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?
And you don’t understand the mechanics of nature and it’s your problem alone.
Oddly enough, I was unaware that successful reproduction between organisms whose most recent common ancestor lived well over a billion years ago was a prediction of common descent.
Yeah. Actually if common design was true there’s no reason why the designer couldn’t have put together some weird hybrid between a rose bush and a chimp. So right back at you: where’s the evidence for any such freak IDiots?
In science, one proceeds from the known to the unknown. So one sees that chimps give rise to chimps, roses to roses, and notes that similarities in life are due to reproduction. Well, that makes sense within reproducing populations, but what of similarities across populations that don’t interbreed?
That actually was a sort of puzzle, with mules and breeding of pigeons, mice, and dogs. Eventually, of course, it seemed that certain types of similarities are indeed due to reproduction of traits across generations and even across populations that no longer interbreed. The trouble for creationists is that there simply isn’t any point at which this evidently becomes impossible, nor where the evidence changes significantly, because they want it to be impossible.
So, where science reasoned and experimented using the known and extended it into the unknown, they reason from the unknown into the known, and end up wiping out knowledge. Aha, we don’t know how prokaryotes gave rise to eukaryotes (some good ideas, little nailed down certainly), hence like (DNA) does not give rise to like (DNA) where eukaryotes and prokaryotes are concerned, and therefore like giving rise to like doesn’t generally hold.
Except at the species level, and anywhere else they decide it does.
So instead of furthering knowledge, they seek to destroy it. Like gives rise to like is what they prefer to claim, but they end up denying it for DNA sequences wherever these give results that aren’t approved. It isn’t just the results that IDists/creationists bollix, it’s process, it’s fundamental reasoning, it’s the bases for knowledge.
Glen Davidson
Tiger lilies. Dog roses. Bee Orchids. Ha! Explain that one, Creationists!
I do find the response somewhat gobsmacking. Sal seems to follow the chimp and rose branches back to their meeting and imagine that, to have a common ancestor, it must have been a bit like a chimp and a bit like a rose. This unicellular organism …
Lock a bunch of creationists in a room with some keyboards, and eventually the most ridiculously stupid things will get typed.
I suggest that Sal should present this conundrum to one of the professors in the course he is doing so well in.
Oh, my sides hurt.
Response in Moderation Issues.
Rumraket had already posted a comment demonstrating your claim to be wrong by the time you reposted it. You should try reading instead of just writing.
And that, that chimp will have mutations in it’s genome, and those mutations affect it’s morphology, behavior and so on. And those changes affect reproductive success.
And if we extrapolate this same effect over long timescales, it makes some pretty clear predictions (multiple nesting hierarchies of shared derived characteristics).
And so on and so forth. Creationism has no such predictions at all, it’s all just mindless rationalizations after the fact. If we didn’t observe such similarities, you would be EVEN MORE confident they had to arise by design. In fact that’s what you are doing most of the time, try to claim the dissimilarities between distantly related taxons, sitting in different clades, or even domains, are evidence of design.
That’s why you constantly blather about the prokaryote-eukaryote divide. You can’t have it both ways, you can’t both claim that similarity is evidence of common design AND that dissimilarity is evidence of… COMMON DESIGN. What the fuck dude? You’re coming up with these idiotic excuses ad-hoc every time. Whatever we see you just stick into a foregone conclusion and say “that’s what the designer wanted”. It’s literally unfalsifiable. You don’t predict any PATTERNS, you just rationalize all the time.
“Mechanically infeasible changes” between the hominid skulls, but it’s totally fine for the “dog kind”.
You people are fucking lunatics.
phoodoo,
Although you were not able to back up your evidence about the amylase enzyme existing in dogs and absent from wolfs, your over thesis about dog and wolf not sharing a common ancestor is worth additional research.
Jesus, colewd.
I’ve highlighted a word to help you out:
colewd,
Sure. Research away.
And be sure to give us progress reports, for laughs.
It is all about comparitiveness.
It is just a presumption that likeness in genetic data between creatures is the evidence/or proof of common descent.
Yet thats just a line of reasoning.
Its bot genetic scientific evidence for common descent. Its a human construction of basic common data.
Alright.
Is it reasonable? NO! If a creator made biology on a common blueprint as done in physics or anything then like body parts would have like dna at atomic levels.
So dna likeness would not be a trail back to a origin, a common origin.
Evolutionists are saying that God could not create basic kinds of creatures with eyeballs straight off, and from a common blueprint including dna, BUT ONLY eyeball likeness is possibly from common descent.
No way around it.
The evolutionist position on genetic likeness equals common descent is just a line of reasoning . whether true or not.
Robert,
WTF?
We’ve learned not to expect reasoning in your comments, Robert.
Glen Davidson
You know, if I might be permitted a bit of regional chauvinism, what our eccentrics lack in firepower (of the literal *or* metaphorical kind) and homicidal rage, they make up for in sheer Non Sequituraliciousness.
colewd,
I don’t know what you mean here. Dogs that have been domesticated, who get their diets from humans have adapted to better digest carbohydrates. What do you mean I haven’t been able to back up that evidence? Here:
http://www.livescience.com/26513-starchy-human-diet-domesticated-dogs.html
If you just accept that what the morons here say is true, you will be terribly mislead.
Phylogeny recapitulates orogeny.
Mountains from pushing things too far.
Patrick,
Oh dear Patrick, you have such a fundamentally incorrect understanding of the concept of “demonstrating”.
I fear I better not delve into the more tough words for you, when you haven’t even gotten to “demonstrating” yet. When Rumraket says that the reason we have convergent evolution is because the laws of physics never change, the word demonstrating should never even be in the same continent as that feeble rationalization attempt.
Instead of telling other people to read, perhaps you and Richard should go attend a nursery school together, so they can put pictures of ice cream of the keys for you to drool on when you tap?
phoodoo, to Patrick:
phoo,
Even your attempts at insults are failures.
keiths,
You mean I should have suggested pictures of fairies with butthurts, because that makes them drool more?
As you wish, you know them better than me keiths.
Robert Byers,
Likewise familial and forensic DNA testing. Do you propose these should be inadmissible in court? “The DNA certainly matches that of my client, Your Honour, but I submit that this is just a line of reasoning. Were you there?”.
phoodoo,
Yes, I have seen this claim cited several times. Your original claim was that this enzyme existed in the saliva of man and dogs and not wolves. I did some research and found several studies that refute your claim. This seems harder to explain with evolution than the same enzyme reproduced more frequently in the pancreas. Case one requires the evolution of a new sequence case 2 does not. This is an interesting study because it is claimed to have happened in the last 50k years. I have always assumed that this transition from the grey wolf to the dog was supported by evolution. I am grateful that you brought up that this transition may not be necessary true. I personally am very skeptical of UCD, however continue to believe that some transitions may have happened by isolated populations. The dog/wolf is a fascinating case study.
Moved a couple of comments to Guano (and came close on a couple more). Please address the ideas, not the person.
I’m merely falsifying the implicit claim of OP that there is no circular reasoning in arguing phylogeny proves Universal Common Ancestry (UCA).
In the case of species like chimps, or better yet, ring species and hybridization experiments, there is experimental evidence confirming a claim of common descent from some ancestor. Chimps descend from chimps, ring species from some common ancestor:
https://en.wikipedia.org/wiki/Ring_species
YECs are hyper evolutionists and accept the orchard model. For example, Kale, Brocolli, Brussel sprouts, etc. come from the same ancestor. Dog, coyotes, jackals, wolves descend from the same species as demonstrated by hybridization.
The problem for UCA is in absence of experimental evidence, the inference that “similarity implies common descent” is circular. This is really in evidenced by the fact evolutionists themselves resort to horizontal gene transfer, convergence, endosymbiosis to argue for the origin of similarity.
If one will allow convergence in some cases, why not in all cases? The answer is ad hoc application of common descent. UCA is based on lots of circular reasoning and ad hoc explanations of similarity.
Isn’t “we don’t know for sure” the appropriate skeptical and circumspect evaluation? If UCA floats your boat, go for it, but let’s not pretend UCA has experimental verification to other fields of biology like say anatomy and physiology or molecular biology or synthetic biology.
If you said, “this phylogeny is faith-based and hasn’t been experimentally demonstrated as feasible” I’d be fine with that.
colewd,
You keep saying UCD. You keep saying UCD then talking about some minor node.
That said, I do find it hilarious that you base your assertion on dog/wolf unrelatedness on one site. This is exactly the kind of thing I’m talking about.
stcordova,
How are you doing that by bringing in ‘mechanical feasibility’? You haven’t addressed the argument in the OP at all. Circular reasoning is a logical fallacy, and you seem not to have addressed the reasoning on logical grounds.
I ask again for actual sequence pairs we can look at where inferring descent is NOT circular, and another where it IS, to see how you are differentially addressing the ‘circularity question’ in each case. There’s more to it than pairwise comparison, but that’s a start.
Or are you saying that assuming descent from sequence similarity is circular in every instance?
stcordova,
Do you have an actual example of unresolvable convergence at the molecular level?
stcordova,
Hybridisation means only recent common ancestry [eta – and only then in sexual linages]. It cannot be diagnostic of all possible instances of common ancestry. Clearly.
If this is not quote mining, it’s a close relative. If I can find a single site from which I can extract a single sentence which on its face seems to support my preferred position, then I’m fully satisfied. No need to look elsewhere because (1) elsewhere might refute my position, yet (2) I knew I was right even before I found my one congenial source.
Are you willing to say that “like produces like” in biology is experimentally unverified? Because that’s what evidence for phylogeny is about.
You’re claiming that biological information is reproduced by life, except where you don’t like that conclusion. It makes no sense.
Glen Davidson
Flint,
Just to be clear, I meant ‘site’ as in genetic locus, not website. It’s genome mining, but he’s off the hook on quote mining!
Allan Miller,
Sal’s argument of circular reasoning is the inference of common decent without homologies being well established. IMHO the scientific claims are way ahead of the evidence and that makes the discussion very difficult form the scientific side. This is a source of emotion and frustration that has become part of this discussion. What are the real standards to establish a homology? If they are poor then Sal’s circular argument is right. If they are tight then the argument is not circular and you win the gambit. I bring up dogs and wolves to get just one node over the goal line of a solidly established homology. Since in evolutionary terms it is fairly recent and has a good chance of being reconciled.
If you are not willing to rigorously support the current homologies by evidence that they evolved by isolated populations then the argument is indeed circular.
colewd,
Not at all. Population isolation does not have much to do with it, and nor does ‘mechanical feasibility’. All you and Sal are doing is making the assertion ‘the argument is circular’, and then bringing in some irrelevance that you declare makes it so. You are not supporting the case that the argument is circular.
Is it circular to infer that sequence similarity in dogs and wolves indicates common ancestry? If you answer that question in the negative, we could proceed from there to find out where circularity comes into the case at higher taxonomic levels. If you answer that question in the positive, I wonder how you might be inferring that common ancestry? Do you have evidence of population isolation?
colewd,
Did you actually look at John’s ratites paper? One of many thousands using multiple lines of evidence to establish phylogeny?
Agreed, and thus even if UCA is true, it cannot be verified experimentally, and at the very least which similarities are due to UCA, horizontal gene transfer, convergence or special creation.
I took a cursory look at the aaRS gene (because being a Noah’s ark hyperevolutionist YLC/YEC) I’ve been interested in molecular clocking. Here is the wiki entry on aaRS:
The bolded isn’t an isolated case. I’ve been saying doesn’t of times, taxonomic nested molecular hierarchies are not the same as phylogenetic molecular hierarchies. This is a case in point, and there are lots more.
The fundamental reason I don’t believe in UCA is that I think if a miracle created the first life, then a miracle could in principle create all the species lines as well.
Was it a Black Swan, God-made creation, exceptional statistic event? There may not be formal experimental resolution to the question, but I don’t think the implicit picture of UCA whereby things evolve by ordinary mechanisms over long periods is theoretically or empirically supported. You can’t use phylogenetic arguments to argue for statistical feasibility of evolving things like orphan genes or evolving the wiring of blood circulatory systems in reptiles.
There is also the waiting time problem that even Durrett and Schmidt admit is substantial. The assumption of UCA doesn’t solve these theoretical problems.
I look at stuff like the anatomy diagram below, and I raises the questions of mechanical feasibility (btw, the species lines would like form a nice taxonomic nested hierarchy).
colewd,
Are you ever going to read Theobald?
ETA: That goes for you, too, Sal.
Meanwhile, “common design” can be inferred in biology without life ever having been shown to be designed by observed designers/design processes, let alone by any that can be shown to have existed in the vicinity of earth when life arose.
We’re supposed to provide evidence for the evidence itself (“like produces like,” unless they’re not happy with it), while they can “infer design” without any good evidence for the requisite designer or even for credible design in the first place. Creationist logic.
Glen Davidson
Can you provide a link again, sorry to ask. I did look at it a long time ago.
I already said I there is a non-random nested hierchical structure for molecular taxonomies.
There isn’t however a conflict-free hierarchical structure from proposed phylogeneis.
The nested molecular taxonomies of individual genes are not the same as the supposed nested hierarchies of supposed phylogenetic trees.
A taxonomic hierarchy puts birds and fish in separate groups. A phylogenetic hierarchy says the ancestor of birds are fish-like creatures. Phylogeneticists will invoke “birds and fish descended from the same ancestor who founded the clade” but then when pressed to describe the ancestor of birds, their description of the ancestor looks like fish! If it looks like fish, swims like a fish, mates with other fishes, it is a fish, and therefore not the ancestor of birds.
I may look at PHYLYP when I get around to it.
stcordova,
All of these should stand out from the simplistic ‘tree’ assumption. And they do; how do you think they are identified? If there is a good tree signal, noise upon it can be very informative. After all, horizontal transfer is still a descent relationship, just not a vertical one. Likewise paralogs and tandem repeats.
This is a point I make repeatedly: the ‘orchard model’ can be tested. Creationists are so busy denying phylogenetic methods at all levels, they don’t realise it would be an ideal method to reveal Creation in all its glory. Because the ground of the orchard would stick out like a sore thumb. There would be no global convergence, simply a set of local convergences. One might suspect why they do not take on that challenge, preferring instead to deny the entirety.
Hybridisation is not, incidentally, an independent test of relationship in the sense implied by the ‘circularity’ brigade. It depends upon sequence similarity for its success. Too far apart, sequentially speaking, and meiosis fails in F1, even if the gene set works.
It is no less circular (and no more) than direct pairwise sequence comparison. Chromosome alignment and recombination involve a search for homologous sequence. Scare quotes can be taken as read.
Where’s the evidence that coyotes and wolves share a common ancestor if you reject phylogenetic principles?
Sal:
29+ Evidences for Macroevolution:
The Scientific Case for Common Descent
You mean circularly reasoned avoidance of theoretical statistical barriers like total reworking of translation and regulation not to mention morphological barriers.
The only “evidence” UCAists give that multicellularity emerged from a common unicellular eukaryotic ancestor is similarity. When pressed for answers how this is reasonable theoretically given the substantial problems of evolving new proteins and cell types and cellular inter-signaling, the objections are claimed to be moot because “we can build a phylogenetic tree”. Anyone can build a phylogenetic tree that shows elephants descended from birds since elephants are closer to birds than they are to fish.
Instead, the objection to the physical, statistical, mechanical barriers to evolving things naturally is with the ability to construct phylogenetic trees. It’s circular reasoning.
Every anatomical, chemical, physiological, population genetic objection posed has been responded to by appealing to the ability to fabricate a phylogenetic tree. That’s no answer to the objection, it is circular reasoning and appealing to something that for all we know is total imagination.
Nor is that a requirement to be able to reliably and justifiably infer that commen descent is true. Theobald directly addresses that particular objection.
FIrst a quick comment. I read 29 evidences a long time ago. The problem with that essay is that Theobald’s essay gives the highly misleading impression the falsifications listed are the only ones! The mechanical objections which I’ve posted on many times at TSZ are serious enough objections to falsify at least some macro-evolutionary transitions, not the least of which is the prokaryote-eukaryote transition. Even Woese and Ventner have objections, maybe not with the exact words of macro evolution, but they know….
I look at the other essay. Thanks again.