge base.
John Harhsman disputed my claim histones provided a means of Random Access Memory.
After he criticized my remark, I thought to myself, “this guy is cluless”
From the Stem Cell Handbook 2013, the chapter entitled “Quantitative Approaches to Model Pluripotency and Differentiation in Stem Cells”
http://link.springer.com/chapter/10.1007/978-1-4614-7696-2_4?no-access=true
As to the never ending litany of “Sal doesn’t understand”, actually it looks like I was like minded with some pretty smart researchers. Get a load of the diagram below!
Confirms an OP I wrote earlier:
Take that John, learn some biology. There is more to biology than phylogeny. You’re knowledge base need some serious expansion and updating.
This is relevant to the issue of the Bromo Domains “readers” of epigenetic memory. I pointed out such inserted domains in genes make a mockery of the idea that differences in orthologous genes between species don’t have functional significance. It’s not the random walk that is in so many phylogenetic models. The changes require coordination. This supports the notion of Common Design over Common Descent, because the patterns of differences in orthologs may not be due to mindless random mutation on functionless regions, but rather designed regions toward a functional goal.
Anyway you embarrassed yourself by showing how obsolete your knowledge base was because I referred to DNA serving as a scaffold for epigenetic memory. It’s not arrogance on my part to point out your ignorance John Harshman.
LOL.
Perhaps there is epigenetic memory. But the idea that it is “random access memory” is laughably absurd.
Neil Rickert,
Ah yes, Sal fails to see any difference between “histones are RAM units” and “epigenetic memory is analogous to RAM”.
Ever one to reify the analogy, our Sal.
And misrepresent what others have written.
And “point to” things, as if that settles anything.
And absolutely hilarious that he would link to the epigenetics post of his, where he got slapped around pretty badly. Although [turn off the irony meters] that thread does end with him demanding a retraction and an apology because someone claimed he wrote something that he did not.
ROFL
“I referred to it”.
Well then I guess that’s all that needs to be said. You followed your “make-my-post-look-scientific”-template well. It has a reference, a quote and a nice picture. Some cutting edge buzzwords and claims that the opposition’s knowledge is “obsolete”.
Haha, you can’t make this dumbfuckery up. All it needs to really top it off as a classic Sal-manoeuvre is to put some buzzword that ends on –ome in there, and that you call the journal or the institution of the authors, “cutting edge”, “prestigious”, or “elite researchers”.
At this point I’m pretty confident I could script a chat-bot to argue with John Harshman at least as competently as you.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035703
So how does this relate to the question of Common Descent vs. Common Design. Histones are only one class of proteins that have sections that can be reversibly written, read, and erased. But we’re finding maybe most proteins have the same ability to have their amino acids reversibly written, read, and erased!!!!
So it’s not just the chromatin that is biological computer, perhaps the entire cell!
What are some of the “readers”? The bromo domain pictured about is but one of them. The problem for the claim of random mutation is these domains that carry out all sorts of function are spread across genes that aren’t really paralogs, orthologs, whatever. Even basic transcription and translational genes that are in primitive form in bacteria have domains appearing simultaneously in the gene sets in complex eukaryotes. It’s like a global copy-and-paste from one gene to many genes happened simultaneously.
Why would this simultaneous pasting into pre-existing genes have to happen from a functional standpoint? If there is a newly evolved signal in chromatin and it needs a specialized reader for all the regulatory genes that will read it, the reader has to be present in all the proteins that will read the signal.
The bromo domain reader, for example, has to be inserted into all the proteins that read the acetyl marks on lysines.
This also involves machinery to implement positioning of the read head to the right address in every affected protein. Thus we see genome wide adjustments to implement new features.
What phylogeneticists model as a random walk sort of falls apart when it requires entails coordinated change among genes. The Promiscuous Domains illustrate the problem. Hence, Common Design is a better argument than Common Descent for the patterns of diversity since the patterns of diversity entails so much coordinated simultaneous change. Phylogeneticists usually don’t pick up these subtleties because their models are simplistic. They tend to think, “oh well this amino acid is different in this species, therefore it can’t have much functional significance.” Not so.
In no way at all. lol
HOLY SHIT!!!!!!!!!!!!! If you’d used twice as many exclamation marks you would have massively increased how much sense your “argument” here makes.
Perhaps chromatin isn’t a biological computer at all. Perhaps it some times is. Perhaps, perhaps not. Regardless, you’re still not explaining why there is a nested hiearchy.
Awe shucks, thanks.
You’re right I can’t make this fumbduckery up.
I can’t especially if my comment has (as you said):
You said:
If you could, that would totally awesome! That way the bot can get John up to speed on the latest cutting edge developments in biology that he keeps ignoring.
In fact, since you know my template so well, you can do the job for me. We all benefit.
I learn, you learn, John learns, every body learns more cutting edge science by using “Sal’s Template” for debating evolutionists.
stcordova,
In exon selection does this mean alternative splicing? What is causing the chromatin to be modified?
Why is that a problem for random mutations? The genes in different species are not identical, so whatever you think is constrained, there’s some species out there where that constrained thing is different, yet still works.
What the hell does this even mean? “Domains appearing simultaneously in the gene sets”? You’re just blathering. You probably don’t even know what you’re really saying. This is even less comprehensible than stream-of-consciousness stuff.
What do phylogeneticists model as a random walk? Does selection play a role? Does epistasis? Have you accounted for that?
Does it require that, and does it fall apart if it does? You just brainlessly declare this. You just babble out claims, obscure speculations, and barely tangential factoids.
What promiscous domains, and why are those words capitalized?
You just say stuff. You literally just stuff your posts with a random mix of technical terms from the molecular biology literature. Oh god it could not be any more obvious that you really have no goddamn clue what you’re even doing here.
Go away, you are an embarassment to everything you pretend to stand for you complete and utter fake. Is it any wonder you look up to the simly fraud and charlatan, Joel Osteen?
Are we talking the nested hierarchy based on novel complex structures (old-school Linnaean style grouping approach) or the MULTIPLE conflicting nested hierarchies in phylogentic trees? There is an important distinction.
For example birds have: beaks, feathers, wings and legs. Fish don’t. One may argue feathers, beaks, wing and legs have some correspondence to fish parts — OK, but it’s obvious they are different enough to call a bird a bird and a fish not a bird. The only place birds and mammals and other tetrapods are called “Sarcopterygiian fish” are by phylogeneticists wanting to minimize the obvious differences between birds and fish.
Mammary glands are a defining characteristic of mammals. How do you reflect this “synapomorphy” (gag, I hate using that term, but if I’m going to use Sal’s template, I guess I should use evolutionary jargon) in a phylogentic protein algorithm?
and
All this to point out, there is a difference between the nested hierarchies of structural classification and the nested hierarchies of the multiple conflicted nested hierarchies created by phylogenetic methods.
Joe didn’t mention the extinct school of systematics. The Pheneticists:
The co-founder of creationists Baraminology, Walter ReMine, is a Pheneticist.
But back to your question, are you talking about nested hierarchies based on structure and behavior, or the conflicting nested hierarchies based on phylogeny. These nested hierarchies aren’t the same, that’s why pheneticists got a bad rap for the good work they did.
Nobody learns anything from your brainless gish-gallops. There is no informative content, it’s just some barely coherent stream of buzzwords and rhetoric.
It’s all something you do in place of actually making reasoned arguments or trying to increase understanding.
The template seems to consist of a combination of these:
1. Use as many “cutting edge” buzzwords you can that end on –ome or –omics. Phosphoproteome? Proteomics? Glycome? Fuuuuuck that is so fancy and cutting edge.
Which is particularly silly seeing you do when it becomes obvious that you learned a new word. A few weeks ago all your posts had to mention Hidden Markov Models. Omg that’s so clever, you must really know your shit when you use that word. It’s based on hidden markov models? Whoah! Why didn’t you just say so? That makes it sooo fancy and technical.
It has both read and write states analogous to RAM? OH MAN, that’s so technical-fancy. I guess that means… something technical. And that word, methylation. Me-thy-la-tion. Sounds fancy too. Only someone really smart and knowledgeable would use it, so it must be really really significant.
2. Cite some journal article, and call the journal prestigious, the authors elite, and their institution “well respected” or something along those lines.
3. Mention credentials, achievements and honors of all sorts, academic or economic, institutional or purely superficial. Inflate inflate inflate!
Dr PhD, has multiple patents, works at “prestigious” institution, studied under famous elite “highly respected” professor bla bla bla.
4. How much money they got from the NIH, how much money the NIH has, and how they’re all “hard working lab researchers”. Mention the money. Anything less than tens of millions of dollars are barely worth talking about. If lots of money was invested, someone must really know their shit, and when you cite their work, by implication your words and your conclusion must be equally well supported and important. Or something.
Not those useless “theoreticians”. No, focus on the people in the lab, doing the work, the guys who are there with their real hands-on experience. Not those arrogant academics sitting in their offices behind their computers. Dem book-learned peoples. Fucking democrats!
5. Pictures and figures with graphs and diagrams. Lots of numbers and abbreviations. Lots of arrows and tables with numbers and more abbreviations. Some cartoons that show steps of how lots of molecules interact. It looks so fancy and technical. And you wouldn’t just post those, you must really really know your stuff when you can attach a figure to your post.
After all, Bill Cole is really impressed by it. That’s how you know it works.
Both. And what is the degree and significance of that conflict? Give concrete examples from the literature, where you calculate the degree of incongruence and show it’s statistical significance.
The ones in the paper I linked to on promiscuous domains and the domains in the papers in the bibliography. Pleckstrin was one of them.
You can’t just willy-nilly copy a domain out of a gene and shove in a random place in the genome and expect it to work like the fine-tuned machines like we see with chromatin remodeling proteins.
55-milliion dollar net worth Joel Osteen? He preached one of my favorite sermons of all time. His theology may not agree with mine, but his sermon was inspirational. I listened to this sermon about 5 times. I’d like to listen to I more. For your listening pleasure if you haven’t heard a nice sermon in a long time, this is a good one by Joel:
https://youtu.be/rjAg9DyD0xw
Yeah, that guy. I can see how much money he has is inspirational to you. What other quality in a person could possibly matter at all? Hospitality?
Yes.
No one really knows all the details. We have a few sketchy details. We know if knock this gene out, chromatin won’t be modified one way. If we add this modification, chromatin will be modified another way. The problem is we don’t have sufficient detail because the lab techniques don’t have the requisite technology to track every molecular interaction in real time inside the cell.
All the mechanisms of what will trigger an alternative splice aren’t well known. We know parts of the mechanisms, but we see through a glass darkly right now.
Not to worry John. Anyone who dares criticize one of Sal’s remarks is cluless. He’s a creationist version of keiths.
Because he doesn’t understand the topics that he loves to pontificate on, Sal often shoots himself in the foot, like citing Yamanaka’s Nobel Prize in support of his contention that HDACs/HATs are more important than conventional transcription factors. That’s always fun.
And I particularly enjoy it when, as often happens, Sal’s attempts to sound oh-so-erudite cause him to fall flat on his face, like confusing HDA10 (the HDAC gene) with 10-HDA (the bee pheromone in Royal Jelly) or [my favorite for personal reasons] confusing human methionine adenosyltrasferases (MAT isozymes) with the yeast MATing Type locus, ‘cos, y’know, they’re both abbreviated ‘MAT’. That’s not the only time he’s assumed that genes with similar names must be homologs. Cyctochrome c = cytochrome oxidase, anyone?
But, as you note, it appears to be sufficient for snowing the rubes. No wonder he hero-worships Joel Osteen…
Cordovaomics?
Don’t kid yourself, Mung. Your quirks may differ from Sal’s, but you’re right down there at his level.
keiths,
Welcome back keths! I thought you’d started your own blog? Was I just dreaming about it???
I’m working on my own blog why-evolution-is-false?
What do you think of the name?
You mean like I had no clue how to refute Ohno’s nylonase hypothesis — you know, the one Ken Miller and Dennis Venema keep promoting? C’mon, you’re just upset with me. You know I have a little bit of a clue.
Well, hey I’m glad someone is impressed. I have a fan club of 1 person. That’s enough to make me keep visiting here. Bill’s approval counts for lot.
But back to more technical matters, the issue of the Taxnomic vs. Phylogenetic nested hierarchies. I asked which would you like to discuss. You said:
You requested:
You mean a refence, a quote, and a nice picture like I’ve been doing according to Sal’s template? Yesiree, I can do that.
Actually, most of my casino math doesn’t involve confidence intervals and p-values, but rather mean and standard deviation and expected values. So I can’t help you there except to say, “do you really need that to see an elephant isn’t a duck? Quack quack quack.”
But first taxonomic nested hierarchies. Unlike supposed phylogenies, there isn’t a hypothetical right answer how to group things together. If someone wants to classify creatures as to whether they lay eggs or not, they can do that. It’s not necessarily right or wrong any more than which way someone wants to take a look at a relational database. There is of course, like with relational databases, some relationships that seem to be the preferred viewpoint as the data may naturally make itself amenable to one way of classifying things over another.
So let’s look at the vertebrates.
Creatures with beaks, feathers, and wings we can put together in the group we call birds (aves).
Creatures with mammary glands we can put together in a group called mammals. Mammals with placentas we put in the group of Placental Mammals. Mammals that carry their young in a pouch form the group called Marsupial Mammals. Mammals that lay eggs are monotremes.
We can also group together creatures of that live in the water and have fins, particularly lobed-fins — AKA the Sarcopterygiian fish like lungfish and coelecanths. If we define Sarcopterygiian in terms of lobed-fins then birds and elephants don’t belong in the Sarcopterygiian group. But if one wants to equivocate and redefine terms band obfuscate the issue one can insist that birds and elephants are lobed-finned fishes. It doesn’t really seem like a natural way for grouping things together. Seems this would only be done if one wanted to prove a fish can give rise to a giraffe after enough time. Me on the other hand, think after N-generations, the descendant of a lobed-finned fish will be a lobe-finned fish, not a duck. Quack quack quack.
We also see birds, mammals, fish are members of vertebrates which are members of animals which are members of eukaryotes. Hence we have a nice taxonomic hierarchy for present day characters. It says nothing about any evolutionary history, it’s just the way things are laid out. The problem with phylogeny is it tries to lay out an evolutionary past. The past is not the present! Taxnomic old-school Linnaean nested hierarchies deal with the present, evolutionary phylogenies deal with the past. Evolutionists like to conflate the two nested hierarchies like they conflate and equivocate so many other things. They are not the same thing. I hope we can agree on that.
But back to the nested hierarchy based on taxonomy. We see Humans nest in Primates, Primates nest in Placental Mammals, Placental Mammals nest in Mammals, Mammals Nest in Veretbrates, Vertebrates nest in Animals, Animals nest within Eukaryotes. That’s a nice taxonomic nested hierarchy.
The taxonomic nested hierarchy also naturally says birds and fish don’t belong in the same group. “Birds of a feather flock together.”
Linnaeus saw these hierchical patterns. His sample of data points wasn’t as good as ours today, so his taxonomic nested hierarchy does merit some revision. But some things are still evident. A lungfish is not a duck. Quack, quack, quack…this follows from the natural taxonomic grouping that a bird is not a fish.
The nested hierarchy formed in the way described (where we put mammals in the mammal group based on mammary glands, etc. and we put birds in the group with feathers, wings, beaks, and we put Sarcopterygiian fish in the group with lobed fins) does not agree with multiple conflicting phylogenetic nested hieararchies for vertebrates except when it agrees. More on that in another comment.
But that hopefully shows how a taxonomic nested hierarchy can be constructed, at least in principle. There is not any one absolute way of imposing and classifying things, but some classification schemes seem so much more natural than others like noting that lobed-finned Sacropterygian fishes are not ducks, quack quack quack.
Sal:
Heh.
So for the evolutionists having a hard time with taxonomic classification, this is a duck. It is not a lobed-finned Sarcopterygiian fish.
And this is a lungfish, a Sarcopterygiian lobe-finned fish. Taxnomically speaking it’s not a duck…quack quack quack.
It musta evolved… look like the whale that walked on the street of….chinesesisco
My long time friend Casey Luskin reported what evolutionists believe:
Well I just showed pictures of birds and real sarcopterygiian fish from a taxonomic stand point. What Axel Meyer said is not true taxonomically speaking, but I guess evolutionarily speaking it is. I guess.
I guess “we are sarcopterygian fish” in the sense that Caitlyn Jenner is a real woman. Or better yet this 52 year old man Stefonknee is a six-year old girl. Please tell me this is a story from The Onion.
http://www.dailymail.co.uk/femail/article-3356084/I-ve-gone-child-Husband-father-seven-52-leaves-wife-kids-live-transgender-SIX-YEAR-OLD-girl-named-Stefonknee.html
Ok, so I explained the taxonomic nested hierarchy that provides a classification for the PRESENT. Further, there isn’t necessarily a right or wrong way to classify things, where as phylogenetic nested hierarchies try to explain the PAST like a genealogy — as in who was the parent of whom. The two are not the same hierarchy, and especially bad for the phylogenetic nested hierarchy, even though in principle there can be only one true hierarchy, the odds of re-constructing the true hierarchy exactly are astronomically remote. One may or may not get a good approximation, but what’s bad is that for particularly deep phylogenies, it may not be possible and becomes a pointless exercise.
But there is also a problem of cherry picking and distorting the data with regard to phylogenetic reconstruction, and then the question of whether miracles are needed to make common descent even work.
The nasty issue for phylogeny is what to do with characters that are so unique and complex, that the characters look like they had no ancestor. I provided one such example system that applies to all genes in the two major divisions of life: Prokaryotes (bacteria and archaea) and Eukaryotes.
Prokaryotic genes where “X” is represents a coding segment:
XXXXXXXXX
Eukaryotic gene (minus a few exceptions where X is the exon that approximates a segment of the corresponding gene in bacteria and i is the intron:
iiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiii
This Eukaryotic feature is a major innovation involving spliceosomal introns. If I tried to put this through phylogeny software to infer a phylogenetic tree it’s going to sort of barf because you have two separate lineages that seem to have to be force-fitted to argue they have a common ancestor.
Sure you can say the X’s are shared, but the i’s sort of just poofed on the scene in a functionally coordinated way (the creature would be otherwise dead without the coordination). This doesn’t agree with any sort of ordinary mechanistic model where small gradual changes happen. It’s a POOF, it looks miraculous. There aren’t really good phylogenetic models to handle POOF except to say a feature is there without traceable ancestor.
So I posed the question earlier, “can life be structured in such a way that one would accept it was of miraculous origin”. If one says, “no”, then I respect a right for a person to believe that, but the problem then is that if there were a miracle for the emergence of life, they’d never recognize it.
If they said, “yes”, then what would be their criteria? My criteria for asserting a miracle happened is that the structure involved would require events that are so extraordinary and improbably far from ordinary expectation, that it is indistinguishable from a miracle.
Let me illustrate some of the illegitimacy of applying phylogenetic methods and pretending no miracles are needed. Someone can build the cytochrome-C protein phylogeny that connects Prokaryotes and Eukaryotes, but they have to edit out the rather big POOF involving the spliceosomal introns which also entail the simultaneous emergence of the spliceosome. When Dayhoff built here cytochrome-C phylogeny, she didn’t point out the rather obvious problem of introns as her phylogeny was only protein based, not DNA based!
The spliceosome is one of the most complex molecular machines in a cell. Phylogeneticists give this beautiful looking diagram of cytochrome-c evolution as suggesting gradual change, all the while the suppress mention of the rather gigantic POOF needed to make the phylogeny work in the first place, the spliceosomal introns in the Eukaryotic version of the cytochrome-c gene. This will be true of all genes shared between Eukaryotes and Prokaryotes.
This sort of data mangling is ok for comparisons, but to pretend this proves common is not very straight up, imho, since the miraculous structure of the Eukaryotic cytochrome-C gene (or any such gene) is not even mentioned.
So to me, the truly parsimonious explanation is that Eukaryotes did not descend from Prokaryotes, nor vice versa, nor did they share a common ancestor because Eukaryotes have features without ancestors. Same could be said for prokaryotes.
If then there is not common descent between the major species groups, the patterns of similarity must be by common design, not common descent. I also showed the patterns of diversity are also likely by design.
I will talk a little more about some of the problems with molecular phylogenetic trees, some of which I have shown can be built with computer software. It was provident Rumraket provided an example to test out the MEGA software by Nei as I’ll run in on actual gene sets too….
But before that, let me summarize my position. I believe in Common Design for this simple reason: “God must have done it because evolution can’t.” It’s that simple.
These last few posts by Sal, succinct:
LMFAO!
Fortunately, we’re not stuck believing that evolution produced life simply because Sal can’t make a case for design.
We’ve got all of that evidence that Sal fails constantly to explain. At all.
Glen Davidson
So as Rumraket requested, I dealt first with the taxonomic nested hierarchy. It was rather easy to see a fish is not a bird, a Sarcoperyggian fish like a coelechanth is not a bird like a duck, quack quack quack, nor a mammal like cow, moooooo moooooo…..
From wiki on vertebrates:
So within vertebrates we have mammals taxonomically united by mammary glands; birds taxonomically united by feathers, beaks and wings; Sarcopterygian fish united by lobed-fins. Of course one could come up with an other classification scheme out of convenience, and there isn’t necessarily a right or wrong answer, but on thing is brutally apparent, each group has defining complex features. I called them orphan systems, orphan features, whatever… Hopefully it is clear then a bird is not a fish because of the aggregation of such features by members of each group.
John Harshman seemed to have a hard time comprehending the relevance of the basic anatomical differences not to mention his understanding of the molecular bases was a bit obsolete.
The problem for common descent is that it doesn’t explain the origin of these defining features (like mammary glands) that define groups like mammals. I pointed out, such defining features that are without ancestors are a problem for invoking common descent, because things without ancestors break out of the pattern of common descent. So the radical differences are not explained by common descent, therefore there was no common descent. “God must have done it because common descent can’t.” If so, then the patterns of similarity must necessarily be by common design.
That said, there is a problem of cherry picking and fudging with regard to the phylogenetic methods. It’s actually very two-faced and full of obfuscations and confusion.
On the one hand it looks superficially like common descent must be true because all the vertebrates like fish, birds, mammals share common designs. OK, so, let’s for the sake of argument assume common descent. We then can say, “we have a branching pattern where there was a common ancestor vertebrate that had descendants that are fish, birds, mammals, etc.”.
Ah, but what looks at first look like evidence for common descent simultaneously becomes problematic when we try to characterize what the common ancestor must look like. Michael Denton, in the book Evolution a Theory in Crisis was keen to point out the Typological Perception of Biology whereby we have types of creatures like fish, mammals, birds. Typology poses a problem for macro evolution. Here is why.
The branching pattern looks good on paper until we try to fill in the details. Evolutionists say, “a fish branched into other fish, birds, and mammals.” The problem however is if you take the taxonomic characteristics associated with the vertebrate groups such as:
birds: beak, feathers, wings
mammals: mammary glands
Sarcopterygiian fish: lobed-fins
It becomes problematic to build a phylogeny that shows nice gradual transitions. What evolutionists want to do is make the lobed-finned fish branch into giraffes, parrots, frogs, dinosaurs through slow gradual evolutionary transitions. But this doesn’t work so well because of the problem of missing links! Mammals have sweat glands and mammary glands, fish don’t have them. What are the transitional states from no mammary gland to a functioning mammary gland?
So, if we were to aggregate all the data we would see birds would still be birds and not fish, and it looks like macroevolution is not likely. The aggregated data suggests that a fish will give rise to another fish not a bird. So this leaves Darwinists in a bad position. What should they do when confronted with taxonomic facts. IGNORE THEM, cherry pick and fudge the data. That’s the way to do it if you don’t have a credible case.
They will then take a gene here and there that is shared by both birds and Sarcopterygiian fish and then make a nested phylogenetic hierarchy that superficially might make it look like a bird is closer to a lungfish than a another fish. But that’s not really a balanced treatment of the data, because if I then pointed out lungfish don’t have beaks, feathers, and wings it becomes harder to argue fish are more similar to birds than to other fish. That is cherry picking!!!
And to make the phylogenetic programs pump out nested hierarchies that put the bird in the same group as Sarcopterygiian fish, one might have to do some fudging to boot with outgroups and deletion of other species in the data set used to construct the phylogeny. I learned how to fudge the data just like a professional phylogenticist.
So on the one hand the evolutionists want to demonstrate the strong branching a pattern where birds aren’t fish and tell one story to the public, and then on the other hand put out a different conflicting branching pattern that says birds are fish! They then pretend there is no conflict! That’s being two-faced.
I called evolutionary biologist Nick Matke for being two-faced, which turns out to be endemic to the whole industry:
You can see the two-faced nature of the conflicting phylogenetic trees by looking a the tree generated by Cox1 (which looks more like the taxonomic nested hierarchy where birds aren’t fisg) vs. the one built by BMP2 homologs (where birds ARE fish). The one built by BMP2 homologs was deliberately fudged to conform to John Harshman’s foregone conclusion. Unlike taxonomy where there isn’t necessarily a right or wrong way to build the nested taxonomic hierarchy, two conflicting phylogenetic nested trees cannot both be right!
I don’t like the two-faced nature of evolutionary biology. It’s not like other scientific disciplines like chemistry and physics.
Larry Moran picked up on your UD post. He was not impressed!
There’s a nice comment by Gordon Davisson too!
I had forgotten about that… that.. impossibly dense post of yours.
A Jaw is the conceptual ancestor? No further proof that you don’t understand, and spend very little time reasoning about this subject, could even be hoped for.
The absence of mechanistically feasible transitions proves “God did it because evolution can’t.”
If Larry can’t deal with the actual argument, he knocks down an argument I didn’t make. Well done Larry.
More correctly a creature with a jaw. Thanks for your editorial suggestion to improve my choice of words.
Well it’s nice that you can just declare the transitions mechanistically infeasible.
What you seem unable to fathom is that the very fact of the phylogenetic tree demonstrates the feasibility of the transitions. There wouldn’t be a nesting hierachy if the transitions did not take place in history.
You obviously disagree, you think there still would be a nesting hiearchy, and you have called the creationist explanation for this fact “common design”. But as this thread is a 4000-post proof of, there actually is no such thing as creatist account called “common design” from which an explanation of the nesting hiearchy of life emerges.
So we’re back to square one, where we began: You are brainlessly declaring a conclusion contradicted by the data we have. And we can only go round and round. We will ask you to explain why there is a nesting hiearchy again, you will blather something vacuous like “common design”. We will then point out that that vacuous phrase does not have an actual mechanism that actually explains why there should be a nested hiearchy. And the cycle repeats anew.
Rumraket,
4 comments would be evidence that common design is a vacuous argument. 4000?