I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.
Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.
If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.
One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.
Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.
That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).
Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.
The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”
So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.
So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.
CURSES! My dastardly plan was foiled!
Seriously, aren’t we getting a little paranoid here?
And you still haven’t learned anything. Remarkable.
No, we insist that you at least understand that what defines a clade is a shared trait. Like having a jaw, or vertebrae, and so on.
Yes we answered you that the nesting hiearchy isn’t defined by superficial similarity, but that a clade is defined by shared characters.
LOL, no. The “implicit claim” is that the traits of the bird are more similar to the Lungfish (than the traits of the chicken are to the Tuna), because the traits of the chicken are derived from a common ancestor shared with the lungfish more recently, than they are similar to the traits of the Tuna, because the traits shared between the Tuna and chicken diverged longer ago. Even that’s not all there is to it, because it is also the case a linage of descendants of the sarcopterygii common ancestor adapted to life on Land (causing significant morphological change away from the “typological fish-like anatomy”, meanwhile other lineages stayed in the water and so were kept more adapted to aquatic life since that time, which explains why the animals that never left the sea are still more similar to each other, than they are to their closer (chronological) relatives on land.
There is no claim, implicit or otherwise, that the Lungfish is more similar to the chicken than it is to the Tuna. You’ve managed to completely misunderstand how this works.
Please understand. The implicit claim is that the morphological and genetic distance between chickenLungfish, is smaller than the morphological and genetic distance between chickenTuna.
It is NOT claimed that the similarity TunaLungfish is smaller than chickenLungfish.
You don’t estimate similarity by branching order on a phylogenetic tree, because mere branching order won’t tell you whether the lineage has gone through some period of adaptation to a different environment.
You do that by looking at the organism.
No, we need arguing that there is convergence of independent phylogenies on a single hiearchy. Nobody has claimed it isn’t possible to construct a phylogenetic tree that shows some incongruent branches.
But while on that subject, you have failed for soon to be five thousand posts to account for the fact that there is such convergence of independent phylogenies. And you seem to have completely ignored the statistical aspect of this argument.
The accuracy of the prediction of common descent that independent phylogenetic trees will match which a high degree of statistical significance, can be verified to several hundred orders of magnitude for orders such as primates. That is how much the trees agree.
And by “which gene” and a “different tree” you mean when one picks a particular subunit from a mitochondrial protein (by mistake because one doesn’t even know that cytochrome c oxidase subunit 1 isn’t cytochrome c), and a taxon sample of about 17, you get a tree with two or three incongruent branches compared to the commonly accepted one. The statistical significance of which is P ≤ 8.601*10^-11.
Wow Sal, your COX1 incongruence is really significant.
Could it be the one converged on by 251 nuclear genes?
I did too, AND gave you a link to a website explaining the whole deal in excruciating detail.
Don’t read it though: I want you to remain confused.
So true, don’t let reality dissuade you from what you know by intuition.
Sorry I should have rephrased this. What it means is that the similarity of the trees [Sal’s COX1 tree vs “canonical” Euteleostomi] (despite the incongruent branches) is extremely highly significant.
The
most
similar?
Seriously, we’re in Robert Byers’ territory now. Who can even say if a thylacine is “more similar” to a wolf or to a kangaroo? What we can say is that the thylacine and kangaroo are more closely related to each other than the wolf is to either one, due to derived characters.
Glen Davidson
But you got a problem here. You can construct 3 clades, mutually incompatible with each other if one allows only one hierarchy.
1. Tuna and Lungfish share gills.
2. But Lungfish have lung-like organ that they share with tetrapods.
3. And the walking cave fish (actinogypterii) has a pelvic girdle similar to tetrapods.
So
1. Tuna and Lungfish (Actinogypterii and Sarcopterygii)
2. Lungfsh and Tetrapod (Sacropterygii and Tetrapod)
3. Walking Cavefish and Tetrapod (Actinogypterii and Tetrapod)
You’ll say, well a fish added a lung, and then the tetrapod removed the gill and the walking cave fish is a convergence. But those are ad hoc/post hoc rationalizaitons based on circularly reasoned common descent. Your approach aren’t constructed with wholesome structural arguments and natural groupings, they are cherry picked as exemplified by the problem above.
If you did a more comprehensive grouping, vs. the cherry picked approach, the shared characters would create these groups more natrually when a more representative set of characters are used.
1. Birds
2. Mammals
3. various fish kinds
They share vertebral columns, so they all three nest within vertebrates.
The skeletal structure is hardly superficial. If you defined the clade by shared characters, you’d put the birds in one group and the fish in the other just looking at the skeletons. They would all nest under vertebrates, however. In contrast, you and John Harshman would put the birds with the lungfish to the exclusion of the tuna.
You haven’t explained why in terms of the data. All you say is “you explained it already” when you never have. An explanation involves list of characters.
Once I started showing the skeletal diagrams, you guys suddenly started being really obtuse in your “explanations”.
I mean looking at the skeletons, they all have a spine. Fine, we form a clade with a spine. We notice the pigeons and other birds have feathered wings. So we put the two fish looking fish in the fish clade and the birds in another. You haven’t justified putting the birds (tetrapod) with the lungfish (Sarcopterygii) to the exclusion of the walking cave fish (actinogypterii).
Rumraket,
How many generations do you think the phylogenetic signal will stay intact?
Lets see if you can make the case that the convergent signal is sustainable among many generations. If not the argument is mute.
The two computers I will use as an example that nest are the mac notebook pro and the mac air. The circuits are very similar except where long term memory is concerned. One supports a mechanical disc drive and the other supports a solid state drive made of flash memory. Due to the lack of a mechanical disc drive the mac air is thinner lighter and uses less battery power.
They both share the same processor and logic circuits interactive memory circuits and other general electronics. They both are a single foldable unit with attached display and keyboard. So both have internal and external similarities and differences. Both were designed inside the same company.
Neither is currently capable of self replication 🙂
Corneel,
🙂
Well, for one thing, the pelvis of Panderichthys and Tiktaalik are more similar to the pelvis of a bird than the pelvis of a walking cave fish. And there are a lot of little characters like that, things you won’t see unless you actually look.
Let’s consider those birds. Wouldn’t feathered wings connect birds with a lot of dinosaurs? How do you deal with that? Further, what about all the characters connecting birds with other dinosaurs, other archosaurs, other diapsids, other amniotes, other tetrapods? Do you accept those groups too?
And if you accept them, what do they mean? Why are there so many groups within groups?
Going the other direction, why are there all those groups within birds? At what point does nested hierarchy for unknown reasons turn into nested hierarchy due to descent? Clearly you can’t draw a line, but why can’t you?
Perhaps because we humans tend to categorize everything into ever smaller groupings.
peace
Stereotyping does the opposite
peace
Even the ablest expositions can be resisted.
stcordova,
Okey-dokey, let’s put this claim to the test.
Here is a nice post on The Sigmodontines. One of the things I notice is a blissful lack of awareness among Creationists of the sheer variety of species in nature. They’ll think ‘rats’ and they’ll think ‘mice’. And that’s pretty much it. Well, this group are the ‘New World rats and mice’, distinct from the lab versions of these critters whose annotated genomes you may hit on a random BLAST of a mammal gene. 430 species in 82 genera (the Designer has been a busy little bee!), many lacking common names.
As Darren Naish notes in his enthusiastic post, the relations of these are ‘a confusing mess’. People can’t quite decide whether to place the group inside Muridae (the more familiar ‘rats and mice’), or whether they belong with hamsters in a sister group, or whether the whole lot, hamsters and gerbils and all, should go in Muridae. And within Sigmodontines there are a couple of competing phylogenies, which molecular data is starting to sort out but – it’s a huge group – still a work in progress.
So is this – the failure to come up with The One True Tree – seriously evidence against common descent of the clade? And does anyone seriously doubt that they nest within the rodents?
If they are not all commonly descended, how many Rodent Kinds are there? If more than one, why is the base of a Kind not visible to analysis?
And, as there is a live debate about these relations, which of the participants in this debate is using circular reasoning? They can’t all be!
Corneel,
I think we need to stop responding to requests for definitions with definitions. It only sows confusion. Mind, I tried the alternative for phunzies with phoodoo over phitness, but I was just being evasive!
One way of putting it is that the thylacine and kangaroo have a descent which is closer than each other than either of them do to the wolf, but the thylacine and wolf have a structural design which is closer than either do to the kangaroo.
Common design and common descent produce different groupings but, in their own right, each are valid ways of looking at overall patterns.
The weighing of characters is an interesting subject in itself, and I’m pretty sure subject to debate among cladists. What is interesting is when the total aggregate (to borrow a term Darwin used) of characters are subjected to phylogenetic analysis, you get a nested hiearchy. And this nested hiearchy can be compared to independently derived hiearchies from shared “putative” orthologous genes, and they converge on a very similar phylogeny.
So far, the only one who is even trying to account for this fact on a “design explanation” is Bill Cole. Though his attempts are completely nonsensical most of the time. And in the few cases they aren’t just incomprehensible blather, they’re instantly falsifiable (and have been shown to be false repeatedly).
Why are the trees so similar? Why do independent data sets converge on a very similar overall phylogeny? It follows immediately from common descent, as I demonstrated with a simple example that even had unrealistically high odds of reversal and homoplasy.
Any attempt to make my simulated example more realistic wrt gene/genome size, number of generations, and mutation rate, will really just increase the strength of the similarity between the independent gene trees (by making the odds of reversal and homoplasy smaller).
It won’t be many when the genes I made are only 20 nucleotides long, we agree on that much.
Maybe 30-40 ish generations will completely screw it up. I honestly don’t know how to calculate it, but some of the more math-savvy around here can probably easily figure that out.
I have generated a new example where the genes are 300 nucleotides long and there are five such genes for each species. That’s a 1500 nucleotide genome. Still very unrealistic, but much much bigger than my previous example.
I found a website with a nice collection of tools for doing these kinds of things which made it much easier to do it with more realistic values.
http://www.bioinformatics.org/sms2/index.html.
This time, I generated a phylogeny where there were multiple generations of copying and mutation between each splitting event. An average of ten generations happened happened between splits, and an average of one mutation happened every “generation”. That means the mutation rate was roughly 1 in 1500 (the whole genome) pr generation.
The true phylogeny looks is attached here at the bottom.
The most distantly related species at the leaves (ends of the branches) are separated by 100 generations in total. There are 100 generations between species A and M, for example.
Notice the smallest “clades” in this phylogeny.
((M,L)K)
((G,H)(I,J))
((D,E)F)
((B,C)A)
These in turn sit in larger clades, but I can’t be bothered typing that out, you can see it easily in the picture.
I then went ahead and submitted all the genes to the maximum likelihood analysis, using empirical base frequencies and 1:1 transition/transversion bias. Here’s the gene 1 phylogeny:
It is exactly correct. It is absolutely identical to the true phylogeny, all the clades are identical.
Gene 2:
Same thing, identical to the true phylogeny, and identical to gene 1.
Here are gene 3, 4, and 5 phylogenies side by side:
The clades are identical.
There is total convergence. There is zero ambiguity.
If that were the claim, there would be no problem. But Sal maintains that only one of those groupings is valid, and that is the one that every person not brainwashed by phylogenetics immediately recognises as a natural grouping.
So which one is it? The grouping of the carnivores – herbivore or the grouping of the marsupial – placental animals? Both involve designed POOFamporphies, right?
You should do an OP. 🙂
Right. We think it’s limited to beetles. I wonder where we got that idea.
Rumraket or anyone else…..
Should we expect mito chondrial gene trees in vertebrates or eukaryotic groups in general to accord with the nuclear gene trees.
But the spine is primitive not advanced so we can’t use that.
Why would you insist that Salvador understand something that is wrong? That seems slightly odd.
First, according to John, what defines a clade is monophyly.
Rumraket,
This may depend on what generation the measurement is taken. Too early you won’t have any signal as the genes will still be almost the same. To late and you will have sequential garbage. Yes, I made up sequential garbage but I think you get it 🙂
EDIT!!!!
Posted to by mistake to this thread. The reposting to the right thread is here.
EDIT!!!
I earlier posted to the wrong thread. The posting in the correct location is here:
Nope, that’s a dwarf crocodile. The true gharial is Gavialis gangeticus.
Mung,
So you read one thing Haldane says? Even as a smartass one-liner, that’s quite a fail.
We definitely should. But you must distinguish between the true mitochondrial tree and your estimate of that tree, which might not be the same thing if you have performed a poor analysis. As, in the case of COX I, you have.
Well it’s mine and no one else’s claim and I get the feeling you will have a problem with the reason why I think there are convergences and such similarities between species that are of a relatively distant relationship, and it has more to do with their inner nature than the environment in which they exist.
I’m not arguing for Sal.
I believe that evolution has an overall direction equivalent to the way that the development of an individual multi-cellular animal has an overall direction. So the marsupial – placental grouping is equivalent to the likes of the white and grey matter of the CNS, the latter being a more advanced form of the former. The carnivores – herbivore grouping would be equivalent to the phalanges of the avian fore and aft limbs, their common designs lie deeper in the formation of the individual.
Wrong. I would say with the multiple instances of novel features that converge in the various life forms that appear are in need of a more plausible explanation than that which is proposed by the theories of blind evolution. It is these theories which require them to be POOFed into existence.
I also read his “haldane’s dilemma” paper.
Yes and I even agree. I’m glad to see you’ve caught on to this, it shows you are at least thinking about what factors affect phylogenetic analysis. It is correct that if you do it too early, no mutations have happened to distinguish one orthologoue from another, and too late the whole gene has mutated so there’s no information left about it’s ancestry(at least in sequence alone).
I heard he had an inordinate fondness for rabbits in the precambrian.
CharlieM,
I was trying to communicate, rather ineffectively as it turns out, that common design is meant to be an alternative to common descent. I am happy for you that you found a way to accommodate both, but several people in this thread consider the two to be mutually exclusive.
Since John Harshman started complaining about me highlighting his teams sequencing work in his thread on crocodiles, I’ll do so here. He invited critiques of his hypothesis, but when I started trying to examine the details he whines. No good deed goes unpunished.
First the issue of mis-identfication.
I put this search in UNIPROT: “c-myc gharial”
As “c-myc” and “gharial” was the subject of the paper.
So I got this entry:
Tomistoma schlegelii (False gharial)
http://www.uniprot.org/uniprot/Q7T243
and this entry:
Gavialis gangeticus (Indian gharial)
http://www.uniprot.org/uniprot/Q7T242
So I put this “false” gharial into BLASTP and do a restricted search with “crocodiles (taxid:8493)”. The ONLY 100% coverage and 100% identity hit was:
https://www.ncbi.nlm.nih.gov/protein/AAP41723.1?report=genbank&log$=prottop&blast_rank=1&RID=3JW8HPYM013
Mecistops cataphractus (African slender-snouted crocodile)
The next closest ones were American crocodiles. Anyone doubt me can run the same blast search.
Many of the hits had John Harshman listed as lead author.
So, why didn’t “Tomistoma schlegelii (False gharial)” show up?
FWIW, many creationists think many crocodiles descended from a created kind. The morphological differences are suspected to be due to heterozysity in the ancestor that becomes specialized in the descendants.
At issue is John is building his case on 1130 bases of DNA!!!!!
Note:
So John is sampling 1130 bases out of possibly 3,000,000,000 bases to make all his inferences. So all this phylogenetic trees based on 1130 bases out of 3,000,000,000. But it does look impressive that all this analysis was done on this measily fragment:
I would think one would like a bigger sample size, and further, maybe identify genes and alleles involved in making the morphological differences. Of course, that would take time and money and resources not presently available, so instead go the easy route and take 1,130 bases out of 3,000,000,000, subject it to fancy shmancy math, all to find one measily difference in one amino acid residue out of 195 residues.
I mean, I could have told you the sequences of one measily fragment take from the “false” gharial was 99.5% similar to the one measily fragment taken out of the true gharial without all that math. But of course it looks so impressive to throw that data into PAUP* and come up with some profound looking analysis.
Given each human being is 0.5% different than any other human being, why wouldn’t we think its possible two creatures with only 0.5% difference in one measily fragment might be descended from the same created kind?
I looked at any possible hybridization experiments. That would suggest, if the creatures could interbreed, they are the same created kind.
With more data on alleles or genetic difference that cause the morphological differences, we could have an explanation for the different morphologies.
Instead, John prefers to build his case on a tiny fragment like this:
Reminds me of the proverb about observational bias:
https://en.wikipedia.org/wiki/Streetlight_effect
In sum, I would suspect the crocs descended from a common ancestor created kind. Do I know for sure? No. But I wouldn’t think looking at a measly 1130 DNA fragment that codes for only 195 amino acids will enlighten the issue that much no matter how many maximum parsimony, maximum likelihood, baysian analytics supported by a hundreds of boostratps exploring tens of thousand of possible phylogenetic trees will give much of an answer. That’s the way to pretend you actually didn’t something of value when in fact you’re extrapolating from 1130 bases an inference that might be better captured by looking at 3,000,000 bases.
No I did not!!!!!!!
I said many groupings are possible conceptually. It is one of utility. However, certain groupings based on overall similarity are more geometrically and physiologically sensible. Some groupings are absurd if one is considering the total set of possible characters (which is all the molecules in one creature compared with all the molecules in another).
I did say, phylogeneticists must in principle argue only one tree is the correct one, but they can’t ever seem to ever find THE right tree.
Here is a creationist essay that that guesses the “false” and true gharials are commonly descended from a created kind that was on Noah’s ark:
https://answersingenesis.org/creation-science/baraminology/an-initial-estimate-toward-identifying-and-numbering-the-ark-turtle-and-crocodile-kinds/
Do we know for sure if they descended from a created kind? No. Do we believe it? Doesn’t matter one way or another in the scheme of things whether one croc descended from another crock.
It does matter however if a lungfish can give rise to a Kangaroo. That I find implausible from ordinary mechanisms. It would take a miracle.
Thanks John.
A YEC Vetrinarian, Jean Lightener, has given her opinion on the Avian created kinds. She and I have a different philosophy about what creationism is. I come from the school of anti-evolutionism which is different from the Baraminologists and model builders. The baraminilogists are obsessed with identifying created kinds, anti-evolutionists (like me) are from the “don’t know, don’t care about Baramin” school of thought.
I believe Baramin exist, I don’t now exactly what they are, except to say, I doubt a lungfish and pigeon are from the same created kind.
https://answersingenesis.org/creation-science/baraminology/an-initial-estimate-of-avian-ark-kinds/
John asked about his crocodile paper:
In the opinion of the YECs at Answers In Genesis, NOTHING! So maybe for a change God might agree with something John Harshman published. Yay!
No it doesn’t if the nested-hierarchy is independently definable by POOFs with no ancestors rather than nested hierarchies definable by variations on shared genes. Common descent might explain the latter (gene trees), it doesn’t explain the former (POOF trees).
Further if the differences in the branches of the gene tree entail substantial coordinated change rather than random copying mistakes, then common descent is a pretty shaky explanation for the pattern of difference.
I gave an poignant example comparing the phosphor proteome of the Topoisomerase II protein in yeast vs. humans.
This is indicative that the amino acid differences between species entails a different Random Access Memory structure between species, not accidental changes due to copying errors.
Rumraket’s assertion on gene tree phylogeny (not morphological phylogeny)might have held some water 20 years ago, but a lot has changed in our knowledge. That’s slowly becoming an antiquated view because the species specific differences in proteins highlight regions of interest to medical researchers, such as shown below with yeast in row 1 and humans in row 2 of the topoisomerase II protein.
Click to enlarge:
http://theskepticalzone.com/wp/wp-content/uploads/2017/12/phosphorylation_comparisons_v2.png
Rumraket,
An example of the where your random mutation model fails is at a very simple level in the phospho proteome of Topoisomerse II. The locations of phosphorylation occur on the Serines and Threonines that are frequently followed by an aspartic acid “D”.
So you’ll see the dipeptide pair “SD”….”SD”…. in so many places that correspond the “S” being a location of readable/writable/erasable molecular memory. That motif of “SD” repeated over and over doesn’t look like a random copying error to me.
Please don’t be an ass. This is the wrong thread, and I wasn’t complaining about you examining the details. I complained about you posting sequences for no reason. Please take this back to the right place.
No idea why you misidentified two sequences, but it appears to have something to do with your confused method of locating them.
No, that’s not the right question. The question is why you would do such a ridiculous search on protein sequences when the data are DNA sequences, the GenBank accession numbrers are listed in the paper, and you could download the whole alignment as a unit.
Yeah, that idea of the sorting of original heterozygosity is just not tenable based on the data. What’s wrong with 1130 bases?
I see you have flooded this thread with discussion that properly belongs elsewhere. I won’t respond here any further. If you want to talk, take it to the right place. And please edit your posts down to what actually makes a relevant point. Assume I already know what sequences look like.
Dammit, stop quote-mining me to me.
Given that your number is wrong, and each human being is 0.5% different from a chimpanzee (and only around 0.05% different from another human), it appears you have just proven the humans and chimps are the same kind. Good work.
“Given each human being is 0.5% different than any other human being”
Sal,
Unless your parents are twins, I don’t think you can get 0.5% genetic resemblance…
What are your sources?