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.

5,163 thoughts on “Common Design vs. Common Descent

  1. Rumraket:

    Just wanted to point this out because creationists mistakenly think that geologic strata and fossils are dated by circular reasoning:

    Including Sal, of course:

    Besides, lots of rock strata are dated with index fossils! Circular reasoning.

    Derp.

  2. keiths: And ‘commonly descended’ sequences are those that pass from ancestors to descendants; that is, all of them. Are you aware of any sequences that are exclusively transmitted horizontally?

    Commonly descended sequences are sequences that derive from the same ancestral sequence, i.e. sequences that are homologs. The point Allan is trying to get across is that from this perspective it is irrelevant whether they were passed exclusively from ancestors to descendants.

    Now if you want to infer common descent of species you are of course correct to point out that HGT pollutes the phylogenetic signal. But it is good to keep in mind that you are discussing at a different biological level then.

  3. Corneel,

    The point Allan is trying to get across is that from this perspective it is irrelevant whether they were passed exclusively from ancestors to descendants.

    He is going well beyond that, arguing that the term ‘common descent’ should encompass horizontal transfers as well as vertical inheritance. Hence his statement:

    You appear to want to restrict the term ‘common descent’ to vertical inheritance.

    He’s right about that. I do think that HGT should be excluded from ‘common descent’, because it isn’t a form of descent.

    There’s no benefit to redefining ‘common descent’ to include HGT. The current meaning works just fine, and the vertical/horizontal distinction is worth maintaining.

    Also, the rationale Allan offered for the redefinition was invalid, as I explained here.

  4. Corneel: The point Allan is trying to get across is that from this perspective it is irrelevant whether they were passed exclusively from ancestors to descendants.

    Hmmm, I thought the point he was making is any new variation entering the gene pool, by whatever method, that is heritable, is going to have its own nested hierarchy. HGT is a source of variation – subject to vertical inheritance.

    Ditto symbiogenesis.

  5. Rumraket,
    Sure, we have our powder dry and ready! I was going to mention relative and absolute dating of fossils and I did mention radiometrics.

  6. PS

    I’m no expert, certainly not on trilobites. They have become the next shiny thing for me and I’m very appreciative of any links, suggestions and info that others may like to provide.

    Thanks in advance to all who feel inclined!

  7. Alan Fox: Hmmm, I thought the point he was making is any new variation entering the gene pool, by whatever method, that is heritable, is going to have its own nested hierarchy. HGT is a source of variation – subject to vertical inheritance.

    As I understand it, that was one of the points that Allan was making, and the one that keiths appeared to understand, but chose to minimize. AIUI, Allan also made the point that the inserted sequence has its own pre-insertion phylogeny, which is also informative. keiths is making a false dichotomy for the purpose of argumentation. Hence my question about human somatotropin genes.
    The ‘signal’ for an objective nested hierarchy across species is confounded by HGT, iff the HGT is a) unrecognized and b) occurred across a significant taxonomic distance.
    keiths made a similar error of dichotomous thinking regarding “guided evolution”. As long as the guider is not making a deliberate effort to obscure the phylogenetic signal (a devil-placed-the-fossils silly assumption), then we expect (partially) guided evolution to produce an ONH.
    And gene duplication is horizontal, rather than vertical, descent.

  8. DNA_Jock: Allan also made the point that the inserted sequence has its own pre-insertion phylogeny, which is also informative.

    Indeed. I guess sequences inserted by HGT will also have their own future phylogeny, if the population from which the HGT’d genes came from continues to survive.

    ETA: Might have been clearer to say “in the population from which the sequences were transferred into another species, if the original population continues to survive”. It’s almost a sort of bifurcation of that sequence.

  9. Is keiths trying to manufacture a controversy again?

    He seems to be arguing that only certain sequences can be inherited due to common descent. That would mean that only the sequences present in the LUCA could be inherited by common descent.

  10. Rumraket: You are so deeply and intensely biased and it shows.

    Natural selection wouldn’t work without bias. Do you get emotionally upset at natural selection?

    Rumraket: Now we a similar situation with Trilobites. Trackways that look like the ancestors of trilobites, yet creationists will selectively decide to reject trackways now that they fit the evolutionary chronology.

    I don’t have any problem with trilobite tracks. I have a problem with the assertion that they are necessarily made by the ancestors of trilobites. They could have been made by actual trilobites.

    The reasoning seems to be that if they were made by actual trilobites, why are there no shells to go with them. So we have evidence of trilobites (the tracks) and we have evidence of no trilobites (no shells) and then we reason it must have been something that evolved into a trilobite. That’s fine as a hypothesis. But somehow it becomes fact, when it reality it is speculation.

    ETA:

    Trackways that look like the ancestors of trilobites

    You don’t know what the tracks of the ancestors of trilobites look like. Just admit it and move on.

  11. Mung: I don’t have any problem with trilobite tracks. I have a problem with the assertion that they are necessarily made by the ancestors of trilobites. They could have been made by actual trilobites.

    Well, there are instances of tracks and burrows associated with fossil specimens, so it’s possible to compare tracks where the culprit is known to tracks of uncertain origin. Bear in mind there’s a time difference. Tracks and no hard parts appear before tracks and hard parts.

    The reasoning seems to be that if they were made by actual trilobites, why are there no shells to go with them. So we have evidence of trilobites (the tracks) and we have evidence of no trilobites (no shells) and then we reason it must have been something that evolved into a trilobite. That’s fine as a hypothesis. But somehow it becomes fact, when it reality it is speculation.

    It could be more than speculation. You too can look through Galileo’s telescope and decide for yourself. There’s plenty of information on line.

  12. Am I the only one here who has read Henry Gee? You cannot look at fossils and infer ancestors. Much less look at tracks and infer ancestors.

  13. Mung: You cannot look at fossils and infer ancestors.

    What is stopping someone from comparing fossil morphology?

  14. Mung: Natural selection wouldn’t work without bias. Do you get emotionally upset at natural selection?

    Do you always make silly but fallacious equivocations like that?

    I don’t have any problem with trilobite tracks. I have a problem with the assertion that they are necessarily made by the ancestors of trilobites.

    So do I. I wonder who said that they were necessarily made by the ancestors of trilobites. Can you quote them?

    The reasoning seems to be that if they were made by actual trilobites, why are there no shells to go with them.

    Actually the question is, if they were made by trilobites similar to the ones we have fossils of, why are there no contemporaneous fossils of them?

    To which one possible and entirely plausible answer is that the tracks are from a species similar to the ancestors of trilobites before armored protection had evolved.

    So we have evidence of trilobites (the tracks)

    What? So now you’re saying the tracks alone are evidence of trilobites?

    and we have evidence of no trilobites (no shells)

    What is evidence of no trilobites? Are you talking about the tracks here again?

    You don’t know what the tracks of the ancestors of trilobites look like. Just admit it and move on.

    My guess is they look at lot like the tracks that actual trilobites make, but likely without leaving marks that indicate they are dragging along a chitinious exoskeleton.

    And then I can google and see if paleontologists are thinking along the same lines: http://www.trilobites.info/trace.htm
    “What are ichnofossils?
    They are trace fossils: preserved tracks or other signs of the behaviors of animals in the substrate. Ichnofossils can provide some very intriguing insights on the ecology and behavior of an extinct animal such as a trilobite. It is very rare that the animal itself is found in direct association with the ichnofossil it created, but that kind of co-occurrence allows scientists to link ichnofossils with the species that created them. In fact, in the pre-Cambrian fossil record, there are no trilobites, but there are trace fossils which very closely resemble those made by trilobites, suggesting that before trilobites developed their hard calcite shells, their ancestors were crawling about leaving traces. While there are hundreds of named ichnofossil types, there are three main named categories of ichnofossils associated with trilobites: Rusophycus, Cruziana, and Diplichnites, described below.”

    Well fuck me. It’s almost like a thinking person could figure this out.

  15. As this thread seems to be gaining in popularity, I’ve amended the publish date to bring it on to the front page.

  16. Detecting similarities and therefore nested taxnomic hierarchies does not need the assumption of plylogeny!

    The software and algorithms that detect similarity or kinship among amino acid and DNA sequences need not assume common descent. In fact all it does is measure similarity.

    One such method of detecting similarity used by some people trying to predict common descent of proteins is Needleman-Wunsch. Another is BLAST. There are some others.

    Now what happens if I put a common designed amino acid sequence through one of these gizmos?

    Here is a calculator:

    http://experiments.mostafa.io/public/needleman-wunsch/

    A hypothetical section of a protein might be:

    “ABIGAILLOVESSAL” (as in Abby Smith Loves Sal)

    and another hypothetical section of a protein is

    “ABIGAILHATESSAL” (as in Abby Smith Hates Sal)

    In fact, I pumped the two sequences through another similarity measuring program, the NIH NCBI BLASTP program and got 80% identity with an e-value of e^-10 !!!! It’s got some hints of homology, that’s fer sure….

    Try it right here:
    https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

    Below is the Needleman-Wunsch comparison of
    these two “protein” fragments.

    Click here for a slightly bigger image:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/10/abbylovessal-1024×819.png

    or better yet go to the website and enter the text yourself:

    http://experiments.mostafa.io/public/needleman-wunsch/

    And see the “phylogeny” it demonstrates.

    Random chance is unlikely an explanation the similarity. Did you need reason from the designer (me) to deduce that this was or was not the product of common descent? Eh, it’s irrelevant to observing similarity. Similarity proves similarity, everything else is by a guessed inference. These issues obviously extend to the question of common design and common descent.

    The same can be extended to making Theobald’s prediction of non-random relations using Hidden Markov models. Ergo, there Theobald’s program doesn’t prove common descent, it only proves non-random similarity!

    PS
    Abby’s own words about me after we stopped getting along so well.

    http://endogenousretrovirus.blogspot.com/2007/09/in-which-erv-eats-sals-soul.html

    You. You Sal Cordova. You cottage cheese dripping pussy.

  17. stcordova: Detecting similarities and therefore nested taxnomic hierarchies does not need the assumption of plylogeny!

    You still don’t know the difference between detecting similarities and finding nested taxonomic hierarchies?

    It’s that difference that matters, and it seems you are either unable or unwilling to comprehend this fact.

    Glen Davidson

  18. stcordova: The software and algorithms that detect similarity or kinship among amino acid and DNA sequences need not assume common descent. In fact all it does is measure similarity.

    The latter part is a misconception I held myself. It isn’t actually correct, but I’ll let John explain that part. Or actually, I think you’re confusing how phylogenies of species are inferred, from how homology is inferred using a sequence alignment.

    The former just shows how confused you are. It is not merely the fact that you can put a number of sequences into an algorithm that infers a phylogeny, and get a tree out, that implies common descent. You can do that for anything.

    It is that phylogenies constructed using independent data sets are highly similar, that implies a common genealogical relationship. The consilience of independent phylogenies. The extremely high level of statistical significance of how similar trees made using different data, are.

    This point is made all the stronger when you consider that actually used phylogenetic aglorithms(as in algorithms used to construct phylogenies, not merely align sequences) do not group by similarity:
    Watch this: Maximum Parsimony method.

  19. I just put the above mentioned sequences into CLUSTAL Omega which uses Hidden Markov Models and even got phylogenetic trees!!!!

    So if a designer decides to create thing in a certain way, phylogenetic methods will generate completely bogus imaginary histories!

    To go to CLUSTAL OMEGA goto:

    https://www.ebi.ac.uk/Tools/msa/clustalo/

    To enter the protein segments ““ABIGAILLOVESSAL” and
    “ABIGAILHATESSAL” (whereby “B” is aspartic acid or asparagine), enter:

    >seq1
    abigaillovessal

    >seq2
    abigailhatessal

    Clustal will generate an alignment and phylogenetic tree. The alignment is REAL the phylogenetic tree using hidden markov modeling is completely BOGUS. Ergo, phylogeny isn’t unequivocally proven by similarity.

  20. Oh, Sal,
    We’ve been over this BLAST thing before.
    That is also the thread where Sal derided John Harshman for his statement “mtEve is not the MRCA of all female humans”. Much hilarity ensued 🙂

  21. Rumraket:

    The former just shows how confused you are. It is not merely the fact that you can put a number of sequences into an algorithm that infers a phylogeny, and get a tree out, that implies common descent. You can do that for anything.

    It is that phylogenies constructed using independent data sets are highly similar, that implies a common genealogical relationship. The consilience of independent phylogenies. The extremely high level of statistical significance of how similar trees made using different data, are.

    I obviously disagree. The designer can also put similarities in several data sets if he chooses, ergo the phylogeny can still be BOGUS!

    John seems to think to prove common design, I have to explain the why the designer wanted to do business a certain way. This is like asking someone to explain to a little kid why Mozart or Rachmaninoff chose certain notes of musical work. No explanation is needed to suspect common design. If common descent will not generate the pattern of Orphan Systems without miracles, then Common Descent it isn’t an explanation, it’s just an article of faith.

    Orphan Systems are a problem for common descent because they have no ancestor. Missing ancestors suggest common design by miracle. At some point, though it would be difficult, it would be worth looking at the MRCA issue in more detail.

    There is also something that I find very interesting which I mentioned in another thread:

    http://theskepticalzone.com/wp/chargaff-parity-rule-2-biasednon-random-mutations/comment-page-2/#comment-111817

    Note the differing GC content in bacteria. This doesn’t look like an unbiased random walk. The bacteria also with extreme CG content or scarcity would be good candidates for estimating MRCAs based on sequence divergence within the species lines.

    I should also mention, John Harshman’s invocation of Coalescence Theory won’t apply to the MRCA of two reproductively isolated populations. Some sort of molecular clocking would appear in order.

    Actinobacteria : some have 75% GC some have 37%

  22. Oh, Sal,
    We’ve been over this BLAST thing before.
    That is also the thread where Sal derided John Harshman for his statement “mtEve is not the MRCA of all female humans”. Much hilarity ensued

    That’s a misrepresentation on your part. Before you go further, have you figured out how to draw straight lines yet, I learned that in elementary school, but apparently you couldn’t apply that skill otherwise you’d see your errors. 🙂

    http://theskepticalzone.com/wp/in-slight-defense-of-granville-sewell-a-lehninger-larry-moran-l-boltzmann/comment-page-34/#comment-153739

    And have you figured out 1.5% does not equal 0.1%.
    http://theskepticalzone.com/wp/some-evidence-alus-and-sines-arent-junk-and-garbologists-are-wrong/comment-page-3/#comment-140116

    Besides you ended up criticizing what is now textbook stuff on Alus when you criticized me.

  23. stcordova: The designer can also put similarities in several data sets if he chooses, ergo the phylogeny can still be BOGUS!

    But Sal the designer could design ALL POSSIBLE IMAGINARY OR REAL DATA SETS. It is a completely unfalsifiable conjecture. There isn’t a data set imaginable that yields a pattern, that you could not just claim is what the designer wanted to design.

    The designer could also choose NOT to let different data sets yield the same phylogeny by an algorithm that doesn’t group by similarity. So you have no reason to EXPECT that the designer DID do that.

    On the other hand, common descent absolutely DEMANDS that the independent data sets yield highly congruent phylogenies. So common descent PREDICTS consilience of independent data sets, while design is only compatible with it in ad-hoc fashion.

    You can’t say that consilience of independent phylogenies is evidence of design, without actually knowing beforehand that the designer WANTED TO produce consilience of independent phylogenies. Do you know that? No, you don’t. So given that THERE IS consilience of independent phylogenies, this fact is evidence of common descent, but it cannot be evidence of a designer you don’t actually know how implemented it’s design.

    And please don’t do the Affirming the Consequent-fallacy and claim that the detected consilience of independent phylogenies, is evidence that the designer wanted to design consilience of independent phylogenies.

    Think. Just think for a moment.

  24. stcordova: John seems to think to prove common design, I have to explain the why the designer wanted to do business a certain way. This is like asking someone to explain to a little kid why Mozart or Rachmaninoff chose certain notes of musical work

    No, it’s like asking why Dangledorff wrote only music that mimics bird songs.

    The only good answer would be that Dangledorff copied bird songs. Which would be ridiculous of him to do, given his job as composer and choir director.

    Or, why does God intricately cause weather to appear as if it were ruled by physics? Gee, maybe it’s actually because it is ruled by physics and not intricately planned by God.

    See, we have an explanation, and all you can do is say it’s done by God and that you don’t have to give us any reason because it’s God.

    Glen Davidson

  25. stcordova: If common descent will not generate the pattern of Orphan Systems without miracles, then Common Descent it isn’t an explanation, it’s just an article of faith.

  26. GlenDavidson:
    I would expect a miracle–or design–to break the patterns of common descent.

    Sal just says that miracles made the patterns.

    Glen Davidson

    The idea that miracles “explain” the nested hiearchy is pretty much like the idea that miracle explain the appearance of starlight from very distant sources in a young universe.

    Oh btw, besides starlight, gravitational waves also confirm astronomical distances. Standard Candles can now be correlated with Standard Sirens.

    So God put the nested hiearchy there to fool us. He made the starlight appear distant to fool us. He made the gravitational waves appear distant to fool us. And so on and so forth ad infinitum.

  27. The idea that miracles “explain” the nested hiearchy is pretty much like the idea that miracle explain the appearance of starlight from very distant sources in a young universe.

    Not necessarily.

    About a decade about I was invited by this YEC who got 6 million in science grants to be his PhD physics student. But since it was in Australia, I had to decline.

    https://uncommondescent.com/creationism/yec-john-harnett-accumulates-almost-5-7-million-dollars-in-science-grants/

    Hartnett released this critique of the Big Bang:
    https://arxiv.org/abs/1107.2485

    And there may be mechanisms of spatial variation and direction influenced speed of light. There is a lot we don’t know. I explained some of my views here:
    https://uncommondescent.com/creationism/distant-starlight-the-thorn-in-the-side-of-yec-can-there-be-a-middle-ground/

    and red shifts may be in the eye of the beholder:
    https://www.reddit.com/r/Creation/comments/2p53uw/astronomic_redshifts_are_in_the_eye_of_the/

    and an experiment I’ve been working on and off:

    https://www.reddit.com/r/Creation/comments/45j6vt/update_on_cahill_relativity_experiment_attempting/

  28. stcordova: I just put the above mentioned sequences into CLUSTAL Omega which uses Hidden Markov Models and even got phylogenetic trees!!!!

    No you didn’t. You can’t get a phylogenetic tree for two sequences. You need at least four before there can be a tree, or three if you assume a perfect molecular clock. Did I mention that every time you type anything you expose your ignorance?

    The designer can also put similarities in several data sets if he chooses, ergo the phylogeny can still be BOGUS!

    Of course it can. A god who chooses to counterfeit common descent is undistinguishable from common descent. But is that the story you want to put out?

    John seems to think to prove common design, I have to explain the why the designer wanted to do business a certain way. This is like asking someone to explain to a little kid why Mozart or Rachmaninoff chose certain notes of musical work. No explanation is needed to suspect common design. If common descent will not generate the pattern of Orphan Systems without miracles, then Common Descent it isn’t an explanation, it’s just an article of faith.

    So you have no explanation for the nested hierarchy. Don’t you realize that’s a damaging admission?

    Orphan Systems are a problem for common descent because they have no ancestor. Missing ancestors suggest common design by miracle. At some point, though it would be difficult, it would be worth looking at the MRCA issue in more detail.

    You throw this term “orphan systems” around a lot, but its definition seems unusually flexible. Some of your orphan systems have clear ancestry. A few of them don’t. But if we accept that any of them could only have come about by miracle, isn’t it a more parsimonious explanation for all the data that god introduced them into existing lineages rather than creating lineages separately? That would explain the similarities, the differences, and the pattern simultaneously. So why aren’t you a theistic evolutionist like Michael Behe?

    I should also mention, John Harshman’s invocation of Coalescence Theory won’t apply to the MRCA of two reproductively isolated populations. Some sort of molecular clocking would appear in order.

    Actually, coalescence theory will apply to reproductively isolated populations. I’m not sure what your reference to “molecular clocking” is supposed to mean.

  29. Is it me or is it becoming pretty much diagnostic of Sal’s posts that they reveal something about his psychology? Somehow it all has to do with

    1. Money and funding.
    2. Pretentious titles and speaking engagements, not to mention fancy technical jargon.
    3. Women, sex and feminism.

    It seems to me the whole thing reduces to ego. For Sal, this whole creationism vs evolution thing is about ego and status.

    Do you have a girlfriend Sal? When was the last time you got laid anyway? (and didn’t pay for it).

  30. Rumraket: I wonder who said that they were necessarily made by the ancestors of trilobites. Can you quote them?

    I never claimed that someone said that they were necessarily made by the ancestors of trilobites. So why would you expect that I ought to be able to quote someone saying that?

  31. Mung: I never claimed that someone said that they were necessarily made by the ancestors of trilobites. So why would you expect that I ought to be able to quote someone saying that?

    Oh so you were responding to an imaginary claim nobody actually made. Okay.

  32. Rumraket: And then I can google and see if paleontologists are thinking along the same lines:

    LoL. Or you could have just read Corneel’s post and followed that link, like I did.

    Do you always re-invent the wheel?

  33. Alan Fox: What is stopping someone from comparing fossil morphology?

    Lack of access to fossils. Lack of interest. A gambling addiction. The list is almost endless.

  34. I like the word orphan.

    Orphans are miracles, ya know, because they don’t have ancestors.

  35. Rumraket asks:

    Do you have a girlfriend Sal? When was the last time you got laid anyway? (and didn’t pay for it).

    Now now, no need to denigrate an un-attractive revolting guy like me.

    But as far as paying for it, never have, for reasons I outlined in the following link when describing two separate incidents when I was approached by women of the evening:

    https://shadowtolight.wordpress.com/2017/09/25/did-overconfidence-hasten-the-demise-of-the-new-atheists/#comment-20267

    But if you’re asking because you want to hookup with me, and if you’re a boy, I’m not into that. Sorry.

  36. John Harshman:

    You can’t get a phylogenetic tree for two sequences.

    Well CLUSTAL OMEGA provided one anyway. 🙂

  37. John Harshman:

    You need at least four before there can be a tree

    CLUSTAL OMEGA lets me make them with two, but just to humor you, below is the cladogram generated via hidden Markov Models from my intelligently designed sequences with common designs.

    The input “protein” fragments were:

    >seq1
    ABIGAILLOVESSAL

    >seq2
    ABIGAILHATESSAL

    >seq3
    ABIGAILLOVESDOGS

    >seq4
    ABIGAILLOVESERVS

    The phylogenetic cladogram is provided below. There, now you can build a theory of common descent from something that was actually created by common design.

    FWIW, it looks like a gap penalty was imposed to make the longer sequences closer in similarity.

  38. John, to Sal:

    So you have no explanation for the nested hierarchy. Don’t you realize that’s a damaging admission?

    Just to hammer the point home, Sal cannot explain why the Designer, out of the trillions of possibilities available to him, just happened to choose one from the tiny fraction that would make common descent appear to be true, by yielding an objective nested hierarchy.

    It’s laughable.

  39. stcordova,

    I bet your two-sequence “tree” is just a line connecting them, right?

    Of course it gives you a tree with four sequences. You will always get a tree no matter what the data look like. I don’t think Clustal will even produce polytomies. That’s how neighbor-joining works; it arbitrarily breaks polytomies. As has been explained to you too many times to count, it’s not just the ability to be put into a tree that makes us conclude that data result from common descent. It’s the hierarchical structure of the data. And of course a creator who wants to simulate common descent can produce a hierarchy identical to that resulting from common descent.

    Now, whatever do you think this shows?

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