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.
Allan Miller,
Not everyone in the population Allan, some, some! Where are the SOME with traits just like the rest of their species, but also with a new trait? A group of cats in their population with a horn like growth that can eccolate. A pocket of mice that have fangs with poison. A sub-species of tigers, that have stingers forming on their ass.
If you can’t point to new features that seem to be evolving as a result of a a reproductive advantage, then why believe it EVER happened.
stcordova,
Quit with the point-scoring. It’s not a ‘taxonomy’ either, but I wasn’t referring to the diagram, but to your general use of cyt-c in your phylogenetic arguments.
There’s a number of issues here. First, 500, 1000, even 5000 years is an evolutionary eye-dropper of change. It’s a blink of an eye from an evolutionary time-frame stand point. You need tens of thousands, hundreds of thousands, and even millions of years to “see” any monumental changes and even in those time-frames whole bunches of species won’t change much if at all. Why? Because again you have to consider the environment. Something in the environment has to promote a given change. And environments tend to stay pretty stable for long periods of time. As such, once all or nearly all of the niches are filled, there’s not going to be a lot of pressure for organism variation to become fixed. I can occur – look at spotted/barred/sparred owl adaptations for instance – but you likely won’t see many.
But here’s the other problem with your issue above. You seem to think that any all changes should become “pocketed” in some sense. Why? Most changes don’t offer anything. Six and seven fingers don’t do anything for humans, so why would you expect there to be pockets of such traits?
No there should not be. There should only be continuums of traits for which there’s some selective pressure. Pepper moth shading is a great example of such a pocket. So is increase in “sparring” on owls instead of “spotting” across populations of barred and spotted owls. But things like three kidneys (which actually do crop up from time to time) are just not something that’s likely to persist unless the environment changes.
phoodoo,
If something provides a reproductive advantage, it is likely to rapidly become fixed. Widespread examples of partially-fixed advantageous traits is not an expectation of evolutionary theory.
You seem to be imagining quite large changes happening all at once as well. That, too, is not an expectation.
You seem to be criticising evolution for not providing the things that only you expects to see.
This one in particular is something I think most people really misunderstand. I think this is one of the primary misunderstandings that leads to many people not getting evolution.
It depends on what you’re trying to say. As Alan has been trying to tell you, those two words mean different things. Interspecific = between species; intraspecific = within species. Which one do you mean?
Adding a smiley to nonsense doesn’t transform it to sense. Yes, isolated populations diverge. But it takes quite a while, and by the time they’ve diverged enough to see they may well also have become separate species. And we do see divergence between isolated populations. How is this a problem?
Again, you have no clue about how we estimate the character states at ancestral nodes. Would you be interested in learning?
Taxonomy is not phylogeny; true. But phylogeny is the only explanation for the nested hierarchical structure of taxonomy, and these days taxonomy is expected to conform to phylogeny. Thus no taxonomic group “fish”, just Vertebrata, Gnathostomata, Osteichthyes, each of which could be called “fish”, and each of which includes humans. No group that includes everything you would consider “fish” does not also include humans, though certainly some groups that don’t include everything, e.g. Teleostei, don’t include humans.
Once again: BLAST is not a method of phylogenetic analysis. I cited an actual paper with an actual phylogenetic analysis. You could, if you liked, use the accession numbers given in that paper and do BLAST with them. But what do you think it would show that the tree I posted wouldn’t show better?
The really weird thing is that cytochrome c doesn’t support his claims. He’s seeing something that isn’t there.
Allan Miller,
What did it look like when the first creatures got eyes Allan (not everyone had these eyes originally right, so at some point some had them and some didn’t. And yet they were the same animal)? When the first creatures got stingers? When the first creatures got kidneys. When the first creatures starting to flap wings. If we could go back in time to when that happened, what would it look like?
There wouldn’t be every creature with a stinging like device in their population, right? Some would have top be different enough from their brothers to give them an advantage right?
What did the advantage of a rack of horns look like, to all the other creatures who first didn’t have them? What did the creatures who got the first poison fangs look like to the ones who didn’t have them yet? What did a spleen look like, before everyone had spleens?
Surely there was a time of novelty. A time when a feature looked entirely new to the population. if we could go back in time, could we see it then?
And so, in 10,000 years, when there are new features, won’t they have to start sometime, like now? What would it look like after 100 years. 500 years? When could you actually see novelty?
Never? There is never a time during the whole process when a feature looks novel compared to the others around it? Then how did it ever confer an advantage if it never was novel.
What, you mean like this:
https://www.sciencedaily.com/releases/2011/08/110802201836.htm
or this:
https://en.wikipedia.org/wiki/Odd-toed_ungulate
or maybe this:
http://water.usgs.gov/nawqa/ecology/pubs/FishSppTraits_abstract.pdf
Or this:
https://msu.edu/~swensonn/LiuEtAl_2012_pone.pdf
I’m betting none of these meet your criteria, but then I think it’s your criteria that needs adjusting and not the theory that explains the above.
Sure it is because we can actually have better molecular clocks to see the actual rates of micro-evolution and when the real MRCAs likely existed. I made a quasi testable prediction about intra specific variation in microbial species that the MRCAs will be relatively recent.
This has medical significance, and you total ignored the papers I cited to the effect that the medical community was astonished to find the actual rates of molecular evolution when they compared the ancestors in the refrigerators to the extant creatures today. It was in that same discussion where you said something about mtDNA Eve. And the other prediction of widespread astonishment at the MRCA dates of “living fossils”.
colewd,
The extract says why. You are more likely to get fusion if telomeric sequences are eroded before it happens. Each round of replication sacrifices a few bases off the ends, so they shorten with age. Therefore, post-fusion, there will be less telomeric sequence to begin with, if the fusion occurred between chromosomes with shortened telomeres.
If only there were some search tool you could use.
phoodoo,
All you are saying is ‘nothing you can ever say can convince me about evolution’. So fine, let us take that as read, shall we? What more can I say?
stcordova,
Hi Sal
I read your attachment, thanks. I agree that orphan genes are highly problematic for the UCD hypothesis. If someone is tampering with the database that is highly disappointing. I also would like to see the fussed telomere debated in more detail. An evolutionist on UD named Python was challenging Tompkins work was creating counter argument material but gave up for some reason.
There are lots of UCD debates going on at UD that contain much more detail discussion that is going on here. VJT is supporting this effort with the help of Washington university professor Joshua Swamadass. I don’t doubt that at the end of the day we may find that there are real ancestral relationships among some species but I think UCD as an over arching theory is almost certainly wrong.
You yourself just said in this discussion, if we looked at the ancestor of birds, it would look like a fish moreso than a bird. So you claim cytochrome C affirms that fish-like creatures are the ancestor of birds? On what grounds?
At best it suggests the ancestor of a bird was a bird and the ancestor of a fish was a fish, and maybe there might be some TBD vertebrate ancestor (VCA) of both birds and fish, but not that birds descended from fish any more than fish descended from birds.
The most impartial phylogeny is TBD or unspecified for the common ancestor of vertebrates, anything more is making up narratives that go beyond the limits of uncertainty imposed by the data itself. Like I said, such speculation have no utility, they are not subject to direct experimental confirmation and when the narrative is checked for consistency such as against avoiding ad-hoc use of molecular clocks, it fails on those grounds as well. There is no utility for such theories except maybe for entertainment.
I claim birds today descended from bird like creatures in the past. That’s why their cytcochrome C proteins are similar. Do you have a problem with that?
You’re the one arguing fish-like creatures were the ancestors of birds. You have to do some creative ad hoc klugery to argue a bird descended from a fish from the Dayhoff cytocrhome-C diagram.
Taxonomies (like the Dayhoff diagram) are not phylogenies, and this isn’t the first time a taxonomic analysis highlighted problems with phylogenies.
But since that diagram doesn’t include lungfish and coelecanths, perhaps we can fill in the missing pieces if someone would provide a set of accession numbers for cytochrome-C that we can all agree is a credible and then rebuild the diagram for vertebrates using Smith-Waterman or some other impartial computational comparison technique.
Like cats, perhaps.
🙂
John Harshman,
observation: is the process of collecting data through either observation.
experiment: Is the means of validating a hypothesis
Steps of the Scientific Method
Observation/Research
Hypothesis
Prediction
Experimentation
Conclusion
I’m sympathetic to Jeff’s work, but even he revised his similarity figures from 70% back up to 90% between chimps and humans.
I think there is great similarity between chimps and men and good similarity between mice and men. If we didn’t have the leverage of such similarities we’d have to be doing rather cruel experiments of genetic engineering on humans in order to elucidate our own biology. It is better we can genetically engineer flies and rats with missing limbs and other horrendous birth defects in order to understand our own genes.
I have less problem with acknowledging the substantial similarity between humans and other creatures than other creationists because I view he similarity as gift from God to help us understand ourselves.
Specifically with regard to teleomere fusion, one difficulty is the current sequencing technology. A lot of modern sequencing techniques like Illumina take the DNA of a chromosome and break it up into little segments of 300 base pairs or so. The old style Sanger sequencing (which what was used for the Human Genome project) has segments of about 700 base pairs. Then like a jigsaw puzzle these are computationally “reassembled”. No one knows the fidelity of the reassembly process, especially for Chimps. Pac Bio sequencers may help since they can sequence longer molecules. Teleomeres are extremely long, probably longer than our sequencers can handle.
All this to say, I think the whole debate is still way to premature. If I were a businessman trying to make a financial decision on who was right, I’d think to myself, there isn’t enough information, and unless there were substantial rewards for making a gamble, it’s too close to call.
Now of course personally I think there will be an issue with Chimp/Human ancestry, but I don’t think I have as good a case with that as I do with arguing against the common ancestor of bacteria and man.
I think in time we’ll get a clearer picture, and that the Orphan Gene arguments will be a better line of reasoning, plus study of human orphan genes has medical significance.
I wish I could provide you with more data to settle some of your questions, but my intuition says we don’t have quite enough today, maybe a few years from now.
Based on a cursory search, it seems to me that Sal is simply rehashing Denton’s Evolution: A Theory in Crisis
colewd,
Hard to do an experiment without collecting data and observing. And experiment is THE means of validating a hypothesis?
To do an experiment is simply to create a partially-controlled local version of a phenomenon. It is not the only means of investigating a phenomenon.
But anyways, what evolutionary experiment would you like to see conducted?
It’s pretty certain that Sal and doodoo are copying stuff from Ken Ham stupid sites, which they don’t understand and for which they lack the knowledge to evaluate.
I sit here lurking, wondering if they will ever come up with something that isn’t copied from a creationist site. And older than dirt.
stcordova,
You don’t have to rely on sequencing. You can create an RNA probe. Attach a dye and voila! There they are, glowing like things that aren’t really there. Or use PCR primers, or sequence-specific restriction enzymes.
No idea whether anyone has***, but probing for intra-chromosome telomeric sequence does not seem like a particular technological problem awaiting NGS.
*** [eta – yes, of course they have. I used a secret method I am not at liberty to divulge to detect this].
colewd,
Yet the evidence for common descent is many, many orders of magnitude better than the evidence for separate creation. It’s been pointed out to you, but you and Sal have ignored it. Why?
That’s a rhetorical question. The answer, as we all know, is religion. Dogma trumps evidence for you and Sal, and you will continue believing the most ridiculous things against a mountain of contrary evidence if dogma demands it.
It’s a terrible way to live.
colewd,
For your convenience, here are my questions again:
Why is God so determined to make it appear that common descent is true? Why is he obsessed with mimicking evolution to a precision of dozens of decimal places?
And why not draw the obvious conclusion — the same conclusion drawn by intelligent and scientifically literate folks whose brains aren’t addled by religion? The evidence overwhelmingly supports common descent because common descent is true.
Separate creation, like the other forms of ID, is a fantasy. It’s completely undermined by science.
stcordova,
I agree this hypothesis has hurdles
-missing genes that are present in other species
-chromosome count difference
-number of proteins with different sequences
-alternative splicing differences
-gene expression differences
Well, when you put it that way, the gap between Chimps and Man does look unbridgeable. 🙂
Is any of these in any way a “hurdle”? There is a clear and well-known mechanism for each. Gene loss is common. Chromosomal fusion (which we have already discussed!) accounts for the difference, and in fact explains all the data better than whatever your alternative might be. Simple mutation and fixation at credible rates explains the protein differences. I don’t know about differences in alternative splicing (in fact I think it isn’t as common as some think), but it’s the sort of thing that small mutations can account for. Same with gene expression differences; they’re expected.
Now put that against the clear nested hierarchy within primates, the nature of the various differences, which are well within expected parameters for a separation of a few million years, the biogeographic consistency with the fossil record, and the fossil record itself. If you didn’t have a prior commitment to separate creation of humans, presumably within the last few thousand years, the answer would be obvious.
This seems to be an explanation only for similarity between humans and other creatures. But other creatures are also similar to other creatures. Are chickens similar to peacocks to help peacocks understand themselves? Are acacia trees similar to fave bean plants to help the fava bean plants understand themselves? An explanation that works only for one species should be a suspect explanation. On the other hand, common descent presents an immediate explanation for the pattern of similarities and differences among all species. Better.
I said nothing about “the ancestor of birds”; it isn’t even clear what you mean by that. I was talking about the common ancestor of birds and their closest living non-tetrapod relatives, lungfish. Now, your cytochrome c table doesn’t have any lungfish so far. What it does have is several teleosts and a lamprey. We can work with that. If we assume a good enough molecular clock, we can even use the distances as is. That assumption is generally unwarranted, but work with me anyway. The lamprey is more or less equidistant from all the other vertebrates in the table. Therefore those vertebrates are a clade to which the lamprey is sister. The various tetrapods are more or less equidistant from all the teleosts. Therefore the tetrapods are a clade to which the teleosts, also a clade, are sister. If you imagine just that tree, and try to suppose how to map “fishiness” onto it, you will see that fishiness arose in the ancestral vertebrate and was lost (transformed to tetrapodiness) in the tetrapod ancestor. It would be conceivable that fishiness was gained twice, independently, in the lamprey and teleost ancestral lineages, but that’s less parsimonious as a hypothesis. If you added some sharks, lungfish, and coelacanths to the table, and if there were still a molecular clock, you would find them all on branches that would force even more independent origins of fishiness if you insisted on the bird-fish ancestor being non-fishy. In a nutshell, that’s how it works.
Word salad. If you’re trying to say that the most recent common ancestor of all birds was a bird, that’s certainly true. If you’re trying to say that the most recent common ancestor of all fish was a fish, that’s true also. But the most recent common ancestor of all fish is also ancestral to birds. If a lamprey is a fish, that’s true from the cyt-c table. If a lamprey isn’t a fish, you’d have to add some fish that aren’t acanthopterygians to see that, because teleosts are not enough to test the assertion.
And now we see a list of buzzphrases I have complained about before:
Ancestral state estimation is not speculation; it’s an objective conclusion based on algorithmic optimization of data onto trees that were themselves algorithmically constructed from data.
Direct experimental confirmation is not the gold standard of science; all science is inference from observation, whether that observation results from experiment or otherwise.
You are the one making ad-hoc use of molecular clocks, as your use exclusively of BLAST to make claims about phylogeny requires. As I have pointed out, real phylogenetic analyses make no such assumption.
No. It’s true. You seem not to be aware that there are groups within groups, and similarities within similarities. All birds form a group; that group is part of Amniota, which forms a group; that group is part of Tetrapoda, which forms a group; that group is part of Osteichthyes, which forms a group, and includes mostly fish. Also, because the first several basal divergences within Osteichthyes, on the lineage leading to Tetrapoda, are fish, the clear implications that tetrapods are descended from fish. The fossil record confirms that.
Not the ancestors. Birds had many ancestors at various levels of the tree. Some ancestors, i.e. the ones rootward of Tetrapoda. The cytochrome-c table tells us that if lampreys are fish and we assume a clock. If we don’t assume a clock, we need to do an actual phylogenetic analysis, which can be done with distances if you must. You need to look at a few outgroups outside vertebrates, but I’m pretty sure it would work out to give the standard tree. Again, adding some different fish would help, and you still wouldn’t want to assume a clock.
First, that diagram isn’t a taxonomy. A taxonomy is an indented list of taxa within taxa. What you have there is a distance matrix. Second, I don’t understand what the problem with phylogenies highlighted by that matrix might be. Can you explain?
Pretty sure the cells of that table are just a count of the number of sites that differ between the two species. No need for any other comparison technique. Distance measures are not the first choice for phylogenetic analysis, but they can be better than nothing. Try neighbor joining as a first shot. I believe PHYLIP would do that for you.
Just so you know, I have no idea what that or anything else in that post was supposed to mean.
DNA_Jock,
Leading somewhere Jock! Progressing, get it??
Let’s take your implied premise of evolution, that this can go somewhere. That this can lead to novelty.
First, can this mutation even be passed along.
Second, many of you whacky evolutionists now subscribe to the neutral theory; that this can drift for a while, as long as it causes no harm (until the one day when it becomes really useful!). So show me Jock, where are the pockets of cats with these kinds of mutations, the beginnings of a new lineage? Are they out there, and we just haven’t studied them enough to know? is that what you believe Jock?
We know that animals get mutations Jock. So since they have been getting mutations for centuries, where are some new lines that are forming, some new branches of evolution, that are in their infancy, just like the eyeball was?
Maybe you are as bright as Robin, and you think poodles are that, huh? One day poodles can become a new class of animal, a big ball of fur that uses wind as a locomotion to tumble through the deserts and collect food on its fur.
Your theory sure does its best to hide itself, until it becomes magically complete. Or maybe this cats descendants really will develop thumbs. Then they will be about as smart as you.
keiths,
Well, Jock seems to think that Natural Selection is also obsessed with hiding itself.
The best he can find are lone cats with extra toes. I guess he figures one day these toes will shoot electric webs that catch predators and also can get broadband.
Where does blue stop and red start, Phoodoo?
Richardthughes,
Oh that is so profound Richard. There are spectrums of colors, and thus there are spectrums of cats that can shoot electric webs.
Only I am only seeing one cat. Where the hell did the spectrums go?
Ooh phoodoo, the GSW’s to the lower extremity continue.
You posited, sarcastically,
So I answered “Like cats, perhaps.” with a smiley, and a picture of a cat with polydactyly.
Your riposte:
Yes, yes it can.
ROFL
Where are the ‘pockets of cats’ with these kinds of mutations? To answer your mocking question: in Cardigan (Wales), in Southwestern England and along the Eastern seaboard of North America (in particular Boston, Maine and perhaps most famously, in Key West — “Hemingway’s Cats” FFS!)
Just because YOU haven’t studied them enough to know, doesn’t mean that others are equally ignorant.
My cat was a stray.
ETA: I don’t know anything about electric webs, but my high school buddy who was born polydactyl was a REALLY good scrum-half.
The man who killed my father had six fingers.
I had a dac cat. He had a near death experience. Ate one of our poisonous lizards and stopped breathing. Petting made him purr, and after an hour or so, he started up on his own.
After that, we called him 8 1/2, figuring he’d used that many of his lives.
phoodoo,
Why isn’t blue next to red? When will red make a blue?
DNA_Jock,
When we first moved to the Languedoc, we adopted a stray* with a truncated tail. My wife asked the vet to check for infection, assuming some kind of trauma. Turns out stub-tailed cats are common here. I wonder about whether the mutation is dominant or recessive and whether there is an overall selective pressure for short tail.
*Best cat ever!
How many people subscribe to your theory phoodoo? Just the one is it? You?
Phoodoo has a theory? 😯
But nobody is saying there is a spectrum of cats BECAUSE there is a spectrum of colours. The colors blending into each other is an ANALOGY to the features of organisms. It could be the size, position or shape of limbs. It could even be the color of fur or what have you. You understand how ANALOGIES work, right?
Here’s a lizard on it’s way to becoming a snake. There are many extantly living organisms that are in this transition, with various stages of body-length and size of libs. Just google “nake with legs” or “lizard snake” and look at the pictures.
Here’s a frog (Ascaphus) in the process of evolving a tail, it lives in fast-flowing streams where the extension at the end helps with stability and locomotion when it swims in strong currents.
Handfish. Are they developing into bona fide forelimbs with hands on them? Who knows, I can’t travel in time.
But this is what you asked for.
But what use is half a tail?
Nitpick: individual frogs don’t evolve.
Is the Axolotl in the process of becoming fully aquatic, or more terrestrial? Who knows? Do you think it will stay forever as it is and how could you possibly know this?
There are salamanders that are clearly much more adapted to terrestrial life than others, which can stay on dry land for much longer periods of time without being in or near water. Were they all created as-is? Or did they evolve various degrees of adaptations to terrestrial or aquatic lifestyles?
True. I mean’t as a species, the population as a whole has adapted.
Edit: How do you remove a picture once posted? There isn’t supposed to be one in this post.
Rumraket,
I didn’t doubt it. It’s just I often see folks like phoodoo attack a strawman version of evolution.
Are Elephant-seal limbs in the process of adaptation to aquatic life? Will they become less and less like legs and more and more like fins and flippers? How do you know?
Are Sea-otters becoming more and more adapted to an aquatic lifestyle? Are seals even more aquatic adaptations of prehistoric Otter-like organisms?