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.
Do you want to be my cousin?
Sure. If not me, then who?
- “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 […].”
It isn’t assumed. It’s concluded from testing models against observations.
The assumptions of common descent are that the basic mechanisms of reproduction and population mechanics we see all around us all the time, still take place and also did in the past:
Organisms reproduce, mutations happen and accumulate in the genomes of the organisms that make up the population, those populations some times split up into two or more subpopulations each of which become become increasingly reproductively isolated over time, and the process will repeat and continue independently in both subpopulations.
That is basically it. All of those “assumptions” are observationally confirmed to take place in real populations in the wild and under laboratory conditions. The only true “assumption” that hasn’t been observationally verified is that it also happened before humans were around to record what happened in their surroundings. Which is conceptually equivalent, at the level of reason, to “assuming” that the Earth also had a gravitional pull and an average temperature before we were around to measure it.
You can of course decide to believe that somehow the entirety of the biosphere was madly and radically different in the past, but why would you, other than as part of some effort to make up ad-hoc and irrational excuses to use to reject common descent with?
In any case, given the “assumptions” I described above; that basic reproductive and population mechanics apply and also did in the past, this inexorably leads to a prediction: If the current biosphere is the result of those same basic mechanisms, then certain patterns should be found in the anatomical and genetic characteristics of all organisms on Earth(the prediction is that we should find consilience of independent phylogenies), which are either not predicted, or downright nonsensical, or ridiculously and obviously ad-hoc, on any other explanation you can come up with.
Should I assume that you’ve got it that common ancestry is not an assumption? Can we get past that already?
How? That’s actually a good question. By whatever phenomena might produce them. It depends on the features. For UCD, for example, some of them are still heatedly discussed, like the likelihood that the genetic code could converge, or not, to what it looks like in extant life forms. Lots of tests about that one still going on, more importantly because it is not known how it arose (as far as I know), and whether it “improved,” whether there’s more than one direction for improvement, whether there’s barriers for improvement in one direction or another depending on starting points, etc. Other features are easier, like long and very similar DNA and protein sequences. Etc.
Entropy,
Why did UC Berkeley called universal common descent a working assumption?
All life being connected by ancestry is a very big claim. How do you get from a working assumption to a tested hypothesis? How would you test the hypothesis?
You are correct, Bill. It is a big claim. Yuge, even! And, if it is incorrect, it should be easy to refute.
Alan Fox,
Like refuting the claim that the center of the moon is made of 100 cubic yards of green cheese 🙂
I think that nonlin.org already has that covered. nonlin.org claims that morphology is not independent of molecules and therefore one can’t use them to confirm each other. Presumably nonlin.org would also claim that different parts of the genome are not independent from each other. (Of course when we look at different parts of the genome they are unlikely to evolve in a substantially correlated way, and when we look at some morphological traits and some molecular sequences, the former is very unlikely to be substantially affected by the latter. But that’s never stopped nonlin.org from making these claims.)
Is my car related to other cars? Seriously?
I asked for two very simple things; For you to acknowledge that the “variations” within Felidae have a genetic basis (or just acknowledge they are true breeding; I don’t care that you don’t believe it is encoded in the DNA) and to take position on the Felidae being an originally created group. You have done neither. Instead, you have continued your habit of constantly contradicting yourself, and failing to clearly communicate any argument or point of view.
I said I would not discuss with you unless you clearly articulated your own position, so I’ll stop here. Your rejection of the most basic concepts makes any discussion pointless.
It’s common descent, until it isn’t!
In a world full of sharp objects and moving vehicles, the continued survival of those with minds like Nonlin’s and Bill’s can seem surprising. But then I remind myself that fitness is about propensities and it all makes sense again. Bill and Nonlin have just gotten lucky (so far).
Nah man, the contiued survival of these specimens is evidence of divine intervention. 😀
I don’t know. Ask them. As far as I know, there’s evidence for UCD. There might be much more now (I haven’t checked in quite a while, I have only so much time) . However, my comment was not just about UCD, but about common ancestry in general, which can be established beyond reasonable doubt for many organisms, if not all. Also remember that I mentioned how some features leading to inferring UCD are still under discussion. But other features are much easier. You really should try and read what I write for comprehension Bill. UCD might be harder to establish than common ancestry between subsets of life forms, but there’s evidence. Therefore not an assumption, but a hypothesis that seems to be getting stronger, rather than weaker, as scientists find more ways for testing it. I insist though, for phylogenetic analyses it’s enough if we can establish common ancestry for the group under analysis, before building a tree.
Clear enough?
The understatement of the year. It’s a humongous claim. In the past, I have doubted it to be true, or to be establishable. However, as I said, the evidence points to that being the case. So, not an assumption, but an inference from the data.
I told you already. By analyzing data Bill. By checking for common features and their likelihood of being that similar if they appeared independently.
For some groups of organisms, common ancestry is obvious. As we move farther and farther, it becomes less obvious, but, also, there’s no reason to think that the pattern should not go on father back. Then somebody notices that there’s other ways for comparisons that allows for further push backs, etc. Then somebody notices some feature. What about checking that and see? Etc. etc. etc.
Entropy,
Have you ever heard of some paid, Darwinism online supporters? If by some random chance your have, why the supporters of the theory that is a fact would do it? Why would SCIENTIFIC FACTS NEED VERIFICATION?
Do you have an answer?
Because all new species discovered continue to confirm it. It would be so simple for the data of a newly discovered species to fail to corroborate it’s common descent.
Every new species discovered will have at least some part of it’s genome sequenced and analyzed. Usually things like ribosomal RNA and ribosomal proteins and a few other translation or central metabolism related enzymes are sequenced. Using a primer for a ribosomal gene is implicitly an assumption that the species has ribosomes that are similar enough to known life that those primers will bind to some DNA and a gene can be sequenced.
It could be found that they simply don’t have those genes, or use a radically different genetic code, or opposite-handed sugars and amino acids. Or different bases on their genetic polymers.
You seem to have this misconception that a “working assumption” somehow prevents the scientists from discovering if common descent is false. That’s like saying you have a working assumption that gravity will apply tomorrow. Would that prevent you from discovering the absense of the gravitational force? No it would be pretty obvious if it no longer applied. It’s the same with the characteristics of newly discovered species. Every single one, thousands every year, is another corroboration instead. They could all fail to corroborate the interrelationship of all hitherto known life. But they don’t.
Rumraket,
Rum,
Do you get paid to spread this stuff? Please confirm you believe it, if you by some chance don’t…
J-Mac, to Entropy:
Take your meds, J-Mac.
No I don’t get paid. I think of it like charity. I like helping people in need. I’ll call myself a “Darwinist without borders”. You’re free to donate to the cause of course. Are you an american? If so I suggest you donate to the National Center for Science Education here: https://ncse.secure.force.com/donate?
And of course I believe it because the evidence for it is absolutely overwhelming. Common descent is among the most successful predictive theories in the history of science. I wouldn’t go on the internet to spend so much time explaining and defending something I believed was false.
Entropy,
I do believe that we probably have some common descent so we have common ground here. Do have any examples you can share?
Nope. I haven’t. I haven’t even found anybody calling themselves “Darwinism online supporters.” I don’t understand why you ask me, but I suspect that’s because you cannot read for comprehension.
I never heard of things being theories and facts. I have heard of facts that are explained by theories though. Like gravitation. It’s a phenomenon, a fact, and it’s explained by at least two theories, one by Newton and one by Einstein.
Facts need verification because we, as limited humans, might have missed something. Thus we might need to develop better theories to explain them. More observations would help develop such better theories. For example, Einstein’s theory predicts better the way gravitation works than Newton’s, but that can only been known after making more observations, and noticing that Newton’s theory fails in some cases.
Yep. But I think you will miss the points though.
We’ve been there before. Had you forgotten?
Here:
Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K., Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D., Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences 2008; 105:13462-13467. Here.
Harshman J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and false gharials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 2003; 52:386-402.Here.
Hackett S.J., Kimball R.T., Reddy S., Bowie R.C.K., Braun E.L., Braun M.J., Chojnowski J.L., Cox W.A., Han K.-L., Harshman J., Huddleston C.J., Marks B.D., Miglia K.J., Moore W.A., Sheldon F.H., Steadman D.W., Witt C.C., Yuri T. A phylogenomic study of birds reveals their evolutionary history. Science 2008; 320:1763-1768.Here.
I could go on.
This is not the first time colewd has forgotten previous extensive explanations and asked for that to be explained again.
Also nonlin.org has failed to notice a 5,000-comment-long thread on the evidence for common descent.
Here’s a funny one from the OP:
” Also, the oldest DNA ever found was 700k years old therefore any match between the independent trees is limited.”
Apparently nonlin.org does not get it that the trees inferred from DNA are obtained from present-day organisms. That one can infer trees from these. And compare them from different genes or regions of DNA. Fossil DNA is not necessary.
Joe Felsenstein,
My comment to Entropy that I believe in some amount of common descent is based on my prior comment with John that crocs may share a common ancestor based on low variation in DNA between groups. I also commented that flightless birds do not share that same low variation.
Lets not forget to mention to nonlin the evidence against a wider range of common descent in Sal’s 5000 comment op.
Sal’s flower.
http://www.sci-news.com/genetics/article01036.html
Maybe John could use Ewerts dependency graph as an additional conformation for the common descent of crocs.
You mean that graph you conclusively demonstrated you didn’t understand? Bill, that graph isn’t evidence against common descent. We expect such distributions under common descent. As was explained to you like 50 times.
Rumraket,
How would you expect such distributions unless you explain away contradictions with “we expect such deviations”. When you ignore the existence of contrary evidence and use the silly line that you repeatably explained it you lose credibility.
If you are to become a successful salesman for the NCSE you need to remain credible.
Define “low variation”. Where’s the cutoff? How do you know?
Sal’s flower has been explained many times; It’s actually evidence for common descent. As Joe says, you conveniently forget every argument you don’t like.
I don’t know what “Ewerts dependency graph” is.
I’m pretty certain that Bill probably doesn’t really either. But he’s internalized the words now. He can type them into a browser: D-e-p-e-n-d-e-n-c-y g-r-a-p-h. That’s all it takes for Bill.
Rumraket,
It’s like Groundhog Day in reverse. Each night, Bill forgets every dumb mistake he’s made. The next morning, he starts making them all over again.
Meanwhile, the rest of the world is saying “Christ, not this again.”
Explain how they are contradictions.
Explain how it is contrary evidence.
John Harshman,
Your opponents bring it as an argument against common descent then you make the assertion that it is evidence for common descent. This is what some call denial as a result of indoctrination.
As with UC Berkeley, you use universal common descent as a working assumption.
What I am forgetting is the unsupported assertions. Genes not following a branching pattern is evidence for common descent?
You can assert anything is evidence for common descent.
Why not assert that convergent evolution is evidence for common descent? Why not assert that the sudden appearance of the spliceosome is evidence for common descent?
What has been built here is a theory based on assumptions. When contradictory evidence hits you guys sweep it under the carpet by claiming it was expected and call it a new feature of your theory.
Ewert’s paper was released about a week ago and has been discussed on the peaceful science blog. Ewert participated in the discussion. It argues that gene families follow a dependency chart that is commonly used in software design. The evidence that supports this is a similar pattern we saw in Sal’s flower.
I can’t help but enjoy “science” that is based on assumptions and speculations…
Why doesn’t Harshman provide us with at least some experiments that prove his unfounded speculations? I have challenged him more than once to provide scientific, experimental evidence how flightless birds lost a major organ that supports flight…
Harshman never got back to me.. He felt more comfortable to have my privileges revoked so that his pointless life work would look as if it was scientific…
What a shame!
In another thread I asked when you thought that Darwinism might fall. But your demurred to give an estimate. So you can’t speculate on when something based on unfounded speculations, as you say here, will fall and be replaced by something more along your prefered lines of thinking?
Do you think Darwinism will fall in your lifetime? Or in the next century? The next ten years?
Do you not care to even speculate on a possible time frame? How close do you think you are? Given everything you are asking for is never produced, i.e. the evidence, you must be close, right?
If you read the the papers I cited for Bill you will see that they are neither speculations nor unfounded. They’re analyses of data and the conclusions are very strongly supported by those data. True, they aren’t experiments, but experiments are not the only kind of legitimate science.
I’m not aware of any organs, major or minor, lost by flightless birds. So that challenge is just silly.
No, I thought your privileges should be revoked because you post incoherent, bandwidth-wasting nonsense, not because you challenge my pointless life work.
“Some”? Sounds like an attempt to avoid making an actual claim. If you recall, I explained at great length how the flower supports common descent. I even showed you the trees that demonstrate that support.
No, I use local common descent as a working assumption. And the point of working assumptions is to test them using data. The data in Sal’s flower allow a sort of crude test of common descent of vertebrates. Common descent passes that test.
Ah, but the genes do follow the branching pattern, almost entirely. What you’re forgetting is in fact the support for that assertion. Perhaps you could go back and refresh your memory.
Yes, but the question is whether that assertion is supported by valid argument. I maintain that it was. Of course you have forgotten that argument entirely.
Because there is no credible argument for those assertions?
I do not recognize that claim. You clearly do not remember or completely misunderstand the actual arguments.
If so, then he’s wrong, since Sal’s flower supports common descent. Do you remember my argument for that at all? Simply put: the vast majority of patterns require only a single evolutionary event (either gain or loss, depending) on the accepted tree. The few patterns that require two events are a teeny minority. And that’s what we expect if gains and losses are rare events that are randomly distributed over a tree; two is less likely than one.
I’ve looked at Ewert’s paper. I haven’t analyzed it in detail, but it seems problematic in many respects. I don’t, however, think it’s useful to discuss those problems with you, since I doubt you understand anything at all about the paper and would be incapable of discussing it. Briefly, his “modules” are ad hoc constructions to fit the data, with no functional meaning. Many of them are just redefined nested taxa. Other modules are just extra parameters of fit and, as such must almost inevitably improve the fit of data to model. Anyway, isn’t every tree model isomorphic to some subset of dependency models? If so, how can a tree model, even in theory, fit the data better than a dependency model that’s isomorphic to it?
5/7 …
Again, not for Nonlin who re-writes her bullshit in a way that shows that she cannot read for comprehension, and insists on making the very same mistakes, thus reinforcing my points.
Who the fuck cares? Of course some designed shit can be classified into a nested hierarchy. So what? The real deal would be actually seeing how the magical-being-in-the-sky did things in a way that her magical desires manifested obviously. If her shit can look as if it evolved, then, again, the designer is indistinguishable from no designer at all. This seems like a reinforcement of that admission of defeat Nonlin presented before.
Now designed shit is different to “biologic” shit? No kidding! All this time I thought Nonlin believes that there’s a magical being in the sky puffing “designed” life forms into existence. Now she’s arguing that designed shit and life are different. OK. Since you say so. let’s go by that and call it a day.
John Harshman,
I do; your claim is lineage specific gene loss. What I don’t remember is support beyond this assertion. You have no idea what mechanism could cause the loss and still allow the animals to survive.
I have a rudimentary understanding of the paper.
It can at least be as good if the genes are truly following an ancestral path. As with Sal’s flower the paper is showing they are not. They are following a dependency model. If you look at diagrams 13 and 14 and follow the discussion you will see this. The paper shows another way to look at the data and may be useful.
It’s an observed fact that this happens. Genes that are not useful in the environment are not subject to purifying selection and so initially mutate and degrade and eventually disappear. Heck, it even happened all 12 lineages of the LTEE. Several independent large-scale gene-losses occurred that aren’t selected against because they’re not useful in the particular environment. In fact given that they’re not useful, their loss is beneficial because the organism then doesn’t have to spend time or energy replicating them every new cell division.
So we do have an idea what mechanism could cause such a loss and allow the organism to survive, we’ve seen it happen in real time.
Like Rumraket says, of course I do. But the mechanism of gene loss isn’t relevant to observing the pattern of distribution across taxa. Is it your claim that gene loss doesn’t happen and therefore can’t be an explanation of the pattern? That’s a very strong claim that’s contradicted by (for example) the existence of many fragmentary
pseudogenes in the average genome.
No, not even that much, as revealed by your comment below.
Again, it would be useless to attempt to discuss this with you. That much is clear.
John Harshman,
No, this is not my claim. My claim is that you have not supported the hypothesis that gene loss is the cause of the pattern observed in Sal’s flower.
Ewert has argued that a dependency pattern is a better representation of the data we are observing where gene groups are not following an ancestral pattern.
The reason I didn’t follow up on this, is because, in my potential answers I might mislead you to think that I accept very limited common ancestry, or with the impression that I think that UCA (I prefer to say ancestry that descent, because, well, it’s ancestors that are common, not descendants) is clearly established. Two quite opposing extremes.
As I said, I’m convinced that most-if-not-all life forms share common ancestry, but I also think that there’s some points where common ancestry might be very hard to demonstrate, and, worse, some things where our conceptual frameworks fall apart.
Explaining such philosophical problems would lead to endless and useless discussions, none of which would make magical beings in the sky any more justifiable (quite the contrary). That, again, would require tons of explanations.
So, were I to offer an example, you’d have to understand that it doesn’t imply that I reject deeper common ancestry. Understood so far?
ETA: I’m not paying [much] attention to what others have offered you to avoid entering a discussion where I don’t really know how far the explanations went. But I see that some examples have been offered, which you rejected for reasons I cannot and will not try and understand from what’s posted here. There’s only so much time. I’d rather offer an example myself, even if limited, to test the waters.
Entropy,
I understand. John has offered examples also of which one I would certainly not reject the hypothesis of common descent.
If you had suddenly rejected a deeper common ancestry that would have been a Devine shift indeed. 🙂
Entropy,
I have stipulated for the sake of argument there are philosophical problems with the design argument.
All that being said something going on outside space time that we don’t understand does not have to be labeled as magical beings unless you are advocating an ideology. Magical beings…lying Ted Cruz… all the same labeling technique.
No, your claim was “You have no idea what mechanism could cause the loss and still allow the animals to survive.” That’s an obvious implication that gene loss doesn’t happen because it would cause extinction. If you want to back down from that claim, fine.
So, why is gene loss a good explanation of the pattern? Because it’s highly parsimonious: it explains why almost all the pattern can be explained by single events on a single tree.
I think he’s wrong, and I don’t think you are capable of understanding either his arguments or mine.
Why only one? You haven’t responded on that point.
John Harshman,
Gene loss is a generic statement.
The gene loss we are observing in the pattern is a more specific statement. You have not established that this gene loss is even reasonable.
So are you claiming that for example that 70 genes were lost as a single event? What happens to your parsimony claim if you take away the assumption of common descent?
To quote a well respected scientist.
“Gene loss is a generic statement” is a generic statement. What meaning did you intend to convey?
You are apparently claiming that it isn’t reasonable, or were until you seem to have backed off. Why do you suppose that the particular pattern of gene loss we observe is not likely to have occurred by the suggested, known mechanism?
No, I am claiming that each loss is independent, and that different losses are related only by having happened on the same branch of a particular tree. If you take away common descent (i.e., the tree), the pattern of gene distribution becomes highly unparsiminious. That’s why we like common descent: it’s a parsimonious explanation for the data.
I doubt I would have any trouble explaining this to a 6-year-old. The problem is that you aren’t a 6-year-old and have all manner of treasured misconceptions that prevent you from understanding the simplest things.
A six year old, not a creationist.
John Harshman,
Or perhaps you are the indoctrinated one as evidence by your last response. Time will tell but your dodge here is duly noted.
colewd:
John:
Someone should start compiling a “Best of Bill Cole” list, modeled after FSTDT.
colewd:
dazz:
An important distinction. Most six-year-olds are capable of learning.
I invite anyone reading to decide who is dodging.