Common Trends in Evolution

Does evolution repeat itself? Could evolution repeat itself? Where do people stand in relation to the thoughts of  Gould and Conway Morris?

Gould has a point, everything is in a state of becoming. As Heraclitus would say, all is change. Replay the tape and nothing would be the same. But would or could there be any similar trends? Would life in general proceed in such a radically different way that Gould makes out?

From “Life’s Grandeur”, Gould states:

“…no persuasive or predictable thrust toward progress permeates the history of life…

“Wind the tape of life to the origin of multicellular animals in the Cambrian explosion, let the tape play again from this identical starting point, and the replay will populate the earth (and generate a right tail of life) with a radically different set of creatures. The chance that this alternative set will contain anything remotely like a human being must be effectively nil, while the probability of any kind of creature endowed with self-consciousness must also be extremely small.”

Conway Morris disagrees with Gould’s conclusion. He champions an inevitable path and cites convergent evolution as evidence which suggests this.

In “The Crucible of Creation” he states,

“What we are interested in is not the origin, destiny, or fate of a particular lineage, but the likelihood of the emergence of a particular property, say consciousness. Here the reality of convergence suggests that the tape of life, to use Gould’s metaphor, can run as many times as we like and in principle intelligence will surely emerge.”

I’m interested in what people have to say about this and its relation to topics such as the emergence of bilateral symmetry and differentiation from head to tail, extreme specialization, encephalization, endothermy, caring for young, transitions from aquatic to terrestrial living and other related topics. These processes have occurred multiple times in different lineages over time.

267 thoughts on “Common Trends in Evolution

  1. CharlieM: No I’m not saying that. I’m talking about intrinsic group intelligence.

    Hmmmm, you used to call it group wisdom. So now you are trying to assimilate Intelligent Design doublespeak and decided group wisdom is equipped with foresight and planning as well? Is this wise, Charlie?

  2. CharlieM: Why would amphioxus need a clotting system when it doesn’t even have a system of blood flow? They do not have a heart and lack a circulatory system.

    Lancelets do have a circulatory system.

    ETA I’m using my phone so I’m not going to try posting articles of which there are many. Try googling, Charlie.

  3. colewd to Alan Fox,
    There is no evidence that reproduction and associated variation can re create a sequence.

    Well, I was going to write, “of course not!”, then I remembered transmembranal segments, and I had to admit. to myself, that there’s plenty of evidence that reproduction and associated variation can “re create sequence.” On a longer shot perspective, however, where circumstances are not that specific, I don’t see why we would expect to “re create sequence.” I was going to say that I didn’t see why we’d care either way, then I remembered we’re curious animals, and, of course, many scientists would care to know if “re create sequence” happens. Transmembranal segments being a common problem in terms of misleading homology inferences.

    colewd to Alan Fox,
    Convergent evolution should have been a show stopper for the theory.

    Why? Evolution, convergent or divergent, is evolution. Why would it be a show stopper?

    colewd to Alan Fox,
    You cannot explain this with your extremely tentative lots of needles in the haystack hypothesis.

    What’s the “this” that Alan cannot explain? You lost me. Well, you lost me several times already. I hope Alan didn’t try and guess what you meant. I, for one, would prefer you to clarify, if you can. We’ll see.

  4. Entropy: What’s the “this” that Alan cannot explain?

    I’m guessing Bill is referring to how rare protein function is in sequence space. Dembski’s “upper probability bound” assumed “search” had to hit unique sequences in one bound (pun intended) and the exponential of twenty by sequence length gives an enormous figure. Bill may think Dembski’s proposition made sense.

  5. Corneel:
    CharlieM: As I said previously irreducibly complex systems can be nested.

    Corneel: No, irreducibly complex systems cannot be “nested”, as the simpler system demonstrates that at least some subunits of the more complex system are redundant to perform given function.

    It’s there in a quote provided by Matzke from “Darwin’s Black Box”. Behe writes:

    From the beginning, a new step in the cascade would require both a proenzyme and also an activating enzyme to switch on the proenzyme at the correct time and place. Since each step necessarily requires several parts, not only is the entire blood-clotting system irreducibly complex, but so is each step in the pathway.

    The function of this one step is to produce an enzyme and it cannot do that if one of the components is missing. The function of the entire blood clotting system is to stem the flow of blood and it cannot do that if any of the individual steps after the fork is missing. And possibly if some of the intrinsic or extrinsic steps are missing but this latter possibility is much harder to demonstrate.

  6. CharlieM:

    The function of this one step is to produce an enzyme and it cannot do that if one of the components is missing. The function of the entire blood clotting system is to stem the flow of blood and it cannot do that if any of the individual steps after the fork is missing. And possibly if some of the intrinsic or extrinsic steps are missing but this latter possibility is much harder to demonstrate.

    In theory, any irreducibly complex system may consist of irreducibly complex steps that perform some different subfunction (like the pair of regulating enzymes) but this cannot be true of nested subsets of systems that perform the same function, like the blood clotting cascades in this example.

    Note: The simpler system is lacking some of the components that the more complex system does have. Since in principle the more complex system can be reduced to the components that make up the simple system and still retain its function, it cannot be irreducibly complex.

  7. DNA_Jock:
    CharlieM: He doesn’t argue that partial systems will be non-functional.

    DNA_Jock: Say what? Of course he does. That is what “irreducible” means.

    As Miller demonstrated a partial mousetrap of the design Behe used can function as a not too convincing tie clip. Behe does not dispute this. But he argues that taking parts away from the mousetrap renders it non-functional in its intended purpose as a mousetrap.

    CharlieM: He argues that removing essential parts from specific systems will render them non-functional.

    DNA_Jock: “essential”? What a silly tautology! He argues that removing any part from an IC system will render it non-functional.

    Only with regards to its original function. And not any part in the system. The system can be examined to determine which specific parts can or cannot be removed. A mousetrap could be designed with a cover over the top and still be considered irreducibly complex even if it still functioned with the cover

    CharlieM: The simpler system of the lamprey is still a complete specific system.

    DNA_Jock: Yes. So his original Pandas claim that the human system is “irreducibly complex” is seen to be a God of the Gaps error. That’s why he retreated to the “irreducible core” position, and hoped that the rubes would not notice that his argument is torpedoed when IC becomes a function of our ignorance.

    I haven’t read Pandas other than the quotes Matzke provided. The human system is irreducibly complex in that taking away specific steps in the system will render it unable to form clots.

  8. DNA_Jock:
    CharlieM: By the time he wrote “Darwin’s Black Box”, he would had spent more time researching and thinking about the finer details of the system. It is a more comprehensive treatment of the system. It is easier to argue against his initial thoughts on the system than arguing against his more considered and mature thoughts on it in which he clarifies his meaning.

    DNA_Jock: Well, he does have a habit of misrepresenting critics whilst adjusting his argument to obscure the criticism, but “By the time he wrote Darwin’s Black Box” he was still claiming Christmas Factor etc. were part of the essential irreducible system. That’s Factor IX, Charlie — not seen in the lamprey.

    Where does he say that Christmas factor was one of the essential components that makes the system irreducible? He does say that lack of Christmas factor is a common cause of haemophilia. But could this step be bypassed in some way? He cannot say for certain, so he makes no claims for its essential contribution.

  9. Alan Fox,

    From the content it would seem that Bill means “re create sequence.” But there’s plenty of evidence that this happens all the time, at least for things like transmembranal segments, so, maybe Bill means “genes present in two organisms but absent in the common ancestor,” but the problem here is that Bill assumes that there’s only one “common ancestor”, when he might be pointing to a common ancestor prior to the last common ancestor, thus the gene could still have evolved prior to the separation of the two organisms. How could Bill tell if he’s pointing to the last common ancestor rather than common ancestry before the last? Among microbes there’s another, very frequent, option, more and more scientists discover lateral gene transfer. So, again, what’s the problem? Large etc.

    I’d still like to see if Bill can explain how any of it is a problem for natural phenomena. Why, in the face of all the natural phenomena happening all around us, we should shrug, ignore what we know, and just say “God did it.”

    Seems like Bill is engaged in some philosophically flawed way of thinking. Jump to God-did-it as soon as you encounter some “problem” with your understanding of evolution. Either nature behaves nicely and cleanly the way some creationist expects from a poorly understood phenomenon, or it was The Magical Being In The Sky,

    Again, maybe he can explain?

  10. CharlieM: i agree that proposing a top-down assembly process by some intentional agent or agents seems too much like human creations and inventions where the agent is external to the product. Interference from without.

    Good, we agree on at least that much. Kant called this a distinction between “external teleology” (purposive organization as a result of an agent imposing some ordering configuration on a system) and “internal teleology” (purposive organization as a consequence of how the system organizes itself, e.g. how the whole constrains the parts such that each part contributes to the whole).

    And the practice of any so called science should not become political.

    I don’t think that’s possible or desirable. As the great philosopher Stan Lee once said, “with great power comes great responsibility.” Scientists are given a lot of epistemic authority because we trust them to value objectivity, and that means that they have responsibility for how their theories are understood and applied.

    For them to focus on “pure science” and ignore its real-world repercussions is the attitude of Tom Lehrer’s Wernher von Braun: “when the rockets go up/who cares where they come down?/that’s not my department/says Werner von Braun”

    In Behe’s case, his work is being used by very right-wing political organizations in the US. Either he doesn’t care, or he endorses that connection. Both are morally damning.

    I don’t really care if Behe thinks the the creative agent is God or some alien mad scientist, I just look to see if the concept of irreducible complexity has any merit. I believe it does.

    The concept of irreducible complexity is perfectly fine, though Behe basically just stole it from the general systems theory developed by Ludwig von Bertanffy. (Note: I have no reason to believe that Behe is aware of Bertalanffy or any other systems theorists. On the contrary, I believe that his ignorance of his predecessors leads to a vastly inflated conception of his own importance.). But irreducible complexity doesn’t have any of the implications that Behe thinks it does, about what evolution can or can’t do, or about whether intervening agents are necessary to explain macroevolutionary transitions. Behe insists on a mechanistic understanding of what a complex system is, and that’s why he thinks this concept (which is not even original with him) has the implications that he imagines it does. Once we let go of a mechaistic understanding of a complex system, the rest of Behe’s argument collapses.

    And before we proceed any further, this has been pointed out many times in the scholarship, most pointedly by Stuart Kauffman. I can see that Behe refers to Kauffman a few times in A Mousetrap for Darwin, but to be honest, I’d be surprised if he displays any real understanding of Kauffman’s criticism.

    For whatever it may be worth, here are some theoretical biologists whose work I highly recommend as alternatives to intelligent design:

    Francisco Varela
    Robert Rosen
    Susan Oyama
    Alvaro Moreno

  11. Alan Fox,

    I’m just a simple unfrozen caveman philosopher, but I’m pretty sure that the whole game is given away with this line: “what we consider to be the conceptually simplest route: point mutation.”

    Conceptually simplest — by what criterion of conceptual simplicity? Does the conceptually simplest route also mean the most common kind of mutation? What’s the likelihood of point mutations vs other kinds of mutations that also allow duplicated genes to explore genetic space?

    Is focusing on point mutations really what is “conceptually simplest”? Or is that that focusing on point mutations is just an excuse to make evolution seem more mathematically difficult than it really is?

  12. Alan Fox,

    Bill is having a hard time at Peaceful Science promoting a paper by Mike Behe (with David Snoke). Maybe that’s on his mind:

    The paper itself is not what’s interesting. It’s the argument with Michael Lynch as in the argument between Art Hunt and Doug Axe. What happens when you put together both arguments 🙂

  13. colewd,

    colewd: It’s the argument with Michael Lynch as in the argument between Art Hunt and Doug Axe. What happens when you put together both arguments

    Don’t be shy, Bill. Tell us.

  14. Kantian Naturalist: I’m just a simple unfrozen caveman philosopher

    Oh come now, no false modesty. 😉

    Kantian Naturalist: What’s the likelihood of point mutations vs other kinds of mutations that also allow duplicated genes to explore genetic space?

    Plenty of evidence of duplications resulting in new gene functions. But ID proponents don’t have a great record on considering evidence.

  15. Alan Fox,

    Plenty of evidence of duplications resulting in new gene functions. But ID proponents don’t have a great record on considering evidence.

    How do they retain new gene function? Mutation after duplication? How exactly does this get fixed in the population? How far away from the duplicated sequence are you proposing? Feel free to use Michael Lynches response to Behe as a resource.

  16. colewd to Alan Fox,
    How do they retain new gene function?

    Selection.

    colewd to Alan Fox,
    Mutation after duplication?

    Why would this perplex you? After genes separate their histories, for example by duplication or speciation, they always, always, always, diverge due to mutations. Mutationas are unavoidable.

    colewd to Alan Fox,
    How exactly does this get fixed in the population?

    Selection, drift, and combinations thereof.

    colewd to Alan Fox,
    How far away from the duplicated sequence are you proposing?

    Do you mean how far away from the duplication event? If so, there’s plenty of documented cases with variable distances/divergence from the duplication event. From very close to very far away. It depends on what we’re talking about, the times since duplication, the selection sweeps, etc.

    colewd to Alan Fox,
    Feel free to use Michael Lynches response to Behe as a resource.

    How kind of you.

    What about you explain why, say, if we ignored exact times, number of recombinations, duplications, mutations, etc, it took for something to happen, we should say instead that some magical being in the sky did it until proven otherwise? Why give the magical being fantasy such a stupidly large amount of leeway?

  17. Entropy,

    How kind of you.

    This will help you model how many of these events were feasible in evolutionary time since LVCA (500 MYO). How much did gene duplication and selection/drift contribute to the current gene distribution of vertebrates. Given given an average search of 10^10 trials to find new gene function? (Art Hunt 2004)

    Your alternative theory is the magical Being in the sky delivered the animals as stated in Genesis 1 and duplication selection/drift started from that point. No search required and no claim of lots of needles in the haystack required. The gene pattern easily explained.

    http://www.sci-news.com/genetics/article01036.html

  18. colewd: Given given an average search of 10^10 trials to find new gene function? (Art Hunt 2004)

    “Well, it’s not many when you consider the size of the population.” (Irene Walker 1985)

  19. colewd,

    Glad to see you have stopped referring to a diagram in the 2013 paper by Howe et al. as “Sal’s flower”.

    Learned a couple of (new to me) things this morning. A duplicated gene is an ohnologue and at least two complete genome duplications have occured in the vertebrate line.

  20. Corneel:
    CharlieM: No I’m not saying that. I’m talking about intrinsic group intelligence.

    Corneel: Hmmmm, you used to call it group wisdom. So now you are trying to assimilate Intelligent Design doublespeak and decided group wisdom is equipped with foresight and planning as well? Is this wise, Charlie?

    The ID movement does not have a monopoly on the word “intellegent”. A being can be both intelligent and wise, but intelligence does not necessarily lead to wisdom. Speaking about intrinsic group intelligence leaves open the question of wisdom.

    Wisdom seldom goes along with individual human intelligence. For example, intelligent humans have introduced cane toads into their local environments to deal with pests and in hindsight wished they hadn’t done this. a little wisdom might have given them the foresight to imagine the outcome before it became an actuality.

  21. Alan Fox:
    CharlieM: Why would amphioxus need a clotting system when it doesn’t even have a system of blood flow? They do not have a heart and lack a circulatory system.

    Alan Fox: Lancelets do have a circulatory system.

    ETA I’m using my phone so I’m not going to try posting articles of which there are many. Try googling, Charlie

    You’re right. I should have double checked and researched further before making that claim.

    I should have said that they do have a circulatory system but it does not contain red blood cells to transport oxygen around the body. But I believe the circulatory system is of pretty low pressure and amphioxus also has remarkable regenerative powers. Having a blood clotting system in these creatures would be like putting a 300 horse power Ferrari engine into a Model T Ford.

  22. Corneel:
    CharlieM:

    The function of this one step is to produce an enzyme and it cannot do that if one of the components is missing. The function of the entire blood clotting system is to stem the flow of blood and it cannot do that if any of the individual steps after the fork is missing. And possibly if some of the intrinsic or extrinsic steps are missing but this latter possibility is much harder to demonstrate.

    Corneel: In theory, any irreducibly complex system may consist of irreducibly complex steps that perform some different subfunction (like the pair of regulating enzymes) but this cannot be true of nested subsets of systems that perform the same function, like the blood clotting cascades in this example.

    Of course there cannot be nested subsystems within the system that share the same function. I’m not arguing that a subsystem shares a function, only that it is irreducible regarding the function which it is known to perform. Many of the subsystems here have the function of producing an active protein.

    Corneel: Note: The simpler system is lacking some of the components that the more complex system does have. Since in principle the more complex system can be reduced to the components that make up the simple system and still retain its function, it cannot be irreducibly complex

    There are many examples of blood clotting systems all of varying complexity, but if we want to stick with reality you cannot take any one of these systems, remove an essential step and expect it to remain functional. That is what Behe means when he says it is irreducible.

  23. CharlieM: The ID movement does not have a monopoly on the word “intell[i]gent”.

    The problem is the concept of “Intelligence” in the mind of the average layperson. The way it is used by cdesign proponentists, it is a code word for God. That differs somewhat from your usual brand of Steiner-infused vitalism.

    In addition, by adopting Behe’s talking points you expose yourself to all the usual criticisms of ID creationism. So you believe the blood clotting cascase is IC and therefore cannot have gradually evolved from a simple precursor? Then please explain to us how it did arise. Was it by *poof* perchance? Oh, you don’t know?

  24. CharlieM: There are many examples of blood clotting systems all of varying complexity, but if we want to stick with reality you cannot take any one of these systems, remove an essential step and expect it to remain functional. That is what Behe means when he says it is irreducible.

    By arguing that certain integrated biological systems are IC, Behe is trying to establish that these are highly unlikely to have evolved by any of the mechanisms in standard evolutionary accounts. This is NOT the same as the tautological statement that a system ceases functioning when you remove an essential step.

    You are backpedaling again, this time on Behe’s behalf. Please stop that.

  25. Kantian Naturalist,

    This post has given me a lot to think about. Some of the names I am familiar with, some not.

    I’ve previously watched videos of conferences organized by the Mind & Life Institute featuring the Dali Lama and Varela among others. This article gives a brief history of these meetings.

    I found Rosen on Wikipedia and it says this:

    Rosen disputes that the functional capability of a biologically active protein can be investigated purely using the genetically encoded sequence of amino acids. This is because, he said, a protein must undergo a process of folding to attain its characteristic three-dimensional shape before it can become functionally active in the system. Yet, only the amino acid sequence is genetically coded. The mechanisms by which proteins fold are not completely known. He concluded, based on examples such as this, that phenotype cannot always be directly attributed to genotype and that the chemically active aspect of a biologically active protein relies on more than the sequence of amino acids, from which it was constructed: there must be some other important factors at work, that he did not however attempt to specify or pin down

    Through searching Rosen I came across Joe Norman who I’d also like to know more about. He wrote:

    …the modern mind misses that in the organic and living unfolding of the world, wholes are generated by and out of other wholes, and the parts we observe are very often descended from the elaboration and internal differentiation of a whole whose existence precedes them.

    I like that thinking. and I believe his point is valid.

    Thanks for that informative post. I’ll enjoy taking a it of time to mull it over. Behe might stimulate my thinking but that does not mean I agree with him wholeheartedly.

    I don’t know if Behe mistakenly believes he was the first to coined the term “irreducibly complex”, but I don’t believe a concept like that belongs to any individual and so can’t be stolen.

  26. Alan Fox,

    Learned a couple of (new to me) things this morning. A duplicated gene is an ohnologue and at least two complete genome duplications have occured in the vertebrate line.

    Good to hear you did some research. Since it offends people I will take your suggestion and call it Howe et al. There was also a gene duplication in the Lenski experiment but no subsequent functional de novo gene sequences.

    The concept of LUCA and LVCA (vertebrate) appears to be wrong. Interesting how the world changes with evidence. Cheers.

  27. CharlieM: I should have said that they do have a circulatory system

    Yes.

    but…

    Oh dear!

    …it does not contain red blood cells to transport oxygen around the body.

    So smaller animals with slower metabolisms can manage without haemoglobin and erythrocytes. That’s not IC then.

    But I believe the circulatory system is of pretty low pressure…

    Have you checked? Why is that a bug and not a feature? The ancestral morphology doesn’t need haemoglobin, erythrocytes, clotting mechanisms but such adaptations can evolve.

    …and amphioxus also has remarkable regenerative powers. Having a blood clotting system in these creatures would be like putting a 300 horse power Ferrari engine into a Model T Ford.

    That is a poor analogy that doesn’t make sense to me. Evolution occurs in parallel. Does amphioxus have “remarkable regenerative powers” by the way?

  28. colewd: Good to hear you did some research. Since it offends people I will take your suggestion and call it Howe et al.

    It seems reasonable to attribute the original authors.

  29. colewd: There was also a gene duplication in the Lenski experiment but no subsequent functional de novo gene sequences.

    Learned something else this evening. Your remark about a duplication event prompted me to search and I came across a 2017 paper by Lenski that I don’t recall reading before. I’ll read it carefully later but a qick glance doesn’t elucidate what you are referring to. Could you elaborate?

    ETA correct link

  30. colewd: The concept of LUCA and LVCA (vertebrate) appears to be wrong.

    To whom? And why? Because the concept of common descent is so well evidenced and so explanatory, it seems perverse to suggest it is flat out wrong.

  31. Alan Fox,

    To whom? And why? Because the concept of common descent is so well evidenced and so explanatory, it seems perverse to suggest it is flat out wrong.

    Common descent and the concept of LUCA and LVCA are different. We all agree there is some level of common descent.

    The idea of more than one tree is starting to gain steam by new genomic evidence.

  32. Alan Fox,

    Learned something else this evening. Your remark about a duplication event prompted me to search and I came across a 2017 paper by Lenski that I don’t recall reading before. I’ll read it carefully later but a qick glance doesn’t elucidate what you are referring to. Could you elaborate?

    Thanks for the paper. On first glance I only see one fixed duplication event. That of a promoter allowing for citrate consumption in an aerobic environment. Let me know if you see it differently.

    What is striking is the limited fixation despite billions of mutations. This is consistent with the Lynch/Behe discussion.

  33. colewd: The idea of more than one tree is starting to gain steam by new genomic evidence.

    Which would be? An alternative explanation as to why there is effectively one genetic code for the whole of life on Earth would be needed.

  34. Alan Fox,

    Which would be? An alternative explanation as to why there is effectively one genetic code for the whole of life on Earth would be needed.

    A common design concept such as the ASCI standard in computer science. Common descent is a possible explanation when you see a high level of similarities like the one you mentioned but becomes problematic when you see lots of differences like in the Howe et al Venn diagram.

  35. colewd: The idea of more than one tree is starting to gain steam by new genomic evidence.

    When I first learned about evolution, I assumed several trees — perhaps one for each phylum. But that was before the work of Crick & Watson. By now, it seems pretty clear that those are all part of the same tree.

  36. colewd: A common design concept such as the ASCI standard in computer science.

    I assume that is supposed to be ASCII.

    I got into computing with computers that spoke EBCDIC rather than ASCII. But they still counted as arising from the earlier von Neumann design.

  37. Neil Rickert,

    Which would be? An alternative explanation as to why there is effectively one genetic code for the whole of life on Earth would be needed.

    If this was the only data I would agree.

  38. CharlieM: Through searching Rosen I came across Joe Norman who I’d also like to know more about. He wrote:

    …the modern mind misses that in the organic and living unfolding of the world, wholes are generated by and out of other wholes, and the parts we observe are very often descended from the elaboration and internal differentiation of a whole whose existence precedes them.

    I like that thinking. and I believe his point is valid.

    Yep, that’s just Kant, from “Critique of Teleological Judgment” in Critique of Judgment. The big questions in philosophy of biology since Kant have been:

    1. realism vs heuristic: is teleology just a necessity about how we need to think about life, or is teleology a genuinely real property of life?

    2. teleology vs mechanism: can we understand teleology and mechanism as different kinds of objectively knowable causal structures, or is teleology somehow not fully knowable from a scientific, third-person standpoint?

    3. form and math: can formal causes be described mathematically? Or does a commitment to mathematical descriptions eliminate formal causes and leave us only with efficient causes?

  39. Alan Fox:
    It seems reasonable to attribute the original authors.

    Rather than some guy who discusses DNA without understanding what it means.

  40. colewd:
    This will help you model how many of these events were feasible in evolutionary time since LVCA (500 MYO).

    I’m not trying to make any models.

    colewd:
    How much did gene duplication and selection/drift contribute to the current gene distribution of vertebrates.

    I don’t know. I doubt we have thee data for all vertebrates.

    colewd:
    Given given an average search of 10^10 trials to find new gene function?(Art Hunt 2004)

    Sorry, I could not find that reference. I doubt that figure is right though. What makes you think that figure should work for all cases in vertebrate evolution?

    colewd:
    Your alternative theory is the magical Being in the sky delivered the animals as stated in Genesis 1 and duplication selection/drift started from that point. No search required and no claim of lots of needles in the haystack required. The gene pattern easily explained.

    This doesn’t answer my question. That’s a lot of leeway, and you added the problem of referring in particular to one of the most absurd magical beings in the sky. You want to “solve” a problem by appealing to an absurd fantasy just because you think that’s easy. Do you really think that’s sound?

    Try and put yourself in my shoes. I have, on the one hand, natural phenomena. I can test some of it, I can see patterns that betray divergence from common ancestors.

    Say I didn’t have a complete picture, but the patterns are there. So, I can infer histories, and then use the most promising results to explore further, and then I find more things that work well, rejecting things that don’t work, gaining better understanding in the process, new findings allowing further exploration, etc. So, suppose, again, that we don’t have a complete answer, or precise numbers for every event, for every new function. Hell, suppose your numbers are in line with scientists know (I doubt it, but let’s suppose for the sake of argument). Well, from where I sit that means that we have to examine the assumptions behind those numbers. Maybe one assumption is that each sequence has to build up from random assemblies of amino-acids. Well, then let’s study how that actually works to see if the assumption holds. But rejecting natural phenomena because our assumptions are wrong?

    Should we reject gravitation because Newton’s laws (which have their own assumptions) failed with Mercury? Wouldn’t it be better to find further data, make different models? Discover which assumptions were wrong? Instead you’d want us to reject gravitation altogether, as if the phenomena of gravitation cared about whether we model it correctly or not. When models fail we check the models. Wee don’t reject thee phenomena.

    On the other “side”, if we can even call if a side, I see a ridiculous proposition, with absurd fantasies on top of one another, in a book compiled from oral tradition tales, barely put together. Then again, It doesn’t really explain anything, like why would it all look as common ancestry? Why would, for example, proteins doing the very same biochemical process in different organisms, still show divergence patterns that serve no purpose? Why do divergence patterns at different levels align with each other in a way that tells the same common ancestry story?

    You see? You want me to reject nature, reality, for a fantasy. You think it’s easy: find problematic assumptions, don’t even examine them, don’t even try and make them explicit, and reject nature altogether. I prefer to aim for actual understanding. Sorry.

  41. Entropy,

    Should we reject gravitation because Newton’s laws (which have their own assumptions) failed with Mercury? Wouldn’t it be better to find further data, make different models? Discover which assumptions were wrong? Instead you’d want us to reject gravitation altogether, as if the phenomena of gravitation cared about whether we model it correctly or not. When models fail we check the models. Wee don’t reject thee phenomena.

    In this case you have a workable model that could be improved and worked very well for local effects. In the case of animals we have pretty good models on how they reproduce down to the molecular level.

    The origin of new animals is beyond science at this point as there is no model that can approximate their genetic origin. Guessing based on limited data leads to faulty conclusions and misleading assumptions. The reality is their existence appears to be the starting point for science as mercury’s existence is the starting point for determining its orbit.

    You see? You want me to reject nature, reality, for a fantasy. You think it’s easy: find problematic assumptions, don’t even examine them, don’t even try and make them explicit, and reject nature altogether. I prefer to aim for actual understanding. Sorry.

    I want you to take your models as far as you can but then recognize their limits when the evidence of those limits is supported by the observation. Especially when you are unable to model the observation.

    Rejecting the possibility of a created universe may lead to very poor scientific assumptions. When you label God a magical being you are assuming His non existence which is circular reasoning. A rational universe that allows for scientific models is evidence of His existence.

  42. Corneel:
    Kantian Naturalist: the great philosopher Stan Lee

    Corneel: Marvelous guy!

    Yep. Some might say a comic genius. 🙂

  43. Corneel: CharlieM: The ID movement does not have a monopoly on the word “intell[i]gent”.

    The problem is the concept of “Intelligence” in the mind of the average layperson. The way it is used by cdesign proponentists, it is a code word for God. That differs somewhat from your usual brand of Steiner-infused vitalism.

    I’m sure I’ve heard Behe saying up front that he believes the designer is God. He also says that design can be investigated without considering who or what the designer is.

    Corneel: In addition, by adopting Behe’s talking points you expose yourself to all the usual criticisms of ID creationism. So you believe the blood clotting cascase is IC and therefore cannot have gradually evolved from a simple precursor? Then please explain to us how it did arise. Was it by *poof* perchance? Oh, you don’t know?

    I would look at any particular irreducible complex system on its own merits. In the case of the lamprey blood clotting system I would like to know, if it evolved from a simpler system, how any extra step came to be gradually inserted into the system. To get fibrin from fibrinogen requires an activator of prothrombin to produce thrombin. No activator of prothrombin, no blood clot. But if that is all that the system consists of then fibrin would be produced constantly and the blood circulation would come to a sticky end. The system needs to be inhibited once the fibrin has done its job. Fibrin needs to be produced in the right amount, quickly enough to stem the leak but not in amounts that would be detrimental to the circulation. And don’t forget that the blood clotting system is normally inactive, but prepared for any forthcoming ruptures. It sits in waiting for events that have not happened yet.

    I have been made aware of creatures such as lampreys with a relatively simple system and creatures such as lancelets with no system at all, but I haven’t seen any evidence or demonstration of anything in between. The lamprey system may seen simple looking at the diagram but that is deceiving. It is still a complex, sophisticated system if we think about the details of all the processes involved. We should not take the diagram as reality.

  44. Corneel:
    CharlieM: There are many examples of blood clotting systems all of varying complexity, but if we want to stick with reality you cannot take any one of these systems, remove an essential step and expect it to remain functional. That is what Behe means when he says it is irreducible.

    Corneel: By arguing that certain integrated biological systems are IC, Behe is trying to establish that these are highly unlikely to have evolved by any of the mechanisms in standard evolutionary accounts. This is NOT the same as the tautological statement that a system ceases functioning when you remove an essential step.

    You are backpedaling again, this time on Behe’s behalf. Please stop that.

    I am simply explaining what I understand an irreducibly complex system is.

    I think it is an additional matter as to whether or not an irreducible system could be achieved through standard evolutionary means. I think it depends on the system. Some no doubt could, but I have strong doubts that it is possible for all of them. Apart from just so stories, I haven’t seen much evidence that the blood clotting system could have come about through blind evolutionary processes.

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