During recent discussions on phylogeny, we saw a distinct failure to communicate, probably felt by both sides. The ‘evos’ attempted to consider the role of molecular data in determining relationship. Given that an obvious cause of common sequence is common descent, due to the significant but not perfect fidelity of the DNA replication process, the phylogenetic inference is that sequence similarity is indicative of common descent. This, critics feel, is a circular argument.
In this, they may be following Jonathan Wells in Icons of Evolution. His criticism is that “homology is inferred from common ancestry, then turned around and used as evidence for common ancestry”. Yet in molecular genetics, the term ‘homology’ tends to be used to indicate sequence similarity alone, not a descent relationship. DNA probes and separate-strand annealing rely upon ‘high homology’, meaning only complementary sequence. The similarity is an observation, not an inference. If one had two sequences, XXXXXXXY and XXXXXXXZ, they certainly aren’t inferred to be similar: they really are similar. The retention of similarity (with variations) in a line of descent is also an observation. It is not clear to me where the circularity comes in in putting those two observations together and inferring that sequence similarity is supportive of common descent. Particularly when other sites are brought in to the analysis. Each site verifies the assumption for the other(s); Creationists on the other hand lump the whole into a composite sequence, and expect ‘independence’ to come from something other than sequence identity. You can’t verify genes using genes, or something.
Well, if the argument is circular, we must apply that razor to within-species comparisons as well – paternity testing, forensics, molecular genealogy and ethnic investigations must all be based upon circular reasoning too. Which I suspect no-one would try and argue in court. Broadening this out to between-gene-pool sequence similarity, among species that are even termed ‘closely related’, we presumably don’t have a major problem with sequence being commonly derived from a common ancestor there either. So the question is: as one goes ‘upwards’ in the Linnaean classification system, where does the circularity arise, if it is not there throughout? The differences identified between higher taxa are inevitably greater than those at lower, as one would expect from the same process of descent with modification that explains similarity among relatives, extended in time. As time goes on, the similarities erode and the differences increase. But there is no boundary detectable, no clear transition at which ‘circular reasoning’ comes in, nor where there is an abrupt difference as would be expected from separate origins. Differences remain a matter of degree, albeit confounded by rare events and inevitable statistical artefacts.
The Creationist alternative for sequence similarity is ‘Common Design’. I confess I can never make any sense of this. At what point does Common Descent stop and Common Design take over? In a process whereby a Designer generated in initial version of a sequence, and then allowed nature to take its course, the similarities between subsequent lineages would actually be due to Common Descent, not the initial Design.
OK, we might propose a Designer making separate taxa. The similarities in sequences between any two such taxa could be termed Common Design. But members of Taxon A and Taxon B are still commonly descended from that point on, from the moment of creation. So you can never separate out Common Design completely from Common Descent. In any process where similarities were initiated by Common Design, residual within-taxon similarities still indicate Common Descent from those points. The exact same kind of data has two completely different explanations across that assumed boundary, which is extravagant and inconsistent. The boundary is not a real boundary in the data.
If we follow the differences in Taxons A and B back, attempting to reverse out evolutionary history, we get to a point where the ‘ur-sequences’ exhibit a high degree of sequence similarity. Something which, if we observed it today, would strongly support a genetic relationship. So what would persuade us that, at that point in history, the relationship was not, in fact, genetic?
Common Design is sometimes invoked as ‘like creatures need like DNA’. But if we envisage the Design occurring at a high enough taxonomic level, we are saying that some very unalike ‘creatures’ had like DNA, at the moment they were … created. They only have unalike DNA now, after a few million years of separate change.
Further, none of this helps explain genetic similarities at loci that have little to do with phenotypic difference. One of the principal markers used in paternity testing are SINEs – a kind of transposon. Intergenic examples have no apparent phenotypic effect, and vary in humans (obviously, or they’d be no use). But there are also SINE inserts that are held in common between humans and chimps, others that are diagnostic at still higher taxonomic levels. They can’t all be essential to the form of the members of the clade they are restricted to – can they?
I’ve taken a somewhat circuitous route to my point, and the reason for the title. Consider the following not-very-treelike tree.
It represents the result of extensive phylogenetic analysis of the entire eukaryote clade. Reminiscent of those ‘you are here’ pictures of the Milky Way, ‘animals’ are all stuffed in the red box at bottom right. That’s everything: vertebrates, insects, sponges, nematodes … Fungi are just above, and land plants, seaweeds and Volvocales at about 11 o’clock. That’s pretty much it for multicellular life. The tree overwhelmingly consists of unicellular eukaryotes of bewildering diversity – what used to be called protists, and still are when we aren’t being cladistically rigorous. Never mind beetles, thats what the designer has an inordinate fondness for! If we had no place on this tree, I suspect people would have no problem with it, or the methods used to infer it. Of course we notice the multicellular life more than anything else. They’re bigger. It’s us, it’s our pets, food, materials and enemies. But most of the tree is minute, and does not indulge colonial clumping, amendments of which cause the ‘mechanical impossibility’ arguments ranged against phylogeny.
The discussions involved in resolving and testing these ‘protistan’ branches are surprisingly heated. It’s not just a question of assuming a relationship; the relationships are teased out of the data. If there were no relationship, that too would be apparent from the data. So where, in the progression to the interior of this diagram, and trying not to be bamboozled by the contents of that little red box, does circular reasoning come into it? Likewise, where does Common Design take over from Common Descent as the cause of similarity?
That’s not my argument. I already showed examples like Marsupial Placental convergence where corresponding similar forms (marsupial rat vs. placental rat) can’t in principle be due to common descent.
By way of extension if a fish can’t physically evolve into birds, then there is no point in assuming birds descended from a fish.
Here is an editorially improved version of the circular reasoning argument used by Allan Miller and John and the TSZ evolutionists : “it’s physically possible to evolve a fish into a bird because we can build phylogenetic trees, we can build phylogenetic trees because it is physically possible to evolve a fish into a bird.”
But I falsified that line of reasoning by referring to the PHYLIP programs ability to build phylogenies from things that can’t possibly give birth to other things. I’ve proven my point, similarity does not necessarily imply common descent.
I gave examples of what would persuade me that a group of species is united by common descent: hybridization and having physical examples of common ancestors vs. missing links that evolutionists say are likely to remain missing.
If there’s a tree, thee’s common descent. If there’s evidence for the tree there’s evidence for CD. Think about it, it’s not rocket science
colewd,
It appears that your real objection is not to common descent but to natural causes of change. Would you agree that a hybrid theory is possible: that there is common descent but that particular mutations, perhaps even macromutations, were forced into being by some unknown entity or principle? And would this not have the happy consequence of removing your objection while allowing you to accept the evidence of phylogenetic trees?
That has the advantage that it is indeed a circular argument. But it has the disadvantage that you made it up yourself; nobody else has said it. Shouldn’t you be arguing against what people have actually said rather than making up your own material?
Ok, so provide your circular reasoning in your own words. Why again do you believe a non-existent-in-the-fossil-record Sarcopterygii fish evolved into a bird?
Not only that, Sal was was in fact told that he was pulling a strawman when he first tried that. He then tweaked the argument with the amusing outcome that it wasn’t circular anymore. And when that was pointed out to him he goes back to the original strawman… ironically he’s trapped in his own vicious circle of fails and fallacies
This is a standard claim of creationists. It seems to give them “pew cred” to be able to tell a story of their struggle out of the depths of depravity.
Two arguments from incredulity for the price of one.
The evidence shows that modern birds evolved, with all tetrapods, from an ancestor you would probably call a fish (not a modern fish, of course). Other than your personal incredulity, inflamed by your religious beliefs, on what basis do you claim that it is physically impossible?
Are you unaware of other evolutionary algorithms?
That’s quite a claim. Got any evidence for it that takes into consideration natural selection?
I think you should start by explaining why you expect every creature that ever lived to be represented in the fossil record.
Else why the problem?
Why do you think god of the gaps is a good argument?
Do you accept that modern birds evolved from dinosaurs or is that too big a difference in phenotype to fit in with your “kinds”?
That would be cool. I could even accept that DNA_jock descended from a monkey.
This question incorporates one of your major fallacies, which I have explained many times and you have always ignored. We don’t know if any ancestors of modern birds exist in the fossil record. While it’s unlikely that any particular ancestor has been found, given the spotty nature of the record, it may be likely that at least one ancestor on that lineage has been found, given the large number of ancestors. But even if so, there’s no way to recognize it, that is to distinguish it from close cousins. Does that sound in any way familiar to you?
So we can’t call any fossil an ancestor. But why isn’t a cousin just as good? What you really need is something that shows the intermediate conditions you find so implausible. If we line up a fairly fine series of intermediates (and will you agree that we can?), doesn’t that show at least mechanical feasibility of those transitions that the fossil record preserves?
Of course the main evidence isn’t fossils, per se. It’s that very strong nested hierarchy in both genetic and morphological characters, the latter including fossils. Fossils just add another line of evidence. Tell me again what lets you ignore that evidence.
Now, if we accept that phylogenetic tree as real evidence of descent — and you have advanced no alternative explanation for the data — that tree implies certain features will be present at ancestral nodes. The fossils reinforce that explanation, as many of them strongly resemble the predicted ancestors, even though we can’t say they actually are ancestors. Among those features of that predicted tetrapod ancestor are a great many fishy ones, and so we would find it reasonable to call it a fish.
OK, spot the circularity.
I have started a new thread in which you can answer questions of that sort, hopefully without deflecting them facetiously.
Cute, but it was a serious question. It doesn’t make much sense to talk about the ancient fish to modern bird scenario if you don’t accept the evidence for more recent transitions. Do you accept that modern birds evolved from dinosaurs?
Sal is a believer. If he was ever an evilutionist, he was a believer.
He abysmal understanding of evolution now argues against him ever being an informed evilutionist. Hell, he doesn’t even understand sex. He seems to think that one mitochondrion or one y-chromosome becoming fixed in a population means that there were no other reproducing people in the population.
Here’s a sex question for you Sal: Assuming there was a mitochondrial Eve, does that mean all her genes and all her chromosomes have been inherited by modern women?
Don’t know, don’t care until you have something like a hybridization experiment and solving the fish-to-reptile transition. If you don’t have repeatable experiments, then isn’t “don’t know for sure” an acceptable answer?
Not to mention I don’t think interpretation of the fossil record being millions of years old is possible in principle because of things like the
Faint Young Sun Paradox
If the Earth is an ice ball during the supposed pre-Cambrian and Cambrian, then millions of years interpretation of the fossil record is false. There’s data for you and some hard core astrophysics. The irony is that to salvage the millions of years fossil record claim, one has to invoke millions of years of Global Warming and greenhouse gases.
I told you I was an evolutionist once upon a time, and I’ve stated reasons why I no longer find it believable, but absurd. I could be wrong, but so could you guys. But if evolutionary theory makes you happy and puts a smile on your face every morning when you ponder it, I respect that because believing in Creator God does those things for me. 🙂
That’s a similarity argument again, not an argument in terms of physical possibibility. Unless you have living soft-tissue it is really hard to say how feasible one transition is to another.
I don’t find it believable, but if you pony up some hybridization experiments, then you can make it believable. Why the rush to judgment?
It doesn’t make much sense to even talk about dinosaur to bird evolution if there is a problem evolving fish to amphibians to reptiles to dinosaurs. I provided one example of a barrier to reptile evolution in the issue of extant hearts (lizzards, snakes, turtles, crocodiles).
What you are providing are necessary but not sufficient conditions for verification. I provided sufficient (but not necessary) criteria : hybridization and/or an extant common ancestor or fossil in the direct line to the species in question. We have lungfish in the fossil record. It is completely believable lungfish today descended from lungfish like those in the fossil record.
If evolutionists want to represent evolutionary theory on par with experimental sciences, then maybe they should limit their major claims on things they can actually experimentally verify like say the evolution of Brassica (cabbage, kale, broccoli, brussel sprouts, etc.). Even the YECs would be on board with such a version of evolution because YECs are hyper-evolutionists.
I have no problem with phylogenetics for these applications which I listed elsewhere: selecting model organisms, tracing the origin disease figuring defenses to new viruses, maximizing diversity of endangered species in an attempt preserve them, tracing ancestry and population movements like that after the tower of babel (which by the way, does confirm the migration from the area of Biblical Babel). But all of these cases, isolated common descent is demonstrated as feasible experimentally.
So by this reasoning, you do have issues with the idea that all “fish” have a common ancestor?
Yeah, I get that you have a problem with relatedness across classes. I’m trying to determine where your line of “ok…I can imagine that these organisms are related” lies.
Except no one who understands evolution makes the latter claim at all. We don’t think we can build phylogenetic trees because it is physically possible to evolve a fish into a bird; that’s a conclusion derived from phylogenetic relationships.
No, you “falsified” a strawman.
So, the grouping of organisms within Class is invalid as far as you are concerned?
So hybridization is not a necessary prerequisite, but you demand hybridization and “solving the fish-to-reptile transition”. This is both so incoherent and so stupid given that distant species couldn’t possibly have hybridized.
I’ll follow your lead and will only believe in god when you can draw square circles
Btw, I forgot to thank you for doing the BLAST searches on sharks. I apologize for the delay in responding to your earlier comment.
Well if they can’t hybridize and you can’t find in the fossil record those missing links, then isn’t “we don’t know for sure in light of the uncertainties” a more appropriate skeptical response, than “common descent is as proven as the theory of gravity”. I was merely pointing out, if one wants to advertise a theory as proven as gravity, you should have experiments to prove extreme claims.
I have hypothesis that is provable by experiment. A lungfish gives will give birth to a lungfish over N generations, where N is a large number. Confirmed for N small, by way of extrapolation believable to N large, and confirmed by fossil record of Lungfish 300 million years ago. There are fossil ancestors in the direct line to existing lunfish in the fossil record, and btw they look like lungfish. That’s the form of a scientific theory.
This is not the form of a scientific theory: Birds descended from lobe finned fishes. No experiments, no fossils in the direct line, but we can assert the common ancestor line existed even though we can’t even provide detailed theoretical descriptions of the common ancestors we assert existed but can’t find in the fossil record and which we say will never likely be found, but we accept it as true anyway since we can put data in PHYLIP and generate branching phylogenetic trees just like we can put data on lego buildings and generate branching phylogenetic trees too. That doesn’t look like scientific theory to me….
Of course not, you seem to somehow forget that hybridization is some arbitrary criteria you just imposed to yourself, and you pretend that should apply to everyone else too. You dismiss all the molecular data and everything else that challenges your preconceptions.
So what? Please stop cherry picking. And that doesn’t mean that nothing evolved from Lungfish or some close relative. You’re pulling once again the classic strawman “why are there still monkeys”
So your “theory” is because there were lungfish 300 million years ago, then evolution is false and special creation is true… and 6000 years tops. No that doesn’t look like a scientific theory to me
What are the odds that PHYLIP will generate a branching tree from data that doesn’t represent a branching tree?
Actually I should amend what I said and add something I referred to before, namely the concept of a Ring Spcies.
If we can hybridize a bird with a reptile, a reptile with an amphibian, an amphibian with a fish, then that demonstrates Birds and Fish are sort of a Ring “species” (claide or whatever you want to call it). That would also be a sufficient evidence of common descent in the absence of direct hybridization but through a Ring of hybridizations.
But for starters, mating a bird with a reptile like a turtle might be a little strange.
Did you also read Joe’s and John’s responses to my questions on those, explaining the similarities and why BLAST is unreliable for phylogenetic analisis?
Pretty much 100%. That’s why “produces a branching tree” is not the criterion for supposing that data support a phylogeny. You have to add some test to show that the support is above chance levels. PHYLIP includes a program for bootstrapping for just that reason. Bootstrapping is a method, introduced to phylogenetics by Joe, that can be used to estimate the consistency of support of the data for particular parts of the tree. Data that don’t represent a branching tree are not expected to give strong bootstrap support for very many branches.
That whole thing about “square circles” went right over your head, then?
How do you know that the fossils are ancestors in the direct line to existing lungfish? Which fossils, by the way? And are lungfish a “kind”? Incidentally, what makes this an experiment?
Thanks, this is all so fascinating… I often wish I had gone with evolutionary biology for my college choice.
I just put the following in PHYLIP Pars program that represents the characters of my hypothetical Lego creatures such that “1” represents an appendage, and “0” represents that same appendage lacking.
The lego creatures are :
Alpha
Beta
Gamma
Delta
Epsilon
Here is the PHYLIP PARS input file:
Here is the beautiful family tree of lego creatures where we identify the grandma lego creature and grand kid lego creature.
It has to be true since we used the models pioneered by Wagner that was originated by Eck and Dayhoff (1966) and by Kluge and Farris:
If you have a point to make, please say what it is. If it’s just agreeing with my point, please say so.
Don’t you think that’s all entirely besides the point after the bootstrap mention that you mysteriously left out from your quote Sal?
That’s quite a lot of words to avoid answering a simple question. Do you accept that modern birds evolved from dinosaurs? It’s a simple yes or no question.
colewd,
Fer Chrissakes. You people have no idea what circular reasoning actually means.
stcordova,
What utter bollocks. We can build phylogenetic trees because the data permits organisation in that way. We can gain confidence in those trees by wider sampling and discovering that this too converges on the same relationships. The data drives the result, not the ‘assumptions’.
stcordova,
Essentially, and for no particularly good reason, you are restricting common descent to species that fall within the BSC as single biospecies.
How much hybridisation are you allowing here? If a zygote is formed but aborts at 6 weeks, is that a pass or a fail? If F1 meiosis commences but no gametes mature, again: pass or fail? If sperm cannot enter the egg unaided but can be injected and proceed normally from then on – again, pass or fail?
You are trying to dichotomise a continuum.
Hybridisation of a slightly different kind was once a frequent technique, before molecular sequence data became available. Separate out single DNA strands from 2 species and allow them to anneal, and the degree of complementarity affects the melting point, due to the hydrogen bonding of complementary sequence. Some pretty good estimates of genetic distance were obtained by this method, since confirmed and refined by actual sequence analysis.
For this method to work, there has to be better-than-random alignment. The DNA from within a gene pool gives the highest melting point. Then related species. Then genera, then families … there is no discontinuity.
Again, we would have Sal’s arbitrary cutoff where the exact same test is admissible at one taxonomic level, but not at another. Despite the data itself exhibiting shading, with no boundary.
this is a good point about the nature of comparitiveness which is the essence of evolutionary biology in most of its subjects of claimed evidence.
INow I say marsupials are just placentals with adaptation due to migration to areas.
Thats beside the point here however.
They do have to say there is fantastic likeness in creatures they say are absolutely unrelated except at a very early stage of a creature non description. A rat thing etc.
So convergent evolution must indeed threaten the line of reasoning of comparing biology to discover origin.
Whether body or dna. The same equation.
with the marsupial/placental model, by thier beliefs, there is already proof positive comparitiveness is based on what you compare and thats all there is.
Its just a line of reasoning and not a scientific investigation.
Robert Byers,
Convergence threatens evolutionary theory not one whit.
Do lego creatures reproduce and accumulate mutations over time? No.
That’s it, that’s your argument going nowhere. How hard is it to fathom that only when it is already known that organisms reproduce and yield branching genealogical relationships does it make sense to attempt to elucidate and test those relationships phylogenetically?
It doesn’t matter that you CAN arrange human inventions into nesting hiearchies when you don’t have any reason to do so in the first place. You DO have such a reason for living organisms.
There is no predictive model for lego creature “genealogies” that predicts anything. You can’t observationally falsify your relationship because nothing is being predicted. There are no genetic sequences to compare with your character states, for example. Your lego creatures do not reproduce and leave descendants with slight variations.
Your argument is a colossal failure of logic and critical thinking.
Rumraket,
Sal’s fail also forgets to add other character states and check for congruence on the same tree. The hierarchies corroborate each other (or, sometimes, not, which is how they detect anomalies such as HGT etc).
Sal’s entire oeuvre is one big Gish Gallop. In His entire history of internet posting he has never followed any argument to its logical conclusion and fitted the pieces together in a consilient framework.
Everything he has written is a variation on god of the gaps. No experimental evidence and mechanical infeasibility have replaced missing links.
Sal is now sulking in his tent. Who will be his Patroclus?
Patrick, you’d think.
Glen Davidson
He’s learned well from the IDists how not to think scientifically. Which works fine with some audiences, not so much with those that value evidence and good inferences from that.
He exemplifies the harm to individuals that creationist/ID causes, as he seems to lack the capacity even to grasp the value of a theoretical framework that ties otherwise disparate phenomena together into a coherent whole, versus a conspiracy-minded bunch of uncoordinated attacks on that coherent whole. At least when the subject is evolutionary biology, anyway.
Glen Davidson
At least he is at peace with himself.
He has the peace that replaceth all understanding.
It is said to be bliss.
Glen Davidson
petrushka,
He clearly isn’t. Hence the flounce.
He’s a cognitive dissonance bomb on the verge of exploding.
He went from evolutionist to OEC to YEC… is he just about to triple down and go full blown flat-earther?
John Harshman,
Maybe he put you on ignore.
I was being snide. If he were at peace, there would be no reason for Pascal’s wager.
And no reason for grasping at straw men.
petrushka,
I know, you were just setting up for your “peace that replaceth all understanding” jab.
I just wanted to emphasize Sal’s discomfiture. He will never find good arguments for his kooky kreationist views, and I think he is starting to realize that, in fits and starts.
Some advice to the youngsters out there: Don’t make the mistake that Sal is making. If you pick your beliefs first, and then demand that reality conform to them, you will be disappointed again and again, as Sal is.
No need to spend your life fighting the truth. It doesn’t accomplish anything worthwhile, and it’s a losing battle anyway.