Moderator’s remark: this post is long enough to need a “more” tag. But the wordpress editor will only allow me to add that at the very beginning or the very end. So here it is at the very beginning.
- “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution. This is the idea that the “tree of life” classification of organisms is somehow objective despite being a creation of very zealous “evolution” advocates. The three basic assumptions of cladistics models are: a) Any group of organisms are related by descent from a common ancestor (UCD – universal common descent); b) There is a bifurcating pattern of cladogenesis; c) Change in characteristics occurs in lineages over time. Although not explicit, UCD (“descent from a common ancestor”) here means by a Darwinian “natural selection mechanism” and not by a process generated by a designer that also happens to make use of biologic reproduction.
- No assumption can be tested by the model that uses them. That is why they’re called ‘assumptions’ and not ‘conclusions’. Instead, assumptions have to be tested independently through an entirely separated method or be accepted as axioms. An UCD “mechanism” has never been observed or proved elsewhere and is not “self-evidently true”, therefore not a valid axiom. Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis. Furthermore the conclusions of any “cladistic analysis” will always and trivially be compatible with the UCD assumption in that model.
- Hypothesis testing requires an alternative (null) hypothesis and a procedure that demonstrates how the data available is compatible with the successful hypothesis and at the same time is statistically incompatible with the alternative hypothesis. In the “cladistic analysis” case, the alternative hypothesis to UCD is “common design”, and of course UCD cannot be an assumption of such an analysis. However this rule is violated twice, first by the use of an assumption also presented as conclusion, and second by the prejudiced rejection of the alternative “common design” hypothesis before analysis. This clearly demonstrates that “cladistic analysis” can never be logically used as proof of UCD. What “cladistic analysis” is instead is ‘curve fitting’ where the cladistics model is best fitted to certain (conveniently selected!) morphologic/biochemical/genetic biologic data points.
- The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative in a biologic comparative analysis as designers have maximum flexibility. This is not surprising as designers are free to incorporate whatever mechanism they want, including intelligent “selection” (human breeders do!) and “common descent” (human breeders do!) if they so desire.
- The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false. On one hand, we do know the history of the automobile, so a proper classification must be able to reconstruct their unique “evolution”. Yes, vehicle share parts, so to get to the actual development tree, we must group them differently than organisms since mass production works differently than biologic reproduction. On the other hand, organisms may not be uniquely classified as demonstrated by the numerous revisions and exceptions to the “tree of life”, and in any case, “uniquely classified” is an absolute claim that can never be proven since it is impossible to compare the infinity of possible organism classifications.
- The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry fails. Anatomy is not independent of biochemistry. Also, the oldest DNA ever found was 700k years old therefore any match between the independent trees is limited. This is not to say that the fossil record is complete, or that fossils can be positively linked to one another and the living without – once again – presupposing UCD. The claim that “there is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry” is false as the ‘designer’ hypothesis produces the same result when one designer creates all morphologies, and furthermore “I cannot think of an alternative reason why…” is not a valid argument.
- A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure. To decide the position of a certain organism, the human creators of the “tree” have to decide which morphologic/biochemical/genetic characteristics to include and what weight to attach to each of those measures. This further supports the claim that “cladistic analysis” is ‘curve fitting’ rather than ‘hypothesis testing’ – if a tree must be built, a tree will be built as in this example: “The close relationship between animals and fungi was suggested by Thomas Cavalier-Smith in 1987, […] and was supported by later genetic studies. Early phylogenies placed fungi near the plants and other groups that have mitochondria with flat cristae, but this character varies. More recently, it has been said that holozoa (animals) and holomycota (fungi) are much more closely related to each other than either is to plants […].”
And what are those mechanisms that human communities provide? You haven’t shown us any yet, just descriptions of language change. The change itself is a categorically different thing from the mechanism that causes the change.
That doesn’t follow. Why should language necessarily change with changes in the human community? Different human communities have been making use of one and the same language (Latin, Spanish, English) throughout history, haven’t they ?
Annoying, isn’t it? If people refuse to accept perfectly valid mechanisms as such.
There you go: The mechanisms of evolutionary change are natural selection, genetic drift, mutation and migration. They make as much sense as sound shifts and borrowing in linguistics. Take it or leave it.
Granted for dialects. Anything specific for new languages?
I would say the population splitting, being part of speciation, can be argued to be both a macroevolutionary and a microevolutionary process.
Someone has to decide! Don’t they?
I honestly tire of repeating myself just because people want to put me in a creationist box.
That they do not interbreed is an important piece of data. But there’s no way to assign any sort of degree of “don’t breed together” or estimate the distance between the species based upon “don’t breed together.”
So it doesn’t enter into how close or how fat on the tree are they, that is true. But that piece of data is also not ignored, because it’s the basis for separating them on the tree in the first place.
IOW, they are placed close on the tree for other reasons. But it does not follow that the data of interbreeding is ignored. The gap is reflected in the tree.
No, I just want to understand why you believe in common descent.
(node) THIS IS A GAP BETWEEN THE NODES (node)
ETA: failed attempt to draw a tree, lol.
Sure, if you’re only measurement is sequence comparison. If you cannot isolate cause here what is the next possibility?
This is a much more technical question than you imagine. Is there anything to macroevolution beyond accumulated microevolution? Yes, there is species selection, the differential speciation and extinction of taxa with certain fixed characters. The question there is whether species selection is in any way important in evolution.
But of course that isn’t even what you’re talking about. You’re actually trying to insinuate that mutation, selection, and drift can’t accumulate to result in big changes within populations. Do you have any evidence to support that claim?
And of course you have no better evidence for language evolution either. You have never seen one language change into another. All you have are various disconnected historical fragments for a very few languages. There are gaps between even such well-attested changes as Latin into French, not the smooth transformation by infinitesimal steps you demand for evolution.
And you seem ignorant of the history of your own field. The beginnings of recognition of Indo-European resulted from comparison of Latin and Sanskrit, but there are no intermediate steps attested between them at all. This was long before there was any study of sound laws or any processes of language change. What you demand for evolution is far beyond anything you accept in linguistics.
That makes two of us. 🙂
And not even a very good one. =p
But if you don’t know why you believe in common descent, how could anyone else know? I know why I believe (poor word choice, but go with it), and I know good reasons to believe, but I can’t examine your thoughts, just your words. So the question is valid, and only you can answer it. Why do you believe in common descent?
I believe we may have a catch-22 situation here. If I remember, Erik has previously criticized biology for not (in his imagination, at least) being supported by mathematics, and now because Joe applies mathematics to biology, suddenly he isn’t a biologist at all.
But it’s a “hypothesis” of re-use, right? Re-use implies some original use. Do you think the shark version is the original, or the human version, or something else? This is how you might go about putting some meat on the bones of the re-use hypothesis.
And how do you know it is possible in this scenario? I don’t see how you could possibly know that. We know re-use occurs in software development, therefore we know re-use is possible in the case of human and shark PRPF8 isn’t going to cut it as a logical argument, because it just doesn’t follow.
You are going far beyond what Winston is claiming in his paper, so I caution you. His paper lends no support for any of this.
So another question you need to address is how the human and or shark lineages managed to survive without this PRPF8 gene until it was introduced in a case of re-use.
Also, what else would have been required in addition to that gene, because re-use of that gene alone is a non-starter. It would be just another stretch of junk DNA when introduced by the designer. So if you can’t explain how that gene just happened to work when inserted you don’t really have a re-use hypothesis.
So still no “common design hypothesis.” Keep working on it though.
I doubt it 🙂
Nor can it eliminate invisible aliens or any number of other “possibilities.”
Behe accepts common descent because he finds the evidence compelling. You say you accept the consensus and it appears reasonable to you, yet (again) you constantly challenge the arguments and the evidence that led to that consensus, and convinced Behe.
Your problem is total lack of internal consistency.
No, it does not. The component could be designed for multiple applications like a memory chip is.
The data shows similar or the same genes appearing in many different organisms. A possible explanation is design. We look at software modules showing a similar pattern which we know is designed. It is an argument from analogy.
This is a problem only for your version of reuse. If the components sequence was designed for multiple use and was part of the original make up of both Sharks and Humans then your question is answered. Both sharks and humans always had this component.
We don’t have evidence of aliens. We do have evidence of highly similar sequences appearing in different organisms. We have evidence of different software modules appearing in different software programs, evidence of different computer brands having the same memory components.
The evidence is following a design pattern which is a point Winston was making in his paper.
You have no idea what Behe’s current thinking on this subject is.
A meaningless statement Bill. 🙂
A dependency graph is not a design pattern. If you want to know about design patterns you can google the phrase.
Think it possible your may be mistaken 🙂
In a technical sense no amount of microevolution can ever amount to macroevolution, since microevolution is defined as evolution below the species level. Lots and lots of evolution below the species level, and then some more evolution below the species level, is all still evolution below the species level. By calling it microevolution we basically define it to not be macroevolution.
But of course that’s a definitional issue. It raises the question whether it is actually even possible to have endless microevolution, or will the accumulating change unavoidably lead to a descendant population so genetically (and/or morphologically) different from an ancestral one that speciation will have occurred?
To return to reproductive isolation, it is importantly different in microevolution and macroevolution. In microevolution, it means that the separated populations of the originally same species ceased to have contact – they could still yield offspring, but don’t. In macroevolution, it means that the different species cannot yield offspring even if they wanted.
In the context of macroevolution, my question is: Were those species (say, ancestors of apes and humans) ever able to yield offspring? How do you demonstrate that? What is the evidence?
You are the biologist here. I assume that the evidence for accumulating mutation, selection, and drift has already been collected and you can readily show how it results in macroevolutionary changes.
Please don’t play the fool. Just place the different editions of Shakespeare over the centuries side by side and take a look. Or Beowulf. Or Caesar in Latin and Italian. Or Plato in Ancient, Medieval, and Modern Greek. This should be a striking illustration of language change, even though the more correct way is to observe the gradual changes in phonology, morphology, vocabulary, etc. over the centuries – paradigmatic changes, not syntagmatic.
What does it matter how knowledge of the evolution of specifically Indo-European came about? Prior to that, there was knowledge of Semitic, Romance, German, Celtic, Turkic, Finno-Ugric, etc. languages. Studies of Indo-European built on those, did not change anything in principle. That words change was always known by e.g. manuscript copyists. It is arguably already noted in the Bible itself.
I have that book right here in front of me. Want to quote something specific from it that you think supports your claim?
It doesn’t include a dependency graph in it’s list of design patterns. Now, to be sure, there are design patterns not in this book, perhaps it is in some other book, but I probably have that book too. 🙂
Want to try again?
Sorry, but this makes no sense. No wonder the conversations between you and Bill are so entertaining. 🙂
What are the taxonomic ranks that are “below the species level”?
As you know (okay, maybe you don’t), dialects form a continuum. Dialects geographically close barely have any difference. Dialects geographically far away have lots of serious differences. The continuum is genuinely gradual also in time – generations back to back talk the same language, but generations centuries apart don’t. And demographic issues and politics compound the complications, so that in different places, in different times, from different viewpoints, the border between a dialect and a (related) language is rather fluid. It is fluid because the continuum is genuine, unbroken but incrementally and indefinitely pliable.
There are two possibilities with comparing linguistic change to biological change. Both Darwin and Theobald use the analogy. The analogy is either false – I can pick on so many false assumptions in Darwin’s and Theobald’s presentations that at least their linguistic ideas are certainly wrong, but this still leaves the possibility that they got the biology right – or true. If the analogy is true, then biological species should form a genuine unbroken continuum, just like related languages and dialects do. However, I don’t see how biological facts on the ground back it up. There are species that have remained unchanged from Jurassic or Triassic period – something that could not happen with a language, it’s impossible for a language not to change over a long time -, while other species that have gone extinct may genuinely have gone extinct, being supplanted or replaced instead of surviving in some wildly different current form. What demonstrates that macroevolution occurs incrementally? Microevolution, yes, but macro is the question.
So, the analogy is either false – and linguistic change is something quite different from biological change and the two cannot be fruitfully compared – or true. You decide.
I am claiming that the reuse of components is a design pattern. I have given you evidence for things that are designed, computers and software. Within these systems are reused components. I have said that these reused components represent design pattern.
You have claimed that a dependency graph is not a design pattern which I don’t object to since I never claimed it was. Looking at a dependency graph you can see a design patten inside as represented by the reuse of components.
So here is Wiki’s definition:
So lets look at PRPF8. It is a mission critical component for eukaryotic cells. It is the largest protein in the spliceosome. Splicing is a design concept used to allow the same MRNA to build different protein isoforms. This protein is found in all vertebrae and is highly conserved.
So lets see if we can “tweak” the definition to conform to our analogy.
Looks like PRPF8 (and the rest of the spliceosome) fits the bill of a design pattern.
Those would be subspecies. But I don’t understand the question. Rumraket made no mention of taxonomic ranks. By “below the species level” he refers to change in allele frequencies within a population.
Still, I don’t see his point. Change in allele frequencies within a population (or perhaps in two populations) is what commonly results in speciation, and a continuous series of ancestor-descendant populations can pass through several speciation events, microevolving all the while and resulting in macroevolutionary change by any definition.
So you should probably stop saying things like “it seems reasonable to me” or “I have or don’t have compelling reasons to doubt it” because you’ve thrown reason out of the window
ok, so my acceptance of common descent is unreasonable. I’ll continue to believe it anyways until I have a better reason to abandon it. If that’s ok with you.
ok, sure, that too may be throwing reason out the window, and unreasonable, but right now I just can’t gin up the outrage needed to change my minds about it.
Then why were you appealing to Winston’s paper? It’s about the dependency graph as a better model for a certain set of data that he examines. It has nothing to do with re-use or design patterns.
Winston’s paper had dependency graphs which I looked at. Within those dependency graphs I saw design patterns or reused components that did not follow a straight inheritance pattern.
Do you not see that a design pattern and a dependency graph are closely related? Without the design pattern the dependency graph would not be a useful tool.
I think so. You argue like someone who rejects it, so…
You seem to have no reason to accept it, so what would be a reason to abandon it?
OK, OK. I won’t pester you anymore if that helps
It was really just semantical, not important to the discussion.
In the thread I linked to above did you ever suggest a book for me to read where the author presented the evidence for universal common descent? If not I agree that you should not pester me any more, because you already had your chance.
Is there any set of data that we could not explain as the result of “common design”? It predicts anything and everything (and therefore predicts nothing).
Bill, Joe appears to have a far better grasp of “the common design hypothesis” than I do, so I think I’ll defer to him.
I think the time has finally come to end this very productive discussion (I get the sense that TSZ was set up to have discussions only. I hope I’m wrong) and test experimentally whether nested hierarchies are actually valid…
How do we test them?
I don’t mean to put Harshman on the spot, but he is the one who objected to one of the experiments I was performing… Maybe he can propose some clear-cut experiment that could test these speculations and end them forever…
I have been particularly intrigued by the evolution of flightless birds as some of you my know… Surprisingly, one of my favorite experimental scientists who have performed mutagenesis experiments for over 30 years, WE Loennig, seems to disagree with me on this issue…
So, I’d propose an experiment that would put the some flightless birds under selective pressure to regain the bone they apparently had lost while adapting to the environment…
“Ostriches, emus, cassowaries, rheas, and kiwis can’t fly. Unlike most birds, their flat breastbones lack the keel that anchors the strong pectoral muscles required for flight. Their puny wings can’t possibly lift their heavy bodies off the ground.”
What can be done to restore that breastbone?
I think that Harashman and his supporters could communicate with Dr. Loennig and come up with some kind of a solution…This is one of the time opportunity for evolutionists and “creationists” to cooperate to kill a rebel… lol
Try jumping off a 10 story building and flapping your arms till you evolve wings. Just kidding, please, don’t.
Last I checked, genealogies go back several generations to specific ancestors. Say grandma was cremated and grandpa’s DNA was also lost during a war. Then your family tree will be very stunted if you rely only on DNA…or you get some vague and meaningless maps of origins: https://www.ancestry.com/ And on a practical basis, the DNA of long lost relatives from “the old country” are nowhere to be found since no one will go check the DNA of whole populations to trace one’s ancestry.
Of course we need other identifiers. Why is this news to you?
There are no 10 story buildings here…It’s not allowed..
Don’t write comments like that unless you don’t care about being responsible for someone’s death…
1. That is a valid hypothesis of creation. It is not for me to say “this is what happened”. Unless shown, we will never know EXACTLY how creation happens. You do realize that this “footnote” completely invalidates Darwinism and it’s neo, right?
2. No one cares “not an example of…” The rest of your answer is plain silly. Repeat after me: “of course it is and example of ID and very intelligent for humans to try to do something only God does”. Point is, remember when Venter or someone else reports genetic manipulations, all those are examples of ID and in fact not at all supportive of Darwinist evolution.
3. Simple. “Common ancestry” is seen every day in all engineered products around you. All those are examples of ID and not supportive of Darwinist evolution. Next time you see a tree of life think “similar to the tree of automobile evolution, not to the imaginary Darwinist evolution”.
hence the “just kidding” part. A disclaimer very much like this one… you never know with creationists involved
1. You’re not addressing my comment. Instead you present yet another baseless scenario.
2. Comparisons of same entities are different on different levels. As examples of Intelligent Design, it makes perfect sense to compare life with watches. Nice try, won’t fly. But the irony remains on you since you were just protesting ‘non-biologic ancestry’.
Why do you always involve the” reproductive” parts of one gender when you comment?
Of course “cladistics [is] a model that was meant to test the assumption of universal common ancestry” in a circular logic.
I already showed this: http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchy
Is siesta still a great part of the Spanish culture?
What? that’s bollocks
Well, we have been there before… It keeps coming up so, what does that mean?
KN will soon attack me with his own story about his friendly deviators…
Because it’s wrong news. I know people who work on this.
The main issue is with phylogenies. Why do you think we can’t reconstruct them if we only have DNA from living species? I work on this, have written and distributed computer programs to do it, and have carried out computer simulations to check how well it works.
Have you done any of these? There are whole books on the subject. I know because I wrote one. There are also multiple people here at TSZ, in this thread, who have worked in the area and know a lot (John Harshman, in particular).
Perhaps you can point us to scientific papers that explain why we’re all wrong. Loud ill-explained declarations on a website don’t count.