Common Design vs. Common Descent

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.

3,738 thoughts on “Common Design vs. Common Descent

  1. John Harshman:

    Define “blew up”.

    Perhaps a picture will explain. I’ll post it in a bit.

    Thanks again.

  2. Alright, here goes nothing. I downloaded the cytochrome c protein alignment from unitprot:
    http://www.uniprot.org/align/A2017111048CF0A2DF181CEB7EC2BC48F8F5F3B059871B1K.aln.

    Uploaded it to an online maximum likelihood phylogenetic tree-service here:
    IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.

    Put E coli as the outgroup, didn’t touch any other of the default settings, and got this result. https://i.imgur.com/XIHJJBf.jpg

  3. Identity and coverage of some selected pairs of Cytocrome-C COX1:

    Accession numbers:

    Lungfish: P_387474.1
    Coelecanth: BAF43538.1
    Salmon: NP_008447.1
    human: AEG23663.1

    now some comparisons:

    Lungfish vs. Salmon : 99% coverage 95% identity
    Lungfish vs. human: 98% coverage 85% identity
    Salmon vs. human: 99% coverage 87% identity
    Colecanth vs. human: 99% coverage 86% identity
    Lungfish vs. Coelacanth: 99% coverage 93% identity

    Given the Salmon and Lungfish are closer to Lungfish and Coelecanth, it will likely give a low confidence tree trying to resolve the structure of teleostomi.

  4. Ok, as I thought, the Teleostomi clade doesn’t have good resolution with the Cox1 gene except to say, in the 99% confidence interval, Tetrapods should be excluded from Teleostomi. That’s how I read it. It confirms my claim, mammals aren’t fish. I force-rooted the tree with a shark as outgroup, per John’s request, something I protested, but I did it anyway.

    First the caption of the cladogram:

    Figure. Molecular Phylogenetic analysis by Maximum Likelihood method
    The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [1]. The tree with the highest log likelihood (-3516.8986) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 17 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 513 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [2].

    1. Jones D.T., Taylor W.R., and Thornton J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282.
    2. Tamura K., Stecher G., Peterson D., Filipski A., and Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution30: 2725-2729.

    click link below to enlarge:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/v2_ml_550boot.png

  5. Sal announces:

    It confirms my claim, mammals aren’t fish.

    Ponder the multiple levels of idiocy wrapped up in that statement.

  6. Just for grins, I present the UPGMA pure distance tree. I at first guessed it would create the most Linnaen-looking arrangement. It didn’t. It probably won’t help the Baraminologists, or maybe it will. I don’t know.

    Figure. Evolutionary relationships of taxa
    The evolutionary history was inferred using the UPGMA method [1]. The optimal tree with the sum of branch length = 0.57733391 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (550 replicates) are shown next to the branches [2]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method [3] and are in the units of the number of amino acid substitutions per site. The analysis involved 17 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 513 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [4].

    1. Sneath P.H.A. and Sokal R.R. (1973). Numerical Taxonomy. Freeman, San Francisco.
    2. Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.

    click for to see larger image:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/v2_upgma_550boot.png

  7. This is the Minimum Evolution phylogenetic tree, with shark as outgroup.

    Figure. Evolutionary relationships of taxa
    The evolutionary history was inferred using the Minimum Evolution method [1]. The optimal tree with the sum of branch length = 0.57498119 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (550 replicates) are shown next to the branches [2]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method [3] and are in the units of the number of amino acid substitutions per site. The ME tree was searched using the Close-Neighbor-Interchange (CNI) algorithm [4] at a search level of 1. The Neighbor-joining algorithm [5] was used to generate the initial tree. The analysis involved 17 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 513 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [6].

    1. Rzhetsky A. and Nei M. (1992). A simple method for estimating and testing minimum evolution trees. Molecular Biology and Evolution 9:945-967.
    2. Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.

    click to see enlarged image:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/v2_me_550boot_shark_rooted.png

  8. We may dismiss the rooting of both of these latest trees from Salkvador. The distance matrix tree has such low bootstrap supports that most of the important interior branches are very ill-supported. The other tree (parsimony, as I recall) has only 35% bootstrap support on the one branch that conflicts with conventional trees for these groups, and only 50% support for the lungfish-coelacanth clade.

    The correct rooting (from other trees by other people) will be on the branch that connects the shark/ray clade to the rest of the tree.

    Sal is also yet to reveal to us how “taxonomy” is determined without reference to phylogenies.

  9. Joe Felsenstein,

    Thank you for you comment, but this diagram shows 99% confidence that the tetrapods don’t belong anywhere around the fish

    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/v2_ml_550boot.png

    It seems to me no matter what phylogenetic method is applied, it’s going to have to contend with the fact that mammals look the most remote of the groups relative to lungfish. But we keep hearing in the press we’re so close to lungfish. As far as Cox1, we aren’t:

    Lungfish vs. Salmon : 99% coverage 95% identity
    Lungfish vs. human: 98% coverage 85% identity
    Salmon vs. human: 99% coverage 87% identity
    Colecanth vs. human: 99% coverage 86% identity
    Lungfish vs. Coelacanth: 99% coverage 93% identity

    So, yes the interior nodes look awful, but isn’t there 99% confidence the mammals don’t belong anywhere near the lungfish. That is superficially also what the above distances suggest.

  10. John Harshman,

    Regarding your question as to what I meant when I said Gallus gallus blew my cladogram up — perhaps a picture is worth a thousand words.

    The accesion number is BAD11116.1, why the prefix “BAD”? Does that mean something?

    Some default BLAST comparisons:

    Lungfish vs. Chicken: 98% coverage 90% identity
    Human vs. Chicken: 99% coverage 86% identity
    Salamander (YP_626701.1) vs. Chicken: 99% coverage 89% identity
    Salmon (NP_008447.1) vs Chicken : 99% coverage 99% identity
    Coelecanth (BAF43538.1) vs Chicken: 99% coverage 89% identity

    I try to start with the something not computationally intensive compared to Maximum Likelihood. So here is the Neighbor Joining Tree even before I could root it with the shark.

    Figure. Evolutionary relationships of taxa
    The evolutionary history was inferred using the Neighbor-Joining method [1]. The optimal tree with the sum of branch length = 6.68512784 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (550 replicates) are shown next to the branches [2]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method [3] and are in the units of the number of amino acid substitutions per site. The analysis involved 18 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 513 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [4].

    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/chicken_nj.png

  11. The first nice paper on the topic was in 2004 published by the society of molecular biology and evolution of which Joe Felsenstein was president at one time.

    https://www.ncbi.nlm.nih.gov/pubmed/15128875

    The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear genes.

    Abstract
    The origin of tetrapods is a major outstanding issue in vertebrate phylogeny. Each of the three possible principal hypotheses (coelacanth, lungfish, or neither being the sister group of tetrapods) has found support in different sets of data. In an attempt to resolve the controversy, sequences of 44 nuclear genes encoding amino acid residues at 10,404 positions were obtained and analyzed. However, this large set of sequences did not support conclusively one of the three hypotheses. Apparently, the coelacanth, lungfish, and tetrapod lineages diverged within such a short time interval that at this level of analysis, their relationships appear to be an irresolvable trichotomy.

    A quick look at the paper and I wasn’t able to see the gene names and accession numbers. But, I’ll move on to a more recent paper. I just that posted that for reference.

  12. This is the more recent paper including the gene names it used for the study:

    https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-4-49

    My comment on the cladogram in the paper? The scaling is a little misleading. There is a bigger gap between the coelacanth/lungfish clade vs. the near fish clades. The major difference between by Cox1 diagram and this one is the relative positioning of the fish, but it is clear even from the diagram the fish and tetrapods split, tetrapods aren’t fish any more than humans are insects as shown in this cladogram:
    https://cdn.thinglink.me/api/image/658283169543356417/1240/10/scaletowidth

    But anyway, here is the diagram in the paper that studied 43 genes. I may look at a few in that paper:
    2F1756-0500-4-49/MediaObjects/13104_2010_Article_804_Fig2_HTML.jpg

  13. Sal: whether we are “close to” fish, and whether we “really are” fish is irrelevant to the main point: your own tree shows that we have more recent common ancestors with coelacanths, and with lungfish, than we do with salmon or tuna.

    Making a monophyletic group then mandates putting us tetrapods in the same clade as lungfish and as coelacanths. If you want to call those “fish” feel free. But then there is a clade that includes salmon, tuna, lungfish, coelacanths, and all tetrapods. The common ancestor of that clade is also then something that, if you saw it, you would say “fish”. There is a larger, more inclusive clade that also includes the sharks and rays, and if you call them “fish” too you get an earlier common ancestor, a placoderm, that you would also call a “fish”.

    One can go on and ask whether you would call a lamprey or a hagfish a “fish”.

    All this has been explained to you a zillion times, to little avail. People are bailing out of the discussion, so you will probably be able declare victory.

    Now, as to “taxonomy”, we have not yet heard how you would do it without referring to reconstructions of the phylogeny. Let us know. You can’t ask Linnaeus as, alas, he is inconveniently dead. (By the way, late in life Linnaeus started to wonder whether some of the closely similar species might not be genealogically related).

  14. Joe Felsenstein:

    Now, as to “taxonomy”, we have not yet heard how you would do it without referring to reconstructions of the phylogeny.

    Thank you again for your time.

    My answer to your question is based on shared characteristics.

    Plants share characteristics with other plants that they don’t share with animals. Same for animals. Within animals we have those that share the characteristics of vertebrates. Within vertebrates there are some that have characteristics of ray-finned fish, some the characteristics of amphibians, some the characteristics of mammals. Mammals share the characteristic of mammary glands. So like Linnaeus we can often group things together based on shared characteristics.

    Hence, I like the Transformed Cladists and the Pheneticists.

    At the molecular level, the taxonomies are defined in terms of almost pure structure and chemical and physical function. They are frequently arranged hierarchically, but the hierarchies being conceptual are not unique and are mostly created out of utility. In fact, I’m finding some of the classifications pre-dated any attempt at phylogeny.

    So we may or may not be able to put things in a hierarchical structure unequivocally. Does it really matter in the scheme of things whether we do or we don’t find an unequivocal way of arranging them in a hierarchy?

    Now, I’m really not trying to be combative, but I’m just pointing out something that can be confirmed by further investigation of gene banks as I am doing.

    Some people come out and say we’re close to lungfish or coelecanths, the creatures supposedly in the Sarcopterygiian clade. I find it really bothersome that within vertebrates, for some genes, the most sequence-divergent lines are humans vs. Lungfish or humans vs. coelecanths. It seems straining at gnats to say whether the coelacanth or lungfish is more sequence related to tetrapods, when the sequence distance between them and tetrapods is among the widest in the vertebrates. So cladograms like this don’t even seem consistent with molecular data:

    https://en.wikipedia.org/wiki/Teleostomi

    Whereas this hierarchical arrangement I find more pleasing:
    https://en.wikipedia.org/wiki/Vertebrate

    Class Agnatha (jawless fishes)
    Class Chondrichthyes (cartilaginous fishes)
    Class Osteichthyes (bony fishes)
    Class Amphibia (amphibians)
    Class Reptilia (reptiles)
    Class Aves (birds)
    Class Mammalia (mammals)

    The gene data may or may not reconstruct the Linnaen Hierarchy. We’ll see, but I would presume Mammals have genes that birds don’t and vice versa. There are also transposable elements and introns, etc that distinguish groups.

    But I found this paper that even uses the word CREATION!
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1762380/

    Lineage-specific Gene Families

    2,278 gene families are found in only a subset of extant taxa and likely arose more recently (Table 1; “Creations”).

    And as far as the coelacanth and lungfish tetrapod issue, we don’t have to do just gene-tree phylogeny, we could survey which genes are in the tetrapods only and vice versa. Isn’t that a measure of distance too?

    So we can do taxonomy base on shared characters of extant organisms. We may or may not be able to arrange them in an unequivocal hierarchical relationship. If there are multiple conceptual hierarchies of things, as there are in the world of protein taxonomy, that doesn’t seem like a bad thing personally.

    There was a paper advocating a Linnaen approach to protein taxonomy:
    https://www.ncbi.nlm.nih.gov/pubmed/11988462

    Abstract

    Genome sequencing and structural genomics projects are providing new insights into the evolutionary history ofprote in domains. As methods for sequence and structure comparison improve, more distantly related domains are shown to be homologous. Thus there is a need for domain families to be classified within a hierarchy similar to Linnaeus’ Systema Naturae, the classification of species.

    Thanks any way for your time.

  15. Joe, to Sal:

    All this has been explained to you a zillion times, to little avail. People are bailing out of the discussion, so you will probably be able declare victory.

    Boring people to death won’t constitute a scientific victory for Sal.

    And of course, the elephant is still in the room. Sal cannot explain, and will never be able to explain, why the Designer mimics common descent to a precision of dozens of decimal places.

    “Common design” is a non-starter. It collapses under the weight of its ridiculous assumptions.

  16. stcordova: Plants share characteristics with other plants that they don’t share with animals.

    But I have heard from a reliable source that plants have ovaries, so I guess they should be grouped with vertebrates based on that character.

    Other decisions are more complicated though. Are rhinoceroses to be grouped with elephants? And do hyena’s go with cats or with dogs? Can I group harvestmen with spiders?

    stcordova: So we may or may not be able to put things in a hierarchical structure unequivocally. Does it really matter in the scheme of things whether we do or we don’t find an unequivocal way of arranging them in a hierarchy?

    Yes it does, you claimed that the TAXONOMY is real, not an arbitrary construct. If this is true, you should be able to tell us what it is.

  17. stcordova: So we can do taxonomy base on shared characters of extant organisms. We may or may not be able to arrange them in an unequivocal hierarchical relationship. If there are multiple conceptual hierarchies of things, as there are in the world of protein taxonomy, that doesn’t seem like a bad thing personally.

    That means you reject the objective nested hierarchy, and we are done discussing common design, right?

  18. stcordova:
    Joe Felsenstein,

    Thank you for you comment, but this diagram shows 99% confidence that the tetrapods don’t belong anywhere around the fish

    And here we have Sal Cordova disagreeing with Joe Felsenstein about interpretation of phylogenetic bootstrap numbers. That alone is worth the price of admission. No, Sal, the 99% bootstrap is for sharks vs. everything else.

    It seems to me no matter what phylogenetic method is applied, it’s going to have to contend with the fact that mammals look the most remote of the groups relative to lungfish. But we keep hearing in the press we’re so close to lungfish.

    You don’t know what “close” means in phylogenetics. It refers to cladistic relationships. Raw distance measures are not relevant.

    So, yes the interior nodes look awful, but isn’t there 99% confidence the mammals don’t belong anywhere near the lungfish.That is superficially also what the above distances suggest.

    Again, you misread both the 99% and the portent of the distances.

  19. stcordova,

    Regarding the chicken: either that isn’t Cox I or you have a very, very bad alignment.

    Ah, I believe I may have a solution to your chicken problem. The chicken sequence (probably all bird sequences) has a one-residue insertion very early in the sequence, and I suspect that your alignment is totally screwed up after that, because you haven’t inserted gaps in the other sequences. Am I correct?

  20. stcordova: Here is a cladogram. It’s worth pointing out, the arrangement does not at all mean humans descended from birds or birds from insects:

    Well, we can be glad that you have figured that out, at least.

    My comment on the cladogram in the paper? The scaling is a little misleading. There is a bigger gap between the coelacanth/lungfish clade vs. the near fish clades. The major difference between by Cox1 diagram and this one is the relative positioning of the fish, but it is clear even from the diagram the fish and tetrapods split, tetrapods aren’t fish any more than humans are insects as shown in this cladogram

    There is no scaling in that tree; the branch lengths have no meaning. And it’s clear from the diagram that tetrapods are more closely related to lungfish and coelacanths than to teleosts, which means, if you had the wit to understand it, that tetrapods are descended from “fish”, i.e. they are embedded in the “fish” clade.

  21. Mung, quoting Joe:

    Sal: whether we are “close to” fish, and whether we “really are” fish is irrelevant to the main point:

    Mung:

    So monophyly doesn’t really matter. Thanks for that.

    Christ, Mung. Joe addressed that immediately afterward:

    Sal: whether we are “close to” fish, and whether we “really are” fish is irrelevant to the main point: your own tree shows that we have more recent common ancestors with coelacanths, and with lungfish, than we do with salmon or tuna.

    Making a monophyletic group then mandates putting us tetrapods in the same clade as lungfish and as coelacanths. If you want to call those “fish” feel free. But then there is a clade that includes salmon, tuna, lungfish, coelacanths, and all tetrapods. The common ancestor of that clade is also then something that, if you saw it, you would say “fish”. There is a larger, more inclusive clade that also includes the sharks and rays, and if you call them “fish” too you get an earlier common ancestor, a placoderm, that you would also call a “fish”.

  22. Joe:

    You’re being too hard on Mung. You just have to realize that a rapid rejoinder is Mung’s highest priority.

    If he’s going to make a fool of himself, he might as well do it quickly, I guess.

  23. John Harshman:

    And here we have Sal Cordova disagreeing with Joe Felsenstein about interpretation of phylogenetic bootstrap numbers. That alone is worth the price of admission. No, Sal, the 99% bootstrap is for sharks vs. everything else.

    That was my way of trying to get a response whether I’m right or wrong in the way I’m reading things. I only get 2.5 lectures on phylogenetics as that is only a small part of my bio-informatics class, and here is the chance to supplement my understanding. So thank you for showing me how to properly read as I was misreading.

    Hardly anyone reads this blog, including creationists, most won’t even understand the topics we’re talking about even if they did read it. This is my chance to learn things outside of formal training and take angles that aren’t easily explored in a formal context such as the exploration of nylonases. About the only satisfaction you get is to hear my wrong notes during practice and tinkering sessions as I try out new ideas.

    But you’re the one who wants to insist putting sharks at the root. Look what happens when I make humans the outgroup. When that is done you get a value of 100 below Kangaroos. Does that mean the Tetrapod Kangaroo and everything else below it is 100% confidence. Thanks for proving Kangaroos aren’t in the Sarcopterygiian nor the Teleostomi clade. Kangaroos are mammals they aren’t fish, and with humans (the most sequence distant from the lungfish) are put as the outgroup, you show Tetrapods don’t belong in the Teleostomi nor the Sarcopterygiian clades.

    You don’t seem to be the least bit bothered how the nested hierarchical trees can be redrawn at the whims of the investigator to make it fit his foregone conclusions.

    John Harshman:

    Raw distance measures are not relevant.

    Howler. You need distances that are close enough to suspect homology, distance suggest the closeness of a relationship.

    The distances values are subject to the metrics embedded in the distance measuring techniques, so different distance techniques deliver different distance estimates. But for a given distance metric, a sequence is fundamentally either more similar or more dis-similar than another sequence, so they should have some priority over phylogenetic distances. Why? Look at all the different kinds of nested hierarchical trees that can be drawn from the same data set. That’s not very reassuring about the ability to make inferences about the supposed (mythical) deep past.

    You’ll complain the signal is unresolvable, the coelacanth-lungfish-tetrapod relation is an unresolvable trichotomy, whatever. So just say you don’t know, but you only believe despite the fact you don’t know. Don’t posture like you really know.

    click to enlarge
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/kangaroo.png

  24. Here is something about outgroups, and the problem of circular reasoning:

    https://en.wikipedia.org/wiki/Outgroup_(cladistics)

    he best outgroups satisfy two characteristics:

    They must not be members of the ingroup.

    They must be related to the ingroup, close enough for meaningful comparisons to the ingroup.

    Therefore, an appropriate outgroup must be unambiguously outside the clade of interest in the phylogenetic study. An outgroup that is actually nested within the ingroup will, when it is used to root the phylogeny, result in incorrect conclusions about phylogenetic relationships and trait evolution.[3] In molecular phylogenetics, satisfying the second requirement typically means that DNA or protein sequences from the outgroup can be successfully aligned to sequences from the ingroup.

    So we assume the fossil record is old and that humans evolved from a common ancestor with sharks, but sharks first. You’ll get a certain phylogeny. But if you assume humans are first and through a process of reductive evolution sharks evolved you get a different phylogeny.

    Here is one problem with using sharks:

    Shark to Human: 98% coverage 87% identity
    Shark to Lungfish: 99% coverage 92% identity

    To argue Sharks actually qualify as an outgroup one has to invoke faster molecular clocks for the tetrapods. On what grounds is this invoked? Foregone conclusions. Not any direct empirical measurement.

    A different choice of outgroup gives a different phylogeny. That’s the problem. There are too many adjustable parameters.

  25. Rather than using BLAST, I realized I could use the Jones-Taylor-Thornton (JTT) or any other distance meteric I choose in MEGA 6.0, and it creates distance matrices. Because evolutionists believe Nautlius is outside the clade of teleostomi, I added it.

    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/jones_taylor_thornton_distances.txt

    Looking at it, unless one really wants to impose a forgone conclusion and interpretation of the fossil record, it casts doubt on using Sharks as an outgroup.

    Consider the criteria of Outgroups and whether sharks unequivocally qualify:
    https://en.wikipedia.org/wiki/Outgroup_(cladistics)

    I’d say using the shark, in light of the JTT distance matrices is suspect.

    Instead I used Nautilus for starters and am doing some runs. Given that creationists don’t believe in Universal Common Ancestry, of what use are phylogenetic methods.

    First off, even creationists which to do taxonomic classification. This could be either a convenience way of looking at things or it could be seeing actual patterns that God designed. The one who coined the word “Homology” was the creationist Richard Owen. If God really designed an absolute hierarchical arrangement, then phylogenetic methods will recover this hierarchy. However, I don’t believe the hierarchies are absolute and unequivocal? Why? Remember the flower diagram — humans share genes with chickens and no one else. Even from a creationist standpoint, such patterns will resist imposing an unequivocal absolute hierarchy, we can only make an approximate one. Perhaps that was God’s intention…

    But, some preliminary runs with Nautilus as the outgroup recovered a nice looking approximation of the Linnaen classifications. Since creationists don’t believe in Universal Common Ancestry, the every adjustable parameters of phylogenetic methods are not that troubling, the adjustable parameters are merely lenses for different ways of conceptually organizing God’s creation.

  26. Below is the phylogenetic tree using Nautilus as outgroup. Nautilus is in the phylum molusca in contrast to every other animal represented in the phylum choradate. I guess next round I could try the chordate Tunicate which is not a vertebrate.

    Anyhow this shows how phylogenetic methods can lead creationists to the Disney World of Baramaminlogy and the rebirth of Linnaen Classification based on structure.

    With respect to Cox1, with Nautilus as the out group it recovers approximately the Linnean hierarchy which puts tetrapods outside of the Sacropterygiian and Teleostomi clade. This is also nicely in accord with the constraints of the Jones-Taylor-Thornton distance matrices I linked to earlier.

    I guess I need to add some jawless fish to fill see how well the Linnaen hierarchy is recovered.

    I and some other creationists like Cornelius Hunter and Walter ReMine don’t believe that an absolute unequivocal hierarchy can be imposed on the patterns of similarity diversity in biology. The hierarchy appears on a gene by gene basis, and each gene has a different hierarchy. ReMine argues that these conflicting hierarchies are evidence against Universal Common Ancestry but are also evidence of Common Design.

    Class Agnatha (jawless fishes)
    Class Chondrichthyes (cartilaginous fishes)
    Class Osteichthyes (bony fishes)
    Class Amphibia (amphibians)
    Class Reptilia (reptiles)
    Class Aves (birds)
    Class Mammalia (mammals)

    Here are the parameters of the model for the diagram below:

    Figure. Molecular Phylogenetic analysis by Maximum Likelihood method
    The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [1]. The tree with the highest log likelihood (-5102.4301) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The analysis involved 18 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 510 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [2].

    click for enlarged image:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/nautilus_outgroup.png

  27. John Harshman and others here are arguing for the idea tetrapods have fast molecular clocks and by way of implication the Coelecanths and Lunfish slow ones.

    How does that square with the Jones-Taylor-Thornton matrices created with Tunicata (a chordate, but not a vertebrate):

    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/tunicata_jtt.txt

    The number of changes against human is SMALLER! Look at the differences in distance between Lunfish and Colecanths and the other fishes. You want to invoke slow clocks for the fish-to-fish differences, but then when you compare them to the tunica/vertebrate divergence you have a fast clock fish to tunicate clocks. You can’t have a fast clock and slow clocks at the same time in terms of molecular clocks. It’s inappropriate to apply General Relativity as an explanation. Reductio Ad Absurbdum.

  28. OK, so I got a tunicate as the outgroup. Tunicates are Chordates and not veretebrates. The other creatures listed are Chordates as well but ARE vetebrates. I also added a lamprey which is a Jawless fish. I was able to show a phylogenetic tree with the right parameters will generate something resembling the Creationist Linnaen Hierachy. The main exception is the Amphibains are in there with the fish, but they do group together, which is nice.

    As I said, the clocking issue is a problem for evolutionism as it must simultaneously invoke fast and slow molecular clocks for the fish, with is a contradiction, and hence proof by contradiction against the mainstream narrative.

    With that in mind I went to the distance-based phylogeny. In the case of distance-based phylogeny, bootstrapping actually degrades the desired result, so I only used 1 bootstrap.

    One may object that I just plugged parameters to get my desired result. Well, the sword cuts both ways, that would hold true for evolutionists.

    However, I should point out, if one merely looks at the distance matrices which are OBJECTIVE relative to the technique of affixing values of distance:

    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/tunicata_jtt.txt

    the following tree is faithful to that. The result is everything is now in the 100% confidence interval.

    Here are the model parameters:

    Figure. Evolutionary relationships of taxa
    The evolutionary history was inferred using the UPGMA method [1]. The optimal tree with the sum of branch length = 8.97843289 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1 replicates) are shown next to the branches [2]. The evolutionary distances were computed using the JTT matrix-based method [3] and are in the units of the number of amino acid substitutions per site. The analysis involved 18 amino acid sequences. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 513 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [4].

    1. Sneath P.H.A. and Sokal R.R. (1973). Numerical Taxonomy. Freeman, San Francisco.
    2. Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.

    In any case, click here to see enlarged image:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/linnaeus_vertebrate.png

  29. stcordova: I only get 2.5 lectures on phylogenetics as that is only a small part of my bio-informatics class, and here is the chance to supplement my understanding.

    So maybe you should be a little less arrogant in your pronouncements. You can’t learn if you reject instruction. Almost everything you say is wrong. Is arrogant ignorance a Christian virtue?

    I could point out all the errors and absurdities in that mass of posts, but what would be the purpose? This is one problem with user-friendly phylogenetic software: any idiot can use it to produce nonsense. The solution isn’t to make software hard to use, though. It’s to educate the user. In this case, the solution can’t be applied.

  30. stcordova: That was my way of trying to get a response whether I’m right or wrong in the way I’m reading things.I only get 2.5 lectures on phylogenetics as that is only a small part of my bio-informatics class, and here is the chance to supplement my understanding. So thank you for showing me how to properly read as I was misreading.

    …This is my chance to learn things outside of formal training and take angles that aren’t easily explored in a formal context such as the exploration of nylonases. About the only satisfaction you get is to hear my wrong notes during practice and tinkering sessions as I try out new ideas.

    You mean this whole thread has been Sal’s way of getting others to help him with his homework assignment?!

  31. Sal:

    That was my way of trying to get a response whether I’m right or wrong in the way I’m reading things.

    No, it was your way of asserting that you were right and Joe was wrong:

    Joe:

    We may dismiss the rooting of both of these latest trees from Salkvador. The distance matrix tree has such low bootstrap supports that most of the important interior branches are very ill-supported. The other tree (parsimony, as I recall) has only 35% bootstrap support on the one branch that conflicts with conventional trees for these groups, and only 50% support for the lungfish-coelacanth clade.

    Sal:

    Thank you for you comment, but this diagram shows 99% confidence that the tetrapods don’t belong anywhere around the fish:

    John:

    And here we have Sal Cordova disagreeing with Joe Felsenstein about interpretation of phylogenetic bootstrap numbers. That alone is worth the price of admission. No, Sal, the 99% bootstrap is for sharks vs. everything else.

  32. John Harshman:
    Almost everything you say is wrong.

    I’m afraid not, John. I overturned two claims on nylonase, one in Nature 1983 and one in PNAS by Ohno in 1984.

    The fact I only have a little knowledge in your phylogenetic nomenclature doesn’t mean my claims against common are wrong.

    you should be a little less arrogant in your pronouncements.

    Yes, of course, you’re right. I shouldn’t be so arrogant.

    Thank you very, nevertheless for your generous help in helping me improve my fundamental theses and eliminate technical errors.

    Nothing personal, sorry we have to disagree, but you’ve been immensely helpful in walking me through stuff. Your fix on my mislabeling of Cox1 was immensely helpful, and I owe you a beer (at least) for that. How about Christmas present.

    But seriously, the UPGMA tree which is almost purely distance based is just what the doctor ordered. Linnaeus and the Collin Patterson would be smiling at the beautiful nested hierarchies I can build with MEGA 6.0.

    John Harshman:

    This is one problem with user-friendly phylogenetic software: any idiot can use it to produce nonsense.

    Hear hear.

  33. Regarding the distance metrix there are a variety in MEGA 6.0 starting with Jones-Taylor-Thornton. There is also Dayhoff, p-distance, poisson model, number of differences model. Each distance model can be tried out with the UPGMA tree builder. They returned approximately the same trees.

  34. TomMueller: You mean this whole thread has been Sal’s way of getting others to help him with his homework assignment?!

    That’s the problem with these exercises, I’m afraid that Sal is just using them to refine some nonsense he’ll be peddling to the gullible.

    Glen Daivdson

  35. stcordova:
    The fact I only have a little knowledge in your phylogenetic nomenclature doesn’t mean my claims against common are wrong.

    Agreed. What it means is that you have no way of supporting your claims or of knowing whether you are supporting your claims. It also means you should believe experts on the subject (that would be me and Joe) when we tell you that you haven’t supported your claims or are grossly mistaken about nearly everything.

    But seriously, the UPGMA tree which is almost purely distance based is just what the doctor ordered. Linnaeus and the Collin Patterson would be smiling at the beautiful nested hierarchies I can build with MEGA 6.0.

    That’s you being arrogant again. I don’t think you know how UPGMA works or what its assumptions are. It is in fact entirely distance based, not almost. It assumes (if we wish to interpret its results as meaningful) an exactly perfect molecular clock. Since that assumption is clearly violated, which you can tell based on all the other trees you have produced that don’t make the assumption, UPGMA is a poor method to use with these data. Linnaeus might smile; Colin Patterson would laugh out loud. Don’t try to recruit dead people whose ideas you don’t understand.

    When you agree you need to stop being so arrogant, that’s fine. But it means nothing unless you act on it.

  36. stcordova:
    Regarding the distance metrix there are a variety in MEGA 6.0 starting with Jones-Taylor-Thornton.There is also Dayhoff, p-distance, poisson model, number of differences model.Each distance model can be tried out with the UPGMA tree builder.They returned approximately the same trees.

    GIGO. Until you understand what the various distance measures do and what UPGMA does, you will have no clue about how (or whether) to apply any of them.

  37. stcordova: The fact I only have a little knowledge in your phylogenetic nomenclature doesn’t mean my claims against common are wrong.

    Who, other then yourself, agrees with you? If you’ve convinced no one does that not worry you?

  38. Glen Davidson:

    There is no nested hierarchy, and common design explains the nested hierarchy.

    This message brought to you by Sal–and many other IDists/creationists as well.

    Well, regarding the creationist Linnaeus:
    https://en.wikipedia.org/wiki/Carl_Linnaeus

    The Linnaean system classified nature within a nested hierarchy,

    I agree.

    To quote Linnaeus: “God creates, Linnaeus classifies.” In the modern day, “God created, Sal classifies with the help of user-friendly phylogenetic software.” Yesireee.

  39. stcordova: To quote Linnaeus: “God creates, Linnaeus classifies.” In the modern day, “God created, Sal classifies with the help of user-friendly phylogenetic software.” Yesireee.

    I thought you were going to cut down on the megalomania.

  40. GlenDavidson,

    Sal–the Gary Gaulin of taxonomy.

    Heh. I had a peek at that thread the other day. It looks identical to the last time I read it, about a year ago. Condemned (on both sides) to say the same things for all of eternity.

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