I do think this site needs a thread to discuss phylogenetics and whatever the creationist alternative might be. Let’s start with this quote from Sal Cordova:
stcordova: Insisting on the truth of naturalism in the disguise of evolutionary theory could impede scientific progress in the medical sciences if the whims of some evolutionary biologists like Dan Graur are realized. The National Science Foundation (NSF) has invested 170 million dollars in unresolvable evolutionary phylogenies of little or no utility to medical science.ii To date, no therapies based on the 170 million dollar phylogeny project have come to market. By way of contrast, with the help of research like ENCODE, epigenetic therapies are already being delivered to patients with more such therapies in the pipeline. Therefore, a gambler’s epistemology that seeks to maximize reward in the face of uncertainty would seem a superior approach versus blind insistence on impractical naturalism.
This short paragraph raises a number of questions, a few of which seem like topics for discussion.
1. Assuming for the sake of argument that investing in phylogenetics doesn’t help medical science, why should we ignore other benefits? Is basic knowledge useless unless it contributes directly to human health? Should NSF be concerned only with medical sciences, and if so, shouldn’t it be folded into NIH?
2. Phylogenetics actually does have practical applications, even in medical research. Feel free to discuss that. Me, I’m into knowledge, regardless.
3. What is “unresolvable” intended to mean here? NSF grants, the AToL program in particular, have produced great amounts of phylogenetic resolution. My project, Early Bird, for example. Is it all somehow bogus? How much phylogeny is there, anyway, and how would a creationist tell where it begins and ends?
4. And a minor point: Where does this figure of $170 million come from? Is it the total amount awarded by the NSF Assembling the Tree of Life program from beginning to end? Or does it also count various other programs that have funded systematics research? I find it hard to pull any aggregate info from the NSF web site.
stcordova,
Fair enough. But are you looking for the truth, or to assert your truth?
Please do not mistake your ignorance for mine. And please stop reproducing a figure when you don’t know the source, don’t know how it was generated, and don’t know what it means. I believe what’s below may illuminate one or two of your fundamental misconceptions.
Really? What it tells me is that lampreys are equally closely related to birds and teleosts. If lampreys are fish, then the most parsimonious hypothesis is that the bird/teleost ancestor would be called a fish too. Add in other taxa (again: lungfish, sharks, etc.) and the conclusion would be inescapable.
That makes no sense. That would show that lampreys are descended from birds, if anything. Clearly you have no clue about how to interpret even the simplest, most clocklike data. It’s hard to see what your problem is. When we say birds are descended from fish, we don’t mean any modern species of fish or modern family of fish. We mean that birds are nested within a clade whose basal divergences are all within what we would call fish. The common ancestor of lampreys, carp, and penguins wasn’t a lamprey, or a carp, or a penguin. But it was a vertebrate with gills and fins; what would you call it?
And what this means is that lampreys, being the modern representatives of a very old lineage, should be quite distant from all other vertebrates but equidistant between penguins and carp, and that penguins and carp should be closer to each other than to the lamprey. As we see.
Once more you repeat the fallacy of equating Teleostei with “fish”, as if I had not explained that several times. Your BMP diagram has only teleosts on it. Birds are not descended from teleosts. Birds are descended from an ancestral osteichthyan (the clade of “bony fish”) whose descendants include both sarcopterygians and actinopterygians. Birds are sarcopterygians (as are all tetrapods). Carp are actinopterygians (as are all teleosts). Neither group is descended from the other, but they are both fish.
Here you again seem to fall into the fallacy of supposing that common descent refers to descent of extant species from other extant species. Birds do not descend from the extant clade Amphibia, but the tetrapod ancestor resembled an amphibian in possessing aquatic larvae and metamorphosis. Birds and amphibians do not descend from the extant clade Teleostei, but the osteichthyan ancestor resembled a teleost in possessing gills and fins. Do you know what “paraphyletic” means? “Fish” are paraphyletic. Teleosts, the fish in your BMP diagram, are not.
Another quote mine. Nick refers to the fact that cladograms tell us about cladistic relationships. They don’t declare species to be ancestral to other species. But that isn’t what we mean when we say that fish are ancestral to birds. We mean that any clade we want to call “fish” also contains birds. The ancestor was a fish, but not any extant fish.
Again, nobody says that and I have expressly explained this several times. Lampreys are not ancestral to birds. Lampreys are an extant group with a very long separate history. The ancestor of carp and penguins was a fish, descended from the common ancestor of carp, penguins, and lampreys, and that ancestor was a fish too. Given clocklike evolution, we expect all three taxa to be equidistant from that ancestor, and we expect carp and penguin to be closer to each other than to the lamprey. As we observe.
Yes, I agree, and this is exactly what we would expect from the standard understanding of phylogeny. Teleosts and tetrapods are sister groups (given the taxon sample of the tree you keep showing but don’t understand), and neither is descended from the other. But there are fish that are not teleosts, and if you added some of them you would see the lungfish clustering with the tetrapods and the sharks outside both groups (but closer than lampreys). Again, that’s the standard tree.
Nick didn’t admit anything; he merely repeated the common understanding of what phylogenetic analysis tells us. You understand nothing, perhaps because understanding is not your goal, and you are merely looking for quotes you can mine to score a point or two. The only rational interpretation of the fossil record — that is, the only one that fits the data — is indeed evolutionary. But we don’t need to think about that. The point is that the fossil record actually shows many of the intermediates that you think are mechanically impossible. It refutes your claim even before we try to construct a tree.
But if you want to learn from us you have to start by actually reading and trying to understand what we tell you, without starting from the assumption that you already know both more and better. You have, to choose a trivial example, consistently equated teleosts with fish and have completely ignored every correction. If you won’t pay attention to even the simplest facts, how can you learn anything?
I’m asserting stuff here, and seeing if what I asserted is wrong. You guys have proven me wrong a few times, and that is worth the price of admission. I learned, and have no intention of repeating where I misfired.
That said, I was an evolutionist, and some of the stuff I’ve said here at TSZ that has withstood criticism are the reasons I have continue to accept creationism.
And when I wasn’t outrightly wrong, you’ve shown me on occasion where I need to phrase things better and where some of my asserted data points and terminology points were off and when I was dead wrong.
Keiths for example showed I made a misattribution to Sir Gavin de Beer in a quote. That was a pretty bad error on my part, better to find out early.
Allan Miller showed me the literature is persnickety about how they define when an epigenetic mark is deemed heritable even though it shows up again and again for millions of years — like epigenetic marks associated with X-inactivation.
I thought you guys (TSZ regulars) argued very well about the problems CSI, the law of conservation of information, IDs use of 2nd law, Arrington’s laws of non-contradiction, KF’s transfinity, ID being science, lots of other things — and I sided with you guys, not the UD crowd.
I even got some good pointers that corrected my misunderstanding of statistical mechanics (something about the Liouville theorem).
On the discussion table right now is molecular taxonomy diagrams and the reasonableness of inferring birds descended from fish versus birds and fish proceeding from some unspecified parent. This is relevant to John Harshman’s question of utility.
If I think the math is with you guys, I’ll agree (as I did regarding CSI and Sewell’s 2nd law). But I don’t think the math is with you guys this time.
Speculated evolutionary relationships or actual numerical relationships that I demonstrated at the molecular level?
Regarding BLAST, it is an approximation of Smith-Waterman, and Smith-Waterman is a mathematically optimal alignment algorithm, hardly the quick and dirty you insinuate. The only thing about BLAST being quick and dirty is that the full-blown smith-waterman algorithm would take too long to run, so the guys at NIH NCBI had to put a few heuristics to speed it up, so it will miss occasionally but not by much.
But you protest too much, do you really think the 97% score in BMP2 between Chickens and Turkey’s vs. the 48% score between Chickens and Lampreys is materially wrong? If you don’t think so, then your objection is overstated.
Here is the heart of the problem. Take any “living fossil”. Unless they had a very recent MRCA (most recent common ancestor) the intra specific sequence divergence should be just as great, or at least on the order of their distance between them and other creatures they are related to.
This is what the hypothetical molecular distance chart should look like if I were to buy into the idea fish transitioned into birds:
Coelacanth (sub species 1) vs. Coelacanth (sub species 2) : 40
Coelacanth (sub species 1) vs. Chicken : 40
Coelacanth (sub species 2) vs. Chicken : 40
One can do the same for the aaRS genes in bacteria vs. aaRS in humans. Why are the aaRS genes of the same species of bacteria so similar if they’d been around for millions of years yet the phylogenetic distances between them and other species is so great? The only resolution is they had a recent MRCA, not one far back in time.
The intergroup and intraspecific variation between fishes and other fishes is too small, same with bacteria. The only resolution is to invoke a recent MRCAs, but to do so would be just at tad toward the YLC (young life creationist) or YEC viewpoint.
But the real data show a different picture than would be required to have necessary (but not sufficient) conditions to argue a fish transitioned into a bird.
The irony is that in order to argue universal common ancestry (UCA), one must appeal to the relative immutability of forms to demonstrate common ancestry in the small branches — i.e. vertebrates descend from vertebrates, fish descend from fish, etc. In other words, a nested hierarchy. But the nested hierarchy comes at a price, it enforces immutability of forms which makes belief in transitions (like from fish to bird) less believable if that axiom is adopted.
Thus, the solution to having a phylogeny where birds descend from fish is to have a systematically incoherent theory, which is the evolutionary theory we have today. What evolutionary theory says in effect:
1. we expect after N generations a coelacanth will look like its coelacanth ancestor, which is another coelacanth
2. but we also expect after N generations a coelacanth could look like a bird 😯 In otherwords, we only invoke nested hierarchies in an ad hoc way and dispose of them when we need to argue fish can evolve into birds
A scientific theory should have something to say about expectation, expected values, expected outcomes.
Like I said evolution isn’t coherent as a theory, and until it is a coherent theory like other scientific theories that are actually stated in terms of expectations from theory, phylogenetics doesn’t have much utility except to give inferences from dubious premises.
stcordova,
That’s so vague. ‘The math’, as I have repeatedly mentioned, is used in investigating disease phylogeny, and clades which even the most hardened Creationist would accept are related by common descent. If you think this is wrong, you could
a) Critique the actual math – as mentioned, Joe’s Inferring Phylogenies might be a good resource.
b) Point to the boundary at which it breaks down.
Of course, you aren’t obliged to do anything.
stcordova,
That’s not the only resolution. aaRS genes appear to have been subject to lineage specific losses and significant HGT. They don’t align strongly with other gene trees. But one cannot use this to infer that all the other gene trees contain no information – that the phylogenetics of the entire genomes is represented by aaRSs and aaRSs alone.
You seem to find everything to be represented most accurately by its anomalies. This is by no means the only example of this selective vision. You have one of the lumpiest carpets on the internet.
stcordova,
I am not sure I agree with you that comparing genetics has no value. Where I agree is that UCD is a problematic concept for many reasons you state highlighted by the fact that the molecular evidence is not cooperating very well. What we see is common biochemistry and observing and understanding why it is common and why there are subtle changes to sequences between species kinds would be of value.
The big paradigm shift from the evidence is there is more than one tree. If we come to realize there are billions of trees then certainly the world will look very different to everyone.
To be clear, I have argued we should do comparative anatomy and genetics, but that is not the same as phylogenetic reconstructions which actually hinder actually seeing real similarities. Creationist Richard Owen was a pioneer of comparative anatomy.
For example, as I showed in this diagram:
http://theskepticalzone.com/wp/wp-content/uploads/2016/07/image_10362.jpg
We share some genes with zebra fish, but not with mice. One presenter at ENCODE 2015, Katalin Susztak, researches human kidney disease by studying zebra fish, not mice.
The phylogenetic reconstructions are not needed to see these similarities, and if we obeyed them as a guide to medical research rather than just the raw similarities, we are blinded to the less obvious similarities like between zebra fish and humans that are not found between humans and mice.
Dr. Suztak at ENCODE 2015 (also where Wesley Pike Presented):
stcordova,
My daughter is a published author on a study using zebra fish and not mice, on Cryptococcus infection. The main reason is that they are see-through.
It’s a practical choice, and the closest relative is not always the easiest to deal with. But it would be pointless if we had nothing in common with them at all.
So much less the need for phylogeny to guide medical research! Zebra fish are practical, sometimes more similar in certain features. The last thing on the list of deciding on a creature to study human health is the (possibly make-believe) phylogenetic relationship.
This is exactly the complaint I put forward that precipitated this discussion.
stcordova,
It remains important that there is a phylogenetic relationship. It’s not so much that detailed phylogenetic classification is required before a model organism can be chosen. These kinds of models were chosen long before molecular phylogenetics. But you can’t do everything with chimps (itself a model based upon a relationship criterion).
Any comment on the use of phylogenetic methods and population genetics in pathology?
stcordova,
I agree that this type of diagram continuously improved is what is needed at this point.
Ok, I misunderstood you. Thanks for pointing out my error in not understanding what you said. You never said “lampreys are ancestral to birds”. I stand corrected for not understanding what you were saying.
Which raises the question, what do you think is ancestral to birds AND some extant fish? Can you describe the creature?
Your answer actually will help me respond to the objection you raised:
So what do evolutionists suggest some of the features of the common ancestor of birds and some extant fish is, surely they have some idea since they keep looking for transitionals.
What did the common ancestor of all extant birds and some extant fish (you name the group of your choice) look like. Did it look more like a bird or say something like this:
https://en.wikipedia.org/wiki/Sarcopterygii
What should I tell creationist students about what evolutionists believe regarding the structure, anatomy, physiology, molecular features of the common ancestor of birds and some extant fish. Let’s give it a name since it is a hypothetical construct, how about “fird” or “bish”?
I mentioned the transformed cladists. There is the old school of taxonomy, and we also have the Pheneticists.
Taxonomically or phenetically speaking or molecularly speaking did the “fird” look more like a fish or a bird?
Or are you going to argue that “fird” is taxonomically equidistant from both fish and birds? My bet is you’ll say it looked more similar to fish (name your preferred group).
Did the “fird” have developmental mechanisms, mechansims of respiration, blood circulation, diet, habitat, reproduction etc. more close to a modern fish (name your favorite closest species) or more like a chicken?
The set of question I just posed and the answers I expect you’ll give will highlight the problem with your conception:
But my understanding is the ancestor looked a lot like an extant fish, certainly not equidistant in characters between fish and birds, but darn near close to the archetype of a fish in terms of anatomy, physiology, developmental mechanism, reproduction, etc.
If it looks darn near like a fish, after N-generations, I expect its offspring will still look much like a fish, not a bird.
So that raises the question what you expect the molecular data to say? This is exactly the point of me raising the question of the MRCA of fish and aaRS genes and whatever.
Do you think the descendants of “fird” should be equidistant from each other?
Name some extant fish you think are “firds” descendants. Shouldn’t you expect the fish descendants to be as diverged from each other as they are from birds? Why or why not? I expect whichever way you answer, and if you think about it carefully, you’ll see the problems I’m trying to point out.
I’m not trying to be combative here, but you’re the one who wanted me to respond and defend my position, and I’m responding and defending my position by pointing out some of the incoherencies of UCA phylogenetic reconstructions which argue birds descended from some fish-like creature. It’s a mess, the most sane resolution is to say birds and fish descended from some common vertebrate that didn’t look like a fish, but then what would it look like?
I’m A-OK with it.
I said, and it is a point I can change my wording on, is that when I was talking phylogenetics I was talking about UCA phylogenetics, not Orchard phylogenetics.
Along those lines, there is an excellent creationist population genetics program called Mendel’s Accountant that models Orchard phylogenetics that can be helped to possibly infer the common ancestor of the created kinds.
But along those lines, we infer common ancestry via similarity, even at the molecular level, those fish don’t look like they are closely related to birds (as in mother daughter), they are more sister like in relationships.
The set of questions I just posed to John Harshman requesting a description of “fird” shows why UCA phylogenetics isn’t really compatible with the phylogenetics in pathology. There is equivocation of terms as to what is actually being carried out.
stcordova,
But you said something along the lines of ‘the math is wrong’.
And where lies the discontinuity? If you understand phylogenetics, you ought to understand that this can be used to resolve that very question. Creationists should be all over it. But they aren’t. They flip-flop endlessly about how useless it is and how they fully accept it.
Sal,
How can you hope to challenge “UCA phylogenetics” when you don’t understand phylogenetics at all?
And actually teaching anyone, when he lacks the most basic knowledge of what’s at stake.
Creationism/ID at its usual level of intellection.
Glen Davidson
Glen,
Yes, which is why the answer to his question…
…is don’t tell them anything.
Find someone who understands the science and let him or her explain it to your students. You do them a disservice by pontificating on things you know nothing about.
Sal,
If the evidence is equivocal, how have scientists managed to arrive at this…
Figure 1. The Consensus Phylogenetic Tree of All Life
…out of the more than 10^38 possible trees?
Is it all a big conspiracy?
Since you’re making that assertion and asserting I don’t understand, can you describe some of the characters of the would-be MRCA ancestor of some-extant fish and all birds?
You can start with habitat and behavior. Did it swim or fly, what was the means of propulsion or locomotion?
How about its circulation and respiration, was it more like an avian lung or some other lung.
Apparently you do, so this would seem a basic question to pose to someone insisting and defending John Harshman’s viewpoint.
We aren’t talking philosophy here, but a theoretical scientific question about the characteristics of “fird”. If you don’t like “fird” give me a name of this would-be ancestor, what it looked like.
No it’s a colossal misinterpretation, look at the “ancestors”:
1. mitochondria, nucleus
2. organs nervous system and vascular system
3. vertebrates
4. jaws
5. digits
6. amniotes
7. hair
8. placenta
A common ancestor that is a mere placenta doesn’t make sense! And to drive home the point, from that diagram, the common ancestor of birds and fish is a “digits”.
So, since you feel so informed, how about for the sake of the readers describe what you think the features of the common ancestor of all birds and some fish are.
This is the skeptical zone, and I’m expressing skepticism about the feasibility of such a common ancestor. “Digits” I don’t think counts as a viable common physical ancestor, but it does count as a conceptual (as in intelligently designed) ancestor.
Here is the problem depicted by the diagram below, the “ancestors” are purely conceptual, they make no sense as physical ancestors. A lung by itself won’t give birth, so don’t have the mistaken notion just because you can build a taxonomy diagram like this that this implies you can actually describe viable physical ancestors. They are viable conceptual ancestors even though they are not viable physical ancestors, and this implies intelligently common design, not mindless common descent.
But if you doubt me, how about you describe the common ancestor of all birds and some of the fish.
Here’s a candidate.
How do you explain the commonality of the genetic code across all known plants and animals (with a few rare and interesting minor variations)?
Sal:
Sal,
You can’t possibly be that dim. To understand the significance of the blue and red dots, look at the legend in the bottom right corner of the diagram:
Ignoring the canard “speculated”, you should realize that they are both identical, as far as what you have presented so far. The fact that you don’t understand this is a big problem for you
Nonsense. There is no mathematically optimal alignment algorithm. I don’t even know what that would mean here. Nor is alignment the same as phylogenetic analysis.
Not so much wrong (What would that mean, exactly?) as not phylogenetic information. Your BLAST search would be a statement about phylogeny if 1) BLAST scores were genetic distances and 2) genetic distances were patristic distances and 3) evolution were exactly and perfectly clocklike. But none of these three things is true. But yeah, we would certainly expect BMP2 to be more similar between chickens and turkeys than between chickens and lampreys. It’s no surprise to find that. It’s just that the lesson you draw from that is nonsensical.
There’s the problem, actually: there is no such thing as a living fossil, certainly not on the molecular level. I can’t imagine why you think that’s a thing.
No, that’s what you might see if chickens were descended from a particular extant species of coelacanth, and that species had somehow persisted for hundreds of millions of years while retaining two potentially interbreeding but entirely allopatric populations
John Harshman,
. Nobody makes such a claim. What you would actually expect is that the chicken should be less distant from a lungfish than from a trout.
What do you mean by “the same species of bacteria”? What makes you think that species has been around for millions of years, or any significant fraction of the time separating that species from humans? What makes you think that coalescence shouldn’t happen within bacterial species?
What do you mean by “too small” and what do you mean by “fishes”? You really aren’t making any sense here, and I hope to show you, by dint of frequent repetition, that you have no idea what “too small” or even “fishes” means.
I have no idea why there should be any such price or axiom. Please explain.
There are no such expectations. Morphological evolution can happen at wildly varying rates and run off in all sorts of directions, depending on a host of environmental factors. Molecular evolution is a bit more tractable, especially for junk DNA. It never stops, and the rate is less variable too. Nor are birds descended from coelacanths. Birds are descended from ancient sarcopterygians that belonged to no extant group (other than Sarcopterygia itself, which includes birds). Not coelacanths, not lungfish, not teleosts, not lampreys. This is why I say you need to learn the standard position before you begin to critique it. So far you’ve been attacking nonsensical claims that are yours alone.
What exactly does this mean and what is the evidence for it?
Ah the silence, no one want to venture a guess what the common ancestor of all birds and mammals and amphibians plus a few fish look like. How about a lungfish.
https://en.wikipedia.org/wiki/Lungfish
But then where did the lungfish descend from, ahem, other fish. So is it fair to say evolutionary biologists think birds and giraffes evolved from some fish?
Wow. I generally hesitate to participate in discussions like this, but this comment is difficult to ignore. Hint: those aren’t ancestors. You need to spend some time learning about basic phylogenetic concepts. Felsenstein’s Inferring Phylogenies is probably jumping ahead a bit; I recommend this resource: Tree Thinking, which deals with some of the basic conceptual difficulties early university students have in interpreting phylogenies. (Note: answers to the quiz can be found here)
Once you’ve got the basic concepts down, Joe’s book is technically authoritative (Ziheng Yang’s Molecular Evolution: A Statistical Approach is also an excellent treatment).
A rather curious argument. I have a question for you, but first a point of clarification.
If you are looking at the divergence of a specific gene, then the MRCA that matters is the MRCA for that GENE, not for coelacanths as a whole. Now the question:
can you think of a mechanism that would reduce the intra-specific divergence of any given gene, but could not (in the general scheme of things) reduce the inter-specific divergence of that gene in extant organisms?
stcordova,
Sal, you really have to dial down the arrogance and realize that you understand almost nothing about evolutionary biology, and specifically phylogenetics and the various phylogenetic trees and related diagrams you have been posting.
Take the tree here, with various vertebrate groups and the labels “lungs”, etc., attached to various branches. Those aren’t ancestors; they’re the spots at which ancestors acquired various traits. (That particular one is, incidentally, wrong. The common ancestor of tetrapods and perch had lungs, so the “lung” mark should be moved one branch down.)
To answer “What was the common ancestor or of birds and fish”, well, it wasn’t a fird or a bish. It was a fish. The term “fish” describes a paraphyletic group, and you should start realizing that as a first step. What fish (in the traditional sense) is the closest living relative of birds? That’s actually a little bit ambiguous, but it’s probably lungfish, AKA Dipnoi. It could conceivably be coelacanths. It couldn’t conceivably be anything else. The common ancestor of Dipnoi and birds wasn’t a lungfish, and it wasn’t a bird, but it was a fish. It had gills and lungs. It had bony scales. It had jaws with teeth. It had fins with bones in them, unlike ray-finned fish. It had various technical details of the bones of the skull that we really don’t need to go into. It’s very unlikely that we have found fossils of that common ancestor, and we couldn’t be sure even if we had. But we know quite a lot about what it looked like, and that (surprise!) is one thing phylogenetic analysis is good for: when we construct a tree, we can fit characters to that tree to discover the probably states at ancestral nodes.
And yes, it’s exactly the same sort of thing used to reconstruct the evolution of pathogens. Even there, you have no notion of what you’re talking about.
Second. It’s a basic textbook for understanding phylogenetic trees and how they are derived. Very basic, which is what Sal needs.
I would prefer to say that birds and giraffes are fish, just very highly modified terrestrial ones. How is it possible for you to ask this question at this point in the discussion?
Not possible as has been noted.
Alan provided a link to a possible ancestor above.
Here’s another possibility:
http://www.csmonitor.com/Science/2014/0611/Ancient-tiny-fish-might-be-ancestor-of-almost-all-vertebrates-including-you
Some of that diagram is confusing. “Monocot”, “Protostome”, “Deuterostome”, and “Amniote” are the names of taxa, not characters. The characters should be “one seed leaf”, “blastopore forms the mouth”, “blastopore forms the anus”, and “amnion”, respectively. Also, not every character has been inherited by every descendant; some things have been lost here and there. There are protostomes in which the blastopore forms the anus (brachiopods, for example); whether that’s because of homoplasy or because deuterostomy is actually primitive is not completely clear.
But the main point is clear enough.
1. We can’t actually recognize when fossils are ancestral and when they are not.
2. Wrong ancestor anyway. Sal wants the ancestor of birds and whatever fish is their closest relative (which relative is probably whatever lungfish you prefer), not the ancestor of all vertebrates.
Same two problems with this one:
John Harshman,
How can you validate the existence of a common ancestor without molecular or fossil evidence? How do you know what it looks like. Is it because you assume the theory of common decent is true and then you construct the common ancestor from the features of the decedents?
Well, of course we do have molecular and fossil evidence. It’s just not what you seem to think would be needed, which apparently is a molecule from the actual ancestor or fossil thereof. What we have is a well-resolved and very strongly supported phylogenetic tree relating extant vertebrates, from both molecules and morphology, as well as morphological evidence relating fossils to that tree. You could say that’s what “assume the theory of common descent is true” means, but only to the degree that when we compute the orbit of Mars we “assume the theory of gravity is true”. What you call assumption is an inescapable conclusion based on shitloads of data.
OK, so let’s “assume” that there actually is a tree. If so, we can estimate the condition at any ancestral node using any of several methods. Some of those estimates will be exceedingly good, others not so certain. The ones I have mentioned are way toward the “certain” end of the scale, which is really the best anything can be in science.
I think your idea of what constitutes good evidence and good inference in science needs adjustment.
stcordova,
Hey, there’s another egregious error in your tree: birds ought to be more closely related to lizards than to mice or chimps. Wherever did you get that thing?
I did say “candidate”, John.
John,
Yes, and to reiterate the main point, just in case Sal missed it: that single tree is the consensus tree out of more than 10^38 possibilities.
Under a hypothesis of common design, we would not expect a consensus tree. Yet we see one. The odds of that happening by chance are less than 1 in 10^38.
John Harshman,
I have seen data both for and against common decent. Until you can explain the differences in a reasonable way then assumption of truth becomes a circular argument. This theory appears way ahead of the evidence. Sals diagram that shows likeness of genes appears to be a lot more useful at this point. To start to validate the theory we would need molecular evidence where we could reconcile 2 kinds that we believe share a common ancestor. I have yet seen this done yet we assume the theory is true. As far as the theory of gravity we can reconcile the model through experimentation.
Been moving any planets around lately?
Rumraket,
Yea, and those suckers are heavy 🙂
An assumption of a particular model makes predictions you can test against additional observations.
If we assume common descent is true, we should expect to find X. We find X. Every time. Been doing that for over a century. At this stage, denial is either through some strange psychoemotional phenomenon or straight up ignorance.
This document has existed since 1999: http://www.talkorigins.org/faqs/comdesc/
You don’t have any excuses. Your ignorance looks like an act of will. Literally every issue I’ve ever seen with common descent is refuted in that document. You probably never bothered to read it. You probably just saw the title, skimmed around for a few minutes, then closed it and didn’t bother because you were told some creationist somewhere had written a response. You probably didn’t even read that either, there mere fact that a creationist had “responded” was enough for you.
Here’s what you should do: Read http://www.talkorigins.org/faqs/comdesc/
The whole fucking thing. Twice.
Well, you did. But that doesn’t help. Given the paucity of the chordate and vertebrate fossil records, it’s unlikely that we have discovered that ancestor. There is no way to recognize it in the unlikely event that we have. And that’s a “candidate” for the wrong node anyway. The important thing is that fossils, when integrated into phylogenies, can give us clues about the nature of the ancestor.
colewd,
What is it with creationists and experimentation? The experimental method is not the only way to do science. Observation works fine too. Almost nothing in astronomy or geology or the history of life is amenable to replication by experiment, and yet we know quite a bit about all those.
Here’s how science actually works: you consider the consequences of competing hypotheses and ask what data we would observe if each were true. Then you look at the data and see which one(s) are actually a good fit to the data. If there’s only one, we begin to suspect that one to be true.
I don’t know what data you have seen against common descent, but I’m open to looking at it. What do you have?
colewd:
John:
Or if they insist on thinking of science as experimental, they should recognize that often it’s nature that runs the experiments, not us. And sometimes only once.
keiths,
Or another way to say it is that experiments are nothing more than the setting up of conditions under which certain observations are more likely to be made.