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?
Salvador,
People would probably interact with you differently if you were to say outright that you’re not going to accept any alternative explanation that requires an old Earth.
How old do you believe the Earth is?
ETA: Do you believe that birds might be dinosaurs?
Ha, you’re responding to an old version of a comment.
It was already amended in anticipation of your quibbles and before your latest twit insult. Is that the best you got?
Tom,
You showed an extreme degree of hostility toward me personally when I have striven at TSZ and elsewhere to be cordial, and while at TSZ I never criticized you or your work or even your criticism of my friends.
You instead accused me of psychopathy and all sorts of things. Sorry, I’m not here to make friends or be liked. I had nothing against you personally and for the last years I felt CSI had to be criticized so I had no axe to grind against you.
I used to be an evolutionist, I now think the Earth is young or at the very least the fossil record is young. I don’t think the Cambrian era happened 500 million years ago because 500 million years ago the Earth would have been an iceball:
https://en.wikipedia.org/wiki/Faint_young_Sun_paradox
One thing you got right, my opponents here, thinking they are clever by trying to correct me publicly aren’t as clever as they think.
I used to accept old Earth, I changed my mind. I wasn’t a dogmatist about it. I said as much years ago:
Tom English,
By the way, I mentioned my affiliation with YEC, and it is with the CRS not AIG as you are accusing me of or your insinuation that I’m somehow hiding my YEC views:
And good grief, I explained my views here:
stcordova,
No, Sal, you have been claiming that John Harshman erred when he wrote “mtEve is not the MRCA of all female humans”, and being really condescending and rude about it, to boot.
The error is in fact entirely yours. You have been failing to distinguish between “the MRCA of all (female) humans” and “the MRCA of all (female) humans through a strict matrilineal line”. These are two different things.
As I demonstrated with John (not Harshman, sorry for any confusion, etc, etc.) procreating with both of Eve’s daughters.
You then moved the goal posts, claiming that the “the MRCFA of all (female) humans” was the same as the “the MRCFA of all (female) humans through a strict matrilineal line”.
Again, I demonstrated that you were wrong with my Rose Kennedy example.
When you now write “Also I was referring to the line involving mtDNA, not some some hypothetical scenario where female MRCA has all boys who become father of all humans.” You are admitting that John was right and you were wrong.
I can accept that. It happens a lot.
It’s the misrepresentation that I won’t forgive.
What do you mean by “subspecies”? Is that another typo that I’m not supposed to quibble about, or are you claiming that all lungfish are a single species? Can’t tell. Of course lungfish “radiate” only to other species of lungfish. That’s what clades do. What you’re really saying is that they don’t turn into things you think are all that different-looking, which is a subjective impression. I don’t know what “data we don’t have” you think I’m arguing on, so I can’t comment on that bit, or what “non-discovered, likely non-existent entities” you think my appeal is to.
OK, here you must actually mean “subspecies” as distinct from “species”. How am I supposed to interpret that other than that you are ignorant of lungfish classification? Help me avoid accusing you of ignorance by explaining what that meant in a way that makes sense. You contradicted my very explanation here (past diversity not matching current diversity) and ignored the additional one (tetrapods radiate into a new adaptive zone), both of which are relevant.
No, it means nothing of the sort. Evolutionary history is a combination of mutations and environmental influences (selection). One lineage lived in an environment in which adaptation to land was advantageous. Others, not. Once the land had been filled with tetrapods, there was no further advantage to any other taxa to gain such adaptations. That’s how incumbency works. And what seems right to you is not a good guide.
Why “unwholesome”? Why “interpretation”? I don’t think you know how the algorithms in phylogenetic analysis work or what assumptions they entail.
They assume no such thing. They don’t consider “mechanical feasibility” at all, nor should they. It’s a vague concept you invented that refers only to your ability (or lack thereof) to imagine intermediates. Phylogenetic analyses consider only the data. A strongly supported, consistent tree is an argument in favor of “mechanical feasibility”, even if you can’t imagine the pathway while knowing nothing about the characters involved.
More importantly, I told you the cartoon you presented wasn’t a good guide to anatomy. I could look up some details in my old comparative anatomy text. But why?
Years ago, I passed that question on to anatomy and physiology professors and they referred it to evolutionary biologists like you, and you just referred it to somewhere else.The cartoon helps the evolutionary case since it hides away even more daunting details like developmental mechanisms, specific relocation of muscles for valves, etc.So the cartoon would actually generously strengthen the case for evolution not against it.
I don’t believe you here, unless your anatomy/physiology professors were medical school types who teach only human anatomy. Try someone who teaches comparative vertebrate anatomy. I’m a molecular systematist; I know a bit about anatomy but it isn’t my central focus. But I know enough to tell that you have no argument here.
Nobody has ever said that. Stop with the strawmen. The first half of your sentence is more or less true. I could quibble with words like “prove”, but yeah: the fact that we can construct consistent phylogenies from different data is good evidence for common descent, and common descent shows that ancestors existed, and if they existed they must have been “mechanically feasible”. That much seems obvious. Your claims amount to demanding that I show how to turn a crocodile into a duck, presumably through the intermediary of a crocoduck. More of less what Doug Axe tried to do with proteins. The second part of your sentence is nonsensical. I agree that if anybody said that it would be circular. If.
You, John, Allan gave the most uncharitable interpretation of what I was saying, and he criticized an argument that I wasn’t intending to make. mtDNA means I was talking about the line of descendants defined by mtDNA not some other scenario of decendants like you came up with. But thank you very much for the editorial improvement. You won’t have quibble to make the next time. I expect you guys to make quibbles because that’s about all you’ve got, so I wanted to see your play book, and you won’t have that play the next time.
In contrast, I’ve demonstrated the circularity in John’s reasoning. “We can make phylogenetic trees, therefore common descent without statistical and mechanical miracles is true, common descent without statistical and mechanical miracles is true because we can make phylogenetic trees”.
John doesn’t seem to understand it’s a moot point whether I really understand his phylogenetic methods or not, the issue is his circular reasoning and total disregard for mechanical difficulties, not my understanding of phylogenetic methods. Not you, not Allan, no John has demonstrated otherwise.
You and Allan and Johns evasion of the topic of mechanical feasibility is reassures me I had a good point.
Next, I listed the ancestors that have no representative in the fossil record. A long list. No one really countered except with admission that they don’t expect them to be in the fossil record! That’s a no-go scientific theory.
To a lesser extent, I pointed out the problem of incongruent rates of evolution in the Sarcopterygii lines. Just handwaving responses.
The problem of Taxonomic Restricted Genes? I was just testing it out.
I don’t see it that way, and it’s not your forgiveness I need, I need to know your guys playbook and how good your counter arguments are. You can remove some quibbles from your playbook because the play won’t be available from me in the future.
I dumped the 2nd law ID arguments and CSI long ago, or “ID is science” — you guys haven’t had that play from me in long time, if you ever really did.
The literature on Lungfish mentions subspecies so I mentioned them, example:
It also mentions species, genera, and families. So why did you settle on subspecies? Are you doubling down again? It seems like a conscious attempt to minimize both diversity and disparity in extant lungfish, not to mention the past lungfish you also characterize as “subspecies”. I’m willing to attribute this to ignorance rather than malice, but it has to be attributed to something.
Your made-up quote of me isn’t circular reasoning. It’s repetition of the same statement with different word ordering. And this is the first I’ve heard of “statistical and mechanical miracles”. If the issue is my circular reasoning, then you should at least make a serious attempt to describe the circularity.
Can we at least agree that you don’t understand phylogenetic methods? Because I do think that’s important. Your incorrect assumptions about them permeate your arguments.
Touché
Sure I agree. But that doesn’t have to be the case forever. I already started looking at PHYLIP thanks to you and Joe Felsenstein.
This time two years ago, I didn’t even know about Fasta files. Studied gene browsers at the NIH a couple months ago too.
Not to mention, YECs accept PHYLIP for situations that are mechanically feasible like the Abraham Modal Haplotype which confirms the Biblical Abraham’s dating. PHYLIP has served YECs well for their purposes. So nothing against PHYLIP for believable domains.
Learning PHYLIP and phyologeny is fine with me for situations where it is completely believable that there is a common ancestor — like
1. kale, broccoli, brussell sprouts, cabbage
2. wolves, dogs, coyotes, jackals
3. lions, tigers, panthers, leopards
etc.
This is demonstrated experimentally through hybridization, historical breeding records, and demonstration of rings.
I don’t agree it is applicable to domains like the prokaryote eukaryote transition. The best argument against UCA is in the prokaryote eukaryote transition, but it is the hardest to understand and learn. Multicellular evolution is also a good argument but hard to understand and learn. I was trying out fish to bird evolution.
It’s only important I learn phylogenetic methods to lend some personal credibility to my arguments, even though the argument is correct because phylogenetics does not address the barriers to evolution, phylogenetics for UCA just pretends such barriers don’t exist in the first place.
” it’s a terrific crash, ladies and gentlemen. It’s smoke, and it’s in flames now; and the frame is crashing to the ground, not quite to the mooring mast. Oh, the humanity! “
Thanks to the wonderfulness of the English language, one can go up in flames and down in flames at the same time.
And Sal can have an education and be ignorant all at the same time.
Glen Davidson
stcordova,
I can’t bring myself to attempt a reply to that. Just can’t summon the energy any more.
John Harshman,
And all the world cried…
Sal, the faint young Sun paradox relates to the Archean eon, not the Cambrian. By the time of the Cambrian it would have been close to modern levels.
4. Human, Chimp, Gorilla, Orangutan.
stcordova,
You haven’t even made the ‘circular’ case. You just repeatedly assert it. You have not explained why phylogenetic analysis is legitimate (and presumably non-circular) at one taxonomic level but not at another.
Yeah, sure. Likewise we might evade an argument on the role of planetary alignments or the information to be gleaned from chicken entrails. You would be reassured by that that you had a good point too.
It is mechanically feasible for one species to split into two. That is all you need for common ancestry at a node. What you are mistaking for ‘infeasibility’ is the accumulation of subsequent divergence, which might look infeasible if it happened all at once. There is really nothing more to say: your ‘feasibility’ argument is an irrelevance based on a misunderstanding (Yes! I said it! Sal misunderstands!) of speciation and coalescence. I don’t evade it, I dismiss it as irrelevant.
Could you do us a favor and point out where the “mechanically infeasible” lies in this fossil hominid transition?
And then explain why it’s perfectly fine in the wolf-chihuahua one?
stcordova,
Talk about assuming what you set out to prove … “the argument is correct; I will ignore this minor inconvenience that goes against it because it’s (somehow) circular and does not accept my argument up front”.
Phylogenetics can’t see the barrier; it pretends nothing. It can’t detect the ‘ground’ of your assumed orchard, despite the fact that it should be detectable on phylogenetic analysis. As I said, if (you seemed stung by that ‘if’) you accept or understand phylogenetics at any level (brassicas or canids), you should appreciate that it ought to.
Repeat appeal to the prokaryote-eukaryote boundary is actually outside of the tree in the OP – this frantic leap from twigs to root, let’s pretend there’s nothing in the middle. Let’s allow for argument’s sake that God created eukaryotes. What about the rest of it? Why does the whole allow grouping into a ‘tree’ relationship? Can random data be arranged as a good tree?
All the anomalies you pick on are themselves informative. Instances of HGT, TRG’s and ORFANs, gene loss, all follow the same phylogenetic patterns as their genomic neighbourhood within the taxon. How do we identify these, your very weapons? Phylogenetics. You depend upon it for your arguments against it. Common descent is writ large.
It’s legitimate when the species can make more of the same kind of species. We don’t have to assume feasibility of the individuals of a species descending from another individual of the same species as it is experimentally demonstrated as feasible.
It’s not legitimate if the species can’t make another kind of the same species.
There are situations that is true even by evolutionist standards, like in the case when whatever tree the evolutionists build, they have to plug with convergence or HGT. That’s even acknowledged in the literature, I provided an example with the salamanders. Convergence, as in common architecture, and some evolutionary literature even uses the word “design” as in constrained to the same design.
Look at the Marsupials placental divergence, and marsupial mammals. So there you have common designs that as a matter of principle are not by common descent.
So if we admit there is at least one circumstance as a matter of principle which can rule out phylogeny or common descent we can at least consider other circumstances that rule out common descent.
If you admit some kinds of convergence you can admit others, like the inability of mutation and selection to construct sufficient change. How do you know mutation and selection are sufficient mechanisms to transform a lobe finned fish into a bird. Where are the numbers and theory that say such high specificity systems can actually be evolved? All I get in reply are phylogenetic reconstructions and hand waving, not actual detailed analysis that is expected in other disciplines.
You cannot just assume that mutation and selection will be sufficient to effect change of a species into another and thus justify you can build a phylogenetic trees at all. Such trees are illegitimate if the similarities aren’t due to common descent. I didn’t say the were or were not due to common descent, but you can’t use the ability of to build phylogenies as evidence of common descent.
There is one mode in the PHYLIP program you can just throw in data like this.
and it will build a tree like this:
It doesn’t serve as proof on bit string descended from another. We could take lego buildings with discrete “characters” and pump them into PHYLIP and generate trees, it doesn’t prove the lego buildings descended from each other.
It has to be reasonably possible that one thing can physically descend from the other before we can assert a phylogenetic relationship. Until that is established, it is speculation, and premature to assert common descent.
It looks to me there is well-designed branching pattern, but also well designed evidence that prevents common descent interpretations. The reptilian heart varieties are an example.
If you don’t want to admit God as an answer, then let it be some unknown mechanism or fluke or black swan, but let’s not pretend it’s been established such transitions can actually happen or are ordinary and natural based on what we know about chemistry, physics, anatomy, physiology, development, genetics, epigenetics, transcriptomics, proteomics, epitranscriptomics, epiproteomics, glycomics, etc. Until then, it’s an open scientific question, not a done deal.
PS
I’m aware of that tadpole experiment that got multiple heart chambers by man-made mutations that didn’t become viable adults.
stcordova,
Hybridisation does not demonstrate common descent independently of sequence. Fertile hybrids can only occur between individuals with a high degree of sequence similarity. You are imagining that ‘nature’ testing a sequence relationship is somehow different from us doing so computationally. That’s not the case.
You don’t need to know anything about the organisms the sequences came from. The programs are even tested using artificial datasets, generated from a computational process of descent. These cannot mate with each other. A tree program simply takes sets of sequences, and the same basic operation is performed regardless whether they are from orders, families, species or within a gene pool.
You wish people to assume up front that the data is meaningless, if they can’t think of a way the relationship could be true. That is hardly objective.
The rest of your post, I didn’t even get time to read. Your posts are generally too long, and have not been improved since you discovered how to add pretty pictures.
Lego doesn’t reproduce itself and it doesn’t have a genome that mutates, living organisms do.
Why is it insufficient? It’s apparently sufficient to produce the divergences between all canines, and all felines, in your view, IN LESS THAN 4000 YEARS. That is a lot of variation generated in a very short amount of time. You seem to be okay with hyperspeed evolution.
But even if we add 25 million years of additional change on top, you still don’t think evolution can produce the transition from lobe-finned fish to tetrapods. Even though the requisite fossil representatives in this transition really do exist in an approximate chronologically ordered sequence.
Why? Why can so much change happen in 4000 years just fine, but even further change not happen in 25 million? I mean, besides your contractual committment to put a specific conclusion before any consideration of evidence:
“By definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the scriptural record.” – Answers in Genesis statement of faith.
OK, skimming, I actually asked for an example of molecular convergence, and a reference in which ‘common design’ was invoked as an alternative to common descent in the literature. Your post has neither.
I didn’t say “common design” in the literature, I said
But along those lines:
http://www.journals.uchicago.edu/doi/10.1086/285234
http://europepmc.org/articles/PMC2881246
http://europepmc.org/abstract/MED/18493604
Well my post didn’t have molecular convergence because it would have repeated the earlier citation. You probably demanded it because you didn’t see it in the first place:
But how do you like this cladogram B that makes Dolphins and Bats a Clade under the Prestin protein. Nice convergence, nice “phylogenetic” tree where dolphins and bats share an immediate common ancestor. 🙂
http://www.sciencedirect.com/science/article/pii/S0960982209020740
But I pointed out, your assumption that ubiquitous similarities are due to common descent rather than common design is an assumption. You have evidence of similarities that are simply the same design not due to common descent in the form of convergences or homoplasys.
It’s only an assumption the majority of similarties between disparate taxa are due to common descent, for which you have no proof. The lack of proof starts with those missing common ancestors in the fossil record and missing theoretical justification that such species can eventually evolve into a very different one. Similarity alone is not proof of common descent. Homoplasys, morphological, molecular convergences, etc. are an indisputable counter examples to the supposition “similarity implies common descent”. If we admit these counter examples then we can admit more, like mechanical feasibility.
If evolutionary biologists can’t provide experimental evidence or if they can’t provide workable mechanical theories, then maybe they shouldn’t make advertise evolution as a science proven by actual experiments and rigorous theory (like say on the order of classical mechanics or quantum chemistry).
If they advertise evolutionary theory on the basis of a series of ancestors they purport to have existed but don’t ever expect to see in the fossil record, ancestors from which they can’t construct detailed evolutionary trajectories even conceptually in principle (like the evolution of the reptilian hearts) — then that is a step in the right direction of saying what the true status of the theory really is, namely unproven.
God can answer anything and everything. It is literally unfalsifiable. Even if we saw large-scale morphological transitions right before our eyes you could just mindlessly declare that god did it. This isn’t about not wanting to admit something, it’s about having good reasons to believe it in the first place because what we see is a prediction of the theory. Nesting hierarchies is not a prediction of “there is a god that loves us and created all life”.
stcordova,
Once again, your ‘the anomaly is the rule’ tactic. So how do they detect these signals (as with HGT, TRG, indel etc)? By the fact that the bulk of the genome converges on a different tree. So the anomaly sticks out.
That is, detection of the things you think fatally undermine phylogenetics rely entirely upon phylogenetic analysis for their detection. You are unaware of this, but your ammunition against phylogenetics depends upon phylogenetics. Not the first, nor the last, time a Creationist has depended upon evolutionary theory in order to attack it. It phylogenetics is bollocks, then convergence is no more a phenomenon than any other apparent phylogenetic signal. You can’t have your cake and eat it.
It’s funny how, despite the ‘bigger picture’ of the OP, we have either gone right outside it (prokaryote-eukaryote) or yet again obsessed about the contents of that tiny box marked ‘animals’. 😀
It remains an inescapable fact that the molecular data can be organised into a ‘tree’ relationship, despite anomalies. You can even stick fossils, and morphological and non-functional characters states on it, where you have ’em. Common descent provides a reasonable explanation of that fact. ‘Common design’ does not.
Yeah, there’s nothing circular about this, just the same statement reworded. LMAO what a fail
But if you can be paid to believe YEC, you can believe anything.
But in order for an organism to exploit a new environment it must have the necessary attributes in place to be successful in that environment. Multiple attributes are needed to take advantage of a particular niche. It is the complete anteater, not just a long sticky tongue that allows it to survive on a diet of ants and termites. It has many adaptations working in a coordinated way for this purpose.
It is the specialists which exploit particular niches which are more in danger of extinction than the generalists who are successful in several various niches and can tolerate changing conditions.
I believe that the human line are the hominids who did not specialise in any given niche and the great apes are the ones who changed to fill more specialized niches and so compromised their further evolution. Jos Verhulst made a case which is in agreement with this view in his book Developmental Dynamics in Humans and Other Animals
Here is more evidence which supports this view.
Ignore the rest (which happens to be right there in cladogram A) because you know, looking at the big picture is not your thing, is it?
Depends. All organisms, as regards their history, start in an environment in which they can survive. Rapid climate climate change or a cataclysmic event such as a meteor strike will mean extinction. Evolutionary change occurs over generations. But also some environments, such as the mudskipper’s tidal environment, change, for instance from wet to dry daily and depending on how close to the water’s edge you venture from either direction.
Sure.
I’m easily convinced that clade ancestors would be most likely to have been opportunists rather than specialists
Specialists are more vulnerable to change, sure. Humans can adapt their environment rather than having to adapt to an environment. This does free us as a species from effects of the environment that has allowed us to become cavalier about climate change.
ETA clarity
Ps re anteaters and termites. Arms races happen. Why did termites evolve to produce extremely tough termite mounds? Why are anteaters well adapted to digging into these mounds?
The Designer is a fight fan and revels in blood sport?
Sal,
One thing you might be misconceptualizing (based on the above) is the idea of “lines”. Keep in mind that once you have have any kind of species split (a branching node), both of those groups become the beginning of a new line. So none of those three “lines” you list above were actually single lines. So thinking of one or two of those “lines” as relatively “unchanged” compared to the third is not an accurate picture.
Further, Tetrapodamorph is technically a superclass of Sarcopterygii (as Benton noted in 2004) and thus contains more groups of diversification than than other two.
Now, the question you should be asking (and this is certainly of interest to a number of ichthyologists and paleontologists) is why it seems that so many branches of both Dipnoi and Actinistia came to dead ends and went extinct. I can’t say myself, though I can speculate and offer that all of the potential niches were taken by better adapted competitors by the time they came around. Maybe others hereon have some ideas.
The point is though, those other two groups do not represent single lines of unchanging organisms.
ETA: I should have read ahead before responding. I see John provided a more clear and comprehensive response already. My bad.
Do you have any evidence that termite mounds were less tough in the past or that anteaters were less well equipped?
Anteaters always ensure that they do not decimate a mound to such an extent that it is beyond repair so that it will remain open for lunch in the future. This shows the wisdom of the species.
Not to hand. I’m willing to speculate a little time on finding some.
That’s a bold statement, Charlie. A simpler explanation would be that evolutionary processes generally limit predation. Drive your prey extinct and your own species follows into oblivion, especially when you are entirely dependent on one type of prey.
Anthropomorphism is an easy trap to fall into. I should know having the surname Fox! “The only animal that kills for pleasure!”.
BTW just glancing at Wikipedia, I could be some time!
Just curious Sal, but what defines a “kind”? How does one determined whether a given species is of the “same kind” or “different kind”?
Are turtles and snakes of the “same” or “different” “kinds”? How similar does a species need to be to another species to be the “same kind”? How many distinctions do two species need to have to be “different kinds”?
It certainly seems to me that this “kind” categorization is not only inaccurate, but completely misleading. It does not appear to have any actual value, particularly scientifically. But, I’ll wait and see if you can provide a realistic definition.
ETA: I’ll just note here that to me, this “kind” category really boils down to, “that which I can accept could be related.” It doesn’t strike me as particularly useful then.
Apparently it’s only important to you to learn some buzzwords about phylogenetic methods so that you can sound less uneducated than your co-religionists when you present your argument from personal incredulity.
Re-read what you wrote. Even to you it must be clear that those are the words of a person profoundly uninterested in the evidence.
Allan Miller,
IMHO both common decent and common design are leaps of logic. What we see is similarities and differences in DNA sequences and other features. If the tree shows specie groupings that is fine but to claim they came from a common ancestor is a claim without evidence in all the cases I have seen discussed so far.
If you make the claim w/o validated empirical evidence then your reasoning is circular based the UCD assumption.
The data you discuss does not verify common decent it verifies similarities. Decent is a extraordinary claim that requires extraordinary evidence.
One little correction: “species” is both singular and plural. As for evidence, most people would consider a well-supported tree to be evidence. Why don’t you? What other explanation can you think of for the data?
What would constitute validated empirical evidence?
One more minor correction: it’s “descent”, with an s. Why is descent an extraordinary claim? Do you understand the difference between mere similarity and nested, hierarchical similarity? Again, can you come up with an alternative explanation for this pattern?
So, other than our recent manipulations, how have genes been demonstrated to duplicate and show up in newly-minted organisms? Has it been by design? Has it been by reproduction?
There is no reason to focus on the whole animal, rather than on the genes, except that former fits your desired result. What you say has been demonstrated with organisms within a species (or with fairly closely-related species, at most) has been demonstrated with information, namely that the same information (with or without variation, it can happen either way) comes from reproduction of that information in various ways. Of course I’ve noted this previously and you ignore it to merely repeat your dreary old creationist tropes, because you only deal with what you like to deal with.
It’s the bigger picture, not the little pictures that creationists focus on in a sorry attempt to nickel and dime to death the truths that they don’t want to hear. It’s been well demonstrated that the same information that appears in one organism comes via reproduction and not by design. That is why phylogenetics points ineluctably to evolution and not to the design that creationists desperately want to claim sans evidence.
Observation of breeding doesn’t demonstrate just what you want, that like produces like with respect to whole organisms, but that like produces like when it comes to information. Hence, when you find many of the same genes in non-interbreeding organisms, you have very good reason to recognize that they must have diverged in the past from a common ancestor (HGT is generally less wholesale), using the same observations you claim to deny the same. It’s your silence over issues like this that is telling.
Glen Davidson
It seems to me that both Cole’s and Sal’s arguments boil down to, “if groups of organisms don’t look similar, I can’t imagine how they could possibly be related.” Thing is, neither seems to be able to define how similar things can be before they can be acceptably related vs how similar things can be while still considered unrelated.
ETA: My guess is that anything within a given Class likely equals “kind” or “similar looking enough”, but who knows…
I was an evolutionist once apon a time. The absurdity of evolving a fish in to a birds is one line of reasoning that swayed me away from becoming an evolutionist again once I accepted creation because of the origin of life problem.
I already pointed out to John that it doesn’t matter that I don’t understand how to do Phylogeny reconstructions as it’s a moot point if something can’t evolve via common descent to something else — i.e. just because I can pump data describing the morphology of several lego buildings into PHYLIP software and get a tree does not imply lego buildings can physically give birth to another lego building. Same with the morphological similarities of Marsupial Mammals and Placental Mammals — even evolutionists must admit as a matter of principle, not incredulity, that the astonishing similarities unique to each of the corresponding mammalian forms (like placental rats vs. marsupial rats) are not due to common descent. So I’ve proven “similarity does not necessarily imply common descent” as a matter of principle.
My detractors seem totally unwilling to acknowledge that unless something like a fish can physically evolve into a bird, there is no point in invoking phylogeny. If common descent is true, it can be accepted by demonstrating that it is physically possible to evolve a fish into a bird.
I can accept phylogeny of Kale,brocolli, cabbage, brussel sprouts because they are shown through historical records and hybridization experiments they are physically capable of coming from the same ancestor — and that’s the other thing, we have living examples of the ancestor unlike the missing ancestors in the direct line from lobe finned fishes to birds.
Here are examples of hybridization experiments that would satisfy even a YEC that some Brassica plants evolved from a common ancestor. As I said, YECs are actually hyper evolutionists from an orchard of common ancestors (OCA), they don’t accept slow evolution from a Universal Common Ancestor (UCA).
http://www.ncbi.nlm.nih.gov/pubmed/24232393
Evolutionist will complain, “providing experiment that show UCA is true that will take millions of years, and we can’t possibly reproduce the experiment like other science”. Well then, evolutionists shouldn’t make claims they can’t support experimentally and then turn around and pretend it is a scientific discipline like other scientific disciplines. Just admit it’s an inference (speculation is a better word) despite the absence of fossils in the direct line from lobe finned fishes to birds, etc.
You want to believe it that’s up to you, but for someone who is always demanding repeatable experiments as evidence for design or God, you seem easily willing to believe a bird descended from a fish despite absence reproducible experiments to that effect, despite lack of fossils that are in the direct line from that Sarcopterygii lobe finned fish to a bird. You don’t want to believe in God, then how about a black swan convergence event — that’s the same line of reasoning evolutionists are forced into regarding Placental and Marsupial convergence. So that raises the question, when is common descent just and ad hoc explanation for similarity that is actually by convergence or coincidence (even assuming no God created it).
I already said, I don’t advertise ID nor aspects of creationism as science because of lack of repeatability, but I accept it as true. The absurdity of the fish-to-bird transition is one reason.
John Harshman,
This disagreement goes back to our first discussion. My answer is we don’t have a clue how these species arose. There are too many obstacles to conclude UCD at this point until we understand how DNA can be modified to create new functional protein sequences or RNA control sequences that live in almost infinite mathematical space.
We are 30 years past the introduction of Weasel and it still needs a target to finish. When you make changes to a sequence of 50 characters or more you are going to degrade unless you know the end sequence.
The tree is not evidence, it is organization of evidence. It contains nodes called a common ancestor which is a concept of which appears to lack evidence. For most my life I assumed the tree as a valid theory but the more we discuss this the less solid this hypothesis seems.
I think this theory is very misleading based on the words common decent or universal common decent. IMHO we need a description that is solidly supported by the evidence.