Common Design

One of the densest Creationist tropes has to be ‘Common Design’. It is proposed as a direct competitor to Common Descent – template mediated copying of DNA – as an explanation for the high sequence similarity of two DNA segments. But what is actually held in common? If we look at a particular transposon sequence, and find it is in A and B but not C, and another that is in A but not B, etc, we can generally organise a set of such markers into a ‘tree’ structure, much as would be predicted by Common Descent. But no, we are assured that these apparent markers are in fact part of the ‘design’. If A is a whale, B a pig and C a deer, there is something that is vital for the function of both whale and pig but is definitely not required in deer. Instead, a sequence which, in whale and pig, sits either side of the insertion, runs uninterrupted in the deer. That, too, is functional, supposedly, even though the insert would give a product which was the A/B one with a gap and possibly a frameshift, if it were transcribed.

But this is held to be the case even if the sequence, with and without transposon, is never transcribed. A sequence that does nothing, and organises hierarchically exactly as would be expected of common descent, is nonetheless functional … because?

On observation, there must be some genome pairs that are highly similar because they are commonly descended. We can see it happening. But there are, on this notion, supposed to be identically-patterened runs of similarity that are not due to common descent, but instead result from a completely different cause – some entity bolting together genomes, or parts thereof, from scratch, I guess, and choosing to repeat a known pattern – up to a point – in a manner that fools our most adept molecular taxonomists into seeing descent.

There must be a line in a taxonomy where the one shades into the other – on one side, sequence commonality is all Common Descent; on the other, Common Design. Where does this discontinuity reside? Species, genus, family, order? Is it a gradual transition, gene by gene, or all at once? How could you tell? Why does it not show up in computer analyses of blind datasets?

If I were to provide 3 genomes shorn of all differences, it would be impossible to tell which were commonly descended and which commonly designed from the data. But there must logically be a transition of causes, were I to take the genomes from sufficiently distant species and this idea were true. What persuades us to adopt this causal explanation in preference to that which explains the pattern better: Common Descent?

278 thoughts on “Common Design

  1. stcordova: You can say life is a miracle without knowing all its function.

    But why would you? Reality appears to be sufficient for the origin of life and it’s continued existence. Why bother with miracles at all?

  2. OMagain: But why would you? Reality appears to be sufficient for the origin of life and it’s continued existence. Why bother with miracles at all?

    Just to be annoying, my pet peeve is that the word it’s, with the apostrophe, is a contraction for IT IS. For a possessive (such as “its continued existence”), there is no apostrophe. As a handy rule of thumb, every time anyone inserts that apostrophe, they should spell out IT IS as a substitute (IT IS continued existence). If it doesn’t work, leave the apostrophe out.

  3. Addendum:

    evolutionary biologists:

    We found… 12 reported cases of orphans with experimental evidence for an encoded protein”

    The mainstream now realizes genes are not restricted to protein coding genes, but also RNA generating genes. A few such RNA genes have been mentioned already at TSZ like HOTAIR, X-ist. A study just a year and half later is chipping away at the above claim.

    This is a pre-print of a peer-reviewed paper:
    https://arxiv.org/ftp/arxiv/papers/1507/1507.07744.pdf

    This pipeline resulted in 634 human-specific genes
    (1,029 transcripts), 780 chimpanzee-specific genes (1,307 transcripts) and 1,300 hominoidspecific genes (3,062 transcripts). By adding these numbers the total number of candidate de novo genes was 2,714 (5,398 transcripts) (Figure 2A).
    ….
    About 20% of de novo genes matched annotated lncRNAs or sequence
    entries in the ‘EST’ or ‘nr’ databases. The identification of lncRNAs in the set was not surprising as it has been previously reported that they tend to show low phylogenetic conservation [37,38,45]. The majority of de novo genes were novel genes (~ 80%, Figure 2C).

    This suggest to me it is possible one primate didn’t evolve from another by ordinary means. Something extraordinary induced them to evolve, or maybe they never evolved in the first place. If so, the similarities are the result of common design.

    After all, the evolutionary biologists said the large number of orphan genes is evolutionarily implausible. The writing is on the wall, so to speak.

  4. OMagain:

    But why would you? Reality appears to be sufficient for the origin of life and it’s continued existence. Why bother with miracles at all?

    I don’t think ordinary events are sufficient for the origin of life or the origin of ophan genes or large numbers of functional transposons which were viewed as junk only 10-20 years ago (or so).

    I obviously have a lower threshold for accepting miraculous explanations than you do. How extraordinary would an event have to be to accept a miracle vs an ordinary mechanism or a hallucination?

    If you don’t have a personal stake in the answer to such questions, then I suppose there is no reason to waste brain energy over the question. If you’ll live your life the same way whether life is a miracle or not, then why bother with the question? It would be about as relevant to you personally as whether some random coin buried in the dessert is head or tails.

  5. stcordova,

    Allan Miller: A sequence that does nothing…

    Sal: It’s too early to make such pronouncements.

    I see the argument about genetic entropy went straight past you then. By your logic it’s ‘too early’ to say something is deleterious, so let’s assume nothing is, eh, just in case?

    There must be a fraction of ‘bits’ in the genome which are non-functional, even if one is wrong about a given one. There must also be, even among the fraction that does something, variants whose variations have no effect. Otherwise there would be no possibility of variation.

    Therefore there must be a fraction of genetic differences between species for which the statement ‘makes no functional difference’ will be true.

    What am I risking by considering it true? The fact that, in the future, I might have to change my mind? Jeez, how will I cope?

    And how does this affect phylogenetic analysis?

  6. stcordova,

    If that’s the case, it’s way too early for evolutionary biologists to start advocating deletion of genes from databases merely because it disagrees with their sorry theories. That’s none of their business to be meddling with lab researcher’s databases as to what these lab researchers can and cannot discover.

    Is that really what happened? Honestly, Sal? Someone’s watching, you know.

    Meantime YECs can pontificate to their hearts’ content about what scientists should and shouldn’t be doing!

  7. stcordova,

    The mainstream now realizes genes are not restricted to protein coding genes, but also RNA generating genes.

    When did ‘the mainstream’ discover that? Must have been before 1975 when I went to uni. Nice to see you keeping abreast of the latest trends.

  8. stcordova: The mainstream now realizes genes are not restricted to protein coding genes, but also RNA generating genes.

    What do you mean “now”? Molecular biologists have known about ribosomal and tRNA for 40 years. This isn’t something new.

  9. RNA genes are hardly an unexpected finding for a proponent of RNA world … if true, time was that’s what ‘gene’ would have meant!

  10. stcordova: That means they want to delete 1177 genes from the database only because only 12 reports of proteins that match those genes have come in SO FAR.

    And as they say, if experimental evidence comes in for the rest, they will be listed as bona fide protein coding genes.

    YOU are the one who wants to jump to conclusions, while the researchers want to wait for actual evidence. What they’re doing is entirely appropriate: Don’t list as fact what is not in evidence.

    Keep up the spin Sal.

  11. stcordova: The only thing that can tell you if it’s an orphan is comparative genetics. Meaning you have to have whole genome sequences from multiple closely related species and look for a corresponding homologous coding region. If there’s a homologous DNA sequence in a related taxon, it’s not a true orphan.

    NO!

    If you want to insist that an orphan gene is merely a protein without a homologous protein in another species, but which still has a homologous but untranslated coding region in closely related species, then sure. But why you think that’s a problem for evolution is anyone’s guess.

  12. stcordova: If you get a list of all the alternative splices of every protein in a cell, that is the most comprehensive list of proteins in the cell, therefore you’re not going to miss any proteins in the cell, therefore you’re not going to miss any orphans in the cell.

    You’re not going to miss any orphans even without alternatively spliced proteins.
    An alternatively spliced protein isn’t an orphan protein. Those two things have nothing to do with each other.

    But one cell of one cell type is not enough. It has to be tens of thousands, maybe hundreds of thousands. Who knows.

    Not you, that much is obvious at this point.

    If that’s the case, it’s way too early for evolutionary biologists to start advocating deletion of genes from databases merely because it disagrees with their sorry theories.

    It’s deleted as protein coding genes because they haven’t been shown to be protein coding genes.
    You know, that whole thing about there having to be evidence for something, rather than feeble speculations of desperate creationist minds.

    That’s none of their business to be meddling with lab researcher’s databases as to what these lab researchers can and cannot discover.

    The evolutionary biologists ARE the lab researchers, and they aren’t saying what can or can’t be discovered. They’re correcting the database so it only lists as bona fide protein coding genes, what has been PROVEN with that pesky thing called EMPIRICAL EVIDENCE, is protein coding genes.

    So when the evolutionary biologist lab researchers discover, with real empirical evidence, actual protein coding genes, they will be listed by the evolutionary biologists, in the database. Like the way it should be: You list your findings when you find them and not a second before that.

  13. stcordova: After all, the evolutionary biologists said the large number of orphan genes is evolutionarily implausible.

    And why did they say that? Because they thought the idea of entirely new protein coding regions in DNA sequence, arising de novo in such a short time, was obviously not within the capacity of currently known evolutionary mechanisms.

    Which left another option: They didn’t arise de novo, but from previously non-coding regions that already existed and which either was nonfunctional or had different functions not related to coding for proteins.

    This prediction turned out to be correct. Every putative case of a truly de novo orphan gene, upon closer analysis from comparative genetics (those pesky evolutionary biologist lab researchers and their pesky empirical evidence) has turned out to be just another case of a similar DNA sequence existing in our close relatives, having evolved so it gets transcribed and translated.

  14. stcordova: Since its been a long time since I’ve gotten anything of value from you. You’re now on my ignore list.

    keiths, DNA_Jock, and now Rumraket on Sal’s Ignore list. Three people who have absolutely nothing worthwhile to contribute at TSZ. How appropriate.

  15. And it has nothing to do with the intellectual ass-kickings he’s received from each of us. It’s because we aren’t delivering anything of value to him.

    I am so disappointed in myself.

  16. I accidentally saw Mung’s comment before I logged in.

    Rumraket is NOT on my ignore list, never was. His comments have scientific substance which is more than I can say for Mung’s posts.

    Keiths has a brain, at times brilliant, but in the Granville Sewell thread he couldn’t defend his points. It got tiresome asking him to do a simple entropy calculation with his proposed alternative definitions of entropy.

    DNA_Jock? Does he not know that m must be constant in the following equation, for it to be a straight line:

    y = mx + b

    I pointed out this out to him in the Granville Sewell thread. It’s beneath him to admit his error, yet he just keeps bloviating away. He had a few other howlers. Not worth my time anymore.

  17. stcordova: I accidentally saw Mung’s comment before I logged in.

    My sympathies. Try logging in before looking at comments. That’s what I do.

  18. stcordova:

    DNA_Jock?Does he not know that m must be constant in the followingequation, for it to be a straight line:

    y = mx + b

    Actually, you get a straight line in two cases: where m AND b are both constants, and where m and b change concurrently so as to cancel out.

  19. Flint: Actually, you get a straight line in two cases: where m AND b are both constants, and where m and b change concurrently so as to cancel out.

    Now that Sal has had his blunder pointed out let’s see if it’s beneath him to admit his error and instead just keep bloviating away. FSM knows he’s had plenty of other howlers.

  20. stcordova,

    DNA_Jock? Does he not know that m must be constant in the following equation, for it to be a straight line:

    y = mx + b”

    Regardless of how you change anything in this equation, you will get a straight line. In fact, this equation defines a straight line. And only a straight line.

  21. Sal:

    Keiths has a brain, at times brilliant, but in the Granville Sewell thread he couldn’t defend his points.

    Says the guy who panicked and put me on ignore when he couldn’t defend his view of entropy against my six points.

    That thread was a disaster for you, Sal. Who do you think you’re fooling with your revisionist history?

    It got tiresome asking him to do a simple entropy calculation with his proposed alternative definitions of entropy.

    All because you couldn’t grasp the following simple point: the missing information interpretation of entropy is just that — an interpretation — and it doesn’t change the way entropy is calculated. As I commented at the time:

    Poor Sal. This discussion has been going on for almost a month, and he still doesn’t get that the dispute is over the interpretation of entropy, not its calculation.

  22. Typically when you see this in school, m and b are constants. When that’s true, then yes, it’ll always be a straight line.

    Acartia:
    stcordova,

    DNA_Jock? Does he not know that m must be constant in the following equation, for it to be a straight line:


    y = mx + b”

    Regardless of how you change anything in this equation, you will get a straight line. In fact, this equation defines a straight line. And only a straight line.

  23. stcordova: DNA_Jock? Does he not know that m must be constant in the following equation, for it to be a straight line:

    y = mx + b

    Oh, Sal, your memory must be failing you. In that extremely enjoyable (for me, at least) thread, I tried in vain to introduce to you the idea that Heat Capacity is a function of temperature. The example I used was the melting of ice at a temperature other than 273.15 K.
    I introduced Sal to

    Kirchhoff’s Law of Thermochemistry. (that is: ∂ΔH/∂T = ΔCp, the difference in heat capacities, FYI)

    As I said then, There followed a lot of huffing and puffing from Sal – my favorites were when he referred to ∂ΔH/∂T as a second derivative(!!), and failed to see that IFF ΔCp were a non-zero constant then “ΔH will vary linearly with T.” [Hey! y = mx + b, anyone?] Oh!, how could I forget Sal’s claim that if Cp is a constant then ΔCp = zero? There was evidently some confusion around the meaning of the symbol Δ.
    In a gobsmacking display of ignorance of the First Law of Thermodynamics, Sal wrote:

    The ΔH in question is dispersal of energy from the surroundings to melt the ice, and that is different from the ΔH of a non-existent chemical reaction involving reactants and products and that are used as inputs to Kirchhoff’s laws.

    That struck me as taking wrong to a whole new level, so I showed him an example of researchers using Kirchhoff’s Law (∂ΔH/∂T = ΔCp) to address the question of ice freezing at non-standard temperatures (Szedlak). Sal’s reaction, hilariously, is to use Szedlak’s curve
    ΔH = Lf = L_effecitve = = L_f(Tm) – Integral [(c_w – c-I) dT]
    [sic]
    in an attempt to prove wrong a claim I never made. That’s fine, I don’t mind, because Sal has (inadvertently?) admitted that Kirchhoff’s Law (∂ΔH/∂T = ΔCp) applies to the melting of ice.
    (For readers without calculus background, Sal’s “L_effecitve” equation is identical to ∂ΔH/∂T = ΔCp, just integrated.)

  24. <

    ;Reality appears to be sufficient for the origin of life and it’s continued existence.

    Only if reality means Intelligent Design. The other option isn’t even testable.

  25. Allan Miller: It still remains the case that, if you want Common Design to be the direct alternative to Common Descent,

    It still remains that, if you want Common Descent to be a direct alternative to Common Design, you have to be able to account for the physiological and anatomical differences observed, and you can’t.

    . Common and Spotted Sandpipers must have more Design in common than any more distant taxonomic pair.

    It depends on what process(es) produced the two.

  26. stcordova: Rumraket is NOT on my ignore list, never was.

    My apologies. You failed to include any link in your post to who you were talking to and I made an assumption that appears to have been incorrect.

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