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. Adapa:
    Here cole, another real world example.Scientists for obvious reasons have been extremely interested in HIV – human immunodeficiency virus.The evolutionary history of the virus has been tracked as seen in this 2010 paper.

    The evolution of HIV-1 and the origin of AIDS

    Abstract:The major cause of acquired immune deficiency syndrome (AIDS) is human immunodeficiency virus type 1 (HIV-1). We have been using evolutionary comparisons to trace (i) the origin(s) of HIV-1 and (ii) the origin(s) of AIDS. The closest relatives of HIV-1 are simian immunodeficiency viruses (SIVs) infecting wild-living chimpanzees (Pan troglodytes troglodytes) and gorillas (Gorilla gorilla gorilla) in west central Africa. Phylogenetic analyses have revealed the origins of HIV-1: chimpanzees were the original hosts of this clade of viruses; four lineages of HIV-1 have arisen by independent cross-species transmissions to humans and one or two of those transmissions may have been via gorillas. However, SIVs are primarily monkey viruses: more than 40 species of African monkeys are infected with their own, species-specific, SIVand in at least some host species, the infection seems non-pathogenic. Chimpanzees acquired from monkeys two distinct forms of SIVs that recombined to produce a virus with a unique genome structure. We have found that SIV infection causes CD4þ T-cell depletion and increases mortality in wild chimpanzees, and so the origin of AIDS is more ancient than the origin of HIV-1. Tracing the genetic changes that occurred as monkey viruses adapted to infect first chimpanzees and then humans may provide insights into the causes of the pathogenicity of these viruses.

    You can see the phylogenetic relationship of the different varieties of the virus shown in Figure 2 of the paper.

    Are all these different strains of HIV evidence of a Common Designer?If so the Designer is one sick sadistic bastard.Or did the different genetic sequences arise through known evolutionary processes?

    Showing a scientific paper to colewd is like showing garlic to a vampire. 🙂

  2. Frankie: In what way?

    We just went through that, the lack of new species popping into existence like the Cambrian Explosion. Unless you know something about why design is not still happening or a mechanism of design that would preclude it?

  3. Mung,

    I’d think it was a miracle if identical twins were found to have exactly identical (in every respect) genomes.

    OK … 99.99% identical. I don’t see this ‘gotcha’ changes anything material in the argument.

    Why is the only alternative to their theory that evolutionist can think of the theory of special creation? I wonder how they calculate the probabilities.

    That’s the one usually presented, and the only one that really makes much sense. What’s the middle way, given 2 genomes with 99.99% identity? They inherited some bits but others were …. what?

  4. The big irony is that most genetic differences between species are neutral or even silent substitutions. So the common designer intentionally designed in branching tree patterns of broadly effectless mutations? Or somehow intentionally intervened in the evolutionary process to cause mutations to happen, which have no phenotypic effect? (this is why the whole theistic evolution crap doesn’t make sense either). What a curious thing, it’s almost like the designer is trying to prove evolution happened without any design at all.

  5. Another irony I might have made more of in the OP is that, for molecular sequence, ‘Common Design’ seems most supported where it is least needed, if sequence similarity is the thing to be explained.

    Common Design is not invoked to explain differences, but similarities. So the more similar two genomes, the more commonly designed they are … ?

  6. colewd,

    Have you heard that SINE’s can be front signals for RNA editing? Not making a claim here just asking if you can validate this.

    Transposons, by their very nature, can be co-opted for organismal function in all sorts of ways. They can act in a very similar manner to mutation, with a spectrum of harmful-to-beneficial effect. It is not impossible that a given SINE used in a study is functional. It would be improbable that they all were – each marker is just a single copy, not the entire class of such retroelements. Finding function for some copies does not give that function to all.

    It does not really matter much for their use as markers in phylogeny.

  7. Frankie,

    And my point about the OP being wrong is that Common Design was not invented to combat Common Descent because the concept clearly preceded it.

    OK, I accept your point, although the term itself was coined by Jonathan Sarfati, with a clear semantic intent to be an alternative to the phrase ‘Common Descent’.

  8. colewd:

    Given that mutation can generate sequences that don’t match, non-matching sequences are not evidence against common descent, though clearly they cannot be used in favour of it if non-matching sequence is all there is.

    This is the biggest hurdle for me and you know the source of my skepticism if the different sequences have found function.

    I believe you said that you’ve read Arrival of the Fittest. You should know from that book that functional sequences are observed to be well-connected in sequence space. There is no rational basis for your incredulity.

  9. newton: We just went through that, the lack of new species popping into existence like the Cambrian Explosion. Unless you know something about why design is not still happening or a mechanism of design that would preclude it?

    Speciation is ambiguous – it is not rigorously defined. ID does not prevent speciation as it is currently defined. It doesn’t prevent macroevolution if that is what the designer(s) programmed to happen.

    My point about humans producing humans is that we can not extrapolate Common Descent (large scale) given the mechanism of common descent.

  10. Allan Miller:
    colewd,

    Transposons, by their very nature, can be co-opted for organismal function in all sorts of ways. They can act in a very similar manner to mutation, with a spectrum of harmful-to-beneficial effect. It is not impossible that a given SINE used in a study is functional. It would be improbable that they all were – each marker is just a single copy, not the entire class of such retroelements. Finding function for some copies does not give that function to all.

    It does not really matter much for their use as markers in phylogeny.

    Transposons, by their very nature, are evidence for IDE.

  11. The biggest problem with IDist/creationist use of the “common design” trope is, of course, that it’s used not as a principle, but as an excuse.

    Why do vertebrates all have quite similar eyes? Common design.

    Why do cephalopods all have quite similar eyes? Common design.

    Why don’t cephalopods and vertebrates have quite similar eyes? Creation by an entity that doesn’t need to stick with one “design.”

    Why do cephalopods and vertebrates all have quite similar developmental genes? Once again, common design.

    It’s just an excuse when similarities show up, not something that is entailed by any sort of design principles. Organisms are dissimilar? Well, why not, designs are about creativity (creation, creationism, etc.). Organisms are similar? Well, why not, common design.

    Just ignore the entailed evolutionary patterns by saying “common design,” and return to your meaningless “god did it,” which was always the plan. Nothing’s been explained, no reason for commonality or lack thereof is forthcoming at all, while evolutionary theory does explain it by the divergence and separation of breeding populations.

    IDists/creationists know that there’s no actual reason for “common design,” which is why they’re not troubled when lack of common design shows up repeatedly. They don’t want to explain anything, they merely wish to thwart evolution by bringing up “common design.”

    But because there remains the evolutionary pattern of similarity and dissimilarity according to divergence from common ancestry, and they haven’t in the slightest explained it, the pattern of similarity and dissimilarity remains powerful evidence for evolution. By the same token, the pattern of similarity and dissimilarity is powerful evidence against design, common or otherwise.

    Glen Davidson

  12. GlenDavidson: The biggest problem with IDist/creationist use of the “common design” trope is, of course, that it’s used not as a principle, but as an excuse.

    Cuz Glenn noes all!

    There aren’t any entailed evolutionary patterns, Glenn. Your position doesn’t have a mechanism capable of producing eyes and vision systems. Yours can’t even produce the organisms that have them.

    And please tell us about this alleged lack of common design. I dare you

  13. Adapa: What were the mechanisms ID uses to physically manipulate matter to achieve desired results again?

    Channeling FrankenJoe: When will you people learn that ID is about detecting design, not about the nature of the designer or the mechanisms he uses.

  14. Frankie,

    ID does not prevent speciation as it is currently defined. It doesn’t prevent macroevolution if that is what the designer(s) programmed to happen.”

    ID, as it is defined, doesn’t prevent leprechauns, Santa Clause, the Easter Bunny or the Flying Spaghetti Monster either. What’s your point?

  15. Frankie,

    Transposons, by their very nature, are evidence for IDE.

    No they aren’t. See? Simple assertion can be readily defeated by simple counter-assertion.

    You seem a little indiscriminate in your application of ‘Frankie’s Razor’. If everything is evidence for ‘IDE’, what the hell use is it, as a scientific endeavour?

  16. Frankie: Speciation is ambiguous – it is not rigorously defined.

    So when you said only humans come from humans the concept of the species Homo Sapiens is ambiguous? Fuzzy around the edges so to speak?

    ID does not prevent speciation as it is currently defined. It doesn’t prevent macroevolution if that is what the designer(s) programmed to happen.

    If indeed designers even have the capability to program anything at all,everything might just come fully realized. What we view as microevolution may just be a series of creation events. Designers constantly at work. ID does not prevent that view ,correct?

    My point about humans producing humans is that we can not extrapolate Common Descent (large scale) given the mechanism of common descent.

    Because we cannot view the emergence of new species in real time, ” it is still a ( fill in the blank) ” . So since we can’t observe this emergence, this is evidence against non intelligent evolution. The protestations from biologists that given the mechanisms proposed the time frames are too long for humans to observe this emergence are dismissed out of hand. Is this about correct?

    Now back to my point, since it is possible that the unknown mechanism of ID would result in the emergence of species in real time, our inability to view such emergence is even greater evidence against ID than non intelligent evolution which is incapable of such rapid emergence.

    Unless you know some reason that mechanism and designer are not compatible with ID?

  17. Allan Miller: So the more similar two genomes, the more commonly designed they are … ?

    No, silly person. The more common designers they have in common. There’s no requirement for designers to be monophyletic.

  18. Allan Miller: OK, I accept your point, although the term itself was coined by Jonathan Sarfati, with a clear semantic intent to be an alternative to the phrase ‘Common Descent’.

    Ah, is that where that comes from? I have some Sarfati around somewhere. Do you have a specific book in mind?

  19. Patrick: There is no rational basis for your incredulity.

    Sure there is, and I’ll even explain it to you. It’s your lucky day!

    I believe you said that you’ve read Arrival of the Fittest. You should know from that book that functional sequences are observed to be well-connected in sequence space.

    There’s a whole universe of potential function out there in sequence space, and we don’t know that all functional sequences are well-connected because we don’t know if we have observed all possible functional sequences. At most we could say that the sequences we observe are well-connected.

    In my opinion, it would be an absolute miracle if all of sequence space is functional or if all functional sequences are in fact well-connected in sequence space. Wouldn’t you find that miraculous? I mean, what are the odds of that?

  20. Acartia: Are they house trained?

    I keep them where they can’t get into trouble. I mean, how many times have I quoted Sarfati here?

  21. Frankie: Transposons, by their very nature, are evidence for IDE.

    Transposons, by their very nature, are not evidence for IDE.

  22. Acartia: ID, as it is defined, doesn’t prevent leprechauns, Santa Clause, the Easter Bunny or the Flying Spaghetti Monster either.

    That’s right, these are all designed.

    What’s your point?

    Evolutionism doesn’t prevent them either. Obviously.

    ETA: You left out the tooth fairy.

  23. Mung,

    No, silly person. The more common designers they have in common.

    So (almost) identical twins have the most common designers of all? Triffic!

  24. Mung: In my opinion, it would be an absolute miracle if all of sequence space is functional or if all functional sequences are in fact well-connected in sequence space. Wouldn’t you find that miraculous? I mean, what are the odds of that?

    If “Islands of function” miracles are required to find function. If tons of function everywhere, also a miracle. Way to cover your bases, LOL

  25. Mung,

    In my opinion, it would be an absolute miracle if all of sequence space is functional or if all functional sequences are in fact well-connected in sequence space. Wouldn’t you find that miraculous? I mean, what are the odds of that?

    The designer is very careful to only generate sequences that are connected in this space whose functional density he apparently has no control over.

  26. dazz: Way to cover your bases, LOL

    I know, right! I’m just hoping to help you guys see the miraculous that surrounds you every day. If you believe the universe started out lifeless, the simple fact that you have life is utterly miraculous.

  27. Allan Miller,

    Refuting Evolution 2

    Oh crap, I just started reading it! Humans get rid of the interdigital web, frogs don’t. They are different, so Common Design … If they were commonly descended, they’d be the same! Ribbit!

  28. Mung:

    There is no rational basis for your incredulity.

    Sure there is, and I’ll even explain it to you. It’s your lucky day!

    I believe you said that you’ve read Arrival of the Fittest. You should know from that book that functional sequences are observed to be well-connected in sequence space.

    There’s a whole universe of potential function out there in sequence space, and we don’t know that all functional sequences are well-connected because we don’t know if we have observed all possible functional sequences. At most we could say that the sequences we observe are well-connected.

    Agreed, and I said nothing else.

    In my opinion, it would be an absolute miracle if all of sequence space is functional or if all functional sequences are in fact well-connected in sequence space. Wouldn’t you find that miraculous? I mean, what are the odds of that?

    I agree with that, too.

    None of what you wrote provides a rational basis for colewd’s incredulity. The functional sequences we know about are observed to be connected to other functional sequences closely enough for known evolutionary mechanisms to traverse between them.

  29. The latest from the Sarfati Mines: Some organisms’ genetic codes are as much as 1.5% different!*** A clear strike against Common Descent.

    ***Including ours vs our mitochondria, he omits to mention.

  30. I apologize for any pain i may have caused by suggesting we follow that line of inquiry, lol.

  31. dazz: If “Islands of function” miracles are required to find function. If tons of function everywhere, also a miracle. Way to cover your bases, LOL

    They retreat to “look at the way things are, how unlikely (not that they have any basis for that of course), therefore my chosen deity”

  32. Allan Miller:
    Frankie,

    No they aren’t. See? Simple assertion can be readily defeated by simple counter-assertion.

    You seem a little indiscriminate in your application of ‘Frankie’s Razor’. If everything is evidence for ‘IDE’, what the hell use is it, as a scientific endeavour?

    Transposons carry within their sequence the coding for two of the enzymes required for it to move around. And given that all of our observations and experiences have editing and splicing requiring knowledge, the inference would be that TEs were designed elements that can move around as required/ triggered. (their movements are not haphazard)

  33. So I have the referenced Sarfati book. Chapter 6 is “Common Design Points to Common Ancestry.”

    By this I infer that the authors mean that what ought to be attributed to common design, is attributed instead to common ancestry, by the heathen [evolutionists].

    (Does that go without saying?)

    The chapter consists of three subsections:

    Common Structure = Common Ancestry?
    DNA Comparisons – Subject to Interpretation
    Debunking the “Molecular Clock”

    So we have common agreement between the book and the web page. This immediately raises the question, common descent, or common design?

    You decide.

  34. Patrick: None of what you wrote provides a rational basis for colewd’s incredulity.

    By that sort of reasoning there’s no rational basis for any skepticism.

  35. Sarfati begins his case for “common design” by attacking the idea, propounded by evilutionists, that if some phenotypic feature looks the same between species it’s because those species share a common ancestor from which those features were inherited.

    Sarfati’s claim is that if the species had a common ancestor, the same genetic sequences would lead to the same phenotypic features. But they don’t. And that this is understandable under the hypothesis of a common design, but not so under a hypothesis of common descent.

    Now I am sure that we would all agree that certain houses share a common design. And we’d probably have no objection to attributing this to a common blueprint. So under a common design hypothesis, common blueprint => shared features.

    Yet Sarfiati’s argument is just the opposite of that line of thought. Shared features do not share a common blueprint, and this is seen as evidence for common design.

    Now it seems to me that all we need now is an argument that a common blueprint must be due to a common design for a clear case of heads I win, tails you lose.

    +1 for Common Design!

  36. newton: So when you said only humans come from humans the concept of the species Homo Sapiens is ambiguous? Fuzzy around the edges so to speak?

    If indeed designers even have the capability to program anything at all,everything might just come fully realized. What we view as microevolution may just be a series of creation events. Designers constantly at work. ID does not prevent that view ,correct?

    Because we cannot view the emergence of new species in real time, ” it is still a ( fill in the blank) ” .So since we can’t observe this emergence, this is evidence against non intelligent evolution. The protestations from biologists that given the mechanisms proposed the time frames are too long for humans to observe this emergence are dismissed out of hand. Is this about correct?

    Now back to my point, since it is possible that the unknown mechanism of ID would result in the emergence of species in real time, our inability to view such emergence is even greater evidence against ID than non intelligent evolution which is incapable of such rapid emergence.

    Unless you know some reason that mechanism and designer are not compatible with ID?

    What is the mechanism that can evolve humans starting from some populations of knuckle-walkers?

    My issue is there isn’t any known mechanism that can account for the transformations that had to have occurred. That means it is untestable and not a scientific claim.

  37. Frankie: What is the mechanism that can evolve humans starting from some populations of knuckle-walkers?

    Evolution. Same as the last 1000x you make the same IDiot whine.

  38. Frankie,

    What is the mechanism that can evolve humans starting from some populations of knuckle-walkers?”

    Again with the “mechanisms”. These have been pointed out to you hundreds of times yet you keep asking the same question. Is there some pathology at work here?

    Yet, your position does not have any mechanisms. Nor is it testable. Or falsifiable. Or rational.

  39. Allan Miller: OK … 99.99% identical. I don’t see this ‘gotcha’ changes anything material in the argument.

    Given that identical twins do not share identical genomes, I’d have to see how your argument changes given that fact, since your original argument was based on the mistaken claim that the genomes of identical twins were in fact identical, in all respects.

    p.s. You really need to figure out how links work on this site.

  40. Frankie: What is the mechanism that can evolve humans starting from some populations of knuckle-walkers?

    For ID it could be one step from knuckle draggers to humans.Given the right designer ,anything is possible.

    My issue is there isn’t any known mechanism that can account for the transformations that had to have occurred. That means it is untestable and not a scientific claim.

    Right, without a mechanism of some sort that can be tested,such how man in one step could be transformed from knuckle draggers, you do not have a scientific claim. We agree

  41. Mung: Now it seems to me that all we need now is an argument that a common blueprint must be due to a common design for a clear case of heads I win, tails you lose.

    Well you might go with common design creates a common blueprint which creates common design, rinse and repeat.

  42. Mung: So I have the referenced Sarfati book. Chapter 6 is “Common Design Points to Common Ancestry.”

    And I would agree that’s a terrible formulation. I’d have to read the chapter to see what he actually says, rather than judge it by title only.

    To make it clear, if you have two objects and they’re merely similarity, that does not imply common descent. It never did. This misconception needs to go away and die.

    Things are similar =/= they have a common origin.

    It is only when those things are known to reproduce themselves, and when that method of reproduction entails stochastic accumulation of changes (meaning they will slowly diverge), that their similarity and the particular pattern of dissimilarities in combination with this fact inexorably implies common descent.

    Inheritance, we know there is a mechanism of inheritance and we know how it works. This is what makes all the difference. It’s what predicts the nesting hierarchical patterns of shared derived similarities. When the facts of this mechanism are brought into the equation, the patterns of similarity implies a degree of relatedness (how distantly they are related) that correlates with the degree of similarity.

    It’s not just “oh gee these two things are sorta gray and have lumps, they must have the same dad”. That would be absurd.

  43. Rumraket: To make it clear, if you have two objects and they’re merely similarity, that does not imply common descent. It never did.

    Rather, that sounds like what ID does.

    Argument by analogy.

    Argument by homology–in the right patterns of derivation–is quite a different sort of argument.

    Glen Davidson

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